Social Media and Pathology: Where Are We Now and Why Does it Matter?

PubMed

Isom, James; Walsh, Meggen; Gardner, Jerad M

2017-09-01

Social media has exploded in popularity in recent years. It is a powerful new tool for networking, collaborating, and for the communication and evolution of ideas. It has been increasingly used for business purposes and is now being embraced by physicians including pathologists. Pathology professional organizations and even peer-reviewed pathology journals are now beginning to use social media, as well. There are multiple social media platforms, including Twitter, Facebook, Instagram, LinkedIn, and others. Each platform has different audiences and different ways to share content and interact with other users. This paper discusses the different social media platforms and how they are being used in pathology currently.

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.

[Construction and analysis of a monitoring system with remote real-time multiple physiological parameters based on cloud computing].

PubMed

Zhu, Lingyun; Li, Lianjie; Meng, Chunyan

2014-12-01

There have been problems in the existing multiple physiological parameter real-time monitoring system, such as insufficient server capacity for physiological data storage and analysis so that data consistency can not be guaranteed, poor performance in real-time, and other issues caused by the growing scale of data. We therefore pro posed a new solution which was with multiple physiological parameters and could calculate clustered background data storage and processing based on cloud computing. Through our studies, a batch processing for longitudinal analysis of patients' historical data was introduced. The process included the resource virtualization of IaaS layer for cloud platform, the construction of real-time computing platform of PaaS layer, the reception and analysis of data stream of SaaS layer, and the bottleneck problem of multi-parameter data transmission, etc. The results were to achieve in real-time physiological information transmission, storage and analysis of a large amount of data. The simulation test results showed that the remote multiple physiological parameter monitoring system based on cloud platform had obvious advantages in processing time and load balancing over the traditional server model. This architecture solved the problems including long turnaround time, poor performance of real-time analysis, lack of extensibility and other issues, which exist in the traditional remote medical services. Technical support was provided in order to facilitate a "wearable wireless sensor plus mobile wireless transmission plus cloud computing service" mode moving towards home health monitoring for multiple physiological parameter wireless monitoring.

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

PubMed

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

2012-01-01

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

Concepts for a geostationary-like polar mission

NASA Astrophysics Data System (ADS)

Macdonald, Malcolm; Anderson, Pamela; Carrea, Laura; Dobke, Benjamin; Embury, Owen; Merchant, Chris; Bensi, Paolo

2014-10-01

An evidence-led scientific case for development of a space-based polar remote sensing platform at geostationary-like (GEO-like) altitudes is developed through methods including a data user survey. Whilst a GEO platform provides a nearstatic perspective, multiple platforms are required to provide circumferential coverage. Systems for achieving GEO-like polar observation likewise require multiple platforms however the perspective is non-stationery. A key choice is between designs that provide complete polar view from a single platform at any given instant, and designs where this is obtained by compositing partial views from multiple sensors. Users foresee an increased challenge in extracting geophysical information from composite images and consider the use of non-composited images advantageous. Users also find the placement of apogee over the pole to be preferable to the alternative scenarios. Thus, a clear majority of data users find the "Taranis" orbit concept to be better than a critical inclination orbit, due to the improved perspective offered. The geophysical products that would benefit from a GEO-like polar platform are mainly estimated from radiances in the visible/near infrared and thermal parts of the electromagnetic spectrum, which is consistent with currently proven technologies from GEO. Based on the survey results, needs analysis, and current technology proven from GEO, scientific and observation requirements are developed along with two instrument concepts with eight and four channels, based on Flexible Combined Imager heritage. It is found that an operational system could, mostly likely, be deployed from an Ariane 5 ES to a 16-hour orbit, while a proof-of-concept system could be deployed from a Soyuz launch to the same orbit.

Simulation Platform: a cloud-based online simulation environment.

PubMed

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

2011-09-01

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

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

PubMed

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

2011-11-01

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

Cross-platform learning: on the nature of children's learning from multiple media platforms.

PubMed

Fisch, Shalom M

2013-01-01

It is increasingly common for an educational media project to span several media platforms (e.g., TV, Web, hands-on materials), assuming that the benefits of learning from multiple media extend beyond those gained from one medium alone. Yet research typically has investigated learning from a single medium in isolation. This paper reviews several recent studies to explore cross-platform learning (i.e., learning from combined use of multiple media platforms) and how such learning compares to learning from one medium. The paper discusses unique benefits of cross-platform learning, a theoretical mechanism to explain how these benefits might arise, and questions for future research in this emerging field. Copyright © 2013 Wiley Periodicals, Inc., A Wiley Company.

A Perfect Platform: Combining Contingency Management with Medications for Drug Abuse

PubMed Central

Carroll, Kathleen M.; Rounsaville, Bruce J.

2008-01-01

Contingency management (CM) procedures, which provide concrete reinforcers or rewards contingent on verification of discrete targeted behaviors, such as drug-free urines, have been demonstrated to be effective in a number of clinical trials. However, to date there have been only a few that have capitalized on the unique strengths and capabilities of CM as an ideal platform to improve response to or address weaknesses of many pharmacotherapies used in the treatment of drug abuse. In this review, we describe the multiple potential uses of CM as a platform for pharmacotherapy, including reducing illicit drug use in the context of agonist therapies; fostering medication compliance with antagonists, aversive agents and HIV medications; fostering a period of abstinence prior to initiation of agents used to treat comorbid psychiatric conditions or in the context of vaccines to foster adequate periods of abstinence while titer levels are building; and to enhance the effectiveness of anticraving agents through additive or synergistic effects. Although its multiple strengths render it an almost perfect platform, CM does have some weaknesses that have limited its use to date, including cost, the short-term nature of its effects, and need for training. Future treatment development of CM as a medication platform needs to counter these issues by focusing on CM applications with large potential benefit, developing simple or automated methods for CM delivery and placing greater emphasis on the process of transitioning away from formal CM treatment. PMID:17613963

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

PubMed

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

2015-12-01

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

Twin-Mirrored-Galvanometer Laser-Light-Sheet Generator

NASA Technical Reports Server (NTRS)

Rhodes, David B.; Franke, John M.; Jones, Stephen B.; Leighty, Bradley D.

1991-01-01

Multiple, rotating laser-light sheets generated to illuminate flows in wind tunnels. Designed and developed to provide flexibility and adaptability to wide range of applications. Design includes capability to control size and location of laser-light sheet in real time, to generate horizontal or vertical sheets, to sweep sheet repeatedly through volume, to generate multiple sheets with controllable separation, and to rotate single or multiple laser-light sheets. Includes electronic equipment and laser mounted on adjustable-height platform. Twin-mirrored galvanometer unit supported by tripod to reduce vibration. Other possible applications include use in construction industry to align beams of building. Artistic or display applications also possible.

In vivo miniature robots for natural orifice surgery: State of the art and future perspectives.

PubMed

Tiwari, Manish M; Reynoso, Jason F; Lehman, Amy C; Tsang, Albert W; Farritor, Shane M; Oleynikov, Dmitry

2010-06-27

Natural orifice translumenal endoscopic surgery (NOTES) is the integration of laparoscopic minimally invasive surgery techniques with endoscopic technology. Despite the advances in NOTES technology, the approach presents several unique instrumentation and technique-specific challenges. Current flexible endoscopy platforms for NOTES have several drawbacks including limited stability, triangulation and dexterity, and lack of adequate visualization, suggesting the need for new and improved instrumentation for this approach. Much of the current focus is on the development of flexible endoscopy platforms that incorporate robotic technology. An alternative approach to access the abdominal viscera for either a laparoscopic or NOTES procedure is the use of small robotic devices that can be implanted in an intracorporeal manner. Multiple, independent, miniature robots can be simultaneously inserted into the abdominal cavity to provide a robotic platform for NOTES surgery. The capabilities of the robots include imaging, retraction, tissue and organ manipulation, and precise maneuverability in the abdominal cavity. Such a platform affords several advantages including enhanced visualization, better surgical dexterity and improved triangulation for NOTES. This review discusses the current status and future perspectives of this novel miniature robotics platform for the NOTES approach. Although these technologies are still in pre-clinical development, a miniature robotics platform provides a unique method for addressing the limitations of minimally invasive surgery, and NOTES in particular.

Opening Health Data: What Do Researchers Want? Early Experiences With New York's Open Health Data Platform.

PubMed

Martin, Erika G; Helbig, Natalie; Birkhead, Guthrie S

2015-01-01

Governments are rapidly developing open data platforms to improve transparency and make information more accessible. New York is a leader, with currently the only state platform devoted to health. Although these platforms could build public health departments' capabilities to serve more researchers, agencies have little guidance on releasing meaningful and usable data. Structured focus groups with researchers and practitioners collected stakeholder feedback on potential uses of open health data and New York's open data strategy. Researchers and practitioners attended a 1-day November 2013 workshop on New York State's open health data resources. After learning about the state's open data platform and vision for open health data, participants were organized into 7 focus groups to discuss the essential elements of open data sets, practical challenges to obtaining and using health data, and potential uses of open data. Participants included 33 quantitative health researchers from State University of New York campuses and private partners and 10 practitioners from the New York State Department of Health. There was low awareness of open data, with 67% of researchers reporting never using open data portals prior to the workshop. Participants were interested in data sets that were geocoded, longitudinal, or aggregated to small area granularity and capabilities to link multiple data sets. Multiple environmental conditions and barriers hinder their capacity to use health data for research. Although open data platforms cannot address all barriers, they provide multiple opportunities for public health research and practice, and participants were overall positive about the state's efforts to release open data. Open data are not ideal for some researchers because they do not contain individually identifiable data, indicating a need for tiered data release strategies. However, they do provide important new opportunities to facilitate research and foster collaborations among agencies, researchers, and practitioners.

Development of a Zigbee platform for bioinstrumentation.

PubMed

Cifuentes, Carlos A; Gentiletti, Gabriel G; Suarez, Marco J; Rodriguez, Luis E

2010-01-01

This paper presents the development of a network platform which allows connecting multiple individual wireless devices for transmitting bioelectrics and biomechanics signals for application in a hospital network, or continuous monitoring in a patient's diary life. The Zigbee platform development proposal was made in three stages: 1) Hardware development, including the construction of a prototype network node and the integration of sensors, (2) Evaluation, in order to define the specifications of each node and scope of communication and (3) The Zigbee Network Implementation for bioinstrumentation based on ZigBee Health Care public application profile (ZHC). Finally, this work presents the experimental results based on measurements of Lost Packets and LQI (Link Quality Indicator), and the Zigbee Platform configuration for Bioinstrumentation in operation.

An Integrated Framework for Effective and Efficient Communication with Families in the Adult Intensive Care Unit.

PubMed

Seaman, Jennifer B; Arnold, Robert M; Scheunemann, Leslie P; White, Douglas B

2017-06-01

The increased focus on patient and family-centered care in adult intensive care units (ICUs) has generated multiple platforms for clinician-family communication beyond traditional interdisciplinary family meetings (family meetings)-including family-centered rounds, bedside or telephone updates, and electronic family portals. Some clinicians and administrators are now using these platforms instead of conducting family meetings. For example, some institutions are moving toward using family-centered rounds as the main platform for clinician-family communication, and some physicians rely on brief daily updates to the family at the bedside or by phone, in lieu of family meetings. We argue that although each of these platforms is useful in some circumstances, there remains an important role for family meetings. We outline five goals of clinician-family communication-establishing trust, providing emotional support, conveying clinical information, understanding the patient as a person, and facilitating careful decision making-and we examine the extent to which various communication platforms are likely to achieve the goals. We argue that because no single platform can achieve all communication goals, an integrated strategy is needed. We present a model that integrates multiple communication platforms to effectively and efficiently support families across the arc of an ICU stay. Our framework employs bedside/telephone conversations and family-centered rounds throughout the admission to address high informational needs, along with well-timed family meetings that attend to families' emotions as well as patients' values and goals. This flexible model uses various communication platforms to achieve consistent, efficient communication throughout the ICU stay.

An Integrated Framework for Effective and Efficient Communication with Families in the Adult Intensive Care Unit

PubMed Central

Arnold, Robert M.; Scheunemann, Leslie P.; White, Douglas B.

2017-01-01

The increased focus on patient and family-centered care in adult intensive care units (ICUs) has generated multiple platforms for clinician–family communication beyond traditional interdisciplinary family meetings (family meetings)—including family-centered rounds, bedside or telephone updates, and electronic family portals. Some clinicians and administrators are now using these platforms instead of conducting family meetings. For example, some institutions are moving toward using family-centered rounds as the main platform for clinician–family communication, and some physicians rely on brief daily updates to the family at the bedside or by phone, in lieu of family meetings. We argue that although each of these platforms is useful in some circumstances, there remains an important role for family meetings. We outline five goals of clinician–family communication—establishing trust, providing emotional support, conveying clinical information, understanding the patient as a person, and facilitating careful decision making—and we examine the extent to which various communication platforms are likely to achieve the goals. We argue that because no single platform can achieve all communication goals, an integrated strategy is needed. We present a model that integrates multiple communication platforms to effectively and efficiently support families across the arc of an ICU stay. Our framework employs bedside/telephone conversations and family-centered rounds throughout the admission to address high informational needs, along with well-timed family meetings that attend to families’ emotions as well as patients’ values and goals. This flexible model uses various communication platforms to achieve consistent, efficient communication throughout the ICU stay. PMID:28282227

Treatment patterns in disease-modifying therapy for patients with multiple sclerosis in the United States.

PubMed

Bonafede, Machaon M; Johnson, Barbara H; Wenten, Madé; Watson, Crystal

2013-10-01

Patients with multiple sclerosis (MS) whose disease activity is inadequately controlled with a platform therapy (interferon beta or glatiramer acetate [GA]) may switch to another platform therapy or escalate therapy to natalizumab or fingolimod, which were approved in the US in 2006 and 2010, respectively. The objective of this study was to describe treatment patterns in patients with multiple sclerosis (MS) in the United States who were followed for 2 years after initiating a disease-modifying therapy (DMT). A retrospective observational cohort study was conducted to examine treatment patterns of initial DMT use (on initial therapy for 2 years with and without gaps of ≥ 60 days, medication switching, and discontinuation) among patients with MS who initiated a platform therapy (interferon-β or glatiramer acetate) or natalizumab between January 1, 2007, and September 30, 2009; the first DMT claim was the index. Eligible patients were identified in the MarketScan Commercial and Medicare Supplemental databases based on continuous enrollment for 6 months before (preindex period) and 24 months after their index date, with a diagnosis of MS and no claim for a previous DMT in the 6-month preindex period. Demographics at index and clinical characteristics during the preindex period were also analyzed. A total of 6181 MS patients were included, with 5735 (92.8%) starting on platform therapy. Natalizumab initiators were more likely to stay on index therapy (32.3% vs 16.9%, P < 0.001) and have fewer treatment gaps of ≥ 60 days (44.8% vs 55.3%, P < 0.001) compared with platform initiators. In addition, natalizumab initiators were less likely to switch treatment (13.9% vs 19.1%, P = 0.007) and took longer to switch (400.9 days vs 330.7 days, P < 0.001) compared with platform initiators. Nearly 79% of platform initiators who switched went to another platform therapy. Approximately two thirds of patients who switched to a third DMT (n = 130) switched to another platform therapy. A total of 9% of natalizumab and platform initiators discontinued DMT within the 2 years. Most MS patients initiating DMT started on platform therapy. Natalizumab initiators tended to stay on index therapy, have fewer treatment gaps, and switch less than platform initiators in the 2 years after treatment initiation. Switching between platform therapies is common despite evidence that MS patients on platform therapy may benefit from switching to natalizumab. © 2013 Elsevier HS Journals, Inc. All rights reserved.

Strategies for Time-resolved X-ray Diffraction of Phase Transitions with Laser Compression

NASA Astrophysics Data System (ADS)

Benedetti, Laura Robin; Eggert, J. H.; Bradley, D. K.; Bell, P. M.; Kilkenny, J. D.; Palmer, N.; Petre, R. B.; Rygg, J. R.; Sorce, C.; Collins, G. W.; Boehly, T. R.

2017-10-01

As part of a program to document kinetics of phase transitions under laser-driven dynamic compression, we are designing a platform to make multiple x-ray diffraction measurements during a single laser experiment. Our plans include experimental development at Omega-EP and eventual implementation at NIF. We will present our strategy for designing a robust platform that can effectively document a wide variety of phase transformations by utilizing both streaked and multiple-frame imaging detectors. Preliminary designs utilize a novel CMOS detector designed by Sandia National Lab. Our initial experiments include scoping studies that will focus on photometrics and shielding requirements in the high EMP environment close to the target. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. Lawrence Livermore National Security, LLC, LLNL-ABS-734470.

