Abnormal hippocampal functioning and impaired spatial navigation in depressed individuals: evidence from whole-head magnetoencephalography.

PubMed

Cornwell, Brian R; Salvadore, Giacomo; Colon-Rosario, Veronica; Latov, David R; Holroyd, Tom; Carver, Frederick W; Coppola, Richard; Manji, Husseini K; Zarate, Carlos A; Grillon, Christian

2010-07-01

Dysfunction of the hippocampus has long been suspected to be a key component of the pathophysiology of major depressive disorder. Despite evidence of hippocampal structural abnormalities in depressed patients, abnormal hippocampal functioning has not been demonstrated. The authors aimed to link spatial navigation deficits previously documented in depressed patients to abnormal hippocampal functioning using a virtual reality navigation task. Whole-head magnetoencephalography (MEG) recordings were collected while participants (19 patients diagnosed with major depressive disorder and 19 healthy subjects matched by gender and age) navigated a virtual Morris water maze to find a hidden platform; navigation to a visible platform served as a control condition. Behavioral measures were obtained to assess navigation performance. Theta oscillatory activity (4-8 Hz) was mapped across the brain on a voxel-wise basis using a spatial-filtering MEG source analysis technique. Depressed patients performed worse than healthy subjects in navigating to the hidden platform. Robust group differences in theta activity were observed in right medial temporal cortices during navigation, with patients exhibiting less engagement of the anterior hippocampus and parahippocampal cortices relative to comparison subjects. Left posterior hippocampal theta activity was positively correlated with individual performance within each group. Consistent with previous findings, depressed patients showed impaired spatial navigation. Dysfunction of right anterior hippocampus and parahippocampal cortices may underlie this deficit and stem from structural abnormalities commonly found in depressed patients.

Lactulose:Mannitol Diagnostic Test by HPLC and LC-MSMS Platforms: Considerations for Field Studies of Intestinal Barrier Function and Environmental Enteropathy

PubMed Central

Lee, Gwenyth O.; Kosek, Peter; Lima, Aldo A.M.; Singh, Ravinder; Yori, Pablo P.; Olortegui, Maribel P.; Lamsam, Jesse L.; Oliveira, Domingos B.; Guerrant, Richard L.; Kosek, Margaret

2014-01-01

ABSTRACT Objectives: The lactulose:mannitol (L:M) diagnostic test is frequently used in field studies of environmental enteropathy (EE); however, heterogeneity in test administration and disaccharide measurement has limited the comparison of results between studies and populations. We aim to assess the agreement between L:M measurement between high-performance liquid chromatography with pulsed amperometric detection (HPLC-PAD) and liquid chromatography-tandem mass spectrometry (LC-MSMS) platforms. Methods: The L:M test was administered in a cohort of Peruvian infants considered at risk for EE. A total of 100 samples were tested for lactulose and mannitol at 3 independent laboratories: 1 running an HPLC-PAD platform and 2 running LC-MSMS platforms. Agreement between the platforms was estimated. Results: The Spearman correlation between the 2 LC-MSMS platforms was high (ρ ≥ 0.89) for mannitol, lactulose, and the L:M ratio. The correlation between the HPLC-PAD platform and LC-MSMS platform was ρ = 0.95 for mannitol, ρ = 0.70 for lactulose, and ρ = 0.43 for the L:M ratio. In addition, the HPLC-PAD platform overestimated the lowest disaccharide concentrations to the greatest degree. Conclusions: Given the large analyte concentration range, the improved accuracy of LC-MSMS has important consequences for the assessment of lactulose and mannitol following oral administration in populations at risk for EE. We recommend that researchers wishing to implement a dual-sugar test as part of a study of EE use an LC-MSMS platform to optimize the accuracy of results and increase comparability between studies. PMID:24941958

PRELIMINARY RESULTS OF BTDF CALIBRATION OF TRANSMISSIVE SOLAR DIFFUSERS FOR REMOTE SENSING.

PubMed

Georgiev, Georgi T; Butler, James J; Thome, Kurt; Cooksey, Catherine; Ding, Leibo

2016-01-01

Satellite instruments operating in the reflected solar wavelength region require accurate and precise determination of the optical properties of their diffusers used in pre-flight and post-flight calibrations. The majority of recent and current space instruments use reflective diffusers. As a result, numerous Bidirectional Reflectance Distribution Function (BRDF) calibration comparisons have been conducted between the National Institute of Standards and Technology (NIST) and other industry and university-based metrology laboratories. However, based on literature searches and communications with NIST and other laboratories, no Bidirectional Transmittance Distribution Function (BTDF) measurement comparisons have been conducted between National Measurement Laboratories (NMLs) and other metrology laboratories. On the other hand, there is a growing interest in the use of transmissive diffusers in the calibration of satellite, air-borne, and ground-based remote sensing instruments. Current remote sensing instruments employing transmissive diffusers include the Ozone Mapping and Profiler Suite instrument (OMPS) Limb instrument on the Suomi-National Polar-orbiting Partnership (S-NPP) platform,, the Geostationary Ocean Color Imager (GOCI) on the Korea Aerospace Research Institute's (KARI) Communication, Ocean, and Meteorological Satellite (COMS), the Ozone Monitoring Instrument (OMI) on NASA's Earth Observing System (EOS) Aura platform, the Tropospheric Emissions: Monitoring of Pollution (TEMPO) instrument and the Geostationary Environmental Monitoring Spectrometer (GEMS).. This ensemble of instruments requires validated BTDF measurements of their on-board transmissive diffusers from the ultraviolet through the near infrared. This paper presents the preliminary results of a BTDF comparison between the NASA Diffuser Calibration Laboratory (DCL) and NIST on quartz and thin Spectralon samples.

Preliminary Results of BTDF Calibration of Transmissive Solar Diffusers for Remote Sensing

NASA Technical Reports Server (NTRS)

Georgiev, Georgi T.; Butler, James J.; Thome, Kurt; Cooksey, Catherine; Ding, Leibo

2016-01-01

Satellite instruments operating in the reflected solar wavelength region require accurate and precise determination of the optical properties of their diffusers used in pre-flight and post-flight calibrations. The majority of recent and current space instruments use reflective diffusers. As a result, numerous Bidirectional Reflectance Distribution Function (BRDF) calibration comparisons have been conducted between the National Institute of Standards and Technology (NIST) and other industry and university-based metrology laboratories. However, based on literature searches and communications with NIST and other laboratories, no Bidirectional Transmittance Distribution Function (BTDF) measurement comparisons have been conducted between National Measurement Laboratories (NMLs) and other metrology laboratories. On the other hand, there is a growing interest in the use of transmissive diffusers in the calibration of satellite, air-borne, and ground-based remote sensing instruments. Current remote sensing instruments employing transmissive diffusers include the Ozone Mapping and Profiler Suite instrument (OMPS) Limb instrument on the Suomi-National Polar-orbiting Partnership (S-NPP) platform,, the Geostationary Ocean Color Imager (GOCI) on the Korea Aerospace Research Institute's (KARI) Communication, Ocean, and Meteorological Satellite (COMS), the Ozone Monitoring Instrument (OMI) on NASA's Earth Observing System (EOS) Aura platform, the Tropospheric Emissions: Monitoring of Pollution (TEMPO) instrument and the Geostationary Environmental Monitoring Spectrometer (GEMS).. This ensemble of instruments requires validated BTDF measurements of their on-board transmissive diffusers from the ultraviolet through the near infrared. This paper presents the preliminary results of a BTDF comparison between the NASA Diffuser Calibration Laboratory (DCL) and NIST on quartz and thin Spectralon samples.

PRELIMINARY RESULTS OF BTDF CALIBRATION OF TRANSMISSIVE SOLAR DIFFUSERS FOR REMOTE SENSING

PubMed Central

Georgiev, Georgi T.; Butler, James J.; Thome, Kurt; Cooksey, Catherine; Ding, Leibo

2016-01-01

Satellite instruments operating in the reflected solar wavelength region require accurate and precise determination of the optical properties of their diffusers used in pre-flight and post-flight calibrations. The majority of recent and current space instruments use reflective diffusers. As a result, numerous Bidirectional Reflectance Distribution Function (BRDF) calibration comparisons have been conducted between the National Institute of Standards and Technology (NIST) and other industry and university-based metrology laboratories. However, based on literature searches and communications with NIST and other laboratories, no Bidirectional Transmittance Distribution Function (BTDF) measurement comparisons have been conducted between National Measurement Laboratories (NMLs) and other metrology laboratories. On the other hand, there is a growing interest in the use of transmissive diffusers in the calibration of satellite, air-borne, and ground-based remote sensing instruments. Current remote sensing instruments employing transmissive diffusers include the Ozone Mapping and Profiler Suite instrument (OMPS) Limb instrument on the Suomi-National Polar-orbiting Partnership (S-NPP) platform,, the Geostationary Ocean Color Imager (GOCI) on the Korea Aerospace Research Institute’s (KARI) Communication, Ocean, and Meteorological Satellite (COMS), the Ozone Monitoring Instrument (OMI) on NASA’s Earth Observing System (EOS) Aura platform, the Tropospheric Emissions: Monitoring of Pollution (TEMPO) instrument and the Geostationary Environmental Monitoring Spectrometer (GEMS).. This ensemble of instruments requires validated BTDF measurements of their on-board transmissive diffusers from the ultraviolet through the near infrared. This paper presents the preliminary results of a BTDF comparison between the NASA Diffuser Calibration Laboratory (DCL) and NIST on quartz and thin Spectralon samples. PMID:28003712

Update on the Comparison of Second-Order Loads on a Tension Leg Platform for Wind Turbines

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

Gueydon, Sebastien; Jonkman, Jason

2016-07-01

In comparison to other kinds of floaters (like a spar or a semisubmersible), the tension leg platform has several notable advantages: its vertical motions are negligible, its weight is lighter, and its mooring system's footprint is smaller. Although a tension leg platform has a negligible response to first-order vertical wave loads, the second-order wave loads need to be addressed. This paper follows up on a verification study of second-order wave loads on a tension leg platform for wind turbines done by the Maritime Research Institute of The Netherlands and National Renewable Energy Laboratory and it brings some corrections to itsmore » conclusions.« less

ESTEST: An Open Science Platform for Electronic Structure Research

ERIC Educational Resources Information Center

Yuan, Gary

2012-01-01

Open science platforms in support of data generation, analysis, and dissemination are becoming indispensible tools for conducting research. These platforms use informatics and information technologies to address significant problems in open science data interoperability, verification & validation, comparison, analysis, post-processing,…

Synthesis of three-dimensional calcium carbonate nanofibrous structure from eggshell using femtosecond laser ablation

PubMed Central

2011-01-01

Background Natural biomaterials from bone-like minerals derived from avian eggshells have been considered as promising bone substitutes owing to their biodegradability, abundance, and lower price in comparison with synthetic biomaterials. However, cell adhesion to bulk biomaterials is poor and surface modifications are required to improve biomaterial-cell interaction. Three-dimensional (3D) nanostructures are preferred to act as growth support platforms for bone and stem cells. Although there have been several studies on generating nanoparticles from eggshells, no research has been reported on synthesizing 3D nanofibrous structures. Results In this study, we propose a novel technique to synthesize 3D calcium carbonate interwoven nanofibrous platforms from eggshells using high repetition femtosecond laser irradiation. The eggshell waste is value engineered to calcium carbonate nanofibrous layer in a single step under ambient conditions. Our striking results demonstrate that by controlling the laser pulse repetition, nanostructures with different nanofiber density can be achieved. This approach presents an important step towards synthesizing 3D interwoven nanofibrous platforms from natural biomaterials. Conclusion The synthesized 3D nanofibrous structures can promote biomaterial interfacial properties to improve cell-platform surface interaction and develop new functional biomaterials for a variety of biomedical applications. PMID:21251288

Whole-body concentrations of elements in three fish species from offshore oil platforms and natural areas in the Southern California Bight, USA

USGS Publications Warehouse

Love, Milton S.; Saiki, Michael K.; May, Thomas W.; Yee, Julie L.

2013-01-01

elements. Forty-two elements were excluded from statistical comparisons as they (1) consisted of major cations that were unlikely to accumulate to potentially toxic concentrations; (2) were not detected by the analytical procedures; or (3) were detected at concentrations too low to yield reliable quantitative measurements. The remaining 21 elements consisted of aluminum, arsenic, barium, cadmium, chromium, cobalt, copper, gallium, iron, lead, lithium, manganese, mercury, nickel, rubidium, selenium, strontium, tin, titanium, vanadium, and zinc. Statistical comparisons of these elements indicated that none consistently exhibited higher concentrations at oil platforms than at natural areas. However, the concentrations of copper, selenium, titanium, and vanadium in Pacific sanddab were unusual because small individuals exhibited either no differences between oil platforms and natural areas or significantly lower concentrations at oil platforms than at natural areas, whereas large individuals exhibited significantly higher concentrations at oil platforms than at natural areas.

A Hardware-in-the-Loop Simulation Platform for the Verification and Validation of Safety Control Systems

NASA Astrophysics Data System (ADS)

Rankin, Drew J.; Jiang, Jin

2011-04-01

Verification and validation (V&V) of safety control system quality and performance is required prior to installing control system hardware within nuclear power plants (NPPs). Thus, the objective of the hardware-in-the-loop (HIL) platform introduced in this paper is to verify the functionality of these safety control systems. The developed platform provides a flexible simulated testing environment which enables synchronized coupling between the real and simulated world. Within the platform, National Instruments (NI) data acquisition (DAQ) hardware provides an interface between a programmable electronic system under test (SUT) and a simulation computer. Further, NI LabVIEW resides on this remote DAQ workstation for signal conversion and routing between Ethernet and standard industrial signals as well as for user interface. The platform is applied to the testing of a simplified implementation of Canadian Deuterium Uranium (CANDU) shutdown system no. 1 (SDS1) which monitors only the steam generator level of the simulated NPP. CANDU NPP simulation is performed on a Darlington NPP desktop training simulator provided by Ontario Power Generation (OPG). Simplified SDS1 logic is implemented on an Invensys Tricon v9 programmable logic controller (PLC) to test the performance of both the safety controller and the implemented logic. Prior to HIL simulation, platform availability of over 95% is achieved for the configuration used during the V&V of the PLC. Comparison of HIL simulation results to benchmark simulations shows good operational performance of the PLC following a postulated initiating event (PIE).

Use of nonlinear design optimization techniques in the comparison of battery discharger topologies for the space platform

NASA Technical Reports Server (NTRS)

Sable, Dan M.; Cho, Bo H.; Lee, Fred C.

1990-01-01

A detailed comparison of a boost converter, a voltage-fed, autotransformer converter, and a multimodule boost converter, designed specifically for the space platform battery discharger, is performed. Computer-based nonlinear optimization techniques are used to facilitate an objective comparison. The multimodule boost converter is shown to be the optimum topology at all efficiencies. The margin is greatest at 97 percent efficiency. The multimodule, multiphase boost converter combines the advantages of high efficiency, light weight, and ample margin on the component stresses, thus ensuring high reliability.

Urban search mobile platform modeling in hindered access conditions

NASA Astrophysics Data System (ADS)

Barankova, I. I.; Mikhailova, U. V.; Kalugina, O. B.; Barankov, V. V.

2018-05-01

The article explores the control system simulation and the design of the experimental model of the rescue robot mobile platform. The functional interface, a structural functional diagram of the mobile platform control unit, and a functional control scheme for the mobile platform of secure robot were modeled. The task of design a mobile platform for urban searching in hindered access conditions is realized through the use of a mechanical basis with a chassis and crawler drive, a warning device, human heat sensors and a microcontroller based on Arduino platforms.

Novel Single-Cell Analysis Platform Based on a Solid-State Zinc-Coadsorbed Carbon Quantum Dots Electrochemiluminescence Probe for the Evaluation of CD44 Expression on Breast Cancer Cells.

PubMed

Qiu, Youyi; Zhou, Bin; Yang, Xiaojuan; Long, Dongping; Hao, Yan; Yang, Peihui

2017-05-24

A novel single-cell analysis platform was fabricated using solid-state zinc-coadsorbed carbon quantum dot (ZnCQDs) nanocomposites as an electrochemiluminescence (ECL) probe for the detection of breast cancer cells and evaluation of the CD44 expression level. Solid-state ZnCQDs nanocomposite probes were constructed through the attachment of ZnCQDs to gold nanoparticles and then the loading of magnetic beads to amplify the ECL signal, exhibiting a remarkable 120-fold enhancement of the ECL intensity. Hyaluronic acid (HA)-functionalized solid-state probes were used to label a single breast cancer cell by the specific recognition of HA with CD44 on the cell surface, revealing more stable, sensitive, and effective tagging in comparison with the water-soluble CQDs. This strategy exhibited a good analytical performance for the analysis of MDA-MB-231 and MCF-7 single cells with linear range from 1 to 18 and from 1 to 12 cells, respectively. Furthermore, this single-cell analysis platform was used for evaluation of the CD44 expression level of these two cell lines, in which the MDA-MB-231 cells revealed a 2.8-5.2-fold higher CD44 expression level. A total of 20 single cells were analyzed individually, and the distributions of the ECL intensity revealed larger variations, indicating the high cellular heterogeneity of the CD44 expression level on the same cell line. The as-proposed single-cell analysis platform might provide a novel protocol to effectively study the individual cellular function and cellular heterogeneity.

Comparison of aerial imagery from manned and unmanned aircraft platforms for monitoring cotton growth

USDA-ARS?s Scientific Manuscript database

Unmanned aircraft systems (UAS) have emerged as a low-cost and versatile remote sensing platform in recent years, but little work has been done on comparing imagery from manned and unmanned platforms for crop assessment. The objective of this study was to compare imagery taken from multiple cameras ...

3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces.

PubMed

Xiong, Yi; Esquivel-Rodriguez, Juan; Sael, Lee; Kihara, Daisuke

2014-01-01

The increasing number of uncharacterized protein structures necessitates the development of computational approaches for function annotation using the protein tertiary structures. Protein structure database search is the basis of any structure-based functional elucidation of proteins. 3D-SURFER is a web platform for real-time protein surface comparison of a given protein structure against the entire PDB using 3D Zernike descriptors. It can smoothly navigate the protein structure space in real-time from one query structure to another. A major new feature of Release 2.0 is the ability to compare the protein surface of a single chain, a single domain, or a single complex against databases of protein chains, domains, complexes, or a combination of all three in the latest PDB. Additionally, two types of protein structures can now be compared: all-atom-surface and backbone-atom-surface. The server can also accept a batch job for a large number of database searches. Pockets in protein surfaces can be identified by VisGrid and LIGSITE (csc) . The server is available at http://kiharalab.org/3d-surfer/.

Told through the wine: A liquid chromatography-mass spectrometry interplatform comparison reveals the influence of the global approach on the final annotated metabolites in non-targeted metabolomics.

PubMed

Díaz, Ramon; Gallart-Ayala, Hector; Sancho, Juan V; Nuñez, Oscar; Zamora, Tatiana; Martins, Claudia P B; Hernández, Félix; Hernández-Cassou, Santiago; Saurina, Javier; Checa, Antonio

2016-02-12

This work focuses on the influence of the selected LC-HRMS platform on the final annotated compounds in non-targeted metabolomics. Two platforms that differed in columns, mobile phases, gradients, chromatographs, mass spectrometers (Orbitrap [Platform#1] and Q-TOF [Platform#2]), data processing and marker selection protocols were compared. A total of 42 wines samples from three different protected denomination of origin (PDO) were analyzed. At the feature level, good (O)PLS-DA models were obtained for both platforms (Q(2)[Platform#1]=0.89, 0.83 and 0.72; Q(2)[Platform#2]=0.86, 0.86 and 0.77 for Penedes, Ribera del Duero and Rioja wines respectively) with 100% correctly classified samples in all cases. At the annotated metabolite level, platforms proposed 9 and 8 annotated metabolites respectively which were identified by matching standards or the MS/MS spectra of the compounds. At this stage, there was no coincidence among platforms regarding the suggested metabolites. When screened on the raw data, 6 and 5 of these compounds were detected on the other platform with a similar trend. Some of the detected metabolites showed complimentary information when integrated on biological pathways. Through the use of some examples at the annotated metabolite level, possible explanations of this initial divergence on the results are presented. This work shows the complications that may arise on the comparison of non-targeted metabolomics platforms even when metabolite focused approaches are used in the identification. Copyright © 2016 Elsevier B.V. All rights reserved.

A versatile modular bioreactor platform for Tissue Engineering

PubMed Central

Schuerlein, Sebastian; Schwarz, Thomas; Krziminski, Steffan; Gätzner, Sabine; Hoppensack, Anke; Schwedhelm, Ivo; Schweinlin, Matthias; Walles, Heike

2016-01-01

Abstract Tissue Engineering (TE) bears potential to overcome the persistent shortage of donor organs in transplantation medicine. Additionally, TE products are applied as human test systems in pharmaceutical research to close the gap between animal testing and the administration of drugs to human subjects in clinical trials. However, generating a tissue requires complex culture conditions provided by bioreactors. Currently, the translation of TE technologies into clinical and industrial applications is limited due to a wide range of different tissue‐specific, non‐disposable bioreactor systems. To ensure a high level of standardization, a suitable cost‐effectiveness, and a safe graft production, a generic modular bioreactor platform was developed. Functional modules provide robust control of culture processes, e.g. medium transport, gas exchange, heating, or trapping of floating air bubbles. Characterization revealed improved performance of the modules in comparison to traditional cell culture equipment such as incubators, or peristaltic pumps. By combining the modules, a broad range of culture conditions can be achieved. The novel bioreactor platform allows using disposable components and facilitates tissue culture in closed fluidic systems. By sustaining native carotid arteries, engineering a blood vessel, and generating intestinal tissue models according to a previously published protocol the feasibility and performance of the bioreactor platform was demonstrated. PMID:27492568

A versatile modular bioreactor platform for Tissue Engineering.

PubMed

Schuerlein, Sebastian; Schwarz, Thomas; Krziminski, Steffan; Gätzner, Sabine; Hoppensack, Anke; Schwedhelm, Ivo; Schweinlin, Matthias; Walles, Heike; Hansmann, Jan

2017-02-01

Tissue Engineering (TE) bears potential to overcome the persistent shortage of donor organs in transplantation medicine. Additionally, TE products are applied as human test systems in pharmaceutical research to close the gap between animal testing and the administration of drugs to human subjects in clinical trials. However, generating a tissue requires complex culture conditions provided by bioreactors. Currently, the translation of TE technologies into clinical and industrial applications is limited due to a wide range of different tissue-specific, non-disposable bioreactor systems. To ensure a high level of standardization, a suitable cost-effectiveness, and a safe graft production, a generic modular bioreactor platform was developed. Functional modules provide robust control of culture processes, e.g. medium transport, gas exchange, heating, or trapping of floating air bubbles. Characterization revealed improved performance of the modules in comparison to traditional cell culture equipment such as incubators, or peristaltic pumps. By combining the modules, a broad range of culture conditions can be achieved. The novel bioreactor platform allows using disposable components and facilitates tissue culture in closed fluidic systems. By sustaining native carotid arteries, engineering a blood vessel, and generating intestinal tissue models according to a previously published protocol the feasibility and performance of the bioreactor platform was demonstrated. © 2017 The Authors. Biotechnology Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Inconsistencies between Academic E-Book Platforms: A Comparison of Metadata and Search Results

ERIC Educational Resources Information Center

Wiersma, Gabrielle; Tovstiadi, Esta

2017-01-01

This article presents the results of a study of academic e-books that compared the metadata and search results from major academic e-book platforms. The authors collected data and performed a series of test searches designed to produce the same result regardless of platform. Testing, however, revealed metadata-related errors and significant…

Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells

PubMed Central

Maouche, Seraya; Poirier, Odette; Godefroy, Tiphaine; Olaso, Robert; Gut, Ivo; Collet, Jean-Phillipe; Montalescot, Gilles; Cambien, François

2008-01-01

Background In this study we assessed the respective ability of Affymetrix and Illumina microarray methodologies to answer a relevant biological question, namely the change in gene expression between resting monocytes and macrophages derived from these monocytes. Five RNA samples for each type of cell were hybridized to the two platforms in parallel. In addition, a reference list of differentially expressed genes (DEG) was generated from a larger number of hybridizations (mRNA from 86 individuals) using the RNG/MRC two-color platform. Results Our results show an important overlap of the Illumina and Affymetrix DEG lists. In addition, more than 70% of the genes in these lists were also present in the reference list. Overall the two platforms had very similar performance in terms of biological significance, evaluated by the presence in the DEG lists of an excess of genes belonging to Gene Ontology (GO) categories relevant for the biology of monocytes and macrophages. Our results support the conclusion of the MicroArray Quality Control (MAQC) project that the criteria used to constitute the DEG lists strongly influence the degree of concordance among platforms. However the importance of prioritizing genes by magnitude of effect (fold change) rather than statistical significance (p-value) to enhance cross-platform reproducibility recommended by the MAQC authors was not supported by our data. Conclusion Functional analysis based on GO enrichment demonstrates that the 2 compared technologies delivered very similar results and identified most of the relevant GO categories enriched in the reference list. PMID:18578872

LipidQC: Method Validation Tool for Visual Comparison to SRM 1950 Using NIST Interlaboratory Comparison Exercise Lipid Consensus Mean Estimate Values.

PubMed

Ulmer, Candice Z; Ragland, Jared M; Koelmel, Jeremy P; Heckert, Alan; Jones, Christina M; Garrett, Timothy J; Yost, Richard A; Bowden, John A

2017-12-19

As advances in analytical separation techniques, mass spectrometry instrumentation, and data processing platforms continue to spur growth in the lipidomics field, more structurally unique lipid species are detected and annotated. The lipidomics community is in need of benchmark reference values to assess the validity of various lipidomics workflows in providing accurate quantitative measurements across the diverse lipidome. LipidQC addresses the harmonization challenge in lipid quantitation by providing a semiautomated process, independent of analytical platform, for visual comparison of experimental results of National Institute of Standards and Technology Standard Reference Material (SRM) 1950, "Metabolites in Frozen Human Plasma", against benchmark consensus mean concentrations derived from the NIST Lipidomics Interlaboratory Comparison Exercise.

Snaps, Selfies, and Shares: How Three Popular Social Media Platforms Contribute to the Sociocultural Model of Disordered Eating Among Young Women.

PubMed

Saunders, Jessica F; Eaton, Asia A

2018-06-01

The current study aimed to integrate and test the sociocultural model of disordered eating with theories explaining the impact of mass media on the development of disordered eating for users of three popular social networking platforms. Young women social networking site (SNS) users (age 18-24) who had never received an eating disorder diagnosis (N = 637) completed questions capturing their SNS gratifications and usage, body surveillance, social comparisons, body dissatisfaction, and eating pathology. Measures were administered in one online session. Model relationships were similar across users of all three SNS platforms: Facebook, Instagram, and Snapchat. Users of all platforms demonstrated a significant positive relationship between upward comparisons and disordered eating outcomes, and between body surveillance and disordered eating outcomes, although differences between models did emerge. Empirical findings support extending the sociocultural model of disordered eating to include SNS uses and gratifications.

New Database Manipulation Tools in the Easy-Learning On-Line Platform

ERIC Educational Resources Information Center

Radescu, Radu; Davidescu, Andrei; Pupezescu, Valentin

2011-01-01

The present paper deals with the new ORM (object-relational mapping) tool introduced in the easy-learning platform. Propel 1.5 is the latest version of Propel, one of the ORMs fully compatible with the Symfony framework, and in comparison with the older versions and it has drastically improved the way the easy-learning platform can manipulate its…

STR-validator: an open source platform for validation and process control.

PubMed

Hansson, Oskar; Gill, Peter; Egeland, Thore

2014-11-01

This paper addresses two problems faced when short tandem repeat (STR) systems are validated for forensic purposes: (1) validation is extremely time consuming and expensive, and (2) there is strong consensus about what to validate but not how. The first problem is solved by powerful data processing functions to automate calculations. Utilising an easy-to-use graphical user interface, strvalidator (hereafter referred to as STR-validator) can greatly increase the speed of validation. The second problem is exemplified by a series of analyses, and subsequent comparison with published material, highlighting the need for a common validation platform. If adopted by the forensic community STR-validator has the potential to standardise the analysis of validation data. This would not only facilitate information exchange but also increase the pace at which laboratories are able to switch to new technology. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Performance of MCNP4A on seven computing platforms

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

Hendricks, J.S.; Brockhoff, R.C.

1994-12-31

The performance of seven computer platforms has been evaluated with the MCNP4A Monte Carlo radiation transport code. For the first time we report timing results using MCNP4A and its new test set and libraries. Comparisons are made on platforms not available to us in previous MCNP timing studies. By using MCNP4A and its 325-problem test set, a widely-used and readily-available physics production code is used; the timing comparison is not limited to a single ``typical`` problem, demonstrating the problem dependence of timing results; the results are reproducible at the more than 100 installations around the world using MCNP; comparison ofmore » performance of other computer platforms to the ones tested in this study is possible because we present raw data rather than normalized results; and a measure of the increase in performance of computer hardware and software over the past two years is possible. The computer platforms reported are the Cray-YMP 8/64, IBM RS/6000-560, Sun Sparc10, Sun Sparc2, HP/9000-735, 4 processor 100 MHz Silicon Graphics ONYX, and Gateway 2000 model 4DX2-66V PC. In 1991 a timing study of MCNP4, the predecessor to MCNP4A, was conducted using ENDF/B-V cross-section libraries, which are export protected. The new study is based upon the new MCNP 25-problem test set which utilizes internationally available data. MCNP4A, its test problems and the test data library are available from the Radiation Shielding and Information Center in Oak Ridge, Tennessee, or from the NEA Data Bank in Saclay, France. Anyone with the same workstation and compiler can get the same test problem sets, the same library files, and the same MCNP4A code from RSIC or NEA and replicate our results. And, because we report raw data, comparison of the performance of other compute platforms and compilers can be made.« less

Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

PubMed Central

Lasitschka, Bärbel; Jones, David; Northcott, Paul; Hutter, Barbara; Jäger, Natalie; Kool, Marcel; Taylor, Michael; Lichter, Peter; Pfister, Stefan; Wolf, Stephan; Brors, Benedikt; Eils, Roland

2013-01-01

The emergence of high-throughput, next-generation sequencing technologies has dramatically altered the way we assess genomes in population genetics and in cancer genomics. Currently, there are four commonly used whole-genome sequencing platforms on the market: Illumina’s HiSeq2000, Life Technologies’ SOLiD 4 and its completely redesigned 5500xl SOLiD, and Complete Genomics’ technology. A number of earlier studies have compared a subset of those sequencing platforms or compared those platforms with Sanger sequencing, which is prohibitively expensive for whole genome studies. Here we present a detailed comparison of the performance of all currently available whole genome sequencing platforms, especially regarding their ability to call SNVs and to evenly cover the genome and specific genomic regions. Unlike earlier studies, we base our comparison on four different samples, allowing us to assess the between-sample variation of the platforms. We find a pronounced GC bias in GC-rich regions for Life Technologies’ platforms, with Complete Genomics performing best here, while we see the least bias in GC-poor regions for HiSeq2000 and 5500xl. HiSeq2000 gives the most uniform coverage and displays the least sample-to-sample variation. In contrast, Complete Genomics exhibits by far the smallest fraction of bases not covered, while the SOLiD platforms reveal remarkable shortcomings, especially in covering CpG islands. When comparing the performance of the four platforms for calling SNPs, HiSeq2000 and Complete Genomics achieve the highest sensitivity, while the SOLiD platforms show the lowest false positive rate. Finally, we find that integrating sequencing data from different platforms offers the potential to combine the strengths of different technologies. In summary, our results detail the strengths and weaknesses of all four whole-genome sequencing platforms. It indicates application areas that call for a specific sequencing platform and disallow other platforms. This helps to identify the proper sequencing platform for whole genome studies with different application scopes. PMID:23776689

Replicated computational results (RCR) report for "BLIS: A framework for rapidly instantiating BLAS functionality"

DOE PAGES

Willenbring, James Michael

2015-06-03

“BLIS: A Framework for Rapidly Instantiating BLAS Functionality” includes single-platform BLIS performance results for both level-2 and level-3 operations that is competitive with OpenBLAS, ATLAS, and Intel MKL. A detailed description of the configuration used to generate the performance results was provided to the reviewer by the authors. All the software components used in the comparison were reinstalled and new performance results were generated and compared to the original results. After completing this process, the published results are deemed replicable by the reviewer.

I want what you've got: Cross platform portabiity and human-robot interaction assessment.

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

Julie L. Marble, Ph.D.*.; Douglas A. Few; David J. Bruemmer

2005-08-01

Human-robot interaction is a subtle, yet critical aspect of design that must be assessed during the development of both the human-robot interface and robot behaviors if the human-robot team is to effectively meet the complexities of the task environment. Testing not only ensures that the system can successfully achieve the tasks for which it was designed, but more importantly, usability testing allows the designers to understand how humans and robots can, will, and should work together to optimize workload distribution. A lack of human-centered robot interface design, the rigidity of sensor configuration, and the platform-specific nature of research robot developmentmore » environments are a few factors preventing robotic solutions from reaching functional utility in real word environments. Often the difficult engineering challenge of implementing adroit reactive behavior, reliable communication, trustworthy autonomy that combines with system transparency and usable interfaces is overlooked in favor of other research aims. The result is that many robotic systems never reach a level of functional utility necessary even to evaluate the efficacy of the basic system, much less result in a system that can be used in a critical, real-world environment. Further, because control architectures and interfaces are often platform specific, it is difficult or even impossible to make usability comparisons between them. This paper discusses the challenges inherent to the conduct of human factors testing of variable autonomy control architectures and across platforms within a complex, real-world environment. It discusses the need to compare behaviors, architectures, and interfaces within a structured environment that contains challenging real-world tasks, and the implications for system acceptance and trust of autonomous robotic systems for how humans and robots interact in true interactive teams.« less

PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species[W][OA

PubMed Central

Mutwil, Marek; Klie, Sebastian; Tohge, Takayuki; Giorgi, Federico M.; Wilkins, Olivia; Campbell, Malcolm M.; Fernie, Alisdair R.; Usadel, Björn; Nikoloski, Zoran; Persson, Staffan

2011-01-01

The model organism Arabidopsis thaliana is readily used in basic research due to resource availability and relative speed of data acquisition. A major goal is to transfer acquired knowledge from Arabidopsis to crop species. However, the identification of functional equivalents of well-characterized Arabidopsis genes in other plants is a nontrivial task. It is well documented that transcriptionally coordinated genes tend to be functionally related and that such relationships may be conserved across different species and even kingdoms. To exploit such relationships, we constructed whole-genome coexpression networks for Arabidopsis and six important plant crop species. The interactive networks, clustered using the HCCA algorithm, are provided under the banner PlaNet (http://aranet.mpimp-golm.mpg.de). We implemented a comparative network algorithm that estimates similarities between network structures. Thus, the platform can be used to swiftly infer similar coexpressed network vicinities within and across species and can predict the identity of functional homologs. We exemplify this using the PSA-D and chalcone synthase-related gene networks. Finally, we assessed how ontology terms are transcriptionally connected in the seven species and provide the corresponding MapMan term coexpression networks. The data support the contention that this platform will considerably improve transfer of knowledge generated in Arabidopsis to valuable crop species. PMID:21441431

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species.

PubMed

Wang, Yi; Coleman-Derr, Devin; Chen, Guoping; Gu, Yong Q

2015-07-01

Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that is useful for genome wide comparisons and visualization of orthologous clusters. OrthoVenn provides coverage of vertebrates, metazoa, protists, fungi, plants and bacteria for the comparison of orthologous clusters and also supports uploading of customized protein sequences from user-defined species. An interactive Venn diagram, summary counts, and functional summaries of the disjunction and intersection of clusters shared between species are displayed as part of the OrthoVenn result. OrthoVenn also includes in-depth views of the clusters using various sequence analysis tools. Furthermore, OrthoVenn identifies orthologous clusters of single copy genes and allows for a customized search of clusters of specific genes through key words or BLAST. OrthoVenn is an efficient and user-friendly web server freely accessible at http://probes.pw.usda.gov/OrthoVenn or http://aegilops.wheat.ucdavis.edu/OrthoVenn. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A simplified method in comparison with comprehensive interaction incremental dynamic analysis to assess seismic performance of jacket-type offshore platforms

NASA Astrophysics Data System (ADS)

Zolfaghari, M. R.; Ajamy, A.; Asgarian, B.

2015-12-01

The primary goal of seismic reassessment procedures in oil platform codes is to determine the reliability of a platform under extreme earthquake loading. Therefore, in this paper, a simplified method is proposed to assess seismic performance of existing jacket-type offshore platforms (JTOP) in regions ranging from near-elastic to global collapse. The simplified method curve exploits well agreement between static pushover (SPO) curve and the entire summarized interaction incremental dynamic analysis (CI-IDA) curve of the platform. Although the CI-IDA method offers better understanding and better modelling of the phenomenon, it is a time-consuming and challenging task. To overcome the challenges, the simplified procedure, a fast and accurate approach, is introduced based on SPO analysis. Then, an existing JTOP in the Persian Gulf is presented to illustrate the procedure, and finally a comparison is made between the simplified method and CI-IDA results. The simplified method is very informative and practical for current engineering purposes. It is able to predict seismic performance elasticity to global dynamic instability with reasonable accuracy and little computational effort.

Earth observing system instrument pointing control modeling for polar orbiting platforms

NASA Technical Reports Server (NTRS)

Briggs, H. C.; Kia, T.; Mccabe, S. A.; Bell, C. E.

1987-01-01

An approach to instrument pointing control performance assessment for large multi-instrument platforms is described. First, instrument pointing requirements and reference platform control systems for the Eos Polar Platforms are reviewed. Performance modeling tools including NASTRAN models of two large platforms, a modal selection procedure utilizing a balanced realization method, and reduced order platform models with core and instrument pointing control loops added are then described. Time history simulations of instrument pointing and stability performance in response to commanded slewing of adjacent instruments demonstrates the limits of tolerable slew activity. Simplified models of rigid body responses are also developed for comparison. Instrument pointing control methods required in addition to the core platform control system to meet instrument pointing requirements are considered.

An Analysis of Fish Communities on Structured Habitat in the Northwestern Gulf of Mexico: Potential Impacts of "Rigs-to-Reefs" Programs and a Comparison with Natural Banks

NASA Astrophysics Data System (ADS)

Wetz, J. J.; Ajemian, M. J.; Streich, M.; Stunz, G. W.

2016-02-01

Artificial habitat in the northwestern Gulf of Mexico is predominantly comprised of both active and reefed oil and gas platforms. In the last few decades, Texas alone has converted over 140 decommissioned oil and gas platforms into permitted artificial reefs. Despite the predominance of this habitat type, the associated fish communities remain poorly studied and few comparisons with natural habitat have been done. Using remotely operated vehicles in 2012 and 2013, we documented fish assemblages surrounding 15 artificial structures and several natural banks located on the Texas shelf. Artificial sites were variable in depth (30-84 m), number of structures, and vertical relief. Both structure type and relief influenced species richness and community structure at these sites. However, bottom depth was most influential with a shift in community composition and high diversity observed at approximately 60 m depth. In this same region, drowned coralgal reefs (the South Texas Banks) provide natural hard substrate with relief up to 20 m. Comparisons between these natural habitats and artificial reefs with similar depths and relief clearly demonstrate fish community differences, perhaps indicating differences in habitat function. To attain species-specific management goals, reefing programs should carefully consider the ambient environmental conditions (i.e., depth) and proximity of natural habitats, as these will most certainly affect the fish assemblage and characteristics of exploited fisheries species.

Research on private cloud computing based on analysis on typical opensource platform: a case study with Eucalyptus and Wavemaker

NASA Astrophysics Data System (ADS)

Yu, Xiaoyuan; Yuan, Jian; Chen, Shi

2013-03-01

Cloud computing is one of the most popular topics in the IT industry and is recently being adopted by many companies. It has four development models, as: public cloud, community cloud, hybrid cloud and private cloud. Except others, private cloud can be implemented in a private network, and delivers some benefits of cloud computing without pitfalls. This paper makes a comparison of typical open source platforms through which we can implement a private cloud. After this comparison, we choose Eucalyptus and Wavemaker to do a case study on the private cloud. We also do some performance estimation of cloud platform services and development of prototype software as cloud services.

Carboxylate platform: the MixAlco process part 1: comparison of three biomass conversion platforms.

PubMed

Holtzapple, Mark T; Granda, Cesar B

2009-05-01

To convert biomass to liquid fuels, three platforms are compared: thermochemical, sugar, and carboxylate. To create a common basis, each platform is fed "ideal biomass," which contains polysaccharides (68.3%) and lignin (31.7%). This ratio is typical of hardwood biomass and was selected so that when gasified and converted to hydrogen, the lignin has sufficient energy to produce ethanol from the carboxylic acids produced by the carboxylate platform. Using balanced chemical reactions, the theoretical yield and energy efficiency were determined for each platform. For all platforms, the ethanol yield can be increased by 71% to 107% by supplying external hydrogen produced from other sources (e.g., solar, wind, nuclear, fossil fuels). The alcohols can be converted to alkanes with a modest loss of energy efficiency (3 to 5 percentage points). Of the three platforms considered, the carboxylate platform has demonstrated the highest product yields.

Comparison of performance of three commercial platforms for warfarin sensitivity genotyping.

PubMed

Babic, Nikolina; Haverfield, Eden V; Burrus, Julie A; Lozada, Anthony; Das, Soma; Yeo, Kiang-Teck J

2009-08-01

We performed a 3-way comparison on the Osmetech eSensor, AutoGenomics INFINITI, and a real-time PCR method (Paragonx reagents/Stratagene RT-PCR platform) for their FDA-cleared warfarin panels, and additional polymorphisms (CYP2C9*5, *6, and 11 and extended VKORC1 panels) where available. One hundred de-identified DNA samples were used in this IRB-approved study. Accuracy was determined by comparison of genotyping results across three platforms. Any discrepancy was resolved by bi-directional sequencing. The CYP4F2 on Osmetech was validated by bi-directional sequencing. Accuracies for CYP2C9*2 and *3 were 100% for all 3 platforms. VKORC1 3673 genotyping accuracies were 100% on eSensor and 97% on Infiniti. CYP2C9*5, *6 and *11 showed 100% concordance between eSensor and Infiniti. VKORC1 6484 and 9041 variants compared between ParagonDx and Infiniti analyzer were 100% (6484) and 99% (9041) concordant. CYP4F2 was 100% concordant with sequencing results. The time required to generate the results from automated DNA extraction-to-result was approximately 8h on Infiniti, and 4h on eSensor and ParagonDx, respectively. Overall, we observed excellent CYP2C9*2 and *3 genotyping accuracy for all three platforms. For VKORC1 3673 genotyping, eSensor demonstrated a slightly higher accuracy than the Infiniti, and CYP4F2 on Osmetech was 100% accurate.

Biohydrogen | Bioenergy | NREL

Science.gov Websites

two renewable platforms for sustainable hydrogen production. One platform is based on the microbial Metabolism in Rubrivivax gelatinosus, PLOS One (2014) Comparison of transcriptional profiles of Clostridium (2012) View all NREL biohydrogen publications. Capabilities Photo of two women and one man in a

Measuring water fluxes in forests: The need for integrative platforms of analysis

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

Ward, Eric J.

To understand the importance of analytical tools such as those provided by Berdanier et al. (2016) in this issue of Tree Physiology, one must understand both the grand challenges facing Earth system modelers, as well as the minutia of engaging in ecophysiological research in the field. It is between these two extremes of scale that many ecologists struggle to translate empirical research into useful conclusions that guide our understanding of how ecosystems currently function and how they are likely to change in the future. Likewise, modelers struggle to build complexity into their models that match this sophisticated understanding of howmore » ecosystems function, so that necessary simplifications required by large scales do not themselves change the conclusions drawn from these simulations. As both monitoring technology and computational power increase, along with the continual effort in both empirical and modeling research, the gap between the scale of Earth system models and ecological observations continually closes. In addition, this creates a need for platforms of model–data interaction that incorporate uncertainties in both simulations and observations when scaling from one to the other, moving beyond simple comparisons of monthly or annual sums and means.« less

Measuring water fluxes in forests: The need for integrative platforms of analysis

DOE PAGES

Ward, Eric J.

2016-08-09

To understand the importance of analytical tools such as those provided by Berdanier et al. (2016) in this issue of Tree Physiology, one must understand both the grand challenges facing Earth system modelers, as well as the minutia of engaging in ecophysiological research in the field. It is between these two extremes of scale that many ecologists struggle to translate empirical research into useful conclusions that guide our understanding of how ecosystems currently function and how they are likely to change in the future. Likewise, modelers struggle to build complexity into their models that match this sophisticated understanding of howmore » ecosystems function, so that necessary simplifications required by large scales do not themselves change the conclusions drawn from these simulations. As both monitoring technology and computational power increase, along with the continual effort in both empirical and modeling research, the gap between the scale of Earth system models and ecological observations continually closes. In addition, this creates a need for platforms of model–data interaction that incorporate uncertainties in both simulations and observations when scaling from one to the other, moving beyond simple comparisons of monthly or annual sums and means.« less

D-Amino acid oxidase bio-functionalized platforms: Toward an enhanced enzymatic bio-activity

NASA Astrophysics Data System (ADS)

Herrera, Elisa; Valdez Taubas, Javier; Giacomelli, Carla E.

2015-11-01

The purpose of this work is to study the adsorption process and surface bio-activity of His-tagged D-amino acid oxidase (DAAO) from Rhodotorula gracilis (His6-RgDAAO) as the first step for the development of an electrochemical bio-functionalized platform. With such a purpose this work comprises: (a) the His6-RgDAAO bio-activity in solution determined by amperometry, (b) the adsorption mechanism of His6-RgDAAO on bare gold and carboxylated modified substrates in the absence (substrate/COO-) and presence of Ni(II) (substrate/COO- + Ni(II)) determined by reflectometry, and (c) the bio-activity of the His6-RgDAAO bio-functionalized platforms determined by amperometry. Comparing the adsorption behavior and bio-activity of His6-RgDAAO on these different solid substrates allows understanding the contribution of the diverse interactions responsible for the platform performance. His6-RgDAAO enzymatic performance in solution is highly improved when compared to the previously used pig kidney (pk) DAAO. His6-RgDAAO exhibits an amperometrically detectable bio-activity at concentrations as low as those expected on a bio-functional platform; hence, it is a viable bio-recognition element of D-amino acids to be coupled to electrochemical platforms. Moreover, His6-RgDAAO bio-functionalized platforms exhibit a higher surface activity than pkDAAO physically adsorbed on gold. The platform built on Ni(II) modified substrates present enhanced bio-activity because the surface complexes histidine-Ni(II) provide with site-oriented, native-like enzymes. The adsorption mechanism responsible of the excellent performance of the bio-functionalized platform takes place in two steps involving electrostatic and bio-affinity interactions whose prevalence depends on the degree of surface coverage.

Increased Functional MEG Connectivity as a Hallmark of MRI-Negative Focal and Generalized Epilepsy.

PubMed

Li Hegner, Yiwen; Marquetand, Justus; Elshahabi, Adham; Klamer, Silke; Lerche, Holger; Braun, Christoph; Focke, Niels K

2018-05-15

Epilepsy is one of the most prevalent neurological diseases with a high morbidity. Accumulating evidence has shown that epilepsy is an archetypical neural network disorder. Here we developed a non-invasive cortical functional connectivity analysis based on magnetoencephalography (MEG) to assess commonalities and differences in the network phenotype in different epilepsy syndromes (non-lesional/cryptogenic focal and idiopathic/genetic generalized epilepsy). Thirty-seven epilepsy patients with normal structural brain anatomy underwent a 30-min resting state MEG measurement with eyes closed. We only analyzed interictal epochs without epileptiform discharges. The imaginary part of coherency was calculated as an indicator of cortical functional connectivity in five classical frequency bands. This connectivity measure was computed between all sources on individually reconstructed cortical surfaces that were surface-aligned to a common template. In comparison to healthy controls, both focal and generalized epilepsy patients showed widespread increased functional connectivity in several frequency bands, demonstrating the potential of elevated functional connectivity as a common pathophysiological hallmark in different epilepsy types. Furthermore, the comparison between focal and generalized epilepsies revealed increased network connectivity in bilateral mesio-frontal and motor regions specifically for the generalized epilepsy patients. Our study indicated that the surface-based normalization of MEG sources of individual brains enables the comparison of imaging findings across subjects and groups on a united platform, which leads to a straightforward and effective disclosure of pathological network characteristics in epilepsy. This approach may allow for the definition of more specific markers of different epilepsy syndromes, and increased MEG-based resting-state functional connectivity seems to be a common feature in MRI-negative epilepsy syndromes.

A Comparison and Contrast in Alternative Learning versus Traditional Learning

ERIC Educational Resources Information Center

Simmons, Mia A.

2013-01-01

Preparation for today's influenced technology professional world starts with structure of primary and secondary educational learning environments. The student learning platforms should be aligned in some ways to professional working platforms. This quantitative correlational ex post facto study compared the effectiveness of learning modalities in…

Comparison of Comparative Genomic Hybridization Technologies across Microarray Platforms

EPA Science Inventory

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

Mine or Theirs, Where Do Users Go? A Comparison of E-Journal Usage at the OhioLINK Electronic Journal Center Platform versus the Elsevier ScienceDirect Platform

ERIC Educational Resources Information Center

Swanson, Juleah

2015-01-01

This research provides librarians with a model for assessing and predicting which platforms patrons will use to access the same content, specifically comparing usage at the Ohio Library and Information Network (OhioLINK) Electronic Journal Center (EJC) and at Elsevier's ScienceDirect from 2007 to 2013. Findings show that in the earlier years, the…

openECA Detailed Design Document

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

Robertson, Russell

This document describes the functional and non-functional requirements for: The openECA platform The included analytic systems that will: Validate the operational readiness and performance of the openECA platform Provide out-of-box value to those that implement the openECA platform with an initial collection of analytics

The Unified Astronomy Thesaurus: Semantic Metadata for Astronomy and Astrophysics

NASA Astrophysics Data System (ADS)

Frey, Katie; Accomazzi, Alberto

2018-05-01

Several controlled vocabularies have been developed and used by the astronomical community, each designed to serve a specific need and a specific group. The Unified Astronomy Thesaurus (UAT) attempts to provide a highly structured controlled vocabulary that will be relevant and useful across the entire discipline, regardless of content or platform. Because classifying articles and data will be the two major functions of the UAT, we examine the UAT in comparison with the Astronomical Subject Keywords used by major publications and the JWST Science Keywords used by STScI’s Astronomer’s Proposal Tool.

Robot-assisted laparoendoscopic single site adrenalectomy: A comparison of 3 different port platforms with 3 case reports.

PubMed

Kan, Hung-Cheng; Pang, See-Tong; Wu, Chun-Te; Chang, Ying-Hsu; Liu, Chung-Yi; Chuang, Cheng-Keng; Lin, Po-Hung

2017-12-01

Laparoscopic adrenalectomy is currently the standard of care for adrenal lesion. Minimal invasive laparoscopic surgery such as laparoendoscopic single site surgery (LESS) and natural orifice transluminal endoscopic surgery (NOTES) have been developed to improve cosmetic outcomes and reduce postoperative pain. However, there are still some problems related to instruments and port limitation during LESS surgery. Robot-assisted laparoscopic surgery may help to overcome these problems, and port platforms selection is an important issue. Three cases received robot-assisted LESS adrenalectomy due to adrenal tumor were enrolled. Blood loss, hospital stay, and analgesia injection were compared. Preoperative evaluations were done in a usual manner. Benign tumors were suspect for two patients, while metastatic tumor could not be excluded for the other patient with prior malignancy history. The pathology reports were all benign adrenal cortical adenoma after operation. Three different port platforms, Da Vinci Single-Site Surgical Platform, GelPOINT, and homemade glove port were used. Trans-peritoneal approach was used for two patients, while the other one received trans-retroperitoneal approach. The advantage and disadvantage of different port platforms were discussed. All patients underwent the operation smoothly without major complications or conversion to open surgery. Blood loss amount was small, hospital stay was short, and only one patient received one single dose of opioid analgesia injection after the surgery. The main problems of LESS are the loss of a working triangle and the limitations of the instruments. Robot-assisted LESS may help surgeons overcome part of these problems. Many different port platforms are available, and based on our initial experience, we believe that the GelPoint may be a more suitable platform, for it maintains the endo-wrist function of the Da Vinci instruments, and allows the surgeon to design the position of ports freely to minimize external and internal collision. Copyright © 2017 The Authors. Published by Wolters Kluwer Health, Inc. All rights reserved.

Cloud computing for comparative genomics with windows azure platform.

PubMed

Kim, Insik; Jung, Jae-Yoon; Deluca, Todd F; Nelson, Tristan H; Wall, Dennis P

2012-01-01

Cloud computing services have emerged as a cost-effective alternative for cluster systems as the number of genomes and required computation power to analyze them increased in recent years. Here we introduce the Microsoft Azure platform with detailed execution steps and a cost comparison with Amazon Web Services.

Multiplex immunoassay for persistent organic pollutants in tilapia: Comparison of imaging- and flow cytometry-based platforms using spectrally encoded paramagnetic microspheres

USDA-ARS?s Scientific Manuscript database

Recent developments in spectrally encoded microspheres (SEMs)-based technologies provide high multiplexing possibilities. Most SEMs-based assays required a flow cytometer with sophisticated fluidics and optics. The new imaging superparamagnetic SEMs-based platform transports SEMs with considerably ...

Cloud Computing for Comparative Genomics with Windows Azure Platform

PubMed Central

Kim, Insik; Jung, Jae-Yoon; DeLuca, Todd F.; Nelson, Tristan H.; Wall, Dennis P.

2012-01-01

Cloud computing services have emerged as a cost-effective alternative for cluster systems as the number of genomes and required computation power to analyze them increased in recent years. Here we introduce the Microsoft Azure platform with detailed execution steps and a cost comparison with Amazon Web Services. PMID:23032609

Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy.

PubMed

Jung, Ki-Hong; Dardick, Christopher; Bartley, Laura E; Cao, Peijian; Phetsom, Jirapa; Canlas, Patrick; Seo, Young-Su; Shultz, Michael; Ouyang, Shu; Yuan, Qiaoping; Frank, Bryan C; Ly, Eugene; Zheng, Li; Jia, Yi; Hsia, An-Ping; An, Kyungsook; Chou, Hui-Hsien; Rocke, David; Lee, Geun Cheol; Schnable, Patrick S; An, Gynheung; Buell, C Robin; Ronald, Pamela C

2008-10-06

Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics.

Amine-functionalized diatom frustules: a platform for specific and sensitive detection of nitroaromatic explosive derivative.

PubMed

Selvaraj, Viji; Thomas, Neethi; Anthuvan, Allen Joseph; Nagamony, Ponpandian; Chinnuswamy, Viswanathan

2017-12-14

In the present study, an attempt was made to develop a proof of concept for the detection of nitroaromatic explosive derivatives through the photoluminescence (PL) quenching process using functionalized diatom frustules as a sensing platform. The diatom frustules are composed of nanostructured, highly porous biogenic silica material and emit strong, visible blue PL upon UV excitation. PL-active biosilica was isolated from the marine diatom Nitzschia sp. and was amine-functionalized to develop a sensing platform. Functionalized diatom frustules were further characterized using field emission scanning electron microscope and a series of spectroscopic methods. When nitroaromatic compounds were bound to the functionalized diatom frustules biosilica, the PL intensity from the functionalized biosilica was partially quenched due to the electrophilic nature of the nitro (-NO) groups. The quenching process confirmed the Meisenheimer complex formation and was investigated by using Fourier transform infrared spectroscopy and time-resolved photoluminescence studies. The developed platform was further evaluated for its sensitivity and specificity, and the limit of detection (LOD) of the assay was determined as 1 μM for a series of nitroaromatic explosive compounds. In conclusion, the developed sensing platform will have great utility in the development of on-site detection platforms for sensitive detection of warfare explosive nitroaromatic compounds from the environment.

Should biomedical research be like Airbnb?

PubMed

Bonazzi, Vivien R; Bourne, Philip E

2017-04-01

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

Should biomedical research be like Airbnb?

PubMed Central

Bonazzi, Vivien R.

2017-01-01

The thesis presented here is that biomedical research is based on the trusted exchange of services. That exchange would be conducted more efficiently if the trusted software platforms to exchange those services, if they exist, were more integrated. While simpler and narrower in scope than the services governing biomedical research, comparison to existing internet-based platforms, like Airbnb, can be informative. We illustrate how the analogy to internet-based platforms works and does not work and introduce The Commons, under active development at the National Institutes of Health (NIH) and elsewhere, as an example of the move towards platforms for research. PMID:28388615

CANDO and the infinite drug discovery frontier

PubMed Central

Minie, Mark; Chopra, Gaurav; Sethi, Geetika; Horst, Jeremy; White, George; Roy, Ambrish; Hatti, Kaushik; Samudrala, Ram

2014-01-01

The Computational Analysis of Novel Drug Opportunities (CANDO) platform (http://protinfo.org/cando) uses similarity of compound–proteome interaction signatures to infer homology of compound/drug behavior. We constructed interaction signatures for 3733 human ingestible compounds covering 48,278 protein structures mapping to 2030 indications based on basic science methodologies to predict and analyze protein structure, function, and interactions developed by us and others. Our signature comparison and ranking approach yielded benchmarking accuracies of 12–25% for 1439 indications with at least two approved compounds. We prospectively validated 49/82 ‘high value’ predictions from nine studies covering seven indications, with comparable or better activity to existing drugs, which serve as novel repurposed therapeutics. Our approach may be generalized to compounds beyond those approved by the FDA, and can also consider mutations in protein structures to enable personalization. Our platform provides a holistic multiscale modeling framework of complex atomic, molecular, and physiological systems with broader applications in medicine and engineering. PMID:24980786

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.

Flexible, secure agent development framework

DOEpatents

Goldsmith,; Steven, Y [Rochester, MN

2009-04-07

While an agent generator is generating an intelligent agent, it can also evaluate the data processing platform on which it is executing, in order to assess a risk factor associated with operation of the agent generator on the data processing platform. The agent generator can retrieve from a location external to the data processing platform an open site that is configurable by the user, and load the open site into an agent substrate, thereby creating a development agent with code development capabilities. While an intelligent agent is executing a functional program on a data processing platform, it can also evaluate the data processing platform to assess a risk factor associated with performing the data processing function on the data processing platform.

Intensity-modulated radiotherapy (IMRT) for carcinoma of the maxillary sinus: A comparison of IMRT planning systems

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

Ahmed, Raef S.; Ove, Roger; Duan, Jun

2006-10-01

The treatment of maxillary sinus carcinoma with forward planning can be technically difficult when the neck also requires radiotherapy. This difficulty arises because of the need to spare the contralateral face while treating the bilateral neck. There is considerable potential for error in clinical setup and treatment delivery. We evaluated intensity-modulated radiotherapy (IMRT) as an improvement on forward planning, and compared several inverse planning IMRT platforms. A composite dose-volume histogram (DVH) was generated from a complex forward planned case. We compared the results with those generated by sliding window fixed field dynamic multileaf collimator (MLC) IMRT, using sets of coplanarmore » beams. All setups included an anterior posterior (AP) beam, and 3-, 5-, 7-, and 9-field configurations were evaluated. The dose prescription and objective function priorities were invariant. We also evaluated 2 commercial tomotherapy IMRT delivery platforms. DVH results from all of the IMRT approaches compared favorably with the forward plan. Results for the various inverse planning approaches varied considerably across platforms, despite an attempt to prescribe the therapy similarly. The improvement seen with the addition of beams in the fixed beam sliding window case was modest. IMRT is an effective means of delivering radiotherapy reliably in the complex setting of maxillary sinus carcinoma with neck irradiation. Differences in objective function definition and optimization algorithms can lead to unexpected differences in the final dose distribution, and our evaluation suggests that these factors are more significant than the beam arrangement or number of beams.« less

Evidence for differential control of tibial position in perturbed unilateral stance after acute ACL rupture.

PubMed

Chmielewski, T L; Ramsey, D K; Snyder-Mackler, L

2005-01-01

Functional outcomes in anterior cruciate ligament-deficient "potential copers" and "non-copers" may be related to their knee stabilization strategies. Therefore, the purpose of this study was to differentiate dynamic knee stabilization strategies of potential copers and non-copers through analysis of sagittal plane knee angle and tibia position during disturbed and undisturbed unilateral standing. Ten uninjured potential coper and non-coper subjects stood in unilateral stance on a platform that translated anteriorly, posteriorly and laterally. Knee angle and tibia position with reference to the femur were calculated before and after platform movement. During perturbation trials, potential copers maintained kinematics that were similar to uninjured subjects across conditions. Conversely, non-copers stood with greater knee flexion than uninjured subjects and a tibia position that was more posterior than the other groups. Both non-copers and potential copers demonstrated small changes in tibia position following platform movement, but direction of movement was not similar. The similarities between the knee kinematics of potential copers and uninjured subjects suggest that potential copers compensated well from their injury by utilizing analogous dynamic knee stabilization strategies. In comparison to the other groups, by keeping the knee in greater flexion and the tibia in a more posterior position, non-copers appear to constrain the tibia in response to a challenging task, which is consistent with a "stiffening strategy". Based on the poor functional outcomes of non-copers, a stiffening strategy does not lead to dynamic knee stability, and the strategy may increase compressive forces which could contribute to or exacerbate articular cartilage degeneration.

EGFR mutation detection in ctDNA from NSCLC patient plasma: A cross-platform comparison of leading technologies to support the clinical development of AZD9291.

PubMed

Thress, Kenneth S; Brant, Roz; Carr, T Hedley; Dearden, Simon; Jenkins, Suzanne; Brown, Helen; Hammett, Tracey; Cantarini, Mireille; Barrett, J Carl

2015-12-01

To assess the ability of different technology platforms to detect epidermal growth factor receptor (EGFR) mutations, including T790M, from circulating tumor DNA (ctDNA) in advanced non-small cell lung cancer (NSCLC) patients. A comparison of multiple platforms for detecting EGFR mutations in plasma ctDNA was undertaken. Plasma samples were collected from patients entering the ongoing AURA trial (NCT01802632), investigating the safety, tolerability, and efficacy of AZD9291 in patients with EGFR-sensitizing mutation-positive NSCLC. Plasma was collected prior to AZD9291 dosing but following clinical progression on a previous EGFR-tyrosine kinase inhibitor (TKI). Extracted ctDNA was analyzed using two non-digital platforms (cobas(®) EGFR Mutation Test and therascreen™ EGFR amplification refractory mutation system assay) and two digital platforms (Droplet Digital™ PCR and BEAMing digital PCR [dPCR]). Preliminary assessment (38 samples) was conducted using all four platforms. For EGFR-TKI-sensitizing mutations, high sensitivity (78-100%) and specificity (93-100%) were observed using tissue as a non-reference standard. For the T790M mutation, the digital platforms outperformed the non-digital platforms. Subsequent assessment using 72 additional baseline plasma samples was conducted using the cobas(®) EGFR Mutation Test and BEAMing dPCR. The two platforms demonstrated high sensitivity (82-87%) and specificity (97%) for EGFR-sensitizing mutations. For the T790M mutation, the sensitivity and specificity were 73% and 67%, respectively, with the cobas(®) EGFR Mutation Test, and 81% and 58%, respectively, with BEAMing dPCR. Concordance between the platforms was >90%, showing that multiple platforms are capable of sensitive and specific detection of EGFR-TKI-sensitizing mutations from NSCLC patient plasma. The cobas(®) EGFR Mutation Test and BEAMing dPCR demonstrate a high sensitivity for T790M mutation detection. Genomic heterogeneity of T790M-mediated resistance may explain the reduced specificity observed with plasma-based detection of T790M mutations versus tissue. These data support the use of both platforms in the AZD9291 clinical development program. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Task 1: Whole-body concentrations of elements in kelp bass (Paralabrax clathratus), kelp rockfish (Sebastes atrovirens), and Pacific sanddab (Citharichthys sordidus) from offshore oil platforms and natural areas in the Southern California Bight

USGS Publications Warehouse

Love, Milton S.