National Community Solar Platform

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

Rupert, Bart

This project was created to provide a National Community Solar Platform (NCSP) portal known as Community Solar Hub, that is available to any entity or individual who wants to develop community solar. This has been done by providing a comprehensive portal to make CEC’s solutions, and other proven community solar solutions, externally available for everyone to access – making the process easy through proven platforms to protect subscribers, developers and utilities. The successful completion of this project provides these tools via a web platform and integration APIs, a wide spectrum of community solar projects included in the platform, multiple groupsmore » of customers (utilities, EPCs, and advocates) using the platform to develop community solar, and open access to anyone interested in community solar. CEC’s Incubator project includes web-based informational resources, integrated systems for project information and billing systems, and engagement with customers and users by community solar experts. The combined effort externalizes much of Clean Energy Collective’s industry-leading expertise, allowing third parties to develop community solar without duplicating expensive start-up efforts. The availability of this platform creates community solar projects that are cheaper to build and cheaper to participate in, furthering the goals of DOE’s SunShot Initiative. Final SF 425 Final SF 428 Final DOE F 2050.11 Final Report Narrative« less

Systemic lupus erythematosus diagnostics in the ‘omics’ era

PubMed Central

Arriens, Cristina; Mohan, Chandra

2014-01-01

Systemic lupus erythematosus is a complex autoimmune disease affecting multiple organ systems. Currently, diagnosis relies upon meeting at least four out of eleven criteria outlined by the ACR. The scientific community actively pursues discovery of novel diagnostics in the hope of better identifying susceptible individuals in early stages of disease. Comprehensive studies have been conducted at multiple biological levels including: DNA (or genomics), mRNA (or transcriptomics), protein (or proteomics) and metabolites (or metabolomics). The ‘omics’ platforms allow us to re-examine systemic lupus erythematosus at a greater degree of molecular resolution. More importantly, one is hopeful that these ‘omics’ platforms may yield newer biomarkers for systemic lupus erythematosus that can help clinicians track the disease course with greater sensitivity and specificity. PMID:24860621

SysBioCube: A Data Warehouse and Integrative Data Analysis Platform Facilitating Systems Biology Studies of Disorders of Military Relevance

DTIC Science & Technology

2013-12-18

include interactive gene and methylation profiles, interactive heatmaps, cytoscape network views, integrative genomics viewer ( IGV ), and protein-protein...single chart. The website also provides an option to include multiple genes. Integrative Genomics Viewer ( IGV )1, is a high-performance desktop tool for

Bellerophon

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

Lingerfelt, Eric J; Messer, II, Otis E

2017-01-02

The Bellerophon software system supports CHIMERA, a production-level HPC application that simulates the evolution of core-collapse supernovae. Bellerophon enables CHIMERA's geographically dispersed team of collaborators to perform job monitoring and real-time data analysis from multiple supercomputing resources, including platforms at OLCF, NERSC, and NICS. Its multi-tier architecture provides an encapsulated, end-to-end software solution that enables the CHIMERA team to quickly and easily access highly customizable animated and static views of results from anywhere in the world via a cross-platform desktop application.

Cross-Platform Learning: On the Nature of Children's Learning from Multiple Media Platforms

ERIC Educational Resources Information Center

Fisch, Shalom M.

2013-01-01

It is increasingly common for an educational media project to span several media platforms (e.g., TV, Web, hands-on materials), assuming that the benefits of learning from multiple media extend beyond those gained from one medium alone. Yet research typically has investigated learning from a single medium in isolation. This paper reviews several…

A Software Platform for Post-Processing Waveform-Based NDE

NASA Technical Reports Server (NTRS)

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

2007-01-01

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

Multiple advanced logic gates made of DNA-Ag nanocluster and the application for intelligent detection of pathogenic bacterial genes† †Electronic supplementary information (ESI) available: Chemicals, materials and DNA sequences used in the investigation, the construction of YES, AND, OR, XOR and INH logic gates, CD and PAGE experimental results. See DOI: 10.1039/c7sc05246d

PubMed Central

Lin, Xiaodong; Deng, Jiankang; Lyu, Yanlong; Qian, Pengcheng; Li, Yunfei

2018-01-01

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. PMID:29675221

Cellular computational platform and neurally inspired elements thereof

DOEpatents

Okandan, Murat

2016-11-22

A cellular computational platform is disclosed that includes a multiplicity of functionally identical, repeating computational hardware units that are interconnected electrically and optically. Each computational hardware unit includes a reprogrammable local memory and has interconnections to other such units that have reconfigurable weights. Each computational hardware unit is configured to transmit signals into the network for broadcast in a protocol-less manner to other such units in the network, and to respond to protocol-less broadcast messages that it receives from the network. Each computational hardware unit is further configured to reprogram the local memory in response to incoming electrical and/or optical signals.

XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets.

PubMed

Yu, Yao; Hu, Hao; Bohlender, Ryan J; Hu, Fulan; Chen, Jiun-Sheng; Holt, Carson; Fowler, Jerry; Guthery, Stephen L; Scheet, Paul; Hildebrandt, Michelle A T; Yandell, Mark; Huff, Chad D

2018-04-06

High-throughput sequencing data are increasingly being made available to the research community for secondary analyses, providing new opportunities for large-scale association studies. However, heterogeneity in target capture and sequencing technologies often introduce strong technological stratification biases that overwhelm subtle signals of association in studies of complex traits. Here, we introduce the Cross-Platform Association Toolkit, XPAT, which provides a suite of tools designed to support and conduct large-scale association studies with heterogeneous sequencing datasets. XPAT includes tools to support cross-platform aware variant calling, quality control filtering, gene-based association testing and rare variant effect size estimation. To evaluate the performance of XPAT, we conducted case-control association studies for three diseases, including 783 breast cancer cases, 272 ovarian cancer cases, 205 Crohn disease cases and 3507 shared controls (including 1722 females) using sequencing data from multiple sources. XPAT greatly reduced Type I error inflation in the case-control analyses, while replicating many previously identified disease-gene associations. We also show that association tests conducted with XPAT using cross-platform data have comparable performance to tests using matched platform data. XPAT enables new association studies that combine existing sequencing datasets to identify genetic loci associated with common diseases and other complex traits.

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.

[Orange Platform].

PubMed

Toba, Kenji

2017-07-01

The Organized Registration for the Assessment of dementia on Nationwide General consortium toward Effective treatment in Japan (ORANGE platform) is a recently established nationwide clinical registry for dementia. This platform consists of multiple registries of patients with dementia stratified by the following clinical stages: preclinical, mild cognitive impairment, early-stage, and advanced-stage dementia. Patients will be examined in a super-longitudinal fashion, and their lifestyle, social background, genetic risk factors, and required care process will be assessed. This project is also notable because the care registry includes information on the successful, comprehensive management of patients with dementia. Therefore, this multicenter prospective cohort study will contribute participants to all clinical trials for Alzheimer's disease as well as improve the understanding of individuals with dementia.

Polymeric scaffolds for three-dimensional culture of nerve cells: a model of peripheral nerve regeneration

PubMed Central

Ayala-Caminero, Radamés; Pinzón-Herrera, Luis; Martinez, Carol A. Rivera; Almodovar, Jorge

2018-01-01

Understanding peripheral nerve repair requires the evaluation of 3D structures that serve as platforms for 3D cell culture. Multiple platforms for 3D cell culture have been developed, mimicking peripheral nerve growth and function, in order to study tissue repair or diseases. To recreate an appropriate 3D environment for peripheral nerve cells, key factors are to be considered including: selection of cells, polymeric biomaterials to be used, and fabrication techniques to shape and form the 3D scaffolds for cellular culture. This review focuses on polymeric 3D platforms used for the development of 3D peripheral nerve cell cultures. PMID:29515936

Blue guardian: an open architecture for rapid ISR demonstration

NASA Astrophysics Data System (ADS)

Barrett, Donald A.; Borntrager, Luke A.; Green, David M.

2016-05-01

Throughout the Department of Defense (DoD), acquisition, platform integration, and life cycle costs for weapons systems have continued to rise. Although Open Architecture (OA) interface standards are one of the primary methods being used to reduce these costs, the Air Force Rapid Capabilities Office (AFRCO) has extended the OA concept and chartered the Open Mission System (OMS) initiative with industry to develop and demonstrate a consensus-based, non-proprietary, OA standard for integrating subsystems and services into airborne platforms. The new OMS standard provides the capability to decouple vendor-specific sensors, payloads, and service implementations from platform-specific architectures and is still in the early stages of maturation and demonstration. The Air Force Research Laboratory (AFRL) - Sensors Directorate has developed the Blue Guardian program to demonstrate advanced sensing technology utilizing open architectures in operationally relevant environments. Over the past year, Blue Guardian has developed a platform architecture using the Air Force's OMS reference architecture and conducted a ground and flight test program of multiple payload combinations. Systems tested included a vendor-unique variety of Full Motion Video (FMV) systems, a Wide Area Motion Imagery (WAMI) system, a multi-mode radar system, processing and database functions, multiple decompression algorithms, multiple communications systems, and a suite of software tools. Initial results of the Blue Guardian program show the promise of OA to DoD acquisitions, especially for Intelligence, Surveillance and Reconnaissance (ISR) payload applications. Specifically, the OMS reference architecture was extremely useful in reducing the cost and time required for integrating new systems.

The rare and undiagnosed diseases diagnostic service - application of massively parallel sequencing in a state-wide clinical service.

PubMed

Baynam, Gareth; Pachter, Nicholas; McKenzie, Fiona; Townshend, Sharon; Slee, Jennie; Kiraly-Borri, Cathy; Vasudevan, Anand; Hawkins, Anne; Broley, Stephanie; Schofield, Lyn; Verhoef, Hedwig; Walker, Caroline E; Molster, Caron; Blackwell, Jenefer M; Jamieson, Sarra; Tang, Dave; Lassmann, Timo; Mina, Kym; Beilby, John; Davis, Mark; Laing, Nigel; Murphy, Lesley; Weeramanthri, Tarun; Dawkins, Hugh; Goldblatt, Jack

2016-06-11

The Rare and Undiagnosed Diseases Diagnostic Service (RUDDS) refers to a genomic diagnostic platform operating within the Western Australian Government clinical services delivered through Genetic Services of Western Australia (GSWA). GSWA has provided a state-wide service for clinical genetic care for 28 years and it serves a population of 2.5 million people across a geographical area of 2.5milion Km(2). Within this context, GSWA has established a clinically integrated genomic diagnostic platform in partnership with other public health system managers and service providers, including but not limited to the Office of Population Health Genomics, Diagnostic Genomics (PathWest Laboratories) and with executive level support from the Department of Health. Herein we describe report presents the components of this service that are most relevant to the heterogeneity of paediatric clinical genetic care. Briefly the platform : i) offers multiple options including non-genetic testing; monogenic and genomic (targeted in silico filtered and whole exome) analysis; and matchmaking; ii) is delivered in a patient-centric manner that is resonant with the patient journey, it has multiple points for entry, exit and re-entry to allow people access to information they can use, when they want to receive it; iii) is synchronous with precision phenotyping methods; iv) captures new knowledge, including multiple expert review; v) is integrated with current translational genomic research activities and best practice; and vi) is designed for flexibility for interactive generation of, and integration with, clinical research for diagnostics, community engagement, policy and models of care. The RUDDS has been established as part of routine clinical genetic services and is thus sustainable, equitably managed and seeks to translate new knowledge into efficient diagnostics and improved health for the whole community.

Multiple emulsions as effective platforms for controlled anti-cancer drug delivery.

PubMed

Dluska, Ewa; Markowska-Radomska, Agnieszka; Metera, Agata; Tudek, Barbara; Kosicki, Konrad

2017-09-01

Developing pH-responsive multiple emulsion platforms for effective glioblastoma multiforme therapy with reduced toxicity, a drug release study and modeling. Cancer cell line: U87 MG, multiple emulsions with pH-responsive biopolymer and encapsulated doxorubicin (DOX); preparation of multiple emulsions in a Couette-Taylor flow biocontactor, in vitro release study of DOX (fluorescence intensity analysis), in vitro cytotoxicity study (alamarBlue cell viability assay) and numerical simulation of DOX release rates. The multiple emulsions offered a high DOX encapsulation efficiency (97.4 ± 1%) and pH modulated release rates of a drug. Multiple emulsions with a low concentration of DOX (0.02 μM) exhibited broadly advanced cell (U87 MG) cytotoxicity than free DOX solution used at the same concentration. Emulsion platforms could be explored for potential delivery of chemotherapeutics in glioblastoma multiforme therapy.

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

Generalized platform for antibody detection using the antibody catalyzed water oxidation pathway.

PubMed

Welch, M Elizabeth; Ritzert, Nicole L; Chen, Hongjun; Smith, Norah L; Tague, Michele E; Xu, Youyong; Baird, Barbara A; Abruña, Héctor D; Ober, Christopher K

2014-02-05

Infectious diseases, such as influenza, present a prominent global problem including the constant threat of pandemics that initiate in avian or other species and then pass to humans. We report a new sensor that can be specifically functionalized to detect antibodies associated with a wide range of infectious diseases in multiple species. This biosensor is based on electrochemical detection of hydrogen peroxide generated through the intrinsic catalytic activity of all antibodies: the antibody catalyzed water oxidation pathway (ACWOP). Our platform includes a polymer brush-modified surface where specific antibodies bind to conjugated haptens with high affinity and specificity. Hydrogen peroxide provides an electrochemical signal that is mediated by Resorufin/Amplex Red. We characterize the biosensor platform, using model anti-DNP antibodies, with the ultimate goal of designing a versatile device that is inexpensive, portable, reliable, and fast. We demonstrate detection of antibodies at concentrations that fall well within clinically relevant levels.

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.

Robotic Precursor Missions for Mars Habitats

NASA Technical Reports Server (NTRS)

Huntsberger, Terry; Pirjanian, Paolo; Schenker, Paul S.; Trebi-Ollennu, Ashitey; Das, Hari; Joshi, Sajay

2000-01-01

Infrastructure support for robotic colonies, manned Mars habitat, and/or robotic exploration of planetary surfaces will need to rely on the field deployment of multiple robust robots. This support includes such tasks as the deployment and servicing of power systems and ISRU generators, construction of beaconed roadways, and the site preparation and deployment of manned habitat modules. The current level of autonomy of planetary rovers such as Sojourner will need to be greatly enhanced for these types of operations. In addition, single robotic platforms will not be capable of complicated construction scenarios. Precursor robotic missions to Mars that involve teams of multiple cooperating robots to accomplish some of these tasks is a cost effective solution to the possible long timeline necessary for the deployment of a manned habitat. Ongoing work at JPL under the Mars Outpost Program in the area of robot colonies is investigating many of the technology developments necessary for such an ambitious undertaking. Some of the issues that are being addressed include behavior-based control systems for multiple cooperating robots (CAMPOUT), development of autonomous robotic systems for the rescue/repair of trapped or disabled robots, and the design and development of robotic platforms for construction tasks such as material transport and surface clearing.

Networking CD-ROMs: A Tutorial Introduction.

ERIC Educational Resources Information Center

Perone, Karen

1996-01-01

Provides an introduction to CD-ROM networking. Highlights include LAN (local area network) architectures for CD-ROM networks, peer-to-peer networks, shared file and dedicated file servers, commercial software/vendor solutions, problems, multiple hardware platforms, and multimedia. Six figures illustrate network architectures and a sidebar contains…

Platform for efficient switching between multiple devices in the intensive care unit.

PubMed

De Backere, F; Vanhove, T; Dejonghe, E; Feys, M; Herinckx, T; Vankelecom, J; Decruyenaere, J; De Turck, F

2015-01-01

This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". Handheld computers, such as tablets and smartphones, are becoming more and more accessible in the clinical care setting and in Intensive Care Units (ICUs). By making the most useful and appropriate data available on multiple devices and facilitate the switching between those devices, staff members can efficiently integrate them in their workflow, allowing for faster and more accurate decisions. This paper addresses the design of a platform for the efficient switching between multiple devices in the ICU. The key functionalities of the platform are the integration of the platform into the workflow of the medical staff and providing tailored and dynamic information at the point of care. The platform is designed based on a 3-tier architecture with a focus on extensibility, scalability and an optimal user experience. After identification to a device using Near Field Communication (NFC), the appropriate medical information will be shown on the selected device. The visualization of the data is adapted to the type of the device. A web-centric approach was used to enable extensibility and portability. A prototype of the platform was thoroughly evaluated. The scalability, performance and user experience were evaluated. Performance tests show that the response time of the system scales linearly with the amount of data. Measurements with up to 20 devices have shown no performance loss due to the concurrent use of multiple devices. The platform provides a scalable and responsive solution to enable the efficient switching between multiple devices. Due to the web-centric approach new devices can easily be integrated. The performance and scalability of the platform have been evaluated and it was shown that the response time and scalability of the platform was within an acceptable range.

Design of the compact high-resolution imaging spectrometer (CHRIS), and future developments

NASA Astrophysics Data System (ADS)

Cutter, Mike; Lobb, Dan

2017-11-01

The CHRIS instrument was launched on ESA's PROBA platform in October 2001, and is providing hyperspectral images of selected ground areas at 17m ground sampling distance, in the spectral range 415nm to 1050nm. Platform agility allows image sets to be taken at multiple view angles in each overpass. The design of the instrument is briefly outlined, including design of optics, structures, detection and in-flight calibration system. Lessons learnt from construction and operation of the experimental system, and possible design directions for future hyperspectral systems, are discussed.

Integrative set enrichment testing for multiple omics platforms

PubMed Central

2011-01-01

Background Enrichment testing assesses the overall evidence of differential expression behavior of the elements within a defined set. When we have measured many molecular aspects, e.g. gene expression, metabolites, proteins, it is desirable to assess their differential tendencies jointly across platforms using an integrated set enrichment test. In this work we explore the properties of several methods for performing a combined enrichment test using gene expression and metabolomics as the motivating platforms. Results Using two simulation models we explored the properties of several enrichment methods including two novel methods: the logistic regression 2-degree of freedom Wald test and the 2-dimensional permutation p-value for the sum-of-squared statistics test. In relation to their univariate counterparts we find that the joint tests can improve our ability to detect results that are marginal univariately. We also find that joint tests improve the ranking of associated pathways compared to their univariate counterparts. However, there is a risk of Type I error inflation with some methods and self-contained methods lose specificity when the sets are not representative of underlying association. Conclusions In this work we show that consideration of data from multiple platforms, in conjunction with summarization via a priori pathway information, leads to increased power in detection of genomic associations with phenotypes. PMID:22118224

An organophosphonate strategy for functionalizing silicon photonic biosensors

PubMed Central

Shang, Jing; Cheng, Fang; Dubey, Manish; Kaplan, Justin M.; Rawal, Meghana; Jiang, Xi; Newburg, David S.; Sullivan, Philip A.; Andrade, Rodrigo B.; Ratner, Daniel M.

2012-01-01

Silicon photonic microring resonators have established their potential for label-free and low-cost biosensing applications. However, the long-term performance of this optical sensing platform requires robust surface modification and biofunctionalization. Herein, we demonstrate a conjugation strategy based on an organophosphonate surface coating and vinyl sulfone linker to biofunctionalize silicon resonators for biomolecular sensing. To validate this method, a series of glycans, including carbohydrates and glycoconjugates, were immobilized on divinyl sulfone (DVS)/organophosphonate-modified microrings and used to characterize carbohydrate-protein and norovirus particle interactions. This biofunctional platform was able to orthogonally detect multiple specific carbohydrate-protein interactions simultaneously. Additionally, the platform was capable of reproducible binding after multiple regenerations by high-salt, high-pH or low-pH solutions and after 1-month storage in ambient conditions. This remarkable stability and durability of the organophosphonate immobilization strategy will facilitate the application of silicon microring resonators in various sensing conditions, prolong their lifetime, and minimize the cost for storage and delivery; these characteristics are requisite for developing biosensors for point-of-care and distributed diagnostics and other biomedical applications. In addition, the platform demonstrated its ability to characterize carbohydrate-mediated host-virus interactions, providing a facile method for discovering new anti-viral agents to prevent infectious disease. PMID:22220731

TMAP - A Versatile Mobile Robot

NASA Astrophysics Data System (ADS)

Weiss, Joel A.; Simmons, Richard K.

1989-03-01

TMAP, the Teleoperated Mobile All-purpose Platform, provides the Army with a low cost, light weight, flexibly designed, modularly expandable platform for support of maneuver forces and light infantry units. The highly mobile, four wheel drive, diesel-hydraulic platform is controllable at distances of up to 4km from a portable operator control unit using either fiber optic or RF control links. The Martin Marietta TMAP system is based on a hierarchical task decomposition Real-time Control System architecture that readily supports interchange of mission packages and provides the capability for simple incorporation of supervisory control concepts leading to increased system autonomy and resulting force multiplication. TMAP has been designed to support a variety of missions including target designation, anti-armor, anti-air, countermine, and reconnaissance/surveillance. As a target designation system TMAP will provide the soldier with increased survivability and effectiveness by providing substantial combat standoff, and the firepower effectiveness of several manual designator operators. Force-on-force analysis of simulated TMAP engagements indicate that TMAP should provide significant force multiplication for the Army in Air-Land Battle 2000.

Device Data Ingestion for Industrial Big Data Platforms with a Case Study †

PubMed Central

Ji, Cun; Shao, Qingshi; Sun, Jiao; Liu, Shijun; Pan, Li; Wu, Lei; Yang, Chenglei

2016-01-01

Despite having played a significant role in the Industry 4.0 era, the Internet of Things is currently faced with the challenge of how to ingest large-scale heterogeneous and multi-type device data. In response to this problem we present a heterogeneous device data ingestion model for an industrial big data platform. The model includes device templates and four strategies for data synchronization, data slicing, data splitting and data indexing, respectively. We can ingest device data from multiple sources with this heterogeneous device data ingestion model, which has been verified on our industrial big data platform. In addition, we present a case study on device data-based scenario analysis of industrial big data. PMID:26927121

Template reporter bacteriophage platform and multiple bacterial detection assays based thereon

NASA Technical Reports Server (NTRS)

Goodridge, Lawrence (Inventor)

2007-01-01

The invention is a method for the development of assays for the simultaneous detection of multiple bacteria. A bacteria of interest is selected. A host bacteria containing plasmid DNA from a T even bacteriophage that infects the bacteria of interest is infected with T4 reporter bacteriophage. After infection, the progeny bacteriophage are plating onto the bacteria of interest. The invention also includes single-tube, fast and sensitive assays which utilize the novel method.

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

PubMed Central

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

2015-01-01

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

Digital Storytelling: Reinventing Literature Circles

ERIC Educational Resources Information Center

Tobin, Maryann Tatum

2012-01-01

New literacies in reading research demand the study of comprehension skills using multiple modalities through a more complex, multi-platform view of reading. Taking into account the robust roll of technology in our daily lives, this article presents an update to the traditional literature circle lesson to include digital storytelling and…

Modular Countermine Payload for Small Robots

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

Herman Herman; Doug Few; Roelof Versteeg

2010-04-01

Payloads for small robotic platforms have historically been designed and implemented as platform and task specific solutions. A consequence of this approach is that payloads cannot be deployed on different robotic platforms without substantial re-engineering efforts. To address this issue, we developed a modular countermine payload that is designed from the ground-up to be platform agnostic. The payload consists of the multi-mission payload controller unit (PCU) coupled with the configurable mission specific threat detection, navigation and marking payloads. The multi-mission PCU has all the common electronics to control and interface to all the payloads. It also contains the embedded processormore » that can be used to run the navigational and control software. The PCU has a very flexible robot interface which can be configured to interface to various robot platforms. The threat detection payload consists of a two axis sweeping arm and the detector. The navigation payload consists of several perception sensors that are used for terrain mapping, obstacle detection and navigation. Finally, the marking payload consists of a dual-color paint marking system. Through the multi-mission PCU, all these payloads are packaged in a platform agnostic way to allow deployment on multiple robotic platforms, including Talon and Packbot.« less

Modular countermine payload for small robots

NASA Astrophysics Data System (ADS)

Herman, Herman; Few, Doug; Versteeg, Roelof; Valois, Jean-Sebastien; McMahill, Jeff; Licitra, Michael; Henciak, Edward

2010-04-01

Payloads for small robotic platforms have historically been designed and implemented as platform and task specific solutions. A consequence of this approach is that payloads cannot be deployed on different robotic platforms without substantial re-engineering efforts. To address this issue, we developed a modular countermine payload that is designed from the ground-up to be platform agnostic. The payload consists of the multi-mission payload controller unit (PCU) coupled with the configurable mission specific threat detection, navigation and marking payloads. The multi-mission PCU has all the common electronics to control and interface to all the payloads. It also contains the embedded processor that can be used to run the navigational and control software. The PCU has a very flexible robot interface which can be configured to interface to various robot platforms. The threat detection payload consists of a two axis sweeping arm and the detector. The navigation payload consists of several perception sensors that are used for terrain mapping, obstacle detection and navigation. Finally, the marking payload consists of a dual-color paint marking system. Through the multimission PCU, all these payloads are packaged in a platform agnostic way to allow deployment on multiple robotic platforms, including Talon and Packbot.

Automated platform for designing multiple robot work cells

NASA Astrophysics Data System (ADS)

Osman, N. S.; Rahman, M. A. A.; Rahman, A. A. Abdul; Kamsani, S. H.; Bali Mohamad, B. M.; Mohamad, E.; Zaini, Z. A.; Rahman, M. F. Ab; Mohamad Hatta, M. N. H.

2017-06-01

Designing the multiple robot work cells is very knowledge-intensive, intricate, and time-consuming process. This paper elaborates the development process of a computer-aided design program for generating the multiple robot work cells which offer a user-friendly interface. The primary purpose of this work is to provide a fast and easy platform for less cost and human involvement with minimum trial and errors adjustments. The automated platform is constructed based on the variant-shaped configuration concept with its mathematical model. A robot work cell layout, system components, and construction procedure of the automated platform are discussed in this paper where integration of these items will be able to automatically provide the optimum robot work cell design according to the information set by the user. This system is implemented on top of CATIA V5 software and utilises its Part Design, Assembly Design, and Macro tool. The current outcomes of this work provide a basis for future investigation in developing a flexible configuration system for the multiple robot work cells.

A Self-Sustained Wireless Multi-Sensor Platform Integrated with Printable Organic Sensors for Indoor Environmental Monitoring

PubMed Central

Wu, Chun-Chang; Chuang, Wen-Yu; Wu, Ching-Da; Su, Yu-Cheng; Huang, Yung-Yang; Huang, Yang-Jing; Peng, Sheng-Yu; Yu, Shih-An; Lin, Chih-Ting; Lu, Shey-Shi

2017-01-01

A self-sustained multi-sensor platform for indoor environmental monitoring is proposed in this paper. To reduce the cost and power consumption of the sensing platform, in the developed platform, organic materials of PEDOT:PSS and PEDOT:PSS/EB-PANI are used as the sensing films for humidity and CO2 detection, respectively. Different from traditional gas sensors, these organic sensing films can operate at room temperature without heating processes or infrared transceivers so that the power consumption of the developed humidity and the CO2 sensors can be as low as 10 μW and 5 μW, respectively. To cooperate with these low-power sensors, a Complementary Metal-Oxide-Semiconductor (CMOS) system-on-chip (SoC) is designed to amplify and to read out multiple sensor signals with low power consumption. The developed SoC includes an analog-front-end interface circuit (AFE), an analog-to-digital convertor (ADC), a digital controller and a power management unit (PMU). Scheduled by the digital controller, the sensing circuits are power gated with a small duty-cycle to reduce the average power consumption to 3.2 μW. The designed PMU converts the power scavenged from a dye sensitized solar cell (DSSC) module into required supply voltages for SoC circuits operation under typical indoor illuminance conditions. To our knowledge, this is the first multiple environmental parameters (Temperature/CO2/Humidity) sensing platform that demonstrates a true self-powering functionality for long-term operations. PMID:28353680

A standalone perfusion platform for drug testing and target validation in micro-vessel networks

PubMed Central

Zhang, Boyang; Peticone, Carlotta; Murthy, Shashi K.; Radisic, Milica

2013-01-01

Studying the effects of pharmacological agents on human endothelium includes the routine use of cell monolayers cultivated in multi-well plates. This configuration fails to recapitulate the complex architecture of vascular networks in vivo and does not capture the relationship between shear stress (i.e. flow) experienced by the cells and dose of the applied pharmacological agents. Microfluidic platforms have been applied extensively to create vascular systems in vitro; however, they rely on bulky external hardware to operate, which hinders the wide application of microfluidic chips by non-microfluidic experts. Here, we have developed a standalone perfusion platform where multiple devices were perfused at a time with a single miniaturized peristaltic pump. Using the platform, multiple micro-vessel networks, that contained three levels of branching structures, were created by culturing endothelial cells within circular micro-channel networks mimicking the geometrical configuration of natural blood vessels. To demonstrate the feasibility of our platform for drug testing and validation assays, a drug induced nitric oxide assay was performed on the engineered micro-vessel network using a panel of vaso-active drugs (acetylcholine, phenylephrine, atorvastatin, and sildenafil), showing both flow and drug dose dependent responses. The interactive effects between flow and drug dose for sildenafil could not be captured by a simple straight rectangular channel coated with endothelial cells, but it was captured in a more physiological branching circular network. A monocyte adhesion assay was also demonstrated with and without stimulation by an inflammatory cytokine, tumor necrosis factor-α. PMID:24404058

A Self-Sustained Wireless Multi-Sensor Platform Integrated with Printable Organic Sensors for Indoor Environmental Monitoring.

PubMed

Wu, Chun-Chang; Chuang, Wen-Yu; Wu, Ching-Da; Su, Yu-Cheng; Huang, Yung-Yang; Huang, Yang-Jing; Peng, Sheng-Yu; Yu, Shih-An; Lin, Chih-Ting; Lu, Shey-Shi

2017-03-29

A self-sustained multi-sensor platform for indoor environmental monitoring is proposed in this paper. To reduce the cost and power consumption of the sensing platform, in the developed platform, organic materials of PEDOT:PSS and PEDOT:PSS/EB-PANI are used as the sensing films for humidity and CO₂ detection, respectively. Different from traditional gas sensors, these organic sensing films can operate at room temperature without heating processes or infrared transceivers so that the power consumption of the developed humidity and the CO₂ sensors can be as low as 10 μW and 5 μW, respectively. To cooperate with these low-power sensors, a Complementary Metal-Oxide-Semiconductor (CMOS) system-on-chip (SoC) is designed to amplify and to read out multiple sensor signals with low power consumption. The developed SoC includes an analog-front-end interface circuit (AFE), an analog-to-digital convertor (ADC), a digital controller and a power management unit (PMU). Scheduled by the digital controller, the sensing circuits are power gated with a small duty-cycle to reduce the average power consumption to 3.2 μW. The designed PMU converts the power scavenged from a dye sensitized solar cell (DSSC) module into required supply voltages for SoC circuits operation under typical indoor illuminance conditions. To our knowledge, this is the first multiple environmental parameters (Temperature/CO₂/Humidity) sensing platform that demonstrates a true self-powering functionality for long-term operations.

An Interactive Platform to Visualize Data-Driven Clinical Pathways for the Management of Multiple Chronic Conditions.

PubMed

Zhang, Yiye; Padman, Rema

2017-01-01

Patients with multiple chronic conditions (MCC) pose an increasingly complex health management challenge worldwide, particularly due to the significant gap in our understanding of how to provide coordinated care. Drawing on our prior research on learning data-driven clinical pathways from actual practice data, this paper describes a prototype, interactive platform for visualizing the pathways of MCC to support shared decision making. Created using Python web framework, JavaScript library and our clinical pathway learning algorithm, the visualization platform allows clinicians and patients to learn the dominant patterns of co-progression of multiple clinical events from their own data, and interactively explore and interpret the pathways. We demonstrate functionalities of the platform using a cluster of 36 patients, identified from a dataset of 1,084 patients, who are diagnosed with at least chronic kidney disease, hypertension, and diabetes. Future evaluation studies will explore the use of this platform to better understand and manage MCC.

Performance Analysis and Scaling Behavior of the Terrestrial Systems Modeling Platform TerrSysMP in Large-Scale Supercomputing Environments

NASA Astrophysics Data System (ADS)

Kollet, S. J.; Goergen, K.; Gasper, F.; Shresta, P.; Sulis, M.; Rihani, J.; Simmer, C.; Vereecken, H.

2013-12-01

In studies of the terrestrial hydrologic, energy and biogeochemical cycles, integrated multi-physics simulation platforms take a central role in characterizing non-linear interactions, variances and uncertainties of system states and fluxes in reciprocity with observations. Recently developed integrated simulation platforms attempt to honor the complexity of the terrestrial system across multiple time and space scales from the deeper subsurface including groundwater dynamics into the atmosphere. Technically, this requires the coupling of atmospheric, land surface, and subsurface-surface flow models in supercomputing environments, while ensuring a high-degree of efficiency in the utilization of e.g., standard Linux clusters and massively parallel resources. A systematic performance analysis including profiling and tracing in such an application is crucial in the understanding of the runtime behavior, to identify optimum model settings, and is an efficient way to distinguish potential parallel deficiencies. On sophisticated leadership-class supercomputers, such as the 28-rack 5.9 petaFLOP IBM Blue Gene/Q 'JUQUEEN' of the Jülich Supercomputing Centre (JSC), this is a challenging task, but even more so important, when complex coupled component models are to be analysed. Here we want to present our experience from coupling, application tuning (e.g. 5-times speedup through compiler optimizations), parallel scaling and performance monitoring of the parallel Terrestrial Systems Modeling Platform TerrSysMP. The modeling platform consists of the weather prediction system COSMO of the German Weather Service; the Community Land Model, CLM of NCAR; and the variably saturated surface-subsurface flow code ParFlow. The model system relies on the Multiple Program Multiple Data (MPMD) execution model where the external Ocean-Atmosphere-Sea-Ice-Soil coupler (OASIS3) links the component models. TerrSysMP has been instrumented with the performance analysis tool Scalasca and analyzed on JUQUEEN with processor counts on the order of 10,000. The instrumentation is used in weak and strong scaling studies with real data cases and hypothetical idealized numerical experiments for detailed profiling and tracing analysis. The profiling is not only useful in identifying wait states that are due to the MPMD execution model, but also in fine-tuning resource allocation to the component models in search of the most suitable load balancing. This is especially necessary, as with numerical experiments that cover multiple (high resolution) spatial scales, the time stepping, coupling frequencies, and communication overheads are constantly shifting, which makes it necessary to re-determine the model setup with each new experimental design.