2009-01-01

Resource managers are concerned that offshore oil platforms in the Southern California Bight may be contributing to environmental contaminants accumulated by marine fishes. To examine this possibility, 18 kelp bass (Paralabrax clathratus), 80 kelp rockfish (Sebastes atrovirens), and 98 Pacific sanddab (Citharichthys sordidus) were collected from five offshore oil platforms and 10 natural areas during 2005-2006 for whole-body analysis of 63 elements. The natural areas, which served as reference sites, were assumed to be relatively uninfluenced by contaminants originating from platforms. Forty-two elements were excluded from statistical comparisons for one of three reasons: they consisted of major cations that were unlikely to accumulate to potentially toxic concentrations under ambient exposure conditions; they were not detected by the analytical procedures; or they were detected at concentrations too low to yield reliable quantitative measurements. The remaining 21 elements consisted of aluminum, arsenic, barium, cadmium, chromium, cobalt, copper, gallium, iron, lead, lithium, manganese, mercury, nickel, rubidium, selenium, strontium, tin, titanium, vanadium, and zinc. Statistical comparisons of these 21 elements indicated that none consistently exhibited higher concentrations at oil platforms than at natural areas. Eight comparisons yielded significant interaction effects between total length (TL) of the fish and the two habitat types (oil platforms and natural areas). This indicated that relations between certain elemental concentrations (i.e., copper, rubidium, selenium, tin, titanium, and vanadium) and habitat type varied by TL of affected fish species. To better understand these interactions, we examined elemental concentrations in very small and very large individuals of affected species. Although significant interactions were detected for rubidium, tin, and selenium in kelp rockfish, the concentrations of these elements did not differ significantly between oil platforms and natural areas over the TL range of sampled fish. However, for selenium, titanium, and vanadium in Pacific sanddab, small individuals (average TL, 13.0 cm) exhibited significantly lower concentrations at oil platforms than at natural areas, whereas large individuals (average TL, 27.5 cm) exhibited higher concentrations at oil platforms than at natural areas. For copper in Pacific sanddab, small individuals did not exhibit differences between oil platforms and natural areas, whereas large individuals exhibited significantly higher concentrations at oil platforms than at natural areas. On the other hand, for tin in Pacific sanddab, small individuals did not exhibit differences between oil platforms and natural areas, whereas large individuals exhibited significantly lower concentrations at oil platforms than at natural areas. Although concentrations of arsenic, cadmium, chromium, lead, mercury, and selenium in fishes from some platforms and natural areas equaled or exceeded literature-based toxicity thresholds for fish and fish-eating wildlife, studies are still needed to document evidence of toxicity from these elements. When estimates of elemental concentrations in skinless fillets were compared to risk-based consumption limits for humans, the concentrations of arsenic, cadmium, mercury, and tin in fish from a mix of oil platforms and natural areas were sufficiently elevated to suggest a need for further study of inorganic arsenic, cadmium, mercury, and tributyltin.

Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing.

PubMed

Waryah, Charlene Babra; Moses, Colette; Arooj, Mahira; Blancafort, Pilar

2018-01-01

The completion of genome, epigenome, and transcriptome mapping in multiple cell types has created a demand for precision biomolecular tools that allow researchers to functionally manipulate DNA, reconfigure chromatin structure, and ultimately reshape gene expression patterns. Epigenetic editing tools provide the ability to interrogate the relationship between epigenetic modifications and gene expression. Importantly, this information can be exploited to reprogram cell fate for both basic research and therapeutic applications. Three different molecular platforms for epigenetic editing have been developed: zinc finger proteins (ZFs), transcription activator-like effectors (TALEs), and the system of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins. These platforms serve as custom DNA-binding domains (DBDs), which are fused to epigenetic modifying domains to manipulate epigenetic marks at specific sites in the genome. The addition and/or removal of epigenetic modifications reconfigures local chromatin structure, with the potential to provoke long-lasting changes in gene transcription. Here we summarize the molecular structure and mechanism of action of ZF, TALE, and CRISPR platforms and describe their applications for the locus-specific manipulation of the epigenome. The advantages and disadvantages of each platform will be discussed with regard to genomic specificity, potency in regulating gene expression, and reprogramming cell phenotypes, as well as ease of design, construction, and delivery. Finally, we outline potential applications for these tools in molecular biology and biomedicine and identify possible barriers to their future clinical implementation.

Comparison of scientific computing platforms for MCNP4A Monte Carlo calculations

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

Hendricks, J.S.; Brockhoff, R.C.

1994-04-01

The performance of seven computer platforms is evaluated with the widely used and internationally available MCNP4A Monte Carlo radiation transport code. All results are reproducible and are presented in such a way as to enable comparison with computer platforms not in the study. The authors observed that the HP/9000-735 workstation runs MCNP 50% faster than the Cray YMP 8/64. Compared with the Cray YMP 8/64, the IBM RS/6000-560 is 68% as fast, the Sun Sparc10 is 66% as fast, the Silicon Graphics ONYX is 90% as fast, the Gateway 2000 model 4DX2-66V personal computer is 27% as fast, and themore » Sun Sparc2 is 24% as fast. In addition to comparing the timing performance of the seven platforms, the authors observe that changes in compilers and software over the past 2 yr have resulted in only modest performance improvements, hardware improvements have enhanced performance by less than a factor of [approximately]3, timing studies are very problem dependent, MCNP4Q runs about as fast as MCNP4.« less

KSC-08pd1246

NASA Image and Video Library

2008-05-02

CAPE CANAVERAL, Fla. -- Artist's rendering of the Constellation Program's Ares V rocket on the mobile launcher platform (left) and the Ares I rocket on the platform (right) with the space shuttle in between for comparison. The tower of the mobile launcher will have multiple platforms for personnel access and will be approximately 390 feet tall. The tower will be used in the assembly, testing and servicing of the Ares rockets at Kennedy and will also transport the Ares rockets to the launch pad and provide ground support for launches.

Open source acceleration of wave optics simulations on energy efficient high-performance computing platforms

NASA Astrophysics Data System (ADS)

Beck, Jeffrey; Bos, Jeremy P.

2017-05-01

We compare several modifications to the open-source wave optics package, WavePy, intended to improve execution time. Specifically, we compare the relative performance of the Intel MKL, a CPU based OpenCV distribution, and GPU-based version. Performance is compared between distributions both on the same compute platform and between a fully-featured computing workstation and the NVIDIA Jetson TX1 platform. Comparisons are drawn in terms of both execution time and power consumption. We have found that substituting the Fast Fourier Transform operation from OpenCV provides a marked improvement on all platforms. In addition, we show that embedded platforms offer some possibility for extensive improvement in terms of efficiency compared to a fully featured workstation.

The capacity to adapt to changing balance threats: a comparison of children with cerebral palsy and typically developing children.

PubMed

Burtner, P A; Woollacott, M H; Craft, G L; Roncesvalles, M N

2007-01-01

This study investigated differences in reactive balance abilities of typically developing children and those with spastic diplegia. Recovery from balance threats was compared by: (i) Platform velocity and amplitude thresholds: Speed and size of platform movement at which children required assistance to remain upright, (ii) percentage of trials with feet-in-place vs. loss of balance, and (iii) center of pressure measures. Participants included 8 children with spastic diplegic cerebral palsy, 15 developmentally matched children (similar walking stages) and 21 age-matched control children. Backward platform movements graded as easy, moderate and difficult were unexpectedly imposed on children standing on a moveable platform. Children with cerebral palsy (CP) had lower platform velocity thresholds, greater percentages of loss of balance trials, increased distances and increased frequency of directional changes in center-of-pressure (COP) trajectories than control children. Older children with CP fell more often than those under 5 years. Greatest differences between children with and without CP were found in comparisons based on age rather than developmental levels. Using balance perturbations that challenged children with CP to the limits of their balance abilities effectively identified age performance differences and differences compared to typically developing children. Implications for rehabilitation programs are presented.

Multiscale Modelling of Relationships between Protein Classes and Drug Behavior Across all Diseases Using the CANDO Platform

PubMed Central

Samudrala, Ram

2015-01-01

We have examined the effect of eight different protein classes (channels, GPCRs, kinases, ligases, nuclear receptors, proteases, phosphatases, transporters) on the benchmarking performance of the CANDO drug discovery and repurposing platform (http://protinfo.org/cando). The first version of the CANDO platform utilizes a matrix of predicted interactions between 48278 proteins and 3733 human ingestible compounds (including FDA approved drugs and supplements) that map to 2030 indications/diseases using a hierarchical chem and bio-informatic fragment based docking with dynamics protocol (> one billion predicted interactions considered). The platform uses similarity of compound-proteome interaction signatures as indicative of similar functional behavior and benchmarking accuracy is calculated across 1439 indications/diseases with more than one approved drug. The CANDO platform yields a significant correlation (0.99, p-value < 0.0001) between the number of proteins considered and benchmarking accuracy obtained indicating the importance of multitargeting for drug discovery. Average benchmarking accuracies range from 6.2 % to 7.6 % for the eight classes when the top 10 ranked compounds are considered, in contrast to a range of 5.5 % to 11.7 % obtained for the comparison/control sets consisting of 10, 100, 1000, and 10000 single best performing proteins. These results are generally two orders of magnitude better than the average accuracy of 0.2% obtained when randomly generated (fully scrambled) matrices are used. Different indications perform well when different classes are used but the best accuracies (up to 11.7% for the top 10 ranked compounds) are achieved when a combination of classes are used containing the broadest distribution of protein folds. Our results illustrate the utility of the CANDO approach and the consideration of different protein classes for devising indication specific protocols for drug repurposing as well as drug discovery. PMID:25694071

Increased risk of aseptic loosening for 43,525 rotating-platform vs. fixed-bearing total knee replacements

PubMed Central

Gothesen, Oystein; Lygre, Stein Hakon L; Lorimer, Michelle; Graves, Stephen; Furnes, Ove

2017-01-01

Background and purpose — Given similar functional outcomes with mobile and fixed bearings, a difference in survivorship may favor either. This study investigated the risk of aseptic loosening for the most used subtypes of mobile-bearing rotating-platform knees, in Norway and Australia. Patients and methods — Primary TKRs reported to the Norwegian and Australian joint registries, between 2003 and 2014, were analyzed with aseptic loosening as primary end-point and all revisions as secondary end-point. We hypothesized that no difference would be found in the rate of revision between rotating-platform and the most used fixed-bearing TKRs, or between keeled and non-keeled tibia. Kaplan–Meier estimates and curves, and Cox regression relative risk estimates adjusted for age, sex, and diagnosis were used for comparison. Results — The rotating-platform TKRs had an increased risk of revision for aseptic loosening compared with the most used fixed-bearing knees, in Norway (RR =6, 95% CI 4–8) and Australia (RR =2.1, 95% CI 1.8–2.5). The risk of aseptic loosening as a reason for revision was highest in Norway compared with Australia (RR =1.7, 95% CI 1.4–2.0). The keeled tibial component had the same risk of aseptic loosening as the non-keeled tibia (Australia). Fixation method and subtypes of the tibial components had no impact on the risk of aseptic loosening in these mobile-bearing knees. Interpretation — The rotating-platform TKRs in this study appeared to have a higher risk of revision for aseptic loosening than the most used fixed-bearing TKRs. PMID:28929828

Effects of Second-Order Sum- and Difference-Frequency Wave Forces on the Motion Response of a Tension-Leg Platform Considering the Set-down Motion

NASA Astrophysics Data System (ADS)

Wang, Bin; Tang, Yougang; Li, Yan; Cai, Runbo

2018-04-01

This paper presents a study on the motion response of a tension-leg platform (TLP) under first- and second-order wave forces, including the mean-drift force, difference and sum-frequency forces. The second-order wave force is calculated using the full-field quadratic transfer function (QTF). The coupled effect of the horizontal motions, such as surge, sway and yaw motions, and the set-down motion are taken into consideration by the nonlinear restoring matrix. The time-domain analysis with 50-yr random sea state is performed. A comparison of the results of different case studies is made to assess the influence of second-order wave force on the motions of the platform. The analysis shows that the second-order wave force has a major impact on motions of the TLP. The second-order difference-frequency wave force has an obvious influence on the low-frequency motions of surge and sway, and also will induce a large set-down motion which is an important part of heave motion. Besides, the second-order sum-frequency force will induce a set of high-frequency motions of roll and pitch. However, little influence of second-order wave force is found on the yaw motion.

An exergame system based on force platforms and body key-point detection for balance training.

PubMed

Lavarda, Marcos D; de Borba, Pedro A; Oliveira, Matheus R; Borba, Gustavo B; de Souza, Mauren A; Gamba, Humberto R

2016-08-01

Postural instability affects a large number of people and can compromise even simple activities of the daily routine. Therapies for balance training can strongly benefit from auxiliary devices specially designed for this purpose. In this paper, we present a system for balance training that uses the metaphor of a game, what contributes to the motivation and engagement of the patients during a treatment. Such approach is usually named exergame, in which input devices for posturographic assessment and a visual output perform the interaction with the subject. The proposed system uses two force platforms, one positioned under the feet and the other under the hip of the subject. The force platforms employ regular load cells and a microcontroller-based signal acquisition module to capture and transmit the samples to a computer. Moreover, a computer vision module performs body key-point detection, based on real time segmentation of markers attached to the subject. For the validation of the system, we conducted experiments with 20 neurologically intact volunteers during two tests: comparison of the stabilometric parameters obtained from the system with those obtained from a commercial baropodometer and the practice of several exergames. Results show that the proposed system is completely functional and can be used as a versatile tool for balance training.

A Physical Heart Failure Simulation System Utilizing the Total Artificial Heart and Modified Donovan Mock Circulation.

PubMed

Crosby, Jessica R; DeCook, Katrina J; Tran, Phat L; Betterton, Edward; Smith, Richard G; Larson, Douglas F; Khalpey, Zain I; Burkhoff, Daniel; Slepian, Marvin J

2017-07-01

With the growth and diversity of mechanical circulatory support (MCS) systems entering clinical use, a need exists for a robust mock circulation system capable of reliably emulating and reproducing physiologic as well as pathophysiologic states for use in MCS training and inter-device comparison. We report on the development of such a platform utilizing the SynCardia Total Artificial Heart and a modified Donovan Mock Circulation System, capable of being driven at normal and reduced output. With this platform, clinically relevant heart failure hemodynamics could be reliably reproduced as evidenced by elevated left atrial pressure (+112%), reduced aortic flow (-12.6%), blunted Starling-like behavior, and increased afterload sensitivity when compared with normal function. Similarly, pressure-volume relationships demonstrated enhanced sensitivity to afterload and decreased Starling-like behavior in the heart failure model. Lastly, the platform was configured to allow the easy addition of a left ventricular assist device (HeartMate II at 9600 RPM), which upon insertion resulted in improvement of hemodynamics. The present configuration has the potential to serve as a viable system for training and research, aimed at fostering safe and effective MCS device use. © 2016 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Efficient Comparison between Windows and Linux Platform Applicable in a Virtual Architectural Walkthrough Application

NASA Astrophysics Data System (ADS)

Thubaasini, P.; Rusnida, R.; Rohani, S. M.

This paper describes Linux, an open source platform used to develop and run a virtual architectural walkthrough application. It proposes some qualitative reflections and observations on the nature of Linux in the concept of Virtual Reality (VR) and on the most popular and important claims associated with the open source approach. The ultimate goal of this paper is to measure and evaluate the performance of Linux used to build the virtual architectural walkthrough and develop a proof of concept based on the result obtain through this project. Besides that, this study reveals the benefits of using Linux in the field of virtual reality and reflects a basic comparison and evaluation between Windows and Linux base operating system. Windows platform is use as a baseline to evaluate the performance of Linux. The performance of Linux is measured based on three main criteria which is frame rate, image quality and also mouse motion.

The chemiluminescence based Ziplex automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip expression profiles.

PubMed

Quinn, Michael C J; Wilson, Daniel J; Young, Fiona; Dempsey, Adam A; Arcand, Suzanna L; Birch, Ashley H; Wojnarowicz, Paulina M; Provencher, Diane; Mes-Masson, Anne-Marie; Englert, David; Tonin, Patricia N

2009-07-06

As gene expression signatures may serve as biomarkers, there is a need to develop technologies based on mRNA expression patterns that are adaptable for translational research. Xceed Molecular has recently developed a Ziplex technology, that can assay for gene expression of a discrete number of genes as a focused array. The present study has evaluated the reproducibility of the Ziplex system as applied to ovarian cancer research of genes shown to exhibit distinct expression profiles initially assessed by Affymetrix GeneChip analyses. The new chemiluminescence-based Ziplex gene expression array technology was evaluated for the expression of 93 genes selected based on their Affymetrix GeneChip profiles as applied to ovarian cancer research. Probe design was based on the Affymetrix target sequence that favors the 3' UTR of transcripts in order to maximize reproducibility across platforms. Gene expression analysis was performed using the Ziplex Automated Workstation. Statistical analyses were performed to evaluate reproducibility of both the magnitude of expression and differences between normal and tumor samples by correlation analyses, fold change differences and statistical significance testing. Expressions of 82 of 93 (88.2%) genes were highly correlated (p < 0.01) in a comparison of the two platforms. Overall, 75 of 93 (80.6%) genes exhibited consistent results in normal versus tumor tissue comparisons for both platforms (p < 0.001). The fold change differences were concordant for 87 of 93 (94%) genes, where there was agreement between the platforms regarding statistical significance for 71 (76%) of 87 genes. There was a strong agreement between the two platforms as shown by comparisons of log2 fold differences of gene expression between tumor versus normal samples (R = 0.93) and by Bland-Altman analysis, where greater than 90% of expression values fell within the 95% limits of agreement. Overall concordance of gene expression patterns based on correlations, statistical significance between tumor and normal ovary data, and fold changes was consistent between the Ziplex and Affymetrix platforms. The reproducibility and ease-of-use of the technology suggests that the Ziplex array is a suitable platform for translational research.

Gut bacterial diversity of the tribes of India and comparison with the worldwide data

PubMed Central

Dehingia, Madhusmita; Thangjam devi, Kanchal; Talukdar, Narayan C.; Talukdar, Rupjyoti; Reddy, Nageshwar; Mande, Sharmila S.; Deka, Manab; Khan, Mojibur R.

2015-01-01

The gut bacteria exert phenotypic traits to the host but the factors which determine the gut bacterial profile (GBP) is poorly understood. This study aimed to understand the effect of ethnicity and geography on GBP of Mongoloid and Proto-Australoid tribes of India. Fecal bacterial diversity was studied in fifteen tribal populations representing four geographic regions (Assam, Telangana, Manipur and Sikkim) by DGGE followed by NGS analysis on Illumina MiSeq platform. Geography and diet had significant effect on GBP of the Indian tribes which was dominated by Prevotella. The effects were more prominent with lower taxonomic levels, indicating probable functional redundancy of the core GBP. A comparison with the worldwide data revealed that GBP of the Indian population was similar to the Mongolian population (Mongolia). The bacterial genera Faecalibacterium, Eubacterium, Clostridium, Blautia, Ruminococcus and Roseburia were found to be core genera in the representative populations of the world. PMID:26689136

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

PubMed Central

Nookaew, Intawat; Papini, Marta; Pornputtapong, Natapol; Scalcinati, Gionata; Fagerberg, Linn; Uhlén, Matthias; Nielsen, Jens

2012-01-01

RNA-seq, has recently become an attractive method of choice in the studies of transcriptomes, promising several advantages compared with microarrays. In this study, we sought to assess the contribution of the different analytical steps involved in the analysis of RNA-seq data generated with the Illumina platform, and to perform a cross-platform comparison based on the results obtained through Affymetrix microarray. As a case study for our work we, used the Saccharomyces cerevisiae strain CEN.PK 113-7D, grown under two different conditions (batch and chemostat). Here, we asses the influence of genetic variation on the estimation of gene expression level using three different aligners for read-mapping (Gsnap, Stampy and TopHat) on S288c genome, the capabilities of five different statistical methods to detect differential gene expression (baySeq, Cuffdiff, DESeq, edgeR and NOISeq) and we explored the consistency between RNA-seq analysis using reference genome and de novo assembly approach. High reproducibility among biological replicates (correlation ≥0.99) and high consistency between the two platforms for analysis of gene expression levels (correlation ≥0.91) are reported. The results from differential gene expression identification derived from the different statistical methods, as well as their integrated analysis results based on gene ontology annotation are in good agreement. Overall, our study provides a useful and comprehensive comparison between the two platforms (RNA-seq and microrrays) for gene expression analysis and addresses the contribution of the different steps involved in the analysis of RNA-seq data. PMID:22965124

Roles of Chemical Functionality and Pore Curvature in the Design of Nanoporous Proton Conductors

DOE PAGES

Jackson, Grayson L.; Perroni, Dominic V.; Mahanthappa, Mahesh K.

2017-10-03

Nanoporous proton-transporting media are critical components in fuel cells and other electrochemical devices, yet general molecular design criteria for new materials with enhanced performance remain obscure. Aqueous lyotropic liquid crystals (LLCs) comprise a platform for detailed studies of the molecular-level features governing proton transport in monodisperse, water-filled nanopores lined with well-defined chemical functionalities. Here, we report new alkylsulfonic acid LLCs that exhibit H+ conductivities as high as σ = 380 mS/cm at 80°C, which rival those of more acidic, perfluorinated polymers, thus demonstrating that the acidity of the pore functionality is not the sole determinant of proton transport. Direct experimentalmore » comparisons of LLCs with convex and concave nanopores of similar dimensions indicate that H+ conductivities therein sensitively depend on the hydration state of the acid functionalities and the pore curvature. These experiments suggest that judicious manipulation of pore curvature provides a new means for optimizing the activities of proton-exchange membranes and nanoporous solid acid catalysts.« less

Comparison of precision and speed in laparoscopic and robot-assisted surgical task performance.

PubMed

Zihni, Ahmed; Gerull, William D; Cavallo, Jaime A; Ge, Tianjia; Ray, Shuddhadeb; Chiu, Jason; Brunt, L Michael; Awad, Michael M

2018-03-01

Robotic platforms have the potential advantage of providing additional dexterity and precision to surgeons while performing complex laparoscopic tasks, especially for those in training. Few quantitative evaluations of surgical task performance comparing laparoscopic and robotic platforms among surgeons of varying experience levels have been done. We compared measures of quality and efficiency of Fundamentals of Laparoscopic Surgery task performance on these platforms in novices and experienced laparoscopic and robotic surgeons. Fourteen novices, 12 expert laparoscopic surgeons (>100 laparoscopic procedures performed, no robotics experience), and five expert robotic surgeons (>25 robotic procedures performed) performed three Fundamentals of Laparoscopic Surgery tasks on both laparoscopic and robotic platforms: peg transfer (PT), pattern cutting (PC), and intracorporeal suturing. All tasks were repeated three times by each subject on each platform in a randomized order. Mean completion times and mean errors per trial (EPT) were calculated for each task on both platforms. Results were compared using Student's t-test (P < 0.05 considered statistically significant). Among novices, greater errors were noted during laparoscopic PC (Lap 2.21 versus Robot 0.88 EPT, P < 0.001). Among expert laparoscopists, greater errors were noted during laparoscopic PT compared with robotic (PT: Lap 0.14 versus Robot 0.00 EPT, P = 0.04). Among expert robotic surgeons, greater errors were noted during laparoscopic PC compared with robotic (Lap 0.80 versus Robot 0.13 EPT, P = 0.02). Among expert laparoscopists, task performance was slower on the robotic platform compared with laparoscopy. In comparisons of expert laparoscopists performing tasks on the laparoscopic platform and expert robotic surgeons performing tasks on the robotic platform, expert robotic surgeons demonstrated fewer errors during the PC task (P = 0.009). Robotic assistance provided a reduction in errors at all experience levels for some laparoscopic tasks, but no benefit in the speed of task performance. Robotic assistance may provide some benefit in precision of surgical task performance. Copyright © 2017 Elsevier Inc. All rights reserved.

Relationships between chlorophyll density and ocean radiance as measured by U2/OCS: Algorithms, examples and comparison

NASA Technical Reports Server (NTRS)

Kim, H. H.; Hart, W. D.

1983-01-01

An ocean atmosphere radiative transfer process computation method which is suitable for determining lower boundary ocean albedo and other radiation components from spectral measurements of upwelling radiance taken from a high altitude platform is described. The method was applied to a set of color scanner data taken from slope water of the South Atlantic Bight to determine the influence of cholorophyll-a pigments in the sea on the ratio of upwelling radiance to down welling irradiance as a function of wavelength. The resulting chlorophyll concentrations are compared with measurements made by ships stationed along the flight path.

Impact of MOODLE Platform on the Pedagogy of Students and Staff: Cross-Curricular Comparison

ERIC Educational Resources Information Center

Jackson, Emerson Abraham

2017-01-01

In the current Information Age, technology is taking the lead in moving teaching and learning beyond that which was once viewed as typically didactic approach to knowledge acquisition. The outcome of this research paper have explored the importance of MOODLE learning platform and its contribution in promoting flexible teaching, and the need for…

A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data.

PubMed

Siretskiy, Alexey; Sundqvist, Tore; Voznesenskiy, Mikhail; Spjuth, Ola

2015-01-01

New high-throughput technologies, such as massively parallel sequencing, have transformed the life sciences into a data-intensive field. The most common e-infrastructure for analyzing this data consists of batch systems that are based on high-performance computing resources; however, the bioinformatics software that is built on this platform does not scale well in the general case. Recently, the Hadoop platform has emerged as an interesting option to address the challenges of increasingly large datasets with distributed storage, distributed processing, built-in data locality, fault tolerance, and an appealing programming methodology. In this work we introduce metrics and report on a quantitative comparison between Hadoop and a single node of conventional high-performance computing resources for the tasks of short read mapping and variant calling. We calculate efficiency as a function of data size and observe that the Hadoop platform is more efficient for biologically relevant data sizes in terms of computing hours for both split and un-split data files. We also quantify the advantages of the data locality provided by Hadoop for NGS problems, and show that a classical architecture with network-attached storage will not scale when computing resources increase in numbers. Measurements were performed using ten datasets of different sizes, up to 100 gigabases, using the pipeline implemented in Crossbow. To make a fair comparison, we implemented an improved preprocessor for Hadoop with better performance for splittable data files. For improved usability, we implemented a graphical user interface for Crossbow in a private cloud environment using the CloudGene platform. All of the code and data in this study are freely available as open source in public repositories. From our experiments we can conclude that the improved Hadoop pipeline scales better than the same pipeline on high-performance computing resources, we also conclude that Hadoop is an economically viable option for the common data sizes that are currently used in massively parallel sequencing. Given that datasets are expected to increase over time, Hadoop is a framework that we envision will have an increasingly important role in future biological data analysis.

QGene 4.0, an extensible Java QTL-analysis platform.

PubMed

Joehanes, Roby; Nelson, James C

2008-12-01

Of many statistical methods developed to date for quantitative trait locus (QTL) analysis, only a limited subset are available in public software allowing their exploration, comparison and practical application by researchers. We have developed QGene 4.0, a plug-in platform that allows execution and comparison of a variety of modern QTL-mapping methods and supports third-party addition of new ones. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Software and documentation are available at http://coding.plantpath.ksu.edu/qgene. Source code is available on request.

A comparison of measured radiances from AIRS and HIRS across different cloud types

NASA Astrophysics Data System (ADS)

Schreier, M. M.; Kahn, B. H.; Staten, P.

2015-12-01

The observation of Earth's atmosphere with passive remote sensing instruments is ongoing for decades and resulting in a long-term global dataset. Two prominent examples are operational satellite platforms from the National Oceanic and Atmospheric Administration (NOAA) or research platforms like NASA's Earth Observing System (EOS). The observed spectral ranges of these observations are often similar among the different platforms, but have large differences when it comes to resolution, accuracy and quality control. Our approach is to combine different kinds of instruments at the pixel-scale to improve the characterization of infrared radiances. We focus on data from the High-resolution Infrared Radiation Sounder (HIRS) and compare the observations to radiances from the Atmospheric Infrared Sounder (AIRS) on Aqua. The high spectral resolution of AIRS is used to characterize and possibly recalibrate the observed radiances from HIRS. Our approach is unique in that we use additional information from other passive instruments on the same platforms including the Advanced Very High Resolution Radiometer (AVHRR) and the MODerate resolution Imaging Spectroradiometer (MODIS). We will present comparisons of radiances from HIRS and AIRS within different types of clouds that are determined from the imagers. In this way, we can analyze and select the most homogeneous conditions for radiance comparisons and a possible re-calibration of HIRS. We hope to achieve a cloud-type-dependent calibration and quality control for HIRS, which can be extrapolated into the past via inter-calibration of the different HIRS instruments beyond the time of AIRS.

Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein-Protein Interaction Data.

PubMed

Pokharel, Yuba Raj; Saarela, Jani; Szwajda, Agnieszka; Rupp, Christian; Rokka, Anne; Lal Kumar Karna, Shibendra; Teittinen, Kaisa; Corthals, Garry; Kallioniemi, Olli; Wennerberg, Krister; Aittokallio, Tero; Westermarck, Jukka

2015-12-01

High content protein interaction screens have revolutionized our understanding of protein complex assembly. However, one of the major challenges in translation of high content protein interaction data is identification of those interactions that are functionally relevant for a particular biological question. To address this challenge, we developed a relevance ranking platform (RRP), which consist of modular functional and bioinformatic filters to provide relevance rank among the interactome proteins. We demonstrate the versatility of RRP to enable a systematic prioritization of the most relevant interaction partners from high content data, highlighted by the analysis of cancer relevant protein interactions for oncoproteins Pin1 and PME-1. We validated the importance of selected interactions by demonstration of PTOV1 and CSKN2B as novel regulators of Pin1 target c-Jun phosphorylation and reveal previously unknown interacting proteins that may mediate PME-1 effects via PP2A-inhibition. The RRP framework is modular and can be modified to answer versatile research problems depending on the nature of the biological question under study. Based on comparison of RRP to other existing filtering tools, the presented data indicate that RRP offers added value especially for the analysis of interacting proteins for which there is no sufficient prior knowledge available. Finally, we encourage the use of RRP in combination with either SAINT or CRAPome computational tools for selecting the candidate interactors that fulfill the both important requirements, functional relevance, and high confidence interaction detection. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

VOLTTRON 3.0: User Guide

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

Lutes, Robert G.; Haack, Jereme N.; Katipamula, Srinivas

This document is a user guide for the deployment of the transactional network platform and agent/application development within VOLTTRON. The intent of this user guide is to provide a description of the functionality of the transactional network platform. This document describes how to deploy the platform, including installation, use, guidance, and limitations. It also describes how additional features can be added to enhance its current functionality.

VOLTTRON 2.0: User Guide

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

Lutes, Robert G.; Haack, Jereme N.; Katipamula, Srinivas

This document is a user guide for the deployment of the transactional network platform and agent/application development within VOLTTRON. The intent of this user guide is to provide a description of the functionality of the transactional network platform. This document describes how to deploy the platform, including installation, use, guidance, and limitations. It also describes how additional features can be added to enhance its current functionality.

Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB)

NASA Astrophysics Data System (ADS)

Ghani, Nur Syatila Ab; Firdaus-Raih, Mohd

2018-04-01

The three-dimensional structure of a protein can provide insights regarding its function. Functional relationship between proteins can be inferred from fold and sequence similarities. In certain cases, sequence or fold comparison fails to conclude homology between proteins with similar mechanism. Since the structure is more conserved than the sequence, a constellation of functional residues can be similarly arranged among proteins of similar mechanism. Local structural similarity searches are able to detect such constellation of amino acids among distinct proteins, which can be useful to annotate proteins of unknown function. Detection of such patterns of amino acids on a large scale can increase the repertoire of important 3D motifs since available known 3D motifs currently, could not compensate the ever-increasing numbers of uncharacterized proteins to be annotated. Here, a computational platform for an automated detection of 3D motifs is described. A fuzzy-pattern searching algorithm derived from IMagine an Amino Acid 3D Arrangement search EnGINE (IMAAAGINE) was implemented to develop an automated method for searching of hypothetical patterns of amino acid side chains in Protein Data Bank (PDB), without the need for prior knowledge on related sequence or structure of pattern of interest. We present an example of the searches, which is the detection of a hypothetical pattern derived from known structural motif of C2H2 structural pattern from zinc fingers. The conservation of particular patterns of amino acid side chains in unrelated proteins is highlighted. This approach can act as a complementary method for available structure- and sequence-based platforms and may contribute in improving functional association between proteins.

Understanding the Cray X1 System

NASA Technical Reports Server (NTRS)

Cheung, Samson

2004-01-01

This paper helps the reader understand the characteristics of the Cray X1 vector supercomputer system, and provides hints and information to enable the reader to port codes to the system. It provides a comparison between the basic performance of the X1 platform and other platforms that are available at NASA Ames Research Center. A set of codes, solving the Laplacian equation with different parallel paradigms, is used to understand some features of the X1 compiler. An example code from the NAS Parallel Benchmarks is used to demonstrate performance optimization on the X1 platform.

Validation of a multiplex electrochemiluminescent immunoassay platform in human and mouse samples

PubMed Central

Bastarache, J.A.; Koyama, T.; Wickersham, N.E; Ware, L.B.

2014-01-01

Despite the widespread use of multiplex immunoassays, there are very few scientific reports that test the accuracy and reliability of a platform prior to publication of experimental data. Our laboratory has previously demonstrated the need for new assay platform validation prior to use of biologic samples from large studies in order to optimize sample handling and assay performance. In this study, our goal was to test the accuracy and reproducibility of an electrochemiluminescent multiplex immunoassay platform (Meso Scale Discovery, MSD®) and compare this platform to validated, singleplex immunoassays (R&D Systems®) using actual study subject (human plasma and mouse bronchoalveolar lavage fluid (BALF) and plasma) samples. We found that the MSD platform performed well on intra- and inter-assay comparisons, spike and recovery and cross-platform comparisons. The mean intra-assay CV% and range for MSD was 3.49 (0.0-10.4) for IL-6 and 2.04 (0.1-7.9) for IL-8. The correlation between values for identical samples measured on both MSD and R&D was R=0.97 for both analytes. The mouse MSD assay had a broader range of CV% with means ranging from 9.5-28.5 depending on the analyte. The range of mean CV% was similar for single plex ELISAs at 4.3-23.7 depending on the analyte. Regardless of species or sample type, CV% was more variable at lower protein concentrations. In conclusion, we validated a multiplex electrochemiluminscent assay system and found that it has superior test characteristics in human plasma compared to mouse BALF and plasma. Both human and MSD assays compared favorably to well-validated singleplex ELISA's PMID:24768796

Benchmarking of dynamic simulation predictions in two software platforms using an upper limb musculoskeletal model

PubMed Central

Saul, Katherine R.; Hu, Xiao; Goehler, Craig M.; Vidt, Meghan E.; Daly, Melissa; Velisar, Anca; Murray, Wendy M.

2014-01-01

Several opensource or commercially available software platforms are widely used to develop dynamic simulations of movement. While computational approaches are conceptually similar across platforms, technical differences in implementation may influence output. We present a new upper limb dynamic model as a tool to evaluate potential differences in predictive behavior between platforms. We evaluated to what extent differences in technical implementations in popular simulation software environments result in differences in kinematic predictions for single and multijoint movements using EMG- and optimization-based approaches for deriving control signals. We illustrate the benchmarking comparison using SIMM-Dynamics Pipeline-SD/Fast and OpenSim platforms. The most substantial divergence results from differences in muscle model and actuator paths. This model is a valuable resource and is available for download by other researchers. The model, data, and simulation results presented here can be used by future researchers to benchmark other software platforms and software upgrades for these two platforms. PMID:24995410

Benchmarking of dynamic simulation predictions in two software platforms using an upper limb musculoskeletal model.

PubMed

Saul, Katherine R; Hu, Xiao; Goehler, Craig M; Vidt, Meghan E; Daly, Melissa; Velisar, Anca; Murray, Wendy M

2015-01-01

Several opensource or commercially available software platforms are widely used to develop dynamic simulations of movement. While computational approaches are conceptually similar across platforms, technical differences in implementation may influence output. We present a new upper limb dynamic model as a tool to evaluate potential differences in predictive behavior between platforms. We evaluated to what extent differences in technical implementations in popular simulation software environments result in differences in kinematic predictions for single and multijoint movements using EMG- and optimization-based approaches for deriving control signals. We illustrate the benchmarking comparison using SIMM-Dynamics Pipeline-SD/Fast and OpenSim platforms. The most substantial divergence results from differences in muscle model and actuator paths. This model is a valuable resource and is available for download by other researchers. The model, data, and simulation results presented here can be used by future researchers to benchmark other software platforms and software upgrades for these two platforms.

Quantitative genetic-interaction mapping in mammalian cells

PubMed Central

Roguev, Assen; Talbot, Dale; Negri, Gian Luca; Shales, Michael; Cagney, Gerard; Bandyopadhyay, Sourav; Panning, Barbara; Krogan, Nevan J

2013-01-01

Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ~11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape. PMID:23407553

Protein Sequence Annotation Tool (PSAT): A centralized web-based meta-server for high-throughput sequence annotations

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

Leung, Elo; Huang, Amy; Cadag, Eithon

In this study, we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resultingmore » functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. Lastly, PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequencebased genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome.« less

Protein Sequence Annotation Tool (PSAT): A centralized web-based meta-server for high-throughput sequence annotations

DOE PAGES

Leung, Elo; Huang, Amy; Cadag, Eithon; ...

2016-01-20

In this study, we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resultingmore » functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. Lastly, PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequencebased genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome.« less

A Versatile Bioorthogonal Copper-free Click Chemistry Platform to Functionalize Cisplatin Prodrugs

PubMed Central

Pathak, Rakesh K.; McNitt, Christopher D.; Popik, Vladimir V.; Dhar, Shanta

2015-01-01

The ability to rationally design and construct a platform technology to develop new platinum(IV) [Pt(IV)] prodrugs with functionalities for installation of targeting moieties, delivery systems, fluorescent reporters from a single precursor with the ability to release biologically active cisplatin using well-defined chemistry is critical for discovering new platinum-based therapeutics. With limited numbers of possibilities by considering the sensitivity of Pt(IV) centers to reduction, thiols, etc, we used a strain promoted azide alkyne cycloaddition (SPAAC) approach to provide a novel platform where new functionalities can easily be installed on cisplatin prodrugs from a single Pt(IV) precursor. The ability of this platform to be incorporated in nano-delivery vehicle and conjugation to fluorescent reporters were also investigated. PMID:24756923

Copper-free click-chemistry platform to functionalize cisplatin prodrugs.

PubMed

Pathak, Rakesh K; McNitt, Christopher D; Popik, Vladimir V; Dhar, Shanta

2014-06-02

The ability to rationally design and construct a platform technology to develop new platinum(IV) [Pt(IV)] prodrugs with functionalities for installation of targeting moieties, delivery systems, fluorescent reporters from a single precursor with the ability to release biologically active cisplatin by using well-defined chemistry is critical for discovering new platinum-based therapeutics. With limited numbers of possibilities considering the sensitivity of Pt(IV) centers, we used a strain-promoted azide-alkyne cycloaddition approach to provide a platform, in which new functionalities can easily be installed on cisplatin prodrugs from a single Pt(IV) precursor. The ability of this platform to be incorporated in nanodelivery vehicle and conjugation to fluorescent reporters were also investigated. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tuning cell adhesion by direct nanostructuring silicon into cell repulsive/adhesive patterns

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

Premnath, Priyatha, E-mail: priyatha.premnath@ryerson.ca; Tavangar, Amirhossein, E-mail: atavanga@ryerson.ca; Tan, Bo, E-mail: tanbo@ryerson.ca

2015-09-10

Developing platforms that allow tuning cell functionality through incorporating physical, chemical, or mechanical cues onto the material surfaces is one of the key challenges in research in the field of biomaterials. In this respect, various approaches have been proposed and numerous structures have been developed on a variety of materials. Most of these approaches, however, demand a multistep process or post-chemical treatment. Therefore, a simple approach would be desirable to develop bio-functionalized platforms for effectively modulating cell adhesion and consequently programming cell functionality without requiring any chemical or biological surface treatment. This study introduces a versatile yet simple laser approachmore » to structure silicon (Si) chips into cytophobic/cytophilic patterns in order to modulate cell adhesion and proliferation. These patterns are fabricated on platforms through direct laser processing of Si substrates, which renders a desired computer-generated configuration into patterns. We investigate the morphology, chemistry, and wettability of the platform surfaces. Subsequently, we study the functionality of the fabricated platforms on modulating cervical cancer cells (HeLa) behaviour. The results from in vitro studies suggest that the nanostructures efficiently repel HeLa cells and drive them to migrate onto untreated sites. The study of the morphology of the cells reveals that cells evade the cytophobic area by bending and changing direction. Additionally, cell patterning, cell directionality, cell channelling, and cell trapping are achieved by developing different platforms with specific patterns. The flexibility and controllability of this approach to effectively structure Si substrates to cell-repulsive and cell-adhesive patterns offer perceptible outlook for developing bio-functionalized platforms for a variety of biomedical devices. Moreover, this approach could pave the way for developing anti-cancer platforms that selectively repel cancer cells while favoring the adhesion of normal cells. - Highlights: • Si platforms with cytophobic/philic patterns were developed to program cell growth. • Both nanotopography and chemistry contributed to the cytophobic property. • Cytophobic zones efficiently repel and drive HeLa cells to migrate to adhesive sites. • The approach enables cell patterning, directionality, channelling, and trapping. • This approach paves the way for developing anti-cancer platforms.« less

A Structured and Unstructured grid Relocatable ocean platform for Forecasting (SURF)

NASA Astrophysics Data System (ADS)

Trotta, Francesco; Fenu, Elisa; Pinardi, Nadia; Bruciaferri, Diego; Giacomelli, Luca; Federico, Ivan; Coppini, Giovanni

2016-11-01

We present a numerical platform named Structured and Unstructured grid Relocatable ocean platform for Forecasting (SURF). The platform is developed for short-time forecasts and is designed to be embedded in any region of the large-scale Mediterranean Forecasting System (MFS) via downscaling. We employ CTD data collected during a campaign around the Elba island to calibrate and validate SURF. The model requires an initial spin up period of a few days in order to adapt the initial interpolated fields and the subsequent solutions to the higher-resolution nested grids adopted by SURF. Through a comparison with the CTD data, we quantify the improvement obtained by SURF model compared to the coarse-resolution MFS model.

Comparison of the LEGO Mindstorms NXT and EV3 Robotics Education Platforms

ERIC Educational Resources Information Center

Sherrard, Ann; Rhodes, Amy

2014-01-01

The release of the latest LEGO Mindstorms EV3 robotics platform in September 2013 has provided a dilemma for many youth robotics leaders. There is a need to understand the differences in the Mindstorms NXT and EV3 in order to make future robotics purchases. In this article the differences are identified regarding software, hardware, sensors, the…

49 CFR 37.42 - Service in an Integrated Setting to Passengers at Intercity, Commuter, and High-Speed Rail...

Code of Federal Regulations, 2012 CFR

2012-10-01

... plates, ramps or other appropriate devices; (4) Mini-high platforms, with multiple mini-high platforms or... chooses a means of meeting the performance standard other than using car-borne lifts, it must perform a comparison of the costs (capital, operating, and life-cycle costs) of car-borne lifts and the means chosen by...

49 CFR 37.42 - Service in an Integrated Setting to Passengers at Intercity, Commuter, and High-Speed Rail...

Code of Federal Regulations, 2014 CFR

2014-10-01

... plates, ramps or other appropriate devices; (4) Mini-high platforms, with multiple mini-high platforms or... chooses a means of meeting the performance standard other than using car-borne lifts, it must perform a comparison of the costs (capital, operating, and life-cycle costs) of car-borne lifts and the means chosen by...

49 CFR 37.42 - Service in an integrated setting to passengers at intercity, commuter, and high-speed rail...

Code of Federal Regulations, 2011 CFR

2011-10-01

... plates, ramps or other appropriate devices; (4) Mini-high platforms, with multiple mini-high platforms or... chooses a means of meeting the performance standard other than using car-borne lifts, it must perform a comparison of the costs (capital, operating, and life-cycle costs) of car-borne lifts and the means chosen by...

49 CFR 37.42 - Service in an Integrated Setting to Passengers at Intercity, Commuter, and High-Speed Rail...

Code of Federal Regulations, 2013 CFR

2013-10-01

... plates, ramps or other appropriate devices; (4) Mini-high platforms, with multiple mini-high platforms or... chooses a means of meeting the performance standard other than using car-borne lifts, it must perform a comparison of the costs (capital, operating, and life-cycle costs) of car-borne lifts and the means chosen by...

Cortical gyrification is abnormal in children with prenatal alcohol exposure.

PubMed

Hendrickson, Timothy J; Mueller, Bryon A; Sowell, Elizabeth R; Mattson, Sarah N; Coles, Claire D; Kable, Julie A; Jones, Kenneth L; Boys, Christopher J; Lim, Kelvin O; Riley, Edward P; Wozniak, Jeffrey R

2017-01-01

Prenatal alcohol exposure (PAE) adversely affects early brain development. Previous studies have shown a wide range of structural and functional abnormalities in children and adolescents with PAE. The current study adds to the existing literature specifically on cortical development by examining cortical gyrification in a large sample of children with PAE compared to controls. Relationships between cortical development and intellectual functioning are also examined. Included were 92 children with PAE and 83 controls ages 9-16 from four sites in the Collaborative Initiative on FASD (CIFASD). All PAE participants had documented heavy PAE. All underwent a formal evaluation of physical anomalies and dysmorphic facial features. MRI data were collected using modified matched protocols on three platforms (Siemens, GE, and Philips). Cortical gyrification was examined using a semi-automated procedure. Whole brain group comparisons using Monte Carlo z-simulation for multiple comparisons showed significantly lower cortical gyrification across a large proportion of the cerebral cortex amongst PAE compared to controls. Whole brain comparisons and ROI based analyses showed strong positive correlations between cortical gyrification and IQ (i.e. less developed cortex was associated with lower IQ). Abnormalities in cortical development were seen across the brain in children with PAE compared to controls. Cortical gyrification and IQ were strongly correlated, suggesting that examining mechanisms by which alcohol disrupts cortical formation may yield clinically relevant insights and potential directions for early intervention.

Assembly Platform For Use In Outer Space

NASA Technical Reports Server (NTRS)

Rao, Niranjan S.; Buddington, Patricia A.

1995-01-01

Report describes conceptual platform or framework for use in assembling other structures and spacecraft in outer space. Consists of three fixed structural beams comprising central beam and two cross beams. Robotic manipulators spaced apart on platform to provide telerobotic operation of platform by either space-station or ground crews. Platform and attached vehicles function synergistically to achieve maximum performance for intended purposes.

Development of a Low-Cost Arduino-Based Sonde for Coastal Applications.

PubMed

Lockridge, Grant; Dzwonkowski, Brian; Nelson, Reid; Powers, Sean

2016-04-13

This project addresses the need for an expansion in the monitoring of marine environments by providing a detailed description of a low cost, robust, user friendly sonde, built on Arduino Mega 2560 (Mega) and Arduino Uno (Uno) platforms. The sonde can be made without specialized tools or training and can be easily modified to meet individual application requirements. The platform allows for internal logging of multiple parameters of which conductivity, temperature, and GPS position are demonstrated. Two design configurations for different coastal hydrographic applications are highlighted to show the robust and versatile nature of this sensor platform. The initial sonde design was intended for use on a Lagrangian style surface drifter that recorded measurements of temperature; salinity; and position for a deployment duration of less than 24 h. Functional testing of the sensor consisted of a 55 h comparison with a regularly maintained water quality sensor (i.e., YSI 6600 sonde) in Mobile Bay, AL. The temperature and salinity data were highly correlated and had acceptable RMS errors of 0.154 °C and 1.35 psu for the environmental conditions. A second application using the sonde platform was designed for longer duration (~3-4 weeks); subsurface (1.5-4.0 m depths) deployment, moored to permanent structures. Design alterations reflected an emphasis on minimizing power consumption, which included the elimination of the GPS capabilities, increased battery capacity, and power-saving software modifications. The sonde designs presented serve as templates that will expand the hydrographic measurement capabilities of ocean scientists, students, and teachers.

Development of a Low-Cost Arduino-Based Sonde for Coastal Applications

PubMed Central

Lockridge, Grant; Dzwonkowski, Brian; Nelson, Reid; Powers, Sean

2016-01-01

This project addresses the need for an expansion in the monitoring of marine environments by providing a detailed description of a low cost, robust, user friendly sonde, built on Arduino Mega 2560 (Mega) and Arduino Uno (Uno) platforms. The sonde can be made without specialized tools or training and can be easily modified to meet individual application requirements. The platform allows for internal logging of multiple parameters of which conductivity, temperature, and GPS position are demonstrated. Two design configurations for different coastal hydrographic applications are highlighted to show the robust and versatile nature of this sensor platform. The initial sonde design was intended for use on a Lagrangian style surface drifter that recorded measurements of temperature; salinity; and position for a deployment duration of less than 24 h. Functional testing of the sensor consisted of a 55 h comparison with a regularly maintained water quality sensor (i.e., YSI 6600 sonde) in Mobile Bay, AL. The temperature and salinity data were highly correlated and had acceptable RMS errors of 0.154 °C and 1.35 psu for the environmental conditions. A second application using the sonde platform was designed for longer duration (~3–4 weeks); subsurface (1.5–4.0 m depths) deployment, moored to permanent structures. Design alterations reflected an emphasis on minimizing power consumption, which included the elimination of the GPS capabilities, increased battery capacity, and power-saving software modifications. The sonde designs presented serve as templates that will expand the hydrographic measurement capabilities of ocean scientists, students, and teachers. PMID:27089337

A novel real time imaging platform to quantify macrophage phagocytosis.

PubMed

Kapellos, Theodore S; Taylor, Lewis; Lee, Heyne; Cowley, Sally A; James, William S; Iqbal, Asif J; Greaves, David R

2016-09-15

Phagocytosis of pathogens, apoptotic cells and debris is a key feature of macrophage function in host defense and tissue homeostasis. Quantification of macrophage phagocytosis in vitro has traditionally been technically challenging. Here we report the optimization and validation of the IncuCyte ZOOM® real time imaging platform for macrophage phagocytosis based on pHrodo® pathogen bioparticles, which only fluoresce when localized in the acidic environment of the phagolysosome. Image analysis and fluorescence quantification were performed with the automated IncuCyte™ Basic Software. Titration of the bioparticle number showed that the system is more sensitive than a spectrofluorometer, as it can detect phagocytosis when using 20× less E. coli bioparticles. We exemplified the power of this real time imaging platform by studying phagocytosis of murine alveolar, bone marrow and peritoneal macrophages. We further demonstrate the ability of this platform to study modulation of the phagocytic process, as pharmacological inhibitors of phagocytosis suppressed bioparticle uptake in a concentration-dependent manner, whereas opsonins augmented phagocytosis. We also investigated the effects of macrophage polarization on E. coli phagocytosis. Bone marrow-derived macrophage (BMDM) priming with M2 stimuli, such as IL-4 and IL-10 resulted in higher engulfment of bioparticles in comparison with M1 polarization. Moreover, we demonstrated that tolerization of BMDMs with lipopolysaccharide (LPS) results in impaired E. coli bioparticle phagocytosis. This novel real time assay will enable researchers to quantify macrophage phagocytosis with a higher degree of accuracy and sensitivity and will allow investigation of limited populations of primary phagocytes in vitro. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Feasibility of observer system for determining orientation of balloon borne observational platforms

NASA Technical Reports Server (NTRS)

Nigro, N. J.; Gagliardi, J. C.

1982-01-01

The instantaneous orientation (i.e., the attitude) of the LACATE instrumentation platform with respect to a local vertical is discussed. An observer model for predicting the orientation of balloon-borne research platforms is described. Determination of the platform orientation as a function of time is addressed.

A survey on platforms for big data analytics.

PubMed

Singh, Dilpreet; Reddy, Chandan K

The primary purpose of this paper is to provide an in-depth analysis of different platforms available for performing big data analytics. This paper surveys different hardware platforms available for big data analytics and assesses the advantages and drawbacks of each of these platforms based on various metrics such as scalability, data I/O rate, fault tolerance, real-time processing, data size supported and iterative task support. In addition to the hardware, a detailed description of the software frameworks used within each of these platforms is also discussed along with their strengths and drawbacks. Some of the critical characteristics described here can potentially aid the readers in making an informed decision about the right choice of platforms depending on their computational needs. Using a star ratings table, a rigorous qualitative comparison between different platforms is also discussed for each of the six characteristics that are critical for the algorithms of big data analytics. In order to provide more insights into the effectiveness of each of the platform in the context of big data analytics, specific implementation level details of the widely used k-means clustering algorithm on various platforms are also described in the form pseudocode.

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.

mirEX: a platform for comparative exploration of plant pri-miRNA expression data.

PubMed

Bielewicz, Dawid; Dolata, Jakub; Zielezinski, Andrzej; Alaba, Sylwia; Szarzynska, Bogna; Szczesniak, Michal W; Jarmolowski, Artur; Szweykowska-Kulinska, Zofia; Karlowski, Wojciech M

2012-01-01

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. RT-qPCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. A web-based mirEX interface can be accessed at http://bioinfo.amu.edu.pl/mirex.

Eight-Channel AC Magnetosusceptometer of Magnetic Nanoparticles for High-Throughput and Ultra-High-Sensitivity Immunoassay

PubMed Central

Chieh, Jen-Jie; Wei, Wen-Chun; Chen, Hsin-Hsein; Lee, Yen-Fu; Lin, Feng-Chun; Chiang, Ming-Hsien; Chiu, Ming-Jang; Horng, Herng-Er; Yang, Shieh-Yueh

2018-01-01

An alternating-current magnetosusceptometer of antibody-functionalized magnetic nanoparticles (MNPs) was developed for immunomagnetic reduction (IMR). A high-sensitivity, high-critical-temperature superconducting quantum interference device was used in the magnetosusceptometer. Minute levels of biomarkers of early-stage neurodegeneration diseases were detectable in serum, but measuring each biomarker required approximately 4 h. Hence, an eight-channel platform was developed in this study to fit minimal screening requirements for Alzheimer’s disease. Two consistent results were measured for three biomarkers, namely Aβ40, Aβ42, and tau protein, per human specimen. This paper presents the instrument configuration as well as critical characteristics, such as the low noise level variations among channels, a high signal-to-noise ratio, and the coefficient of variation for the biomarkers’ IMR values. The instrument’s ultrahigh sensitivity levels for the three biomarkers and the substantially shorter total measurement time in comparison with the previous single- and four-channels platforms were also demonstrated in this study. Thus, the eight-channel instrument may serve as a powerful tool for clinical high-throughput screening of Alzheimer’s disease. PMID:29601532

Year 2 Report: Protein Function Prediction Platform

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

Zhou, C E

2012-04-27

Upon completion of our second year of development in a 3-year development cycle, we have completed a prototype protein structure-function annotation and function prediction system: Protein Function Prediction (PFP) platform (v.0.5). We have met our milestones for Years 1 and 2 and are positioned to continue development in completion of our original statement of work, or a reasonable modification thereof, in service to DTRA Programs involved in diagnostics and medical countermeasures research and development. The PFP platform is a multi-scale computational modeling system for protein structure-function annotation and function prediction. As of this writing, PFP is the only existing fullymore » automated, high-throughput, multi-scale modeling, whole-proteome annotation platform, and represents a significant advance in the field of genome annotation (Fig. 1). PFP modules perform protein functional annotations at the sequence, systems biology, protein structure, and atomistic levels of biological complexity (Fig. 2). Because these approaches provide orthogonal means of characterizing proteins and suggesting protein function, PFP processing maximizes the protein functional information that can currently be gained by computational means. Comprehensive annotation of pathogen genomes is essential for bio-defense applications in pathogen characterization, threat assessment, and medical countermeasure design and development in that it can short-cut the time and effort required to select and characterize protein biomarkers.« less

AutoFACT: An Automatic Functional Annotation and Classification Tool

PubMed Central

Koski, Liisa B; Gray, Michael W; Lang, B Franz; Burger, Gertraud

2005-01-01

Background Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets. Results We present AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it (1) analyzes nucleotide and protein sequence data; (2) determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; (3) assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and (4) generates output in HTML, text and GFF formats for the user's convenience. We have compared AutoFACT to four well-established annotation pipelines. The error rate of functional annotation is estimated to be only between 1–2%. Comparison of AutoFACT to the traditional top-BLAST-hit annotation method shows that our procedure increases the number of functionally informative annotations by approximately 50%. Conclusion AutoFACT will serve as a useful annotation tool for smaller sequencing groups lacking dedicated bioinformatics staff. It is implemented in PERL and runs on LINUX/UNIX platforms. AutoFACT is available at . PMID:15960857

Engineering of Surface Chemistry for Enhanced Sensitivity in Nanoporous Interferometric Sensing Platforms.

PubMed

Law, Cheryl Suwen; Sylvia, Georgina M; Nemati, Madieh; Yu, Jingxian; Losic, Dusan; Abell, Andrew D; Santos, Abel

2017-03-15

We explore new approaches to engineering the surface chemistry of interferometric sensing platforms based on nanoporous anodic alumina (NAA) and reflectometric interference spectroscopy (RIfS). Two surface engineering strategies are presented, namely (i) selective chemical functionalization of the inner surface of NAA pores with amine-terminated thiol molecules and (ii) selective chemical functionalization of the top surface of NAA with dithiol molecules. The strong molecular interaction of Au 3+ ions with thiol-containing functional molecules of alkane chain or peptide character provides a model sensing system with which to assess the sensitivity of these NAA platforms by both molecular feature and surface engineering. Changes in the effective optical thickness of the functionalized NAA photonic films (i.e., sensing principle), in response to gold ions, are monitored in real-time by RIfS. 6-Amino-1-hexanethiol (inner surface) and 1,6-hexanedithiol (top surface), the most sensitive functional molecules from approaches i and ii, respectively, were combined into a third sensing strategy whereby the NAA platforms are functionalized on both the top and inner surfaces concurrently. Engineering of the surface according to this approach resulted in an additive enhancement in sensitivity of up to 5-fold compared to previously reported systems. This study advances the rational engineering of surface chemistry for interferometric sensing on nanoporous platforms with potential applications for real-time monitoring of multiple analytes in dynamic environments.

The Association Between Video Game Play and Cognitive Function: Does Gaming Platform Matter?

PubMed

Huang, Vivian; Young, Michaelia; Fiocco, Alexandra J

2017-11-01

Despite consumer growth, few studies have evaluated the cognitive effects of gaming using mobile devices. This study examined the association between video game play platform and cognitive performance. Furthermore, the differential effect of video game genre (action versus nonaction) was explored. Sixty undergraduate students completed a video game experience questionnaire, and we divided them into three groups: mobile video game players (MVGPs), console/computer video game players (CVGPs), and nonvideo game players (NVGPs). Participants completed a cognitive battery to assess executive function, and learning and memory. Controlling for sex and ethnicity, analyses showed that frequent video game play is associated with enhanced executive function, but not learning and memory. MVGPs were significantly more accurate on working memory performances than NVGPs. Both MVGPs and CVGPs were similarly associated with enhanced cognitive function, suggesting that platform does not significantly determine the benefits of frequent video game play. Video game platform was found to differentially associate with preference for action video game genre and motivation for gaming. Exploratory analyses show that sex significantly effects frequent video game play, platform and genre preference, and cognitive function. This study represents a novel exploration of the relationship between mobile video game play and cognition and adds support to the cognitive benefits of frequent video game play.

Mesenchymal stem cell mechanobiology and emerging experimental platforms

PubMed Central

MacQueen, Luke; Sun, Yu; Simmons, Craig A.

2013-01-01

Experimental control over progenitor cell lineage specification can be achieved by modulating properties of the cell's microenvironment. These include physical properties of the cell adhesion substrate, such as rigidity, topography and deformation owing to dynamic mechanical forces. Multipotent mesenchymal stem cells (MSCs) generate contractile forces to sense and remodel their extracellular microenvironments and thereby obtain information that directs broad aspects of MSC function, including lineage specification. Various physical factors are important regulators of MSC function, but improved understanding of MSC mechanobiology requires novel experimental platforms. Engineers are bridging this gap by developing tools to control mechanical factors with improved precision and throughput, thereby enabling biological investigation of mechanics-driven MSC function. In this review, we introduce MSC mechanobiology and review emerging cell culture platforms that enable new insights into mechanobiological control of MSCs. Our main goals are to provide engineers and microtechnology developers with an up-to-date description of MSC mechanobiology that is relevant to the design of experimental platforms and to introduce biologists to these emerging platforms. PMID:23635493

Feasibility of Floating Platform Systems for Wind Turbines: Preprint

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

Musial, W.; Butterfield, S.; Boone, A.

This paper provides a general technical description of several types of floating platforms for wind turbines. Platform topologies are classified into multiple- or single-turbine floaters and by mooring method. Platforms using catenary mooring systems are contrasted to vertical mooring systems and the advantages and disadvantages are discussed. Specific anchor types are described in detail. A rough cost comparison is performed for two different platform architectures using a generic 5-MW wind turbine. One platform is a Dutch study of a tri-floater platform using a catenary mooring system, and the other is a mono-column tension-leg platform developed at the National Renewable Energymore » Laboratory. Cost estimates showed that single unit production cost is $7.1 M for the Dutch tri-floater, and $6.5 M for the NREL TLP concept. However, value engineering, multiple unit series production, and platform/turbine system optimization can lower the unit platform costs to $4.26 M and $2.88 M, respectively, with significant potential to reduce cost further with system optimization. These foundation costs are within the range necessary to bring the cost of energy down to the DOE target range of $0.05/kWh for large-scale deployment of offshore floating wind turbines.« less

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

Gueydon, Sebastien; Jonkman, Jason

In comparison to other kinds of floaters (like a spar or a semisubmersible), the tension leg platform has several notable advantages: its vertical motions are negligible, its weight is lighter, and its mooring system's footprint is smaller. Although a tension leg platform has a negligible response to first-order vertical wave loads, the second-order wave loads need to be addressed. This paper follows up on a verification study of second-order wave loads on a tension leg platform for wind turbines done by the Maritime Research Institute of The Netherlands and National Renewable Energy Laboratory and it brings some corrections to itsmore » conclusions.« less

Geosynchronous platform definition study. Volume 6: Geosynchronous program evaluation and recommendations

NASA Technical Reports Server (NTRS)

Myers, H. L.