Multiple piece turbine rotor blade

DOEpatents

Jones, Russell B; Fedock, John A

2013-05-21

A multiple piece turbine rotor blade with a shell having an airfoil shape and secured between a spar and a platform with the spar including a tip end piece. a snap ring fits around the spar and abuts against the spar tip end piece on a top side and abuts against a shell on the bottom side so that the centrifugal loads from the shell is passed through the snap ring and into the spar and not through a tip cap dovetail slot and projection structure.

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-01-01

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

NGAP: A (Brief) Update PaaS, IaaS, Onbording, and the Future

NASA Technical Reports Server (NTRS)

McLaughlin, Brett; Pawloski, Andrew

2016-01-01

NASA ESDIS has charged the EED2 program with delivering a NASA-compliant, secure, cloud-based platform for application hosting. More than just a move to the cloud, this has forced us to examine all aspects of application hosting, from resource management to system administration, patching to monitoring, deployment to multiple environments. The result of this mandate is NGAP, the NASA General Application Platform. In this presentation, we will also discuss the various applications we are supporting and targeting, and their architectures including NGAPs move to support both PaaS and IaaS architectures.

Multiple piece turbine rotor blade

DOEpatents

Kimmel, Keith D.; Plank, William L.

2016-07-19

A spar and shell turbine rotor blade with a spar and a tip cap formed as a single piece, the spar includes a bottom end with dovetail or fir tree slots that engage with slots on a top end of a root section, and a platform includes an opening on a top surface for insertion of the spar in which a shell made from an exotic high temperature resistant material is secured between the tip cap and the platform. The spar is tapered to form thinner walls at the tip end to further reduce the weight and therefore a pulling force due to blade rotation. The spar and tip cap piece is made from a NiAL material to further reduce the weight and the pulling force.

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

NASA Astrophysics Data System (ADS)

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

2012-02-01

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

Reconfigurable, Cognitive Software-Defined Radio

NASA Technical Reports Server (NTRS)

Bhat, Arvind

2015-01-01

Software-defined radio (SDR) technology allows radios to be reconfigured to perform different communication functions without using multiple radios to accomplish each task. Intelligent Automation, Inc., has developed SDR platforms that switch adaptively between different operation modes. The innovation works by modifying both transmit waveforms and receiver signal processing tasks. In Phase I of the project, the company developed SDR cognitive capabilities, including adaptive modulation and coding (AMC), automatic modulation recognition (AMR), and spectrum sensing. In Phase II, these capabilities were integrated into SDR platforms. The reconfigurable transceiver design employs high-speed field-programmable gate arrays, enabling multimode operation and scalable architecture. Designs are based on commercial off-the-shelf (COTS) components and are modular in nature, making it easier to upgrade individual components rather than redesigning the entire SDR platform as technology advances.

Modular cryogenic interconnects for multi-qubit devices.

PubMed

Colless, J I; Reilly, D J

2014-11-01

We have developed a modular interconnect platform for the control and readout of multiple solid-state qubits at cryogenic temperatures. The setup provides 74 filtered dc-bias connections, 32 control and readout connections with -3 dB frequency above 5 GHz, and 4 microwave feed lines that allow low loss (less than 3 dB) transmission 10 GHz. The incorporation of a radio-frequency interposer enables the platform to be separated into two printed circuit boards, decoupling the simple board that is bonded to the qubit chip from the multilayer board that incorporates expensive connectors and components. This modular approach lifts the burden of duplicating complex interconnect circuits for every prototype device. We report the performance of this platform at milli-Kelvin temperatures, including signal transmission and crosstalk measurements.

Immunohistochemistry for predictive biomarkers in non-small cell lung cancer.

PubMed

Mino-Kenudson, Mari

2017-10-01

In the era of targeted therapy, predictive biomarker testing has become increasingly important for non-small cell lung cancer. Of multiple predictive biomarker testing methods, immunohistochemistry (IHC) is widely available and technically less challenging, can provide clinically meaningful results with a rapid turn-around-time and is more cost efficient than molecular platforms. In fact, several IHC assays for predictive biomarkers have already been implemented in routine pathology practice. In this review, we will discuss: (I) the details of anaplastic lymphoma kinase (ALK) and proto-oncogene tyrosine-protein kinase ROS (ROS1) IHC assays including the performance of multiple antibody clones, pros and cons of IHC platforms and various scoring systems to design an optimal algorithm for predictive biomarker testing; (II) issues associated with programmed death-ligand 1 (PD-L1) IHC assays; (III) appropriate pre-analytical tissue handling and selection of optimal tissue samples for predictive biomarker IHC.

Immunohistochemistry for predictive biomarkers in non-small cell lung cancer

PubMed Central

2017-01-01

In the era of targeted therapy, predictive biomarker testing has become increasingly important for non-small cell lung cancer. Of multiple predictive biomarker testing methods, immunohistochemistry (IHC) is widely available and technically less challenging, can provide clinically meaningful results with a rapid turn-around-time and is more cost efficient than molecular platforms. In fact, several IHC assays for predictive biomarkers have already been implemented in routine pathology practice. In this review, we will discuss: (I) the details of anaplastic lymphoma kinase (ALK) and proto-oncogene tyrosine-protein kinase ROS (ROS1) IHC assays including the performance of multiple antibody clones, pros and cons of IHC platforms and various scoring systems to design an optimal algorithm for predictive biomarker testing; (II) issues associated with programmed death-ligand 1 (PD-L1) IHC assays; (III) appropriate pre-analytical tissue handling and selection of optimal tissue samples for predictive biomarker IHC. PMID:29114473

RMG An Open Source Electronic Structure Code for Multi-Petaflops Calculations

NASA Astrophysics Data System (ADS)

Briggs, Emil; Lu, Wenchang; Hodak, Miroslav; Bernholc, Jerzy

RMG (Real-space Multigrid) is an open source, density functional theory code for quantum simulations of materials. It solves the Kohn-Sham equations on real-space grids, which allows for natural parallelization via domain decomposition. Either subspace or Davidson diagonalization, coupled with multigrid methods, are used to accelerate convergence. RMG is a cross platform open source package which has been used in the study of a wide range of systems, including semiconductors, biomolecules, and nanoscale electronic devices. It can optionally use GPU accelerators to improve performance on systems where they are available. The recently released versions (>2.0) support multiple GPU's per compute node, have improved performance and scalability, enhanced accuracy and support for additional hardware platforms. New versions of the code are regularly released at http://www.rmgdft.org. The releases include binaries for Linux, Windows and MacIntosh systems, automated builds for clusters using cmake, as well as versions adapted to the major supercomputing installations and platforms. Several recent, large-scale applications of RMG will be discussed.

A Naturalistic Investigation of Media Multitasking While Studying and the Effects on Exam Performance

ERIC Educational Resources Information Center

Patterson, Michael C.

2017-01-01

The present study investigated the use of multiple digital media technologies, including social networking platforms, by students while preparing for an examination (media multitasking) and the subsequent effects on exam performance. The level of media multitasking (number of simultaneous media technologies) and duration of study were used as…

A lectin-coupled, targeted proteomic mass spectrometry (MRM MS) platform for identification of multiple liver cancer biomarkers in human plasma.

PubMed

Ahn, Yeong Hee; Shin, Park Min; Oh, Na Ree; Park, Gun Wook; Kim, Hoguen; Yoo, Jong Shin

2012-09-18

Aberrantly glycosylated proteins related to liver cancer progression were captured with specific lectin and identified from human plasma by multiple reaction monitoring (MRM) mass spectrometry as multiple biomarkers for hepatocellular carcinoma (HCC). The lectin fractionation for fucosylated protein glycoforms in human plasma was conducted with a fucose-specific aleuria aurantia lectin (AAL). Following tryptic digestion of the lectin-captured fraction, plasma samples from 30 control cases (including 10 healthy, 10 hepatitis B virus [HBV], and 10 cirrhosis cases) and 10 HCC cases were quantitatively analyzed by MRM to identify which glycoproteins are viable HCC biomarkers. A1AG1, AACT, A1AT, and CERU were found to be potent biomarkers to differentiate HCC plasma from control plasmas. The AUROC generated independently from these four biomarker candidates ranged from 0.73 to 0.92. However, the lectin-coupled MRM assay with multiple combinations of biomarker candidates is superior statistically to those generated from the individual candidates with AUROC more than 0.95, which can be an alternative to the immunoassay inevitably requiring tedious development of multiple antibodies against biomarker candidates to be verified. Eventually the lectin-coupled, targeted proteomic mass spectrometry (MRM MS) platform was found to be efficient to identify multiple biomarkers from human plasma according to cancer progression. Copyright © 2012 Elsevier B.V. All rights reserved.

Modular nonvolatile solid state recorder (MONSSTR) update

NASA Astrophysics Data System (ADS)

Klang, Mark R.; Small, Martin B.; Beams, Tom

2001-12-01

Solid state recorders have begun replacing traditional tape recorders in fulfilling the requirement to record images on airborne platforms. With the advances in electro-optical, IR, SAR, Multi and Hyper-spectral sensors and video recording requirements, solid state recorders have become the recorder of choice. Solid state recorders provide the additional storage, higher sustained bandwidth, less power, less weight and smaller footprint to meet the current and future recording requirements. CALCULEX, Inc., manufactures a non-volatile flash memory solid state recorder called the MONSSTR (Modular Non-volatile Solid State Recorder). MONSSTR is being used to record images from many different digital sensors on high performance aircraft such as the RF- 4, F-16 and the Royal Air Force Tornado. MONSSTR, with its internal multiplexer, is also used to record instrumentation data. This includes multiple streams of PCM and multiple channels of 1553 data. Instrumentation data is being recorded by MONSSTR systems in a range of platforms including F-22, F-15, F-16, Comanche Helicopter and US Navy torpedos. MONSSTR can also be used as a cockpit video recorder. This paper will provide an update of the MONSSTR.

Highly stable multi-anchored magnetic nanoparticles for optical imaging within biofilms

DOE PAGES

Stone, R. C.; Fellows, B. D.; Qi, B.; ...

2015-08-05

Magnetic nanoparticles are the next tool in medical diagnoses and treatment in many different biomedical applications, including magnetic hyperthermia as alternative treatment for cancer and bacterial infections, as well as the disruption of biofilms. The colloidal stability of the magnetic nanoparticles in a biological environment is crucial for efficient delivery. A surface that can be easily modifiable can also improve the delivery and imaging properties of the magnetic nanoparticle by adding targeting and imaging moieties, providing a platform for additional modification. The strategy presented in this paper includes multiple nitroDOPA anchors for robust binding to the surface tied to themore » same polymer backbone as multiple poly(ethylene oxide) chains for steric stability. This approach provides biocompatibility and enhanced stability in fetal bovine serum (FBS) and phosphate buffer saline (PBS). As a proof of concept, these polymer-particles complexes were then modified with a near infrared dye and utilized in characterizing the integration of magnetic nanoparticles in biofilms. Finally, the work presented in this manuscript describes the synthesis and characterization of a nontoxic platform for the labeling of near IR-dyes for bioimaging.« less

The 2008 North Atlantic Spring Bloom Experiment I: Overview and Strategy

NASA Astrophysics Data System (ADS)

D'Asaro, E. A.; Lee, C.; Perry, M.; Fennel, K.; Rehm, E.; Gray, A.; Briggs, N.; Gudmundsson, K.

2008-12-01

The 2008 North Atlantic Spring Bloom Experiment (NAB08) aimed to understand carbon export from this globally important event by combining a new generation of autonomous floats and gliders equipped with a new generation of sensors, and traditional and modern shipboard observational methods. Measurements were made from early April to late June 2008 in a region southeast of Iceland near the JGOFS and MLML sites. Although Sverdrup's classical explanation for the bloom is probably broadly correct, previous observations have revealed a large degree of spatial and temporal variability, often on scales of a few kilometers, which have made detailed tests of Sverdrup's hypothesis difficult. The experiment was designed to continuously sample the bloom and its temporal and spatial 'patchiness' from the pre-bloom, wintertime conditions through the Spring and early Summer. The spatial scales were sampled by 4 Seagliders operating together as a mobile array. Measurements were made in a Lagrangian, water-following coordinate system which minimized the effects of horizontal advection and most clearly separated temporal and spatial scales. The coordinate system was defined by two Lagrangian Floats, one of which was chosen as the center of the Seaglider array. Proper measurement of the bloom by the autonomous vehicles required a robust and redundant array of sensors measuring key physical, chemical and biological variables including temperature, salinity, spectral light, oxygen, multiple optical proxies for carbon (chlorophyll fluorescence, beam-c attenuation and optical backscatter coefficients) and nitrate. Redundant measurements were made whenever possible, with nearly identical sensors on many platforms and multiple sensors measuring similar quantities on the same platform. Such care is clearly necessary, since the current generation of biogeochemical sensor require considerable efforts in calibration and interpretation. The autonomous platforms provided good coverage in space and time, but could not sample the entire range of processes that control the bloom. More detailed measurements and multiple calibrations of the autonomous platforms were made on 4 cruises, particularly a 21-day Knorr cruise in May 2008 that included collaborators from five US and five international institutions. These measurements included nutrients; particulate organic carbon and nitrogen; characterization of plankton composition and physiology by size, imaging, genomics, HPLC pigments, absorption spectra, 14C-primary productivity, and variable fluorescence; particle flux from floating sediment traps; and ADCP and CTD measurements. The experiment clearly demonstrated the ability of autonomous platforms to make biogeochemically relevant measurements of blooms. Its success, however, required intensive shipboard support for sensor calibration and interpretation. Further development of sensor technology, validation protocols, and understanding is clearly required if these measurements are to made routinely and easily.

Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design.

PubMed

Pine, P Scott; Munro, Sarah A; Parsons, Jerod R; McDaniel, Jennifer; Lucas, Anne Bergstrom; Lozach, Jean; Myers, Timothy G; Su, Qin; Jacobs-Helber, Sarah M; Salit, Marc

2016-06-24

Highly multiplexed assays for quantitation of RNA transcripts are being used in many areas of biology and medicine. Using data generated by these transcriptomic assays requires measurement assurance with appropriate controls. Methods to prototype and evaluate multiple RNA controls were developed as part of the External RNA Controls Consortium (ERCC) assessment process. These approaches included a modified Latin square design to provide a broad dynamic range of relative abundance with known differences between four complex pools of ERCC RNA transcripts spiked into a human liver total RNA background. ERCC pools were analyzed on four different microarray platforms: Agilent 1- and 2-color, Illumina bead, and NIAID lab-made spotted microarrays; and two different second-generation sequencing platforms: the Life Technologies 5500xl and the Illumina HiSeq 2500. Individual ERCC controls were assessed for reproducible performance in signal response to concentration among the platforms. Most demonstrated linear behavior if they were not located near one of the extremes of the dynamic range. Performance issues with any individual ERCC transcript could be attributed to detection limitations, platform-specific target probe issues, or potential mixing errors. Collectively, these pools of spike-in RNA controls were evaluated for suitability as surrogates for endogenous transcripts to interrogate the performance of the RNA measurement process of each platform. The controls were useful for establishing the dynamic range of the assay, as well as delineating the useable region of that range where differential expression measurements, expressed as ratios, would be expected to be accurate. The modified Latin square design presented here uses a composite testing scheme for the evaluation of multiple performance characteristics: linear performance of individual controls, signal response within dynamic range pools of controls, and ratio detection between pairs of dynamic range pools. This compact design provides an economical sample format for the evaluation of multiple external RNA controls within a single experiment per platform. These results indicate that well-designed pools of RNA controls, spiked into samples, provide measurement assurance for endogenous gene expression studies.

EMPOWER-support of patient empowerment by an intelligent self-management pathway for patients: study protocol.

PubMed

Mantwill, Sarah; Fiordelli, Maddalena; Ludolph, Ramona; Schulz, Peter J

2015-03-20

Diabetes education together with patient empowerment has shown to be key to effective self-management behavior. When delivered through information and communication technologies (ICT), this solution has shown to lead to better health outcomes. However, the potential of ICT and their integration into the healthcare environment have not yet been fully exploited. ICT should be in particular used to facilitate communication and information exchange between patient and healthcare providers. In addition, systems should include components facilitating behavior change using empowerment approaches such as goal-setting. Funded by the European Commission (FP7-ICT-2011-288209) a web/mobile based platform (EMPOWER) has been developed, which aims at supporting self-management activities of diabetes patients and their treating physicians in Germany and Turkey. The platform semantically integrates multiple information sources, such as electronic and personal health records (EHR/PHR). Patients can register patterns of daily living, record blood glucose levels, design disease management plans and set long- and short-term goals. The project actively involves the treating physician, who has the possibility to set recommendations for the patient and to monitor his/her progress on the platform. In the test-phase of EMPOWER, patients will be assigned to an intervention group and a control group. Data will be collected at baseline and three months after the intervention started. In addition, qualitative interviews will be conducted to collect extra information on usability and usefulness. Outcome measures include amongst others the Problem Areas in Diabetes questionnaire (PAID), the Summary of Diabetes Self-Care Activities and scales evaluating doctor-patient interaction. Physiological parameters, such as physical activity or blood glucose levels will be collected via the platform. Further, log files and number of logins will serve as independent variables. The interplay between multiple sources, including EHR, patients' own registered information and physicians' recommendations on one platform can have important practice implications. It might not only improve self-management activities in diabetes patients but it will also facilitate physician's work, and ultimately the physician patient relationship. The trial has been registered with Deutsches Register Klinischer Studien (German register of clinical trials) under DRKS00007699 on January 30, 2015.

Multiple Intelligences: The Most Effective Platform for Global 21st Century Educational and Instructional Methodologies

ERIC Educational Resources Information Center

McFarlane, Donovan A.

2011-01-01

This paper examines the theory of Multiple Intelligences (MI) as the most viable and effective platform for 21st century educational and instructional methodologies based on the understanding of the value of diversity in today's classrooms and educational institutions, the unique qualities and characteristics of individual learners, the…

A multicolor panel of TALE-KRAB based transcriptional repressor vectors enabling knockdown of multiple gene targets

PubMed Central

Zhang, Zhonghui; Wu, Elise; Qian, Zhijian; Wu, Wen-Shu

2014-01-01

Stable and efficient knockdown of multiple gene targets is highly desirable for dissection of molecular pathways. Because it allows sequence-specific DNA binding, transcription activator-like effector (TALE) offers a new genetic perturbation technique that allows for gene-specific repression. Here, we constructed a multicolor lentiviral TALE-Kruppel-associated box (KRAB) expression vector platform that enables knockdown of multiple gene targets. This platform is fully compatible with the Golden Gate TALEN and TAL Effector Kit 2.0, a widely used and efficient method for TALE assembly. We showed that this multicolor TALE-KRAB vector system when combined together with bone marrow transplantation could quickly knock down c-kit and PU.1 genes in hematopoietic stem and progenitor cells of recipient mice. Furthermore, our data demonstrated that this platform simultaneously knocked down both c-Kit and PU.1 genes in the same primary cell populations. Together, our results suggest that this multicolor TALE-KRAB vector platform is a promising and versatile tool for knockdown of multiple gene targets and could greatly facilitate dissection of molecular pathways. PMID:25475013

A multicolor panel of TALE-KRAB based transcriptional repressor vectors enabling knockdown of multiple gene targets.

PubMed

Zhang, Zhonghui; Wu, Elise; Qian, Zhijian; Wu, Wen-Shu

2014-12-05

Stable and efficient knockdown of multiple gene targets is highly desirable for dissection of molecular pathways. Because it allows sequence-specific DNA binding, transcription activator-like effector (TALE) offers a new genetic perturbation technique that allows for gene-specific repression. Here, we constructed a multicolor lentiviral TALE-Kruppel-associated box (KRAB) expression vector platform that enables knockdown of multiple gene targets. This platform is fully compatible with the Golden Gate TALEN and TAL Effector Kit 2.0, a widely used and efficient method for TALE assembly. We showed that this multicolor TALE-KRAB vector system when combined together with bone marrow transplantation could quickly knock down c-kit and PU.1 genes in hematopoietic stem and progenitor cells of recipient mice. Furthermore, our data demonstrated that this platform simultaneously knocked down both c-Kit and PU.1 genes in the same primary cell populations. Together, our results suggest that this multicolor TALE-KRAB vector platform is a promising and versatile tool for knockdown of multiple gene targets and could greatly facilitate dissection of molecular pathways.

Multiple Experimental Platform Consistency at NIF

NASA Astrophysics Data System (ADS)

Benedetti, L. R.; Barrios, M. A.; Bradley, D. K.; Eder, D. C.; Khan, S. F.; Izumi, N.; Jones, O. S.; Ma, T.; Nagel, S. R.; Peterson, J. L.; Rygg, J. R.; Spears, B. K.; Town, R. P.

2013-10-01

ICF experiments at NIF utilize several platforms to assess different metrics of implosion quality. In addition to the point design-a target capsule of DT ice inside a thin plastic ablator-notable platforms include: (i) Symmetry Capsules(SymCaps), mass-adjusted CH capsules filled with DT gas for similar hydrodynamic performance without the need for a DT crystal; (ii) D:3He filled SymCaps, designed for low neutron yield implosions to accommodate a variety of x-ray and optical diagnostics; and (iii) Convergent Ablators, SymCaps coupled with x-radiography to assess in-flight velocity and symmetry of the implosion over ~1 ns before stagnation and burn. These platforms are expected to be good surrogates for one another, and their hohlraum and implosion performance variations have been simulated in detail. By comparing results of similar experiments, we isolate platform-specific variations. We focus on the symmetry, convergence, and timing of x-ray emission as observed in each platform as this can be used to infer stagnation pressure and temperature. This work performed under the auspices of the U.S. Dept. of Energy by LLNL under Contract DE-AC52-07NA27344. LLNL-ABS-640865.

An intelligent monitoring and management system for cross-enterprise biomedical data sharing platform

NASA Astrophysics Data System (ADS)

Wang, Tusheng; Yang, Yuanyuan; Zhang, Jianguo

2013-03-01

In order to enable multiple disciplines of medical researchers, clinical physicians and biomedical engineers working together in a secured, efficient, and transparent cooperative environment, we had designed an e-Science platform for biomedical imaging research and application cross multiple academic institutions and hospitals in Shanghai by using grid-based or cloud-based distributed architecture and presented this work in SPIE Medical Imaging conference held in San Diego in 2012. However, when the platform integrates more and more nodes over different networks, the first challenge is that how to monitor and maintain all the hosts and services operating cross multiple academic institutions and hospitals in the e-Science platform, such as DICOM and Web based image communication services, messaging services and XDS ITI transaction services. In this presentation, we presented a system design and implementation of intelligent monitoring and management which can collect system resource status of every node in real time, alert when node or service failure occurs, and can finally improve the robustness, reliability and service continuity of this e-Science platform.

A high-content image-based method for quantitatively studying context-dependent cell population dynamics

PubMed Central

Garvey, Colleen M.; Spiller, Erin; Lindsay, Danika; Chiang, Chun-Te; Choi, Nathan C.; Agus, David B.; Mallick, Parag; Foo, Jasmine; Mumenthaler, Shannon M.

2016-01-01

Tumor progression results from a complex interplay between cellular heterogeneity, treatment response, microenvironment and heterocellular interactions. Existing approaches to characterize this interplay suffer from an inability to distinguish between multiple cell types, often lack environmental context, and are unable to perform multiplex phenotypic profiling of cell populations. Here we present a high-throughput platform for characterizing, with single-cell resolution, the dynamic phenotypic responses (i.e. morphology changes, proliferation, apoptosis) of heterogeneous cell populations both during standard growth and in response to multiple, co-occurring selective pressures. The speed of this platform enables a thorough investigation of the impacts of diverse selective pressures including genetic alterations, therapeutic interventions, heterocellular components and microenvironmental factors. The platform has been applied to both 2D and 3D culture systems and readily distinguishes between (1) cytotoxic versus cytostatic cellular responses; and (2) changes in morphological features over time and in response to perturbation. These important features can directly influence tumor evolution and clinical outcome. Our image-based approach provides a deeper insight into the cellular dynamics and heterogeneity of tumors (or other complex systems), with reduced reagents and time, offering advantages over traditional biological assays. PMID:27452732

Feature-aided multiple target tracking in the image plane

NASA Astrophysics Data System (ADS)

Brown, Andrew P.; Sullivan, Kevin J.; Miller, David J.

2006-05-01

Vast quantities of EO and IR data are collected on airborne platforms (manned and unmanned) and terrestrial platforms (including fixed installations, e.g., at street intersections), and can be exploited to aid in the global war on terrorism. However, intelligent preprocessing is required to enable operator efficiency and to provide commanders with actionable target information. To this end, we have developed an image plane tracker which automatically detects and tracks multiple targets in image sequences using both motion and feature information. The effects of platform and camera motion are compensated via image registration, and a novel change detection algorithm is applied for accurate moving target detection. The contiguous pixel blob on each moving target is segmented for use in target feature extraction and model learning. Feature-based target location measurements are used for tracking through move-stop-move maneuvers, close target spacing, and occlusion. Effective clutter suppression is achieved using joint probabilistic data association (JPDA), and confirmed target tracks are indicated for further processing or operator review. In this paper we describe the algorithms implemented in the image plane tracker and present performance results obtained with video clips from the DARPA VIVID program data collection and from a miniature unmanned aerial vehicle (UAV) flight.

A high-content image-based method for quantitatively studying context-dependent cell population dynamics

NASA Astrophysics Data System (ADS)

Garvey, Colleen M.; Spiller, Erin; Lindsay, Danika; Chiang, Chun-Te; Choi, Nathan C.; Agus, David B.; Mallick, Parag; Foo, Jasmine; Mumenthaler, Shannon M.

2016-07-01

Tumor progression results from a complex interplay between cellular heterogeneity, treatment response, microenvironment and heterocellular interactions. Existing approaches to characterize this interplay suffer from an inability to distinguish between multiple cell types, often lack environmental context, and are unable to perform multiplex phenotypic profiling of cell populations. Here we present a high-throughput platform for characterizing, with single-cell resolution, the dynamic phenotypic responses (i.e. morphology changes, proliferation, apoptosis) of heterogeneous cell populations both during standard growth and in response to multiple, co-occurring selective pressures. The speed of this platform enables a thorough investigation of the impacts of diverse selective pressures including genetic alterations, therapeutic interventions, heterocellular components and microenvironmental factors. The platform has been applied to both 2D and 3D culture systems and readily distinguishes between (1) cytotoxic versus cytostatic cellular responses; and (2) changes in morphological features over time and in response to perturbation. These important features can directly influence tumor evolution and clinical outcome. Our image-based approach provides a deeper insight into the cellular dynamics and heterogeneity of tumors (or other complex systems), with reduced reagents and time, offering advantages over traditional biological assays.

Seismicity map tools for earthquake studies

NASA Astrophysics Data System (ADS)

Boucouvalas, Anthony; Kaskebes, Athanasios; Tselikas, Nikos

2014-05-01

We report on the development of new and online set of tools for use within Google Maps, for earthquake research. We demonstrate this server based and online platform (developped with PHP, Javascript, MySQL) with the new tools using a database system with earthquake data. The platform allows us to carry out statistical and deterministic analysis on earthquake data use of Google Maps and plot various seismicity graphs. The tool box has been extended to draw on the map line segments, multiple straight lines horizontally and vertically as well as multiple circles, including geodesic lines. The application is demonstrated using localized seismic data from the geographic region of Greece as well as other global earthquake data. The application also offers regional segmentation (NxN) which allows the studying earthquake clustering, and earthquake cluster shift within the segments in space. The platform offers many filters such for plotting selected magnitude ranges or time periods. The plotting facility allows statistically based plots such as cumulative earthquake magnitude plots and earthquake magnitude histograms, calculation of 'b' etc. What is novel for the platform is the additional deterministic tools. Using the newly developed horizontal and vertical line and circle tools we have studied the spatial distribution trends of many earthquakes and we here show for the first time the link between Fibonacci Numbers and spatiotemporal location of some earthquakes. The new tools are valuable for examining visualizing trends in earthquake research as it allows calculation of statistics as well as deterministic precursors. We plan to show many new results based on our newly developed platform.

A Droplet Microfluidic Platform for Automating Genetic Engineering.

PubMed

Gach, Philip C; Shih, Steve C C; Sustarich, Jess; Keasling, Jay D; Hillson, Nathan J; Adams, Paul D; Singh, Anup K

2016-05-20

We present a water-in-oil droplet microfluidic platform for transformation, culture and expression of recombinant proteins in multiple host organisms including bacteria, yeast and fungi. The platform consists of a hybrid digital microfluidic/channel-based droplet chip with integrated temperature control to allow complete automation and integration of plasmid addition, heat-shock transformation, addition of selection medium, culture, and protein expression. The microfluidic format permitted significant reduction in consumption (100-fold) of expensive reagents such as DNA and enzymes compared to the benchtop method. The chip contains a channel to continuously replenish oil to the culture chamber to provide a fresh supply of oxygen to the cells for long-term (∼5 days) cell culture. The flow channel also replenished oil lost to evaporation and increased the number of droplets that could be processed and cultured. The platform was validated by transforming several plasmids into Escherichia coli including plasmids containing genes for fluorescent proteins GFP, BFP and RFP; plasmids with selectable markers for ampicillin or kanamycin resistance; and a Golden Gate DNA assembly reaction. We also demonstrate the applicability of this platform for transformation in widely used eukaryotic organisms such as Saccharomyces cerevisiae and Aspergillus niger. Duration and temperatures of the microfluidic heat-shock procedures were optimized to yield transformation efficiencies comparable to those obtained by benchtop methods with a throughput up to 6 droplets/min. The proposed platform offers potential for automation of molecular biology experiments significantly reducing cost, time and variability while improving throughput.

A Randomized Trial Comparing Classical Participatory Design to VandAID, an Interactive CrowdSourcing Platform to Facilitate User-centered Design.

PubMed

Dufendach, Kevin R; Koch, Sabine; Unertl, Kim M; Lehmann, Christoph U

2017-10-26

Early involvement of stakeholders in the design of medical software is particularly important due to the need to incorporate complex knowledge and actions associated with clinical work. Standard user-centered design methods include focus groups and participatory design sessions with individual stakeholders, which generally limit user involvement to a small number of individuals due to the significant time investments from designers and end users. The goal of this project was to reduce the effort for end users to participate in co-design of a software user interface by developing an interactive web-based crowdsourcing platform. In a randomized trial, we compared a new web-based crowdsourcing platform to standard participatory design sessions. We developed an interactive, modular platform that allows responsive remote customization and design feedback on a visual user interface based on user preferences. The responsive canvas is a dynamic HTML template that responds in real time to user preference selections. Upon completion, the design team can view the user's interface creations through an administrator portal and download the structured selections through a REDCap interface. We have created a software platform that allows users to customize a user interface and see the results of that customization in real time, receiving immediate feedback on the impact of their design choices. Neonatal clinicians used the new platform to successfully design and customize a neonatal handoff tool. They received no specific instruction and yet were able to use the software easily and reported high usability. VandAID, a new web-based crowdsourcing platform, can involve multiple users in user-centered design simultaneously and provides means of obtaining design feedback remotely. The software can provide design feedback at any stage in the design process, but it will be of greatest utility for specifying user requirements and evaluating iterative designs with multiple options.

A wireless modular multi-modal multi-node patch platform for robust biosignal monitoring.

PubMed

Pantelopoulos, Alexandros; Saldivar, Enrique; Roham, Masoud

2011-01-01

In this paper a wireless modular, multi-modal, multi-node patch platform is described. The platform comprises low-cost semi-disposable patch design aiming at unobtrusive ambulatory monitoring of multiple physiological parameters. Owing to its modular design it can be interfaced with various low-power RF communication and data storage technologies, while the data fusion of multi-modal and multi-node features facilitates measurement of several biosignals from multiple on-body locations for robust feature extraction. Preliminary results of the patch platform are presented which illustrate the capability to extract respiration rate from three different independent metrics, which combined together can give a more robust estimate of the actual respiratory rate.

Hyperspectral imaging to monitor simultaneously multiple protein subtypes and live track their spatial dynamics: a new platform to screen drugs for CNS diseases

NASA Astrophysics Data System (ADS)

Labrecque, S.; Sylvestre, J.-P.; Marcet, S.; Mangiarini, F.; Verhaegen, M.; De Koninck, P.; Blais-Ouellette, S.

2015-03-01

In the past decade, the efficacy of existing therapies and the discovery of innovative treatments for Central Nervous System (CNS) diseases have been limited by the lack of appropriate methods to investigate complex molecular processes at the synaptic level. In order to better understand the fundamental mechanisms that regulate diseases of the CNS, a fast fluorescence hyperspectral imaging platform was designed to track simultaneously various neurotransmitter receptors trafficking in and out of synapses. With this hyperspectral imaging platform, it was possible to image simultaneously five different synaptic proteins, including subtypes of glutamate receptors (mGluR, NMDAR, AMPAR), postsynaptic density proteins, and signaling proteins. This new imaging platform allows fast simultaneous acquisitions of at least five fluorescent markers in living neurons with a high spatial resolution. This technique provides an effective method to observe several synaptic proteins at the same time, thus study how drugs for CNS impact the spatial dynamics of these proteins.