1973-01-01

The programmatic analyses conducted to achieve the objectives of the study are presented. The characteristics are examined of alternate geosynchronous programs based on servicing concepts, geosynchronous platform configurations, and equipment definitions which have evolved during the study. The logistics support necessary to carry out programs using these systems is defined considering alternate approaches for on-orbit servicing. The costs of the resultant programs are then determined and the alternate program approaches compared. Conventional programs with expendable satellites are also defined to the extent necessary to permit comparison with on-orbit serviced platform programs.

An open source platform for multi-scale spatially distributed simulations of microbial ecosystems

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

Segre, Daniel

2014-08-14

The goal of this project was to develop a tool for facilitating simulation, validation and discovery of multiscale dynamical processes in microbial ecosystems. This led to the development of an open-source software platform for Computation Of Microbial Ecosystems in Time and Space (COMETS). COMETS performs spatially distributed time-dependent flux balance based simulations of microbial metabolism. Our plan involved building the software platform itself, calibrating and testing it through comparison with experimental data, and integrating simulations and experiments to address important open questions on the evolution and dynamics of cross-feeding interactions between microbial species.

Environmental control and life support technologies for advanced manned space missions

NASA Technical Reports Server (NTRS)

Powell, F. T.; Wynveen, R. A.; Lin, C.

1986-01-01

Regenerative environmental control and life support system (ECLSS) technologies are found by the present evaluation to have reached a degree of maturity that recommends their application to long duration manned missions. The missions for which regenerative ECLSSs are attractive in virtue of the need to avoid expendables and resupply requirements have been identified as that of the long duration LEO Space Station, long duration stays at GEO, a permanently manned lunar base (or colony), manned platforms located at the earth-moon libration points L4 or L5, a Mars mission, deep space exploration, and asteroid exploration. A comparison is made between nonregenerative and regenerative ECLSSs in the cases of 10 essential functions.

A high-performance spatial database based approach for pathology imaging algorithm evaluation

PubMed Central

Wang, Fusheng; Kong, Jun; Gao, Jingjing; Cooper, Lee A.D.; Kurc, Tahsin; Zhou, Zhengwen; Adler, David; Vergara-Niedermayr, Cristobal; Katigbak, Bryan; Brat, Daniel J.; Saltz, Joel H.

2013-01-01

Background: Algorithm evaluation provides a means to characterize variability across image analysis algorithms, validate algorithms by comparison with human annotations, combine results from multiple algorithms for performance improvement, and facilitate algorithm sensitivity studies. The sizes of images and image analysis results in pathology image analysis pose significant challenges in algorithm evaluation. We present an efficient parallel spatial database approach to model, normalize, manage, and query large volumes of analytical image result data. This provides an efficient platform for algorithm evaluation. Our experiments with a set of brain tumor images demonstrate the application, scalability, and effectiveness of the platform. Context: The paper describes an approach and platform for evaluation of pathology image analysis algorithms. The platform facilitates algorithm evaluation through a high-performance database built on the Pathology Analytic Imaging Standards (PAIS) data model. Aims: (1) Develop a framework to support algorithm evaluation by modeling and managing analytical results and human annotations from pathology images; (2) Create a robust data normalization tool for converting, validating, and fixing spatial data from algorithm or human annotations; (3) Develop a set of queries to support data sampling and result comparisons; (4) Achieve high performance computation capacity via a parallel data management infrastructure, parallel data loading and spatial indexing optimizations in this infrastructure. Materials and Methods: We have considered two scenarios for algorithm evaluation: (1) algorithm comparison where multiple result sets from different methods are compared and consolidated; and (2) algorithm validation where algorithm results are compared with human annotations. We have developed a spatial normalization toolkit to validate and normalize spatial boundaries produced by image analysis algorithms or human annotations. The validated data were formatted based on the PAIS data model and loaded into a spatial database. To support efficient data loading, we have implemented a parallel data loading tool that takes advantage of multi-core CPUs to accelerate data injection. The spatial database manages both geometric shapes and image features or classifications, and enables spatial sampling, result comparison, and result aggregation through expressive structured query language (SQL) queries with spatial extensions. To provide scalable and efficient query support, we have employed a shared nothing parallel database architecture, which distributes data homogenously across multiple database partitions to take advantage of parallel computation power and implements spatial indexing to achieve high I/O throughput. Results: Our work proposes a high performance, parallel spatial database platform for algorithm validation and comparison. This platform was evaluated by storing, managing, and comparing analysis results from a set of brain tumor whole slide images. The tools we develop are open source and available to download. Conclusions: Pathology image algorithm validation and comparison are essential to iterative algorithm development and refinement. One critical component is the support for queries involving spatial predicates and comparisons. In our work, we develop an efficient data model and parallel database approach to model, normalize, manage and query large volumes of analytical image result data. Our experiments demonstrate that the data partitioning strategy and the grid-based indexing result in good data distribution across database nodes and reduce I/O overhead in spatial join queries through parallel retrieval of relevant data and quick subsetting of datasets. The set of tools in the framework provide a full pipeline to normalize, load, manage and query analytical results for algorithm evaluation. PMID:23599905

High-throughput screening based on label-free detection of small molecule microarrays

NASA Astrophysics Data System (ADS)

Zhu, Chenggang; Fei, Yiyan; Zhu, Xiangdong

2017-02-01

Based on small-molecule microarrays (SMMs) and oblique-incidence reflectivity difference (OI-RD) scanner, we have developed a novel high-throughput drug preliminary screening platform based on label-free monitoring of direct interactions between target proteins and immobilized small molecules. The screening platform is especially attractive for screening compounds against targets of unknown function and/or structure that are not compatible with functional assay development. In this screening platform, OI-RD scanner serves as a label-free detection instrument which is able to monitor about 15,000 biomolecular interactions in a single experiment without the need to label any biomolecule. Besides, SMMs serves as a novel format for high-throughput screening by immobilization of tens of thousands of different compounds on a single phenyl-isocyanate functionalized glass slide. Based on the high-throughput screening platform, we sequentially screened five target proteins (purified target proteins or cell lysate containing target protein) in high-throughput and label-free mode. We found hits for respective target protein and the inhibition effects for some hits were confirmed by following functional assays. Compared to traditional high-throughput screening assay, the novel high-throughput screening platform has many advantages, including minimal sample consumption, minimal distortion of interactions through label-free detection, multi-target screening analysis, which has a great potential to be a complementary screening platform in the field of drug discovery.

High precision Hugoniot measurements of D2 near maximum compression

NASA Astrophysics Data System (ADS)

Benage, John; Knudson, Marcus; Desjarlais, Michael

2015-11-01

The Hugoniot response of liquid deuterium has been widely studied due to its general importance and to the significant discrepancy in the inferred shock response obtained from early experiments. With improvements in dynamic compression platforms and experimental standards these results have converged and show general agreement with several equation of state (EOS) models, including quantum molecular dynamics (QMD) calculations within the Generalized Gradient Approximation (GGA). This approach to modeling the EOS has also proven quite successful for other materials and is rapidly becoming a standard approach. However, small differences remain among predictions obtained using different local and semi-local density functionals; these small differences show up in the deuterium Hugoniot at ~ 30-40 GPa near the region of maximum compression. Here we present experimental results focusing on that region of the Hugoniot and take advantage of advancements in the platform and standards, resulting in data with significantly higher precision than that obtained in previous studies. These new data may prove to distinguish between the subtle differences predicted by the various density functionals. Results of these experiments will be presented along with comparison to various QMD calculations. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin company, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Platinum nanoparticles functionalized nitrogen doped graphene platform for sensitive electrochemical glucose biosensing.

PubMed

Yang, Zhanjun; Cao, Yue; Li, Juan; Jian, Zhiqin; Zhang, Yongcai; Hu, Xiaoya

2015-04-29

In this work, we reported an efficient platinum nanoparticles functionalized nitrogen doped graphene (PtNPs@NG) nanocomposite for devising novel electrochemical glucose biosensor for the first time. The fabricated PtNPs@NG and biosensor were characterized using transmission electron microscopy, high-resolution transmission electron microscopy, X-ray photoelectron spectroscopy, static water contact angle, UV-vis spectroscopy, electrochemical impedance spectra and cyclic voltammetry, respectively. PtNPs@NG showed large surface area and excellent biocompatibility, and enhanced the direct electron transfer between enzyme molecules and electrode surface. The glucose oxidase (GOx) immobilized on PtNPs@NG nanocomposite retained its bioactivity, and exhibited a surface controlled, quasi-reversible and fast electron transfer process. The constructed glucose biosensor showed wide linear range from 0.005 to 1.1mM with high sensitivity of 20.31 mA M(-1) cm(-2). The detection limit was calculated to be 0.002 mM at signal-to-noise of 3, which showed 20-fold decrease in comparison with single NG-based electrochemical biosensor for glucose. The proposed glucose biosensor also demonstrated excellent selectivity, good reproducibility, acceptable stability, and could be successfully applied in the detection of glucose in serum samples at the applied potential of -0.33 V. This research provided a promising biosensing platform for the development of excellent electrochemical biosensors. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

On Dreams and Motivation: Comparison of Freud's and Hobson's Views.

PubMed

Boag, Simon

2016-01-01

The merits of Freudian dream theory continue to be debated and both supporters and critics appeal to empirical evidence to support their respective positions. What receives much less attention is the theoretical coherency of either Freudian dream theory or alternative perspectives. This paper examines Freudian dream theory and J. Allan Hobson's alternative position by addressing the role of motivation in dreams. This paper first discusses motivation in Freudian theory and its relation to dreams and disguise-censorship. The role of motivation in Hobson's theory is then considered. Hobson's claim that dream plot and content selection is random and based on design error and functional imbalance is then discussed in relation to the protoconsciousness theory proposal that dreams serve an adaptive function. While there are apparent inconsistencies in Hobson's position, his appeal to emotions and instincts provides a preliminary platform for understanding the role of motivation in dreams that is consonant with the Freudian position.

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.

Microfluidic platform combining droplets and magnetic tweezers: application to HER2 expression in cancer diagnosis.

PubMed

Ferraro, Davide; Champ, Jérôme; Teste, Bruno; Serra, Marco; Malaquin, Laurent; Viovy, Jean-Louis; de Cremoux, Patricia; Descroix, Stephanie

2016-05-09

The development of precision medicine, together with the multiplication of targeted therapies and associated molecular biomarkers, call for major progress in genetic analysis methods, allowing increased multiplexing and the implementation of more complex decision trees, without cost increase or loss of robustness. We present a platform combining droplet microfluidics and magnetic tweezers, performing RNA purification, reverse transcription and amplification in a fully automated and programmable way, in droplets of 250nL directly sampled from a microtiter-plate. This platform decreases sample consumption about 100 fold as compared to current robotized platforms and it reduces human manipulations and contamination risk. The platform's performance was first evaluated on cell lines, showing robust operation on RNA quantities corresponding to less than one cell, and then clinically validated with a cohort of 21 breast cancer samples, for the determination of their HER2 expression status, in a blind comparison with an established routine clinical analysis.

End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

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

Linshiz, Gregory; Jensen, Erik; Stawski, Nina

Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening. Here, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform’s capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, andmore » proteogenic and metabolic output analysis. Finally, taken together, we demonstrate the microfluidic platform’s potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis.« less

End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

DOE PAGES

Linshiz, Gregory; Jensen, Erik; Stawski, Nina; ...

2016-02-02

Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening. Here, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform’s capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, andmore » proteogenic and metabolic output analysis. Finally, taken together, we demonstrate the microfluidic platform’s potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis.« less

Carbohydrate Cluster Microarrays Fabricated on 3-Dimensional Dendrimeric Platforms for Functional Glycomics Exploration

PubMed Central

Zhou, Xichun; Turchi, Craig; Wang, Denong

2009-01-01

We reported here a novel, ready-to-use bioarray platform and methodology for construction of sensitive carbohydrate cluster microarrays. This technology utilizes a 3-dimensional (3-D) poly(amidoamine) starburst dendrimer monolayer assembled on glass surface, which is functionalized with terminal aminooxy and hydrazide groups for site-specific coupling of carbohydrates. A wide range of saccharides, including monosaccharides, oligosaccharides and polysaccharides of diverse structures, are applicable for the 3-D bioarray platform without prior chemical derivatization. The process of carbohydrate coupling is effectively accelerated by microwave radiation energy. The carbohydrate concentration required for microarray fabrication is substantially reduced using this technology. Importantly, this bioarray platform presents sugar chains in defined orientation and cluster configurations. It is, thus, uniquely useful for exploration of the structural and conformational diversities of glyco-epitope and their functional properties. PMID:19791771

pH-triggered conduction of amine-functionalized single ZnO wire integrated on a customized nanogap electronic platform

PubMed Central

2014-01-01

The electrical conductance response of single ZnO microwire functionalized with amine-groups was tested upon an acid pH variation of a solution environment after integration on a customized gold electrode array chip. ZnO microwires were easily synthesized by hydrothermal route and chemically functionalized with aminopropyl groups. Single wires were deposited from the solution and then oriented through dielectrophoresis across eight nanogap gold electrodes on a platform single chip. Therefore, eight functionalized ZnO microwire-gold junctions were formed at the same time, and being integrated on an ad hoc electronic platform, they were ready for testing without any further treatment. Experimental and simulation studies confirmed the high pH-responsive behavior of the amine-modified ZnO-gold junctions, obtaining in a simple and reproducible way a ready-to-use device for pH detection in the acidic range. We also compared this performance to bare ZnO wires on the same electronic platform, showing the superiority in pH response of the amine-functionalized material. PMID:24484615

Geostationary platform systems concepts definition study. Volume 2: Technical, book 2

NASA Technical Reports Server (NTRS)

1980-01-01

A selected concept for a geostationary platform is defined in sufficient detail to identify requirements for supporting research and technology, space demonstrations, GFE interfaces, costs, and schedules. This system consists of six platforms in geostationary orbit (GEO) over the Western Hemisphere and six over the Atlantic, to satisfy the total payload set associated with the nominal traffic model. Each platform is delivered to low Earth orbit (LEO) in a single shuttle flight, already mated to its LEO to GEO transfer vehicle and ready for deployment and transfer to GEO. An alternative concept is looked at briefly for comparison of configuration and technology requirements. This alternative consists of two large platforms, one over the Western Hemisphere consisting of three docked modules, and one over the Atlantic (two docked modules), to satisfy a high traffic model. The modules are full length orbiter cargo bay payloads, mated at LEO to orbital transfer vehicles (OTVs) delivered in other shuttle flights, for transfer to GEO, rendezvous, and docking. A preliminary feasibility study of an experimental platform is also performed to demonstrate communications and platform technologies required for the operational platforms of the 1990s.

Application and Mechanics Analysis of Multi-Function Construction Platforms in Prefabricated-Concrete Construction

NASA Astrophysics Data System (ADS)

Wang, Meihua; Li, Rongshuai; Zhang, Wenze

2017-11-01

Multi-function construction platforms (MCPs) as an “old construction technology, new application” of the building facade construction equipment, its efforts to reduce labour intensity, improve labour productivity, ensure construction safety, shorten the duration of construction and other aspects of the effect are significant. In this study, the functional analysis of the multi-function construction platforms is carried out in the construction of the assembly building. Based on the general finite element software ANSYS, the static calculation and dynamic characteristics analysis of the MCPs structure are analysed, the simplified finite element model is constructed, and the selection of the unit, the processing and solution of boundary are under discussion and research. The maximum deformation value, the maximum stress value and the structural dynamic characteristic model are obtained. The dangerous parts of the platform structure are analysed, too. Multiple types of MCPs under engineering construction conditions are calculated, so as to put forward the rationalization suggestions for engineering application of the MCPs.

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 work and results may be outdated when this paper is published.

Standardized Methods to Generate Mock (Spiked) Clinical Specimens by Spiking Blood or Plasma with Cultured Pathogens

PubMed Central

Dong, Ming; Fisher, Carolyn; Añez, Germán; Rios, Maria; Nakhasi, Hira L.; Hobson, J. Peyton; Beanan, Maureen; Hockman, Donna; Grigorenko, Elena; Duncan, Robert

2016-01-01

Aims To demonstrate standardized methods for spiking pathogens into human matrices for evaluation and comparison among diagnostic platforms. Methods and Results This study presents detailed methods for spiking bacteria or protozoan parasites into whole blood and virus into plasma. Proper methods must start with a documented, reproducible pathogen source followed by steps that include standardized culture, preparation of cryopreserved aliquots, quantification of the aliquots by molecular methods, production of sufficient numbers of individual specimens and testing of the platform with multiple mock specimens. Results are presented following the described procedures that showed acceptable reproducibility comparing in-house real-time PCR assays to a commercially available multiplex molecular assay. Conclusions A step by step procedure has been described that can be followed by assay developers who are targeting low prevalence pathogens. Significance and Impact of Study The development of diagnostic platforms for detection of low prevalence pathogens such as biothreat or emerging agents is challenged by the lack of clinical specimens for performance evaluation. This deficit can be overcome using mock clinical specimens made by spiking cultured pathogens into human matrices. To facilitate evaluation and comparison among platforms, standardized methods must be followed in the preparation and application of spiked specimens. PMID:26835651

Comparative Performance of Reagents and Platforms for Quantitation of Cytomegalovirus DNA by Digital PCR

PubMed Central

Gu, Z.; Sam, S. S.; Sun, Y.; Tang, L.; Pounds, S.; Caliendo, A. M.

2016-01-01

A potential benefit of digital PCR is a reduction in result variability across assays and platforms. Three sets of PCR reagents were tested on two digital PCR systems (Bio-Rad and RainDance), using three different sets of PCR reagents for quantitation of cytomegalovirus (CMV). Both commercial quantitative viral standards and 16 patient samples (n = 16) were tested. Quantitative accuracy (compared to nominal values) and variability were determined based on viral standard testing results. Quantitative correlation and variability were assessed with pairwise comparisons across all reagent-platform combinations for clinical plasma sample results. The three reagent sets, when used to assay quantitative standards on the Bio-Rad system, all showed a high degree of accuracy, low variability, and close agreement with one another. When used on the RainDance system, one of the three reagent sets appeared to have a much better correlation to nominal values than did the other two. Quantitative results for patient samples showed good correlation in most pairwise comparisons, with some showing poorer correlations when testing samples with low viral loads. Digital PCR is a robust method for measuring CMV viral load. Some degree of result variation may be seen, depending on platform and reagents used; this variation appears to be greater in samples with low viral load values. PMID:27535685

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

PubMed Central

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

2006-01-01

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

Sedimentological evolution of the Cretaceous carbonate platform of Chiapas (Mexico)

NASA Astrophysics Data System (ADS)

Cros, Pierre; Michaud, François; Fourcade, Eric; Fleury, Jean-Jacques

1998-07-01

The Cretaceous epicontinental carbonate platform of Chiapas (south-east of Mexico) extends along a 200 km NW-SE narrow strip, north of the Sierra Madre basement, from Ocozocoautla to Comitan. In the western and central domain, three stratigraphic sections of the Sierra Madre Formation (late Aptian to early Senonian) display well exposed facies sequences enabling broad facies correlations about: (1) The successive transgressive-regressive stages, (2) the different subsidence rates controlling the outer to inner platform environmental evolution, (3) the conditions of tectonically controlled partial platform drowning during Campanian-Maastrichtian. Three other sections through the eastern Maastrichtian carbonate platform area record the changes from limestone to dolomite during the Angostura Maastrichtian platform stage. This evolution of thickness and facies in the occidental domain of Piedra Parada and in the central domain of Guadalupe Victoria and Julian Grajales illustrates the settlement process of the carbonate platform and the general decreasing of the thickness of the Sierra Madre Formation from west to east. The eastern platform domain (Comitan) crops out extensively and enables new correlations along a south-north transect. The Sierra Madre Formation and Angostura Formation documents continuous carbonate platform sedimentation with foraminifers, rudists and dasycladacean algae during Campanian and Maastrichtian. These sections permit palaeogeographical comparisons of depositional conditions of the Mexican margin of the Maya block.

Feasibility of observer system for determining orientation of balloon borne observational platforms

NASA Technical Reports Server (NTRS)

Nigro, N. J.; Gagliardi, J. C.

1982-01-01

An observer model for predicting the orientation of balloon borne research platforms was developed. The model was employed in conjunction with data from the LACATE mission in order to determine the platform orientation as a function of time.

Unmanned aerial system nadir reflectance and MODIS nadir BRDF-adjusted surface reflectances intercompared over Greenland

NASA Astrophysics Data System (ADS)

Faulkner Burkhart, John; Kylling, Arve; Schaaf, Crystal B.; Wang, Zhuosen; Bogren, Wiley; Storvold, Rune; Solbø, Stian; Pedersen, Christina A.; Gerland, Sebastian

2017-07-01

Albedo is a fundamental parameter in earth sciences, and many analyses utilize the Moderate Resolution Imaging Spectroradiometer (MODIS) bidirectional reflectance distribution function (BRDF)/albedo (MCD43) algorithms. While derivative albedo products have been evaluated over Greenland, we present a novel, direct comparison with nadir surface reflectance collected from an unmanned aerial system (UAS). The UAS was flown from Summit, Greenland, on 210 km transects coincident with the MODIS sensor overpass on board the Aqua and Terra satellites on 5 and 6 August 2010. Clear-sky acquisitions were available from the overpasses within 2 h of the UAS flights. The UAS was equipped with upward- and downward-looking spectrometers (300-920 nm) with a spectral resolution of 10 nm, allowing for direct integration into the MODIS bands 1, 3, and 4. The data provide a unique opportunity to directly compare UAS nadir reflectance with the MODIS nadir BRDF-adjusted surface reflectance (NBAR) products. The data show UAS measurements are slightly higher than the MODIS NBARs for all bands but agree within their stated uncertainties. Differences in variability are observed as expected due to different footprints of the platforms. The UAS data demonstrate potentially large sub-pixel variability of MODIS reflectance products and the potential to explore this variability using the UAS as a platform. It is also found that, even at the low elevations flown typically by a UAS, reflectance measurements may be influenced by haze if present at and/or below the flight altitude of the UAS. This impact could explain some differences between data from the two platforms and should be considered in any use of airborne platforms.

Comparison of Four PD-L1 Immunohistochemical Assays in Lung Cancer.

PubMed

Hendry, Shona; Byrne, David J; Wright, Gavin M; Young, Richard J; Sturrock, Sue; Cooper, Wendy A; Fox, Stephen B

2018-03-01

Four different programmed death ligand 1 immunohistochemical assays are approved or in development as companion or complementary diagnostics to different immunotherapeutic agents in lung carcinoma. We sought to determine whether these assays are technically equivalent and whether one antibody can be used on an alternate staining platform. Serial sections of tissue microarrays constructed from 368 cases of resected lung cancer were stained for 22C3 and 28-8 on the Dako Link 48 platform (Dako, Carpinteria, Ca) and for SP142 and SP263 on the Ventana Benchmark Ultra platform (Ventana Medical Systems, Tucson, AZ) strictly as per product insert. A protocol was developed to use the 22C3 antibody on the Ventana Benchmark Ultra platform. Differences in mean tumor cell and immune cell staining were observed between the four assays (p < 0.001). Differences between 22C3 and 28-8 were not statistically significant. Concordance of tumor cell scores was good (intraclass correlation coefficient [ICC] = 0.674), particularly when SP142 was excluded as an outlier (ICC = 0.755). The highest concordance was seen between 22C3 and 28-8 (ICC = 0.812). Concordance was poor for immune cell staining (ICC = 0.212). When dichotomized according to clinically relevant cutoffs, pairwise comparisons showed poor to moderate concordance (κ = 0.196-0.578), with positive percent agreement ranging from 15.1% to 90.0%. The 22C3 antibody performed comparably on the Dako Link 48 platform and the alternate Ventana Benchmark Ultra platform (ICC = 0.921, κ = 0.897). Concordance between the four programmed death ligand 1 immunohistochemical assays when performed and scored as intended show that apart from 28-8 and 22C3, they cannot be used interchangeably in clinical practice. A protocol was successfully developed to use 22C3 on an alternate platform, which may help to overcome some barriers to implementation. Copyright © 2017 International Association for the Study of Lung Cancer. All rights reserved.

[Porting Radiotherapy Software of Varian to Cloud Platform].

PubMed

Zou, Lian; Zhang, Weisha; Liu, Xiangxiang; Xie, Zhao; Xie, Yaoqin

2017-09-30

To develop a low-cost private cloud platform of radiotherapy software. First, a private cloud platform which was based on OpenStack and the virtual GPU hardware was builded. Then on the private cloud platform, all the Varian radiotherapy software modules were installed to the virtual machine, and the corresponding function configuration was completed. Finally the software on the cloud was able to be accessed by virtual desktop client. The function test results of the cloud workstation show that a cloud workstation is equivalent to an isolated physical workstation, and any clients on the LAN can use the cloud workstation smoothly. The cloud platform transplantation in this study is economical and practical. The project not only improves the utilization rates of radiotherapy software, but also makes it possible that the cloud computing technology can expand its applications to the field of radiation oncology.

Comprehensive comparison of three commercial human whole-exome capture platforms.

PubMed

Asan; Xu, Yu; Jiang, Hui; Tyler-Smith, Chris; Xue, Yali; Jiang, Tao; Wang, Jiawei; Wu, Mingzhi; Liu, Xiao; Tian, Geng; Wang, Jun; Wang, Jian; Yang, Huangming; Zhang, Xiuqing

2011-09-28

Exome sequencing, which allows the global analysis of protein coding sequences in the human genome, has become an effective and affordable approach to detecting causative genetic mutations in diseases. Currently, there are several commercial human exome capture platforms; however, the relative performances of these have not been characterized sufficiently to know which is best for a particular study. We comprehensively compared three platforms: NimbleGen's Sequence Capture Array and SeqCap EZ, and Agilent's SureSelect. We assessed their performance in a variety of ways, including number of genes covered and capture efficacy. Differences that may impact on the choice of platform were that Agilent SureSelect covered approximately 1,100 more genes, while NimbleGen provided better flanking sequence capture. Although all three platforms achieved similar capture specificity of targeted regions, the NimbleGen platforms showed better uniformity of coverage and greater genotype sensitivity at 30- to 100-fold sequencing depth. All three platforms showed similar power in exome SNP calling, including medically relevant SNPs. Compared with genotyping and whole-genome sequencing data, the three platforms achieved a similar accuracy of genotype assignment and SNP detection. Importantly, all three platforms showed similar levels of reproducibility, GC bias and reference allele bias. We demonstrate key differences between the three platforms, particularly advantages of solutions over array capture and the importance of a large gene target set.

A single-layer platform for Boolean logic and arithmetic through DNA excision in mammalian cells

PubMed Central

Weinberg, Benjamin H.; Hang Pham, N. T.; Caraballo, Leidy D.; Lozanoski, Thomas; Engel, Adrien; Bhatia, Swapnil; Wong, Wilson W.

2017-01-01

Genetic circuits engineered for mammalian cells often require extensive fine-tuning to perform their intended functions. To overcome this problem, we present a generalizable biocomputing platform that can engineer genetic circuits which function in human cells with minimal optimization. We used our Boolean Logic and Arithmetic through DNA Excision (BLADE) platform to build more than 100 multi-input-multi-output circuits. We devised a quantitative metric to evaluate the performance of the circuits in human embryonic kidney and Jurkat T cells. Of 113 circuits analysed, 109 functioned (96.5%) with the correct specified behavior without any optimization. We used our platform to build a three-input, two-output Full Adder and six-input, one-output Boolean Logic Look Up Table. We also used BLADE to design circuits with temporal small molecule-mediated inducible control and circuits that incorporate CRISPR/Cas9 to regulate endogenous mammalian genes. PMID:28346402

Lipid Raft Redox Signaling: Molecular Mechanisms in Health and Disease

PubMed Central

Zhou, Fan; Katirai, Foad

2011-01-01

Abstract Lipid rafts, the sphingolipid and cholesterol-enriched membrane microdomains, are able to form different membrane macrodomains or platforms upon stimulations, including redox signaling platforms, which serve as a critical signaling mechanism to mediate or regulate cellular activities or functions. In particular, this raft platform formation provides an important driving force for the assembling of NADPH oxidase subunits and the recruitment of other related receptors, effectors, and regulatory components, resulting, in turn, in the activation of NADPH oxidase and downstream redox regulation of cell functions. This comprehensive review attempts to summarize all basic and advanced information about the formation, regulation, and functions of lipid raft redox signaling platforms as well as their physiological and pathophysiological relevance. Several molecular mechanisms involving the formation of lipid raft redox signaling platforms and the related therapeutic strategies targeting them are discussed. It is hoped that all information and thoughts included in this review could provide more comprehensive insights into the understanding of lipid raft redox signaling, in particular, of their molecular mechanisms, spatial-temporal regulations, and physiological, pathophysiological relevances to human health and diseases. Antioxid. Redox Signal. 15, 1043–1083. PMID:21294649

Validation of the three web quality dimensions of a minimally invasive surgery e-learning platform.

PubMed

Ortega-Morán, Juan Francisco; Pagador, J Blas; Sánchez-Peralta, Luisa Fernanda; Sánchez-González, Patricia; Noguera, José; Burgos, Daniel; Gómez, Enrique J; Sánchez-Margallo, Francisco M

2017-11-01

E-learning web environments, including the new TELMA platform, are increasingly being used to provide cognitive training in minimally invasive surgery (MIS) to surgeons. A complete validation of this MIS e-learning platform has been performed to determine whether it complies with the three web quality dimensions: usability, content and functionality. 21 Surgeons participated in the validation trials. They performed a set of tasks in the TELMA platform, where an e-MIS validity approach was followed. Subjective (questionnaires and checklists) and objective (web analytics) metrics were analysed to achieve the complete validation of usability, content and functionality. The TELMA platform allowed access to didactic content with easy and intuitive navigation. Surgeons performed all tasks with a close-to-ideal number of clicks and amount of time. They considered the design of the website to be consistent (95.24%), organised (90.48%) and attractive (85.71%). Moreover, they gave the content a high score (4.06 out of 5) and considered it adequate for teaching purposes. The surgeons scored the professional language and content (4.35), logo (4.24) and recommendations (4.20) the highest. Regarding functionality, the TELMA platform received an acceptance of 95.24% for navigation and 90.48% for interactivity. According to the study, it seems that TELMA had an attractive design, innovative content and interactive navigation, which are three key features of an e-learning platform. TELMA successfully met the three criteria necessary for consideration as a website of quality by achieving more than 70% of agreements regarding all usability, content and functionality items validated; this constitutes a preliminary requirement for an effective e-learning platform. However, the content completeness, authoring tool and registration process required improvement. Finally, the e-MIS validity methodology used to measure the three dimensions of web quality in this work can be applied to other clinical areas or training fields. Copyright © 2017 Elsevier B.V. All rights reserved.

A comparison of selected vertical wind measurement techniques on basis of the EUCAARI IMPACT observations

NASA Astrophysics Data System (ADS)

Arabas, S.; Baehr, C.; Boquet, M.; Dufournet, Y.; Pawlowska, H.; Siebert, H.; Unal, C.

2009-04-01

The poster presents a comparison of selected methods for determination of the vertical wind in the boundary layer used during the EUCAARI IMPACT campaign that took place in May 2008 in The Netherlands. The campaign covered a monthlong intensified ground-based and airborne measurements in the vicinity of the CESAR observatory in Cabauw. Ground-based vertical wind remote sensing was carried out using the Leosphere WindCube WLS70 IR Doppler lidar, Vaisala LAP3000 radar wind-profiler and the TUDelft TARA S-band radar. In-situ airborne measurements were performed using an ultrasonic anemometer (on the ACTOS helicopter underhung platform) and a 5-hole pressure probe (on the SAFIRE ATR-42 airplane radome). Several in-situ anemometers were deployed on the 200-meter high tower of the CESAR observatory. A summary of the characteristics and principles of the considered techniques is presented. A comparison of the results obtained from different platforms depicts the capabilities of each technique and highlights the time, space and velocity resolutions.

An overview of sensor calibration inter-comparison and applications

USGS Publications Warehouse

Xiong, Xiaoxiong; Cao, Changyong; Chander, Gyanesh

2010-01-01

Long-term climate data records (CDR) are often constructed using observations made by multiple Earth observing sensors over a broad range of spectra and a large scale in both time and space. These sensors can be of the same or different types operated on the same or different platforms. They can be developed and built with different technologies and are likely operated over different time spans. It has been known that the uncertainty of climate models and data records depends not only on the calibration quality (accuracy and stability) of individual sensors, but also on their calibration consistency across instruments and platforms. Therefore, sensor calibration inter-comparison and validation have become increasingly demanding and will continue to play an important role for a better understanding of the science product quality. This paper provides an overview of different methodologies, which have been successfully applied for sensor calibration inter-comparison. Specific examples using different sensors, including MODIS, AVHRR, and ETM+, are presented to illustrate the implementation of these methodologies.

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

PubMed

Severgnini, Marco; Bicciato, Silvio; Mangano, Eleonora; Scarlatti, Francesca; Mezzelani, Alessandra; Mattioli, Michela; Ghidoni, Riccardo; Peano, Clelia; Bonnal, Raoul; Viti, Federica; Milanesi, Luciano; De Bellis, Gianluca; Battaglia, Cristina

2006-06-01

Meta-analysis of microarray data is increasingly important, considering both the availability of multiple platforms using disparate technologies and the accumulation in public repositories of data sets from different laboratories. We addressed the issue of comparing gene expression profiles from two microarray platforms by devising a standardized investigative strategy. We tested this procedure by studying MDA-MB-231 cells, which undergo apoptosis on treatment with resveratrol. Gene expression profiles were obtained using high-density, short-oligonucleotide, single-color microarray platforms: GeneChip (Affymetrix) and CodeLink (Amersham). Interplatform analyses were carried out on 8414 common transcripts represented on both platforms, as identified by LocusLink ID, representing 70.8% and 88.6% of annotated GeneChip and CodeLink features, respectively. We identified 105 differentially expressed genes (DEGs) on CodeLink and 42 DEGs on GeneChip. Among them, only 9 DEGs were commonly identified by both platforms. Multiple analyses (BLAST alignment of probes with target sequences, gene ontology, literature mining, and quantitative real-time PCR) permitted us to investigate the factors contributing to the generation of platform-dependent results in single-color microarray experiments. An effective approach to cross-platform comparison involves microarrays of similar technologies, samples prepared by identical methods, and a standardized battery of bioinformatic and statistical analyses.

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.

Definition, analysis and development of an optical data distribution network for integrated avionics and control systems

NASA Technical Reports Server (NTRS)

Burns, R. R.

1981-01-01

The potential and functional requirements of fiber optic bus designs for next generation aircraft are assessed. State-of-the-art component evaluations and projections were used in the system study. Complex networks were decomposed into dedicated structures, star buses, and serial buses for detailed analysis. Comparisons of dedicated links, star buses, and serial buses with and without full duplex operation and with considerations for terminal to terminal communication requirements were obtained. This baseline was then used to consider potential extensions of busing methods to include wavelength multiplexing and optical switches. Example buses were illustrated for various areas of the aircraft as potential starting points for more detail analysis as the platform becomes definitized.

[Construction and application of an onboard absorption analyzer device for CDOM].

PubMed

Lin, Jun-Fang; Sun, Zhao-Hua; Cao, Wen-Xi; Hu, Shui-Bo; Xu, Zhan-Tang

2013-04-01

Colored dissolved organic matter (CDOM) plays an important role in marine ecosystems. In order to solve the current problems in measurement of CDOM absorption, an automated onboard analyzer based on liquid core waveguides (Teflon AF LWCC/LCW) was constructed. This analyzer has remarkable characteristics including adjusted optical pathlength, wide measurement range, and high sensitivity. The model of filtration and injection can implement the function of automated filtration, sample injection, and LWCC cleaning. The LabVIEW software platform can efficiently control the running state of the analyzer and acquire real time data including light absorption spectra, GPS data, and CTW data. By the comparison experiments and shipboard measurements, it was proved that the analyzer was reliable and robust.

Complexiton and solitary wave solutions of the coupled nonlinear Maccari’s system using two integration schemes

NASA Astrophysics Data System (ADS)

Inc, Mustafa; Aliyu, Aliyu Isa; Yusuf, Abdullahi; Baleanu, Dumitru; Nuray, Elif

2018-01-01

In this paper, we consider a coupled nonlinear Maccari’s system (CNMS) which describes the motion of isolated waves localized in a small part of space. There are some integration tools that are adopted to retrieve the solitary wave solutions. They are the modified F-Expansion and the generalized projective Riccati equation methods. Topological, non-topological, complexiton, singular and trigonometric function solutions are derived. A comparison between the results in this paper and the well-known results in the literature is also given. The derived structures of the obtained solutions offer a rich platform to study the nonlinear CNMS. Numerical simulation of the obtained solutions are presented with interesting figures showing the physical meaning of the solutions.

The hollow fiber bioreactor as a stroma-supported, serum-free ex vivo expansion platform for human umbilical cord blood cells.

PubMed

Xue, Cao; Kwek, Kenneth Y C; Chan, Jerry K Y; Chen, Qingfeng; Lim, Mayasari

2014-07-01

The bone marrow microenvironment plays an integral role in the regulation of hematopoiesis. Residing stromal cells and the extracellular matrix in the bone marrow microenvironment provide biological signals that control hematopoietic stem cell (HSC) function. In this study, we developed a bio-mimetic co-culture platform using the hollow fiber bioreactor (HFBR) for ex vivo expansion of HSCs. We evaluated the efficacy of such a platform in comparison to standard cultures performed on tissue culture polystyrene (TCP), using a human stromal cell line (HS-5) as stromal support, co-cultured with lineage-depleted human cord blood cells in serum-free medium supplemented with a cytokine cocktail. Our results showed that the performance of the HFBR in supporting total cell and CD34(+) progenitor cell expansion was comparable to that of cultures on TCP. Cells harvested from the HFBR had a higher clonogenic ability. The performance of ex vivo-expanded cells from the HFBR in hematopoietic reconstitution in humanized mice was comparable to that of the TCP control. Scanning electron microscopy revealed that stroma cell growth inside the HFBR created a three-dimensional cell matrix architecture. These findings demonstrate the feasibility of utilizing the HFBR for creating a complex cell matrix architecture, which may provide good in vitro mimicry of the bone marrow, supporting large-scale expansion of HSCs. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Continental-scale quantification of landscape values using social media data.

PubMed

van Zanten, Boris T; Van Berkel, Derek B; Meentemeyer, Ross K; Smith, Jordan W; Tieskens, Koen F; Verburg, Peter H

2016-11-15

Individuals, communities, and societies ascribe a diverse array of values to landscapes. These values are shaped by the aesthetic, cultural, and recreational benefits and services provided by those landscapes. However, across the globe, processes such as urbanization, agricultural intensification, and abandonment are threatening landscape integrity, altering the personally meaningful connections people have toward specific places. Existing methods used to study landscape values, such as social surveys, are poorly suited to capture dynamic landscape-scale processes across large geographic extents. Social media data, by comparison, can be used to indirectly measure and identify valuable features of landscapes at a regional, continental, and perhaps even worldwide scale. We evaluate the usefulness of different social media platforms-Panoramio, Flickr, and Instagram-and quantify landscape values at a continental scale. We find Panoramio, Flickr, and Instagram data can be used to quantify landscape values, with features of Instagram being especially suitable due to its relatively large population of users and its functional ability of allowing users to attach personally meaningful comments and hashtags to their uploaded images. Although Panoramio, Flickr, and Instagram have different user profiles, our analysis revealed similar patterns of landscape values across Europe across the three platforms. We also found variables describing accessibility, population density, income, mountainous terrain, or proximity to water explained a significant portion of observed variation across data from the different platforms. Social media data can be used to extend our understanding of how and where individuals ascribe value to landscapes across diverse social, political, and ecological boundaries.

Land User and Land Cover Maps of Europe: a Webgis Platform

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Fahl, F. C.; Minghini, M.; Molinari, M. E.

2016-06-01

This paper presents the methods and implementation processes of a WebGIS platform designed to publish the available land use and land cover maps of Europe at continental scale. The system is built completely on open source infrastructure and open standards. The proposed architecture is based on a server-client model having GeoServer as the map server, Leaflet as the client-side mapping library and the Bootstrap framework at the core of the front-end user interface. The web user interface is designed to have typical features of a desktop GIS (e.g. activate/deactivate layers and order layers by drag and drop actions) and to show specific information on the activated layers (e.g. legend and simplified metadata). Users have the possibility to change the base map from a given list of map providers (e.g. OpenStreetMap and Microsoft Bing) and to control the opacity of each layer to facilitate the comparison with both other land cover layers and the underlying base map. In addition, users can add to the platform any custom layer available through a Web Map Service (WMS) and activate the visualization of photos from popular photo sharing services. This last functionality is provided in order to have a visual assessment of the available land coverages based on other user-generated contents available on the Internet. It is supposed to be a first step towards a calibration/validation service that will be made available in the future.

Land Ice Verification and Validation Kit

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

2015-07-15

To address a pressing need to better understand the behavior and complex interaction of ice sheets within the global Earth system, significant development of continental-scale, dynamical ice-sheet models is underway. The associated verification and validation process of these models is being coordinated through a new, robust, python-based extensible software package, the Land Ice Verification and Validation toolkit (LIVV). This release provides robust and automated verification and a performance evaluation on LCF platforms. The performance V&V involves a comprehensive comparison of model performance relative to expected behavior on a given computing platform. LIVV operates on a set of benchmark and testmore » data, and provides comparisons for a suite of community prioritized tests, including configuration and parameter variations, bit-4-bit evaluation, and plots of tests where differences occur.« less

Overview of the TOPEX/Poseidon Platform Harvest Verification Experiment

NASA Technical Reports Server (NTRS)

Morris, Charles S.; DiNardo, Steven J.; Christensen, Edward J.

1995-01-01

An overview is given of the in situ measurement system installed on Texaco's Platform Harvest for verification of the sea level measurement from the TOPEX/Poseidon satellite. The prelaunch error budget suggested that the total root mean square (RMS) error due to measurements made at this verification site would be less than 4 cm. The actual error budget for the verification site is within these original specifications. However, evaluation of the sea level data from three measurement systems at the platform has resulted in unexpectedly large differences between the systems. Comparison of the sea level measurements from the different tide gauge systems has led to a better understanding of the problems of measuring sea level in relatively deep ocean. As of May 1994, the Platform Harvest verification site has successfully supported 60 TOPEX/Poseidon overflights.

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.

Embedding Task-Based Neural Models into a Connectome-Based Model of the Cerebral Cortex.

PubMed

Ulloa, Antonio; Horwitz, Barry

2016-01-01

A number of recent efforts have used large-scale, biologically realistic, neural models to help understand the neural basis for the patterns of activity observed in both resting state and task-related functional neural imaging data. An example of the former is The Virtual Brain (TVB) software platform, which allows one to apply large-scale neural modeling in a whole brain framework. TVB provides a set of structural connectomes of the human cerebral cortex, a collection of neural processing units for each connectome node, and various forward models that can convert simulated neural activity into a variety of functional brain imaging signals. In this paper, we demonstrate how to embed a previously or newly constructed task-based large-scale neural model into the TVB platform. We tested our method on a previously constructed large-scale neural model (LSNM) of visual object processing that consisted of interconnected neural populations that represent, primary and secondary visual, inferotemporal, and prefrontal cortex. Some neural elements in the original model were "non-task-specific" (NS) neurons that served as noise generators to "task-specific" neurons that processed shapes during a delayed match-to-sample (DMS) task. We replaced the NS neurons with an anatomical TVB connectome model of the cerebral cortex comprising 998 regions of interest interconnected by white matter fiber tract weights. We embedded our LSNM of visual object processing into corresponding nodes within the TVB connectome. Reciprocal connections between TVB nodes and our task-based modules were included in this framework. We ran visual object processing simulations and showed that the TVB simulator successfully replaced the noise generation originally provided by NS neurons; i.e., the DMS tasks performed with the hybrid LSNM/TVB simulator generated equivalent neural and fMRI activity to that of the original task-based models. Additionally, we found partial agreement between the functional connectivities using the hybrid LSNM/TVB model and the original LSNM. Our framework thus presents a way to embed task-based neural models into the TVB platform, enabling a better comparison between empirical and computational data, which in turn can lead to a better understanding of how interacting neural populations give rise to human cognitive behaviors.

Design and Performance of a Spectrometer for Deployment on MISSE 7

NASA Technical Reports Server (NTRS)

Pippin, Gary; Beymer, Jim; Robb, Andrew; Longino, James; Perry, George; Stewart, Alan; Finkenor, Miria

2009-01-01

A spectrometer for reflectance and transmission measurements of samples exposed to the space environment has been developed for deployment on the Materials on the International Space Station Experiment (MISSE) 7. The instrument incorporates a miniature commercial fiber optic coupled spectrometer with a computer control system for detector operation, sample motion and illumination. A set of three spectrometers were recently integrated on the MISSE7 platform with launch and deployment on the International Space Station scheduled for summer of this year. The instrument is one of many active experiments on the platform. The performance of the instrument prior to launch will be discussed. Data from samples measured in the laboratory will be compared to those from the instrument prior to launch. These comparisons will illustrate the capabilities of the current design. The space environment challenges many materials. When in operation on the MISSE 7 platform, the new spectrometer will provide real time data on the how the space environment affects the optical properties of thermal control paints and optical coatings. Data obtained from comparison of pre and post flight measurements on hundreds of samples exposed on previous MISSE platforms have been reported at these meetings. With the new spectrometer and the ability to correlate measured changes with time on orbit and the occurrence of both natural events and human activities, a better understanding of the processes responsible for degradation of materials in space will be possible.

categoryCompare, an analytical tool based on feature annotations

PubMed Central

Flight, Robert M.; Harrison, Benjamin J.; Mohammad, Fahim; Bunge, Mary B.; Moon, Lawrence D. F.; Petruska, Jeffrey C.; Rouchka, Eric C.

2014-01-01

Assessment of high-throughput—omics data initially focuses on relative or raw levels of a particular feature, such as an expression value for a transcript, protein, or metabolite. At a second level, analyses of annotations including known or predicted functions and associations of each individual feature, attempt to distill biological context. Most currently available comparative- and meta-analyses methods are dependent on the availability of identical features across data sets, and concentrate on determining features that are differentially expressed across experiments, some of which may be considered “biomarkers.” The heterogeneity of measurement platforms and inherent variability of biological systems confounds the search for robust biomarkers indicative of a particular condition. In many instances, however, multiple data sets show involvement of common biological processes or signaling pathways, even though individual features are not commonly measured or differentially expressed between them. We developed a methodology, categoryCompare, for cross-platform and cross-sample comparison of high-throughput data at the annotation level. We assessed the utility of the approach using hypothetical data, as well as determining similarities and differences in the set of processes in two instances: (1) denervated skin vs. denervated muscle, and (2) colon from Crohn's disease vs. colon from ulcerative colitis (UC). The hypothetical data showed that in many cases comparing annotations gave superior results to comparing only at the gene level. Improved analytical results depended as well on the number of genes included in the annotation term, the amount of noise in relation to the number of genes expressing in unenriched annotation categories, and the specific method in which samples are combined. In the skin vs. muscle denervation comparison, the tissues demonstrated markedly different responses. The Crohn's vs. UC comparison showed gross similarities in inflammatory response in the two diseases, with particular processes specific to each disease. PMID:24808906

A Unique Model Platform for C4 Plant Systems and Synthetic Biology

DTIC Science & Technology

2015-12-10

International Conference in Bioinformatics , Sydney, Australia, July 31 - August 2, 2014.  Nielsen LK (2015) Genome scale metabolic and regulatory...the comparison of transcriptome proteome and central metabolome in mature and immature tissue. Preliminary data were obtained suggesting successful...guide the comparison of transcriptome, proteome and central metabolome in mature and immature tissue. Preliminary data were obtained suggesting

Computation of Nonlinear Hydrodynamic Loads on Floating Wind Turbines Using Fluid-Impulse Theory: Preprint

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

Kok Yan Chan, G.; Sclavounos, P. D.; Jonkman, J.

2015-04-02

A hydrodynamics computer module was developed for the evaluation of the linear and nonlinear loads on floating wind turbines using a new fluid-impulse formulation for coupling with the FAST program. The recently developed formulation allows the computation of linear and nonlinear loads on floating bodies in the time domain and avoids the computationally intensive evaluation of temporal and nonlinear free-surface problems and efficient methods are derived for its computation. The body instantaneous wetted surface is approximated by a panel mesh and the discretization of the free surface is circumvented by using the Green function. The evaluation of the nonlinear loadsmore » is based on explicit expressions derived by the fluid-impulse theory, which can be computed efficiently. Computations are presented of the linear and nonlinear loads on the MIT/NREL tension-leg platform. Comparisons were carried out with frequency-domain linear and second-order methods. Emphasis was placed on modeling accuracy of the magnitude of nonlinear low- and high-frequency wave loads in a sea state. Although fluid-impulse theory is applied to floating wind turbines in this paper, the theory is applicable to other offshore platforms as well.« less

Preparation of highly multiplexed small RNA sequencing libraries.

PubMed

Persson, Helena; Søkilde, Rolf; Pirona, Anna Chiara; Rovira, Carlos

2017-08-01

MicroRNAs (miRNAs) are ~22-nucleotide-long small non-coding RNAs that regulate the expression of protein-coding genes by base pairing to partially complementary target sites, preferentially located in the 3´ untranslated region (UTR) of target mRNAs. The expression and function of miRNAs have been extensively studied in human disease, as well as the possibility of using these molecules as biomarkers for prognostication and treatment guidance. To identify and validate miRNAs as biomarkers, their expression must be screened in large collections of patient samples. Here, we develop a scalable protocol for the rapid and economical preparation of a large number of small RNA sequencing libraries using dual indexing for multiplexing. Combined with the use of off-the-shelf reagents, more samples can be sequenced simultaneously on large-scale sequencing platforms at a considerably lower cost per sample. Sample preparation is simplified by pooling libraries prior to gel purification, which allows for the selection of a narrow size range while minimizing sample variation. A comparison with publicly available data from benchmarking of miRNA analysis platforms showed that this method captures absolute and differential expression as effectively as commercially available alternatives.

Development of quantum dots-based biosensor towards on-farm detection of subclinical ketosis.

PubMed

Weng, Xuan; Chen, Longyan; Neethirajan, Suresh; Duffield, Todd

2015-10-15

Early detection of dairy animal health issues allows the producer or veterinarian to intervene before the animals' production levels, or even survival, is threatened. An increased concentration of β-hydroxybutyrate (βHBA) is a key biomarker for diagnosis of subclinical ketosis (SCK), and provides information on the health stress in cows well before any external symptoms are observable. In this study, quantum dots (QDs) modified with cofactor nicotinamide adenine dinucleotide (NAD(+)) were prepared for the sensing event, by which the βHBA concentration in the cow's blood and milk samples was determined via fluorescence analysis of the functionalized QDs. The detection was performed on a custom designed microfluidic platform combining with a low cost and miniaturized optical sensor. The sensing mechanism was first validated by a microplate reader method and then applied to the microfluidic platform. Standard βHBA solution, βHBA in blood and milk samples from cows were successfully measured by this novel technology with a detection limit at a level of 35 µM. Side by side comparison of the developed microfluidic biosensor with a commercial kit presented its good performance. Copyright © 2015 Elsevier B.V. All rights reserved.

Spatial optimization for decentralized non-potable water reuse

NASA Astrophysics Data System (ADS)

Kavvada, Olga; Nelson, Kara L.; Horvath, Arpad

2018-06-01

Decentralization has the potential to reduce the scale of the piped distribution network needed to enable non-potable water reuse (NPR) in urban areas by producing recycled water closer to its point of use. However, tradeoffs exist between the economies of scale of treatment facilities and the size of the conveyance infrastructure, including energy for upgradient distribution of recycled water. To adequately capture the impacts from distribution pipes and pumping requirements, site-specific conditions must be accounted for. In this study, a generalized framework (a heuristic modeling approach using geospatial algorithms) is developed that estimates the financial cost, the energy use, and the greenhouse gas emissions associated with NPR (for toilet flushing) as a function of scale of treatment and conveyance networks with the goal of determining the optimal degree of decentralization. A decision-support platform is developed to assess and visualize NPR system designs considering topography, economies of scale, and building size. The platform can be used for scenario development to explore the optimal system size based on the layout of current or new buildings. The model also promotes technology innovation by facilitating the systems-level comparison of options to lower costs, improve energy efficiency, and lower greenhouse gas emissions.

Chemical Conversions of Biomass-Derived Platform Chemicals over Copper-Silica Nanocomposite Catalysts.

PubMed

Upare, Pravin P; Hwang, Young Kyu; Lee, Jong-Min; Hwang, Dong Won; Chang, Jong-San

2015-07-20

Biomass and biomass-derived carbohydrates have a high extent of functionality, unlike petroleum, which has limited functionality. In biorefinery applications, the development of methods to control the extent of functionality in final products intended for use as fuels and chemicals is a challenge. In the chemical industry, heterogeneous catalysis is an important tool for the defunctionalization of functionalized feedstocks and biomass-derived platform chemicals to produce value-added chemicals. Herein, we review the recent progress in this field, mainly of vapor phase chemical conversion of biomass-derived C4 -C6 carboxylic acids and esters using copper-silica nanocomposite catalysts. We also demonstrate that these nanocomposite catalysts very efficiently convert biomass-derived platform chemicals into cyclic compounds, such as lactones and hydrofurans, with high selectivities and yields. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Test strategies for industrial testers for converter controls equipment

NASA Astrophysics Data System (ADS)

Oleniuk, P.; Di Cosmo, M.; Kasampalis, V.; Nisbet, D.; Todd, B.; Uznański, S.

2017-04-01

Power converters and their controls electronics are key elements for the operation of the CERN accelerator complex, having a direct impact on its availability. To prevent early-life failures and provide means to verify electronics, a set of industrial testers is used throughout the converters controls electronics' life cycle. The roles of the testers are to validate mass production during the manufacturing phase and to provide means to diagnose and repair failed modules that are brought back from operation. In the converter controls electronics section of the power converters group in the technology department of CERN (TE/EPC/CCE), two main test platforms have been adopted: a PXI platform for mixed analogue-digital functional tests and a JTAG Boundary-Scan platform for digital interconnection and functional tests. Depending on the functionality of the device under test, the appropriate test platforms are chosen. This paper is a follow-up to results presented at the TWEPP 2015 conference, adding the boundary scan test platform and the first results from exploitation of the test system. This paper reports on the test software, hardware design and test strategy applied for a number of devices that has resulted in maximizing test coverage and minimizing test design effort.

Development and Comparison of Technical Solutions for Electricity Monitoring Equipment

NASA Astrophysics Data System (ADS)

Potapovs, A.; Obushevs, A.

2017-12-01

The paper focuses on the elaboration of a demand-side management platform for optimal energy management strategies; the topicality is related to the description and comparison of the developed electricity monitoring and control equipment. The article describes two versions based on Atmega328 and STM32 microcontrollers, a lower and higher level of precision, and other distinct performance parameters. At the end of the article, the results of the testing of the two types of equipment are given and their comparison is made.

Quantum cryptography: Theoretical protocols for quantum key distribution and tests of selected commercial QKD systems in commercial fiber networks

NASA Astrophysics Data System (ADS)

Jacak, Monika; Jacak, Janusz; Jóźwiak, Piotr; Jóźwiak, Ireneusz

2016-06-01

The overview of the current status of quantum cryptography is given in regard to quantum key distribution (QKD) protocols, implemented both on nonentangled and entangled flying qubits. Two commercial R&D platforms of QKD systems are described (the Clavis II platform by idQuantique implemented on nonentangled photons and the EPR S405 Quelle platform by AIT based on entangled photons) and tested for feasibility of their usage in commercial TELECOM fiber metropolitan networks. The comparison of systems efficiency, stability and resistivity against noise and hacker attacks is given with some suggestion toward system improvement, along with assessment of two models of QKD.

IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes

PubMed Central

Ng, I-Man; Tsai, Shang-Chi

2017-01-01

Abstract Alternative splicing (AS), a mechanism by which different forms of mature messenger RNAs (mRNAs) are generated from the same gene, widely occurs in the metazoan genomes. Knowledge about isoform variants and abundance is crucial for understanding the functional context in the molecular diversity of the species. With increasing transcriptome data of model and non-model species, a database for visualization and comparison of AS events with up-to-date information is needed for further research. IsoPlot is a publicly available database with visualization tools for exploration of AS events, including three major species of mosquitoes, Aedes aegypti, Anopheles gambiae, and Culex quinquefasciatus, and fruit fly Drosophila melanogaster, the model insect species. IsoPlot includes not only 88,663 annotated transcripts but also 17,037 newly predicted transcripts from massive transcriptome data at different developmental stages of mosquitoes. The web interface enables users to explore the patterns and abundance of isoforms in different experimental conditions as well as cross-species sequence comparison of orthologous transcripts. IsoPlot provides a platform for researchers to access comprehensive information about AS events in mosquitoes and fruit fly. Our database is available on the web via an interactive user interface with an intuitive graphical design, which is applicable for the comparison of complex isoforms within or between species. Database URL: http://isoplot.iis.sinica.edu.tw/ PMID:29220459

Children's Media Comprehension: The Relationship between Media Platform, Executive Functioning Abilities, and Age

ERIC Educational Resources Information Center

Menkes, Susan M.

2012-01-01

Children's media comprehension was compared for material presented on television, computer, or touchscreen tablet. One hundred and thirty-two children were equally distributed across 12 groups defined by age (4- or 6-years-olds), gender, and the three media platforms. Executive functioning as measured by attentional control, cognitive…

Metadata Harvesting in Regional Digital Libraries in the PIONIER Network

ERIC Educational Resources Information Center

Mazurek, Cezary; Stroinski, Maciej; Werla, Marcin; Weglarz, Jan

2006-01-01

Purpose: The paper aims to present the concept of the functionality of metadata harvesting for regional digital libraries, based on the OAI-PMH protocol. This functionality is a part of regional digital libraries platform created in Poland. The platform was required to reach one of main objectives of the Polish PIONIER Programme--to enrich the…

Shift of microRNA profile upon orthotopic xenografting of glioblastoma spheroid cultures.

PubMed

Halle, Bo; Thomassen, Mads; Venkatesan, Ranga; Kaimal, Vivek; Marcusson, Eric G; Munthe, Sune; Sørensen, Mia D; Aaberg-Jessen, Charlotte; Jensen, Stine S; Meyer, Morten; Kruse, Torben A; Christiansen, Helle; Schmidt, Steffen; Mollenhauer, Jan; Schulz, Mette K; Andersen, Claus; Kristensen, Bjarne W

2016-07-01

Glioblastomas always recur despite surgery, radiotherapy and chemotherapy. A key player in the therapeutic resistance may be immature tumor cells with stem-like properties (TSCs) escaping conventional treatment. A group of promising molecular targets are microRNAs (miRs). miRs are small non-coding RNAs exerting post-transcriptional regulation of gene expression. In this study we aimed to identify over-expressed TSC-related miRs potentially amenable for therapeutic targeting. We used non-differentiated glioblastoma spheroid cultures (GSCs) containing TSCs and compared these to xenografts using a NanoString nCounter platform. This revealed 19 over-expressed miRs in the non-differentiated GSCs. Additionally, non-differentiated GSCs were compared to neural stem cells (NSCs) using a microarray platform. This revealed four significantly over-expressed miRs in the non-differentiated GSCs in comparison to the NSCs. The three most over-expressed miRs in the non-differentiated GSCs compared to xenografts were miR-126, -137 and -128. KEGG pathway analysis suggested the main biological function of these over-expressed miRs to be cell-cycle arrest and diminished proliferation. To functionally validate the profiling results suggesting association of these miRs with stem-like properties, experimental over-expression of miR-128 was performed. A consecutive limiting dilution assay confirmed a significantly elevated spheroid formation in the miR-128 over-expressing cells. This may provide potential therapeutic targets for anti-miRs to identify novel treatment options for GBM patients.

No difference between fixed- and mobile-bearing total knee arthroplasty in activities of daily living and pain: a randomized clinical trial.

PubMed

Amaro, Joicemar Tarouco; Arliani, Gustavo Gonçalves; Astur, Diego Costa; Debieux, Pedro; Kaleka, Camila Cohen; Cohen, Moises

2017-06-01

Until now, there are no definitive conclusions regarding functional differences related to middle- and long-term everyday activities and patient pain following implantation of mobile- and fixed-platform tibial prostheses. The aim of this study was to determine whether there are middle-term differences in knee function and pain in patients undergoing fixed- and mobile-bearing total knee arthroplasty (TKA). Eligible patients were randomized into two groups: the first group received TKA implantation with a fixed tibial platform (group A); the second group received TKA with a mobile tibial platform (group B). Patients were followed up (2 years), and their symptoms and limitations in daily living activities were evaluated using the Knee Outcome Survey-Activities of Daily Living Scale (ADLS), in addition to pain evaluation assessed using the pain visual analogue scale (VAS). There were no significant differences in function and symptoms in the ADLS and VAS between the study groups. The type of platform used in TKA (fixed vs. mobile) does not change the symptoms, function or pain of patients 2 years post-surgery. Although mobile TKAs may have better short-term results, at medium- and long-term follow-up they do not present important clinical differences compared with fixed-platform TKAs. This information is important so that surgeons can choose the most suitable implant for each patient. Randomized clinical trial, Level I.

Microfluidic platform for efficient Nanodisc assembly, membrane protein incorporation, and purification.

PubMed

Wade, James H; Jones, Joshua D; Lenov, Ivan L; Riordan, Colleen M; Sligar, Stephen G; Bailey, Ryan C

2017-08-22

The characterization of integral membrane proteins presents numerous analytical challenges on account of their poor activity under non-native conditions, limited solubility in aqueous solutions, and low expression in most cell culture systems. Nanodiscs are synthetic model membrane constructs that offer many advantages for studying membrane protein function by offering a native-like phospholipid bilayer environment. The successful incorporation of membrane proteins within Nanodiscs requires experimental optimization of conditions. Standard protocols for Nanodisc formation can require large amounts of time and input material, limiting the facile screening of formation conditions. Capitalizing on the miniaturization and efficient mass transport inherent to microfluidics, we have developed a microfluidic platform for efficient Nanodisc assembly and purification, and demonstrated the ability to incorporate functional membrane proteins into the resulting Nanodiscs. In addition to working with reduced sample volumes, this platform simplifies membrane protein incorporation from a multi-stage protocol requiring several hours or days into a single platform that outputs purified Nanodiscs in less than one hour. To demonstrate the utility of this platform, we incorporated Cytochrome P450 into Nanodiscs of variable size and lipid composition, and present spectroscopic evidence for the functional active site of the membrane protein. This platform is a promising new tool for membrane protein biology and biochemistry that enables tremendous versatility for optimizing the incorporation of membrane proteins using microfluidic gradients to screen across diverse formation conditions.