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

A Multilevel Multiset Time-Series Model for Describing Complex Developmental Processes

PubMed Central

Ma, Xin; Shen, Jianping

2017-01-01

The authors sought to develop an analytical platform where multiple sets of time series can be examined simultaneously. This multivariate platform capable of testing interaction effects among multiple sets of time series can be very useful in empirical research. The authors demonstrated that the multilevel framework can readily accommodate this analytical capacity. Given their intention to use the multilevel multiset time-series model to pursue complicated research purposes, their resulting model is relatively simple to specify, to run, and to interpret. These advantages make the adoption of their model relatively effortless as long as researchers have the basic knowledge and skills in working with multilevel growth modeling. With multiple potential extensions of their model, the establishment of this analytical platform for analysis of multiple sets of time series can inspire researchers to pursue far more advanced research designs to address complex developmental processes in reality. PMID:29881094

Extending the scope of pooled analyses of individual patient biomarker data from heterogeneous laboratory platforms and cohorts using merging algorithms.

PubMed

Burke, Órlaith; Benton, Samantha; Szafranski, Pawel; von Dadelszen, Peter; Buhimschi, S Catalin; Cetin, Irene; Chappell, Lucy; Figueras, Francesc; Galindo, Alberto; Herraiz, Ignacio; Holzman, Claudia; Hubel, Carl; Knudsen, Ulla; Kronborg, Camilla; Laivuori, Hannele; Lapaire, Olav; McElrath, Thomas; Moertl, Manfred; Myers, Jenny; Ness, Roberta B; Oliveira, Leandro; Olson, Gayle; Poston, Lucilla; Ris-Stalpers, Carrie; Roberts, James M; Schalekamp-Timmermans, Sarah; Schlembach, Dietmar; Steegers, Eric; Stepan, Holger; Tsatsaris, Vassilis; van der Post, Joris A; Verlohren, Stefan; Villa, Pia M; Williams, David; Zeisler, Harald; Redman, Christopher W G; Staff, Anne Cathrine

2016-01-01

A common challenge in medicine, exemplified in the analysis of biomarker data, is that large studies are needed for sufficient statistical power. Often, this may only be achievable by aggregating multiple cohorts. However, different studies may use disparate platforms for laboratory analysis, which can hinder merging. Using circulating placental growth factor (PlGF), a potential biomarker for hypertensive disorders of pregnancy (HDP) such as preeclampsia, as an example, we investigated how such issues can be overcome by inter-platform standardization and merging algorithms. We studied 16,462 pregnancies from 22 study cohorts. PlGF measurements (gestational age ⩾20 weeks) analyzed on one of four platforms: R&D Systems, AlereTriage, RocheElecsys or AbbottArchitect, were available for 13,429 women. Two merging algorithms, using Z-Score and Multiple of Median transformations, were applied. Best reference curves (BRC), based on merged, transformed PlGF measurements in uncomplicated pregnancy across six gestational age groups, were estimated. Identification of HDP by these PlGF-BRCs was compared to that of platform-specific curves. We demonstrate the feasibility of merging PlGF concentrations from different analytical platforms. Overall BRC identification of HDP performed at least as well as platform-specific curves. Our method can be extended to any set of biomarkers obtained from different laboratory platforms in any field. Merged biomarker data from multiple studies will improve statistical power and enlarge our understanding of the pathophysiology and management of medical syndromes. Copyright © 2015 International Society for the Study of Hypertension in Pregnancy. Published by Elsevier B.V. All rights reserved.

PADF RF localization experiments with multi-agent caged-MAV platforms

NASA Astrophysics Data System (ADS)

Barber, Christopher; Gates, Miguel; Selmic, Rastko; Al-Issa, Huthaifa; Ordonez, Raul; Mitra, Atindra

2011-06-01

This paper provides a summary of preliminary RF direction finding results generated within an AFOSR funded testbed facility recently developed at Louisiana Tech University. This facility, denoted as the Louisiana Tech University Micro- Aerial Vehicle/Wireless Sensor Network (MAVSeN) Laboratory, has recently acquired a number of state-of-the-art MAV platforms that enable us to analyze, design, and test some of our recent results in the area of multiplatform position-adaptive direction finding (PADF) [1] [2] for localization of RF emitters in challenging embedded multipath environments. Discussions within the segmented sections of this paper include a description of the MAVSeN Laboratory and the preliminary results from the implementation of mobile platforms with the PADF algorithm. This novel approach to multi-platform RF direction finding is based on the investigation of iterative path-loss based (i.e. path loss exponent) metrics estimates that are measured across multiple platforms in order to develop a control law that robotically/intelligently positionally adapt (i.e. self-adjust) the location of each distributed/cooperative platform. The body of this paper provides a summary of our recent results on PADF and includes a discussion on state-of-the-art Sensor Mote Technologies as applied towards the development of sensor-integrated caged-MAV platform for PADF applications. Also, a discussion of recent experimental results that incorporate sample approaches to real-time singleplatform data pruning is included as part of a discussion on potential approaches to refining a basic PADF technique in order to integrate and perform distributed self-sensitivity and self-consistency analysis as part of a PADF technique with distributed robotic/intelligent features. These techniques are extracted in analytical form from a parallel study denoted as "PADF RF Localization Criteria for Multi-Model Scattering Environments". The focus here is on developing and reporting specific approaches to self-sensitivity and self-consistency within this experimental PADF framework via the exploitation of specific single-agent caged-MAV trajectories that are unique to this experiment set.

Formation Flight of Multiple UAVs via Onboard Sensor Information Sharing.

PubMed

Park, Chulwoo; Cho, Namhoon; Lee, Kyunghyun; Kim, Youdan

2015-07-17

To monitor large areas or simultaneously measure multiple points, multiple unmanned aerial vehicles (UAVs) must be flown in formation. To perform such flights, sensor information generated by each UAV should be shared via communications. Although a variety of studies have focused on the algorithms for formation flight, these studies have mainly demonstrated the performance of formation flight using numerical simulations or ground robots, which do not reflect the dynamic characteristics of UAVs. In this study, an onboard sensor information sharing system and formation flight algorithms for multiple UAVs are proposed. The communication delays of radiofrequency (RF) telemetry are analyzed to enable the implementation of the onboard sensor information sharing system. Using the sensor information sharing, the formation guidance law for multiple UAVs, which includes both a circular and close formation, is designed. The hardware system, which includes avionics and an airframe, is constructed for the proposed multi-UAV platform. A numerical simulation is performed to demonstrate the performance of the formation flight guidance and control system for multiple UAVs. Finally, a flight test is conducted to verify the proposed algorithm for the multi-UAV system.

Formation Flight of Multiple UAVs via Onboard Sensor Information Sharing

PubMed Central

Park, Chulwoo; Cho, Namhoon; Lee, Kyunghyun; Kim, Youdan

2015-01-01

To monitor large areas or simultaneously measure multiple points, multiple unmanned aerial vehicles (UAVs) must be flown in formation. To perform such flights, sensor information generated by each UAV should be shared via communications. Although a variety of studies have focused on the algorithms for formation flight, these studies have mainly demonstrated the performance of formation flight using numerical simulations or ground robots, which do not reflect the dynamic characteristics of UAVs. In this study, an onboard sensor information sharing system and formation flight algorithms for multiple UAVs are proposed. The communication delays of radiofrequency (RF) telemetry are analyzed to enable the implementation of the onboard sensor information sharing system. Using the sensor information sharing, the formation guidance law for multiple UAVs, which includes both a circular and close formation, is designed. The hardware system, which includes avionics and an airframe, is constructed for the proposed multi-UAV platform. A numerical simulation is performed to demonstrate the performance of the formation flight guidance and control system for multiple UAVs. Finally, a flight test is conducted to verify the proposed algorithm for the multi-UAV system. PMID:26193281

Platform for Post-Processing Waveform-Based NDE

NASA Technical Reports Server (NTRS)

Roth, Don J.

2010-01-01

Signal- and image-processing methods are commonly needed to extract information from the waves, improve resolution of, and highlight defects in an image. Since some similarity exists for all waveform-based nondestructive evaluation (NDE) methods, it would seem that a common software platform containing multiple signal- and image-processing techniques to process the waveforms and images makes sense where multiple techniques, scientists, engineers, and organizations are involved. NDE Wave & Image Processor Version 2.0 software provides a single, integrated signal- and image-processing and analysis environment for total NDE data processing and analysis. It brings some of the most useful algorithms developed for NDE over the past 20 years into a commercial-grade product. The software can import signal/spectroscopic data, image data, and image series data. This software offers the user hundreds of basic and advanced signal- and image-processing capabilities including esoteric 1D and 2D wavelet-based de-noising, de-trending, and filtering. Batch processing is included for signal- and image-processing capability so that an optimized sequence of processing operations can be applied to entire folders of signals, spectra, and images. Additionally, an extensive interactive model-based curve-fitting facility has been included to allow fitting of spectroscopy data such as from Raman spectroscopy. An extensive joint-time frequency module is included for analysis of non-stationary or transient data such as that from acoustic emission, vibration, or earthquake data.

An airborne robotic platform for mapping thermal structure in surface water bodies

NASA Astrophysics Data System (ADS)

Thompson, S. E.; Chung, M.; Detweiler, C.; Ore, J. P.

2015-12-01

The significance of thermal heterogeneities in small surface water bodies as drivers of mixing and for habitat provision is increasingly recognized, yet obtaining three-dimensionally resolved observations of the thermal structure of lakes and rivers remains challenging. For relatively shallow water bodies, observations of water temperature from aerial platforms are attractive: they do not require shoreline access, they can be quickly and easily deployed and redeployed, facilitating repeated sampling, and they can rapidly move between measurement locations, allowing multiple measurements to be made during single flights. However, they are also subject to well-known limitations including payload, flight duration and operability, and their effectiveness as a mobile platform for thermal sensing is still poorly characterized. In this talk, I will introduce an aerial thermal sensing platform that enables water temperature measurements to be made and spatially located throughout a water column, and present preliminary results from initial field experiments comparing in-situ temperature observations to those made from the UAS platform. The results highlight the potential scalability of the platform to provide high-resolution 3D thermal mapping of a ~1 ha lake in 2-3 flights (circa 1 hour), sufficient to resolve diurnal variations. Operability constraints and key needs for further development are also identified.

Device Access Abstractions for Resilient Information Architecture Platform for Smart Grid

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

Dubey, Abhishek; Karsai, Gabor; Volgyesi, Peter

An open application platform distributes the intelligence and control capability to local endpoints (or nodes) reducing total network traffic, improving speed of local actions by avoiding latency, and improving reliability by reducing dependencies on numerous devices and communication interfaces. The platform must be multi-tasking and able to host multiple applications running simultaneously. Given such a system, the core functions of power grid control systems include grid state determination, low level control, fault intelligence and reconfiguration, outage intelligence, power quality measurement, remote asset monitoring, configuration management, power and energy management (including local distributed energy resources, such as wind, solar and energymore » storage) can be eventually distributed. However, making this move requires extensive regression testing of systems to prove out new technologies, such as phasor measurement units (PMU). Additionally, as the complexity of the systems increase with the inclusion of new functionality (especially at the distribution and consumer levels), hidden coupling issues becomes a challenge with possible N-way interactions known and not known by device and application developers. Therefore, it is very important to provide core abstractions that ensure uniform operational semantics across such interactions. Here in this paper, we describe the pattern for abstracting device interactions we have developed for the RIAPS platform in the context of a microgrid control application we have developed.« less

Device Access Abstractions for Resilient Information Architecture Platform for Smart Grid

DOE PAGES

Dubey, Abhishek; Karsai, Gabor; Volgyesi, Peter; ...

2018-06-12

An open application platform distributes the intelligence and control capability to local endpoints (or nodes) reducing total network traffic, improving speed of local actions by avoiding latency, and improving reliability by reducing dependencies on numerous devices and communication interfaces. The platform must be multi-tasking and able to host multiple applications running simultaneously. Given such a system, the core functions of power grid control systems include grid state determination, low level control, fault intelligence and reconfiguration, outage intelligence, power quality measurement, remote asset monitoring, configuration management, power and energy management (including local distributed energy resources, such as wind, solar and energymore » storage) can be eventually distributed. However, making this move requires extensive regression testing of systems to prove out new technologies, such as phasor measurement units (PMU). Additionally, as the complexity of the systems increase with the inclusion of new functionality (especially at the distribution and consumer levels), hidden coupling issues becomes a challenge with possible N-way interactions known and not known by device and application developers. Therefore, it is very important to provide core abstractions that ensure uniform operational semantics across such interactions. Here in this paper, we describe the pattern for abstracting device interactions we have developed for the RIAPS platform in the context of a microgrid control application we have developed.« less

ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models.

PubMed

Marvel, Skylar W; To, Kimberly; Grimm, Fabian A; Wright, Fred A; Rusyn, Ivan; Reif, David M

2018-03-05

Drawing integrated conclusions from diverse source data requires synthesis across multiple types of information. The ToxPi (Toxicological Prioritization Index) is an analytical framework that was developed to enable integration of multiple sources of evidence by transforming data into integrated, visual profiles. Methodological improvements have advanced ToxPi and expanded its applicability, necessitating a new, consolidated software platform to provide functionality, while preserving flexibility for future updates. We detail the implementation of a new graphical user interface for ToxPi (Toxicological Prioritization Index) that provides interactive visualization, analysis, reporting, and portability. The interface is deployed as a stand-alone, platform-independent Java application, with a modular design to accommodate inclusion of future analytics. The new ToxPi interface introduces several features, from flexible data import formats (including legacy formats that permit backward compatibility) to similarity-based clustering to options for high-resolution graphical output. We present the new ToxPi interface for dynamic exploration, visualization, and sharing of integrated data models. The ToxPi interface is freely-available as a single compressed download that includes the main Java executable, all libraries, example data files, and a complete user manual from http://toxpi.org .

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.

Direct Adaptive Rejection of Vortex-Induced Disturbances for a Powered SPAR Platform

NASA Technical Reports Server (NTRS)

VanZwieten, Tannen S.; Balas, Mark J.; VanZwieten, James H.; Driscoll, Frederick R.

2009-01-01

The Rapidly Deployable Stable Platform (RDSP) is a novel vessel designed to be a reconfigurable, stable at-sea platform. It consists of a detachable catamaran and spar, performing missions with the spar extending vertically below the catamaran and hoisting it completely out of the water. Multiple thrusters located along the spar allow it to be actively controlled in this configuration. A controller is presented in this work that uses an adaptive feedback algorithm in conjunction with Direct Adaptive Disturbance Rejection (DADR) to mitigate persistent, vortex-induced disturbances. Given the frequency of a disturbance, the nominal DADR scheme adaptively compensates for its unknown amplitude and phase. This algorithm is extended to adapt to a disturbance frequency that is only coarsely known by including a Phase Locked Loop (PLL). The PLL improves the frequency estimate on-line, allowing the modified controller to reduce vortex-induced motions by more than 95% using achievable thrust inputs.

Measurement of cell respiration and oxygenation in standard multichannel biochips using phosphorescent O2-sensitive probes.

PubMed

Kondrashina, Alina V; Papkovsky, Dmitri B; Dmitriev, Ruslan I

2013-09-07

Measurement of cell oxygenation and oxygen consumption is useful for studies of cell bioenergetics, metabolism, mitochondrial function, drug toxicity and common pathophysiological conditions. Here we present a new platform for such applications which uses commercial multichannel biochips (μ-slides, Ibidi) and phosphorescent O2 sensitive probes. This platform was evaluated with both extracellular and intracellular O2 probes, several different cell types and treatments including mitochondrial uncoupling and inhibition, depletion of extracellular Ca(2+) and inhibition of V-ATPase and histone deacetylases. The results show that compared to the standard microwell plates currently used, the μ-slide platform provides facile O2 measurements with both suspension and adherent cells, higher sensitivity and reproducibility, and faster measurement time. It also allows re-perfusion and multiple treatments of cells and multi-parametric analyses in conjunction with other probes. Optical measurements are conducted on standard fluorescence readers and microscopes.

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.

Development of a virtual multidisciplinary lung cancer tumor board in a community setting.

PubMed

Stevenson, Marvaretta M; Irwin, Tonia; Lowry, Terry; Ahmed, Maleka Z; Walden, Thomas L; Watson, Melanie; Sutton, Linda

2013-05-01

Creating an effective platform for multidisciplinary tumor conferences can be challenging in the rural community setting. The Duke Cancer Network created an Internet-based platform for a multidisciplinary conference to enhance the care of patients with lung cancer. This conference incorporates providers from different physical locations within a rural community and affiliated providers from a university-based cancer center 2 hours away. An electronic Web conferencing tool connects providers aurally and visually. Conferences were set up using a commercially available Web conferencing platform. The video platform provides a secure Web site coupled with a secure teleconference platform to ensure patient confidentiality. Multiple disciplines are invited to participate, including radiology, radiation oncology, thoracic surgery, pathology, and medical oncology. Participants only need telephone access and Internet connection to participate. Patient histories and physicals are presented, and the Web conferencing platform allows radiologic and histologic images to be reviewed. Treatment plans for patients are discussed, allowing providers to coordinate care among the different subspecialties. Patients who need referral to the affiliated university-based cancer center for specialized services are identified. Pertinent treatment guidelines and journal articles are reviewed. On average, there are 10 participants with one to two cases presented per session. The use of a Web conferencing platform allows subspecialty providers throughout the community and hours away to discuss lung cancer patient cases. This platform increases convenience for providers, eliminating travel to a central location. Coordination of care for patients requiring multidisciplinary care is facilitated, shortening evaluation time before definitive treatment plan.

Optofluidic devices for biomolecule sensing and multiplexing

NASA Astrophysics Data System (ADS)

Ozcelik, Damla

Optofluidics which integrates photonics and microfluidics, has led to highly compact, sensitive and adaptable biomedical sensors. Optofluidic biosensors based on liquid-core anti-resonant reflecting optical waveguides (LC-ARROWs), have proven to be a highly sensitive, portable, and reconfigurable platform for fluorescence spectroscopy and detection of single biomolecules such as proteins, nucleic acids, and virus particles. However, continued improvements in sensitivity remain a major goal as we approach the ultimate limit of detecting individual bio-particles labeled by single or few fluorophores. Additionally, the ability to simultaneously detect and identify multiple biological particles or biomarkers is one of the key requirements for molecular diagnostic tests. The compactness and adaptability of these platforms can further be advanced by introducing tunability, integrating off-chip components, designing reconfigurable and customizable devices, which makes these platforms very good candidates for many different applications. The goal of this thesis was to introduce new elements in these LC-ARROW optofluidics platforms that provide major enhancements in their functionality, making them more sensitive, compact, customizable and multiplexed. First, a novel integrated tunable spectral filter that achieves effective elimination of background noise on the ARROW platform was demonstrated. A unique dual liquid-core design enabled the independent multi-wavelength tuning of the spectral filter by adjusting the refractive index and chemical properties of the liquid. In order to enhance the detection sensitivity of the platform, Y-splitter waveguides were integrated to create multiple excitation spots for each target molecule. A powerful signal processing algorithm was used to analyze the data to improve the signal-to-noise ratio (SNR) of the collected data. Next, the design, optimization and characterization of the Y-splitter waveguides are presented; and single influenza virus detection with an improved SNR was demonstrated using this platform. Finally, multiplexing capacity is introduced to the ARROW detection platform by integrating multi-mode interference (MMI) waveguides. MMI waveguides create wavelength dependent multiple excitation spots at the excitation region, allowing the spectral multiplexed detection of multiple different target molecules based on the excitation pattern, without the need for additional spectral filters. Successful spectral multiplexed detection of three different types of influenza viruses is achieved by using separate wavelengths and combination of wavelengths. This multiplexing capacity is further enhanced by taking advantage of the spatial properties of the MMI pattern, designing triple liquid-core waveguides that intersect the MMI waveguide in different locations. Furthermore, the spectral and spatial multiplexing capacities are combined in these triple liquid-core MMI platforms, allowing these devices to distinguish multiple different targets and samples simultaneously.

A Stream lined Approach for the Payload Customer in Identifying Payload Design Requirements

NASA Technical Reports Server (NTRS)

Miller, Ladonna J.; Schneider, Walter F.; Johnson, Dexer E.; Roe, Lesa B.

2001-01-01

NASA payload developers from across various disciplines were asked to identify areas where process changes would simplify their task of developing and flying flight hardware. Responses to this query included a central location for consistent hardware design requirements for middeck payloads. The multidisciplinary team assigned to review the numerous payload interface design documents is assessing the Space Shuttle middeck, the SPACEHAB Inc. locker, as well as the MultiPurpose Logistics Module (MPLM) and EXpedite the PRocessing of Experiments to Space Station (EXPRESS) rack design requirements for the payloads. They are comparing the multiple carriers and platform requirements and developing a matrix which illustrates the individual requirements, and where possible, the envelope that encompasses all of the possibilities. The matrix will be expanded to form an overall envelope that the payload developers will have the option to utilize when designing their payload's hardware. This will optimize the flexibility for payload hardware and ancillary items to be manifested on multiple carriers and platforms with minimal impact to the payload developer.

Use of baculovirus expression system for generation of virus-like particles: successes and challenges.

PubMed

Liu, Fuxiao; Wu, Xiaodong; Li, Lin; Liu, Zengshan; Wang, Zhiliang

2013-08-01

The baculovirus expression system (BES) has been one of the versatile platforms for the production of recombinant proteins requiring multiple post-translational modifications, such as folding, oligomerization, phosphorylation, glycosylation, acylation, disulfide bond formation and proteolytic cleavage. Advances in recombinant DNA technology have facilitated application of the BES, and made it possible to express multiple proteins simultaneously in a single infection and to produce multimeric proteins sharing functional similarity with their natural analogs. Therefore, the BES has been used for the production of recombinant proteins and the construction of virus-like particles (VLPs), as well as for the development of subunit vaccines, including VLP-based vaccines. The VLP, which consists of one or more structural proteins but no viral genome, resembles the authentic virion but cannot replicate in cells. The high-quality recombinant protein expression and post-translational modifications obtained with the BES, along with its capacity to produce multiple proteins, imply that it is ideally suited to VLP production. In this article, we critically review the pros and cons of using the BES as a platform to produce both enveloped and non-enveloped VLPs. Copyright © 2013 Elsevier Inc. All rights reserved.

Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing.

PubMed

Park, Bongsoo; Park, Jongsun; Cheong, Kyeong-Chae; Choi, Jaeyoung; Jung, Kyongyong; Kim, Donghan; Lee, Yong-Hwan; Ward, Todd J; O'Donnell, Kerry; Geiser, David M; Kang, Seogchan

2011-01-01

The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate species identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation for Fusarium classification. Genomes of four Fusarium species have been published with more being currently sequenced. The Cyber infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) was built to support archiving and utilization of rapidly increasing data and knowledge and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them later using multiple tools without requiring repeated copying-and-pasting of sequences. The FCP is designed to serve as an online community forum for sharing and preserving accumulated experience and knowledge to support future research and education.

CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing.

PubMed

Angiuoli, Samuel V; Matalka, Malcolm; Gussman, Aaron; Galens, Kevin; Vangala, Mahesh; Riley, David R; Arze, Cesar; White, James R; White, Owen; Fricke, W Florian

2011-08-30

Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software. We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms. The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing.

Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing

PubMed Central

Park, Bongsoo; Park, Jongsun; Cheong, Kyeong-Chae; Choi, Jaeyoung; Jung, Kyongyong; Kim, Donghan; Lee, Yong-Hwan; Ward, Todd J.; O'Donnell, Kerry; Geiser, David M.; Kang, Seogchan

2011-01-01

The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate species identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation for Fusarium classification. Genomes of four Fusarium species have been published with more being currently sequenced. The Cyber infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) was built to support archiving and utilization of rapidly increasing data and knowledge and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them later using multiple tools without requiring repeated copying-and-pasting of sequences. The FCP is designed to serve as an online community forum for sharing and preserving accumulated experience and knowledge to support future research and education. PMID:21087991

Status of development of LCOS projection displays for F-22A, F/A-18E/F, and JSF cockpits

NASA Astrophysics Data System (ADS)

Kalmanash, Michael H.

2001-09-01

Projection display technology has been found to be an attractive alternative to direct view flat panel displays in many avionics applications. The projection approach permits compact high performance systems to be tailored to specific platform needs while using a complement of commercial off the shelf (COTS) components, including liquid crystal on silicon (LCOS) microdisplay imagers. A common projection engine used on multiple platforms enables improved performance, lower cost and shorter development cycles. This paper provides a status update for projection displays under development for the F-22A, the F/A-18E/F and the Lockheed Joint Strike Fighter (JSF) aircraft.

Jungle Computing: Distributed Supercomputing Beyond Clusters, Grids, and Clouds

NASA Astrophysics Data System (ADS)

Seinstra, Frank J.; Maassen, Jason; van Nieuwpoort, Rob V.; Drost, Niels; van Kessel, Timo; van Werkhoven, Ben; Urbani, Jacopo; Jacobs, Ceriel; Kielmann, Thilo; Bal, Henri E.

In recent years, the application of high-performance and distributed computing in scientific practice has become increasingly wide spread. Among the most widely available platforms to scientists are clusters, grids, and cloud systems. Such infrastructures currently are undergoing revolutionary change due to the integration of many-core technologies, providing orders-of-magnitude speed improvements for selected compute kernels. With high-performance and distributed computing systems thus becoming more heterogeneous and hierarchical, programming complexity is vastly increased. Further complexities arise because urgent desire for scalability and issues including data distribution, software heterogeneity, and ad hoc hardware availability commonly force scientists into simultaneous use of multiple platforms (e.g., clusters, grids, and clouds used concurrently). A true computing jungle.

Portability and Cross-Platform Performance of an MPI-Based Parallel Polygon Renderer

NASA Technical Reports Server (NTRS)

Crockett, Thomas W.

1999-01-01

Visualizing the results of computations performed on large-scale parallel computers is a challenging problem, due to the size of the datasets involved. One approach is to perform the visualization and graphics operations in place, exploiting the available parallelism to obtain the necessary rendering performance. Over the past several years, we have been developing algorithms and software to support visualization applications on NASA's parallel supercomputers. Our results have been incorporated into a parallel polygon rendering system called PGL. PGL was initially developed on tightly-coupled distributed-memory message-passing systems, including Intel's iPSC/860 and Paragon, and IBM's SP2. Over the past year, we have ported it to a variety of additional platforms, including the HP Exemplar, SGI Origin2OOO, Cray T3E, and clusters of Sun workstations. In implementing PGL, we have had two primary goals: cross-platform portability and high performance. Portability is important because (1) our manpower resources are limited, making it difficult to develop and maintain multiple versions of the code, and (2) NASA's complement of parallel computing platforms is diverse and subject to frequent change. Performance is important in delivering adequate rendering rates for complex scenes and ensuring that parallel computing resources are used effectively. Unfortunately, these two goals are often at odds. In this paper we report on our experiences with portability and performance of the PGL polygon renderer across a range of parallel computing platforms.

Iowa Flood Information System: Towards Integrated Data Management, Analysis and Visualization

NASA Astrophysics Data System (ADS)

Demir, I.; Krajewski, W. F.; Goska, R.; Mantilla, R.; Weber, L. J.; Young, N.

2012-04-01

The Iowa Flood Information System (IFIS) is a web-based platform developed by the Iowa Flood Center (IFC) to provide access to flood inundation maps, real-time flood conditions, flood forecasts both short-term and seasonal, flood-related data, information and interactive visualizations for communities in Iowa. The key element of the system's architecture is the notion of community. Locations of the communities, those near streams and rivers, define basin boundaries. The IFIS provides community-centric watershed and river characteristics, weather (rainfall) conditions, and streamflow data and visualization tools. Interactive interfaces allow access to inundation maps for different stage and return period values, and flooding scenarios with contributions from multiple rivers. Real-time and historical data of water levels, gauge heights, and rainfall conditions are available in the IFIS by streaming data from automated IFC bridge sensors, USGS stream gauges, NEXRAD radars, and NWS forecasts. Simple 2D and 3D interactive visualizations in the IFIS make the data more understandable to general public. Users are able to filter data sources for their communities and selected rivers. The data and information on IFIS is also accessible through web services and mobile applications. The IFIS is optimized for various browsers and screen sizes to provide access through multiple platforms including tablets and mobile devices. The IFIS includes a rainfall-runoff forecast model to provide a five-day flood risk estimate for around 500 communities in Iowa. Multiple view modes in the IFIS accommodate different user types from general public to researchers and decision makers by providing different level of tools and details. River view mode allows users to visualize data from multiple IFC bridge sensors and USGS stream gauges to follow flooding condition along a river. The IFIS will help communities make better-informed decisions on the occurrence of floods, and will alert communities in advance to help minimize damage of floods. This presentation provides an overview and live demonstration of the tools and interfaces in the IFIS developed to date to provide a platform for one-stop access to flood related data, visualizations, flood conditions, and forecast.

Iowa Flood Information System

NASA Astrophysics Data System (ADS)

Demir, I.; Krajewski, W. F.; Goska, R.; Mantilla, R.; Weber, L. J.; Young, N.

2011-12-01

The Iowa Flood Information System (IFIS) is a web-based platform developed by the Iowa Flood Center (IFC) to provide access to flood inundation maps, real-time flood conditions, flood forecasts both short-term and seasonal, flood-related data, information and interactive visualizations for communities in Iowa. The key element of the system's architecture is the notion of community. Locations of the communities, those near streams and rivers, define basin boundaries. The IFIS provides community-centric watershed and river characteristics, weather (rainfall) conditions, and streamflow data and visualization tools. Interactive interfaces allow access to inundation maps for different stage and return period values, and flooding scenarios with contributions from multiple rivers. Real-time and historical data of water levels, gauge heights, and rainfall conditions are available in the IFIS by streaming data from automated IFC bridge sensors, USGS stream gauges, NEXRAD radars, and NWS forecasts. Simple 2D and 3D interactive visualizations in the IFIS make the data more understandable to general public. Users are able to filter data sources for their communities and selected rivers. The data and information on IFIS is also accessible through web services and mobile applications. The IFIS is optimized for various browsers and screen sizes to provide access through multiple platforms including tablets and mobile devices. The IFIS includes a rainfall-runoff forecast model to provide a five-day flood risk estimate for around 500 communities in Iowa. Multiple view modes in the IFIS accommodate different user types from general public to researchers and decision makers by providing different level of tools and details. River view mode allows users to visualize data from multiple IFC bridge sensors and USGS stream gauges to follow flooding condition along a river. The IFIS will help communities make better-informed decisions on the occurrence of floods, and will alert communities in advance to help minimize damage of floods. This presentation provides an overview of the tools and interfaces in the IFIS developed to date to provide a platform for one-stop access to flood related data, visualizations, flood conditions, and forecast.

Flood Risk Management in Iowa through an Integrated Flood Information System

NASA Astrophysics Data System (ADS)

Demir, Ibrahim; Krajewski, Witold

2013-04-01

The Iowa Flood Information System (IFIS) is a web-based platform developed by the Iowa Flood Center (IFC) to provide access to flood inundation maps, real-time flood conditions, flood forecasts both short-term and seasonal, flood-related data, information and interactive visualizations for communities in Iowa. The key element of the system's architecture is the notion of community. Locations of the communities, those near streams and rivers, define basin boundaries. The IFIS provides community-centric watershed and river characteristics, weather (rainfall) conditions, and streamflow data and visualization tools. Interactive interfaces allow access to inundation maps for different stage and return period values, and flooding scenarios with contributions from multiple rivers. Real-time and historical data of water levels, gauge heights, and rainfall conditions are available in the IFIS by streaming data from automated IFC bridge sensors, USGS stream gauges, NEXRAD radars, and NWS forecasts. Simple 2D and 3D interactive visualizations in the IFIS make the data more understandable to general public. Users are able to filter data sources for their communities and selected rivers. The data and information on IFIS is also accessible through web services and mobile applications. The IFIS is optimized for various browsers and screen sizes to provide access through multiple platforms including tablets and mobile devices. The IFIS includes a rainfall-runoff forecast model to provide a five-day flood risk estimate for around 1100 communities in Iowa. Multiple view modes in the IFIS accommodate different user types from general public to researchers and decision makers by providing different level of tools and details. River view mode allows users to visualize data from multiple IFC bridge sensors and USGS stream gauges to follow flooding condition along a river. The IFIS will help communities make better-informed decisions on the occurrence of floods, and will alert communities in advance to help minimize damage of floods. This presentation provides an overview and live demonstration of the tools and interfaces in the IFIS developed to date to provide a platform for one-stop access to flood related data, visualizations, flood conditions, and forecast.

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.

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 ...

Duel between an ASAT with Multiple Kill Vehicles and a Space-Based Weapons Platform with Kinetic Energy Weapons

DTIC Science & Technology

1986-01-01

b~l~l Ec B-J COPYl OF 2 COPIES AD-A241 820 �liJiil I~ I III 111 r11 III lii II - IDA MEMORANDUM REPORT M-144 DUEL BETWEEN AN ASAT WITH MULTIPLE...20301-7100 ELEMENT NO. NO. NO. ACC3SSION NO. _____ ____ ____ ____ ____ _ ____ _ _T-3__187 I1I TITLE (include S*CuHWl CWia cetlonVi Duel Between an ASAT...neceuaiy andi identd by b~lock number) iA ,mathematical model is described for a duel beltween a ground-based anti-satellite (ASAT) and a space-based

MyDiabetesMyWay: An Evolving National Data Driven Diabetes Self-Management Platform.