Investigating structure-property relationships of biomineralized calcium phosphate compounds as fluorescent quenching-recovery platform

NASA Astrophysics Data System (ADS)

Wang, Liuzheng; He, Xiang; Zhang, Wei; Liu, Yong; Banks, Craig E.; Zhang, Ying

2018-02-01

The structure-property relationship between biomineralized calcium phosphate compounds upon a fluorescent quenching-recovery platform and their distinct crystalline structure and surficial functional groups are investigated. A fluorescence-based sensing platform is shown to be viable for the sensing of 8-hydroxy-2-deoxy-guanosine in simulated systems.

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

Akyol, Bora A.; Allwardt, Craig H.; Beech, Zachary W.

VOLTTRON is a flexible, reliable, and scalable platform for distributed control and sensing. VOLTTRON serves in four primary roles: •A reference platform for researchers to quickly develop control applications for transactive energy. •A reference platform with flexible data store support for energy analytics applications either in academia or in commercial enterprise. •A platform from which commercial enterprise can develop products without license issues and easily integrate into their product line. •An accelerator to drive industry adoption of transactive energy and advanced building energy analytics. Pacific Northwest National Laboratory, with funding from the U.S. Department of Energy’s Building Technologies Office, developedmore » and maintains VOLTTRON as an open-source community project. VOLTTRON source code includes agent execution software; agents that perform critical services that enable and enhance VOLTTRON functionality; and numerous agents that utilize the platform to perform a specific function (fault detection, demand response, etc.). The platform supports energy, operational, and financial transactions between networked entities (equipment, organizations, buildings, grid, etc.) and enhance the control infrastructure of existing buildings through the use of open-source device communication, control protocols, and integrated analytics.« less

Spiral: Automated Computing for Linear Transforms

NASA Astrophysics Data System (ADS)

Püschel, Markus

2010-09-01

Writing fast software has become extraordinarily difficult. For optimal performance, programs and their underlying algorithms have to be adapted to take full advantage of the platform's parallelism, memory hierarchy, and available instruction set. To make things worse, the best implementations are often platform-dependent and platforms are constantly evolving, which quickly renders libraries obsolete. We present Spiral, a domain-specific program generation system for important functionality used in signal processing and communication including linear transforms, filters, and other functions. Spiral completely replaces the human programmer. For a desired function, Spiral generates alternative algorithms, optimizes them, compiles them into programs, and intelligently searches for the best match to the computing platform. The main idea behind Spiral is a mathematical, declarative, domain-specific framework to represent algorithms and the use of rewriting systems to generate and optimize algorithms at a high level of abstraction. Experimental results show that the code generated by Spiral competes with, and sometimes outperforms, the best available human-written code.

Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms

PubMed Central

Li, Jun; Riehle, Michelle M; Zhang, Yan; Xu, Jiannong; Oduol, Frederick; Gomez, Shawn M; Eiglmeier, Karin; Ueberheide, Beatrix M; Shabanowitz, Jeffrey; Hunt, Donald F; Ribeiro, José MC; Vernick, Kenneth D

2006-01-01

Background Complete genome annotation is a necessary tool as Anopheles gambiae researchers probe the biology of this potent malaria vector. Results We reannotate the A. gambiae genome by synthesizing comparative and ab initio sets of predicted coding sequences (CDSs) into a single set using an exon-gene-union algorithm followed by an open-reading-frame-selection algorithm. The reannotation predicts 20,970 CDSs supported by at least two lines of evidence, and it lowers the proportion of CDSs lacking start and/or stop codons to only approximately 4%. The reannotated CDS set includes a set of 4,681 novel CDSs not represented in the Ensembl annotation but with EST support, and another set of 4,031 Ensembl-supported genes that undergo major structural and, therefore, probably functional changes in the reannotated set. The quality and accuracy of the reannotation was assessed by comparison with end sequences from 20,249 full-length cDNA clones, and evaluation of mass spectrometry peptide hit rates from an A. gambiae shotgun proteomic dataset confirms that the reannotated CDSs offer a high quality protein database for proteomics. We provide a functional proteomics annotation, ReAnoXcel, obtained by analysis of the new CDSs through the AnoXcel pipeline, which allows functional comparisons of the CDS sets within the same bioinformatic platform. CDS data are available for download. Conclusion Comprehensive A. gambiae genome reannotation is achieved through a combination of comparative and ab initio gene prediction algorithms. PMID:16569258

Nanofilter platform based on functionalized carbon nanotubes for adsorption and elimination of Acrolein, a toxicant in cigarette smoke

NASA Astrophysics Data System (ADS)

Yoosefian, Mehdi; Pakpour, Atef; Etminan, Nazanin

2018-06-01

This paper discusses the use of carboxylated single-walled carbon nanotube as a general nanofilter platform for the removal of acrolein carcinogen from cigarette smoke. The analyses carried out in the detailed study of the electronic and structural effects of the adsorption of acrolein onto COOH loaded on single-walled carbon nanotube under the density functional theory framework. The results of Bader theory of atoms in molecules, natural bond orbital, molecular potential electron surface and density of state confirm the potential application of the suggested nanofilter platform.

Shared Platform for South African Earth and Environmental Observation Systems: Recent Developments and Improvements

NASA Astrophysics Data System (ADS)

Hugo, Wim

2013-04-01

Over the past 3 years, SAEON has worked with a number of stakeholders and funders to establish a shared platform for the management of dissemination of E&EO research outputs, data sets, and services. This platform is strongly aligned with GEO principles and architecture, allowing direct integration with the GEOSS Broker. The platform has two important characteristics: 1. It reduces the cost and lead time of provision of similar infrastructure for future initiatives. 2. The platform is domain-agnostic to some degree, and can be used for non E&EO applications. Projects to achive this is under way at present. The paper describes the application of the platform for a variety of user communities and initiatives (SAEON Data Portal, South African Earth Observation System, Risk and Vulnerability Atlas, BioEnergy Atlas, National Spatial Information Framework, ICSU World Data System Components, and many more), and demonstrates use cases utilising a distributed, service oriented architecture. Significant improvements have been made to the interoperability functions available to end users and content providers, and these are demonstrated and discussed in detail. Functions include • Creation and persistence of composite maps, as well as time series or scatter charts, supporting a variety of standardized data sources. • Search facilities have been extended to allow analysis and filtering of primary search results, and to deal with large meta-data collections. • In addition, data sources, data listings, news items, images, search results, and other platform content can, with increasing flexibility, be accessed as standardized services that are processed in standardized clients, allowing creation of a rich user interface, and permitting the inclusion of platform functionality into external websites and resources. This shift to explicit service-oriented, peer-to-peer architecture is a preparation for increased distributed processing and content composition, and will support the concept of virtualization of 'science gateways' based on the platform, in support of a growing number of domains and initiatives.

Pre-Hardware Optimization of Spacecraft Image Processing Software Algorithms and Hardware Implementation

NASA Technical Reports Server (NTRS)

Kizhner, Semion; Flatley, Thomas P.; Hestnes, Phyllis; Jentoft-Nilsen, Marit; Petrick, David J.; Day, John H. (Technical Monitor)

2001-01-01

Spacecraft telemetry rates have steadily increased over the last decade presenting a problem for real-time processing by ground facilities. This paper proposes a solution to a related problem for the Geostationary Operational Environmental Spacecraft (GOES-8) image processing application. Although large super-computer facilities are the obvious heritage solution, they are very costly, making it imperative to seek a feasible alternative engineering solution at a fraction of the cost. The solution is based on a Personal Computer (PC) platform and synergy of optimized software algorithms and re-configurable computing hardware technologies, such as Field Programmable Gate Arrays (FPGA) and Digital Signal Processing (DSP). It has been shown in [1] and [2] that this configuration can provide superior inexpensive performance for a chosen application on the ground station or on-board a spacecraft. However, since this technology is still maturing, intensive pre-hardware steps are necessary to achieve the benefits of hardware implementation. This paper describes these steps for the GOES-8 application, a software project developed using Interactive Data Language (IDL) (Trademark of Research Systems, Inc.) on a Workstation/UNIX platform. The solution involves converting the application to a PC/Windows/RC platform, selected mainly by the availability of low cost, adaptable high-speed RC hardware. In order for the hybrid system to run, the IDL software was modified to account for platform differences. It was interesting to examine the gains and losses in performance on the new platform, as well as unexpected observations before implementing hardware. After substantial pre-hardware optimization steps, the necessity of hardware implementation for bottleneck code in the PC environment became evident and solvable beginning with the methodology described in [1], [2], and implementing a novel methodology for this specific application [6]. The PC-RC interface bandwidth problem for the class of applications with moderate input-output data rates but large intermediate multi-thread data streams has been addressed and mitigated. This opens a new class of satellite image processing applications for bottleneck problems solution using RC technologies. The issue of a science algorithm level of abstraction necessary for RC hardware implementation is also described. Selected Matlab functions already implemented in hardware were investigated for their direct applicability to the GOES-8 application with the intent to create a library of Matlab and IDL RC functions for ongoing work. A complete class of spacecraft image processing applications using embedded re-configurable computing technology to meet real-time requirements, including performance results and comparison with the existing system, is described in this paper.

Synthesis of a novel poly-thiolated magnetic nano-platform for heavy metal adsorption. Role of thiol and carboxyl functions

NASA Astrophysics Data System (ADS)

Odio, Oscar F.; Lartundo-Rojas, Luis; Palacios, Elia Guadalupe; Martínez, Ricardo; Reguera, Edilso

2016-11-01

We report a novel strategy for the synthesis of magnetic nano-platforms containing free thiol groups. It first involves the synthesis of a poly(acrylic acid) copolymer containing disulfide bridges between the linear chains through di-ester linkages, followed by the anchoring of this new ligand to magnetite nanoparticles using a ligand exchange reaction. Finally, free sbnd SH groups are obtained by treating the resulting disulfide-functionalized magnetic nano-system with tributyl phosphine as reducing agent. The characterization of the resulting 17 nm nanoparticles (Fe3O4@PAA-HEDred) by FTIR and TGA confirms the attachment of the copolymer through iron carboxylates. XRD, TEM and magnetic measurements indicate an increase in the inorganic core diameter and the occurrence of strong magnetic inter-particle interactions during the exchange reaction, although coercitivity and remanence drop to near zero at room temperature. Afterwards, Fe3O4@PAA-HEDred nanoparticles were tested as sorbent for Pb2+ and Cd2+ cations in aqueous media. XPS measurements were performed in order to unravel the role of both carboxyl and thiol functions in the adsorption process. For the sake of comparison, the same study was performed using bare Fe3O4 nanoparticles and a nanosystem with disulfide groups (Fe3O4@DMSA). The joint analysis of the Pb 4f, Cd 3d, Fe 2p and S 2p high resolution spectra for the nanostructured materials indicates that metal-sulfur interactions are dominant if free sbnd SH groups are present, but if not, the main adsorption route entails metal-carboxyl interactions. Even in presence of unbound thiol moieties, carboxyl groups participate due to favoured steric availability.

Microfluidic platform for assessing pancreatic islet functionality through dielectric spectroscopy

PubMed Central

Heileman, K.; Daoud, J.; Hasilo, C.; Gasparrini, M.; Paraskevas, S.; Tabrizian, M.

2015-01-01

Human pancreatic islets are seldom assessed for dynamic responses to external stimuli. Thus, the elucidation of human islet functionality would provide insights into the progression of diabetes mellitus, evaluation of preparations for clinical transplantation, as well as for the development of novel therapeutics. The objective of this study was to develop a microfluidic platform for in vitro islet culture, allowing the multi-parametric investigation of islet response to chemical and biochemical stimuli. This was accomplished through the fabrication and implementation of a microfluidic platform that allowed the perifusion of islet culture while integrating real-time monitoring using impedance spectroscopy, through microfabricated, interdigitated electrodes located along the microchamber arrays. Real-time impedance measurements provide important dielectric parameters, such as cell membrane capacitance and cytoplasmic conductivity, representing proliferation, differentiation, viability, and functionality. The perifusion of varying glucose concentrations and monitoring of the resulting impedance of pancreatic islets were performed as proof-of-concept validation of the lab-on-chip platform. This novel technique to elucidate the underlying mechanisms that dictate islet functionality is presented, providing new information regarding islet function that could improve the evaluation of islet preparations for transplantation. In addition, it will lead to a better understanding of fundamental diabetes-related islet dysfunction and the development of therapeutics through evaluation of potential drug effects. PMID:26339324

FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants1

PubMed Central

Tohge, Takayuki; Klie, Sebastian; Fernie, Alisdair R.

2016-01-01

Gene duplications generate new genes that can acquire similar but often diversified functions. Recent studies of gene coexpression networks have indicated that, not only genes, but also pathways can be multiplied and diversified to perform related functions in different parts of an organism. Identification of such diversified pathways, or modules, is needed to expand our knowledge of biological processes in plants and to understand how biological functions evolve. However, systematic explorations of modules remain scarce, and no user-friendly platform to identify them exists. We have established a statistical framework to identify modules and show that approximately one-third of the genes of a plant’s genome participate in hundreds of multiplied modules. Using this framework as a basis, we implemented a platform that can explore and visualize multiplied modules in coexpression networks of eight plant species. To validate the usefulness of the platform, we identified and functionally characterized pollen- and root-specific cell wall modules that multiplied to confer tip growth in pollen tubes and root hairs, respectively. Furthermore, we identified multiplied modules involved in secondary metabolite synthesis and corroborated them by metabolite profiling of tobacco (Nicotiana tabacum) tissues. The interactive platform, referred to as FamNet, is available at http://www.gene2function.de/famnet.html. PMID:26754669

Characteristics of train noise in above-ground and underground stations with side and island platforms

NASA Astrophysics Data System (ADS)

Shimokura, Ryota; Soeta, Yoshiharu

2011-04-01

Railway stations can be principally classified by their locations, i.e., above-ground or underground stations, and by their platform styles, i.e., side or island platforms. However, the effect of the architectural elements on the train noise in stations is not well understood. The aim of the present study is to determine the different acoustical characteristics of the train noise for each station style. The train noise was evaluated by (1) the A-weighted equivalent continuous sound pressure level ( LAeq), (2) the amplitude of the maximum peak of the interaural cross-correlation function (IACC), (3) the delay time ( τ1) and amplitude ( ϕ1) of the first maximum peak of the autocorrelation function. The IACC, τ1 and ϕ1 are related to the subjective diffuseness, pitch and pitch strength, respectively. Regarding the locations, the LAeq in the underground stations was 6.4 dB higher than that in the above-ground stations, and the pitch in the underground stations was higher and stronger. Regarding the platform styles, the LAeq on the side platforms was 3.3 dB higher than on the island platforms of the above-ground stations. For the underground stations, the LAeq on the island platforms was 3.3 dB higher than that on the side platforms when a train entered the station. The IACC on the island platforms of the above-ground stations was higher than that in the other stations.

Solving the problem of comparing whole bacterial genomes across different sequencing platforms.

PubMed

Kaas, Rolf S; Leekitcharoenphon, Pimlapas; Aarestrup, Frank M; Lund, Ole

2014-01-01

Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. We developed two different procedures for identifying variable sites and inferring phylogenies in WGS data across multiple platforms. The methods were evaluated on three bacterial data sets and sequenced on three different platforms (Illumina, 454, Ion Torrent). We show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. It is concluded that the cause of the success of these new procedures is due to a validation of all informative sites that are included in the analysis. The procedures are available as web tools.

Pro-ana versus Pro-recovery: A Content Analytic Comparison of Social Media Users' Communication about Eating Disorders on Twitter and Tumblr.

PubMed

Branley, Dawn B; Covey, Judith

2017-01-01

Objectives: To compare how people communicate about eating disorders on two popular social media platforms - Twitter and Tumblr. Materials and Methods: Thematic analysis was conducted to characterize the types of communications posted, and a content analysis was undertaken of between-platform differences. Results: Three types of content (pro-ana, anti-ana, and pro-recovery) were posted on each platform. Overall, across both platforms, extreme pro-ana posts were in the minority compared to anti-ana and pro-recovery. Pro-ana posts (including 'thinspiration') were more common on Twitter than Tumblr, whereas anti-ana and pro-recovery posts were more common on Tumblr. Conclusion: The findings have implications for future research and health care relating to the treatment and prevention of eating disorders. Developers of future interventions targeting negative pro-ana content should remain aware of the need to avoid any detrimental impact on positive online support.

Compact and lightweight support platform with electromagnetic disturbance elimination for interferometer on reversed field pinch Keda Torus eXperiment

NASA Astrophysics Data System (ADS)

Mao, Wenzhe; Yuan, Peng; Zheng, Jian; Ding, Weixing; Li, Hong; Lan, Tao; Liu, Adi; Liu, Wandong; Xie, Jinlin

2016-11-01

A compact and lightweight support platform has been used as a holder for the interferometer system on the Keda Torus eXperiment (KTX), which is a reversed field pinch device. The vibration caused by the interaction between the time-varying magnetic field and the induced current driven in the metal optical components has been measured and, following comparison with the mechanical vibration of the KTX device and the refraction effect of the ambient turbulent air flow, has been identified as the primary vibration source in this case. To eliminate this electromagnetic disturbance, nonmetallic epoxy resin has been selected as the material for the support platform and the commercially available metal optical mounts are replaced. Following these optimization steps and mechanical reinforcements, the stability of the interferometer platform has improved significantly. The phase shift caused by the vibration has been reduced to the level of background noise.

Comparison of MagNA Pure 96, Chemagic MSM1, and QIAamp MinElute for hepatitis B virus nucleic acid extraction.

PubMed

Kang, Seong-Ho; Lee, Eun Hee; Park, Geon; Jang, Sook Jin; Moon, Dae Soo

2012-01-01

This study was designed to compare two automated systems and one manual system for hepatitis B virus (HBV) nucleic acid extraction. The two automated systems were the MagNA Pure 96 system (Roche Applied Science, Manheim, Germany) and the Chemagic system (Chemagen, Baesweiler, Germany), and the manual system was the QIAamp system (Qiagen, Hilden, Germany). Sixty-eight samples that were within the detection range of the Cobas Ampliprep/Cobas TaqMan (CAP/CTM) platform (Roche Molecular Systems, Manheim, Germany) were selected. Extracted viral nucleic acids from the three systems were quantified using an AccuPower HBV Quantitative PCR kit (Bioneer, Daejon, Korea). The MagNA Pure 96 system and QIAamp system did not detect viral loads in one sample. The Chemagic system did not detect low viral loads in nine samples (range, 26-290 IU/mL by the CAP/CTM platform). Comparisons of the viral loads of the samples from the MagNA Pure 96 system, the Chemagic system, and the QIAamp system with those from the CAP/CTM platform yielded correlation coefficients of 0.977, 0.914, and 0.967, respectively. Comparisons of the MagNA Pure 96 system and the Chemagic system with the QIAamp system yielded correlation coefficients of 0.987 and 0.939, respectively. The MagNA Pure 96 system demonstrated better performance than the Chemagic system for HBV nucleic acid extraction. The MagNA Pure 96 system demonstrated comparable performance with the QIAamp system.

Self-assembled monolayers of 1-alkenes on oxidized platinum surfaces as platforms for immobilized enzymes for biosensing

NASA Astrophysics Data System (ADS)

Alonso, Jose Maria; Bielen, Abraham A. M.; Olthuis, Wouter; Kengen, Servé W. M.; Zuilhof, Han; Franssen, Maurice C. R.

2016-10-01

Alkene-based self-assembled monolayers grafted on oxidized Pt surfaces were used as a scaffold to covalently immobilize oxidase enzymes, with the aim to develop an amperometric biosensor platform. NH2-terminated organic layers were functionalized with either aldehyde (CHO) or N-hydroxysuccinimide (NHS) ester-derived groups, to provide anchoring points for enzyme immobilization. The functionalized Pt surfaces were characterized by X-ray photoelectron spectroscopy (XPS), static water contact angle (CA), infrared reflection absorption spectroscopy (IRRAS) and atomic force microscopy (AFM). Glucose oxidase (GOX) was covalently attached to the functionalized Pt electrodes, either with or without additional glutaraldehyde crosslinking. The responses of the acquired sensors to glucose concentrations ranging from 0.5 to 100 mM were monitored by chronoamperometry. Furthermore, lactate oxidase (LOX) and human hydroxyacid oxidase (HAOX) were successfully immobilized onto the PtOx surface platform. The performance of the resulting lactate sensors was investigated for lactate concentrations ranging from 0.05 to 20 mM. The successful attachment of active enzymes (GOX, LOX and HAOX) on Pt electrodes demonstrates that covalently functionalized PtOx surfaces provide a universal platform for the development of oxidase enzyme-based sensors.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

Parameter Estimation for Thurstone Choice Models

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

Vojnovic, Milan; Yun, Seyoung

We consider the estimation accuracy of individual strength parameters of a Thurstone choice model when each input observation consists of a choice of one item from a set of two or more items (so called top-1 lists). This model accommodates the well-known choice models such as the Luce choice model for comparison sets of two or more items and the Bradley-Terry model for pair comparisons. We provide a tight characterization of the mean squared error of the maximum likelihood parameter estimator. We also provide similar characterizations for parameter estimators defined by a rank-breaking method, which amounts to deducing one ormore » more pair comparisons from a comparison of two or more items, assuming independence of these pair comparisons, and maximizing a likelihood function derived under these assumptions. We also consider a related binary classification problem where each individual parameter takes value from a set of two possible values and the goal is to correctly classify all items within a prescribed classification error. The results of this paper shed light on how the parameter estimation accuracy depends on given Thurstone choice model and the structure of comparison sets. In particular, we found that for unbiased input comparison sets of a given cardinality, when in expectation each comparison set of given cardinality occurs the same number of times, for a broad class of Thurstone choice models, the mean squared error decreases with the cardinality of comparison sets, but only marginally according to a diminishing returns relation. On the other hand, we found that there exist Thurstone choice models for which the mean squared error of the maximum likelihood parameter estimator can decrease much faster with the cardinality of comparison sets. We report empirical evaluation of some claims and key parameters revealed by theory using both synthetic and real-world input data from some popular sport competitions and online labor platforms.« less

The Mobile Aircraft Maintenance Office Concept from a Wide Area Perspective

DTIC Science & Technology

2003-03-01

significant improvements in wireless network data rates, and enhanced mobile application platforms offers an opportunity to effectively integrate m...hardware, and mobile application platforms housing the necessary middleware software comprise the mobile landscape. The m-business network...devices. Lastly, an investigation into mobile application platforms will reveal the middleware functionality required to successfully extend suitable e

A Case Study of Design and Usability Evaluation of the Collaborative Problem Solving Instructional Platform System

ERIC Educational Resources Information Center

Chao, Jen-Yi; Chao, Shu-Jen; Yao, Lo-Yi; Liu, Chuan-His

2016-01-01

This study used Focus Group to analyze user requirements for user interface so as to understand what capabilities of the Collaborative Problem Solving (CPS) Instructional Platform were expected by users. After 12 focus group interviews, the following four functions had been identified as essential to the CPS Instructional Platform: CPS…

Investigating structure–property relationships of biomineralized calcium phosphate compounds as fluorescent quenching–recovery platform

PubMed Central

Wang, Liuzheng; He, Xiang; Zhang, Wei; Liu, Yong; Zhang, Ying

2018-01-01

The structure–property relationship between biomineralized calcium phosphate compounds upon a fluorescent quenching–recovery platform and their distinct crystalline structure and surficial functional groups are investigated. A fluorescence-based sensing platform is shown to be viable for the sensing of 8-hydroxy-2-deoxy-guanosine in simulated systems. PMID:29515827

A gimbal platform stabilization for topographic applications

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

Michele, Mangiameli, E-mail: michele.mangiameli@dica.unict.it; Giuseppe, Mussumeci

2015-03-10

The aim of this work is the stabilization of a Gimbal platform for optical sensors acquisitions in topographic applications using mobile vehicles. The stabilization of the line of sight (LOS) consists in tracking the command velocity in presence of nonlinear noise due to the external environment. The hardware architecture is characterized by an Ardupilot platform that allows the control of both the mobile device and the Gimbal. Here we developed a new approach to stabilize the Gimbal platform, which is based on neural network. For the control system, we considered a plant that represents the transfer function of the servomore » system control model for an inertial stabilized Gimbal platform. The transductor used in the feed-back line control is characterized by the Rate Gyro transfer function installed onboard of Ardupilot. For the simulation and investigation of the system performance, we used the Simulink tool of Matlab. Results show that the hardware/software approach is efficient, reliable and cheap for direct photogrammetry, as well as for general purpose applications using mobile vehicles.« less

Coupling chemical and biological catalysis: a flexible paradigm for producing biobased chemicals.

PubMed

Schwartz, Thomas J; Shanks, Brent H; Dumesic, James A

2016-04-01

Advances in metabolic engineering have allowed for the development of new biological catalysts capable of selectively de-functionalizing biomass to yield platform molecules that can be upgraded to biobased chemicals using high efficiency continuous processing allowed by heterogeneous chemical catalysis. Coupling these disciplines overcomes the difficulties of selectively activating COH bonds by heterogeneous chemical catalysis and producing petroleum analogues by biological catalysis. We show that carboxylic acids, pyrones, and alcohols are highly flexible platforms that can be used to produce biobased chemicals by this approach. More generally, we suggest that molecules with three distinct functionalities may represent a practical upper limit on the extent of functionality present in the platform molecules that serve as the bridge between biological and chemical catalysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Silicon Field Effect Transistors as Dual-Use Sensor-Heater Hybrids

PubMed Central

Reddy, Bobby; Elibol, Oguz H.; Nair, Pradeep R.; Dorvel, Brian R.; Butler, Felice; Ahsan, Zahab; Bergstrom, Donald E.; Alam, Muhammad A.; Bashir, Rashid

2011-01-01

We demonstrate the temperature mediated applications of a previously proposed novel localized dielectric heating method on the surface of dual purpose silicon field effect transistor (FET) sensor-heaters and perform modeling and characterization of the underlying mechanisms. The FETs are first shown to operate as electrical sensors via sensitivity to changes in pH in ionic fluids. The same devices are then demonstrated as highly localized heaters via investigation of experimental heating profiles and comparison to simulation results. These results offer further insight into the heating mechanism and help determine the spatial resolution of the technique. Two important biosensor platform applications spanning different temperature ranges are then demonstrated: a localized heat-mediated DNA exchange reaction and a method for dense selective functionalization of probe molecules via the heat catalyzed complete desorption and reattachment of chemical functionalization to the transistor surfaces. Our results show that the use of silicon transistors can be extended beyond electrical switching and field-effect sensing to performing localized temperature controlled chemical reactions on the transistor itself. PMID:21214189

Differential 3’ processing of specific transcripts expands regulatory and protein diversity across neuronal cell types

PubMed Central

Jereb, Saša; Hwang, Hun-Way; Van Otterloo, Eric; Govek, Eve-Ellen; Fak, John J; Yuan, Yuan; Hatten, Mary E

2018-01-01

Alternative polyadenylation (APA) regulates mRNA translation, stability, and protein localization. However, it is unclear to what extent APA regulates these processes uniquely in specific cell types. Using a new technique, cTag-PAPERCLIP, we discovered significant differences in APA between the principal types of mouse cerebellar neurons, the Purkinje and granule cells, as well as between proliferating and differentiated granule cells. Transcripts that differed in APA in these comparisons were enriched in key neuronal functions and many differed in coding sequence in addition to 3’UTR length. We characterize Memo1, a transcript that shifted from expressing a short 3’UTR isoform to a longer one during granule cell differentiation. We show that Memo1 regulates granule cell precursor proliferation and that its long 3’UTR isoform is targeted by miR-124, contributing to its downregulation during development. Our findings provide insight into roles for APA in specific cell types and establish a platform for further functional studies. PMID:29578408

On Dreams and Motivation: Comparison of Freud’s and Hobson’s Views

PubMed Central

Boag, Simon

2017-01-01

The merits of Freudian dream theory continue to be debated and both supporters and critics appeal to empirical evidence to support their respective positions. What receives much less attention is the theoretical coherency of either Freudian dream theory or alternative perspectives. This paper examines Freudian dream theory and J. Allan Hobson’s alternative position by addressing the role of motivation in dreams. This paper first discusses motivation in Freudian theory and its relation to dreams and disguise-censorship. The role of motivation in Hobson’s theory is then considered. Hobson’s claim that dream plot and content selection is random and based on design error and functional imbalance is then discussed in relation to the protoconsciousness theory proposal that dreams serve an adaptive function. While there are apparent inconsistencies in Hobson’s position, his appeal to emotions and instincts provides a preliminary platform for understanding the role of motivation in dreams that is consonant with the Freudian position. PMID:28111554

Direct Comparison of a Tablet Computer and a Personal Digital Assistant for Point-of-Care Documentation in Eye Care

PubMed Central

Silvey, Garry M.; Macri, Jennifer M.; Lee, Paul P.; Lobach, David F.

2005-01-01

New mobile computing devices including personal digital assistants (PDAs) and tablet computers have emerged to facilitate data collection at the point of care. Unfortunately, little research has been reported regarding which device is optimal for a given care setting. In this study we created and compared functionally identical applications on a Palm operating system-based PDA and a Windows-based tablet computer for point-of-care documentation of clinical observations by eye care professionals when caring for patients with diabetes. Eye-care professionals compared the devices through focus group sessions and through validated usability surveys. We found that the application on the tablet computer was preferred over the PDA for documenting the complex data related to eye care. Our findings suggest that the selection of a mobile computing platform depends on the amount and complexity of the data to be entered; the tablet computer functions better for high volume, complex data entry, and the PDA, for low volume, simple data entry. PMID:16779128

Comparison of response times of a mobile-web EHRs system using PHP and JSP languages.

PubMed

De la Torre-Díez, Isabel; Antón-Rodríguez, Míriam; Díaz-Pernas, Francisco Javier; Perozo-Rondón, Freddy José

2012-12-01

Performance evaluation is highly important in the Electronic Health Records (EHRs) system implementation. Response time's measurement can be considered as one manner to make that evaluation. In the e-health field, after the creation of EHRs available through different platforms such as Web and/or mobile, a performance evaluation is necessary. The operation of the system in the right way is essential. In this paper, a comparison of the response times for the MEHRmobile system is presented. The first version uses PHP language with a MySQL database and the second one employs JSP with an eXist database. Both versions have got the same functionalities. In addition to the technological aspects, a significant difference is the way the information is stored. The main goal of this paper is choosing the version which offers better response times. We have created a new benchmark to calculate the response times. Better results have been obtained for the PHP version. Nowadays, this version is being used for specialists from Fundación Intras, Spain.

Modeling human-machine interactions for operations room layouts

NASA Astrophysics Data System (ADS)

Hendy, Keith C.; Edwards, Jack L.; Beevis, David

2000-11-01

The LOCATE layout analysis tool was used to analyze three preliminary configurations for the Integrated Command Environment (ICE) of a future USN platform. LOCATE develops a cost function reflecting the quality of all human-human and human-machine communications within a workspace. This proof- of-concept study showed little difference between the efficacy of the preliminary designs selected for comparison. This was thought to be due to the limitations of the study, which included the assumption of similar size for each layout and a lack of accurate measurement data for various objects in the designs, due largely to their notional nature. Based on these results, the USN offered an opportunity to conduct a LOCATE analysis using more appropriate assumptions. A standard crew was assumed, and subject matter experts agreed on the communications patterns for the analysis. Eight layouts were evaluated with the concepts of coordination and command factored into the analysis. Clear differences between the layouts emerged. The most promising design was refined further by the USN, and a working mock-up built for human-in-the-loop evaluation. LOCATE was applied to this configuration for comparison with the earlier analyses.

Effects of Messages Delivered by Mobile Phone on Increasing Compliance With Shoulder Exercises Among Patients With a Frozen Shoulder.

PubMed

Chen, Hui-Chun; Chuang, Tai-Yuan; Lin, Pi-Chu; Lin, Yen-Kuang; Chuang, Yeu-Hui

2017-07-01

The aim of this study was to examine the effects of reminders, encouragement, and educational messages delivered by mobile phone on shoulder exercise compliance and improvements in shoulder function among patients with a frozen shoulder. A randomized controlled trial design was used. A convenience sample of patients with a frozen shoulder in an orthopedic outpatient clinic was recruited. All participants were instructed on how to do shoulder exercises and were provided with a printed pamphlet about shoulder exercises. Then, the intervention group received reminders, encouragement, and educational messages by mobile phone daily for the next 2 weeks, while the comparison group did not. The intervention group had higher compliance with shoulder exercises than did the comparison group (t = 2.263, p = .03) and had significant improvements in shoulder forward flexion (F = 12.067, p = .001), external rotation (F = 13.61, p = .001), and internal rotation (F = 5.903, p = .018) compared to those in the comparison group after the 2-week intervention. The text messages significantly increased patient compliance with shoulder exercises and thus improved patients' shoulder range of motion. Hospital or clinics can send appropriate messages to patients via text message platforms in order to remind and encourage them to do shoulder exercises. © 2017 Sigma Theta Tau International.

The skin microbiome in psoriatic arthritis: methodology development and pilot data.

PubMed

Castelino, Madhura; Eyre, Stephen; Moat, John; Fox, Graeme; Martin, Paul; Ijaz, Umer; Quince, Christopher; Ho, Pauline; Upton, Mathew; Barton, Anne

2015-02-26

Skin microbiota are likely to be important in the development of conditions such as psoriatic arthritis. Profiling the bacterial community in the psosriatic plaques will contribute to our understanding of the role of the skin microbiome in these conditions. The aim of this work was to determine the optimum study design for work on the skin microbiome with use of the MiSeq platform. The objectives were to compare data generated from two platforms for two primer pairs in a low density mock bacterial community. DNA was obtained from two low density mock communities of 11 diverse bacterial strains (with and without human DNA supplementation) and from swabs taken from the skin of four healthy volunteers. The DNA was amplified with primer pairs covering hypervariable regions of the 16S rRNA gene: primers 63F and 519R (V1-V3), and 347F and 803R (V3-V4). The resultant libraries were indexed for the MiSeq and Roche454 platforms and sequenced. Both datasets were de-noised, cleaned of chimeras, and analysed by use of QIIME software (version 1.8.0). No significant difference in the diversity indices at the phylum and the genus level between the platforms was seen. Comparison of the diversity indices for the mock community data for the two primer pairs demonstrated that the V3-V4 hypervariable region had significantly better capture of bacterial diversity than did the V1-V3 region. Amplification with the same primer pairs showed strong concordance within each platform (98·9-99·8%), with negligible effect of spiked human DNA contamination. Comparison at the family level classification between samples processed on the MiSeq and Roche454 platforms using the V3-V4 hypervariable region also showed a high level of concordance (87%), although less so for the V1-V3 primers (10%). The pilot data from healthy volunteers were similar. Results obtained from the V3-V4 16S rRNA hypervariable region, sequencing on the MiSeq and Roche454 platforms, were concordant between replicates, and between each other. These findings suggest that the MiSeq platform, and these primers, is a comparable method for determining skin microbiota to the widely used Roche454 methodology. NIHR Manchester Musculoskeletal Biomedical Research Unit. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Comparison of DESI-MS and LC-MS for the Lipidomic Profiling of Human Cancer Tissue

NASA Astrophysics Data System (ADS)

Abbassi-Ghadi, Nima; Jones, Emrys A.; Gomez-Romero, Maria; Golf, Ottmar; Kumar, Sacheen; Huang, Juzheng; Kudo, Hiromi; Goldin, Rob D.; Hanna, George B.; Takats, Zoltan

2016-02-01

In this study, we make a direct comparison between desorption electrospray ionization-mass spectrometry (DESI-MS) and ultraperformance liquid chromatography-electrospray ionization-mass spectrometry (UPLC-ESI-MS) platforms for the profiling of glycerophospholipid (GPL) species in esophageal cancer tissue. In particular, we studied the similarities and differences in the range of GPLs detected and the congruency of their relative abundances as detected by each analytical platform. The main differences between mass spectra of the two modalities were found to be associated with the variance in adduct formation of common GPLs, rather than the presence of different GPL species. Phosphatidylcholines as formate adducts in UPLC-ESI-MS accounted for the majority of differences in negative ion mode and alkali metal adducts of phosphatidylcholines in DESI-MS for positive ion mode. Comparison of the relative abundance of GPLs, normalized to a common peak, revealed a correlation coefficient of 0.70 ( P < 0.001). The GPL profile detected by DESI-MS is congruent to UPLC-ESI-MS, which reaffirms the role of DESI-MS for lipidomic profiling and a potential premise for quantification.

Arabidopsis phenotyping through Geometric Morphometrics.

PubMed

Manacorda, Carlos A; Asurmendi, Sebastian

2018-06-18

Recently, much technical progress was achieved in the field of plant phenotyping. High-throughput platforms and the development of improved algorithms for rosette image segmentation make it now possible to extract shape and size parameters for genetic, physiological and environmental studies on a large scale. The development of low-cost phenotyping platforms and freeware resources make it possible to widely expand phenotypic analysis tools for Arabidopsis. However, objective descriptors of shape parameters that could be used independently of platform and segmentation software used are still lacking and shape descriptions still rely on ad hoc or even sometimes contradictory descriptors, which could make comparisons difficult and perhaps inaccurate. Modern geometric morphometrics is a family of methods in quantitative biology proposed to be the main source of data and analytical tools in the emerging field of phenomics studies. Based on the location of landmarks (corresponding points) over imaged specimens and by combining geometry, multivariate analysis and powerful statistical techniques, these tools offer the possibility to reproducibly and accurately account for shape variations amongst groups and measure them in shape distance units. Here, a particular scheme of landmarks placement on Arabidopsis rosette images is proposed to study shape variation in the case of viral infection processes. Shape differences between controls and infected plants are quantified throughout the infectious process and visualized. Quantitative comparisons between two unrelated ssRNA+ viruses are shown and reproducibility issues are assessed. Combined with the newest automated platforms and plant segmentation procedures, geometric morphometric tools could boost phenotypic features extraction and processing in an objective, reproducible manner.

Navigation and Positioning System Using High Altitude Platforms Systems (HAPS)

NASA Astrophysics Data System (ADS)

Tsujii, Toshiaki; Harigae, Masatoshi; Harada, Masashi

Recently, some countries have begun conducting feasibility studies and R&D projects on High Altitude Platform Systems (HAPS). Japan has been investigating the use of an airship system that will function as a stratospheric platform for applications such as environmental monitoring, communications and broadcasting. If pseudolites were mounted on the airships, their GPS-like signals would be stable augmentations that would improve the accuracy, availability, and integrity of GPS-based positioning systems. Also, the sufficient number of HAPS can function as a positioning system independent of GPS. In this paper, a system design of the HAPS-based positioning system and its positioning error analyses are described.

Modification to the Joint Platform Allocation Tool (JPAT) to Include Additional Warfighting Functions. Aerial R&S Future

DTIC Science & Technology

2013-07-01

example, System 2 is four P2 platforms with four SN2 and four SN3 items of available equipment to build configura- tions. Image from [10...System 2 is four P2 platforms with four SN2 and four SN3 items of available equipment to build configurations. Image from [10]. UNCLASSIFIED 3

A multi-analyte biosensor for the simultaneous label-free detection of pathogens and biomarkers in point-of-need animal testing.

PubMed

Ewald, Melanie; Fechner, Peter; Gauglitz, Günter

2015-05-01

For the first time, a multi-analyte biosensor platform has been developed using the label-free 1-lambda-reflectometry technique. This platform is the first, which does not use imaging techniques, but is able to perform multi-analyte measurements. It is designed to be portable and cost-effective and therefore allows for point-of-need testing or on-site field-testing with possible applications in diagnostics. This work highlights the application possibilities of this platform in the field of animal testing, but is also relevant and transferable to human diagnostics. The performance of the platform has been evaluated using relevant reference systems like biomarker (C-reactive protein) and serology (anti-Salmonella antibodies) as well as a panel of real samples (animal sera). The comparison of the working range and limit of detection shows no loss of performance transferring the separate assays to the multi-analyte setup. Moreover, the new multi-analyte platform allows for discrimination between sera of animals infected with different Salmonella subtypes.

A forced running wheel system with a microcontroller that provides high-intensity exercise training in an animal ischemic stroke model.

PubMed

Chen, C C; Chang, M W; Chang, C P; Chan, S C; Chang, W Y; Yang, C L; Lin, M T

2014-10-01

We developed a forced non-electric-shock running wheel (FNESRW) system that provides rats with high-intensity exercise training using automatic exercise training patterns that are controlled by a microcontroller. The proposed system successfully makes a breakthrough in the traditional motorized running wheel to allow rats to perform high-intensity training and to enable comparisons with the treadmill at the same exercise intensity without any electric shock. A polyvinyl chloride runway with a rough rubber surface was coated on the periphery of the wheel so as to permit automatic acceleration training, and which allowed the rats to run consistently at high speeds (30 m/min for 1 h). An animal ischemic stroke model was used to validate the proposed system. FNESRW, treadmill, control, and sham groups were studied. The FNESRW and treadmill groups underwent 3 weeks of endurance running training. After 3 weeks, the experiments of middle cerebral artery occlusion, the modified neurological severity score (mNSS), an inclined plane test, and triphenyltetrazolium chloride were performed to evaluate the effectiveness of the proposed platform. The proposed platform showed that enhancement of motor function, mNSS, and infarct volumes was significantly stronger in the FNESRW group than the control group (P<0.05) and similar to the treadmill group. The experimental data demonstrated that the proposed platform can be applied to test the benefit of exercise-preconditioning-induced neuroprotection using the animal stroke model. Additional advantages of the FNESRW system include stand-alone capability, independence of subjective human adjustment, and ease of use.

Computational analyses of spectral trees from electrospray multi-stage mass spectrometry to aid metabolite identification.

PubMed

Cao, Mingshu; Fraser, Karl; Rasmussen, Susanne

2013-10-31

Mass spectrometry coupled with chromatography has become the major technical platform in metabolomics. Aided by peak detection algorithms, the detected signals are characterized by mass-over-charge ratio (m/z) and retention time. Chemical identities often remain elusive for the majority of the signals. Multi-stage mass spectrometry based on electrospray ionization (ESI) allows collision-induced dissociation (CID) fragmentation of selected precursor ions. These fragment ions can assist in structural inference for metabolites of low molecular weight. Computational investigations of fragmentation spectra have increasingly received attention in metabolomics and various public databases house such data. We have developed an R package "iontree" that can capture, store and analyze MS2 and MS3 mass spectral data from high throughput metabolomics experiments. The package includes functions for ion tree construction, an algorithm (distMS2) for MS2 spectral comparison, and tools for building platform-independent ion tree (MS2/MS3) libraries. We have demonstrated the utilization of the package for the systematic analysis and annotation of fragmentation spectra collected in various metabolomics platforms, including direct infusion mass spectrometry, and liquid chromatography coupled with either low resolution or high resolution mass spectrometry. Assisted by the developed computational tools, we have demonstrated that spectral trees can provide informative evidence complementary to retention time and accurate mass to aid with annotating unknown peaks. These experimental spectral trees once subjected to a quality control process, can be used for querying public MS2 databases or de novo interpretation. The putatively annotated spectral trees can be readily incorporated into reference libraries for routine identification of metabolites.

A forced running wheel system with a microcontroller that provides high-intensity exercise training in an animal ischemic stroke model

PubMed Central

Chen, C.C.; Chang, M.W.; Chang, C.P.; Chan, S.C.; Chang, W.Y.; Yang, C.L.; Lin, M.T.

2014-01-01

We developed a forced non-electric-shock running wheel (FNESRW) system that provides rats with high-intensity exercise training using automatic exercise training patterns that are controlled by a microcontroller. The proposed system successfully makes a breakthrough in the traditional motorized running wheel to allow rats to perform high-intensity training and to enable comparisons with the treadmill at the same exercise intensity without any electric shock. A polyvinyl chloride runway with a rough rubber surface was coated on the periphery of the wheel so as to permit automatic acceleration training, and which allowed the rats to run consistently at high speeds (30 m/min for 1 h). An animal ischemic stroke model was used to validate the proposed system. FNESRW, treadmill, control, and sham groups were studied. The FNESRW and treadmill groups underwent 3 weeks of endurance running training. After 3 weeks, the experiments of middle cerebral artery occlusion, the modified neurological severity score (mNSS), an inclined plane test, and triphenyltetrazolium chloride were performed to evaluate the effectiveness of the proposed platform. The proposed platform showed that enhancement of motor function, mNSS, and infarct volumes was significantly stronger in the FNESRW group than the control group (P<0.05) and similar to the treadmill group. The experimental data demonstrated that the proposed platform can be applied to test the benefit of exercise-preconditioning-induced neuroprotection using the animal stroke model. Additional advantages of the FNESRW system include stand-alone capability, independence of subjective human adjustment, and ease of use. PMID:25140816

A Methodology for Improving the Shipyard Planning Process: Using KVA Analysis, Risk Simulation and Strategic Real Options

DTIC Science & Technology

2006-09-30

allocated to intangible assets. With Proctor & Gamble’s $53.5 billion acquisition of Gillette , $31.5 billion or 59% of the total purchase price was... outsourcing , alliances, joint ventures) • Compound Option (platform options) • Sequential Options (stage-gate development, R&D, phased...Comparisons • RO/KVA could enhance outsourcing comparisons between the Government’s Most Efficient Organization (MEO) and private-sector

HaloTag Technology: A Versatile Platform for Biomedical Applications

PubMed Central

2015-01-01

Exploration of protein function and interaction is critical for discovering links among genomics, proteomics, and disease state; yet, the immense complexity of proteomics found in biological systems currently limits our investigational capacity. Although affinity and autofluorescent tags are widely employed for protein analysis, these methods have been met with limited success because they lack specificity and require multiple fusion tags and genetic constructs. As an alternative approach, the innovative HaloTag protein fusion platform allows protein function and interaction to be comprehensively analyzed using a single genetic construct with multiple capabilities. This is accomplished using a simplified process, in which a variable HaloTag ligand binds rapidly to the HaloTag protein (usually linked to the protein of interest) with high affinity and specificity. In this review, we examine all current applications of the HaloTag technology platform for biomedical applications, such as the study of protein isolation and purification, protein function, protein–protein and protein–DNA interactions, biological assays, in vitro cellular imaging, and in vivo molecular imaging. In addition, novel uses of the HaloTag platform are briefly discussed along with potential future applications. PMID:25974629

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.

Development of a software for quantitative evaluation radiotherapy target and organ-at-risk segmentation comparison.

PubMed

Kalpathy-Cramer, Jayashree; Awan, Musaddiq; Bedrick, Steven; Rasch, Coen R N; Rosenthal, David I; Fuller, Clifton D

2014-02-01

Modern radiotherapy requires accurate region of interest (ROI) inputs for plan optimization and delivery. Target delineation, however, remains operator-dependent and potentially serves as a major source of treatment delivery error. In order to optimize this critical, yet observer-driven process, a flexible web-based platform for individual and cooperative target delineation analysis and instruction was developed in order to meet the following unmet needs: (1) an open-source/open-access platform for automated/semiautomated quantitative interobserver and intraobserver ROI analysis and comparison, (2) a real-time interface for radiation oncology trainee online self-education in ROI definition, and (3) a source for pilot data to develop and validate quality metrics for institutional and cooperative group quality assurance efforts. The resultant software, Target Contour Testing/Instructional Computer Software (TaCTICS), developed using Ruby on Rails, has since been implemented and proven flexible, feasible, and useful in several distinct analytical and research applications.

Establishment and Comparison of Two Different Diagnostic Platforms for Detection of DENV1 NS1 Protein

PubMed Central

Tang, Yin-Liang; Chiu, Chien-Yu; Lin, Chun-Yu; Huang, Chung-Hao; Chen, Yen-Hsu; Destura, Raul V.; Chao, Day-Yu; Wu, Han-Chung

2015-01-01

Dengue virus (DENV) infection is currently at pandemic levels, with populations in tropical and subtropical regions at greatest risk of infection. Early diagnosis and management remain the cornerstone for good clinical outcomes, thus efficient and accurate diagnostic technology in the early stage of the disease is urgently needed. Serotype-specific monoclonal antibodies (mAbs) against the DENV1 nonstructural protein 1 (NS1), DA12-4, DA13-2, and DA15-3, which were recently generated using the hybridoma technique, are suitable for use in diagnostic platforms. Immunofluorescence assay (IFA), enzyme-linked immunosorbent assay (ELISA) and Western blot analysis further confirmed the serotype specificity of these three monoclonal antibodies. The ELISA-based diagnostic platform was established using the combination of two highly sensitive mAbs (DA15-3 and DB20-6). The same combination was also used for the flow cytometry-based diagnostic platform. We report here the detection limits of flow cytometry-based and ELISA-based diagnostic platforms using these mAbs to be 0.1 and 1 ng/mL, respectively. The collected clinical patient serum samples were also assayed by these two serotyping diagnostic platforms. The sensitivity and specificity for detecting NS1 protein of DENV1 are 90% and 96%, respectively. The accuracy of our platform for testing clinical samples is more advanced than that of the two commercial NS1 diagnostic platforms. In conclusion, our platforms are suitable for the early detection of NS1 protein in DENV1 infected patients. PMID:26610481

Use of a platform in an automated open-field to enhance assessment of anxiety-like behaviors in mice.

PubMed

Pogorelov, Vladimir M; Lanthorn, Thomas H; Savelieva, Katerina V

2007-05-15

The present report describes a setup for simultaneously measuring anxiety-like behaviors and locomotor activity in mice. Animals are placed in a brightly lit, standard automated open-field (OF) in which a rectangular ceramic platform 8 cm high covers one quadrant of the floor. Mice preferred to stay under the platform, avoiding the area with bright illumination. Activities under and outside the platform were measured for 5 min. Chlordiazepoxide and buspirone dose-dependently increased time spent outside the platform (L-Time) and the light distance to total OF distance ratio (L:T-TD) in both genders without changing total OF distance. By contrast, amphetamine decreased L-Time and L:T-TD in males, thus displaying an anxiogenic effect. Imipramine was without selective effect on L-Time or L:T-TD, but decreased total OF distance at the highest dose indicative of a sedative effect. Drug effects were also evaluated in the OF without platform using conventional anxiety measures. Introduction of the platform into the OF apparatus strongly enhanced the sensitivity to anxiolytics. Comparison of strains differing in activity or anxiety levels showed that L-Time and L:T-TD can be used as measures of anxiety-like behavior independent of locomotor activity. Changes in motor activity are reflected in the total distance traveled under and outside the platform. Therefore, the platform test is fully automated, sensitive to both anxiolytic and anxiogenic effects of drugs and genetic phenotypes with little evidence of gender-specific responses, and can be easily utilized by most laboratories measuring behavior.

Millstone: software for multiplex microbial genome analysis and engineering

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

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering.

PubMed

Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering

DOE PAGES

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.; ...

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Regional Patterns in Invertebrate Assemblages on Offshore Oil Platforms Along the Pacific Outer Continental Shelf

NASA Astrophysics Data System (ADS)

Zaleski, S.; Page, H. M.; Miller, R. J.; Doheny, B.; Dugan, J. E.; Schroeder, D. M.

2016-02-01

Twenty-seven oil and gas platforms are arrayed offshore California from north of Point Conception south to San Pedro Bay (a coastline distance of >300 km). To test the hypothesis that variability in the structure of sessile invertebrate communities on the platforms is associated with regional differences in sea surface temperature, we sampled space-holding invertebrate taxa photographically on 23 platforms and compared the composition and cover of invertebrates among and within regions using multivariate analyses. To explore temporal variability in invertebrate assemblages, we also compared the cover and composition of invertebrates on a subset of platforms in the Santa Barbara Channel (SBC) where data were collected over ten years previously. The composition of invertebrate assemblages differed significantly among regions, and was driven by variation in the relative abundance of certain anemone, bryozoan, tubiferous annelid, sponge, and bivalve taxa. The presence of non-native bryozoan and anemone taxa on some platforms in the south (San Pedro Bay) and southeast SBC contributed to the distinction of these assemblages from the others. Comparison of survey data on the subset of platforms in the SBC surveyed over ten years apart revealed little change in the cover of major space-holding taxa (e.g., anemones Metridium, Corynactis) across platforms, although there was an increase in cover of the non-native bryozoan Watersipora subtorquata between surveys. The existence of geographical patterns in the composition of platform invertebrate assemblages suggests that these assemblages may be useful as barometers of short and longer-term environmental change. For biogeographic transition zones, such as the SBC, monitoring of platform invertebrate assemblages could permit an evaluation of the concept that these zones are particularly susceptible to shifts in the composition of marine species driven by ocean climate.

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 New Cloud Architecture of Virtual Trusted Platform Modules

NASA Astrophysics Data System (ADS)

Liu, Dongxi; Lee, Jack; Jang, Julian; Nepal, Surya; Zic, John

We propose and implement a cloud architecture of virtual Trusted Platform Modules (TPMs) to improve the usability of TPMs. In this architecture, virtual TPMs can be obtained from the TPM cloud on demand. Hence, the TPM functionality is available for applications that do not have physical TPMs in their local platforms. Moreover, the TPM cloud allows users to access their keys and data in the same virtual TPM even if they move to untrusted platforms. The TPM cloud is easy to access for applications in different languages since cloud computing delivers services in standard protocols. The functionality of the TPM cloud is demonstrated by applying it to implement the Needham-Schroeder public-key protocol for web authentications, such that the strong security provided by TPMs is integrated into high level applications. The chain of trust based on the TPM cloud is discussed and the security properties of the virtual TPMs in the cloud is analyzed.

Virtual health platform for medical tourism purposes.

PubMed

Martinez, Debora; Ferriol, Pedro; Tous, Xisco; Cabrer, Miguel; Prats, Mercedes

2008-01-01

This paper introduces an overview of the Virtual Health Platform (VHP), an alternative approach to create a functional PHR system in a medical tourism environment. The proposed platform has been designed in order to be integrated with EHR infrastructures and in this way it expects to be useful and more advantageous to the patient or tourist. Use cases of the VHP and its potential benefits summarize the analysis.

Antibacterial Au nanostructured surfaces

NASA Astrophysics Data System (ADS)

Wu, Songmei; Zuber, Flavia; Brugger, Juergen; Maniura-Weber, Katharina; Ren, Qun

2016-01-01

We present here a technological platform for engineering Au nanotopographies by templated electrodeposition on antibacterial surfaces. Three different types of nanostructures were fabricated: nanopillars, nanorings and nanonuggets. The nanopillars are the basic structures and are 50 nm in diameter and 100 nm in height. Particular arrangement of the nanopillars in various geometries formed nanorings and nanonuggets. Flat surfaces, rough substrate surfaces, and various nanostructured surfaces were compared for their abilities to attach and kill bacterial cells. Methicillin-resistant Staphylococcus aureus, a Gram-positive bacterial strain responsible for many infections in health care system, was used as the model bacterial strain. It was found that all the Au nanostructures, regardless their shapes, exhibited similar excellent antibacterial properties. A comparison of live cells attached to nanotopographic surfaces showed that the number of live S. aureus cells was <1% of that from flat and rough reference surfaces. Our micro/nanofabrication process is a scalable approach based on cost-efficient self-organization and provides potential for further developing functional surfaces to study the behavior of microbes on nanoscale topographies.We present here a technological platform for engineering Au nanotopographies by templated electrodeposition on antibacterial surfaces. Three different types of nanostructures were fabricated: nanopillars, nanorings and nanonuggets. The nanopillars are the basic structures and are 50 nm in diameter and 100 nm in height. Particular arrangement of the nanopillars in various geometries formed nanorings and nanonuggets. Flat surfaces, rough substrate surfaces, and various nanostructured surfaces were compared for their abilities to attach and kill bacterial cells. Methicillin-resistant Staphylococcus aureus, a Gram-positive bacterial strain responsible for many infections in health care system, was used as the model bacterial strain. It was found that all the Au nanostructures, regardless their shapes, exhibited similar excellent antibacterial properties. A comparison of live cells attached to nanotopographic surfaces showed that the number of live S. aureus cells was <1% of that from flat and rough reference surfaces. Our micro/nanofabrication process is a scalable approach based on cost-efficient self-organization and provides potential for further developing functional surfaces to study the behavior of microbes on nanoscale topographies. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06157a

Phytozome Comparative Plant Genomics Portal

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

Goodstein, David; Batra, Sajeev; Carlson, Joseph

2014-09-09

The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

The Construction of Higher Education Entrepreneur Services Network System a Research Based on Ecological Systems Theory

NASA Astrophysics Data System (ADS)

Xue, Jingxin

The article aims to completely, systematically and objectively analyze the current situation of Entrepreneurship Education in China with Ecological Systems Theory. From this perspective, the author discusses the structure, function and its basic features of higher education entrepreneur services network system, and puts forward the opinion that every entrepreneurship organization in higher education institution does not limited to only one platform. Different functional supporting platforms should be combined closed through composite functional organization to form an integrated network system, in which each unit would impels others' development.

Designing scalable product families by the radial basis function-high-dimensional model representation metamodelling technique

NASA Astrophysics Data System (ADS)

Pirmoradi, Zhila; Haji Hajikolaei, Kambiz; Wang, G. Gary

2015-10-01

Product family design is cost-efficient for achieving the best trade-off between commonalization and diversification. However, for computationally intensive design functions which are viewed as black boxes, the family design would be challenging. A two-stage platform configuration method with generalized commonality is proposed for a scale-based family with unknown platform configuration. Unconventional sensitivity analysis and information on variation in the individual variants' optimal design are used for platform configuration design. Metamodelling is employed to provide the sensitivity and variable correlation information, leading to significant savings in function calls. A family of universal electric motors is designed for product performance and the efficiency of this method is studied. The impact of the employed parameters is also analysed. Then, the proposed method is modified for obtaining higher commonality. The proposed method is shown to yield design solutions with better objective function values, allowable performance loss and higher commonality than the previously developed methods in the literature.

A rodent brain-machine interface paradigm to study the impact of paraplegia on BMI performance.

PubMed

Bridges, Nathaniel R; Meyers, Michael; Garcia, Jonathan; Shewokis, Patricia A; Moxon, Karen A

2018-05-31

Most brain machine interfaces (BMI) focus on upper body function in non-injured animals, not addressing the lower limb functional needs of those with paraplegia. A need exists for a novel BMI task that engages the lower body and takes advantage of well-established rodent spinal cord injury (SCI) models to study methods to improve BMI performance. A tilt BMI task was designed that randomly applies different types of tilts to a platform, decodes the tilt type applied and rights the platform if the decoder correctly classifies the tilt type. The task was tested on female rats and is relatively natural such that it does not require the animal to learn a new skill. It is self-rewarding such that there is no need for additional rewards, eliminating food or water restriction, which can be especially hard on spinalized rats. Finally, task difficulty can be adjusted by making the tilt parameters. This novel BMI task bilaterally engages the cortex without visual feedback regarding limb position in space and animals learn to improve their performance both pre and post-SCI.Comparison with Existing Methods: Most BMI tasks primarily engage one hemisphere, are upper-body, rely heavily on visual feedback, do not perform investigations in animal models of SCI, and require nonnaturalistic extrinsic motivation such as water rewarding for performance improvement. Our task addresses these gaps. The BMI paradigm presented here will enable researchers to investigate the interaction of plasticity after SCI and plasticity during BMI training on performance. Copyright © 2018. Published by Elsevier B.V.

A Compendium of Canine Normal Tissue Gene Expression

PubMed Central

Chen, Qing-Rong; Wen, Xinyu; Khan, Javed; Khanna, Chand

2011-01-01

Background Our understanding of disease is increasingly informed by changes in gene expression between normal and abnormal tissues. The release of the canine genome sequence in 2005 provided an opportunity to better understand human health and disease using the dog as clinically relevant model. Accordingly, we now present the first genome-wide, canine normal tissue gene expression compendium with corresponding human cross-species analysis. Methodology/Principal Findings The Affymetrix platform was utilized to catalogue gene expression signatures of 10 normal canine tissues including: liver, kidney, heart, lung, cerebrum, lymph node, spleen, jejunum, pancreas and skeletal muscle. The quality of the database was assessed in several ways. Organ defining gene sets were identified for each tissue and functional enrichment analysis revealed themes consistent with known physio-anatomic functions for each organ. In addition, a comparison of orthologous gene expression between matched canine and human normal tissues uncovered remarkable similarity. To demonstrate the utility of this dataset, novel canine gene annotations were established based on comparative analysis of dog and human tissue selective gene expression and manual curation of canine probeset mapping. Public access, using infrastructure identical to that currently in use for human normal tissues, has been established and allows for additional comparisons across species. Conclusions/Significance These data advance our understanding of the canine genome through a comprehensive analysis of gene expression in a diverse set of tissues, contributing to improved functional annotation that has been lacking. Importantly, it will be used to inform future studies of disease in the dog as a model for human translational research and provides a novel resource to the community at large. PMID:21655323

Technology-Based Feedback and Its Efficacy in Improving Gait Parameters in Patients with Abnormal Gait: A Systematic Review

PubMed Central

Chamorro-Moriana, Gema; Moreno, Antonio José

2018-01-01

This systematic review synthesized and analyzed clinical findings related to the effectiveness of innovative technological feedback for tackling functional gait recovery. An electronic search of PUBMED, PEDro, WOS, CINAHL, and DIALNET was conducted from January 2011 to December 2016. The main inclusion criteria were: patients with modified or abnormal gait; application of technology-based feedback to deal with functional recovery of gait; any comparison between different kinds of feedback applied by means of technology, or any comparison between technological and non-technological feedback; and randomized controlled trials. Twenty papers were included. The populations were neurological patients (75%), orthopedic and healthy subjects. All participants were adults, bar one. Four studies used exoskeletons, 6 load platforms and 5 pressure sensors. The breakdown of the type of feedback used was as follows: 60% visual, 40% acoustic and 15% haptic. 55% used terminal feedback versus 65% simultaneous feedback. Prescriptive feedback was used in 60% of cases, while 50% used descriptive feedback. 62.5% and 58.33% of the trials showed a significant effect in improving step length and speed, respectively. Efficacy in improving other gait parameters such as balance or range of movement is observed in more than 75% of the studies with significant outcomes. Conclusion: Treatments based on feedback using innovative technology in patients with abnormal gait are mostly effective in improving gait parameters and therefore useful for the functional recovery of patients. The most frequently highlighted types of feedback were immediate visual feedback followed by terminal and immediate acoustic feedback. PMID:29316645

Technology-Based Feedback and Its Efficacy in Improving Gait Parameters in Patients with Abnormal Gait: A Systematic Review.

PubMed

Chamorro-Moriana, Gema; Moreno, Antonio José; Sevillano, José Luis

2018-01-06

This systematic review synthesized and analyzed clinical findings related to the effectiveness of innovative technological feedback for tackling functional gait recovery. An electronic search of PUBMED, PEDro, WOS, CINAHL, and DIALNET was conducted from January 2011 to December 2016. The main inclusion criteria were: patients with modified or abnormal gait; application of technology-based feedback to deal with functional recovery of gait; any comparison between different kinds of feedback applied by means of technology, or any comparison between technological and non-technological feedback; and randomized controlled trials. Twenty papers were included. The populations were neurological patients (75%), orthopedic and healthy subjects. All participants were adults, bar one. Four studies used exoskeletons, 6 load platforms and 5 pressure sensors. The breakdown of the type of feedback used was as follows: 60% visual, 40% acoustic and 15% haptic. 55% used terminal feedback versus 65% simultaneous feedback. Prescriptive feedback was used in 60% of cases, while 50% used descriptive feedback. 62.5% and 58.33% of the trials showed a significant effect in improving step length and speed, respectively. Efficacy in improving other gait parameters such as balance or range of movement is observed in more than 75% of the studies with significant outcomes. Treatments based on feedback using innovative technology in patients with abnormal gait are mostly effective in improving gait parameters and therefore useful for the functional recovery of patients. The most frequently highlighted types of feedback were immediate visual feedback followed by terminal and immediate acoustic feedback.

Enhanced hybrid TV platform with multiscreen, advanced EPG and recommendation enablers

NASA Astrophysics Data System (ADS)

Kovacik, Tomas; Bencel, Rastislav; Mato, Jan; Bronis, Roman; Truchly, Peter; Kotuliak, Ivan

2017-05-01

TV watching dramatically changes with introduction of new technologies such as Internet-connected TVs, enriched digital broadcasting (DVB), on-demand content, additional programme information, mobile phones and tablets enabling multiscreen functions etc that offer added values to content consumers. In this paper we propose modular advanced TV platform and its enablers enhancing TV watching. They allow users to receive aside of EPG also additional information about broadcasted content, to be reminded of requested programme, to utilize recommendation and search features, thanks to multiscreen functionality to allow users to take watched content with them or transfer it onto another device. The modularity of the platform allows new features to be added in future.

Space Station Freedom electrical power system hardware commonality with the United States Polar Platform

NASA Technical Reports Server (NTRS)

Rieker, Lorra L.; Haraburda, Francis M.

1989-01-01

The National Aeronautics and Space Administration has adopted the policy to achieve the maximum practical level of commonality for the Space Station Freedom program in order to significantly reduce life cycle costs. Commonality means using identical or similar hardware/software for meeting common sets of functionally similar requirements. Information on how the concept of commonality is being implemented with respect to electric power system hardware for the Space Station Freedom and the U.S. Polar Platform is presented. Included is a historical account of the candidate common items which have the potential to serve the same power system functions on both Freedom and the Polar Platform.

Developing Extracellular Matrix Technology to Treat Retinal or Optic Nerve Injury

PubMed Central

van der Merwe, Yolandi

2015-01-01

Abstract Adult mammalian CNS neurons often degenerate after injury, leading to lost neurologic functions. In the visual system, retinal or optic nerve injury often leads to retinal ganglion cell axon degeneration and irreversible vision loss. CNS axon degeneration is increasingly linked to the innate immune response to injury, which leads to tissue-destructive inflammation and scarring. Extracellular matrix (ECM) technology can reduce inflammation, while increasing functional tissue remodeling, over scarring, in various tissues and organs, including the peripheral nervous system. However, applying ECM technology to CNS injuries has been limited and virtually unstudied in the visual system. Here we discuss advances in deriving fetal CNS-specific ECMs, like fetal porcine brain, retina, and optic nerve, and fetal non-CNS-specific ECMs, like fetal urinary bladder, and the potential for using tissue-specific ECMs to treat retinal or optic nerve injuries in two platforms. The first platform is an ECM hydrogel that can be administered as a retrobulbar, periocular, or even intraocular injection. The second platform is an ECM hydrogel and polymer “biohybrid” sheet that can be readily shaped and wrapped around a nerve. Both platforms can be tuned mechanically and biochemically to deliver factors like neurotrophins, immunotherapeutics, or stem cells. Since clinical CNS therapies often use general anti-inflammatory agents, which can reduce tissue-destructive inflammation but also suppress tissue-reparative immune system functions, tissue-specific, ECM-based devices may fill an important need by providing naturally derived, biocompatible, and highly translatable platforms that can modulate the innate immune response to promote a positive functional outcome. PMID:26478910

Assessment of inlet efficiency through a 3D simulation: numerical and experimental comparison.

PubMed

Gómez, Manuel; Recasens, Joan; Russo, Beniamino; Martínez-Gomariz, Eduardo

2016-10-01

Inlet efficiency is a requirement for characterizing the flow transfers between surface and sewer flow during rain events. The dual drainage approach is based on the joint analysis of both upper and lower drainage levels, and the flow transfer is one of the relevant elements to define properly this joint behaviour. This paper presents the results of an experimental and numerical investigation about the inlet efficiency definition. A full scale (1:1) test platform located in the Technical University of Catalonia (UPC) reproduces both the runoff process in streets and the water entering the inlet. Data from tests performed on this platform allow the inlet efficiency to be estimated as a function of significant hydraulic and geometrical parameters. A reproduction of these tests through a numerical three-dimensional code (Flow-3D) has been carried out simulating this type of flow by solving the RANS equations. The aim of the work was to reproduce the hydraulic performance of a previously tested grated inlet under several flow and geometric conditions using Flow-3D as a virtual laboratory. This will allow inlet efficiencies to be obtained without previous experimental tests. Moreover, the 3D model allows a better understanding of the hydraulics of the flow interception and the flow patterns approaching the inlet.

Evanescent field refractometry in planar optical fiber.

PubMed

Holmes, Christopher; Jantzen, Alexander; Gray, Alan C; Gow, Paul C; Carpenter, Lewis G; Bannerman, Rex H S; Gates, James C; Smith, Peter G R

2018-02-15

This Letter demonstrates a refractometer in integrated optical fiber, a new optical platform that planarizes fiber using flame hydrolysis deposition (FHD). The unique advantage of the technology is survivability in harsh environments. The platform is mechanically robust, and can survive elevated temperatures approaching 1000°C and exposure to common solvents, including acetone, gasoline, and methanol. For the demonstrated refractometer, fabrication was achieved through wet etching an SMF-28 fiber to a diameter of 8 μm before FHD planarization. An external refractive index was monitored using fiber Bragg gratings (FBGs), written into the core of the planarized fiber. A direct comparison to alternative FBG refractometers is made, for which the developed platform is shown to have comparable sensitivity, with the added advantage of survivability in harsh environments.

Development of a PDXP platform on NIF

NASA Astrophysics Data System (ADS)

Whitley, Heather; Schneider, Marilyn; Garbett, Warren; Pino, Jesse; Shepherd, Ronnie; Brown, Colin; Castor, John; Scott, Howard; Ellison, C. Leland; Benedict, Lorin; Sio, Hong; Lahmann, Brandon; Petrasso, Richard; Graziani, Frank

2016-10-01

Over the past several years, we have conducted theoretical investigations of electron-ion coupling and electronic transport in plasmas. In the regime of weakly coupled plasmas, we have identified models that we believe describe the physics well, but experimental measurements are still needed to validate the models. We are developing spectroscopic experiments to study electron-ion equilibration and electron heat transport using a polar direct drive exploding pusher (PDXP) platform at the National Ignition Facility (NIF). Initial measurements are focused on characterizing the laser-target coupling, symmetry of the PDXP implosion, and overall neutron and x-ray signals. We present images from the first set of shots and make comparisons with simulations from ARES and discuss next steps in the platform development. Prepared by LLNL under Contract DE-AC52-07NA27344. LLNL-ABS-697489.

Protective Immunization Against Inhalational Anthrax: A Comparison of Minimally Invasive Delivery Platforms

DTIC Science & Technology

2004-12-15

278 • JID 2005:191 (15 January) • Mikszta et al. M A J O R A R T I C L E Protective Immunization against Inhalational Anthrax: A Comparison of...provides complete protection against inhalational anthrax in rabbits. The novel vaccine/device combi- nations described here have the potential to...have produced documented fatali- ties, the fatality rate of inhalational anthrax is nearly 100% without antibiotic intervention. Inhalational an

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.

Application of online measures to monitor and evaluate multiplatform fusion performance

NASA Astrophysics Data System (ADS)

Stubberud, Stephen C.; Kowalski, Charlene; Klamer, Dale M.

1999-07-01

A primary concern of multiplatform data fusion is assessing the quality and utility of data shared among platforms. Constraints such as platform and sensor capability and task load necessitate development of an on-line system that computes a metric to determine which other platform can provide the best data for processing. To determine data quality, we are implementing an approach based on entropy coupled with intelligent agents. To determine data quality, we are implementing an approach based on entropy coupled with intelligent agents. Entropy measures quality of processed information such as localization, classification, and ambiguity in measurement-to-track association. Lower entropy scores imply less uncertainty about a particular target. When new information is provided, we compuete the level of improvement a particular track obtains from one measurement to another. The measure permits us to evaluate the utility of the new information. We couple entropy with intelligent agents that provide two main data gathering functions: estimation of another platform's performance and evaluation of the new measurement data's quality. Both functions result from the entropy metric. The intelligent agent on a platform makes an estimate of another platform's measurement and provides it to its own fusion system, which can then incorporate it, for a particular target. A resulting entropy measure is then calculated and returned to its own agent. From this metric, the agent determines a perceived value of the offboard platform's measurement. If the value is satisfactory, the agent requests the measurement from the other platform, usually by interacting with the other platform's agent. Once the actual measurement is received, again entropy is computed and the agent assesses its estimation process and refines it accordingly.

Microfluidic platform combining droplets and magnetic tweezers: application to HER2 expression in cancer diagnosis

PubMed Central

Ferraro, Davide; Champ, Jérôme; Teste, Bruno; Serra, Marco; Malaquin, Laurent; Viovy, Jean-Louis; de Cremoux, Patricia; Descroix, Stephanie

2016-01-01

The development of precision medicine, together with the multiplication of targeted therapies and associated molecular biomarkers, call for major progress in genetic analysis methods, allowing increased multiplexing and the implementation of more complex decision trees, without cost increase or loss of robustness. We present a platform combining droplet microfluidics and magnetic tweezers, performing RNA purification, reverse transcription and amplification in a fully automated and programmable way, in droplets of 250nL directly sampled from a microtiter-plate. This platform decreases sample consumption about 100 fold as compared to current robotized platforms and it reduces human manipulations and contamination risk. The platform’s performance was first evaluated on cell lines, showing robust operation on RNA quantities corresponding to less than one cell, and then clinically validated with a cohort of 21 breast cancer samples, for the determination of their HER2 expression status, in a blind comparison with an established routine clinical analysis. PMID:27157697

Microfluidic platform combining droplets and magnetic tweezers: application to HER2 expression in cancer diagnosis

NASA Astrophysics Data System (ADS)

Ferraro, Davide; Champ, Jérôme; Teste, Bruno; Serra, Marco; Malaquin, Laurent; Viovy, Jean-Louis; de Cremoux, Patricia; Descroix, Stephanie

2016-05-01

The development of precision medicine, together with the multiplication of targeted therapies and associated molecular biomarkers, call for major progress in genetic analysis methods, allowing increased multiplexing and the implementation of more complex decision trees, without cost increase or loss of robustness. We present a platform combining droplet microfluidics and magnetic tweezers, performing RNA purification, reverse transcription and amplification in a fully automated and programmable way, in droplets of 250nL directly sampled from a microtiter-plate. This platform decreases sample consumption about 100 fold as compared to current robotized platforms and it reduces human manipulations and contamination risk. The platform’s performance was first evaluated on cell lines, showing robust operation on RNA quantities corresponding to less than one cell, and then clinically validated with a cohort of 21 breast cancer samples, for the determination of their HER2 expression status, in a blind comparison with an established routine clinical analysis.

Sequence Data for Clostridium autoethanogenum using Three Generations of Sequencing Technologies

DOE PAGES

Utturkar, Sagar M.; Klingeman, Dawn Marie; Bruno-Barcena, José M.; ...

2015-04-14

During the past decade, DNA sequencing output has been mostly dominated by the second generation sequencing platforms which are characterized by low cost, high throughput and shorter read lengths for example, Illumina. The emergence and development of so called third generation sequencing platforms such as PacBio has permitted exceptionally long reads (over 20 kb) to be generated. Due to read length increases, algorithm improvements and hybrid assembly approaches, the concept of one chromosome, one contig and automated finishing of microbial genomes is now a realistic and achievable task for many microbial laboratories. In this paper, we describe high quality sequencemore » datasets which span three generations of sequencing technologies, containing six types of data from four NGS platforms and originating from a single microorganism, Clostridium autoethanogenum. The dataset reported here will be useful for the scientific community to evaluate upcoming NGS platforms, enabling comparison of existing and novel bioinformatics approaches and will encourage interest in the development of innovative experimental and computational methods for NGS data.« less

Pro-ana versus Pro-recovery: A Content Analytic Comparison of Social Media Users’ Communication about Eating Disorders on Twitter and Tumblr

PubMed Central

Branley, Dawn B.; Covey, Judith

2017-01-01

Objectives: To compare how people communicate about eating disorders on two popular social media platforms – Twitter and Tumblr. Materials and Methods: Thematic analysis was conducted to characterize the types of communications posted, and a content analysis was undertaken of between-platform differences. Results: Three types of content (pro-ana, anti-ana, and pro-recovery) were posted on each platform. Overall, across both platforms, extreme pro-ana posts were in the minority compared to anti-ana and pro-recovery. Pro-ana posts (including ‘thinspiration’) were more common on Twitter than Tumblr, whereas anti-ana and pro-recovery posts were more common on Tumblr. Conclusion: The findings have implications for future research and health care relating to the treatment and prevention of eating disorders. Developers of future interventions targeting negative pro-ana content should remain aware of the need to avoid any detrimental impact on positive online support. PMID:28848472

Simple diazonium chemistry to develop specific gene sensing platforms.

PubMed

Revenga-Parra, M; García-Mendiola, T; González-Costas, J; González-Romero, E; Marín, A García; Pau, J L; Pariente, F; Lorenzo, E

2014-02-27

A simple strategy for covalent immobilizing DNA sequences, based on the formation of stable diazonized conducting platforms, is described. The electrochemical reduction of 4-nitrobenzenediazonium salt onto screen-printed carbon electrodes (SPCE) in aqueous media gives rise to terminal grafted amino groups. The presence of primary aromatic amines allows the formation of diazonium cations capable to react with the amines present at the DNA capture probe. As a comparison a second strategy based on the binding of aminated DNA capture probes to the developed diazonized conducting platforms through a crosslinking agent was also employed. The resulting DNA sensing platforms were characterized by cyclic voltammetry, electrochemical impedance spectroscopy and spectroscopic ellipsometry. The hybridization event with the complementary sequence was detected using hexaamineruthenium (III) chloride as electrochemical indicator. Finally, they were applied to the analysis of a 145-bp sequence from the human gene MRP3, reaching a detection limit of 210 pg μL(-1). Copyright © 2014 Elsevier B.V. All rights reserved.

Conceptual design study. Science and Applications Space Platform (SASP). Final briefing

NASA Technical Reports Server (NTRS)

1980-01-01

The modularity, shape, and size of the recommended platform concept offers a low investment, early option to demonstrate the system; flexibility to conservative growth; adaptability to great variety of multi or dedicated payload groups; and good dispersion and viewing freedom for payloads. Platform configuration effectively supports 80 to 85% of the NASA/OSS and OSTA payloads. The subsystem approaches recommended are based on cost effective distribution of functions.

A novel tablet computer platform for advanced language mapping during awake craniotomy procedures.

PubMed

Morrison, Melanie A; Tam, Fred; Garavaglia, Marco M; Golestanirad, Laleh; Hare, Gregory M T; Cusimano, Michael D; Schweizer, Tom A; Das, Sunit; Graham, Simon J

2016-04-01

A computerized platform has been developed to enhance behavioral testing during intraoperative language mapping in awake craniotomy procedures. The system is uniquely compatible with the environmental demands of both the operating room and preoperative functional MRI (fMRI), thus providing standardized testing toward improving spatial agreement between the 2 brain mapping techniques. Details of the platform architecture, its advantages over traditional testing methods, and its use for language mapping are described. Four illustrative cases demonstrate the efficacy of using the testing platform to administer sophisticated language paradigms, and the spatial agreement between intraoperative mapping and preoperative fMRI results. The testing platform substantially improved the ability of the surgeon to detect and characterize language deficits. Use of a written word generation task to assess language production helped confirm areas of speech apraxia and speech arrest that were inadequately characterized or missed with the use of traditional paradigms, respectively. Preoperative fMRI of the analogous writing task was also assistive, displaying excellent spatial agreement with intraoperative mapping in all 4 cases. Sole use of traditional testing paradigms can be limiting during awake craniotomy procedures. Comprehensive assessment of language function will require additional use of more sophisticated and ecologically valid testing paradigms. The platform presented here provides a means to do so.

The Extracellular δ-Domain is Essential for the Formation of CD81 Tetraspanin Webs

PubMed Central

Homsi, Yahya; Schloetel, Jan-Gero; Scheffer, Konstanze D.; Schmidt, Thomas H.; Destainville, Nicolas; Florin, Luise; Lang, Thorsten

2014-01-01

CD81 is a ubiquitously expressed member of the tetraspanin family. It forms large molecular platforms, so-called tetraspanin webs that play physiological roles in a variety of cellular functions and are involved in viral and parasite infections. We have investigated which part of the CD81 molecule is required for the formation of domains in the cell membranes of T-cells and hepatocytes. Surprisingly, we find that large CD81 platforms assemble via the short extracellular δ-domain, independent from a strong primary partner binding and from weak interactions mediated by palmitoylation. The δ-domain is also essential for the platforms to function during viral entry. We propose that, instead of stable binary interactions, CD81 interactions via the small δ-domain, possibly involving a dimerization step, play the key role in organizing CD81 into large tetraspanin webs and controlling its function. PMID:24988345

Blood transcriptomic comparison of individuals with and without autism spectrum disorder: A combined-samples mega-analysis.

PubMed

Tylee, Daniel S; Hess, Jonathan L; Quinn, Thomas P; Barve, Rahul; Huang, Hailiang; Zhang-James, Yanli; Chang, Jeffrey; Stamova, Boryana S; Sharp, Frank R; Hertz-Picciotto, Irva; Faraone, Stephen V; Kong, Sek Won; Glatt, Stephen J

2017-04-01

Blood-based microarray studies comparing individuals affected with autism spectrum disorder (ASD) and typically developing individuals help characterize differences in circulating immune cell functions and offer potential biomarker signal. We sought to combine the subject-level data from previously published studies by mega-analysis to increase the statistical power. We identified studies that compared ex vivo blood or lymphocytes from ASD-affected individuals and unrelated comparison subjects using Affymetrix or Illumina array platforms. Raw microarray data and clinical meta-data were obtained from seven studies, totaling 626 affected and 447 comparison subjects. Microarray data were processed using uniform methods. Covariate-controlled mixed-effect linear models were used to identify gene transcripts and co-expression network modules that were significantly associated with diagnostic status. Permutation-based gene-set analysis was used to identify functionally related sets of genes that were over- and under-expressed among ASD samples. Our results were consistent with diminished interferon-, EGF-, PDGF-, PI3K-AKT-mTOR-, and RAS-MAPK-signaling cascades, and increased ribosomal translation and NK-cell related activity in ASD. We explored evidence for sex-differences in the ASD-related transcriptomic signature. We also demonstrated that machine-learning classifiers using blood transcriptome data perform with moderate accuracy when data are combined across studies. Comparing our results with those from blood-based studies of protein biomarkers (e.g., cytokines and trophic factors), we propose that ASD may feature decoupling between certain circulating signaling proteins (higher in ASD samples) and the transcriptional cascades which they typically elicit within circulating immune cells (lower in ASD samples). These findings provide insight into ASD-related transcriptional differences in circulating immune cells. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Blood Transcriptomic Comparison of Individuals with and without Autism Spectrum Disorder: A Combined-Samples Mega-Analysis

PubMed Central

Tylee, Daniel S.; Hess, Jonathan L.; Quinn, Thomas P.; Barve, Rahul; Huang, Hailiang; Zhang-James, Yanli; Chang, Jeffrey; Stamova, Boryana S.; Sharp, Frank R.; Hertz-Picciotto, Irva; Faraone, Stephen V.; Kong, Sek Won; Glatt, Stephen J.

2017-01-01

Blood-based microarray studies comparing individuals affected with autism spectrum disorder (ASD) and typically developing individuals help characterize differences in circulating immune cell functions and offer potential biomarker signal. We sought to combine the subject-level data from previously published studies by mega-analysis to increase the statistical power. We identified studies that compared ex-vivo blood or lymphocytes from ASD-affected individuals and unrelated comparison subjects using Affymetrix or Illumina array platforms. Raw microarray data and clinical meta-data were obtained from seven studies, totaling 626 affected and 447 comparison subjects. Microarray data were processed using uniform methods. Covariate-controlled mixed-effect linear models were used to identify gene transcripts and co-expression network modules that were significantly associated with diagnostic status. Permutation-based gene-set analysis was used to identify functionally related sets of genes that were over- and under-expressed among ASD samples. Our results were consistent with diminished interferon-, EGF-, PDGF-, PI3K-AKT-mTOR-, and RAS-MAPK-signaling cascades, and increased ribosomal translation and NK-cell related activity in ASD. We explored evidence for sex-differences in the ASD-related transcriptomic signature. We also demonstrated that machine-learning classifiers using blood transcriptome data perform with moderate accuracy when data are combined across studies. Comparing our results with those from blood-based studies of protein biomarkers (e.g., cytokines and trophic factors), we propose that ASD may feature decoupling between certain circulating signaling proteins (higher in ASD samples) and the transcriptional cascades which they typically elicit within circulating immune cells (lower in ASD samples). These findings provide insight into ASD-related transcriptional differences in circulating immune cells. PMID:27862943

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.

High Throughput and Mechano-Active Platforms to Promote Cartilage Regeneration and Repair

NASA Astrophysics Data System (ADS)

Mohanraj, Bhavana

Traumatic joint injuries initiate acute degenerative changes in articular cartilage that can lead to progressive loss of load-bearing function. As a result, patients often develop post-traumatic osteoarthritis (PTOA), a condition for which there currently exists no biologic interventions. To address this need, tissue engineering aims to mimic the structure and function of healthy, native counterparts. These constructs can be used to not only replace degenerated tissue, but also build in vitro, pre-clinical models of disease. Towards this latter goal, this thesis focuses on the design of a high throughput system to screen new therapeutics in a micro-engineered model of PTOA, and the development of a mechanically-responsive drug delivery system to augment tissue-engineered approaches for cartilage repair. High throughput screening is a powerful tool for drug discovery that can be adapted to include 3D tissue constructs. To facilitate this process for cartilage repair, we built a high throughput mechanical injury platform to create an engineered cartilage model of PTOA. Compressive injury of functionally mature constructs increased cell death and proteoglycan loss, two hallmarks of injury observed in vivo. Comparison of this response to that of native cartilage explants, and evaluation of putative therapeutics, validated this model for subsequent use in small molecule screens. A primary screen of 118 compounds identified a number of 'hits' and relevant pathways that may modulate pathologic signaling post-injury. To complement this process of therapeutic discovery, a stimuli-responsive delivery system was designed that used mechanical inputs as the 'trigger' mechanism for controlled release. The failure thresholds of these mechanically-activated microcapsules (MAMCs) were influenced by physical properties and composition, as well as matrix mechanical properties in 3D environments. TGF-beta released from the system upon mechano-activation stimulated stem cell chondrogenesis, demonstrating the potential of MAMCs to actively deliver therapeutics within demanding mechanical environments. Taken together, this work advances our capacity to identify and deliver new compounds of clinical relevance to modulate disease progression following traumatic injury using state-of-the-art micro-engineered screening tools and a novel mechanically-activated delivery system. These platforms advance strategies for cartilage repair and regeneration in PTOA and provide new options for the treatment of this debilitating condition.

Embedding Task-Based Neural Models into a Connectome-Based Model of the Cerebral Cortex

PubMed Central

Ulloa, Antonio; Horwitz, Barry

2016-01-01

A number of recent efforts have used large-scale, biologically realistic, neural models to help understand the neural basis for the patterns of activity observed in both resting state and task-related functional neural imaging data. An example of the former is The Virtual Brain (TVB) software platform, which allows one to apply large-scale neural modeling in a whole brain framework. TVB provides a set of structural connectomes of the human cerebral cortex, a collection of neural processing units for each connectome node, and various forward models that can convert simulated neural activity into a variety of functional brain imaging signals. In this paper, we demonstrate how to embed a previously or newly constructed task-based large-scale neural model into the TVB platform. We tested our method on a previously constructed large-scale neural model (LSNM) of visual object processing that consisted of interconnected neural populations that represent, primary and secondary visual, inferotemporal, and prefrontal cortex. Some neural elements in the original model were “non-task-specific” (NS) neurons that served as noise generators to “task-specific” neurons that processed shapes during a delayed match-to-sample (DMS) task. We replaced the NS neurons with an anatomical TVB connectome model of the cerebral cortex comprising 998 regions of interest interconnected by white matter fiber tract weights. We embedded our LSNM of visual object processing into corresponding nodes within the TVB connectome. Reciprocal connections between TVB nodes and our task-based modules were included in this framework. We ran visual object processing simulations and showed that the TVB simulator successfully replaced the noise generation originally provided by NS neurons; i.e., the DMS tasks performed with the hybrid LSNM/TVB simulator generated equivalent neural and fMRI activity to that of the original task-based models. Additionally, we found partial agreement between the functional connectivities using the hybrid LSNM/TVB model and the original LSNM. Our framework thus presents a way to embed task-based neural models into the TVB platform, enabling a better comparison between empirical and computational data, which in turn can lead to a better understanding of how interacting neural populations give rise to human cognitive behaviors. PMID:27536235

The effectiveness of extended care based on Internet and Home Care Platform for Orthopedics after hip replacement surgery in China.

PubMed

Wang, Jie; Tong, Yahui; Jiang, Yingqing; Zhu, Hongxia; Gao, Hui; Wei, Rong; Que, Xianfeng; Gao, Luoluo

2018-05-31

To evaluate the effect of an Internet-based home orthopedic care platform on patients' functional joint recovery, quality of life, and activities of daily living after hip replacement. Most of the functional exercises after arthroplasty are performed outside the hospital. At present, the WeChat platform is used mainly in the inland of China for continuous nursing of patients with chronic disease in the Department of Orthopedics. An experimental design was applied. 400 patients who had undergone hip replacement from April to October 2016 were selected from 18 hospitals with nurse specialists in clinical orthopedics. These patients were randomized into control and intervention groups (n=200 per group).In the control group, only routine nursing care was carried out after discharge. In the intervention group, continuous intervention was performed via the Internet-based orthopedic care platform. The patients in the two groups were compared in terms of functional recovery (Harris hip score), quality of life score (MOS SF-36), and activities of daily living (Barthel index) at 3 and 6 months after discharge. In total, 389 patients were enrolled in this study. There were no significant differences in the baseline data between the two groups. After 6 months of continuous intervention, the mean MOS SF-36 score, Barthel index, and Harris hip score in the intervention group were significantly higher than those in the control group . The study gives full play to the role of clinical nurse specialists, and provides professional home care services to patients in the region after hip replacement through home care orthopedic platform. The platform guides the patients to master the correct disease knowledge and rehabilitation exercise methods, promotes the recovery of joint function, improves the activity of daily living, elevates the quality of life and met the need of long-term management. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

30 CFR 250.915 - What are the CVA's primary responsibilities?

Code of Federal Regulations, 2010 CFR

2010-07-01

... OFFSHORE OIL AND GAS AND SULPHUR OPERATIONS IN THE OUTER CONTINENTAL SHELF Platforms and Structures... or organizations acting as CVAs must not function in any capacity that would create a conflict of... design, fabrication and installation of the platform. ...

A new e-learning platform for radiology education (RadEd).

PubMed

Xiberta, Pau; Boada, Imma

2016-04-01

One of the key elements of e-learning platforms is the content provided to the students. Content creation is a time demanding task that requires teachers to prepare material taking into account that it will be accessed on-line. Moreover, the teacher is restricted by the functionalities provided by the e-learning platforms. In contexts such as radiology where images have a key role, the required functionalities are still more specific and difficult to be provided by these platforms. Our purpose is to create a framework to make teacher's tasks easier, specially when he has to deal with contents where images have a main role. In this paper, we present RadEd, a new web-based teaching framework that integrates a smart editor to create case-based exercises that support image interaction such as changing the window width and the grey scale used to render the image, taking measurements on the image, attaching labels to images and selecting parts of the images, amongst others. It also provides functionalities to prepare courses with different topics, exercises and theory material, and also functionalities to control students' work. Different experts have used RadEd and all of them have considered it a very useful and valuable tool to prepare courses where radiological images are the main component. RadEd provides teachers functionalities to prepare more realistic cases and students the ability to make a more specific diagnosis. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

COMPARISON OF COMPARATIVE GENOMIC HYBRIDIZATIONS TECHNOLOGIES ACROSS MICROARRAY PLATFORMS

EPA Science Inventory

Comparative Genomic Hybridization (CGH) measures DNA copy number differences between a reference genome and a test genome. The DNA samples are differentially labeled and hybridized to an immobilized substrate. In early CGH experiments, the DNA targets were hybridized to metaphase...

Usability studies on e-learning platforms: Preliminary study in USM

NASA Astrophysics Data System (ADS)

Emang, Devinna Win Anak Boniface; Lukman, Raja Nurul Izzati Raja; Kamarulzaman, Muhammad Izzat Syafiq; Zaaba, Zarul Fitri

2017-10-01

This paper explores the end-users' experienced in regards to the usability issues in E-learning platform. An online survey utilising 116 participants were conducted to investigate the end-users understanding and satisfaction on E-learning platform in the Universiti Sains Malaysia (USM). The results indicates that mainly students still experiencing significant challenges in E-learning platform in regards to accessibility, technical terminologies and functionality. On the other hand, the 10 heuristic guideline is chosen to be a referral point to compare five E-learning platforms in order to assess each performance on regards to the usability criteria. Overall, USM E-learning platform can be considered in a good shape. However, there are more works to be done to improve the delivery system of the E-learning if it would like to sustain for a long period of time. Although the result is at the preliminary stage, it provides useful insights to improve the E-learning platform as one of the most popular education platform in Malaysia.

Exploring Inflammatory Disease Drug Effects on Neutrophil Function

PubMed Central

Wu, Xiaojie; Kim, Donghyuk; Young, Ashlyn T.; Haynes, Christy L.

2014-01-01

Neutrophils are critical inflammatory cells; thus, it is important to characterize the effects of drugs on neutrophil function in the context of inflammatory diseases. Herein, chemically guided neutrophil migration, known as chemotaxis, is studied in the context of drug treatment at the single cell level using a microfluidic platform, complemented by cell viability assays and calcium imaging. Three representative drugs known to inhibit surface receptor expression, signaling enzyme activity, and the elevation of intracellular Ca2+ levels, each playing a significant role in neutrophil chemotactic pathways, are used to examine the in vitro drug effects on cellular behaviors. The microfluidic device establishes a stable concentration gradient of chemokines across a cell culture chamber so that neutrophil migration can be monitored under various drug-exposure conditions. Different time- and concentration-dependent regulatory effects were observed by comparing the motility, polarization, and effectiveness of neutrophil chemotaxis in response to the three drugs. Viability assays revealed distinct drug capabilities in reducing neutrophil viability while calcium imaging clarified the role of Ca2+ in the neutrophil chemotactic pathway. This study provides mechanistic insight into the drug effects on neutrophil function, facilitating comparison of current and potential pharmaceutical approaches. PMID:24946254

AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants.

PubMed

Wang, Yi; Thilmony, Roger; Zhao, Yunjun; Chen, Guoping; Gu, Yong Q

2014-01-01

Systems biology analysis of protein modules is important for understanding the functional relationships between proteins in the interactome. Here, we present a comprehensive database named AIM for Arabidopsis (Arabidopsis thaliana) interactome modules. The database contains almost 250,000 modules that were generated using multiple analysis methods and integration of microarray expression data. All the modules in AIM are well annotated using multiple gene function knowledge databases. AIM provides a user-friendly interface for different types of searches and offers a powerful graphical viewer for displaying module networks linked to the enrichment annotation terms. Both interactive Venn diagram and power graph viewer are integrated into the database for easy comparison of modules. In addition, predicted interologs from other plant species (homologous proteins from different species that share a conserved interaction module) are available for each Arabidopsis module. AIM is a powerful systems biology platform for obtaining valuable insights into the function of proteins in Arabidopsis and other plants using the modules of the Arabidopsis interactome. Database URL:http://probes.pw.usda.gov/AIM Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

Solutal and thermal buoyancy effects in self-powered phosphatase micropumps.

PubMed

Valdez, Lyanne; Shum, Henry; Ortiz-Rivera, Isamar; Balazs, Anna C; Sen, Ayusman

2017-04-12

Immobilized enzymes generate net fluid flow when exposed to specific reagents in solution. Thus, they function as self-powered platforms that combine sensing and on-demand fluid pumping. To uncover the mechanism of pumping, we examine the effects of solutal and thermal buoyancy on the behavior of phosphatase-based micropumps, using a series of reactants with known thermodynamic and kinetic parameters. By combining modeling and experiments, we perform the first quantitative comparison of thermal and solutal effects in an enzyme micropump system. Despite the significant exothermicity of the catalyzed reactions, we find that thermal effects play a minimal role in the observed fluid flow. Instead, fluid transport in phosphatase micropumps is governed by the density difference between the reactants and the products of the reaction. This surprising conclusion suggests new design principles for catalytic pumps.

Aptahistochemistry in diagnostic pathology: technical scrutiny and feasibility.

PubMed

Bukari, Bakhtiar A; Citartan, Marimuthu; Ch'ng, Ewe Seng; Bilibana, Mawethu P; Rozhdestvensky, Timofey; Tang, Thean-Hock

2017-05-01

Antibodies have been the workhorse for diagnostic immunohistochemistry to specifically interrogate the expression of certain protein to aid in histopathological diagnosis. This review introduces another dimension of histochemistry that employs aptamers as the core tool, the so-called aptahistochemistry. Aptamers are an emerging class of molecular recognition elements that could recapitulate the roles of antibodies. The many advantageous properties of aptamers suited for this diagnostic platform are scrutinized. An in-depth discussion on the technical aspects of aptahistochemistry is provided with close step-by-step comparison to the more familiarized immunohistochemical procedures, namely functionalization of the aptamer as a probe, antigen retrieval, optimization with emphasis on incubation parameters and visualization methods. This review offers rationales to overcome the anticipated challenges in transition from immunohistochemistry to aptahistochemistry, which is deemed feasible for an average diagnostic pathology laboratory.

A COMSOL-GEMS interface for modeling coupled reactive-transport geochemical processes

NASA Astrophysics Data System (ADS)

Azad, Vahid Jafari; Li, Chang; Verba, Circe; Ideker, Jason H.; Isgor, O. Burkan

2016-07-01

An interface was developed between COMSOL MultiphysicsTM finite element analysis software and (geo)chemical modeling platform, GEMS, for the reactive-transport modeling of (geo)chemical processes in variably saturated porous media. The two standalone software packages are managed from the interface that uses a non-iterative operator splitting technique to couple the transport (COMSOL) and reaction (GEMS) processes. The interface allows modeling media with complex chemistry (e.g. cement) using GEMS thermodynamic database formats. Benchmark comparisons show that the developed interface can be used to predict a variety of reactive-transport processes accurately. The full functionality of the interface was demonstrated to model transport processes, governed by extended Nernst-Plank equation, in Class H Portland cement samples in high pressure and temperature autoclaves simulating systems that are used to store captured carbon dioxide (CO2) in geological reservoirs.

Novel graphene-oxide-coated SPR interfaces for biosensing applications

NASA Astrophysics Data System (ADS)

Volkov, V. S.; Stebunov, Yu. V.; Yakubovsky, D. I.; Fedyanin, D. Yu.; Arsenin, A. V.

2017-09-01

Carbon allotropes-based nanomaterials possess unique physical and chemical properties including high surface area, the possibility of pi-stacking interaction with a wide range of biological objects, rich availability of oxygen-containing functional groups in graphene-oxide (GO), and excellent optical properties, which make them an ideal candidate for use as a universal immobilization platform in SPR biosensing. Here, we propose a new surface plasmon resonance (SPR) biosensing interface for sensitive and selective detection of small molecules. This interface is based on the GO linking layers deposited on the gold/copper surface of SPR sensor chips. To estimate the binding capacity of GO layers, modification of carboxyl groups to N-Hydroxysuccinimide esters was performed in the flow cell of SPR instrument. For comparison, the same procedure was applied to commercial sensor chips based on linking layers of carboxymethylated dextran.

Continuous measurement of breast tumor hormone receptor expression: a comparison of two computational pathology platforms

PubMed Central

Ahern, Thomas P.; Beck, Andrew H.; Rosner, Bernard A.; Glass, Ben; Frieling, Gretchen; Collins, Laura C.; Tamimi, Rulla M.

2017-01-01

Background Computational pathology platforms incorporate digital microscopy with sophisticated image analysis to permit rapid, continuous measurement of protein expression. We compared two computational pathology platforms on their measurement of breast tumor estrogen receptor (ER) and progesterone receptor (PR) expression. Methods Breast tumor microarrays from the Nurses’ Health Study were stained for ER (n=592) and PR (n=187). One expert pathologist scored cases as positive if ≥1% of tumor nuclei exhibited stain. ER and PR were then measured with the Definiens Tissue Studio (automated) and Aperio Digital Pathology (user-supervised) platforms. Platform-specific measurements were compared using boxplots, scatter plots, and correlation statistics. Classification of ER and PR positivity by platform-specific measurements was evaluated with areas under receiver operating characteristic curves (AUC) from univariable logistic regression models, using expert pathologist classification as the standard. Results Both platforms showed considerable overlap in continuous measurements of ER and PR between positive and negative groups classified by expert pathologist. Platform-specific measurements were strongly and positively correlated with one another (rho≥0.77). The user-supervised Aperio workflow performed slightly better than the automated Definiens workflow at classifying ER positivity (AUCAperio=0.97; AUCDefiniens=0.90; difference=0.07, 95% CI: 0.05, 0.09) and PR positivity (AUCAperio=0.94; AUCDefiniens=0.87; difference=0.07, 95% CI: 0.03, 0.12). Conclusion Paired hormone receptor expression measurements from two different computational pathology platforms agreed well with one another. The user-supervised workflow yielded better classification accuracy than the automated workflow. Appropriately validated computational pathology algorithms enrich molecular epidemiology studies with continuous protein expression data and may accelerate tumor biomarker discovery. PMID:27729430

Comparison of Online Survey Recruitment Platforms for Hard-to-Reach Pregnant Smoking Populations: Feasibility Study

PubMed Central

Agas, Jessica Marie; Lee, Melissa; Pan, Julia Lily; Buttenheim, Alison Meredith

2018-01-01

Background Recruiting hard-to-reach populations for health research is challenging. Web-based platforms offer one way to recruit specific samples for research purposes, but little is known about the feasibility of online recruitment and the representativeness and comparability of samples recruited through different Web-based platforms. Objective The objectives of this study were to determine the feasibility of recruiting a hard-to-reach population (pregnant smokers) using 4 different Web-based platforms and to compare participants recruited through each platform. Methods A screener and survey were distributed online through Qualtrics Panel, Soapbox Sample, Reddit, and Amazon Mechanical Turk (mTurk). Descriptive statistics were used to summarize results of each recruitment platform, including eligibility yield, quality yield, income, race, age, and gestational age. Results Of the 3847 participants screened for eligibility across all 4 Web-based platforms, 535 were eligible and 308 completed the survey. Amazon mTurk yielded the fewest completed responses (n=9), 100% (9/9) of which passed several quality metrics verifying pregnancy and smoking status. Qualtrics Panel yielded 14 completed responses, 86% (12/14) of which passed the quality screening. Soapbox Sample produced 107 completed surveys, 67% (72/107) of which were found to be quality responses. Advertising through Reddit produced the highest completion rate (n=178), but only 29.2% (52/178) of those surveys passed the quality metrics. We found significant differences in eligibility yield, quality yield, age, number of previous pregnancies, age of smoking initiation, current smokers, race, education, and income (P<.001). Conclusions Although each platform successfully recruited pregnant smokers, results varied in quality, cost, and percentage of complete responses. Moving forward, investigators should pay careful attention to the percentage yield and cost of online recruitment platforms to maximize internal and external validity. PMID:29661751

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

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.

Structure of frequency-interacting RNA helicase from Neurospora crassa reveals high flexibility in a domain critical for circadian rhythm and RNA surveillance.

PubMed

Morales, Yalemi; Olsen, Keith J; Bulcher, Jacqueline M; Johnson, Sean J

2018-01-01

The FRH (frequency-interacting RNA helicase) protein is the Neurospora crassa homolog of yeast Mtr4, an essential RNA helicase that plays a central role in RNA metabolism as an activator of the nuclear RNA exosome. FRH is also a required component of the circadian clock, mediating protein interactions that result in the rhythmic repression of gene expression. Here we show that FRH unwinds RNA substrates in vitro with a kinetic profile similar to Mtr4, indicating that while FRH has acquired additional functionality, its core helicase function remains intact. In contrast with the earlier FRH structures, a new crystal form of FRH results in an ATP binding site that is undisturbed by crystal contacts and adopts a conformation consistent with nucleotide binding and hydrolysis. Strikingly, this new FRH structure adopts an arch domain conformation that is dramatically altered from previous structures. Comparison of the existing FRH structures reveals conserved hinge points that appear to facilitate arch motion. Regions in the arch have been previously shown to mediate a variety of protein-protein interactions critical for RNA surveillance and circadian clock functions. The conformational changes highlighted in the FRH structures provide a platform for investigating the relationship between arch dynamics and Mtr4/FRH function.

A differential mobility spectrometry/mass spectrometry platform for the rapid detection and quantitation of DNA adduct dG-ABP.

PubMed

Kafle, Amol; Klaene, Joshua; Hall, Adam B; Glick, James; Coy, Stephen L; Vouros, Paul

2013-07-15

There is continued interest in exploring new analytical technologies for the detection and quantitation of DNA adducts, biomarkers which provide direct evidence of exposure and genetic damage in cells. With the goal of reducing clean-up steps and improving sample throughput, a Differential Mobility Spectrometry/Mass Spectrometry (DMS/MS) platform has been introduced for adduct analysis. A DMS/MS platform has been utilized for the analysis of dG-ABP, the deoxyguanosine adduct of the bladder carcinogen 4-aminobiphenyl (4-ABP). After optimization of the DMS parameters, each sample was analyzed in just 30 s following a simple protein precipitation step of the digested DNA. A detection limit of one modification in 10^6 nucleosides has been achieved using only 2 µg of DNA. A brief comparison (quantitative and qualitative) with liquid chromatography/mass spectrometry is also presented highlighting the advantages of using the DMS/MS method as a high-throughput platform. The data presented demonstrate the successful application of a DMS/MS/MS platform for the rapid quantitation of DNA adducts using, as a model analyte, the deoxyguanosine adduct of the bladder carcinogen 4-aminobiphenyl. Copyright © 2013 John Wiley & Sons, Ltd.

"Harder, Better, Faster, Stronger": Negative Comparison on Facebook and Adolescents' Life Satisfaction Are Reciprocally Related.

PubMed

Frison, Eline; Eggermont, Steven

2016-03-01

Social networking sites, such as Facebook, offer adolescent users an ideal platform for negative comparison (i.e., experiencing negative feelings from social comparison). Although such negative comparison on Facebook has been associated with users' well-being, the reciprocal relations between the two remain unclear, particularly in an adolescent sample. To examine this reciprocal process, a two-wave study among a representative sample of Flemish adolescents was set up (N Time1 = 1,840). Data were analyzed using structural equation modeling. Cross-lagged analyses indicated that negative comparison on Facebook predicted decreases in life satisfaction over time. Conversely, lower scores on life satisfaction predicted increases in negative comparison on Facebook. The discussion focuses on the understanding of these findings, key limitations, directions for future research, and implications for prevention and intervention strategies.

Adding Value to the Network: Exploring the Software as a Service and Platform as a Service Models for Mobile Operators

NASA Astrophysics Data System (ADS)

Gonçalves, Vânia

The environments of software development and software provision are shifting to Web-based platforms supported by Platform/Software as a Service (PaaS/SaaS) models. This paper will make the case that there is equally an opportunity for mobile operators to identify additional sources of revenue by exposing network functionalities through Web-based service platforms. By elaborating on the concepts, benefits and risks of SaaS and PaaS, several factors that should be taken into consideration in applying these models to the telecom world are delineated.

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

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.

Friendly Extensible Transfer Tool Beta Version

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

Collins, William P.; Gutierrez, Kenneth M.; McRee, Susan R.

2016-04-15

Often data transfer software is designed to meet specific requirements or apply to specific environments. Frequently, this requires source code integration for added functionality. An extensible data transfer framework is needed to more easily incorporate new capabilities, in modular fashion. Using FrETT framework, functionality may be incorporated (in many cases without need of source code) to handle new platform capabilities: I/O methods (e.g., platform specific data access), network transport methods, data processing (e.g., data compression.).

Assessing the efficacy of perioperative oral carprofen after cranial cruciate surgery using noninvasive, objective pressure platform gait analysis.

PubMed

Horstman, Christopher L; Conzemius, Michael G; Evans, Richard; Gordon, Wanda J

2004-01-01

To document, using pressure platform gait analysis, the effect of perioperative oral carprofen on limb function and pain after cranial cruciate ligament surgery in dogs. Blinded, prospective clinical investigation. Twenty dogs with naturally occurring unilateral cranial cruciate disease. Physiologic indices, subjective pain scoring, and pressure platform gait analyses were performed before and 24, 48, and 72 hours after surgery. Correlations were assessed between methods of evaluation and the data was compared across treatment groups. No strong correlations were noted between physiologic data, subjective scoring systems, or gait analysis data at a walk or stance. Although average measures of limb function were nearly twice as large in dogs treated with carprofen, no significant differences between groups over time were identified. No significant differences were noted in any other measure of pain or limb function. Power analysis of peak vertical force at a walk indicated that significant difference would have been detected had the number of dogs in each group been increased to 35. When limb function was assessed with pressure platform gait analysis no statistical difference was noted between groups with respect to PVF and VI at a walk or stance, although average ground reaction forces for dogs in the carprofen group were greater than the traditional pain management group at all time points. Oral carprofen appears to provide some benefit for the treatment of postoperative orthopedic pain.

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

PubMed

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

2010-01-13

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

Genomics Portals: integrative web-platform for mining genomics data

PubMed Central

2010-01-01

Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org. PMID:20070909

MetaNET--a web-accessible interactive platform for biological metabolic network analysis.

PubMed

Narang, Pankaj; Khan, Shawez; Hemrom, Anmol Jaywant; Lynn, Andrew Michael

2014-01-01

Metabolic reactions have been extensively studied and compiled over the last century. These have provided a theoretical base to implement models, simulations of which are used to identify drug targets and optimize metabolic throughput at a systemic level. While tools for the perturbation of metabolic networks are available, their applications are limited and restricted as they require varied dependencies and often a commercial platform for full functionality. We have developed MetaNET, an open source user-friendly platform-independent and web-accessible resource consisting of several pre-defined workflows for metabolic network analysis. MetaNET is a web-accessible platform that incorporates a range of functions which can be combined to produce different simulations related to metabolic networks. These include (i) optimization of an objective function for wild type strain, gene/catalyst/reaction knock-out/knock-down analysis using flux balance analysis. (ii) flux variability analysis (iii) chemical species participation (iv) cycles and extreme paths identification and (v) choke point reaction analysis to facilitate identification of potential drug targets. The platform is built using custom scripts along with the open-source Galaxy workflow and Systems Biology Research Tool as components. Pre-defined workflows are available for common processes, and an exhaustive list of over 50 functions are provided for user defined workflows. MetaNET, available at http://metanet.osdd.net , provides a user-friendly rich interface allowing the analysis of genome-scale metabolic networks under various genetic and environmental conditions. The framework permits the storage of previous results, the ability to repeat analysis and share results with other users over the internet as well as run different tools simultaneously using pre-defined workflows, and user-created custom workflows.

Profiling post-translational modifications of histones in human monocyte-derived macrophages.

PubMed

Olszowy, Pawel; Donnelly, Maire Rose; Lee, Chanho; Ciborowski, Pawel

2015-01-01

Histones and their post-translational modifications impact cellular function by acting as key regulators in the maintenance and remodeling of chromatin, thus affecting transcription regulation either positively (activation) or negatively (repression). In this study we describe a comprehensive, bottom-up proteomics approach to profiling post-translational modifications (acetylation, mono-, di- and tri-methylation, phosphorylation, biotinylation, ubiquitination, citrullination and ADP-ribosylation) in human macrophages, which are primary cells of the innate immune system. As our knowledge expands, it becomes more evident that macrophages are a heterogeneous population with potentially subtle differences in their responses to various stimuli driven by highly complex epigenetic regulatory mechanisms. To profile post-translational modifications (PTMs) of histones in macrophages we used two platforms of liquid chromatography and mass spectrometry. One platform was based on Sciex5600 TripleTof and the second one was based on VelosPro Orbitrap Elite ETD mass spectrometers. We provide side-by-side comparison of profiling using two mass spectrometric platforms, ion trap and qTOF, coupled with the application of collisional induced and electron transfer dissociation. We show for the first time methylation of a His residue in macrophages and demonstrate differences in histone PTMs between those currently reported for macrophage cell lines and what we identified in primary cells. We have found a relatively low level of histone PTMs in differentiated but resting human primary monocyte derived macrophages. This study is the first comprehensive profiling of histone PTMs in primary human MDM. Our study implies that epigenetic regulatory mechanisms operative in transformed cell lines and primary cells are overlapping to a limited extent. Our mass spectrometric approach provides groundwork for the investigation of how histone PTMs contribute to epigenetic regulation in primary human macrophages.

Introducing meta-services for biomedical information extraction

PubMed Central

Leitner, Florian; Krallinger, Martin; Rodriguez-Penagos, Carlos; Hakenberg, Jörg; Plake, Conrad; Kuo, Cheng-Ju; Hsu, Chun-Nan; Tsai, Richard Tzong-Han; Hung, Hsi-Chuan; Lau, William W; Johnson, Calvin A; Sætre, Rune; Yoshida, Kazuhiro; Chen, Yan Hua; Kim, Sun; Shin, Soo-Yong; Zhang, Byoung-Tak; Baumgartner, William A; Hunter, Lawrence; Haddow, Barry; Matthews, Michael; Wang, Xinglong; Ruch, Patrick; Ehrler, Frédéric; Özgür, Arzucan; Erkan, Güneş; Radev, Dragomir R; Krauthammer, Michael; Luong, ThaiBinh; Hoffmann, Robert; Sander, Chris; Valencia, Alfonso

2008-01-01

We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; ). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations. PMID:18834497

Numerical wind-tunnel simulation for Spar platform

NASA Astrophysics Data System (ADS)

Shen, Wenjun

2017-05-01

ANSYS Fluent software is used in the simulation analysis of numerical wind tunnel model for the upper Spar platform module. Design Modeler (DM), Meshing, FLUENT and CFD-POST are chosen in the numerical calculation. And DM is used to deal with and repair the geometric model, and Meshing is used to mesh the model, Fluent is used to set up and solve the calculation condition, finally CFD-POST is used for post-processing of the results. The wind loads are obtained under different direction and incidence angles. Finally, comparison is made between numerical results and empirical formula.

Comparison of the three optical platforms for measurement of cellular respiration.

PubMed

Kondrashina, Alina V; Ogurtsov, Vladimir I; Papkovsky, Dmitri B

2015-01-01

We compared three optical platforms for measurement of cellular respiration: absolute oxygen consumption rates (OCRs) in hermetically sealed microcuvettes, relative OCRs measured in a 96-well plate with oil seal, and steady-state oxygenation of cells in an open 96-well plate. Using mouse embryonic fibroblasts cell line, the phosphorescent intracellular O2 probe MitoXpress-Intra, and time-resolved fluorescence reader, we determined algorithms for conversion of relative OCRs and cell oxygenation into absolute OCRs, thereby allowing simple high-throughput measurement of absolute OCR values. Copyright © 2014 Elsevier Inc. All rights reserved.

Airborne Science Program: Observing Platforms for Earth Science Investigations

NASA Technical Reports Server (NTRS)

Mace, Thomas H.

2009-01-01

This slide presentation reviews the Airborne Science Program and the platforms used for conducting investigations for the Earth System Science. Included is a chart that shows some of the aircraft and the operational altitude and the endurance of the aircraft, views of the Dryden Aircraft Operation Facility, and some of the current aircraft that the facility operates, and the varieties of missions that are flown and the type of instrumentation. Also included is a chart showing the attributes of the various aircraft (i.e., duration, weight for a payload, maximum altitude, airspeed and range) for comparison

Scoping review and evaluation of SMS/text messaging platforms for mHealth projects or clinical interventions.

PubMed

Iribarren, Sarah J; Brown, William; Giguere, Rebecca; Stone, Patricia; Schnall, Rebecca; Staggers, Nancy; Carballo-Diéguez, Alex

2017-05-01

Mobile technology supporting text messaging interventions (TMIs) continues to evolve, presenting challenges for researchers and healthcare professionals who need to choose software solutions to best meet their program needs. The objective of this review was to systematically identify and compare text messaging platforms and to summarize their advantages and disadvantages as described in peer-reviewed literature. A scoping review was conducted using four steps: 1) identify currently available platforms through online searches and in mHealth repositories; 2) expand evaluation criteria of an mHealth mobile messaging toolkit and integrate prior user experiences as researchers; 3) evaluate each platform's functions and features based on the expanded criteria and a vendor survey; and 4) assess the documentation of platform use in the peer-review literature. Platforms meeting inclusion criteria were assessed independently by three reviewers and discussed until consensus was reached. The PRISMA guidelines were followed to report findings. Of the 1041 potentially relevant search results, 27 platforms met inclusion criteria. Most were excluded because they were not platforms (e.g., guides, toolkits, reports, or SMS gateways). Of the 27 platforms, only 12 were identified in existing mHealth repositories, 10 from Google searches, while five were found in both. The expanded evaluation criteria included 22 items. Results indicate no uniform presentation of platform features and functions, often making these difficult to discern. Fourteen of the platforms were reported as open source, 10 focused on health care and 16 were tailored to meet needs of low resource settings (not mutually exclusive). Fifteen platforms had do-it-yourself setup (programming not required) while the remainder required coding/programming skills or setups could be built to specification by the vendor. Frequently described features included data security and access to the platform via cloud-based systems. Pay structures and reported targeted end-users varied. Peer-reviewed publications listed only 6 of the 27 platforms across 21 publications. The majority of these articles reported the name of the platform used but did not describe advantages or disadvantages. Searching for and comparing mHealth platforms for TMIs remains a challenge. The results of this review can serve as a resource for researchers and healthcare professionals wanting to integrate TMIs into health interventions. Steps to identify, compare and assess advantages and disadvantages are outlined for consideration. Expanded evaluation criteria can be used by future researchers. Continued and more comprehensive platform tools should be integrated into mHealth repositories. Detailed descriptions of platform advantages and disadvantages are needed when mHealth researchers publish findings to expand the body of research on TMI tools for healthcare. Standardized descriptions and features are recommended for vendor sites. Copyright © 2017 Elsevier B.V. All rights reserved.

Emerging microengineering tools for functional analysis and phenotyping of blood cells

PubMed Central

Li, Xiang; Chen, Weiqiang; Li, Zida; Li, Ling; Gu, Hongchen; Fu, Jianping

2014-01-01

The available techniques for assessing blood cell functions are limited considering the various types of blood cells and their diverse functions. In the past decade, rapid advancement in microengineering has enabled an array of blood cell functional measurements that are difficult or impossible to achieve using conventional bulk platforms. Such miniaturized blood cell assay platforms also provide attractive capabilities of reducing chemical consumption, cost, assay time, as well as exciting opportunities of device integration, automation, and assay standardization. This review summarizes these contemporary microengineering tools and discusses their promising potential for constructing accurate in vitro models and rapid clinical diagnosis using minimal amount of whole blood samples. PMID:25283971

Lab on a CD.

PubMed

Madou, Marc; Zoval, Jim; Jia, Guangyao; Kido, Horacio; Kim, Jitae; Kim, Nahui

2006-01-01

In this paper, centrifuge-based microfluidic platforms are reviewed and compared with other popular microfluidic propulsion methods. The underlying physical principles of centrifugal pumping in microfluidic systems are presented and the various centrifuge fluidic functions, such as valving, decanting, calibration, mixing, metering, heating, sample splitting, and separation, are introduced. Those fluidic functions have been combined with analytical measurement techniques, such as optical imaging, absorbance, and fluorescence spectroscopy and mass spectrometry, to make the centrifugal platform a powerful solution for medical and clinical diagnostics and high throughput screening (HTS) in drug discovery. Applications of a compact disc (CD)-based centrifuge platform analyzed in this review include two-point calibration of an optode-based ion sensor, an automated immunoassay platform, multiple parallel screening assays, and cellular-based assays. The use of modified commercial CD drives for high-resolution optical imaging is discussed as well. From a broader perspective, we compare technical barriers involved in applying microfluidics for sensing and diagnostic use and applying such techniques to HTS. The latter poses less challenges and explains why HTS products based on a CD fluidic platform are already commercially available, whereas we might have to wait longer to see commercial CD-based diagnostics.

Knowledge discovery through games and game theory

NASA Astrophysics Data System (ADS)

Smith, James F., III; Rhyne, Robert D.

2001-03-01

A fuzzy logic based expert system has been developed that automatically allocates electronic attack (EA) resources in real-time over many dissimilar platforms. 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. The initial version of the algorithm was optimized using a genetic algorithm employing fitness functions constructed based on expertise. A new approach is being explored that involves embedding the resource manager in a electronic game environment. The game allows a human expert to play against the resource manager in a simulated battlespace with each of the defending platforms being exclusively directed by the fuzzy resource manager and the attacking platforms being controlled by the human expert or operating autonomously under their own logic. This approach automates the data mining problem. The game automatically creates a database reflecting the domain expert's knowledge, it calls a data mining function, a genetic algorithm, for data mining of the database as required. The game allows easy evaluation of the information mined in the second step. The measure of effectiveness (MOE) for re-optimization is discussed. The mined information is extremely valuable as shown through demanding scenarios.

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.

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.

Caspase-8 Binding to Cardiolipin in Giant Unilamellar Vesicles Provides a Functional Docking Platform for Bid

PubMed Central

Perry, Mark; Granjon, Thierry; Gonzalvez, François; Gottlieb, Eyal; Ayala-Sanmartin, Jesus; Klösgen, Beate; Schwille, Petra; Petit, Patrice X.

2013-01-01

Caspase-8 is involved in death receptor-mediated apoptosis in type II cells, the proapoptotic programme of which is triggered by truncated Bid. Indeed, caspase-8 and Bid are the known intermediates of this signalling pathway. Cardiolipin has been shown to provide an anchor and an essential activating platform for caspase-8 at the mitochondrial membrane surface. Destabilisation of this platform alters receptor-mediated apoptosis in diseases such as Barth Syndrome, which is characterised by the presence of immature cardiolipin which does not allow caspase-8 binding. We used a simplified in vitro system that mimics contact sites and/or cardiolipin-enriched microdomains at the outer mitochondrial surface in which the platform consisting of caspase-8, Bid and cardiolipin was reconstituted in giant unilamellar vesicles. We analysed these vesicles by flow cytometry and confirm previous results that demonstrate the requirement for intact mature cardiolipin for caspase-8 activation and Bid binding and cleavage. We also used confocal microscopy to visualise the rupture of the vesicles and their revesiculation at smaller sizes due to alteration of the curvature following caspase-8 and Bid binding. Biophysical approaches, including Laurdan fluorescence and rupture/tension measurements, were used to determine the ability of these three components (cardiolipin, caspase-8 and Bid) to fulfil the minimal requirements for the formation and function of the platform at the mitochondrial membrane. Our results shed light on the active functional role of cardiolipin, bridging the gap between death receptors and mitochondria. PMID:23418437

Effects of the visual-feedback-based force platform training with functional electric stimulation on the balance and prevention of falls in older adults: a randomized controlled trial.

PubMed

Li, Zhen; Wang, Xiu-Xia; Liang, Yan-Yi; Chen, Shu-Yan; Sheng, Jing; Ma, Shao-Jun

2018-01-01

Force platform training with functional electric stimulation aimed at improving balance may be effective in fall prevention for older adults. Aim of the study is to evaluate the effects of the visual-feedback-based force platform balance training with functional electric stimulation on balance and fall prevention in older adults. A single-centre, unblinded, randomized controlled trial was conducted. One hundred and twenty older adults were randomly allocated to two groups: the control group ( n  = 60, one-leg standing balance exercise, 12 min/d) or the intervention group ( n  = 60, force platform training with functional electric stimulation, 12 min/d). The training was provided 15 days a month for 3 months by physical therapists. Medial-lateral and anterior-posterior maximal range of sway with eyes open and closed, the Berg Balance Scale, the Barthel Index, the Falls Efficacy scale-International were assessed at baseline and after the 3-month intervention. A fall diary was kept by each participant during the 6-month follow-up. On comparing the two groups, the intervention group showed significantly decreased ( p  < 0.01) medial-lateral and anterior-posterior maximal range of sway with eyes open and closed. There was significantly higher improvement in the Berg Balance Scale ( p  < 0.05), the Barthel Index ( p  < 0.05) and the Falls Efficacy Scale-International ( p  < 0.05), along with significantly lesser number of injurious fallers ( p  < 0.05), number of fallers ( p  < 0.05), and fall rates ( p  < 0.05) during the 6-month follow-up in the intervention group. This study showed that the visual feedback-based force platform training with functional electric stimulation improved balance and prevented falls in older adults.

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.

Comparison of Two Methods for Estimating the Sampling-Related Uncertainty of Satellite Rainfall Averages Based on a Large Radar Data Set

NASA Technical Reports Server (NTRS)

Lau, William K. M. (Technical Monitor); Bell, Thomas L.; Steiner, Matthias; Zhang, Yu; Wood, Eric F.

2002-01-01

The uncertainty of rainfall estimated from averages of discrete samples collected by a satellite is assessed using a multi-year radar data set covering a large portion of the United States. The sampling-related uncertainty of rainfall estimates is evaluated for all combinations of 100 km, 200 km, and 500 km space domains, 1 day, 5 day, and 30 day rainfall accumulations, and regular sampling time intervals of 1 h, 3 h, 6 h, 8 h, and 12 h. These extensive analyses are combined to characterize the sampling uncertainty as a function of space and time domain, sampling frequency, and rainfall characteristics by means of a simple scaling law. Moreover, it is shown that both parametric and non-parametric statistical techniques of estimating the sampling uncertainty produce comparable results. Sampling uncertainty estimates, however, do depend on the choice of technique for obtaining them. They can also vary considerably from case to case, reflecting the great variability of natural rainfall, and should therefore be expressed in probabilistic terms. Rainfall calibration errors are shown to affect comparison of results obtained by studies based on data from different climate regions and/or observation platforms.

Nanoporous microbead supported bilayers: stability, physical characterization, and incorporation of functional transmembrane proteins.

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

Davis, Ryan W.; Brozik, James A.; Brozik, Susan Marie

2007-03-01

The introduction of functional transmembrane proteins into supported bilayer-based biomimetic systems presents a significant challenge for biophysics. Among the various methods for producing supported bilayers, liposomal fusion offers a versatile method for the introduction of membrane proteins into supported bilayers on a variety of substrates. In this study, the properties of protein containing unilamellar phosphocholine lipid bilayers on nanoporous silica microspheres are investigated. The effects of the silica substrate, pore structure, and the substrate curvature on the stability of the membrane and the functionality of the membrane protein are determined. Supported bilayers on porous silica microspheres show a significant increasemore » in surface area on surfaces with structures in excess of 10 nm as well as an overall decrease in stability resulting from increasing pore size and curvature. Comparison of the liposomal and detergent-mediated introduction of purified bacteriorhodopsin (bR) and the human type 3 serotonin receptor (5HT3R) are investigated focusing on the resulting protein function, diffusion, orientation, and incorporation efficiency. In both cases, functional proteins are observed; however, the reconstitution efficiency and orientation selectivity are significantly enhanced through detergent-mediated protein reconstitution. The results of these experiments provide a basis for bulk ionic and fluorescent dye-based compartmentalization assays as well as single-molecule optical and single-channel electrochemical interrogation of transmembrane proteins in a biomimetic platform.« less

The dark side of hippo signaling: A cancer promoter role.

PubMed

Dunn, Brandon; Ma, Xianjue

2017-10-02

The Hippo signaling pathway regulates organ size and tissue homeostasis. Given this role it is unsurprising that dysregulation of this pathway has implications for cancer progression. A convincing body of literature shows that the Hippo pathway serves a tumor suppressive function with its inactivation leading to massive overgrowth. However, additional studies have also shown that activation of Hippo signaling can promote tumor progression. It remains unknown how a single pathway can produce such diametrically opposed effects. This lack of knowledge is in part due to our inability to make meaningful comparisons from studies which have taken place in a variety of cell types, tissues, and organisms. Recently however, we have published 2 studies using the Drosophila wing disk to study the Hippo pathway and have found that Hippo pathway activation can promote cell migration and invasion while Hippo pathway inactivation leads to overgrowth. Thus we propose here that Drosophila can provide a research platform with which to begin addressing how the Hippo pathway can both enhance and suppress tumor progression due to published pro- and anti-tumor functionalities of the Hippo pathway in the same tissue.

A Genome-wide Analysis of Human Pluripotent Stem Cell-Derived Endothelial Cells in 2D or 3D Culture.

PubMed

Zhang, Jue; Schwartz, Michael P; Hou, Zhonggang; Bai, Yongsheng; Ardalani, Hamisha; Swanson, Scott; Steill, John; Ruotti, Victor; Elwell, Angela; Nguyen, Bao Kim; Bolin, Jennifer; Stewart, Ron; Thomson, James A; Murphy, William L

2017-04-11

A defined protocol for efficiently deriving endothelial cells from human pluripotent stem cells was established and vascular morphogenesis was used as a model system to understand how synthetic hydrogels influence global biological function compared with common 2D and 3D culture platforms. RNA sequencing demonstrated that gene expression profiles were similar for endothelial cells and pericytes cocultured in polyethylene glycol (PEG) hydrogels or Matrigel, while monoculture comparisons identified distinct vascular signatures for each cell type. Endothelial cells cultured on tissue-culture polystyrene adopted a proliferative phenotype compared with cells cultured on or encapsulated in PEG hydrogels. The proliferative phenotype correlated to increased FAK-ERK activity, and knockdown or inhibition of ERK signaling reduced proliferation and expression for cell-cycle genes while increasing expression for "3D-like" vasculature development genes. Our results provide insight into the influence of 2D and 3D culture formats on global biological processes that regulate cell function. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Basin analysis in the Southern Tethyan margin: Facies sequences, stratal pattern and subsidence history highlight extension-to-inversion processes in the Cretaceous Panormide carbonate platform (NW Sicily)

NASA Astrophysics Data System (ADS)

Basilone, Luca; Sulli, Attilio

2018-01-01

In the Mediterranean, the South-Tethys paleomargin experienced polyphased tectonic episodes and paleoenvironmental perturbations during Mesozoic time. The Cretaceous shallow-water carbonate successions of the Panormide platform, outcropping in the northern edge of the Palermo Mountains (NW Sicily), were studied by integrating facies and stratal pattern with backstripping analysis to recognize the tectonics vs. carbonate sedimentation interaction. The features of the Requienid limestone, including geometric configuration, facies sequence, lithological changes and significance of the top-unconformity, highlight that at the end of the Lower Cretaceous the carbonate platform was tectonically dismembered in various rotating fault-blocks. The variable trends of the subsidence curves testify to different responses, both uplift and downthrow, of various platform-blocks impacted by extensional tectonics. Physical stratigraphic and facies analysis of the Rudistid limestone highlight that during the Upper Cretaceous the previously carbonate platform faulted-blocks were subjected to vertical movements in the direction opposite to the displacement produced by the extensional tectonics, indicating a positive tectonic inversion. Comparisons with other sectors of the Southern Tethyan and Adria paleomargins indicate that during the Cretaceous these areas underwent the same extensional and compressional stages occurring in the Panormide carbonate platform, suggesting a regional scale significance, in time and kinematics, for these tectonic events.

Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms.

PubMed

Chen, DaYang; Zhen, HeFu; Qiu, Yong; Liu, Ping; Zeng, Peng; Xia, Jun; Shi, QianYu; Xie, Lin; Zhu, Zhu; Gao, Ya; Huang, GuoDong; Wang, Jian; Yang, HuanMing; Chen, Fang

2018-03-21

Research based on a strategy of single-cell low-coverage whole genome sequencing (SLWGS) has enabled better reproducibility and accuracy for detection of copy number variations (CNVs). The whole genome amplification (WGA) method and sequencing platform are critical factors for successful SLWGS (<0.1 × coverage). In this study, we compared single cell and multiple cells sequencing data produced by the HiSeq2000 and Ion Proton platforms using two WGA kits and then comprehensively evaluated the GC-bias, reproducibility, uniformity and CNV detection among different experimental combinations. Our analysis demonstrated that the PicoPLEX WGA Kit resulted in higher reproducibility, lower sequencing error frequency but more GC-bias than the GenomePlex Single Cell WGA Kit (WGA4 kit) independent of the cell number on the HiSeq2000 platform. While on the Ion Proton platform, the WGA4 kit (both single cell and multiple cells) had higher uniformity and less GC-bias but lower reproducibility than those of the PicoPLEX WGA Kit. Moreover, on these two sequencing platforms, depending on cell number, the performance of the two WGA kits was different for both sensitivity and specificity on CNV detection. The results can help researchers who plan to use SLWGS on single or multiple cells to select appropriate experimental conditions for their applications.

Scoping Review and Evaluation of SMS/text Messaging Platforms for mHealth Projects or Clinical Interventions

PubMed Central

Iribarren, Sarah; Brown, William; Giguere, Rebecca; Stone, Patricia; Schnall, Rebecca; Staggers, Nancy; Carballo-Diéguez, Alex

2017-01-01

Objectives Mobile technology supporting text messaging interventions (TMIs) continues to evolve, presenting challenges for researchers and healthcare professionals who need to choose software solutions to best meet their program needs. The objective of this review was to systematically identify and compare text messaging platforms and to summarize their advantages and disadvantages as described in peer-reviewed literature. Methods A scoping review was conducted using four steps: 1) identify currently available platforms through online searches and in mHealth repositories; 2) expand evaluation criteria of an mHealth mobile messaging toolkit and prior user experiences as researchers; 3) evaluate each platform’s functions and features based on the expanded criteria and a vendor survey; and 4) assess the documentation of platform use in the peer-review literature. Platforms meeting inclusion criteria were assessed independently by three reviewers and discussed until consensus was reached. The PRISMA guidelines were followed to report findings. Results Of the 1041 potentially relevant search results, 27 platforms met inclusion criteria. Most were excluded because they were not platforms (e.g., guides, toolkits, reports, or SMS gateways). Of the 27 platforms, only 12 were identified in existing mHealth repositories, 10 from Google searches, while five were found in both. The expanded evaluation criteria included 22 items. Results indicate no uniform presentation of platform features and functions, often making these difficult to discern. Fourteen of the platforms were reported as open source, 10 focused on health care and 16 were tailored to meet needs of low resource settings (not mutually exclusive). Fifteen platforms had do-it-yourself setup (programming not required) while the remainder required coding/programming skills or setups could be built to specification by the vendor. Frequently described features included data security and access to the platform via cloud-based systems. Pay structures and reported targeted end-users varied. Peer-reviewed publications listed only 6 of the 27 platforms across 21 publications. The majority of these articles reported the name of the platform used but did not describe advantages or disadvantages. Conclusions Searching for and comparing mHealth platforms for TMIs remains a challenge. The results of this review can serve as a resource for researchers and healthcare professionals wanting to integrate TMIs into health interventions. Steps to identify, compare and assess advantages and disadvantages are outlined for consideration. Expanded evaluation criteria can be used by future researchers. Continued and more comprehensive platform tools should be integrated into mHealth repositories. Detailed descriptions of platform advantages and disadvantages are needed when mHealth researchers publish findings to expand the body of research on texting-based tools for healthcare. Standardized descriptions and features are recommended for vendor sites. PMID:28347445

Multiplex cDNA quantification method that facilitates the standardization of gene expression data

PubMed Central

Gotoh, Osamu; Murakami, Yasufumi; Suyama, Akira

2011-01-01

Microarray-based gene expression measurement is one of the major methods for transcriptome analysis. However, current microarray data are substantially affected by microarray platforms and RNA references because of the microarray method can provide merely the relative amounts of gene expression levels. Therefore, valid comparisons of the microarray data require standardized platforms, internal and/or external controls and complicated normalizations. These requirements impose limitations on the extensive comparison of gene expression data. Here, we report an effective approach to removing the unfavorable limitations by measuring the absolute amounts of gene expression levels on common DNA microarrays. We have developed a multiplex cDNA quantification method called GEP-DEAN (Gene expression profiling by DCN-encoding-based analysis). The method was validated by using chemically synthesized DNA strands of known quantities and cDNA samples prepared from mouse liver, demonstrating that the absolute amounts of cDNA strands were successfully measured with a sensitivity of 18 zmol in a highly multiplexed manner in 7 h. PMID:21415008

Solar Occultation Retrieval Algorithm Development

NASA Technical Reports Server (NTRS)

Lumpe, Jerry D.

2004-01-01

This effort addresses the comparison and validation of currently operational solar occultation retrieval algorithms, and the development of generalized algorithms for future application to multiple platforms. initial development of generalized forward model algorithms capable of simulating transmission data from of the POAM II/III and SAGE II/III instruments. Work in the 2" quarter will focus on: completion of forward model algorithms, including accurate spectral characteristics for all instruments, and comparison of simulated transmission data with actual level 1 instrument data for specific occultation events.

Comparison of standard- and nano-flow liquid chromatography platforms for MRM-based quantitation of putative plasma biomarker proteins.

PubMed

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

2012-09-01

The analytical performance of a standard-flow ultra-high-performance liquid chromatography (UHPLC) and a nano-flow high-performance liquid chromatography (HPLC) system, interfaced to the same state-of-the-art triple-quadrupole mass spectrometer, were compared for the multiple reaction monitoring (MRM)-mass spectrometry (MS)-based quantitation of a panel of 48 high-to-moderate-abundance cardiovascular disease-related plasma proteins. After optimization of the MRM transitions for sensitivity and testing for chemical interference, the optimum sensitivity, loading capacity, gradient, and retention-time reproducibilities were determined. We previously demonstrated the increased robustness of the standard-flow platform, but we expected that the standard-flow platform would have an overall lower sensitivity. This study was designed to determine if this decreased sensitivity could be compensated for by increased sample loading. Significantly fewer interferences with the MRM transitions were found for the standard-flow platform than for the nano-flow platform (2 out of 103 transitions compared with 42 out of 103 transitions, respectively), which demonstrates the importance of interference-testing when nano-flow systems are used. Using only interference-free transitions, 36 replicate LC/MRM-MS analyses resulted in equal signal reproducibilities between the two platforms (9.3 % coefficient of variation (CV) for 88 peptide targets), with superior retention-time precision for the standard-flow platform (0.13 vs. 6.1 % CV). Surprisingly, for 41 of the 81 proteotypic peptides in the final assay, the standard-flow platform was more sensitive while for 9 of 81 the nano-flow platform was more sensitive. For these 81 peptides, there was a good correlation between the two sets of results (R(2) = 0.98, slope = 0.97). Overall, the standard-flow platform had superior performance metrics for most peptides, and is a good choice if sufficient sample is available.

Methods for multi-material stereolithography

DOEpatents

Wicker, Ryan [El Paso, TX; Medina, Francisco [El Paso, TX; Elkins, Christopher [Redwood City, CA

2011-06-14

Methods and systems of stereolithography for building cost-efficient and time-saving multi-material, multi-functional and multi-colored prototypes, models and devices configured for intermediate washing and curing/drying is disclosed including: laser(s), liquid and/or platform level sensing system(s), controllable optical system(s), moveable platform(s), elevator platform(s), recoating system(s) and at least one polymer retaining receptacle. Multiple polymer retaining receptacles may be arranged in a moveable apparatus, wherein each receptacle is adapted to actively/passively maintain a uniform, desired level of polymer by including a recoating device and a material fill/remove system. The platform is movably accessible to the polymer retaining receptacle(s), elevator mechanism(s) and washing and curing/drying area(s) which may be housed in a shielded enclosure(s). The elevator mechanism is configured to vertically traverse and rotate the platform, thus providing angled building, washing and curing/drying capabilities. A horizontal traversing mechanism may be included to facilitate manufacturing between components of SL cabinet(s) and/or alternative manufacturing technologies.

A novel 3D bioprinted flexible and biocompatible hydrogel bioelectronic platform.

PubMed

Agarwala, Shweta; Lee, Jia Min; Ng, Wei Long; Layani, Michael; Yeong, Wai Yee; Magdassi, Shlomo

2018-04-15

Bioelectronics platforms are gaining widespread attention as they provide a template to study the interactions between biological species and electronics. Decoding the effect of the electrical signals on the cells and tissues holds the promise for treating the malignant tissue growth, regenerating organs and engineering new-age medical devices. This work is a step forward in this direction, where bio- and electronic materials co-exist on one platform without any need for post processing. We fabricate a freestanding and flexible hydrogel based platform using 3D bioprinting. The fabrication process is simple, easy and provides a flexible route to print materials with preferred shapes, size and spatial orientation. Through the design of interdigitated electrodes and heating coil, the platform can be tailored to print various circuits for different functionalities. The biocompatibility of the printed platform is tested using C2C12 murine myoblasts cell line. Furthermore, normal human dermal fibroblasts (primary cells) are also seeded on the platform to ascertain the compatibility. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

A Design Comparison of Atmospheric Flight Vehicles for the Exploration of Titan

NASA Technical Reports Server (NTRS)

Gasbarre, Joseph F.; Wright, Henry S.; Lewis, Mark J.

2005-01-01

Titan, the largest moon of Saturn, is one of the most scientifically interesting locations in the Solar System. With a very cold atmosphere that is five times as dense as Earth s, and one and a half times the surface pressure, it also provides one of the most aeronautically fascinating environments known to humankind. While this may seem the ideal place to attempt atmospheric flight, many challenges await any vehicle attempting to navigate through it. In addition to these physical challenges, any scientific exploration mission to Titan will most likely have several operational constraints. One difficult constraint is the desire for a global survey of the planet and thus, a long duration flight within the atmosphere. Since many of the scientific measurements that would be unique to a vehicle flying through the atmosphere (as opposed to an orbiting spacecraft) desire near-surface positioning of their associated instruments, the vehicle must also be able to fly within the first scale height of the atmosphere. Another difficult constraint is that interaction with the surface, whether by landing or dropped probe, is also highly desirable from a scientific perspective. Two common atmospheric flight platforms that might be used for this mission are the airplane and airship. Under the assumption of a mission architecture that would involve an orbiting relay spacecraft delivered via aerocapture and an atmospheric flight vehicle delivered via direct entry, designs were developed for both platforms that are unique to Titan. Consequently, after a viable design was achieved for each platform, their advantages and disadvantages were compared. This comparison included such factors as deployment risk, surface interaction capability, mass, and design heritage. When considering all factors, the preferred candidate platform for a global survey of Titan is an airship.

A comparison of the accuracy of the smart sock system to force platform and optical system for measurement of temporal parameters of locomotion

NASA Astrophysics Data System (ADS)

Oks, A.; Katashev, A.; Bernans, E.; Abolins, V.

2017-10-01

The aim of the study was to present a new DAid®Pressure Sock System for feet locomotion monitoring and to verify it’s temporal characteristics by data comparison with the same obtained by two other widely used methods as reference. Designed system is based on sensors which can be knitted directly in the garment or hosiery items. DAid®Pressure Sock System was created for sport and medical applications. Comparison of temporal characteristics of different types of locomotion, obtained using designed system and reference devises, showed good agreement between data.

Seismic and Infrasound Location

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

Arrowsmith, Stephen J.; Begnaud, Michael L.

2014-03-19

This presentation includes slides on Signal Propagation Through the Earth/Atmosphere Varies at Different Scales; 3D Seismic Models: RSTT; Ray Coverage (Pn); Source-Specific Station Corrections (SSSCs); RSTT Conclusions; SALSA3D (SAndia LoS Alamos) Global 3D Earth Model for Travel Time; Comparison of IDC SSSCs to RSTT Predictions; SALSA3D; Validation and Model Comparison; DSS Lines in the Siberian Platform; DSS Line CRA-4 Comparison; Travel Time Δak135; Travel Time Prediction Uncertainty; SALSA3D Conclusions; Infrasound Data Processing: An example event; Infrasound Data Processing: An example event; Infrasound Location; How does BISL work?; BISL: Application to the 2013 DPRK Test; and BISL: Ongoing Research.

Open-WiSe: a solar powered wireless sensor network platform.

PubMed

González, Apolinar; Aquino, Raúl; Mata, Walter; Ochoa, Alberto; Saldaña, Pedro; Edwards, Arthur

2012-01-01

Because battery-powered nodes are required in wireless sensor networks and energy consumption represents an important design consideration, alternate energy sources are needed to provide more effective and optimal function. The main goal of this work is to present an energy harvesting wireless sensor network platform, the Open Wireless Sensor node (WiSe). The design and implementation of the solar powered wireless platform is described including the hardware architecture, firmware, and a POSIX Real-Time Kernel. A sleep and wake up strategy was implemented to prolong the lifetime of the wireless sensor network. This platform was developed as a tool for researchers investigating Wireless sensor network or system integrators.

Ground Simulation of an Autonomous Satellite Rendezvous and Tracking System Using Dual Robotic Systems

NASA Technical Reports Server (NTRS)

Trube, Matthew J.; Hyslop, Andrew M.; Carignan, Craig R.; Easley, Joseph W.

2012-01-01

A hardware-in-the-loop ground system was developed for simulating a robotic servicer spacecraft tracking a target satellite at short range. A relative navigation sensor package "Argon" is mounted on the end-effector of a Fanuc 430 manipulator, which functions as the base platform of the robotic spacecraft servicer. Machine vision algorithms estimate the pose of the target spacecraft, mounted on a Rotopod R-2000 platform, relay the solution to a simulation of the servicer spacecraft running in "Freespace", which performs guidance, navigation and control functions, integrates dynamics, and issues motion commands to a Fanuc platform controller so that it tracks the simulated servicer spacecraft. Results will be reviewed for several satellite motion scenarios at different ranges. Key words: robotics, satellite, servicing, guidance, navigation, tracking, control, docking.

Automatic and integrated micro-enzyme assay (AIμEA) platform for highly sensitive thrombin analysis via an engineered fluorescence protein-functionalized monolithic capillary column.

PubMed

Lin, Lihua; Liu, Shengquan; Nie, Zhou; Chen, Yingzhuang; Lei, Chunyang; Wang, Zhen; Yin, Chao; Hu, Huiping; Huang, Yan; Yao, Shouzhuo

2015-04-21

Nowadays, large-scale screening for enzyme discovery, engineering, and drug discovery processes require simple, fast, and sensitive enzyme activity assay platforms with high integration and potential for high-throughput detection. Herein, a novel automatic and integrated micro-enzyme assay (AIμEA) platform was proposed based on a unique microreaction system fabricated by a engineered green fluorescence protein (GFP)-functionalized monolithic capillary column, with thrombin as an example. The recombinant GFP probe was rationally engineered to possess a His-tag and a substrate sequence of thrombin, which enable it to be immobilized on the monolith via metal affinity binding, and to be released after thrombin digestion. Combined with capillary electrophoresis-laser-induced fluorescence (CE-LIF), all the procedures, including thrombin injection, online enzymatic digestion in the microreaction system, and label-free detection of the released GFP, were integrated in a single electrophoretic process. By taking advantage of the ultrahigh loading capacity of the AIμEA platform and the CE automatic programming setup, one microreaction column was sufficient for many times digestion without replacement. The novel microreaction system showed significantly enhanced catalytic efficiency, about 30 fold higher than that of the equivalent bulk reaction. Accordingly, the AIμEA platform was highly sensitive with a limit of detection down to 1 pM of thrombin. Moreover, the AIμEA platform was robust and reliable to detect thrombin in human serum samples and its inhibition by hirudin. Hence, this AIμEA platform exhibits great potential for high-throughput analysis in future biological application, disease diagnostics, and drug screening.

Acute sleep deprivation preconditions the heart against ischemia/ reperfusion injury: the role of central GABA-A receptors

PubMed Central

Parsa, Hoda; Imani, Alireza; Faghihi, Mahdieh; Riahi, Esmail; Badavi, Mohammad; Shakoori, Abbas; Rastegar, Tayebeh; Aghajani, Marjan; Rajani, Sulail Fatima

2017-01-01

Objective(s): Central γ-aminobutyric acid (GABA) neurotransmission modulates cardiovascular functions and sleep. Acute sleep deprivation (ASD) affects functions of various body organs via different mechanisms. Here, we evaluated the effect of ASD on cardiac ischemia/reperfusion injury (IRI), and studied the role of GABA-A receptor inhibition in central nucleus of amygdala (CeA) by assessing nitric oxide (NO) and oxidative stress. Materials and Methods: The CeA in sixty male Wistar rats was cannulated for saline or bicuculline (GABA-A receptor antagonist) administration. All animals underwent 30 min of coronary occlusion (ischemia), followed by 2 hr reperfusion (IR). The five experimental groups (n=12) included are as follows: IR: received saline; BIC+IR: received Bicuculline; MLP+IR: received saline, followed by the placement of animals in an aquarium with multiple large platforms; ASD+IR: underwent ASD in an aquarium with multiple small platforms; and BIC+ASD+IR: received bicuculline prior to ASD. Results: Bicuculline administration increased the malondialdehyde levels and infarct size, and decreased the NO metabolites levels and endothelial nitric oxide synthase (eNOS) gene expression in infarcted and non-infarcted areas in comparison to IR group. ASD reduced malondialdehyde levels and infarct size and increased NO metabolites, corticosterone levels and eNOS expression in infarcted and non-infarcted areas as compared to the IR group. Levels of malondialdehyde were increased while levels of NO metabolites, corticosterone and eNOS expression in infarcted and non-infarcted areas were reduced in the BIC+ASD+IR as compared to the ASD+IR group. Conclusion: Blockade of GABA-A receptors in the CeA abolishes ASD-induced cardioprotection by suppressing oxidative stress and NO production. PMID:29299201

Acute sleep deprivation preconditions the heart against ischemia/ reperfusion injury: the role of central GABA-A receptors.

PubMed

Parsa, Hoda; Imani, Alireza; Faghihi, Mahdieh; Riahi, Esmail; Badavi, Mohammad; Shakoori, Abbas; Rastegar, Tayebeh; Aghajani, Marjan; Rajani, Sulail Fatima

2017-11-01

Central γ-aminobutyric acid (GABA) neurotransmission modulates cardiovascular functions and sleep. Acute sleep deprivation (ASD) affects functions of various body organs via different mechanisms. Here, we evaluated the effect of ASD on cardiac ischemia/reperfusion injury (IRI), and studied the role of GABA-A receptor inhibition in central nucleus of amygdala (CeA) by assessing nitric oxide (NO) and oxidative stress. The CeA in sixty male Wistar rats was cannulated for saline or bicuculline (GABA-A receptor antagonist) administration. All animals underwent 30 min of coronary occlusion (ischemia), followed by 2 hr reperfusion (IR). The five experimental groups (n=12) included are as follows: IR: received saline; BIC+IR: received Bicuculline; MLP+IR: received saline, followed by the placement of animals in an aquarium with multiple large platforms; ASD+IR: underwent ASD in an aquarium with multiple small platforms; and BIC+ASD+IR: received bicuculline prior to ASD. Bicuculline administration increased the malondialdehyde levels and infarct size, and decreased the NO metabolites levels and endothelial nitric oxide synthase (eNOS) gene expression in infarcted and non-infarcted areas in comparison to IR group. ASD reduced malondialdehyde levels and infarct size and increased NO metabolites, corticosterone levels and eNOS expression in infarcted and non-infarcted areas as compared to the IR group. Levels of malondialdehyde were increased while levels of NO metabolites, corticosterone and eNOS expression in infarcted and non-infarcted areas were reduced in the BIC+ASD+IR as compared to the ASD+IR group. Blockade of GABA-A receptors in the CeA abolishes ASD-induced cardioprotection by suppressing oxidative stress and NO production.

Advanced Silicon Photonic Device Architectures for Optical Communications: Proposals and Demonstrations

NASA Astrophysics Data System (ADS)

Sacher, Wesley David

Photonic integrated circuits implemented on silicon (Si) hold the potential for densely integrated electro-optic and passive devices manufactured by the high-volume fabrication and sophisticated assembly processes used for complementary metal-oxide-semiconductor (CMOS) electronics. However, high index contrast Si photonics has a number of functional limitations. In this thesis, several devices are proposed, designed, and experimentally demonstrated to overcome challenges in the areas of resonant modulation, waveguide loss, fiber-to-chip coupling, and polarization control. The devices were fabricated using foundry services at IBM and A*STAR Institute of Microelectronics (IME). First, we describe coupling modulated microrings, in which the coupler between a microring and the bus waveguide is modulated. The device circumvents the modulation bandwidth vs. resonator linewidth trade-off of conventional intracavity modulated microrings. We demonstrate a Si coupling modulated microring with a small-signal modulation response free of the parasitic resonator linewidth limitations at frequencies up to about 6x the linewidth. Comparisons of eye diagrams show that coupling modulation achieved data rates > 2x the rate attainable with intracavity modulation. Second, we demonstrate a silicon nitride (Si3N4)-on-Si photonic platform with independent Si3N4 and Si waveguides and taper transitions to couple light between the layers. The platform combines the excellent passive waveguide properties of Si3N4 and the compatibility of Si waveguides with electro-optic devices. Within the platform, we propose and demonstrate dual-level, Si3N 4-on-Si, fiber-to-chip grating couplers that simultaneously have wide bandwidths and high coupling efficiencies. Conventional Si and Si3N 4 grating couplers suffer from a trade-off between bandwidth and coupling efficiency. The dual-level grating coupler achieved a peak coupling efficiency of -1.3 dB and a 1-dB bandwidth of 80 nm, a record for the coupling efficiency-bandwidth product. Finally, we describe polarization rotator-splitters and controllers based on mode conversion between the fundamental transverse magnetic polarized mode and a high order transverse electric polarized mode in vertically asymmetric waveguides. We demonstrate the first polarization rotator-splitters and controllers that are fully compatible with standard active Si photonic platforms and extend the concept to our Si3N4-on-Si photonic platform.

A novel approach for simulating the optical misalignment caused by satellite platform vibration in the ground test of satellite optical communication systems.

PubMed

Wang, Qiang; Tan, Liying; Ma, Jing; Yu, Siyuan; Jiang, Yijun

2012-01-16

Satellite platform vibration causes the misalignment between incident direction of the beacon and optical axis of the satellite optical communication system, which also leads to the instability of the laser link and reduces the precision of the system. So how to simulate the satellite platform vibration is a very important work in the ground test of satellite optical communication systems. In general, a vibration device is used for simulating the satellite platform vibration, but the simulation effect is not ideal because of the limited randomness. An approach is reasonable, which uses a natural random process for simulating the satellite platform vibration. In this paper, we discuss feasibility of the concept that the effect of angle of arrival fluctuation is taken as an effective simulation of satellite platform vibration in the ground test of the satellite optical communication system. Spectrum characteristic of satellite platform vibration is introduced, referring to the model used by the European Space Agency (ESA) in the SILEX program and that given by National Aeronautics and Space Development Agency (NASDA) of Japan. Spectrum characteristic of angle of arrival fluctuation is analyzed based on the measured data from an 11.16km bi-directional free space laser transmission experiment. Spectrum characteristic of these two effects is compared. The results show that spectra of these two effects have similar variation trend with the variation of frequency and feasibility of the concept is proved by the comparison results. At last the procedure of this method is proposed, which uses the power spectra of angle of arrival fluctuation to simulate that of the satellite platform vibration. The new approach is good for the ground test of satellite optical communication systems.

Testing tubewell platform color as a rapid screening tool for arsenic and manganese in drinking water wells.

PubMed

Biswas, Ashis; Nath, Bibhash; Bhattacharya, Prosun; Halder, Dipti; Kundu, Amit K; Mandal, Ujjal; Mukherjee, Abhijit; Chatterjee, Debashis; Jacks, Gunnar

2012-01-03

A low-cost rapid screening tool for arsenic (As) and manganese (Mn) in groundwater is urgently needed to formulate mitigation policies for sustainable drinking water supply. This study attempts to make statistical comparison between tubewell (TW) platform color and the level of As and Mn concentration in groundwater extracted from the respective TW (n = 423), to validate platform color as a screening tool for As and Mn in groundwater. The result shows that a black colored platform with 73% certainty indicates that well water is safe from As, while with 84% certainty a red colored platform indicates that well water is enriched with As, compared to WHO drinking water guideline of 10 μg/L. With this guideline the efficiency, sensitivity, and specificity of the tool are 79%, 77%, and 81%, respectively. However, the certainty values become 93% and 38%, respectively, for black and red colored platforms at 50 μg/L, the drinking water standards for India and Bangladesh. The respective efficiency, sensitivity, and specificity are 65%, 85%, and 59%. Similarly for Mn, black and red colored platform with 78% and 64% certainty, respectively, indicates that well water is either enriched or free from Mn at the Indian national drinking water standard of 300 μg/L. With this guideline the efficiency, sensitivity, and specificity of the tool are 71%, 67%, and 76%, respectively. Thus, this study demonstrates that TW platform color can be potentially used as an initial screening tool for identifying TWs with elevated dissolved As and Mn, to make further rigorous groundwater testing more intensive and implement mitigation options for safe drinking water supplies.

Scalable, Lightweight, Integrated and Quick-to-Assemble (SLIQ) Hyperdrives for Functional Circuit Dissection.

PubMed

Liang, Li; Oline, Stefan N; Kirk, Justin C; Schmitt, Lukas Ian; Komorowski, Robert W; Remondes, Miguel; Halassa, Michael M

2017-01-01

Independently adjustable multielectrode arrays are routinely used to interrogate neuronal circuit function, enabling chronic in vivo monitoring of neuronal ensembles in freely behaving animals at a single-cell, single spike resolution. Despite the importance of this approach, its widespread use is limited by highly specialized design and fabrication methods. To address this, we have developed a Scalable, Lightweight, Integrated and Quick-to-assemble multielectrode array platform. This platform additionally integrates optical fibers with independently adjustable electrodes to allow simultaneous single unit recordings and circuit-specific optogenetic targeting and/or manipulation. In current designs, the fully assembled platforms are scalable from 2 to 32 microdrives, and yet range 1-3 g, light enough for small animals. Here, we describe the design process starting from intent in computer-aided design, parameter testing through finite element analysis and experimental means, and implementation of various applications across mice and rats. Combined, our methods may expand the utility of multielectrode recordings and their continued integration with other tools enabling functional dissection of intact neural circuits.

From proteomics to systems biology: MAPA, MASS WESTERN, PROMEX, and COVAIN as a user-oriented platform.

PubMed

Weckwerth, Wolfram; Wienkoop, Stefanie; Hoehenwarter, Wolfgang; Egelhofer, Volker; Sun, Xiaoliang

2014-01-01

Genome sequencing and systems biology are revolutionizing life sciences. Proteomics emerged as a fundamental technique of this novel research area as it is the basis for gene function analysis and modeling of dynamic protein networks. Here a complete proteomics platform suited for functional genomics and systems biology is presented. The strategy includes MAPA (mass accuracy precursor alignment; http://www.univie.ac.at/mosys/software.html ) as a rapid exploratory analysis step; MASS WESTERN for targeted proteomics; COVAIN ( http://www.univie.ac.at/mosys/software.html ) for multivariate statistical analysis, data integration, and data mining; and PROMEX ( http://www.univie.ac.at/mosys/databases.html ) as a database module for proteogenomics and proteotypic peptides for targeted analysis. Moreover, the presented platform can also be utilized to integrate metabolomics and transcriptomics data for the analysis of metabolite-protein-transcript correlations and time course analysis using COVAIN. Examples for the integration of MAPA and MASS WESTERN data, proteogenomic and metabolic modeling approaches for functional genomics, phosphoproteomics by integration of MOAC (metal-oxide affinity chromatography) with MAPA, and the integration of metabolomics, transcriptomics, proteomics, and physiological data using this platform are presented. All software and step-by-step tutorials for data processing and data mining can be downloaded from http://www.univie.ac.at/mosys/software.html.

The 'cube' meta-model for the information system of large health sector organizations--a (platform neutral) mapping tool to integrate information system development with changing business functions and organizational development.

PubMed

Balkányi, László

2002-01-01

To develop information systems (IS) in the changing environment of the health sector, a simple but throughout model, avoiding the techno-jargon of informatics, might be useful for the top management. A platform neutral, extensible, transparent conceptual model should be established. Limitations of current methods lead to a simple, but comprehensive mapping, in the form of a three-dimensional cube. The three 'orthogonal' views are (a) organization functionality, (b) organizational structures and (c) information technology. Each of the cube-sides is described according to its nature. This approach enables to define any kind of an IS component as a certain point/layer/domain of the cube and enables also the management to label all IS components independently form any supplier(s) and/or any specific platform. The model handles changes in organization structure, business functionality and the serving info-system independently form each other. Practical application extends to (a) planning complex, new ISs, (b) guiding development of multi-vendor, multi-site ISs, (c) supporting large-scale public procurement procedures and the contracting, implementation phase by establishing a platform neutral reference, (d) keeping an exhaustive inventory of an existing large-scale system, that handles non-tangible aspects of the IS.

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.

Implementation of Arithmetic and Nonarithmetic Functions on a Label-free and DNA-based Platform

NASA Astrophysics Data System (ADS)

Wang, Kun; He, Mengqi; Wang, Jin; He, Ronghuan; Wang, Jianhua

2016-10-01

A series of complex logic gates were constructed based on graphene oxide and DNA-templated silver nanoclusters to perform both arithmetic and nonarithmetic functions. For the purpose of satisfying the requirements of progressive computational complexity and cost-effectiveness, a label-free and universal platform was developed by integration of various functions, including half adder, half subtractor, multiplexer and demultiplexer. The label-free system avoided laborious modification of biomolecules. The designed DNA-based logic gates can be implemented with readout of near-infrared fluorescence, and exhibit great potential applications in the field of bioimaging as well as disease diagnosis.

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.

Development of an Automated Microfluidic Reaction Platform for Multidimensional Screening: Reaction Discovery Employing Bicyclo[3.2.1]octanoid Scaffolds

PubMed Central

Goodell, John R.; McMullen, Jonathan P.; Zaborenko, Nikolay; Maloney, Jason R.; Ho, Chuan-Xing; Jensen, Klavs F.; Porco, John A.

2010-01-01

An automated, silicon-based microreactor system has been developed for rapid, low-volume, multidimensional reaction screening. Use of the microfluidic platform to identify transformations of densely functionalized bicyclo[3.2.1]octanoid scaffolds will be described. PMID:20560568

Utility-Based Link Recommendation in Social Networks

ERIC Educational Resources Information Center

Li, Zhepeng

2013-01-01

Link recommendation, which suggests links to connect currently unlinked users, is a key functionality offered by major online social networking platforms. Salient examples of link recommendation include "people you may know"' on Facebook and "who to follow" on Twitter. A social networking platform has two types of stakeholder:…

Integrated micro-optofluidic platform for real-time detection of airborne microorganisms

NASA Astrophysics Data System (ADS)

Choi, Jeongan; Kang, Miran; Jung, Jae Hee

2015-11-01

We demonstrate an integrated micro-optofluidic platform for real-time, continuous detection and quantification of airborne microorganisms. Measurements of the fluorescence and light scattering from single particles in a microfluidic channel are used to determine the total particle number concentration and the microorganism number concentration in real-time. The system performance is examined by evaluating standard particle measurements with various sample flow rates and the ratios of fluorescent to non-fluorescent particles. To apply this method to real-time detection of airborne microorganisms, airborne Escherichia coli, Bacillus subtilis, and Staphylococcus epidermidis cells were introduced into the micro-optofluidic platform via bioaerosol generation, and a liquid-type particle collection setup was used. We demonstrate successful discrimination of SYTO82-dyed fluorescent bacterial cells from other residue particles in a continuous and real-time manner. In comparison with traditional microscopy cell counting and colony culture methods, this micro-optofluidic platform is not only more accurate in terms of the detection efficiency for airborne microorganisms but it also provides additional information on the total particle number concentration.

Integrated micro-optofluidic platform for real-time detection of airborne microorganisms

PubMed Central

Choi, Jeongan; Kang, Miran; Jung, Jae Hee

2015-01-01

We demonstrate an integrated micro-optofluidic platform for real-time, continuous detection and quantification of airborne microorganisms. Measurements of the fluorescence and light scattering from single particles in a microfluidic channel are used to determine the total particle number concentration and the microorganism number concentration in real-time. The system performance is examined by evaluating standard particle measurements with various sample flow rates and the ratios of fluorescent to non-fluorescent particles. To apply this method to real-time detection of airborne microorganisms, airborne Escherichia coli, Bacillus subtilis, and Staphylococcus epidermidis cells were introduced into the micro-optofluidic platform via bioaerosol generation, and a liquid-type particle collection setup was used. We demonstrate successful discrimination of SYTO82-dyed fluorescent bacterial cells from other residue particles in a continuous and real-time manner. In comparison with traditional microscopy cell counting and colony culture methods, this micro-optofluidic platform is not only more accurate in terms of the detection efficiency for airborne microorganisms but it also provides additional information on the total particle number concentration. PMID:26522006

The contribution of the androgen receptor (AR) in human spatial learning and memory: A study in women with complete androgen insensitivity syndrome (CAIS).

PubMed

Mueller, S C; Verwilst, T; Van Branteghem, A; T'Sjoen, G; Cools, M

2016-02-01

Few studies have examined the impact of androgen insensitivity on human spatial learning and memory. In the present study, we tested 11 women with complete androgen insensitivity syndrome (CAIS), a rare genetic disorder characterized by complete absence of AR activity, and compared their performance against 20 comparison males and 19 comparison females on a virtual analog of the Morris Water Maze task. The results replicated a main sex effect showing that men relative to women were faster in finding the hidden platform and had reduced heading error. Furthermore, findings indicated that mean performance of women with CAIS was between control women and control men, though the differences were not statistically significant. Effect size estimates (and corresponding confidence intervals) of spatial learning trials showed little difference between women with CAIS and control women but CAIS women differed from men, but not women, on two variables, latency to find the platform and first-move latency. No differences between groups were present during visible platform trials or the probe trial, a measure of spatial memory. Moreover, groups also did not differ on estimates of IQ and variability of performance. The findings are discussed in relation to androgen insensitivity in human spatial learning and memory. Copyright © 2015 Elsevier Inc. All rights reserved.

Artificial Reefs as Surrogate Habitats for Red Snapper in the Northwestern Gulf of Mexico: A Fishery-Independent Comparison of Artificial and Natural Habitats

NASA Astrophysics Data System (ADS)

Streich, M.; Wetz, J. J.; Ajemian, M. J.; Stunz, G. W.

2016-02-01

The goal of our study was to evaluate the relative abundance, size and age structure of Red Snapper among three different habitat types (standing oil and gas platforms, artificial reefs [rigs-to-reefs], and natural banks) in the northwestern Gulf of Mexico. From May 2013 - January 2015, we conducted 140 vertical line sets and captured 1538 Red Snapper ranging in size from 251 to 855 mm TL. Ages determined for 801 of these fish ranged from 2-30 years. No differences were detected in Red Snapper CPUE among the three habitats. However, a comparison of TL and TW distributions suggested that natural banks supported a greater proportion of larger fish than artificial reefs or standing platforms (K-S test, p<0.001). Mean TW-at-age regressions for the most common age groups (ages 3-7) suggested that Red Snapper grew faster at artificial reefs and standing platforms than natural bank habitats (ANCOVA, p<0.05). Mean age was positively correlated with capture depth (r=0.79) suggesting spatial variation in age composition. These results have important implications for artificial reef development and Red Snapper management in the GOM. Further use of standardized, fishery-independent surveys and additional biological data will help elucidate the role artificial structures play in maintaining the Red Snapper population.

Open-source platform to benchmark fingerprints for ligand-based virtual screening

PubMed Central

2013-01-01

Similarity-search methods using molecular fingerprints are an important tool for ligand-based virtual screening. A huge variety of fingerprints exist and their performance, usually assessed in retrospective benchmarking studies using data sets with known actives and known or assumed inactives, depends largely on the validation data sets used and the similarity measure used. Comparing new methods to existing ones in any systematic way is rather difficult due to the lack of standard data sets and evaluation procedures. Here, we present a standard platform for the benchmarking of 2D fingerprints. The open-source platform contains all source code, structural data for the actives and inactives used (drawn from three publicly available collections of data sets), and lists of randomly selected query molecules to be used for statistically valid comparisons of methods. This allows the exact reproduction and comparison of results for future studies. The results for 12 standard fingerprints together with two simple baseline fingerprints assessed by seven evaluation methods are shown together with the correlations between methods. High correlations were found between the 12 fingerprints and a careful statistical analysis showed that only the two baseline fingerprints were different from the others in a statistically significant way. High correlations were also found between six of the seven evaluation methods, indicating that despite their seeming differences, many of these methods are similar to each other. PMID:23721588

[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.

[Web-based support system for medical device maintenance].

PubMed

Zhao, Jinhai; Hou, Wensheng; Chen, Haiyan; Tang, Wei; Wang, Yihui

2015-01-01

A Web-based technology system was put forward aiming at the actual problems of the long maintenance cycle and the difficulties of the maintenance and repairing of medical equipments. Based on analysis of platform system structure and function, using the key technologies such as search engine, BBS, knowledge base and etc, a platform for medical equipment service technician to use by online or offline was designed. The platform provides users with knowledge services and interactive services, enabling users to get a more ideal solution.

Ontology-based, multi-agent support of production management

NASA Astrophysics Data System (ADS)

Meridou, Despina T.; Inden, Udo; Rückemann, Claus-Peter; Patrikakis, Charalampos Z.; Kaklamani, Dimitra-Theodora I.; Venieris, Iakovos S.

2016-06-01

Over the recent years, the reported incidents on failed aircraft ramp-ups or the delayed production in small-lots have increased substantially. In this paper, we present a production management platform that combines agent-based techniques with the Service Oriented Architecture paradigm. This platform takes advantage of the functionality offered by the semantic web language OWL, which allows the users and services of the platform to speak a common language and, at the same time, facilitates risk management and decision making.

openECA Platform and Analytics Alpha Test Results

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

Robertson, Russell

The objective of the Open and Extensible Control and Analytics (openECA) Platform for Phasor Data project is to develop an open source software platform that significantly accelerates the production, use, and ongoing development of real-time decision support tools, automated control systems, and off-line planning systems that (1) incorporate high-fidelity synchrophasor data and (2) enhance system reliability while enabling the North American Electric Reliability Corporation (NERC) operating functions of reliability coordinator, transmission operator, and/or balancing authority to be executed more effectively.

openECA Platform and Analytics Beta Demonstration Results

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

Robertson, Russell

The objective of the Open and Extensible Control and Analytics (openECA) Platform for Phasor Data project is to develop an open source software platform that significantly accelerates the production, use, and ongoing development of real-time decision support tools, automated control systems, and off-line planning systems that (1) incorporate high-fidelity synchrophasor data and (2) enhance system reliability while enabling the North American Electric Reliability Corporation (NERC) operating functions of reliability coordinator, transmission operator, and/or balancing authority to be executed more effectively.

Comparisons of microbiomes in conventional and alternative poultry production systems

USDA-ARS?s Scientific Manuscript database

With the advent of new sequencing technologies and platforms, entire microbiomes are more easily characterized than ever before, while initially used more as a surveying tool to determine what microbial taxa (and their relative abundance) comprise various microbiomes, using microbiome data in a more...

Developing Single Nucleotide Polymorphism markers for the identification of Coffee germplasm

USDA-ARS?s Scientific Manuscript database

Coffee is one of the most widely consumed beverages that represent a multibillion dollar global industry. Accurate identification of coffee cultivars is essential for efficient management, exchange and use of coffee genetic resources. So far a universal platform that can allow data comparison across...

Emerging microengineered tools for functional analysis and phenotyping of blood cells.

PubMed

Li, Xiang; Chen, Weiqiang; Li, Zida; Li, Ling; Gu, Hongchen; Fu, Jianping

2014-11-01

The available techniques for assessing blood cell functions are limited considering the various types of blood cell and their diverse functions. In the past decade, rapid advances in microengineering have enabled an array of blood cell functional measurements that are difficult or impossible to achieve using conventional bulk platforms. Such miniaturized blood cell assay platforms also provide the attractive capabilities of reducing chemical consumption, cost, and assay time, as well as exciting opportunities for device integration, automation, and assay standardization. This review summarizes these contemporary microengineered tools and discusses their promising potential for constructing accurate in vitro models and rapid clinical diagnosis using minimal amounts of whole-blood samples. Copyright © 2014 Elsevier Ltd. All rights reserved.

Overestimation of the 25(OH)D serum concentration with the automated IDS EIA kit.

PubMed

Cavalier, Etienne; Huberty, Véronique; Cormier, Catherine; Souberbielle, Jean-Claude

2011-02-01

We have recently observed an increasing number of patients presenting very high serum levels of 25-hydroxyvitamin D [25(OH)D] (> 150 ng/mL), which, in all cases, had been measured with the IDS EIA kit adapted on different "open" automated platforms. We performed a comparison between the IDS EIA kit adapted on two different "open"automated platforms and the DiaSorin RIA. We found a systematic bias (higher levels with the IDS EIA kit) for concentrations more than 50-60 ng/mL that was less obvious when the IDS EIA was used in its manual procedure. We thus suggest to use the IDS EIA kit in its manual procedure rather than to adapt it on an automated platform, and to interpret cautiously a 25(OH)D greater than 100 ng/mL with this kit. Copyright © 2011 American Society for Bone and Mineral Research.

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.

PubMed

Martin, Daniel B; Holzman, Ted; May, Damon; Peterson, Amelia; Eastham, Ashley; Eng, Jimmy; McIntosh, Martin

2008-11-01

Multiple reaction monitoring (MRM) mass spectrometry identifies and quantifies specific peptides in a complex mixture with very high sensitivity and speed and thus has promise for the high throughput screening of clinical samples for candidate biomarkers. We have developed an interactive software platform, called MRMer, for managing highly complex MRM-MS experiments, including quantitative analyses using heavy/light isotopic peptide pairs. MRMer parses and extracts information from MS files encoded in the platform-independent mzXML data format. It extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1000 precursor-product pairs. Results can be easily output for quantitative comparison of consecutive runs. Additionally MRMer incorporates features that permit the quantitative analysis experiments including heavy and light isotopic peptide pairs. MRMer is open source and provided under the Apache 2.0 license.

GPU-based High-Performance Computing for Radiation Therapy

PubMed Central

Jia, Xun; Ziegenhein, Peter; Jiang, Steve B.

2014-01-01

Recent developments in radiotherapy therapy demand high computation powers to solve challenging problems in a timely fashion in a clinical environment. Graphics processing unit (GPU), as an emerging high-performance computing platform, has been introduced to radiotherapy. It is particularly attractive due to its high computational power, small size, and low cost for facility deployment and maintenance. Over the past a few years, GPU-based high-performance computing in radiotherapy has experienced rapid developments. A tremendous amount of studies have been conducted, in which large acceleration factors compared with the conventional CPU platform have been observed. In this article, we will first give a brief introduction to the GPU hardware structure and programming model. We will then review the current applications of GPU in major imaging-related and therapy-related problems encountered in radiotherapy. A comparison of GPU with other platforms will also be presented. PMID:24486639

A Comparison of Platforms for the Aerial Exploration of Titan

NASA Technical Reports Server (NTRS)

Wright, Henry S.; Gasbarre, Joseph F.; Levine, Joel S.

2005-01-01

Exploration of Titan, envisioned as a follow-on to the highly successful Cassini-Huygens mission, is described in this paper. A mission blending measurements from a dedicated orbiter and an in-situ aerial explorer is discussed. Summary description of the science rationale and the mission architecture, including the orbiter, is provided. The mission has been sized to ensure it can be accommodated on an existing expendable heavy-lift launch vehicle. A launch to Titan in 2018 with a 6-year time of flight to Titan using a combination of Solar Electric Propulsion and aeroassist (direct entry and aerocapture) forms the basic mission architecture. A detailed assessment of different platforms for aerial exploration of Titan has been performed. A rationale for the selection of the airship as the baseline platform is provided. Detailed description of the airship, its subsystems, and its operational strategies are provided.

Metronomic chemotherapy and nanocarrier platforms.

PubMed

Abu Lila, Amr S; Ishida, Tatsuhiro

2017-08-01

The therapeutic concept of administering chemotherapeutic agents continuously at lower doses, relative to the maximum tolerated dose (MTD) without drug-free breaks over extended periods -known as "metronomic chemotherapy"- is a promising approach for anti-angiogenic cancer therapy. In comparison with MTD chemotherapy regimens, metronomic chemotherapy has demonstrated reduced toxicity. However, as a monotherapy, metronomic chemotherapy has failed to provide convincing results in clinical trials. Therapeutic approaches including combining the anti-angiogenic "metronomic" therapy with conventional radio-/chemo-therapy and/or targeted delivery of chemotherapeutic agents to tumor tissues via their encapsulation with nanocarrier-based platforms have proven to potentiate the overall therapeutic outcomes. In this review, therefore, we focused on the mutual contribution made by nanoscale drug delivery platforms to the therapeutic efficacy of metronomic-based chemotherapy. In addition, the influence that the dosing schedule has on the overall therapeutic efficacy of metronomic chemotherapy is discussed. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Results from MARBLE DT Experiments on the National Ignition Facility: Implosion of Foam-Filled Capsules for Studying Thermonuclear Burn in the Presence of Heterogeneous Mix

NASA Astrophysics Data System (ADS)

Murphy, T. J.; Douglas, M. R.; Cardenas, T.; Cooley, J. H.; Gunderson, M. A.; Haines, B. M.; Hamilton, C. E.; Kim, Y.; Lee, M. N.; Oertel, J. A.; Olson, R. E.; Randolph, R. B.; Shah, R. C.; Smidt, J. M.

2017-10-01

The MARBLE campaign on NIF investigates the effect of heterogeneous mix on thermonuclear burn for comparison to a probability distribution function (PDF) burn model. MARBLE utilizes plastic capsules filled with deuterated plastic foam and tritium gas. The ratio of DT to DD neutron yield is indicative of the degree to which the foam and the gas atomically mix. Platform development experiments have been performed to understand the behavior of the foam and of the gas separately using two types of capsule. The first experiments using deuterated foam and tritium gas have been performed. Results of these experiments, and the implications for our understanding of thermonuclear burn in heterogeneously mixed separated reactant experiments will be discussed. This work is supported by US DOE/NNSA, performed at LANL, operated by LANS LLC under contract DE-AC52-06NA25396.

Enhanced bioactivity of internally functionalized cationic dendrimers with PEG cores

PubMed Central

Albertazzi, Lorenzo; Mickler, Frauke M.; Pavan, Giovanni M.; Salomone, Fabrizio; Bardi, Giuseppe; Panniello, Mariangela; Amir, Elizabeth; Kang, Taegon; Killops, Kato L.; Bräuchle, Christoph; Amir, Roey J.; Hawker, Craig J.

2012-01-01

Hybrid dendritic-linear block copolymers based on a 4-arm polyethylene glycol (PEG) core were synthesized using an accelerated AB2/CD2 dendritic growth approach through orthogonal amine/epoxy and thiol-yne chemistries. The biological activity of these 4-arm and the corresponding 2-arm hybrid dendrimers revealed an enhanced, dendritic effect with an exponential increase in cell internalization concomitant with increasing amine end-groups and low cytotoxicity. Furthermore, the ability of these hybrid dendrimers to induce endosomal escape combined with their facile and efficient synthesis makes them attractive platforms for gene transfection. The 4-arm-based dendrimer showed significantly improved DNA binding and gene transfection capabilities in comparison with the 2-arm derivative. These results combined with the MD simulation indicate a significant effect of both the topology of the PEG core and the multivalency of these hybrid macromolecules, on their DNA binding and delivery capablities. PMID:23140570

Comparison of two MAC protocols based on LEO satellite networks

NASA Astrophysics Data System (ADS)

Guan, Mingxiang; Wang, Ruichun

2009-12-01

With the development of LEO satellite communication, it is the basic requirement that various kinds of services will be provided. Considering that weak channel collision detection ability, long propagation delay and heavy load in LEO satellite communication system, a valid adaptive access control protocol APRMA is proposed. Different access probability functions for different services are obtained and appropriate access probabilities for voice and data users are updated slot by slot based on the estimation of the voice traffic and the channel status. Finally simulation results demonstrate that the performance of system is improved by the APRMA compared with the conventional PRMA, with an acceptable trade-off between QoS of voice and delay of data. Also the APRMA protocol will be suitable for HAPS (high altitude platform station) with the characters of weak channel collision detection ability, long propagation delay and heavy load.

Solid organ fabrication: comparison of decellularization to 3D bioprinting.

PubMed

Jung, Jangwook P; Bhuiyan, Didarul B; Ogle, Brenda M

2016-01-01

Solid organ fabrication is an ultimate goal of Regenerative Medicine. Since the introduction of Tissue Engineering in 1993, functional biomaterials, stem cells, tunable microenvironments, and high-resolution imaging technologies have significantly advanced efforts to regenerate in vitro culture or tissue platforms. Relatively simple flat or tubular organs are already in (pre)clinical trials and a few commercial products are in market. The road to more complex, high demand, solid organs including heart, kidney and lung will require substantive technical advancement. Here, we consider two emerging technologies for solid organ fabrication. One is decellularization of cadaveric organs followed by repopulation with terminally differentiated or progenitor cells. The other is 3D bioprinting to deposit cell-laden bio-inks to attain complex tissue architecture. We reviewed the development and evolution of the two technologies and evaluated relative strengths needed to produce solid organs, with special emphasis on the heart and other tissues of the cardiovascular system.

Application of Fourier-transform ion cyclotron resonance mass spectrometry to metabolic profiling and metabolite identification.

PubMed

Ohta, Daisaku; Kanaya, Shigehiko; Suzuki, Hideyuki

2010-02-01

Metabolomics, as an essential part of genomics studies, intends holistic understanding of metabolic networks through simultaneous analysis of a myriad of both known and unknown metabolites occurring in living organisms. The initial stage of metabolomics was designed for the reproducible analyses of known metabolites based on their comparison to available authentic compounds. Such metabolomics platforms were mostly based on mass spectrometry (MS) technologies enabled by a combination of different ionization methods together with a variety of separation steps including LC, GC, and CE. Among these, Fourier-transform ion cyclotron resonance MS (FT-ICR/MS) is distinguished from other MS technologies by its ultrahigh resolution power in mass to charge ratio (m/z). The potential of FT-ICR/MS as a distinctive metabolomics tool has been demonstrated in nontargeted metabolic profiling and functional characterization of novel genes. Here, we discuss both the advantages and difficulties encountered in the FT-ICR/MS metabolomics studies.

Gender differences in patellofemoral load during the epee fencing lunge.

PubMed

Sinclair, J; Bottoms, L

2015-01-01

Clinical analyses have shown that injuries and pain linked specifically to fencing training/competition were prevalent in 92.8% of fencers. Patellofemoral pain is the most common chronic injury in athletic populations and females are considered to be more susceptible to this pathology. This study aimed to examine gender differences in patellofemoral contact forces during the fencing lunge. Patellofemoral contact forces were obtained from eight male and eight female club level epee fencers using an eight-camera 3D motion capture system and force platform data as they completed simulated lunges. Independent t-tests were performed on the data to determine whether gender differences in patellofemoral contact forces were present. The results show that females were associated with significantly greater patellofemoral contact force parameters in comparison with males. This suggests that female fencers may be at greater risk from patellofemoral pathology as a function of fencing training/competition.

A DNA-scaffold platform enhances a multi-enzymatic cycling reaction.

PubMed

Mashimo, Yasumasa; Mie, Masayasu; Kobatake, Eiry

2018-04-01

We explored the co-localization of multiple enzymes on a DNA backbone via a DNA-binding protein, Gene-A* (A*-tag) to increase the efficiency of cascade enzymatic reactions. Firefly luciferase (FLuc) and pyruvate orthophosphate dikinase (PPDK) were genetically fused with A*-tag and modified with single-stranded (ss) DNA via A*-tag. The components were assembled on ssDNA by hybridization, thereby enhancing the efficiency of the cascading bioluminescent reaction producing light emission from pyrophosphate. The activity of A*-tag in each enzyme was investigated with dye-labeled DNA. Co-localization of the enzymes via hybridization was examined using a gel shift assay. The multi-enzyme complex showed significant improvement in the overall efficiency of the cascading reaction in comparison to a mixture of free enzymes. A*-tag is highly convenient for ssDNA modification of versatile enzymes, and it can be used for construction of functional DNA-enzyme complexes.

MISSE in the Materials and Processes Technical Information System (MAPTIS )

NASA Technical Reports Server (NTRS)

Burns, DeWitt; Finckenor, Miria; Henrie, Ben

2013-01-01

Materials International Space Station Experiment (MISSE) data is now being collected and distributed through the Materials and Processes Technical Information System (MAPTIS) at Marshall Space Flight Center in Huntsville, Alabama. MISSE data has been instrumental in many programs and continues to be an important source of data for the space community. To facilitate great access to the MISSE data the International Space Station (ISS) program office and MAPTIS are working to gather this data into a central location. The MISSE database contains information about materials, samples, and flights along with pictures, pdfs, excel files, word documents, and other files types. Major capabilities of the system are: access control, browsing, searching, reports, and record comparison. The search capabilities will search within any searchable files so even if the desired meta-data has not been associated data can still be retrieved. Other functionality will continue to be added to the MISSE database as the Athena Platform is expanded

Application of a laser Doppler vibrometer for air-water to subsurface signature detection

NASA Astrophysics Data System (ADS)

Land, Phillip; Roeder, James; Robinson, Dennis; Majumdar, Arun

2015-05-01

There is much interest in detecting a target and optical communications from an airborne platform to a platform submerged under water. Accurate detection and communications between underwater and aerial platforms would increase the capabilities of surface, subsurface, and air, manned and unmanned vehicles engaged in oversea and undersea activities. The technique introduced in this paper involves a Laser Doppler Vibrometer (LDV) for acousto-optic sensing for detecting acoustic information propagated towards the water surface from a submerged platform inside a 12 gallon water tank. The LDV probes and penetrates the water surface from an aerial platform to detect air-water surface interface vibrations caused by an amplifier to a speaker generating a signal generated from underneath the water surface (varied water depth from 1" to 8"), ranging between 50Hz to 5kHz. As a comparison tool, a hydrophone was used simultaneously inside the water tank for recording the acoustic signature of the signal generated between 50Hz to 5kHz. For a signal generated by a submerged platform, the LDV can detect the signal. The LDV detects the signal via surface perturbations caused by the impinging acoustic pressure field; proving a technique of transmitting/sending information/messages from a submerged platform acoustically to the surface of the water and optically receiving the information/message using the LDV, via the Doppler Effect, allowing the LDV to become a high sensitivity optical-acoustic device. The technique developed has much potential usage in commercial oceanography applications. The present work is focused on the reception of acoustic information from an object located underwater.

Comparison of the Predictive Accuracy of DNA Array-Based Multigene Classifiers across cDNA Arrays and Affymetrix GeneChips

PubMed Central

Stec, James; Wang, Jing; Coombes, Kevin; Ayers, Mark; Hoersch, Sebastian; Gold, David L.; Ross, Jeffrey S; Hess, Kenneth R.; Tirrell, Stephen; Linette, Gerald; Hortobagyi, Gabriel N.; Symmans, W. Fraser; Pusztai, Lajos

2005-01-01

We examined how well differentially expressed genes and multigene outcome classifiers retain their class-discriminating values when tested on data generated by different transcriptional profiling platforms. RNA from 33 stage I-III breast cancers was hybridized to both Affymetrix GeneChip and Millennium Pharmaceuticals cDNA arrays. Only 30% of all corresponding gene expression measurements on the two platforms had Pearson correlation coefficient r ≥ 0.7 when UniGene was used to match probes. There was substantial variation in correlation between different Affymetrix probe sets matched to the same cDNA probe. When cDNA and Affymetrix probes were matched by basic local alignment tool (BLAST) sequence identity, the correlation increased substantially. We identified 182 genes in the Affymetrix and 45 in the cDNA data (including 17 common genes) that accurately separated 91% of cases in supervised hierarchical clustering in each data set. Cross-platform testing of these informative genes resulted in lower clustering accuracy of 45 and 79%, respectively. Several sets of accurate five-gene classifiers were developed on each platform using linear discriminant analysis. The best 100 classifiers showed average misclassification error rate of 2% on the original data that rose to 19.5% when tested on data from the other platform. Random five-gene classifiers showed misclassification error rate of 33%. We conclude that multigene predictors optimized for one platform lose accuracy when applied to data from another platform due to missing genes and sequence differences in probes that result in differing measurements for the same gene. PMID:16049308

Results from a new 193nm die-to-database reticle inspection platform

NASA Astrophysics Data System (ADS)

Broadbent, William H.; Alles, David S.; Giusti, Michael T.; Kvamme, Damon F.; Shi, Rui-fang; Sousa, Weston L.; Walsh, Robert; Xiong, Yalin

2010-05-01

A new 193nm wavelength high resolution reticle defect inspection platform has been developed for both die-to-database and die-to-die inspection modes. In its initial configuration, this innovative platform has been designed to meet the reticle qualification requirements of the IC industry for the 22nm logic and 3xhp memory generations (and shrinks) with planned extensions to the next generation. The 22nm/3xhp IC generation includes advanced 193nm optical lithography using conventional RET, advanced computational lithography, and double patterning. Further, EUV pilot line lithography is beginning. This advanced 193nm inspection platform has world-class performance and the capability to meet these diverse needs in optical and EUV lithography. The architecture of the new 193nm inspection platform is described. Die-to-database inspection results are shown on a variety of reticles from industry sources; these reticles include standard programmed defect test reticles, as well as advanced optical and EUV product and product-like reticles. Results show high sensitivity and low false and nuisance detections on complex optical reticle designs and small feature size EUV reticles. A direct comparison with the existing industry standard 257nm wavelength inspection system shows measurable sensitivity improvement for small feature sizes

Research on Hydrodynamic Interference Suppression of Bottom-Mounted Monitoring Platform with Fairing Structure

NASA Astrophysics Data System (ADS)

Wang, Zhen; Zheng, Yi; Mao, Yu-feng; Wang, Ya-zhou; Yu, Yan-ting; Liu, Hong-ning

2018-03-01

In the disturbance of unsteady flow field under the sea, the monitoring accuracy and precision of the bottom-mounted acoustic monitoring platform will decrease. In order to reduce the hydrodynamic interference, the platform wrapped with fairing structure and separated from the retrieval unit is described. The suppression effect evaluation based on the correlation theory of sound pressure and particle velocity for spherical wave in infinite homogeneous medium is proposed and the difference value between them is used to evaluate the hydrodynamic restraining performance of the bottom-mounted platform under far field condition. Through the sea test, it is indicated that the platform with sparse layers fairing structure (there are two layers for the fairing, in which the inside layer is 6-layers sparse metal net, and the outside layer is 1-layer polyester cloth, and then it takes sparse layers for short) has no attenuation in the sound pressure response to the sound source signal, but obvious suppression in the velocity response to the hydrodynamic noise. The effective frequency of the fairing structure is decreased below 10 Hz, and the noise magnitude is reduced by 10 dB. With the comparison of different fairing structures, it is concluded that the tighter fairing structure can enhance the performance of sound transmission and flow restraining.

In situ characterization of N-carboxy anhydride polymerization in nanoporous anodic alumina.

PubMed

Lau, K H Aaron; Duran, Hatice; Knoll, Wolfgang

2009-03-12

Poly(gamma-benzyl-L-glutamate) (PBLG) has been a popular model polypeptide for a range of physicochemical studies, and its modifiable ester side chains make it an attractive platform for various potential applications. Thin films of Poly(gamma-benzyl-L-glutamate) PBLG were surface grafted within nanoporous anodic alumina (AAO) by surface-initiated polymerization of the N-carboxy anhydride of benzyl-L-glutamate (BLG-NCA). The grafting process was characterized by optical waveguide spectroscopy (OWS), infrared spectroscopy (FT-IR), and scanning electron microscopy (SEM). OWS was able to track the PBLG layer thickness increase in situ, and ex situ FT-IR gave complementary information on the PBLG chain's secondary structure. Transitions in the PBLG growth rate could be correlated with transitions in the polypeptide secondary structure. The emergence of a three-dimensional, anisotropic PBLG morphology within the cylindrical pores of the AAO membrane was also identified as the grafted PBLG average layer thickness increased. Comparison of the PBLG/AAO results with those on a planar silicon dioxide surface indicated that both the conformational transitions and the PBLG nanostructure development could be attributed to the confining geometry within the pores of the nanoporous AAO matrix. The use of a nanoporous AAO matrix, combined with the surface grafting of a thin film of PBLG chains with multiple modifiable side chains, could potentially offer a nanoporous platform with a very high density of functional sites.

LIVVkit: An extensible, python-based, land ice verification and validation toolkit for ice sheet models

NASA Astrophysics Data System (ADS)

Kennedy, Joseph H.; Bennett, Andrew R.; Evans, Katherine J.; Price, Stephen; Hoffman, Matthew; Lipscomb, William H.; Fyke, Jeremy; Vargo, Lauren; Boghozian, Adrianna; Norman, Matthew; Worley, Patrick H.

2017-06-01

To address the pressing need to better understand the behavior and complex interaction of ice sheets within the global Earth system, significant development of continental-scale, dynamical ice sheet models is underway. Concurrent to the development of the Community Ice Sheet Model (CISM), the corresponding verification and validation (V&V) process is being coordinated through a new, robust, Python-based extensible software package, the Land Ice Verification and Validation toolkit (LIVVkit). Incorporated into the typical ice sheet model development cycle, it provides robust and automated numerical verification, software verification, performance validation, and physical validation analyses on a variety of platforms, from personal laptops to the largest supercomputers. LIVVkit operates on sets of regression test and reference data sets, and provides comparisons for a suite of community prioritized tests, including configuration and parameter variations, bit-for-bit evaluation, and plots of model variables to indicate where differences occur. LIVVkit also provides an easily extensible framework to incorporate and analyze results of new intercomparison projects, new observation data, and new computing platforms. LIVVkit is designed for quick adaptation to additional ice sheet models via abstraction of model specific code, functions, and configurations into an ice sheet model description bundle outside the main LIVVkit structure. Ultimately, through shareable and accessible analysis output, LIVVkit is intended to help developers build confidence in their models and enhance the credibility of ice sheet models overall.

The Bigfoot Drive; Experimental Results

NASA Astrophysics Data System (ADS)

Baker, Kevin; Thomas, Cliff; Khan, Shahab; Casey, Daniel; Spears, Brian; Nora, Ryan; Munro, Davis; Eder, David; Milovich, Jose; Berger, Dick; Strozzi, David; Goyon, Clement; Turnbull, David; Ma, Tammy; Izumi, Nobuhiko; Benedetti, Robin; Millot, Marius; Celliers, Peter; Yeamans, Charles; Hatarik, Robert; Landen, Nino; Hurricane, Omar; Callahan, Debbie

2016-10-01

The Bigfoot platform was developed on the National Ignition Facility to investigate low convergence, high adiabat, high rhoR hotspot implosions. This platform was designed to be less susceptible to wall motion, LPI and CBET and to be more robust against capsule hydrodynamic instabilities. To date experimental studies have been carried out at two hohlraum scales, a 5.75 and 5.4 mm diameter hohlraum. We will present experimental results from these tuning campaigns including the shape vs. cone fraction, surrogacy comparisons of self-emission from the capsules vs. radiography of the imploding capsule and doped vs. undoped capsules. Prepared by LLNL under Contract DE-AC52-07NA27344.

Assessing the Quality, Feasibility, and Efficacy of Electronic Patient Platforms Designed to Support Adolescents and Young Adults With Cancer: A Systematic Review Protocol

PubMed Central

McCann, Lisa

2017-01-01

Background A range of innovative websites, mobile technologies, eHealth and mHealth platforms have emerged to support adolescents and young adults (AYAs) with cancer. Previous reviews have identified these various applications and solutions, but no review has summarized the quality, feasibility, and efficacy of existing patient platforms (inclusive of websites, mobile technologies, mHealth and eHealth platforms) developed specifically for young people with cancer. Objective This paper describes the design of a protocol to conduct a review of published studies or reports which describe or report on an existing platform designed specifically for AYAs who have had a cancer diagnosis. Methods A search string was developed using a variety of key words and Medical Subject Heading and applied to bibliographic databases. General data (sample characteristics, patient platform development, design and, if applicable, pilot testing outcomes) will be extracted from reports and studies. Drawing on a previously developed coding schematic, the identified patient platforms will be coded for mode of delivery into (1) automated functions, (2) communicative functions, and (3) use of supplementary modes. An adapted version of the Mobile App Rating Scale (MARS) will be used to assess the of quality of each identified patient platform. The methodological quality of included studies will be assessed using the Quality Assessment Criteria for Evaluating Primary Research Papers from a Variety of Fields (QualSyst). Both authors will independently screen eligible studies for final inclusion and will both be responsible for data extraction and appraisal. Data will be synthesized narratively to provide an overview of identified patient platforms. Results The review began in October 2016 and is currently in progress. The review paper will be submitted for peer-review and publication in the summer of 2017. Conclusions This review will be unique in its focus on assessing, where possible, the quality and efficacy of patient platforms for adolescents and young adults diagnosed with cancer. Results generated from this review will provide an invaluable insight into the utility of modern technology in supporting young people with cancer. PMID:28096067

Earth Observation-Supported Service Platform for the Development and Provision of Thematic Information on the Built Environment - the Tep-Urban Project

NASA Astrophysics Data System (ADS)

Esch, T.; Asamer, H.; Boettcher, M.; Brito, F.; Hirner, A.; Marconcini, M.; Mathot, E.; Metz, A.; Permana, H.; Soukop, T.; Stanek, F.; Kuchar, S.; Zeidler, J.; Balhar, J.

2016-06-01

The Sentinel fleet will provide a so-far unique coverage with Earth observation data and therewith new opportunities for the implementation of methodologies to generate innovative geo-information products and services. It is here where the TEP Urban project is supposed to initiate a step change by providing an open and participatory platform based on modern ICT technologies and services that enables any interested user to easily exploit Earth observation data pools, in particular those of the Sentinel missions, and derive thematic information on the status and development of the built environment from these data. Key component of TEP Urban project is the implementation of a web-based platform employing distributed high-level computing infrastructures and providing key functionalities for i) high-performance access to satellite imagery and derived thematic data, ii) modular and generic state-of-the art pre-processing, analysis, and visualization techniques, iii) customized development and dissemination of algorithms, products and services, and iv) networking and communication. This contribution introduces the main facts about the TEP Urban project, including a description of the general objectives, the platform systems design and functionalities, and the preliminary portfolio products and services available at the TEP Urban platform.

Enhanced zinc consumption causes memory deficits and increased brain levels of zinc

USGS Publications Warehouse

Flinn, J.M.; Hunter, D.; Linkous, D.H.; Lanzirotti, A.; Smith, L.N.; Brightwell, J.; Jones, B.F.

2005-01-01

Zinc deficiency has been shown to impair cognitive functioning, but little work has been done on the effects of elevated zinc. This research examined the effect on memory of raising Sprague-Dawley rats on enhanced levels of zinc (10 ppm ZnCO3; 0.153 mM) in the drinking water for periods of 3 or 9 months, both pre- and postnatally. Controls were raised on lab water. Memory was tested in a series of Morris Water Maze (MWM) experiments, and zinc-treated rats were found to have impairments in both reference and working memory. They were significantly slower to find a stationary platform and showed greater thigmotaxicity, a measure of anxiety. On a working memory task, where the platform was moved each day, zinc-treated animals had longer latencies over both trials and days, swam further from the platform, and showed greater thigmotaxicity. On trials using an Atlantis platform, which remained in one place but was lowered on probe trials, the zinc-treated animals had significantly fewer platform crossings, spent less time in the target quadrant, and did not swim as close to the platform position. They had significantly greater latency on nonprobe trials. Microprobe synchrotron X-ray fluorescence (??SXRF) confirmed that brain zinc levels were increased by adding ZnCO 3 to the drinking water. These data show that long-term dietary administration of zinc can lead to impairments in cognitive function. ?? 2004 Elsevier Inc. All rights reserved.

Everyday Functioning Benefits from an Assisted Living Platform amongst Frail Older Adults and Their Caregivers

PubMed Central

Dupuy, Lucile; Froger, Charlotte; Consel, Charles; Sauzéon, Hélène

2017-01-01

Ambient assisted living technologies (AAL) are regarded as a promising solution to support aging in place. Yet, their efficacy has to be demonstrated in terms of benefits for independent living and for work conditions of caregivers. Hence, the purpose of this study was to assess the benefits of a multi-task AAL platform for both Frail older Individuals (FIs) and professional caregivers with respect to everyday functioning and caregiver burden. In this context, a 6-month field study involved 32 FIs living at home (half of them were equipped by the platform and the remaining half were not, as a control condition) and their caregivers. Everyday functioning measures were reported by frail participants and caregivers. Self-reported burden measures of caregiver were also collected. The main results showed that the caregiver's estimates of everyday functioning of equipped participants were unchanged across time, while they decreased for the control participants. Also, a reduction of self-reported objective burden was obtained after 6 months of AAL intervention for the equipped group, compared to the control group. Overall, these results highlighted the potential of AAL as a relevant environmental support for preventing both functional losses in FIs and objective burden professional caregiver. PMID:29033826

Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression.

PubMed

Zhang, Guosheng; Huang, Kuan-Chieh; Xu, Zheng; Tzeng, Jung-Ying; Conneely, Karen N; Guan, Weihua; Kang, Jian; Li, Yun

2016-05-01

DNA methylation is a key epigenetic mark involved in both normal development and disease progression. Recent advances in high-throughput technologies have enabled genome-wide profiling of DNA methylation. However, DNA methylation profiling often employs different designs and platforms with varying resolution, which hinders joint analysis of methylation data from multiple platforms. In this study, we propose a penalized functional regression model to impute missing methylation data. By incorporating functional predictors, our model utilizes information from nonlocal probes to improve imputation quality. Here, we compared the performance of our functional model to linear regression and the best single probe surrogate in real data and via simulations. Specifically, we applied different imputation approaches to an acute myeloid leukemia dataset consisting of 194 samples and our method showed higher imputation accuracy, manifested, for example, by a 94% relative increase in information content and up to 86% more CpG sites passing post-imputation filtering. Our simulated association study further demonstrated that our method substantially improves the statistical power to identify trait-associated methylation loci. These findings indicate that the penalized functional regression model is a convenient and valuable imputation tool for methylation data, and it can boost statistical power in downstream epigenome-wide association study (EWAS). © 2016 WILEY PERIODICALS, INC.

Sequenced sorghum mutant library- an efficient platform for discovery of causal gene mutations

USDA-ARS?s Scientific Manuscript database

Ethyl methanesulfonate (EMS) efficiently generates high-density mutations in genomes. We applied whole-genome sequencing to 256 phenotyped mutant lines of sorghum (Sorghum bicolor L. Moench) to 16x coverage. Comparisons with the reference sequence revealed >1.8 million canonical EMS-induced G/C to A...

Draft genome sequence of Cryptococcus terricola JCM 24523, an oleaginous yeast capable of expressing exogenous DNA

DOE PAGES

Close, Dan; Ojumu, John O.; Zhang, Gui X.

2016-11-03

Cryptococcus terricola JCM 24523 has recently been identified as an oleaginous yeast capable of converting starch into fatty acids. Here, this draft genome sequence provides a platform for elucidating its fatty acid production potential and supporting comparisons with other oleaginous species.

Comparison of L1000 and Affymetrix Microarray for In Vitro Concentration-Response Gene Expression Profiling (SOT)

EPA Science Inventory

Advances in high-throughput screening technologies and in vitro systems have opened doors for cost-efficient evaluation of chemical effects on a diversity of biological endpoints. However, toxicogenomics platforms remain too costly to evaluate large libraries of chemicals in conc...

Draft genome sequence of Cryptococcus terricola JCM 24523, an oleaginous yeast capable of expressing exogenous DNA

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

Close, Dan; Ojumu, John O.; Zhang, Gui X.

Cryptococcus terricola JCM 24523 has recently been identified as an oleaginous yeast capable of converting starch into fatty acids. Here, this draft genome sequence provides a platform for elucidating its fatty acid production potential and supporting comparisons with other oleaginous species.

Mobile Phone Mood Charting for Adolescents

ERIC Educational Resources Information Center

Matthews, Mark; Doherty, Gavin; Sharry, John; Fitzpatrick, Carol

2008-01-01

Mobile phones may provide a useful and engaging platform for supporting therapeutic services working with adolescents. This paper examines the potential benefits of the mobile phone for self-charting moods in comparison to existing methods in current practice. The paper describes a mobile phone application designed by the authors which allows…

GraphCrunch 2: Software tool for network modeling, alignment and clustering.

PubMed

Kuchaiev, Oleksii; Stevanović, Aleksandar; Hayes, Wayne; Pržulj, Nataša

2011-01-19

Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, GraphCruch 2 implements an algorithm for clustering nodes within a network based solely on their topological similarities. Using GraphCrunch 2, we demonstrate that eukaryotic and viral PPI networks may belong to different graph model families and show that topology-based clustering can reveal important functional similarities between proteins within yeast and human PPI networks. GraphCrunch 2 is a software tool that implements the latest research on biological network analysis. It parallelizes computationally intensive tasks to fully utilize the potential of modern multi-core CPUs. It is open-source and freely available for research use. It runs under the Windows and Linux platforms.

13. Detail, northeast facade, original door from platform to waiting ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

13. Detail, northeast facade, original door from platform to waiting room, now non-functional; note holes in mortar joints used to hold masonry anchors for mounting advertising signs for previous building tenants; view to southwest, 90mm lens. - Southern Pacific Depot, 559 El Camino Real, San Carlos, San Mateo County, CA

Beam Dynamics Simulation Platform and Studies of Beam Breakup in Dielectric Wakefield Structures

NASA Astrophysics Data System (ADS)

Schoessow, P.; Kanareykin, A.; Jing, C.; Kustov, A.; Altmark, A.; Gai, W.

2010-11-01

A particle-Green's function beam dynamics code (BBU-3000) to study beam breakup effects is incorporated into a parallel computing framework based on the Boinc software environment, and supports both task farming on a heterogeneous cluster and local grid computing. User access to the platform is through a web browser.

Explaining University Students' Effective Use of E-Learning Platforms

ERIC Educational Resources Information Center

Moreno, Valter; Cavazotte, Flavia; Alves, Isabela

2017-01-01

Students' success in e-learning programs depends on how they adopt and embed technology into their learning activities. Drawing on the Technology Acceptance Model, we propose a framework to explain students' intention to use e-learning platforms effectively, that is, their intention to fully exploit system's functionalities in leaning processes,…

Noble Metal Nanoparticles for Biosensing Applications

PubMed Central

Doria, Gonçalo; Conde, João; Veigas, Bruno; Giestas, Leticia; Almeida, Carina; Assunção, Maria; Rosa, João; Baptista, Pedro V.

2012-01-01

In the last decade the use of nanomaterials has been having a great impact in biosensing. In particular, the unique properties of noble metal nanoparticles have allowed for the development of new biosensing platforms with enhanced capabilities in the specific detection of bioanalytes. Noble metal nanoparticles show unique physicochemical properties (such as ease of functionalization via simple chemistry and high surface-to-volume ratios) that allied with their unique spectral and optical properties have prompted the development of a plethora of biosensing platforms. Additionally, they also provide an additional or enhanced layer of application for commonly used techniques, such as fluorescence, infrared and Raman spectroscopy. Herein we review the use of noble metal nanoparticles for biosensing strategies—from synthesis and functionalization to integration in molecular diagnostics platforms, with special focus on those that have made their way into the diagnostics laboratory. PMID:22438731

Genetic Constructor: An Online DNA Design Platform.

PubMed

Bates, Maxwell; Lachoff, Joe; Meech, Duncan; Zulkower, Valentin; Moisy, Anaïs; Luo, Yisha; Tekotte, Hille; Franziska Scheitz, Cornelia Johanna; Khilari, Rupal; Mazzoldi, Florencio; Chandran, Deepak; Groban, Eli

2017-12-15

Genetic Constructor is a cloud Computer Aided Design (CAD) application developed to support synthetic biologists from design intent through DNA fabrication and experiment iteration. The platform allows users to design, manage, and navigate complex DNA constructs and libraries, using a new visual language that focuses on functional parts abstracted from sequence. Features like combinatorial libraries and automated primer design allow the user to separate design from construction by focusing on functional intent, and design constraints aid iterative refinement of designs. A plugin architecture enables contributions from scientists and coders to leverage existing powerful software and connect to DNA foundries. The software is easily accessible and platform agnostic, free for academics, and available in an open-source community edition. Genetic Constructor seeks to democratize DNA design, manufacture, and access to tools and services from the synthetic biology community.

Lab-on-a-chip platforms for quantification of multicellular interactions in bone remodeling.

PubMed

George, Estee L; Truesdell, Sharon L; York, Spencer L; Saunders, Marnie M

2018-04-01

Researchers have been using lab-on-a-chip systems to isolate factors for study, simulate laboratory analysis and model cellular, tissue and organ level processes. The technology is increasing rapidly, but the bone field has been slow to keep pace. Novel models are needed that have the power and flexibility to investigate the elegant and synchronous multicellular interactions that occur in normal bone turnover and in disease states in which remodeling is implicated. By removing temporal and spatial limitations and enabling quantification of functional outcomes, the platforms should provide unique environments that are more biomimetic than single cell type systems while minimizing complex systemic effects of in vivo models. This manuscript details the development and characterization of lab-on-a-chip platforms for stimulating osteocytes and quantifying bone remodeling. Our platforms provide the foundation for a model that can be used to investigate remodeling interactions as a whole or as a standard mechanotransduction tool by which isolated activity can be quantified as a function of load. Copyright © 2018 Elsevier Inc. All rights reserved.

Discovery and bio-optimization of human antibody therapeutics using the XenoMouse® transgenic mouse platform.

PubMed

Foltz, Ian N; Gunasekaran, Kannan; King, Chadwick T

2016-03-01

Since the late 1990s, the use of transgenic animal platforms has transformed the discovery of fully human therapeutic monoclonal antibodies. The first approved therapy derived from a transgenic platform--the epidermal growth factor receptor antagonist panitumumab to treat advanced colorectal cancer--was developed using XenoMouse(®) technology. Since its approval in 2006, the science of discovering and developing therapeutic monoclonal antibodies derived from the XenoMouse(®) platform has advanced considerably. The emerging array of antibody therapeutics developed using transgenic technologies is expected to include antibodies and antibody fragments with novel mechanisms of action and extreme potencies. In addition to these impressive functional properties, these antibodies will be designed to have superior biophysical properties that enable highly efficient large-scale manufacturing methods. Achieving these new heights in antibody drug discovery will ultimately bring better medicines to patients. Here, we review best practices for the discovery and bio-optimization of monoclonal antibodies that fit functional design goals and meet high manufacturing standards. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Functional photonic crystal fiber sensing devices

NASA Astrophysics Data System (ADS)

Villatoro, Joel; Finazzi, Vittoria; Pruneri, Valerio

2011-12-01

We report on a functional, highly reproducible and cost effective sensing platform based on photonic crystal fibers (PCFs). The platform consists of a centimeter-length segment of an index-guiding PCF fusion spliced to standard single mode fibers (SMFs). The voids of the PCF are intentionally sealed over an adequate length in the PCF-SMF interfaces. A microscopic collapsed region in the PCF induces a mode field mismatch which combined with the axial symmetry of the structure allow the efficient excitation and recombination or overlapping of azimuthal symmetric modes in the PCF. The transmission or reflection spectrum of the devices exhibits a high-visibility interference pattern or a single, profound and narrow notch. The interference pattern or the notch position shifts when the length of the PCF experiences microelongations or when liquids or coatings are present on the PCF surface. Thus, the platform here proposed can be useful for sensing diverse parameters such as strain, vibration, pressure, humidity, refractive index, gases, etc. Unlike other PCF-based sensing platforms the multiplexing of the devices here proposed is simple for which it is possible to implement PCF-based sensor arrays or networks.

Open-WiSe: A Solar Powered Wireless Sensor Network Platform

PubMed Central

González, Apolinar; Aquino, Raúl; Mata, Walter; Ochoa, Alberto; Saldaña, Pedro; Edwards, Arthur

2012-01-01

Because battery-powered nodes are required in wireless sensor networks and energy consumption represents an important design consideration, alternate energy sources are needed to provide more effective and optimal function. The main goal of this work is to present an energy harvesting wireless sensor network platform, the Open Wireless Sensor node (WiSe). The design and implementation of the solar powered wireless platform is described including the hardware architecture, firmware, and a POSIX Real-Time Kernel. A sleep and wake up strategy was implemented to prolong the lifetime of the wireless sensor network. This platform was developed as a tool for researchers investigating Wireless sensor network or system integrators. PMID:22969396

Semi-physical Simulation Platform of a Parafoil Nonlinear Dynamic System

NASA Astrophysics Data System (ADS)

Gao, Hai-Tao; Yang, Sheng-Bo; Zhu, Er-Lin; Sun, Qing-Lin; Chen, Zeng-Qiang; Kang, Xiao-Feng

2013-11-01

Focusing on the problems in the process of simulation and experiment on a parafoil nonlinear dynamic system, such as limited methods, high cost and low efficiency we present a semi-physical simulation platform. It is designed by connecting parts of physical objects to a computer, and remedies the defect that a computer simulation is divorced from a real environment absolutely. The main components of the platform and its functions, as well as simulation flows, are introduced. The feasibility and validity are verified through a simulation experiment. The experimental results show that the platform has significance for improving the quality of the parafoil fixed-point airdrop system, shortening the development cycle and saving cost.

Continuous measurement of breast tumour hormone receptor expression: a comparison of two computational pathology platforms.

PubMed

Ahern, Thomas P; Beck, Andrew H; Rosner, Bernard A; Glass, Ben; Frieling, Gretchen; Collins, Laura C; Tamimi, Rulla M

2017-05-01

Computational pathology platforms incorporate digital microscopy with sophisticated image analysis to permit rapid, continuous measurement of protein expression. We compared two computational pathology platforms on their measurement of breast tumour oestrogen receptor (ER) and progesterone receptor (PR) expression. Breast tumour microarrays from the Nurses' Health Study were stained for ER (n=592) and PR (n=187). One expert pathologist scored cases as positive if ≥1% of tumour nuclei exhibited stain. ER and PR were then measured with the Definiens Tissue Studio (automated) and Aperio Digital Pathology (user-supervised) platforms. Platform-specific measurements were compared using boxplots, scatter plots and correlation statistics. Classification of ER and PR positivity by platform-specific measurements was evaluated with areas under receiver operating characteristic curves (AUC) from univariable logistic regression models, using expert pathologist classification as the standard. Both platforms showed considerable overlap in continuous measurements of ER and PR between positive and negative groups classified by expert pathologist. Platform-specific measurements were strongly and positively correlated with one another (r≥0.77). The user-supervised Aperio workflow performed slightly better than the automated Definiens workflow at classifying ER positivity (AUC Aperio =0.97; AUC Definiens =0.90; difference=0.07, 95% CI 0.05 to 0.09) and PR positivity (AUC Aperio =0.94; AUC Definiens =0.87; difference=0.07, 95% CI 0.03 to 0.12). Paired hormone receptor expression measurements from two different computational pathology platforms agreed well with one another. The user-supervised workflow yielded better classification accuracy than the automated workflow. Appropriately validated computational pathology algorithms enrich molecular epidemiology studies with continuous protein expression data and may accelerate tumour biomarker discovery. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Comparison of Online Survey Recruitment Platforms for Hard-to-Reach Pregnant Smoking Populations: Feasibility Study.

PubMed

Ibarra, Jose Luis; Agas, Jessica Marie; Lee, Melissa; Pan, Julia Lily; Buttenheim, Alison Meredith

2018-04-16

Recruiting hard-to-reach populations for health research is challenging. Web-based platforms offer one way to recruit specific samples for research purposes, but little is known about the feasibility of online recruitment and the representativeness and comparability of samples recruited through different Web-based platforms. The objectives of this study were to determine the feasibility of recruiting a hard-to-reach population (pregnant smokers) using 4 different Web-based platforms and to compare participants recruited through each platform. A screener and survey were distributed online through Qualtrics Panel, Soapbox Sample, Reddit, and Amazon Mechanical Turk (mTurk). Descriptive statistics were used to summarize results of each recruitment platform, including eligibility yield, quality yield, income, race, age, and gestational age. Of the 3847 participants screened for eligibility across all 4 Web-based platforms, 535 were eligible and 308 completed the survey. Amazon mTurk yielded the fewest completed responses (n=9), 100% (9/9) of which passed several quality metrics verifying pregnancy and smoking status. Qualtrics Panel yielded 14 completed responses, 86% (12/14) of which passed the quality screening. Soapbox Sample produced 107 completed surveys, 67% (72/107) of which were found to be quality responses. Advertising through Reddit produced the highest completion rate (n=178), but only 29.2% (52/178) of those surveys passed the quality metrics. We found significant differences in eligibility yield, quality yield, age, number of previous pregnancies, age of smoking initiation, current smokers, race, education, and income (P<.001). Although each platform successfully recruited pregnant smokers, results varied in quality, cost, and percentage of complete responses. Moving forward, investigators should pay careful attention to the percentage yield and cost of online recruitment platforms to maximize internal and external validity. ©Jose Luis Ibarra, Jessica Marie Agas, Melissa Lee, Julia Lily Pan, Alison Meredith Buttenheim. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 16.04.2018.

miRiadne: a web tool for consistent integration of miRNA nomenclature.

PubMed

Bonnal, Raoul J P; Rossi, Riccardo L; Carpi, Donatella; Ranzani, Valeria; Abrignani, Sergio; Pagani, Massimiliano

2015-07-01

The miRBase is the official miRNA repository which keeps the annotation updated on newly discovered miRNAs: it is also used as a reference for the design of miRNA profiling platforms. Nomenclature ambiguities generated by loosely updated platforms and design errors lead to incompatibilities among platforms, even from the same vendor. Published miRNA lists are thus generated with different profiling platforms that refer to diverse and not updated annotations. This greatly compromises searches, comparisons and analyses that rely on miRNA names only without taking into account the mature sequences, which is particularly critic when such analyses are carried over automatically. In this paper we introduce miRiadne, a web tool to harmonize miRNA nomenclature, which takes into account the original miRBase versions from 10 up to 21, and annotations of 40 common profiling platforms from nine brands that we manually curated. miRiadne uses the miRNA mature sequence to link miRBase versions and/or platforms to prevent nomenclature ambiguities. miRiadne was designed to simplify and support biologists and bioinformaticians in re-annotating their own miRNA lists and/or data sets. As Ariadne helped Theseus in escaping the mythological maze, miRiadne will help the miRNA researcher in escaping the nomenclature maze. miRiadne is freely accessible from the URL http://www.miriadne.org. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Smart CEI Moncloa: An IoT-based Platform for People Flow and Environmental Monitoring on a Smart University Campus

PubMed Central

Vázquez, Enrique

2017-01-01

Internet of Things platforms for Smart Cities are technologically complex and deploying them at large scale involves high costs and risks. Therefore, pilot schemes that allow validating proof of concepts, experimenting with different technologies and services, and fine-tuning them before migrating them to actual scenarios, are especially important in this context. The IoT platform deployed across the engineering schools of the Universidad Politécnica de Madrid in the Moncloa Campus of International Excellence represents a good example of a test bench for experimentation with Smart City services. This paper presents the main features of this platform, putting special emphasis on the technological challenges faced and on the solutions adopted, as well as on the functionality, services and potential that the platform offers. PMID:29292790

Smart CEI Moncloa: An IoT-based Platform for People Flow and Environmental Monitoring on a Smart University Campus.

PubMed

Alvarez-Campana, Manuel; López, Gregorio; Vázquez, Enrique; Villagrá, Víctor A; Berrocal, Julio

2017-12-08

Internet of Things platforms for Smart Cities are technologically complex and deploying them at large scale involves high costs and risks. Therefore, pilot schemes that allow validating proof of concepts, experimenting with different technologies and services, and fine-tuning them before migrating them to actual scenarios, are especially important in this context. The IoT platform deployed across the engineering schools of the Universidad Politécnica de Madrid in the Moncloa Campus of International Excellence represents a good example of a test bench for experimentation with Smart City services. This paper presents the main features of this platform, putting special emphasis on the technological challenges faced and on the solutions adopted, as well as on the functionality, services and potential that the platform offers.

Design and Evaluation of a new mechatronic platform for assessment and prevention of fall risks

PubMed Central

2012-01-01

Background Studying the responses in human behaviour to external perturbations during daily motor tasks is of key importance for understanding mechanisms of balance control and for investigating the functional response of targeted subjects. Experimental platforms as far developed entail a low number of perturbations and, only in few cases, have been designed to measure variables used at run time to trigger events during a certain motor task. Methods This work introduces a new mechatronic device, named SENLY, that provides balance perturbations while subjects carry out daily motor tasks (e.g., walking, upright stance). SENLY mainly consists of two independently-controlled treadmills that destabilize balance by suddenly perturbing belts movements in the horizontal plane. It is also provided with force sensors, which can be used at run time to estimate the ground reaction forces and identify events along the gait cycle in order to trigger the platform perturbation. The paper also describes the customized procedures adopted to calibrate the platform and the first testing trials aimed at evaluating its performance. Results SENLY allows to measure both vertical ground reaction forces and their related location more precisely and more accurately than other platforms of the same size. Moreover, the platform kinematic and kinetic performance meets all required specifications, with a negligible influence of the instrumental noise. Conclusion A new perturbing platform able to reproduce different slipping paradigms while measuring GRFs at run time in order to enable the asynchronous triggering during the gait cycle was designed and developed. Calibration procedures and pilot tests show that SENLY allows to suitably estimate dynamical features of the load and to standardize experimental sessions, improving the efficacy of functional analysis. PMID:22838638

GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants.

PubMed

Tebel, Katrin; Boldt, Vivien; Steininger, Anne; Port, Matthias; Ebert, Grit; Ullmann, Reinhard

2017-01-06

The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multidimensional data analysis and comparison of patient cohorts are needed to assist in the discrimination of clinically relevant CNVs from others. We developed GenomeCAT, a standalone Java application for the analysis and integrative visualization of CNVs. GenomeCAT is composed of three modules dedicated to the inspection of single cases, comparative analysis of multidimensional data and group comparisons aiming at the identification of recurrent aberrations in patients sharing the same phenotype, respectively. Its flexible import options ease the comparative analysis of own results derived from microarray or NGS platforms with data from literature or public depositories. Multidimensional data obtained from different experiment types can be merged into a common data matrix to enable common visualization and analysis. All results are stored in the integrated MySQL database, but can also be exported as tab delimited files for further statistical calculations in external programs. GenomeCAT offers a broad spectrum of visualization and analysis tools that assist in the evaluation of CNVs in the context of other experiment data and annotations. The use of GenomeCAT does not require any specialized computer skills. The various R packages implemented for data analysis are fully integrated into GenomeCATs graphical user interface and the installation process is supported by a wizard. The flexibility in terms of data import and export in combination with the ability to create a common data matrix makes the program also well suited as an interface between genomic data from heterogeneous sources and external software tools. Due to the modular architecture the functionality of GenomeCAT can be easily extended by further R packages or customized plug-ins to meet future requirements.

NOTE: MMCTP: a radiotherapy research environment for Monte Carlo and patient-specific treatment planning

NASA Astrophysics Data System (ADS)

Alexander, A.; DeBlois, F.; Stroian, G.; Al-Yahya, K.; Heath, E.; Seuntjens, J.

2007-07-01

Radiotherapy research lacks a flexible computational research environment for Monte Carlo (MC) and patient-specific treatment planning. The purpose of this study was to develop a flexible software package on low-cost hardware with the aim of integrating new patient-specific treatment planning with MC dose calculations suitable for large-scale prospective and retrospective treatment planning studies. We designed the software package 'McGill Monte Carlo treatment planning' (MMCTP) for the research development of MC and patient-specific treatment planning. The MMCTP design consists of a graphical user interface (GUI), which runs on a simple workstation connected through standard secure-shell protocol to a cluster for lengthy MC calculations. Treatment planning information (e.g., images, structures, beam geometry properties and dose distributions) is converted into a convenient MMCTP local file storage format designated, the McGill RT format. MMCTP features include (a) DICOM_RT, RTOG and CADPlan CART format imports; (b) 2D and 3D visualization views for images, structure contours, and dose distributions; (c) contouring tools; (d) DVH analysis, and dose matrix comparison tools; (e) external beam editing; (f) MC transport calculation from beam source to patient geometry for photon and electron beams. The MC input files, which are prepared from the beam geometry properties and patient information (e.g., images and structure contours), are uploaded and run on a cluster using shell commands controlled from the MMCTP GUI. The visualization, dose matrix operation and DVH tools offer extensive options for plan analysis and comparison between MC plans and plans imported from commercial treatment planning systems. The MMCTP GUI provides a flexible research platform for the development of patient-specific MC treatment planning for photon and electron external beam radiation therapy. The impact of this tool lies in the fact that it allows for systematic, platform-independent, large-scale MC treatment planning for different treatment sites. Patient recalculations were performed to validate the software and ensure proper functionality.

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges.

PubMed

Yin, Zekun; Lan, Haidong; Tan, Guangming; Lu, Mian; Vasilakos, Athanasios V; Liu, Weiguo

2017-01-01

The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics.

Modulating Cellular Recombination Potential through Alterations in RecA Structure and Regulation

PubMed Central

Bakhlanova, Irina V.; Dudkina, Alexandra V.; Baitin, Dima M.; Knight, Kendall L.; Cox, Michael M.; Lanzov, Vladislav A.

2010-01-01

The wild type E. coli RecA protein is a recombinase platform with unrealized recombination potential. We have explored the factors affecting recombination during conjugation with a quantitative assay. Regulatory proteins that affect RecA function have the capacity to increase or decrease recombination frequencies by factors up to 6 fold. Autoinhibition by the RecA C-terminus can affect recombination frequency by factors up to 4 fold. The greatest changes in recombination frequency measured here are brought about by point mutations in the recA gene. RecA variants can increase recombination frequencies by more than 50 fold. The RecA protein thus possesses an inherently broad functional range. The RecA protein of Escherichia coli (EcRecA) is not optimized for recombination function. Instead, much of the recombination potential of EcRecA is structurally suppressed, probably reflecting cellular requirements. One point mutation in EcRecA with a particularly dramatic effect on recombination frequency, D112R, exhibits an enhanced capacity to load onto SSB-coated ssDNA, overcome the effects of regulatory proteins such as PsiB and RecX, and to pair homologous DNAs. Comparisons of key RecA protein mutants reveal two components to RecA recombination function – filament formation and the inherent DNA pairing activity of the formed filaments. PMID:21143322

Microfluidic platform for optimization of crystallization conditions

NASA Astrophysics Data System (ADS)

Zhang, Shuheng; Gerard, Charline J. J.; Ikni, Aziza; Ferry, Gilles; Vuillard, Laurent M.; Boutin, Jean A.; Ferte, Nathalie; Grossier, Romain; Candoni, Nadine; Veesler, Stéphane

2017-08-01

We describe a universal, high-throughput droplet-based microfluidic platform for crystallization. It is suitable for a multitude of applications, due to its flexibility, ease of use, compatibility with all solvents and low cost. The platform offers four modular functions: droplet formation, on-line characterization, incubation and observation. We use it to generate droplet arrays with a concentration gradient in continuous long tubing, without using surfactant. We control droplet properties (size, frequency and spacing) in long tubing by using hydrodynamic empirical relations. We measure droplet chemical composition using both an off-line and a real-time on-line method. Applying this platform to a complicated chemical environment, membrane proteins, we successfully handle crystallization, suggesting that the platform is likely to perform well in other circumstances. We validate the platform for fine-gradient screening and optimization of crystallization conditions. Additional on-line detection methods may well be integrated into this platform in the future, for instance, an on-line diffraction technique. We believe this method could find applications in fields such as fluid interaction engineering, live cell study and enzyme kinetics.

SMART Platforms: Building the App Store for Biosurveillance

PubMed Central

Mandl, Kenneth D.

2013-01-01

Objective To enable public health departments to develop “apps” to run on electronic health records (EHRs) for (1) biosurveillance and case reporting and (2) delivering alerts to the point of care. We describe a novel health information technology platform with substitutable apps constructed around core services enabling EHRs to function as iPhone-like platforms. Introduction Health care information is a fundamental source of data for biosurveillance, yet configuring EHRs to report relevant data to health departments is technically challenging, labor intensive, and often requires custom solutions for each installation. Public health agencies wishing to deliver alerts to clinicians also must engage in an endless array of one-off systems integrations. Despite a $48B investment in HIT, and meaningful use criteria requiring reporting to biosurveillance systems, most vendor electronic health records are architected monolithically, making modification difficult for hospitals and physician practices. An alternative approach is to reimagine EHRs as iPhone-like platforms supporting substitutable apps-based functionality. Substitutability is the capability inherent in a system of replacing one application with another of similar functionality. Methods Substitutability requires that the purchaser of an app can replace one application with another without being technically expert, without requiring re-engineering other applications that they are using, and without having to consult or require assistance of any of the vendors of previously installed or currently installed applications. Apps necessarily compete with each other promoting progress and adaptability. The Substitutable Medical Applications, Reusable Technologies (SMART) Platforms project is funded by a $15M grant from Office of the National Coordinator of Health Information Technology’s Strategic Health IT Advanced Research Projects (SHARP) Program. All SMART standards are open and the core software is open source. The SMART project promotes substitutability through an application programming interface (API) that can be adopted as part of a “container” built around by a wide variety of HIT, providing readonly access to the underlying data model and a software development toolkit to readily create apps. SMART containers are HIT systems, that have implemented the SMART API or a portion of it. Containers marshal data sources and present them consistently across the SMART API. SMART applications consume the API and are substitutable. Results SMART provides a common platform supporting an “app store for biosurveillance” as an approach to enabling one stop shopping for public health departments—to create an app once, and distribute it everywhere. Further, such apps can be readily updated or created—for example, in the case of an emerging infection, an app may be designed to collect additional data at emergency department triage. Or a public health department may widely distribute an app, interoperable with any SMART-enabled EMR, that delivers contextualized alerts when patient electronic records are opened, or through background processes. SMART has sparked an ecosystem of apps developers and attracted existing health information technology platforms to adopt the SMART API—including, traditional, open source, and next generation EHRs, patient-facing platforms and health information exchanges. SMART-enabled platforms to date include the Cerner EMR, the WorldVista EHR, the OpenMRS EHR, the i2b2 analytic platform, and the Indivo X personal health record. The SMART team is working with the Mirth Corporation, to SMART-enable the HealthBridge and Redwood MedNet Health Information Exchanges. We have demonstrated that a single SMART app can run, unmodified, in all of these environments, as long as the underlying platform collects the required data types. Major EHR vendors are currently adapting the SMART API for their products. Conclusions The SMART system enables nimble customization of any electronic health record system to create either a reporting function (outgoing communication) or an alerting function (incoming communication) establishing a technology for a robust linkage between public health and clinical environments.

Platform for combined analysis of functional and biomolecular phenotypes of the same cell.

PubMed

Kelbauskas, L; Ashili, S; Zeng, J; Rezaie, A; Lee, K; Derkach, D; Ueberroth, B; Gao, W; Paulson, T; Wang, H; Tian, Y; Smith, D; Reid, B; Meldrum, Deirdre R

2017-03-16

Functional and molecular cell-to-cell variability is pivotal at the cellular, tissue and whole-organism levels. Yet, the ultimate goal of directly correlating the function of the individual cell with its biomolecular profile remains elusive. We present a platform for integrated analysis of functional and transcriptional phenotypes in the same single cells. We investigated changes in the cellular respiration and gene expression diversity resulting from adaptation to repeated episodes of acute hypoxia in a premalignant progression model. We find differential, progression stage-specific alterations in phenotypic heterogeneity and identify cells with aberrant phenotypes. To our knowledge, this study is the first demonstration of an integrated approach to elucidate how heterogeneity at the transcriptional level manifests in the physiologic profile of individual cells in the context of disease progression.

A review of simulation platforms in surgery of the temporal bone.

PubMed

Bhutta, M F

2016-10-01

Surgery of the temporal bone is a high-risk activity in an anatomically complex area. Simulation enables rehearsal of such surgery. The traditional simulation platform is the cadaveric temporal bone, but in recent years other simulation platforms have been created, including plastic and virtual reality platforms. To undertake a review of simulation platforms for temporal bone surgery, specifically assessing their educational value in terms of validity and in enabling transition to surgery. Systematic qualitative review. Search of the Pubmed, CINAHL, BEI and ERIC databases. Assessment of reported outcomes in terms of educational value. A total of 49 articles were included, covering cadaveric, animal, plastic and virtual simulation platforms. Cadaveric simulation is highly rated as an educational tool, but there may be a ceiling effect on educational outcomes after drilling 8-10 temporal bones. Animal models show significant anatomical variation from man. Plastic temporal bone models offer much potential, but at present lack sufficient anatomical or haptic validity. Similarly, virtual reality platforms lack sufficient anatomical or haptic validity, but with technological improvements they are advancing rapidly. At present, cadaveric simulation remains the best platform for training in temporal bone surgery. Technological advances enabling improved materials or modelling mean that in the future plastic or virtual platforms may become comparable to cadaveric platforms, and also offer additional functionality including patient-specific simulation from CT data. © 2015 John Wiley & Sons Ltd.

Increasing Flight Software Reuse with OpenSatKit

NASA Technical Reports Server (NTRS)

McComas, David C.

2018-01-01

In January 2015 the NASA Goddard Space Flight Center (GSFC) released the Core Flight System (cFS) as open source under the NASA Open Source Agreement (NOSA) license. The cFS is based on flight software (FSW) developed for 12 spacecraft spanning nearly two decades of effort and it can provide about a third of the FSW functionality for a low-earth orbiting scientific spacecraft. The cFS is a FSW framework that is portable, configurable, and extendable using a product line deployment model. However, the components are maintained separately so the user must configure, integrate, and deploy them as a cohesive functional system. This can be very challenging especially for organizations such as universities building cubesats that have minimal experience developing FSW. Supporting universities was one of the primary motivators for releasing the cFS under NOSA. This paper describes the OpenSatKit that was developed to address the cFS deployment challenges and to serve as a cFS training platform for new users. It provides a fully functional out-of-the box software system that includes NASA's cFS, Ball Aerospace's command and control system COSMOS, and a NASA dynamic simulator called 42. The kit is freely available since all of the components have been released as open source. The kit runs on a Linux platform, includes 8 cFS applications, several kit-specific applications, and built in demos illustrating how to use key application features. It also includes the software necessary to port the cFS to a Raspberry Pi and instructions for configuring COSMOS to communicate with the target. All of the demos and test scripts can be rerun unchanged with the cFS running on the Raspberry Pi. The cFS uses a 3-tiered layered architecture including a platform abstraction layer, a Core Flight Executive (cFE) middle layer, and an application layer. Similar to smart phones, the cFS application layer is the key architectural feature for users to extend the FSW functionality to meet their mission-specific requirements. The platform abstraction layer and the cFE layers go a step further than smart phones by providing a platform-agnostic Application Programmer Interface (API) that allows applications to run unchanged on different platforms. OpenSatKit can serve two significant architectural roles that will further help the adoption of the cFS and help create a community of users that can share assets. First, the kit is being enhanced to automate the integration of applications with the goal of creating a virtual cFS "App Store".. Second, a platform certification test suite can be developed that would allow users to verify the port of the cFS to a new platform. This paper will describe the current state of these efforts and future plans.

Developing a Shared Patient-Centered, Web-Based Medication Platform for Type 2 Diabetes Patients and Their Health Care Providers: Qualitative Study on User Requirements.

PubMed

Bernhard, Gerda; Mahler, Cornelia; Seidling, Hanna Marita; Stützle, Marion; Ose, Dominik; Baudendistel, Ines; Wensing, Michel; Szecsenyi, Joachim

2018-03-27

Information technology tools such as shared patient-centered, Web-based medication platforms hold promise to support safe medication use by strengthening patient participation, enhancing patients' knowledge, helping patients to improve self-management of their medications, and improving communication on medications among patients and health care professionals (HCPs). However, the uptake of such platforms remains a challenge also due to inadequate user involvement in the development process. Employing a user-centered design (UCD) approach is therefore critical to ensure that user' adoption is optimal. The purpose of this study was to identify what patients with type 2 diabetes mellitus (T2DM) and their HCPs regard necessary requirements in terms of functionalities and usability of a shared patient-centered, Web-based medication platform for patients with T2DM. This qualitative study included focus groups with purposeful samples of patients with T2DM (n=25), general practitioners (n=13), and health care assistants (n=10) recruited from regional health care settings in southwestern Germany. In total, 8 semistructured focus groups were conducted. Sessions were audio- and video-recorded, transcribed verbatim, and subjected to a computer-aided qualitative content analysis. Appropriate security and access methods, supported data entry, printing, and sending information electronically, and tracking medication history were perceived as the essential functionalities. Although patients wanted automatic interaction checks and safety alerts, HCPs on the contrary were concerned that unspecific alerts confuse patients and lead to nonadherence. Furthermore, HCPs were opposed to patients' ability to withhold or restrict access to information in the platform. To optimize usability, there was consensus among participants to display information in a structured, chronological format, to provide information in lay language, to use visual aids and customize information content, and align the platform to users' workflow. By employing a UCD, this study provides insight into the desired functionalities and usability of patients and HCPs regarding a shared patient-centered, Web-based medication platform, thus increasing the likelihood to achieve a functional and useful system. Substantial and ongoing engagement by all intended user groups is necessary to reconcile differences in requirements of patients and HCPs, especially regarding medication safety alerts and access control. Moreover, effective training of patients and HCPs on medication self-management (support) and optimal use of the tool will be a prerequisite to unfold the platform's full potential. ©Gerda Bernhard, Cornelia Mahler, Hanna Marita Seidling, Marion Stützle, Dominik Ose, Ines Baudendistel, Michel Wensing, Joachim Szecsenyi. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 27.03.2018.

Flight simulator requirements for airline transport pilot training - An evaluation of motion system design alternatives

NASA Technical Reports Server (NTRS)

Lee, A. T.; Bussolari, S. R.

1986-01-01

The effect of motion platform systems on pilot behavior is considered with emphasis placed on civil aviation applications. A dynamic model for human spatial orientation based on the physiological structure and function of the human vestibular system is presented. Motion platform alternatives were evaluated on the basis of the following motion platform conditions: motion with six degrees-of-freedom required for Phase II simulators and two limited motion conditions. Consideration was given to engine flameout, airwork, and approach and landing scenarios.

Integrated testing system FiTest for diagnosis of PCBA

NASA Astrophysics Data System (ADS)

Bogdan, Arkadiusz; Lesniak, Adam

2016-12-01

This article presents the innovative integrated testing system FiTest for automatic, quick inspection of printed circuit board assemblies (PCBA) manufactured in Surface Mount Technology (SMT). Integration of Automatic Optical Inspection (AOI), In-Circuit Tests (ICT) and Functional Circuit Tests (FCT) resulted in universal hardware platform for testing variety of electronic circuits. The platform provides increased test coverage, decreased level of false calls and optimization of test duration. The platform is equipped with powerful algorithms performing tests in a stable and repetitive way and providing effective management of diagnosis.

A novel multifunctional electrochemical platform for simultaneous detection, elimination, and inactivation of pathogenic bacteria based on the Vancomycin-functionalised AgNPs/3D-ZnO nanorod arrays.

PubMed

Yang, Zhiqing; Wang, Yi; Zhang, Dun

2017-12-15

A novel fast, sensitive, and specific multifunctional electrochemical platform has been proposed for simultaneous detection, elimination, and inactivation of pathogenic bacteria for the first time. The platform is constituted with three-dimensional ZnO nanorod arrays (3D-ZnO) decorated with sliver nanoparticles (AgNPs) and functionalized with vancomycin (Van). Based on the specific recognition of Van for Gram-positive bacteria, the fabricated electrochemical platform has presented high detection sensitivity to Staphylococcus aureus with a low detection limit of 330cfu/mL and adaptable bacterial-elimination efficiency (50%) at low concentrations (1000-2000cfu/mL). Moreover, the platform has shown high antibacterial activity (99.99%) arising from the synergistic germicidal effect of the composited antibacterial AgNPs and Van units. The current work could provide new strategies to construct advanced platforms for simultaneous detection, elimination, and inactivation of various pathogenic bacteria. Copyright © 2017 Elsevier B.V. All rights reserved.

Progress in Open-World, Integrative, Collaborative Science Data Platforms (Invited)

NASA Astrophysics Data System (ADS)

Fox, P. A.

2013-12-01

As collaborative, or network science spreads into more Earth and space science fields, both the participants and their funders have expressed a very strong desire for highly functional data and information capabilities that are a) easy to use, b) integrated in a variety of ways, c) leverage prior investments and keep pace with rapid technical change, and d) are not expensive or time-consuming to build or maintain. In response, and based on our accumulated experience over the last decade and a maturing of several key technical approaches, we have adapted, extended, and integrated several open source applications and frameworks that handle major portions of functionality for these platforms. At minimum, these functions include: an object-type repository, collaboration tools, an ability to identify and manage all key entities in the platform, and an integrated portal to manage diverse content and applications, with varied access levels and privacy options. At a conceptual level, science networks (even small ones) deal with people, and many intellectual artifacts produced or consumed in research, organizational and/our outreach activities, as well as the relations among them. Increasingly these networks are modeled as knowledge networks, i.e. graphs with named and typed relations among the 'nodes'. Nodes can be people, organizations, datasets, events, presentations, publications, videos, meetings, reports, groups, and more. In this heterogeneous ecosystem, it is also important to use a set of common informatics approaches to co-design and co-evolve the needed science data platforms based on what real people want to use them for. In this contribution, we present our methods and results for information modeling, adapting, integrating and evolving a networked data science and information architecture based on several open source technologies (Drupal, VIVO, the Comprehensive Knowledge Archive Network; CKAN, and the Global Handle System; GHS). In particular we present both the instantiation of this data platform for the Deep Carbon Observatory, including key functional and non-functional attributes, how the smart mediation among the components is modeled and managed, and discuss its general applicability.

Research resource: Update and extension of a glycoprotein hormone receptors web application.

PubMed

Kreuchwig, Annika; Kleinau, Gunnar; Kreuchwig, Franziska; Worth, Catherine L; Krause, Gerd

2011-04-01

The SSFA-GPHR (Sequence-Structure-Function-Analysis of Glycoprotein Hormone Receptors) database provides a comprehensive set of mutation data for the glycoprotein hormone receptors (covering the lutropin, the FSH, and the TSH receptors). Moreover, it provides a platform for comparison and investigation of these homologous receptors and helps in understanding protein malfunctions associated with several diseases. Besides extending the data set (> 1100 mutations), the database has been completely redesigned and several novel features and analysis tools have been added to the web site. These tools allow the focused extraction of semiquantitative mutant data from the GPHR subtypes and different experimental approaches. Functional and structural data of the GPHRs are now linked interactively at the web interface, and new tools for data visualization (on three-dimensional protein structures) are provided. The interpretation of functional findings is supported by receptor morphings simulating intramolecular changes during the activation process, which thus help to trace the potential function of each amino acid and provide clues to the local structural environment, including potentially relocated spatial counterpart residues. Furthermore, double and triple mutations are newly included to allow the analysis of their functional effects related to their spatial interrelationship in structures or homology models. A new important feature is the search option and data visualization by interactive and user-defined snake-plots. These new tools allow fast and easy searches for specific functional data and thereby give deeper insights in the mechanisms of hormone binding, signal transduction, and signaling regulation. The web application "Sequence-Structure-Function-Analysis of GPHRs" is accessible on the internet at http://www.ssfa-gphr.de/.

CONRAD—A software framework for cone-beam imaging in radiology

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

Maier, Andreas; Choi, Jang-Hwan; Riess, Christian

2013-11-15

Purpose: In the community of x-ray imaging, there is a multitude of tools and applications that are used in scientific practice. Many of these tools are proprietary and can only be used within a certain lab. Often the same algorithm is implemented multiple times by different groups in order to enable comparison. In an effort to tackle this problem, the authors created CONRAD, a software framework that provides many of the tools that are required to simulate basic processes in x-ray imaging and perform image reconstruction with consideration of nonlinear physical effects.Methods: CONRAD is a Java-based state-of-the-art software platform withmore » extensive documentation. It is based on platform-independent technologies. Special libraries offer access to hardware acceleration such as OpenCL. There is an easy-to-use interface for parallel processing. The software package includes different simulation tools that are able to generate up to 4D projection and volume data and respective vector motion fields. Well known reconstruction algorithms such as FBP, DBP, and ART are included. All algorithms in the package are referenced to a scientific source.Results: A total of 13 different phantoms and 30 processing steps have already been integrated into the platform at the time of writing. The platform comprises 74.000 nonblank lines of code out of which 19% are used for documentation. The software package is available for download at http://conrad.stanford.edu. To demonstrate the use of the package, the authors reconstructed images from two different scanners, a table top system and a clinical C-arm system. Runtimes were evaluated using the RabbitCT platform and demonstrate state-of-the-art runtimes with 2.5 s for the 256 problem size and 12.4 s for the 512 problem size.Conclusions: As a common software framework, CONRAD enables the medical physics community to share algorithms and develop new ideas. In particular this offers new opportunities for scientific collaboration and quantitative performance comparison between the methods of different groups.« less

[Usefulness of an online education platform for the medical and surgical emergencies specialty in Mexico].

PubMed

Loria-Castellanos, Jorge

2014-01-01

Determine the usefulness of a Moodle-type education platform for knowledge development with residents in the medical and surgical emergencies (MSE) specialty. This quasi-experimental study compared the departmental evaluations of MSE residents in two Mexican hospital units after they did their academic work using different educational strategies. The control group used a traditional format (classroom-style teaching with guided discussion), while the comparison group had access to a variety of resources (forums, chat, wikis, downloaded files) on a Moodle-type platform. Nonparametric statistics were used. The study was conducted during the 2010 - 2011 and 2011 - 2012 academic years. Three versions of the course were made available online, geared to the academic level of the residents (first, second, or third year). There were statistically significant differences in the mid-year evaluations, and improvements were even greater in the evaluations at the end of the academic year, especially for the third-year residents. In both academic years, the mid-year evaluations reported that only one resident in the control group performed within the average range, while the majority were in the lower range. The resources most used with the platform Moodle were downloaded files (77%) and the forum (63%). Still, 46.4% of the residents said that they encountered some type of limitation when they used the platform, the main one being lack of time (76.9%). The Moodle-type education platform appears to be useful and to offer greater opportunities for knowledge development compared with the traditional strategies. It is recommended that educational strategies based on Moodle-type platforms be implemented for MSE and other medical specialties.

Comparison of three multiplex gastrointestinal platforms for the detection of gastroenteritis viruses

PubMed Central

Chhabra, Preeti; Gregoricus, Nicole; Weinberg, Geoffrey A.; Halasa, Natasha; Chappell, James; Hassan, Ferdaus; Selvarangan, Rangaraj; Mijatovic-Rustempasic, Slavica; Ward, M. Leanne; Bowen, Michael; Payne, Daniel C.; Vinjé, Jan

2018-01-01

Background Viruses are major etiological agents of childhood gastroenteritis. In recent years, several molecular platforms for the detection of viral enteric pathogens have become available. Objective/study design We evaluated the performance of three multiplex platforms including Biofire’s Gastrointestinal Panel (FilmArray), Luminex xTAG® Gastrointestinal Pathogen Panel (GPP), and the TaqMan Array Card (TAC) for the detection of five gastroenteritis viruses using a coded panel of 300 archived stool samples. Results The FilmArray detected a virus in 199 (96.1%) and the TAC in 172 (83.1%) of the 207 samples (187 samples positive for a single virus and 20 samples positive for more than one virus) whereas the GPP detected a virus in 100 (78.7%) of the 127 (97 positive for one virus and three positive for more than one virus) samples. Overall the clinical accuracy was highest for the FilmArray (98%) followed by TAC (97.2%) and GPP (96.9%). The sensitivity of the FilmArray, GPP and TAC platforms was highest for rotavirus (100%, 95.8%, and 89.6%, respectively) and lowest for adenovirus type 40/41 (97.4%, 57.9% and 68.4%). The specificity of the three platforms ranged from 95.6% (rotavirus) to 99.6% (norovirus/sapovirus) for the FilmArray, 99.6% (norovirus) to 100% (rotavirus/adenovirus) for GPP, and 98.9% (astrovirus) to 100% (rotavirus/sapovirus) for TAC. Conclusion The FilmArray demonstrated the best analytical performance followed by TAC. In recent years, the availability of multi-enteric molecular testing platforms has increased significantly and our data highlight the strengths and weaknesses of these platforms. PMID:28889082

Developing a Shared Patient-Centered, Web-Based Medication Platform for Type 2 Diabetes Patients and Their Health Care Providers: Qualitative Study on User Requirements

PubMed Central

Mahler, Cornelia; Seidling, Hanna Marita; Stützle, Marion; Ose, Dominik; Baudendistel, Ines; Wensing, Michel; Szecsenyi, Joachim

2018-01-01

Background Information technology tools such as shared patient-centered, Web-based medication platforms hold promise to support safe medication use by strengthening patient participation, enhancing patients’ knowledge, helping patients to improve self-management of their medications, and improving communication on medications among patients and health care professionals (HCPs). However, the uptake of such platforms remains a challenge also due to inadequate user involvement in the development process. Employing a user-centered design (UCD) approach is therefore critical to ensure that user’ adoption is optimal. Objective The purpose of this study was to identify what patients with type 2 diabetes mellitus (T2DM) and their HCPs regard necessary requirements in terms of functionalities and usability of a shared patient-centered, Web-based medication platform for patients with T2DM. Methods This qualitative study included focus groups with purposeful samples of patients with T2DM (n=25), general practitioners (n=13), and health care assistants (n=10) recruited from regional health care settings in southwestern Germany. In total, 8 semistructured focus groups were conducted. Sessions were audio- and video-recorded, transcribed verbatim, and subjected to a computer-aided qualitative content analysis. Results Appropriate security and access methods, supported data entry, printing, and sending information electronically, and tracking medication history were perceived as the essential functionalities. Although patients wanted automatic interaction checks and safety alerts, HCPs on the contrary were concerned that unspecific alerts confuse patients and lead to nonadherence. Furthermore, HCPs were opposed to patients’ ability to withhold or restrict access to information in the platform. To optimize usability, there was consensus among participants to display information in a structured, chronological format, to provide information in lay language, to use visual aids and customize information content, and align the platform to users’ workflow. Conclusions By employing a UCD, this study provides insight into the desired functionalities and usability of patients and HCPs regarding a shared patient-centered, Web-based medication platform, thus increasing the likelihood to achieve a functional and useful system. Substantial and ongoing engagement by all intended user groups is necessary to reconcile differences in requirements of patients and HCPs, especially regarding medication safety alerts and access control. Moreover, effective training of patients and HCPs on medication self-management (support) and optimal use of the tool will be a prerequisite to unfold the platform’s full potential. PMID:29588269

Massive and Reproducible Production of Liver Buds Entirely from Human Pluripotent Stem Cells.

PubMed

Takebe, Takanori; Sekine, Keisuke; Kimura, Masaki; Yoshizawa, Emi; Ayano, Satoru; Koido, Masaru; Funayama, Shizuka; Nakanishi, Noriko; Hisai, Tomoko; Kobayashi, Tatsuya; Kasai, Toshiharu; Kitada, Rina; Mori, Akira; Ayabe, Hiroaki; Ejiri, Yoko; Amimoto, Naoki; Yamazaki, Yosuke; Ogawa, Shimpei; Ishikawa, Momotaro; Kiyota, Yasujiro; Sato, Yasuhiko; Nozawa, Kohei; Okamoto, Satoshi; Ueno, Yasuharu; Taniguchi, Hideki

2017-12-05

Organoid technology provides a revolutionary paradigm toward therapy but has yet to be applied in humans, mainly because of reproducibility and scalability challenges. Here, we overcome these limitations by evolving a scalable organ bud production platform entirely from human induced pluripotent stem cells (iPSC). By conducting massive "reverse" screen experiments, we identified three progenitor populations that can effectively generate liver buds in a highly reproducible manner: hepatic endoderm, endothelium, and septum mesenchyme. Furthermore, we achieved human scalability by developing an omni-well-array culture platform for mass producing homogeneous and miniaturized liver buds on a clinically relevant large scale (>10 8 ). Vascularized and functional liver tissues generated entirely from iPSCs significantly improved subsequent hepatic functionalization potentiated by stage-matched developmental progenitor interactions, enabling functional rescue against acute liver failure via transplantation. Overall, our study provides a stringent manufacturing platform for multicellular organoid supply, thus facilitating clinical and pharmaceutical applications especially for the treatment of liver diseases through multi-industrial collaborations. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Leveraging zinc interstitials and oxygen vacancies for sensitive biomolecule detection through selective surface functionalization

NASA Astrophysics Data System (ADS)

Radha Shanmugam, Nandhinee; Muthukumar, Sriram; Chaudhry, Shajee; Prasad, Shalini

2015-03-01

In this study, functionally engineered EIS technique was implemented to investigate the influence of surface functionalization on sensitivity of biomolecule detection using nanostructured ZnO platform. Organic molecules with thiol and carboxylic functional groups were chosen to control biomolecule immobilization on zinc and oxygen-terminated 2D planar and 1D nanostructured ZnO surfaces. The amount of functionalization and its influence on charge perturbations at the ZnO-electrolyte interface were studied using fluorescence and EIS measurements. We observed the dependence of charge transfer on both the polarity of platform and concentration of cross-linker molecules. Such selectively modified surfaces were used for detection of cortisol, a major stress indicator. Results demonstrated preferential binding of thiol groups to Zn terminations and thus leveraging ZnO interstitials increases the sensitivity of detection over larger dynamic range with detection limit at 10fg/mL.

Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis.

PubMed

McCourt, Clare M; McArt, Darragh G; Mills, Ken; Catherwood, Mark A; Maxwell, Perry; Waugh, David J; Hamilton, Peter; O'Sullivan, Joe M; Salto-Tellez, Manuel

2013-01-01

Next Generation Sequencing (NGS) has the potential of becoming an important tool in clinical diagnosis and therapeutic decision-making in oncology owing to its enhanced sensitivity in DNA mutation detection, fast-turnaround of samples in comparison to current gold standard methods and the potential to sequence a large number of cancer-driving genes at the one time. We aim to test the diagnostic accuracy of current NGS technology in the analysis of mutations that represent current standard-of-care, and its reliability to generate concomitant information on other key genes in human oncogenesis. Thirteen clinical samples (8 lung adenocarcinomas, 3 colon carcinomas and 2 malignant melanomas) already genotyped for EGFR, KRAS and BRAF mutations by current standard-of-care methods (Sanger Sequencing and q-PCR), were analysed for detection of mutations in the same three genes using two NGS platforms and an additional 43 genes with one of these platforms. The results were analysed using closed platform-specific proprietary bioinformatics software as well as open third party applications. Our results indicate that the existing format of the NGS technology performed well in detecting the clinically relevant mutations stated above but may not be reliable for a broader unsupervised analysis of the wider genome in its current design. Our study represents a diagnostically lead validation of the major strengths and weaknesses of this technology before consideration for diagnostic use.

Development and Validation of an Interactive Internet Platform for Older People: The Healthy Ageing Through Internet Counselling in the Elderly Study.

PubMed

Jongstra, Susan; Beishuizen, Cathrien; Andrieu, Sandrine; Barbera, Mariagnese; van Dorp, Matthijs; van de Groep, Bram; Guillemont, Juliette; Mangialasche, Francesca; van Middelaar, Tessa; Moll van Charante, Eric; Soininen, Hilkka; Kivipelto, Miia; Richard, Edo

2017-02-01

A myriad of Web-based applications on self-management have been developed, but few focus on older people. In the face of global aging, older people form an important target population for cardiovascular prevention. This article describes the full development of an interactive Internet platform for older people, which was designed for the Healthy Ageing Through Internet Counselling in the Elderly (HATICE) study. We provide recommendations to design senior-friendly Web-based applications for a new approach to multicomponent cardiovascular prevention. The development of the platform followed five phases: (1) conceptual framework; (2) platform concept and functional design; (3) platform building (software and content); (4) testing and pilot study; and (5) final product. We performed a meta-analysis, reviewed guidelines for cardiovascular diseases, and consulted end users, experts, and software developers to create the platform concept and content. The software was built in iterative cycles. In the pilot study, 41 people aged ≥65 years used the platform for 8 weeks. Participants used the interactive features of the platform and appreciated the coach support. During all phases adjustments were made to incorporate all improvements from the previous phases. The final platform is a personal, secured, and interactive platform supported by a coach. When carefully designed, an interactive Internet platform is acceptable and feasible for use by older people with basic computer skills. To improve acceptability by older people, we recommend involving the end users in the process of development, to personalize the platform and to combine the application with human support. The interactive HATICE platform will be tested for efficacy in a multinational randomized controlled trial (ISRCTN48151589).

Nitrogen-containing polymers as a platform for CO2 electroreduction.

PubMed

Ponnurangam, Sathish; Chernyshova, Irina V; Somasundaran, Ponisseril

2017-06-01

Heterogeneous electroreduction of CO 2 has received considerable attention in the past decade. However, none of the earlier reviews has been dedicated to nitrogen-containing polymers (N-polymers) as an emerging platform for conversion of CO 2 to industrially useful chemicals. The term 'platform' is used here to underscore that the role of N-polymers is not only to serve as direct catalysts (through loaded metals) but also as co-catalysts/promoters and stabilizing agents. This review covers the current state, advantages, challenges, and prospects of the application of N-polymer-metal composites, also referred as polymer functionalized, coated, or modified electrodes, as well as functional hybrid materials, for the electrocatalytic conversion of CO 2 . It briefly surveys the efficiencies of the N-polymer-metal electrodes already used for this application, methods of their fabrication, and proposed mechanisms of their catalytic activities. Copyright © 2016 Elsevier B.V. All rights reserved.

Strategies to Maximize the Potential of Marine Biomaterials as a Platform for Cell Therapy

PubMed Central

Kim, Hyeongmin; Lee, Jaehwi

2016-01-01

Marine biopolymers have been explored as a promising cell therapy system for efficient cell delivery and tissue engineering. However, the marine biomaterial-based systems themselves have exhibited limited performance in terms of maintenance of cell viability and functions, promotion of cell proliferation and differentiation as well as cell delivery efficiency. Thus, numerous novel strategies have been devised to improve cell therapy outcomes. The strategies include optimization of physical and biochemical properties, provision of stimuli-responsive functions, and design of platforms for efficient cell delivery and tissue engineering. These approaches have demonstrated substantial improvement of therapeutic outcomes in a variety of research settings. In this review, therefore, research progress made with marine biomaterials as a platform for cell therapy is reported along with current research directions to further advance cell therapies as a tool to cure incurable diseases. PMID:26821034

Bioinspired interface for nanobiodevices based on phospholipid polymer chemistry

PubMed Central

Ishihara, Kazuhiko; Takai, Madoka

2009-01-01

This review paper describes novel biointerfaces for nanobiodevices. Biocompatible and non-biofouling surfaces are designed largely based on cell membrane structure, and the preparation and functioning of the bioinspired interface are evaluated and compared between living and artificial systems. A molecular assembly of polymers with a phospholipid polar group has been developed as the platform of the interface. At the surface, protein adsorption is effectively reduced and the subsequent bioreactions are suppressed. Through this platform, biomolecules with a high affinity to the specific molecules are introduced under mild conditions. The activity of the biomolecules is retained even after immobilization. This bioinspired interface is adapted to construct bionanodevices, that is, microfluidic chips and nanoparticles for capturing target molecules and cells. The interface functions well and has a very high efficiency for biorecognition. This bioinspired interface is a promising universal platform that integrates various fields of science and has useful applications. PMID:19324688

The touchscreen operant platform for testing learning and memory in rats and mice

PubMed Central

Horner, Alexa E.; Heath, Christopher J.; Hvoslef-Eide, Martha; Kent, Brianne A.; Kim, Chi Hun; Nilsson, Simon R. O.; Alsiö, Johan; Oomen, Charlotte A.; Holmes, Andrew; Saksida, Lisa M.; Bussey, Timothy J.

2014-01-01

Summary An increasingly popular method of assessing cognitive functions in rodents is the automated touchscreen platform, on which a number of different cognitive tests can be run in a manner very similar to touchscreen methods currently used to test human subjects. This methodology is low stress (using appetitive, rather than aversive reinforcement), has high translational potential, and lends itself to a high degree of standardisation and throughput. Applications include the study of cognition in rodent models of psychiatric and neurodegenerative diseases (e.g., Alzheimer’s disease, schizophrenia, Huntington’s disease, frontotemporal dementia), and characterisation of the role of select brain regions, neurotransmitter systems and genes in rodents. This protocol describes how to perform four touchscreen assays of learning and memory: Visual Discrimination, Object-Location Paired-Associates Learning, Visuomotor Conditional Learning and Autoshaping. It is accompanied by two further protocols using the touchscreen platform to assess executive function, working memory and pattern separation. PMID:24051959

Microgravity vibration isolation: An optimal control law for the one-dimensional case

NASA Technical Reports Server (NTRS)

Hampton, Richard D.; Grodsinsky, Carlos M.; Allaire, Paul E.; Lewis, David W.; Knospe, Carl R.

1991-01-01

Certain experiments contemplated for space platforms must be isolated from the accelerations of the platform. An optimal active control is developed for microgravity vibration isolation, using constant state feedback gains (identical to those obtained from the Linear Quadratic Regulator (LQR) approach) along with constant feedforward gains. The quadratic cost function for this control algorithm effectively weights external accelerations of the platform disturbances by a factor proportional to (1/omega) exp 4. Low frequency accelerations are attenuated by greater than two orders of magnitude. The control relies on the absolute position and velocity feedback of the experiment and the absolute position and velocity feedforward of the platform, and generally derives the stability robustness characteristics guaranteed by the LQR approach to optimality. The method as derived is extendable to the case in which only the relative positions and velocities and the absolute accelerations of the experiment and space platform are available.

Novel droplet platforms for the detection of disease biomarkers.

PubMed

Zec, Helena; Shin, Dong Jin; Wang, Tza-Huei

2014-09-01

Personalized medicine - healthcare based on individual genetic variation - has the potential to transform the way healthcare is delivered to patients. The promise of personalized medicine has been predicated on the predictive and diagnostic power of genomic and proteomic biomarkers. Biomarker screening may help improve health outcomes, for example, by identifying individuals' susceptibility to diseases and predicting how patients will respond to drugs. Microfluidic droplet technology offers an exciting opportunity to revolutionize the accessibility of personalized medicine. A framework for the role of droplet microfluidics in biomarker detection can be based on two main themes. Emulsion-based microdroplet platforms can provide new ways to measure and detect biomolecules. In addition, microdroplet platforms facilitate high-throughput screening of biomarkers. Meanwhile, surface-based droplet platforms provide an opportunity to develop miniaturized diagnostic systems. These platforms may function as portable benchtop environments that dramatically shorten the transition of a benchtop assay into a point-of-care format.

Design and Implementation of Demand Response Information Interactive Service Platform Based on “Internet Plus” Smart Energy

NASA Astrophysics Data System (ADS)

Cui, Gaoying; Fan, Jie; Qin, Yuchen; Wang, Dong; Chen, Guangyan

2017-05-01

In order to promote the effective use of demand response load side resources, promote the interaction between supply and demand, enhance the level of customer service and achieve the overall utilization of energy, this paper briefly explain the background significance of design demand response information platform and current situation of domestic and foreign development; Analyse the new demand of electricity demand response combined with the application of Internet and big data technology; Design demand response information platform architecture, construct demand responsive system, analyse process of demand response strategy formulate and intelligent execution implement; study application which combined with the big data, Internet and demand response technology; Finally, from information interaction architecture, control architecture and function design perspective design implementation of demand response information platform, illustrate the feasibility of the proposed platform design scheme implemented in a certain extent.

Microgravity vibration isolation: An optimal control law for the one-dimensional case

NASA Technical Reports Server (NTRS)

Hampton, R. D.; Grodsinsky, C. M.; Allaire, P. E.; Lewis, D. W.; Knospe, C. R.

1991-01-01

Certain experiments contemplated for space platforms must be isolated from the accelerations of the platforms. An optimal active control is developed for microgravity vibration isolation, using constant state feedback gains (identical to those obtained from the Linear Quadratic Regulator (LQR) approach) along with constant feedforward (preview) gains. The quadratic cost function for this control algorithm effectively weights external accelerations of the platform disturbances by a factor proportional to (1/omega)(exp 4). Low frequency accelerations (less than 50 Hz) are attenuated by greater than two orders of magnitude. The control relies on the absolute position and velocity feedback of the experiment and the absolute position and velocity feedforward of the platform, and generally derives the stability robustness characteristics guaranteed by the LQR approach to optimality. The method as derived is extendable to the case in which only the relative positions and velocities and the absolute accelerations of the experiment and space platform are available.

Development of FEB Test Platform for ATLAS New Small Wheel Upgrade

NASA Astrophysics Data System (ADS)

Lu, Houbing; Hu, Kun; Wang, Xu; Li, Feng; Han, Liang; Jin, Ge

2016-10-01

This concept of test platform is based on the test requirements of the front-end board (FEB) which is developed for the phase I upgrade of the small Thin Gap Chamber(sTGC) detector on New Small Wheel(NSW) of ATLAS. The front-end electronics system of sTGC consists of 1,536 FEBs with about 322,000 readout of strips, wires and pads in total. A test platform for FEB with up to 256 channels has been designed to keep the testing efficiency at a controllable level. We present the circuit model architecture of the platform, and its functions and implementation as well. The firmware based on Field Programmable Gate Array (FPGA) and the software based on PC have been developed, and basic test methods have been established. FEB readout measurements have been performed in analog injection from the test platform, which will provide a fast and efficient test method for the production of FEB.

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.

Crossing Cross-Platform: Comparing Skills Preferences and Convergence Attitudes in Strategic Communication and News Disciplines

ERIC Educational Resources Information Center

Hubbard, Glenn T.; Kang, Jin-Ae; Crawford, Elizabeth Crisp

2016-01-01

National survey of college mass communication students (N = 247) analyzed attitudes on the teaching of print and electronic media skills, using journalism students as comparison group. Previous research had not explored strategic communication student responses to convergence. Found identity variables within public relations (PR) field related to…

Network-Based Professional Development: A Comparison of Statewide Initiatives.

ERIC Educational Resources Information Center

Shotsberger, Paul G.; Stammen, Ronald; Vetter, Ronald; Blue, Gloria; Greer, Edrie

This paper addresses opportunities and issues related to the use of the World Wide Web and high-speed networks as a delivery vehicle for training educators who are geographically dispersed. The benefits and potential pitfalls of using networks as educational platforms are explored from the perspective of various systems specifically being…

Mission Command and the Starfish Organizational Models: A Comparison of Organizational Philosophies in a Decentralized Combat Environment

DTIC Science & Technology

2015-06-12

market. However, in 2004, Netflix changed the home video entertainment landscape from brick and mortar rental outlets to the DVD-by-mail business...competing companies had very different organizational structures and leadership styles. Amazon stayed true to an online brick and mortar platform

A Comparison Between Genotyping-by-sequencing and Array-based Scoring of SNPs for Genomic Prediction Accuracy in Winter Wheat

USDA-ARS?s Scientific Manuscript database

The utilization of DNA molecular markers in plant breeding to maximize selection response via marker assisted selection (MAS) and genomic selection (GS) has the potential to revolutionize plant breeding. A key factor affecting GS applicability is the choice of molecular marker platform. Genotypying-...

Abstract of Capstone

ERIC Educational Resources Information Center

Pack, Della F.

2013-01-01

At the end of the Fall 2011 semester at Big Sandy Community and Technical College (BSCTC) a comparison of grade patterns in multiple CIS 100-Introduction to Computers courses was analyzed. This analysis found online courses returned a higher failure rate than those taught in a classroom setting. Why was there a difference? Is the platform of…

A Comparison of Psychology Curriculum and Instruction: China & America

ERIC Educational Resources Information Center

Huang, Feifei; Garrett, Marta

2015-01-01

As China becomes a more international platform, studying abroad is an increasingly popular choice for Chinese students. Business is the most popular major Chinese students choose when studying abroad but a growing number of Chinese students are interested in psychology. To ensure a meaningful experience, it is essential to understand the…

OVERVIEW OF AN INTERLABORATORY COLLABORATION ON EVALUATING THE EFFECTS OF MODEL HEPATOTOXICANTS ON HEPATIC GENE EXPRESSION

EPA Science Inventory

Evaluating the Effects of Methapyrilene and Clofibrate on Hepatic Gene Expression: A Collaboration Between Laboratories and a Comparison of Platform and Analytical Approaches

Roger G. Ulrich1, John C. Rockett2, G. Gordon Gibson3 and Syril Pettit4

1 Rosetta Inpharmat...

Forex Trading Game in an Online Classroom with Heterogeneous Student Background

ERIC Educational Resources Information Center

Wang, Huabing

2018-01-01

This article presents a teaching exercise using real-time trading platform in an online international finance course with both finance and non-finance majors. The authors discuss their approach to accommodate to the on-line environment with the emphasis on preparation and flexibility, and present a statistical comparison of performance between…

Mobility as a Fusion Enabler

DTIC Science & Technology

2008-07-01

identification sensor is then VrT where T is some reasonable time in comparison to the approach speed of a potentially hostile contact. In fact, if the...effective range of the identification sensor on the mobile platform is VrT = VrA/Vh = h r V VA Further detail of such analysis is ongoing as part

Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities.

PubMed

Heinz, Hendrik; Ramezani-Dakhel, Hadi

2016-01-21

Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance in silico.

Validation of Ocean Color Remote Sensing Reflectance Using Autonomous Floats

NASA Technical Reports Server (NTRS)

Gerbi, Gregory P.; Boss, Emanuel; Werdell, P. Jeremy; Proctor, Christopher W.; Haentjens, Nils; Lewis, Marlon R.; Brown, Keith; Sorrentino, Diego; Zaneveld, J. Ronald V.; Barnard, Andrew H.;

Cross talk between ceramide and redox signaling: implications for endothelial dysfunction and renal disease.

PubMed

Li, Pin-Lan; Zhang, Yang

2013-01-01

Recent studies have demonstrated that cross talk between ceramide and redox signaling modulates various cell activities and functions and contributes to the development of cardiovascular diseases and renal dysfunctions. Ceramide triggers the generation of reactive oxygen species (ROS) and increases oxidative stress in many mammalian cells and animal models. On the other hand, inhibition of ROS-generating enzymes or treatment of antioxidants impairs sphingomyelinase activation and ceramide production. As a mechanism, ceramide-enriched signaling platforms, special cell membrane rafts (MR) (formerly lipid rafts), provide an important microenvironment to mediate the cross talk of ceramide and redox signaling to exert a corresponding regulatory role on cell and organ functions. In this regard, activation of acid sphingomyelinase and generation of ceramide mediate the formation of ceramide-enriched membrane platforms, where transmembrane signals are transmitted or amplified through recruitment, clustering, assembling, or integration of various signaling molecules. A typical such signaling platform is MR redox signaling platform that is centered on ceramide production and aggregation leading to recruitment and assembling of NADPH oxidase to form an active complex in the cell plasma membrane. This redox signaling platform not only conducts redox signaling or regulation but also facilitates a feedforward amplification of both ceramide and redox signaling. In addition to this membrane MR redox signaling platform, the cross talk between ceramide and redox signaling may occur in other cell compartments. This book chapter focuses on the molecular mechanisms, spatial-temporal regulations, and implications of this cross talk between ceramide and redox signaling, which may provide novel insights into the understanding of both ceramide and redox signaling pathways.

Boulder coastal deposits at Favignana Island rocky coast (Sicily, Italy): Litho-structural and hydrodynamic control

NASA Astrophysics Data System (ADS)

Pepe, Fabrizio; Corradino, Marta; Parrino, Nicolò; Besio, Giovanni; Presti, Valeria Lo; Renda, Pietro; Calcagnile, Lucio; Quarta, Gianluca; Sulli, Attilio; Antonioli, Fabrizio

2018-02-01

Boulders are frequently dislodged from rock platforms, transported and deposited along coastal zones by high-magnitude storm waves or tsunamis. Their size and shape are often controlled by the thickness of bedding planes as well as by high-angle to bedding fracture network. We investigate these processes along two coastal areas of Favignana Island by integrating geological data for 81 boulders, 49 rupture surfaces (called sockets) and fracture orientation and spacing with four radiocarbon dates, numerical hydrodynamic analysis, and hindcast numerical simulation data. Boulders are scattered along the carbonate platform as isolated blocks or in small groups, which form, as a whole, a discontinuous berm. Underwater surveys also highlight free boulders with sharp edges and sockets carved out in the rock platform. Boulders are composed of ruditic- to arenitic-size clastic carbonates. Their size ranges from 0.6 to 3.7 m, 0.55 to 2.4 m, and 0.2 to 1 m on the major (A), medium (B), and minor (C) axes, respectively. The highest value of mass estimation is 12.5 t. Almost all of boulders and sockets are characterized by a tabular or bladed shape. The comparisons between a) the fractures spacing and the length of A- and B-axes, and b) the frequency peaks of C-axis with the recurrent thickness of beds measured along the coastal zone demonstrate the litho-structural control in the size and shape of joint-bounded boulders. These comparisons, together with the similarity between the shapes of the boulders and those of the sockets as well as between the lithology of boulders and the areas surrounding the sockets, suggest that blocks originate by detachment from the platform edge. Thus, the most common pre-transport setting is the joint-bounded scenario. Hydrodynamic equations estimate that the storm wave heights necessary to initiate the transport of blocks diverge from 2 m to 8 m for joint-bounded boulders and from few tens of centimeters up to 11 m for submerged boulders. The comparison between the wave heights at the breaking point of the coastal zones with the results of hydrodynamic equations shows that waves approaching the coastline are able to transport all surveyed boulders. Our data suggest that boulders have been transported by several storm events, even in very recent times.

Consistency of Global Modis Aerosol Optical Depths over Ocean on Terra and Aqua Ceres SSF Datasets

NASA Technical Reports Server (NTRS)

Ignatov, Alexander; Minnis, Patrick; Miller, Walter F.; Wielicki, Bruce A.; Remer, Lorraine

2006-01-01

Aerosol retrievals over ocean from the Moderate Resolution Imaging Spectroradiometer (MODIS) onboard Terra and Aqua platforms are available from the Clouds and the Earth's Radiant Energy System (CERES) Single Scanner Footprint (SSF) datasets generated at NASA Langley Research Center (LaRC). Two aerosol products are reported side-by-side. The primary M product is generated by sub-setting and remapping the multi-spectral (0.47-2.1 micrometer) MODIS produced oceanic aerosol (MOD04/MYD04 for Terra/Aqua) onto CERES footprints. M*D04 processing uses cloud screening and aerosol algorithms developed by the MODIS science team. The secondary AVHRR-like A product is generated in only two MODIS bands 1 and 6 (on Aqua, bands 1 and 7). The A processing uses the CERES cloud screening algorithm, and NOAA/NESDIS glint identification, and single-channel aerosol retrieval algorithms. The M and A products have been documented elsewhere and preliminarily compared using 2 weeks of global Terra CERES SSF Edition 1A data in which the M product was based on MOD04 collection 3. In this study, the comparisons between the M and A aerosol optical depths (AOD) in MODIS band 1 (0.64 micrometers), tau(sub 1M) and tau(sub 1A) are re-examined using 9 days of global CERES SSF Terra Edition 2A and Aqua Edition 1B data from 13 - 21 October 2002, and extended to include cross-platform comparisons. The M and A products on the new CERES SSF release are generated using the same aerosol algorithms as before, but with different preprocessing and sampling procedures, lending themselves to a simple sensitivity check to non-aerosol factors. Both tau(sub 1M) and tau(sub 1A) generally compare well across platforms. However, the M product shows some differences, which increase with ambient cloud amount and towards the solar side of the orbit. Three types of comparisons conducted in this study - cross-platform, cross-product, and cross-release confirm the previously made observation that the major area for improvement in the current aerosol processing lies in a more formalized and standardized sampling (and most importantly, cloud screening) whereas optimization of the aerosol algorithm is deemed to be an important yet less critical element.

The Urban Exploitation Platform - An instrument for the global provision of indicators related to sustainable cities and communities

NASA Astrophysics Data System (ADS)

Esch, Thomas; Asamer, Hubert; Hirner, Andreas; Marconcini, Mattia; Metz, Annekatrin; Uereyen, Soner; Zeidler, Julian; Boettcher, Martin; Permana, Hans; Boissier, Enguerran; Mathot, Emmanuel; Soukop, Tomas; Balhar, Jakub; Svaton, Vaclav; Kuchar, Stepan

2017-04-01

The Sentinel fleet will provide a so-far unique coverage with Earth Observation (EO) data and therewith new opportunities for the implementation of methodologies to generate innovative geo-information products and services supporting the SDG targets. It is here where the TEP Urban project is supposed to initiate a step change by providing an open and participatory platform that allows any interested user to easily exploit large-volume EO data pools, in particular those of the European Sentinel and the US Landsat missions, and derive thematic geo-information, metrics and indicators related to the status and development of the built environment. Key component of TEP Urban initiative is the implementation of a web-based platform (https://urban-tep.eo.esa.int) employing distributed high-level computing infrastructures and providing key functionalities for i) high-performance access to satellite imagery and other data sources such as statistics or topographic data, ii) state-of-the-art pre-processing, analysis, and visualization techniques, iii) customized development and dissemination of algorithms, products and services, and iv) networking and communication. This contribution introduces the main facts about the TEP Urban platform, including a description of the general objectives, the platform systems design and functionalities, and the available portfolio of products and services that can directly serve the global provision of indicators for SDG targets, in particular related to SDG 11.

a Real-Time GIS Platform for High Sour Gas Leakage Simulation, Evaluation and Visualization

NASA Astrophysics Data System (ADS)

Li, M.; Liu, H.; Yang, C.

2015-07-01

The development of high-sulfur gas fields, also known as sour gas field, is faced with a series of safety control and emergency management problems. The GIS-based emergency response system is placed high expectations under the consideration of high pressure, high content, complex terrain and highly density population in Sichuan Basin, southwest China. The most researches on high hydrogen sulphide gas dispersion simulation and evaluation are used for environmental impact assessment (EIA) or emergency preparedness planning. This paper introduces a real-time GIS platform for high-sulfur gas emergency response. Combining with real-time data from the leak detection systems and the meteorological monitoring stations, GIS platform provides the functions of simulating, evaluating and displaying of the different spatial-temporal toxic gas distribution patterns and evaluation results. This paper firstly proposes the architecture of Emergency Response/Management System, secondly explains EPA's Gaussian dispersion model CALPUFF simulation workflow under high complex terrain and real-time data, thirdly explains the emergency workflow and spatial analysis functions of computing the accident influencing areas, population and the optimal evacuation routes. Finally, a well blow scenarios is used for verify the system. The study shows that GIS platform which integrates the real-time data and CALPUFF models will be one of the essential operational platforms for high-sulfur gas fields emergency management.

Diamond nanoparticles as a way to improve electron transfer in sol-gel L-lactate biosensing platforms.

PubMed

Briones, M; Casero, E; Vázquez, L; Pariente, F; Lorenzo, E; Petit-Domínguez, M D

2016-02-18

In the present work, we have included for the first time diamond nanoparticles (DNPs) in a sol-gel matrix derived from (3-mercaptopropyl)-trimethoxysilane (MPTS) in order to improve electron transfer in a lactate oxidase (LOx) based electrochemical biosensing platform. Firstly, an exhaustive AFM study, including topographical, surface potential (KFM) and capacitance gradient (CG) measurements, of each step involved in the biosensing platform development was performed. The platform is based on gold electrodes (Au) modified with the sol-gel matrix (Au/MPTS) in which diamond nanoparticles (Au/MPTS/DNPs) and lactate oxidase (Au/MPTS/DNPs/LOx) have been included. For the sake of comparison, we have also characterized a gold electrode directly modified with DNPs (Au/DNPs). Secondly, the electrochemical behavior of a redox mediator (hydroxymethyl-ferrocene, HMF) was evaluated at the platforms mentioned above. The response of Au/MPTS/DNPs/LOx towards lactate was obtained. A linear concentration range from 0.053 mM to 1.6 mM, a sensitivity of 2.6 μA mM(-1) and a detection limit of 16 μM were obtained. These analytical properties are comparable to other biosensors, presenting also as advantages that DNPs are inexpensive, environment-friendly and easy-handled nanomaterials. Finally, the developed biosensor was applied for lactate determination in wine samples. Copyright © 2016 Elsevier B.V. All rights reserved.

A low-power multi-modal body sensor network with application to epileptic seizure monitoring.

PubMed

Altini, Marco; Del Din, Silvia; Patel, Shyamal; Schachter, Steven; Penders, Julien; Bonato, Paolo

2011-01-01

Monitoring patients' physiological signals during their daily activities in the home environment is one of the challenge of the health care. New ultra-low-power wireless technologies could help to achieve this goal. In this paper we present a low-power, multi-modal, wearable sensor platform for the simultaneous recording of activity and physiological data. First we provide a description of the wearable sensor platform, and its characteristics with respect to power consumption. Second we present the preliminary results of the comparison between our sensors and a reference system, on healthy subjects, to test the reliability of the detected physiological (electrocardiogram and respiration) and electromyography signals.

Development of a Turbofan Engine Simulation in a Graphical Simulation Environment

NASA Technical Reports Server (NTRS)

Parker, Khary I.; Guo, Ten-Heui

2003-01-01

This paper presents the development of a generic component level model of a turbofan engine simulation with a digital controller, in an advanced graphical simulation environment. The goal of this effort is to develop and demonstrate a flexible simulation platform for future research in propulsion system control and diagnostic technology. A previously validated FORTRAN-based model of a modern, high-performance, military-type turbofan engine is being used to validate the platform development. The implementation process required the development of various innovative procedures, which are discussed in the paper. Open-loop and closed-loop comparisons are made between the two simulations. Future enhancements that are to be made to the modular engine simulation are summarized.

The numerology of T cell functional diversity

PubMed Central

Haining, W. Nicholas

2013-01-01

Memory T cells are heterogeneous in phenotype and function. In this issue of Immunity Newell et al. (2012) use a new flow cytometry platform to show that the functional heterogeneity in the human T cell compartment is even greater than expected. PMID:22284416

Spontaneous emergence of rogue waves in partially coherent waves: A quantitative experimental comparison between hydrodynamics and optics

NASA Astrophysics Data System (ADS)

El Koussaifi, R.; Tikan, A.; Toffoli, A.; Randoux, S.; Suret, P.; Onorato, M.

2018-01-01

Rogue waves are extreme and rare fluctuations of the wave field that have been discussed in many physical systems. Their presence substantially influences the statistical properties of a partially coherent wave field, i.e., a wave field characterized by a finite band spectrum with random Fourier phases. Their understanding is fundamental for the design of ships and offshore platforms. In many meteorological conditions waves in the ocean are characterized by the so-called Joint North Sea Wave Project (JONSWAP) spectrum. Here we compare two unique experimental results: the first one has been performed in a 270 m wave tank and the other in optical fibers. In both cases, waves characterized by a JONSWAP spectrum and random Fourier phases have been launched at the input of the experimental device. The quantitative comparison, based on an appropriate scaling of the two experiments, shows a very good agreement between the statistics in hydrodynamics and optics. Spontaneous emergence of heavy tails in the probability density function of the wave amplitude is observed in both systems. The results demonstrate the universal features of rogue waves and provide a fundamental and explicit bridge between two important fields of research. Numerical simulations are also compared with experimental results.

Spontaneous emergence of rogue waves in partially coherent waves: A quantitative experimental comparison between hydrodynamics and optics.

PubMed

El Koussaifi, R; Tikan, A; Toffoli, A; Randoux, S; Suret, P; Onorato, M

2018-01-01

Rogue waves are extreme and rare fluctuations of the wave field that have been discussed in many physical systems. Their presence substantially influences the statistical properties of a partially coherent wave field, i.e., a wave field characterized by a finite band spectrum with random Fourier phases. Their understanding is fundamental for the design of ships and offshore platforms. In many meteorological conditions waves in the ocean are characterized by the so-called Joint North Sea Wave Project (JONSWAP) spectrum. Here we compare two unique experimental results: the first one has been performed in a 270 m wave tank and the other in optical fibers. In both cases, waves characterized by a JONSWAP spectrum and random Fourier phases have been launched at the input of the experimental device. The quantitative comparison, based on an appropriate scaling of the two experiments, shows a very good agreement between the statistics in hydrodynamics and optics. Spontaneous emergence of heavy tails in the probability density function of the wave amplitude is observed in both systems. The results demonstrate the universal features of rogue waves and provide a fundamental and explicit bridge between two important fields of research. Numerical simulations are also compared with experimental results.

A Comparison Study for DNA Motif Modeling on Protein Binding Microarray.

PubMed

Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Wong, Hau-San

2016-01-01

Transcription factor binding sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, protein binding microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k = 8∼10). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build TFBS (also known as DNA motif) models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement if choosing di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

New platforms for multi-functional ocular lenses: engineering double-sided functionalized nano-coatings.

PubMed

Mehta, Prina; Justo, Lucas; Walsh, Susannah; Arshad, Muhammad S; Wilson, Clive G; O'Sullivan, Ciara K; Moghimi, Seyed M; Vizirianakis, Ioannis S; Avgoustakis, Konstantinos; Fatouros, Dimitris G; Ahmad, Zeeshan

2015-05-01

A scalable platform to prepare multi-functional ocular lenses is demonstrated. Using rapidly dissolving polyvinylpyrrolidone (PVP) as the active stabilizing matrix, both sides of ocular lenses were coated using a modified scaled-up masking electrohydrodynamic atomization (EHDA) technique (flow rates variable between 5 and 10 µL/min, applied voltage 4-11 kV). Each side was coated (using a specially designed flip-able well) selectively with a pre-determined morphology and model drug substance. PVP nanoparticles (inner side, to be in contact with the cornea, mean size

Platform for combined analysis of functional and biomolecular phenotypes of the same cell

PubMed Central

Kelbauskas, L.; Ashili, S.; Zeng, J.; Rezaie, A.; Lee, K.; Derkach, D.; Ueberroth, B.; Gao, W.; Paulson, T.; Wang, H.; Tian, Y.; Smith, D.; Reid, B.; Meldrum, Deirdre R.

2017-01-01

Functional and molecular cell-to-cell variability is pivotal at the cellular, tissue and whole-organism levels. Yet, the ultimate goal of directly correlating the function of the individual cell with its biomolecular profile remains elusive. We present a platform for integrated analysis of functional and transcriptional phenotypes in the same single cells. We investigated changes in the cellular respiration and gene expression diversity resulting from adaptation to repeated episodes of acute hypoxia in a premalignant progression model. We find differential, progression stage-specific alterations in phenotypic heterogeneity and identify cells with aberrant phenotypes. To our knowledge, this study is the first demonstration of an integrated approach to elucidate how heterogeneity at the transcriptional level manifests in the physiologic profile of individual cells in the context of disease progression. PMID:28300162

Objective Integrated Assessment of Functional Outcomes in Reduction Mammaplasty

PubMed Central

Passaro, Ilaria; Malovini, Alberto; Faga, Angela; Toffola, Elena Dalla

2013-01-01

Background: The aim of our study was an objective integrated assessment of the functional outcomes of reduction mammaplasty. Methods: The study involved 17 women undergoing reduction mammaplasty from March 2009 to June 2011. Each patient was assessed before surgery and 2 months postoperatively with the original association of 4 subjective and objective assessment methods: a physiatric clinical examination, the Roland Morris Disability Questionnaire, the Berg Balance Scale, and a static force platform analysis. Results: All of the tests proved multiple statistically significant associated outcomes demonstrating a significant improvement in the functional status following reduction mammaplasty. Surgical correction of breast hypertrophy could achieve both spinal pain relief and recovery of performance status in everyday life tasks, owing to a muscular postural functional rearrangement with a consistent antigravity muscle activity sparing. Pain reduction in turn could reduce the antalgic stiffness and improved the spinal range of motion. In our sample, the improvement of the spinal range of motion in flexion matched a similar improvement in extension. Recovery of a more favorable postural pattern with reduction of the anterior imbalance was demonstrated by the static force stabilometry. Therefore, postoperatively, all of our patients narrowed the gap between the actual body barycenter and the ideal one. The static force platform assessment also consistently confirmed the effectiveness of an accurate clinical examination of functional impairment from breast hypertrophy. Conclusions: The static force platform assessment might help the clinician to support the diagnosis of functional impairment from a breast hypertrophy with objectively based data. PMID:25289256

Marginal bone response of implants with platform switching and non-platform switching abutments in posterior healed sites: a 1-year prospective study

PubMed Central

Wang, Yun-Chi; Kan, Joseph Y K; Rungcharassaeng, Kitichai; Roe, Phillip; Lozada, Jaime L

2015-01-01

Objectives This 1-year prospective study evaluated the implant success rate and marginal bone response of non-submerged implants with platform and non-platform switching abutments in posterior healed sites. Material and methods Nineteen patients (9 male, 10 female) with posterior partially edentulous spaces, between the ages of 23 and 76 (mean = 55.4 years), were included in this study. A total of 30 implants (15 implants restored with platform switching [PS] abutments [control] and 15 implants restored with non-platform switching [NPS] abutments [test]) were assigned between two groups using a randomization procedure. The definitive abutments with conical connections were placed at the time of surgery, and the definitive restorations were placed at 3 months. All patients were evaluated clinically and radiographically using standardized radiographs at time of implant placement (0), 3, 6 and 12 months after implant placement. Data were analyzed using Friedman test with post hoc pairwise comparisons, Mann–Whitney U-test, and Pearson's chi-square test at the significance level of α = 0.05. Results At 12 months, all 30 implants remained osseointegrated corresponding to a 100% success rate. The overall mean marginal bone level change at 12 months was −0.04 ± 0.08 mm for PS group and −0.19 ± 0.16 mm for NPS group. Statistically significant difference in the marginal bone level change was observed between groups at 0 to 12 months and 3 to 12 months (P < 0.05). Conclusions This 1-year randomized control study suggests that when a conical implant–abutment connection is present, similar peri-implant tissue responses can be achieved with platform switching and non-platform switching abutments. PMID:24383912

Slope and basinal deposits adjacent to isolated carbonate platforms in the Indian Ocean: Sedimentology, geomorphology, and a new 1.2 Ma record of highstand shedding

NASA Astrophysics Data System (ADS)

Counts, J. W.; Jorry, S.; Jouet, G.

2017-12-01

Newly analyzed bathymetric, seismic, and core data from carbonate-topped seamounts in the Mozambique Channel reveals a variety of depositional processes and products operating on platform slopes and adjacent basins. Mass transport complexes (including turbidites and debrites), leveed channel systems with basin-floor fans, and contourites are imaged in high resolution in both seafloor maps and cross-section, and show both differences and similarities compared with platform slopes in the Bahamas and elsewhere. In some, though not all, platforms, increased sedimentation can be observed on the leeward margins, and slope rugosity may be asymmetric with respect to prevailing wind direction. Deposition is also controlled by glacial-interglacial cycles; cores taken from the lower slopes (3000+ m water depth) of carbonate platforms reveal a causative relationship between sea level and aragonite export to the deep ocean. δ18O isotopes from planktonic and benthic foraminifera of two 27-meter cores, reveal a high-resolution, continuous depositional record of carbonate sediment dating back to 1.2 Ma. Sea level rise, as determined by correlation with the LR04 benthic stack, is coincident with increased aragonite flux from platform tops. Gravity flow deposits are also affected by platform flooding—the frequency of turbidite/debrite deposits on pinnacle slopes increases during highstand, although such deposits are also present during glacial episodes. The results reported here are the first record of highstand shedding in the southern Indian Ocean, and provide the longest Quaternary sediment record to date in the region, including the Mid-Brunhes transition (MIS 11) that serves as an analog for the current climate conditions. In addition, this is the first study to describe sedimentation on the slopes of these platforms, providing an important point of comparison that has the potential to influence source-to-sink carbonate facies models.

Developing a Web Platform to Support a Community of Practice: A Mixed Methods Study in Pediatric Physiotherapy.

PubMed

Pratte, Gabrielle; Hurtubise, Karen; Rivard, Lisa; Berbari, Jade; Camden, Chantal

2018-01-01

Web platforms are increasingly used to support virtual interactions between members of communities of practice (CoP). However, little is known about how to develop these platforms to support the implementation of best practices for health care professionals. The aim of this article is to explore pediatric physiotherapists' (PTs) perspectives regarding the utility and usability of the characteristic of a web platform developed to support virtual communities of practice (vCoP). This study adopted an explanatory sequential mixed methods design. A web platform supporting the interactions of vCoP members was developed for PTs working with children with developmental coordination disorder. Specific strategies and features were created to support the effectiveness of the platform across three domains: social, information-quality, and system-quality factors. Quantitative data were collected from a cross-sectional survey (n = 41) after 5 months of access to the web platform. Descriptive statistics were calculated. Qualitative data were also collected from semistructured interviews (n = 9), which were coded, interpreted, and analyzed by using Boucher's Web Ergonomics Conceptual Framework. The utility of web platform characteristics targeting the three key domain factors were generally perceived positively by PTs. However, web platform usability issues were noted by PTs, including problems with navigation and information retrieval. Web platform aiming to support vCoP should be carefully developed to target potential users' needs. Whenever possible, users should co-construct the web platform with vCoP developers. Moreover, each of the developed characteristics (eg, newsletter, search function) should be evaluated in terms of utility and usability for the users.

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

Gramene 2013: comparative plant genomics resources.

PubMed

Monaco, Marcela K; Stein, Joshua; Naithani, Sushma; Wei, Sharon; Dharmawardhana, Palitha; Kumari, Sunita; Amarasinghe, Vindhya; Youens-Clark, Ken; Thomason, James; Preece, Justin; Pasternak, Shiran; Olson, Andrew; Jiao, Yinping; Lu, Zhenyuan; Bolser, Dan; Kerhornou, Arnaud; Staines, Dan; Walts, Brandon; Wu, Guanming; D'Eustachio, Peter; Haw, Robin; Croft, David; Kersey, Paul J; Stein, Lincoln; Jaiswal, Pankaj; Ware, Doreen

2014-01-01

Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Whole-genome alignments complemented by phylogenetic gene family trees help infer syntenic and orthologous relationships. Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts. The pathways section also hosts 10 species-specific metabolic pathways databases developed in-house or by our collaborators using Pathway Tools software, which facilitates searches for pathway, reaction and metabolite annotations, and allows analyses of user-defined expression datasets. Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species. We continue to provide genetic and QTL maps and marker datasets developed by crop researchers. The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology.

Transcriptome Analysis and Development of SSR Molecular Markers in Glycyrrhiza uralensis Fisch.

PubMed Central

Liu, Yaling; Zhang, Pengfei; Song, Meiling; Hou, Junling; Qing, Mei; Wang, Wenquan; Liu, Chunsheng

2015-01-01

Licorice is an important traditional Chinese medicine with clinical and industrial applications. Genetic resources of licorice are insufficient for analysis of molecular biology and genetic functions; as such, transcriptome sequencing must be conducted for functional characterization and development of molecular markers. In this study, transcriptome sequencing on the Illumina HiSeq 2500 sequencing platform generated a total of 5.41 Gb clean data. De novo assembly yielded a total of 46,641 unigenes. Comparison analysis using BLAST showed that the annotations of 29,614 unigenes were conserved. Further study revealed 773 genes related to biosynthesis of secondary metabolites of licorice, 40 genes involved in biosynthesis of the terpenoid backbone, and 16 genes associated with biosynthesis of glycyrrhizic acid. Analysis of unigenes larger than 1 Kb with a length of 11,702 nt presented 7,032 simple sequence repeats (SSR). Sixty-four of 69 randomly designed and synthesized SSR pairs were successfully amplified, 33 pairs of primers were polymorphism in in Glycyrrhiza uralensis Fisch., Glycyrrhiza inflata Bat., Glycyrrhiza glabra L. and Glycyrrhiza pallidiflora Maxim. This study not only presents the molecular biology data of licorice but also provides a basis for genetic diversity research and molecular marker-assisted breeding of licorice. PMID:26571372

Brain Targeting Delivery Facilitated by Ligand-Functionalized Layered Double Hydroxide Nanoparticles.

PubMed

Chen, Weiyu; Zuo, Huali; Zhang, Enqi; Li, Li; Henrich-Noack, Petra; Cooper, Helen; Qian, Yujin; Xu, Zhi Ping

2018-06-20

A delivery platform with highly selective permeability through the blood-brain barrier (BBB) is essential for brain disease treatment. In this research, we designed and prepared a novel target nanoplatform, that is, layered double hydroxide (LDH) nanoparticle conjugated with targeting peptide-ligand Angiopep-2 (Ang2) or rabies virus glycoprotein (RVG) via intermatrix bovine serum albumin for brain targeting. In vitro studies show that functionalization with the target ligand significantly increases the delivery efficiency of LDH nanoparticles to the brain endothelial (bEnd.3) cells and the transcytosis through the simulated BBB model, that is, bEnd.3 cell-constructed multilayer membrane. In vivo confocal neuroimaging of the rat's blood-retina area dynamically demonstrates that LDH nanoparticles modified with peptide ligands have shown a prolonged retention period within the retina vessel in comparison with the pristine LDH group. Moreover, Ang2-modified LDH nanoparticles are found to more specifically accumulate in the mouse brain than the control and RVG-modified LDH nanoparticles after 2 and 48 h intravenous injection. All these findings strongly suggest that Ang2-modified LDHs can serve as an effective targeting nanoplatform for brain disease treatment.

Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome.

PubMed

Verwaaijen, Bart; Wibberg, Daniel; Nelkner, Johanna; Gordin, Miriam; Rupp, Oliver; Winkler, Anika; Bremges, Andreas; Blom, Jochen; Grosch, Rita; Pühler, Alfred; Schlüter, Andreas

2018-02-10

Lettuce (Lactuca sativa, L.) is an important annual plant of the family Asteraceae (Compositae). The commercial lettuce cultivar Tizian has been used in various scientific studies investigating the interaction of the plant with phytopathogens or biological control agents. Here, we present the de novo draft genome sequencing and gene prediction for this specific cultivar derived from transcriptome sequence data. The assembled scaffolds amount to a size of 2.22 Gb. Based on RNAseq data, 31,112 transcript isoforms were identified. Functional predictions for these transcripts were determined within the GenDBE annotation platform. Comparison with the cv. Salinas reference genome revealed a high degree of sequence similarity on genome and transcriptome levels, with an average amino acid identity of 99%. Furthermore, it was observed that two large regions are either missing or are highly divergent within the cv. Tizian genome compared to cv. Salinas. One of these regions covers the major resistance complex 1 region of cv. Salinas. The cv. Tizian draft genome sequence provides a valuable resource for future functional and transcriptome analyses focused on this lettuce cultivar. Copyright © 2017 Elsevier B.V. All rights reserved.

Vector analysis of astigmatism before and after LASIK: a comparison of two different platforms for treatment of high astigmatism.

PubMed

Biscevic, Alma; Bohac, Maja; Koncarevic, Mateja; Anticic, Marija; Dekaris, Iva; Patel, Sudi

2015-12-01

To compare the outcomes of astigmatic laser in-situ keratomileusis (LASIK) procedures between two different platforms using J0 and J45 vector analysis. Patients were divided into four groups, depending on the type of astigmatism and laser platform on which they were treated. Astigmatism was between 2 and 7 diopters (D). One hundred and thirty-five patients with myopic astigmatism (246 eyes) and 102 patients with mixed astigmatism (172 eyes) underwent unremarkable LASIK correction on Wavelight Allegretto Eye-Q 400Hz and Schwind Amaris 750S laser platform. The preoperative and postoperative sphere, negative cylinder [C] and axis (ø) of manifest refractions were subjected to vector analysis by calculations of the standard J0 (cos [4π(ø-90)/360]xC/2) and J45 (sin[4π(ø-90)/360]xC/2). Reporting the key results, we found J0 significantly reduced after LASIK in both groups (p < 0.001) but not J45. There was no significant association between individual pairs of pre and postoperative J0 & J45 values. There was no significant difference between the outcomes of the two platforms. Wavelight Allegretto 400Hz and Schwind Amaris 750S showed excellent results for treating patients with astigmatism, regardless whether it is mixed or myopic astigmatism. The J45 did not reduce significantly possibly because of the low number of eyes with oblique astigmatism. There was no genuine difference post-operatively between groups treated on two different laser platforms according to the vector analyses.

Facebook dethroned: Revealing the more likely social media destinations for college students’ depictions of underage drinking

PubMed Central

Boyle, Sarah C.; Earle, Andrew M.; LaBrie, Joseph W.; Ballou, Kayla

2016-01-01

Studies examining representations of college drinking on social media have almost exclusively focused on Facebook. However, recent research suggests college students may be more influenced by peers’ alcohol-related posts on Instagram and Snapchat, two image-based platforms popular among this demographic. One potential explanation for this differential influence is that qualitative distinctions in the types of alcohol-related content posted by students on these three platforms may exist. Informed by undergraduate focus groups, this study examined the hypothesis that, of the three platforms, students tend to use Instagram most often for photos glamourizing drinking and Snapchat for incriminating photos of alcohol misuse and negative consequences. Undergraduate research assistants aided investigators in developing hypothetical vignettes and photographic examples of posts both glamorizing and depicting negative consequences associated with college drinking. In an online survey, vignette and photo stimuli were followed by counterbalanced paired comparisons that presented each possible pair of social media platforms. Undergraduates (N=196) selected the platform from each pair on which they would be more likely to see each post. Generalized Bradley-Terry models examined the probabilities of platform selections. As predicted, Instagram was seen as the most probable destination (and Facebook least probable) for photos depicting alcohol use as attractive and glamorous. Conversely, Snapchat was selected as the most probable destination (and Facebook least probable) for items depicting negative consequences associated with heavy drinking. Results suggest researchers aiming to mitigate the potential influences associated with college students’ glamorous and consequential alcohol-related photos posted social media posts should shift their focus from Facebook to Instagram and Snapchat. PMID:27776267

Multiple advanced logic gates made of DNA-Ag nanocluster and the application for intelligent detection of pathogenic bacterial genes.

PubMed

Lin, Xiaodong; Liu, Yaqing; Deng, Jiankang; Lyu, Yanlong; Qian, Pengcheng; Li, Yunfei; Wang, Shuo

2018-02-21

The integration of multiple DNA logic gates on a universal platform to implement advance logic functions is a critical challenge for DNA computing. Herein, a straightforward and powerful strategy in which a guanine-rich DNA sequence lighting up a silver nanocluster and fluorophore was developed to construct a library of logic gates on a simple DNA-templated silver nanoclusters (DNA-AgNCs) platform. This library included basic logic gates, YES, AND, OR, INHIBIT, and XOR, which were further integrated into complex logic circuits to implement diverse advanced arithmetic/non-arithmetic functions including half-adder, half-subtractor, multiplexer, and demultiplexer. Under UV irradiation, all the logic functions could be instantly visualized, confirming an excellent repeatability. The logic operations were entirely based on DNA hybridization in an enzyme-free and label-free condition, avoiding waste accumulation and reducing cost consumption. Interestingly, a DNA-AgNCs-based multiplexer was, for the first time, used as an intelligent biosensor to identify pathogenic genes, E. coli and S. aureus genes, with a high sensitivity. The investigation provides a prototype for the wireless integration of multiple devices on even the simplest single-strand DNA platform to perform diverse complex functions in a straightforward and cost-effective way.

Exploring the Function of Online Narratives to Develop Critical Thinking and Localisation of Knowledge in an International Science Program

ERIC Educational Resources Information Center

Hicks, Marianne; Tham, Melissa; Brookes, Rowan

2017-01-01

e-learning practitioners have long recognised the benefits of using online training to achieve knowledge transfer, less is understood about facilitating the sharing of values, attitudes, critical thinking, and localisation using online platforms. In this article an online learning platform in the context of an international scientific program was…

A Real-Time Linux for Multicore Platforms

DTIC Science & Technology

2013-12-20

under ARO support) to obtain a fully-functional OS for supporting real-time workloads on multicore platforms. This system, called LITMUS -RT...to be specified as plugin components. LITMUS -RT is open-source software (available at The views, opinions and/or findings contained in this report... LITMUS -RT (LInux Testbed for MUltiprocessor Scheduling in Real-Time systems), allows different multiprocessor real-time scheduling and

Design and evaluation of NEUROBike: a neurorehabilitative platform for bedridden post-stroke patients.

PubMed

Monaco, Vito; Galardi, Giuseppe; Coscia, Martina; Martelli, Dario; Micera, Silvestro

2012-11-01

Over the past decades, a large number of robotic platforms have been developed which provide rehabilitative treatments aimed at recovering walking abilities in post-stroke patients. Unfortunately, they do not significantly influence patients' performance after three months from the accident. One of the main reasons underlying this result seems to be related to the time of intervention. Specifically, although experimental evidences suggest that early (i.e., first days after the injury) and intense neuro-rehabilitative treatments can significantly favor the functional recovery of post-stroke patients, robots require patients to be verticalized. Consequently, this does not allow them to be treated immediately after the trauma. This paper introduces a new robotic platform, named NEUROBike, designed to provide neuro-rehabilitative treatments to bedridden patients. It was designed to provide an early and well-addressed rehabilitation therapy, in terms of kinesiology, efforts, and fatigue, accounting for exercises functionally related to daily motor tasks. For this purpose, kinematic models of leg-joint angular excursions during both walking and sit-to-stand were developed and implemented in control algorithms leading both passive and active exercises. Finally, a set of pilot tests was carried out to evaluate the performance of the robotic platform on healthy subjects.

Mass Spectrometry-Based Screening Platform Reveals Orco Interactome in Drosophila melanogaster.

PubMed

Yu, Kate E; Kim, Do-Hyoung; Kim, Yong-In; Jones, Walton D; Lee, J Eugene

2018-02-28

Animals use their odorant receptors to receive chemical information from the environment. Insect odorant receptors differ from the G protein-coupled odorant receptors in vertebrates and nematodes, and very little is known about their protein-protein interactions. Here, we introduce a mass spectrometric platform designed for the large-scale analysis of insect odorant receptor protein-protein interactions. Using this platform, we obtained the first Orco interactome from Drosophila melanogaster . From a total of 1,186 identified proteins, we narrowed the interaction candidates to 226, of which only two-thirds have been named. These candidates include the known olfactory proteins Or92a and Obp51a. Around 90% of the proteins having published names likely function inside the cell, and nearly half of these intracellular proteins are associated with the endomembrane system. In a basic loss-of-function electrophysiological screen, we found that the disruption of eight (i.e., Rab5, CG32795, Mpcp, Tom70, Vir-1, CG30427, Eaat1, and CG2781) of 28 randomly selected candidates affects olfactory responses in vivo . Thus, because this Orco interactome includes physiologically meaningful candidates, we anticipate that our platform will help guide further research on the molecular mechanisms of the insect odorant receptor family.

How to Build a Hybrid Neurofeedback Platform Combining EEG and fMRI

PubMed Central

Mano, Marsel; Lécuyer, Anatole; Bannier, Elise; Perronnet, Lorraine; Noorzadeh, Saman; Barillot, Christian

2017-01-01

Multimodal neurofeedback estimates brain activity using information acquired with more than one neurosignal measurement technology. In this paper we describe how to set up and use a hybrid platform based on simultaneous electroencephalography (EEG) and functional magnetic resonance imaging (fMRI), then we illustrate how to use it for conducting bimodal neurofeedback experiments. The paper is intended for those willing to build a multimodal neurofeedback system, to guide them through the different steps of the design, setup, and experimental applications, and help them choose a suitable hardware and software configuration. Furthermore, it reports practical information from bimodal neurofeedback experiments conducted in our lab. The platform presented here has a modular parallel processing architecture that promotes real-time signal processing performance and simple future addition and/or replacement of processing modules. Various unimodal and bimodal neurofeedback experiments conducted in our lab showed high performance and accuracy. Currently, the platform is able to provide neurofeedback based on electroencephalography and functional magnetic resonance imaging, but the architecture and the working principles described here are valid for any other combination of two or more real-time brain activity measurement technologies. PMID:28377691

Open Platform for Limit Protection with Carefree Maneuver Applications

NASA Technical Reports Server (NTRS)

Jeram, Geoffrey J.

2004-01-01

This Open Platform for Limit Protection guides the open design of maneuver limit protection systems in general, and manned, rotorcraft, aerospace applications in particular. The platform uses three stages of limit protection modules: limit cue creation, limit cue arbitration, and control system interface. A common set of limit cue modules provides commands that can include constraints, alerts, transfer functions, and friction. An arbitration module selects the "best" limit protection cues and distributes them to the most appropriate control path interface. This platform adopts a holistic approach to limit protection whereby it considers all potential interface points, including the pilot's visual, aural, and tactile displays; and automatic command restraint shaping for autonomous limit protection. For each functional module, this thesis guides the control system designer through the design choices and information interfaces among the modules. Limit cue module design choices include type of prediction, prediction mechanism, method of critical control calculation, and type of limit cue. Special consideration is given to the nature of the limit, particularly the level of knowledge about it, and the ramifications for limit protection design, especially with respect to intelligent control methods such as fuzzy inference systems and neural networks.

Updating the Micro-Tom TILLING platform.

PubMed

Okabe, Yoshihiro; Ariizumi, Tohru; Ezura, Hiroshi

2013-03-01

The dwarf tomato variety Micro-Tom is regarded as a model system for functional genomics studies in tomato. Various tomato genomic tools in the genetic background of Micro-Tom have been established, such as mutant collections, genome information and a metabolomic database. Recent advances in tomato genome sequencing have brought about a significant need for reverse genetics tools that are accessible to the larger community, because a great number of gene sequences have become available from public databases. To meet the requests from the tomato research community, we have developed the Micro-Tom Targeting-Induced Local Lesions IN Genomes (TILLING) platform, which is comprised of more than 5000 EMS-mutagenized lines. The platform serves as a reverse genetics tool for efficiently identifying mutant alleles in parallel with the development of Micro-Tom mutant collections. The combination of Micro-Tom mutant libraries and the TILLING approach enables researchers to accelerate the isolation of desirable mutants for unraveling gene function or breeding. To upgrade the genomic tool of Micro-Tom, the development of a new mutagenized population is underway. In this paper, the current status of the Micro-Tom TILLING platform and its future prospects are described.

An open platform for personal health record apps with platform-level privacy protection.

PubMed

Van Gorp, P; Comuzzi, M; Jahnen, A; Kaymak, U; Middleton, B

2014-08-01

One of the main barriers to the adoption of Personal Health Records (PHR) systems is their closed nature. It has been argued in the literature that this barrier can be overcome by introducing an open market of substitutable PHR apps. The requirements introduced by such an open market on the underlying platform have also been derived. In this paper, we argue that MyPHRMachines, a cloud-based PHR platform recently developed by the authors, satisfies these requirements better than its alternatives. The MyPHRMachines platform leverages Virtual Machines as flexible and secure execution sandboxes for health apps. MyPHRMachines does not prevent pushing hospital- or patient-generated data to one of its instances, nor does it prevent patients from sharing data with their trusted caregivers. External software developers have minimal barriers to contribute innovative apps to the platform, since apps are only required to avoid pushing patient data outside a MyPHRMachines cloud. We demonstrate the potential of MyPHRMachines by presenting two externally contributed apps. Both apps provide functionality going beyond the state-of-the-art in their application domain, while they did not require any specific MyPHRMachines platform extension. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

Novel intelligent real-time position tracking system using FPGA and fuzzy logic.

PubMed

Soares dos Santos, Marco P; Ferreira, J A F

2014-03-01

The main aim of this paper is to test if FPGAs are able to achieve better position tracking performance than software-based soft real-time platforms. For comparison purposes, the same controller design was implemented in these architectures. A Multi-state Fuzzy Logic controller (FLC) was implemented both in a Xilinx(®) Virtex-II FPGA (XC2v1000) and in a soft real-time platform NI CompactRIO(®)-9002. The same sampling time was used. The comparative tests were conducted using a servo-pneumatic actuation system. Steady-state errors lower than 4 μm were reached for an arbitrary vertical positioning of a 6.2 kg mass when the controller was embedded into the FPGA platform. Performance gains up to 16 times in the steady-state error, up to 27 times in the overshoot and up to 19.5 times in the settling time were achieved by using the FPGA-based controller over the software-based FLC controller. © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

EAQUATE: An International Experiment for Hyper-Spectral Atmospheric Sounding Validation

NASA Technical Reports Server (NTRS)

Taylor, J. P.; Smith, W.; Cuomo, V.; Larar, A.; Zhou, D.; Serio, C.; Maestri, T.; Rizzi, R.; Newman, S.; Antonelli, P.;

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

PubMed Central

Tian, Tian; Liu, Yue; Yan, Hengyu; You, Qi; Yi, Xin; Du, Zhou

2017-01-01

Abstract The agriGO platform, which has been serving the scientific community for >10 years, specifically focuses on gene ontology (GO) enrichment analyses of plant and agricultural species. We continuously maintain and update the databases and accommodate the various requests of our global users. Here, we present our updated agriGO that has a largely expanded number of supporting species (394) and datatypes (865). In addition, a larger number of species have been classified into groups covering crops, vegetables, fish, birds and insects closely related to the agricultural community. We further improved the computational efficiency, including the batch analysis and P-value distribution (PVD), and the user-friendliness of the web pages. More visualization features were added to the platform, including SEACOMPARE (cross comparison of singular enrichment analysis), direct acyclic graph (DAG) and Scatter Plots, which can be merged by choosing any significant GO term. The updated platform agriGO v2.0 is now publicly accessible at http://systemsbiology.cau.edu.cn/agriGOv2/. PMID:28472432

Advanced Platform Systems Technology study. Volume 2: Trade study and technology selection

NASA Technical Reports Server (NTRS)

1983-01-01

Three primary tasks were identified which include task 1-trade studies, task 2-trade study comparison and technology selection, and task 3-technology definition. Task 1 general objectives were to identify candidate technology trade areas, determine which areas have the highest potential payoff, define specific trades within the high payoff areas, and perform the trade studies. In order to satisfy these objectives, a structured, organized approach was employed. Candidate technology areas and specific trades were screened using consistent selection criteria and considering possible interrelationships. A data base comprising both manned and unmanned space platform documentation was used as a source of system and subsystem requirements. When requirements were not stated in the data base documentation, assumptions were made and recorded where necessary to characterize a particular spacecraft system. The requirements and assumptions were used together with the selection criteria to establish technology advancement goals and select trade studies. While both manned and unmanned platform data were used, the study was focused on the concept of an early manned space station.

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.

SPEKTROP DPU: optoelectronic platform for fast multispectral imaging

NASA Astrophysics Data System (ADS)

Graczyk, Rafal; Sitek, Piotr; Stolarski, Marcin

2010-09-01

In recent years it easy to spot and increasing need of high-quality Earth imaging in airborne and space applications. This is due fact that government and local authorities urge for up to date topological data for administrative purposes. On the other hand, interest in environmental sciences, push for ecological approach, efficient agriculture and forests management are also heavily supported by Earth images in various resolutions and spectral ranges. "SPEKTROP DPU: Opto-electronic platform for fast multi-spectral imaging" paper describes architectural datails of data processing unit, part of universal and modular platform that provides high quality imaging functionality in aerospace applications.