PubMed

Wake, Deborah J; He, Jinzhang; Czesak, Anna Maria; Mughal, Fezan; Cunningham, Scott G

2016-09-01

MyDiabetesMyWay (MDMW) is an award-wining national electronic personal health record and self-management platform for diabetes patients in Scotland. This platform links multiple national institutional and patient-recorded data sources to provide a unique resource for patient care and self-management. This review considers the current evidence for online interventions in diabetes and discusses these in the context of current and ongoing developments for MDMW. Evaluation of MDMW through patient reported outcomes demonstrates a positive impact on self-management. User feedback has highlighted barriers to uptake and has guided platform evolution from an education resource website to an electronic personal health record now encompassing remote monitoring, communication tools and personalized education links. Challenges in delivering digital interventions for long-term conditions include integration of data between institutional and personal recorded sources to perform big data analytics and facilitating technology use in those with disabilities, low digital literacy, low socioeconomic status and in minority groups. The potential for technology supported health improvement is great, but awareness and adoption by health workers and patients remains a significant barrier. © 2016 Diabetes Technology Society.

MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.

PubMed

Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

2016-01-01

Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available. We have therefore developed a new pipeline called MutAid to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. It performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid is freely available at https://sourceforge.net/projects/mutaid.

MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics

PubMed Central

Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

2016-01-01

Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available. We have therefore developed a new pipeline called MutAid to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. It performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid is freely available at https://sourceforge.net/projects/mutaid. PMID:26840129

Multidimensional bioseparation with modular microfluidics

DOEpatents

Chirica, Gabriela S.; Renzi, Ronald F.

2013-08-27

A multidimensional chemical separation and analysis system is described including a prototyping platform and modular microfluidic components capable of rapid and convenient assembly, alteration and disassembly of numerous candidate separation systems. Partial or total computer control of the separation system is possible. Single or multiple alternative processing trains can be tested, optimized and/or run in parallel. Examples related to the separation and analysis of human bodily fluids are given.

Programmable bio-nano-chip system for saliva diagnostics

NASA Astrophysics Data System (ADS)

Christodoulides, Nicolaos; De La Garza, Richard; Simmons, Glennon W.; McRae, Michael P.; Wong, Jorge; Kosten, Thomas R.; Miller, Craig S.; Ebersole, Jeffrey L.; McDevitt, John

2014-06-01

This manuscript describes programmable Bio-Nano-Chip (p-BNC) approach that serves as miniaturized assay platform designed for the rapid detection and quantitation of multiple analytes in biological fluids along with the specific applications in salivary diagnostics intended for the point of need (PON). Included here are oral fluid-based tests for local periodontal disease, systemic cardiac disease and multiplexed tests for drugs of abuse.

Drowned carbonate platforms in the Huon Gulf, Papua New Guinea

NASA Astrophysics Data System (ADS)

Webster, Jody M.; Wallace, Laura; Silver, Eli; Applegate, Bruce; Potts, Donald; Braga, Juan Carlos; Riker-Coleman, Kristin; Gallup, Christina

2004-11-01

The western Huon Gulf, Papua New Guinea, is an actively subsiding foreland basin dominated by drowned carbonate platforms. We investigated these platforms using new high-resolution multibeam, side-scan sonar and seismic data, combined with submersible observations and previously published radiometric and sedimentary facies data. The data reveal 14 distinct drowned carbonate platforms and numerous pinnacles/banks that increase in age (˜20-450 kyr) and depth (0.1-2.5 km) NE toward the Ramu-Markham Trench. Superimposed on this overall downward flexing of the platforms toward the trench is a systematic tilting of the deep platforms 15 m/km toward the NW and the shallow platforms 2 m/km toward the SE. This may reflect the encroaching thrust load from the NW (Finisterre Range) and spatial variations in the flexural rigidity of the underlying basement. The drowned platforms form a complex system of promontories and reentrants, with abundant pinnacles and banks preserved at similar depths seaward of the main platforms. This configuration closely mimics the present-day Huon coastline and its seaward islands fringed by modern coral reefs. The platforms retain structural, morphologic, and sedimentary facies evidence of primary platform growth, drowning, and subsequent backstepping, despite some lateral erosion of the platform margins (<100 m slope defacement) by mass wasting. Both platforms and pinnacles are composite features containing multiple terrace levels and notches, corresponding to multiple phases of growth, emergence, and drowning in response to rapid climatic and sea level changes during the evolution of each structure. On the basis of all observational and numerical modeling data, we propose a chronology for the initiation, growth, and drowning of the 14 platforms. Over shorter timescales (≤100 kyr) the rate and amplitude of eustatic sea level changes are critical in controlling initiation, growth, drowning or subaerial exposure, subsequent reinitiation, and final drowning of the platforms. However, continued tectonic subsidence and basement substrate morphology influence the overall backstepping geometry and subsequent tilting of the platforms over longer timescales (≥100-500 kyr).

Controlling multiple security robots in a warehouse environment

NASA Technical Reports Server (NTRS)

Everett, H. R.; Gilbreath, G. A.; Heath-Pastore, T. A.; Laird, R. T.

1994-01-01

The Naval Command Control and Ocean Surveillance Center (NCCOSC) has developed an architecture to provide coordinated control of multiple autonomous vehicles from a single host console. The multiple robot host architecture (MRHA) is a distributed multiprocessing system that can be expanded to accommodate as many as 32 robots. The initial application will employ eight Cybermotion K2A Navmaster robots configured as remote security platforms in support of the Mobile Detection Assessment and Response System (MDARS) Program. This paper discusses developmental testing of the MRHA in an operational warehouse environment, with two actual and four simulated robotic platforms.

Monteris AXiiiS Stereotactic Miniframe for Intracranial Biopsy: Precision, Feasibility, and Ease of Use.

PubMed

Manjila, Sunil; Knudson, Kathleen E; Johnson, Carleton; Sloan, Andrew E

2016-06-01

Stereotactic biopsy is an important and minimally invasive technique used for a variety of indications in neurosurgery. Initially, this technique required a frame, but recently there have been a number of newer, less cumbersome approaches to biopsy including robotic arms, fixed arms, and, more recently, skull-mounted miniframes. Miniframes are attractive because they are disposable and low profile. However, the relatively limited degree of freedom offered by currently available devices necessitates a preplanned burr hole, which in turn limits flexibility and multiple trajectories. The AXiiiS device is a skull-mounted, magnetic resonance imaging-compatible miniframe that provides a similar degree of freedom with a frame while maintaining a low-profile, disposable platform. To assess the image-guided trajectory alignment accuracy using AXiiiS stereotactic miniframe biopsy of intracranial lesions. The accuracy of the AXiiiS device is compared with the Navigus Trajectory Guide as platforms. After approval by our institutional review board, medical records of 10 neurosurgical patients with intracranial pathologies were chosen for AXiiiS stereotactic miniframe biopsy, and histological correlation was obtained. Ten reported cases demonstrate the precision and ease of using the AXiiiS stereotactic miniframe for biopsy of intracranial lesions in conjunction with preoperative magnetic resonance imaging. Multiple trajectories and angles have been used with precision and safety. The AXiiiS stereotactic miniframe is a feasible, safe, and disposable platform for multitrajectory intracranial biopsies. Compared with existing platforms, this novel device provides a more stable base and wider limits of trajectory angles with comparable accuracy and precision.

Maritime Analytics Prototype: Final Development Report

DTIC Science & Technology

2014-04-01

access management platform OpenAM , support for multiple instances of the same type of widget and support for installation specific configuration files to...et de la gestion de l’accès OpenAM , le support pour plusieurs instances du même type de widget et le support des fichiers d’installation de...open source authentication and access management platform OpenAM , support for multiple instances of the same type of widget and support for

Human-Robot Teaming for Hydrologic Data Gathering at Multiple Scales

NASA Astrophysics Data System (ADS)

Peschel, J.; Young, S. N.

2017-12-01

The use of personal robot-assistive technology by researchers and practitioners for hydrologic data gathering has grown in recent years as barriers to platform capability, cost, and human-robot interaction have been overcome. One consequence to this growth is a broad availability of unmanned platforms that might or might not be suitable for a specific hydrologic investigation. Through multiple field studies, a set of recommendations has been developed to help guide novice through experienced users in choosing the appropriate unmanned platforms for a given application. This talk will present a series of hydrologic data sets gathered using a human-robot teaming approach that has leveraged unmanned aerial, ground, and surface vehicles over multiple scales. The field case studies discussed will be connected to the best practices, also provided in the presentation. This talk will be of interest to geoscience researchers and practitioners, in general, as well as those working in fields related to emerging technologies.

EduGATE - basic examples for educative purpose using the GATE simulation platform.

PubMed

Pietrzyk, Uwe; Zakhnini, Abdelhamid; Axer, Markus; Sauerzapf, Sophie; Benoit, Didier; Gaens, Michaela

2013-02-01

EduGATE is a collection of basic examples to introduce students to the fundamental physical aspects of medical imaging devices. It is based on the GATE platform, which has received a wide acceptance in the field of simulating medical imaging devices including SPECT, PET, CT and also applications in radiation therapy. GATE can be configured by commands, which are, for the sake of simplicity, listed in a collection of one or more macro files to set up phantoms, multiple types of sources, detection device, and acquisition parameters. The aim of the EduGATE is to use all these helpful features of GATE to provide insights into the physics of medical imaging by means of a collection of very basic and simple GATE macros in connection with analysis programs based on ROOT, a framework for data processing. A graphical user interface to define a configuration is also included. Copyright © 2012. Published by Elsevier GmbH.

Integrated Display and Simulation for Automatic Dependent Surveillance-Broadcast and Traffic Collision Avoidance System Data Fusion.

PubMed

Wang, Yanran; Xiao, Gang; Dai, Zhouyun

2017-11-13

Automatic Dependent Surveillance-Broadcast (ADS-B) is the direction of airspace surveillance development. Research analyzing the benefits of Traffic Collision Avoidance System (TCAS) and ADS-B data fusion is almost absent. The paper proposes an ADS-B minimum system from ADS-B In and ADS-B Out. In ADS-B In, a fusion model with a variable sampling Variational Bayesian-Interacting Multiple Model (VSVB-IMM) algorithm is proposed for integrated display and an airspace traffic situation display is developed by using ADS-B information. ADS-B Out includes ADS-B Out transmission based on a simulator platform and an Unmanned Aerial Vehicle (UAV) platform. This paper describes the overall implementation of ADS-B minimum system, including theoretical model design, experimental simulation verification, engineering implementation, results analysis, etc. Simulation and implementation results show that the fused system has better performance than each independent subsystem and it can work well in engineering applications.

Development of a Virtual Multidisciplinary Lung Cancer Tumor Board in a Community Setting

PubMed Central

Stevenson, Marvaretta M.; Irwin, Tonia; Lowry, Terry; Ahmed, Maleka Z.; Walden, Thomas L.; Watson, Melanie; Sutton, Linda

2013-01-01

Purpose: Creating an effective platform for multidisciplinary tumor conferences can be challenging in the rural community setting. The Duke Cancer Network created an Internet-based platform for a multidisciplinary conference to enhance the care of patients with lung cancer. This conference incorporates providers from different physical locations within a rural community and affiliated providers from a university-based cancer center 2 hours away. An electronic Web conferencing tool connects providers aurally and visually. Methods: Conferences were set up using a commercially available Web conferencing platform. The video platform provides a secure Web site coupled with a secure teleconference platform to ensure patient confidentiality. Multiple disciplines are invited to participate, including radiology, radiation oncology, thoracic surgery, pathology, and medical oncology. Participants only need telephone access and Internet connection to participate. Results: Patient histories and physicals are presented, and the Web conferencing platform allows radiologic and histologic images to be reviewed. Treatment plans for patients are discussed, allowing providers to coordinate care among the different subspecialties. Patients who need referral to the affiliated university-based cancer center for specialized services are identified. Pertinent treatment guidelines and journal articles are reviewed. On average, there are 10 participants with one to two cases presented per session. Conclusion: The use of a Web conferencing platform allows subspecialty providers throughout the community and hours away to discuss lung cancer patient cases. This platform increases convenience for providers, eliminating travel to a central location. Coordination of care for patients requiring multidisciplinary care is facilitated, shortening evaluation time before definitive treatment plan. PMID:23942505

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Multiple Ships and Multiple Media: A Flexible Telepresence Program

NASA Astrophysics Data System (ADS)

Pelz, M.; Hoeberechts, M.; Riddell, D. J.; Ewing, N.

2016-02-01

Ocean Networks Canada (ONC) uses a number of research and exploration vessels equipped with remotely operated vehicles (ROVs) to maintain the NEPTUNE and VENUS cabled ocean observatories off the west coast of British Columbia, Canada. Maintenance expeditions range from several days to multiple weeks and encompass a range of activities including deploying new instruments, laying cable, recovering platforms, scientific sampling and conducting multibeam and visual surveys. In order to engage the widest possible participation in at-sea work, ONC uses telepresence technology to communicate from ship to shore and back with scientists, students, teachers and online viewers. In this presentation, we explore the challenge of designing a sustainable and flexible telepresence program which can be supported across multiple ship and ROV platforms, sometimes simultaneously. To meet outreach and education objectives, onboard educators conduct presentations to K-12 and post-secondary classrooms, museums and science centres on a daily basis. Online commentary by the educators, dive chief and ROV pilots accompanies the ROV dive footage and is streamed online 24/7 during underwater operations. Sharing the sights and sounds of the expeditions with students and educators ashore, including those in remote and inland communities, creates a unique learning environment for both formal and informal education audiences. As space is always a limiting factor on expeditions, the use of telepresence and other communication media enables ONC to simultaneously achieve engineering and science priorities at sea while communicating the successes and challenges of the expedition back to shore. Scientists and engineers provide guidance for operations from shore using a variety of communication technologies. We give examples from Ocean Networks Canada's most recent expedition, Fall 2015, which involved co-ordinated operations with three vessels - the R/V Thompson, the E/V Nautilus and the C/S Wave Venture.

Real-time Java simulations of multiple interference dielectric filters

NASA Astrophysics Data System (ADS)

Kireev, Alexandre N.; Martin, Olivier J. F.

2008-12-01

An interactive Java applet for real-time simulation and visualization of the transmittance properties of multiple interference dielectric filters is presented. The most commonly used interference filters as well as the state-of-the-art ones are embedded in this platform-independent applet which can serve research and education purposes. The Transmittance applet can be freely downloaded from the site http://cpc.cs.qub.ac.uk. Program summaryProgram title: Transmittance Catalogue identifier: AEBQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5778 No. of bytes in distributed program, including test data, etc.: 90 474 Distribution format: tar.gz Programming language: Java Computer: Developed on PC-Pentium platform Operating system: Any Java-enabled OS. Applet was tested on Windows ME, XP, Sun Solaris, Mac OS RAM: Variable Classification: 18 Nature of problem: Sophisticated wavelength selective multiple interference filters can include some tens or even hundreds of dielectric layers. The spectral response of such a stack is not obvious. On the other hand, there is a strong demand from application designers and students to get a quick insight into the properties of a given filter. Solution method: A Java applet was developed for the computation and the visualization of the transmittance of multilayer interference filters. It is simple to use and the embedded filter library can serve educational purposes. Also, its ability to handle complex structures will be appreciated as a useful research and development tool. Running time: Real-time simulations

Network-based drug discovery by integrating systems biology and computational technologies

PubMed Central

Leung, Elaine L.; Cao, Zhi-Wei; Jiang, Zhi-Hong; Zhou, Hua

2013-01-01

Network-based intervention has been a trend of curing systemic diseases, but it relies on regimen optimization and valid multi-target actions of the drugs. The complex multi-component nature of medicinal herbs may serve as valuable resources for network-based multi-target drug discovery due to its potential treatment effects by synergy. Recently, robustness of multiple systems biology platforms shows powerful to uncover molecular mechanisms and connections between the drugs and their targeting dynamic network. However, optimization methods of drug combination are insufficient, owning to lacking of tighter integration across multiple ‘-omics’ databases. The newly developed algorithm- or network-based computational models can tightly integrate ‘-omics’ databases and optimize combinational regimens of drug development, which encourage using medicinal herbs to develop into new wave of network-based multi-target drugs. However, challenges on further integration across the databases of medicinal herbs with multiple system biology platforms for multi-target drug optimization remain to the uncertain reliability of individual data sets, width and depth and degree of standardization of herbal medicine. Standardization of the methodology and terminology of multiple system biology and herbal database would facilitate the integration. Enhance public accessible databases and the number of research using system biology platform on herbal medicine would be helpful. Further integration across various ‘-omics’ platforms and computational tools would accelerate development of network-based drug discovery and network medicine. PMID:22877768

ScaMo: Realisation of an OO-functional DSL for cross platform mobile applications development

NASA Astrophysics Data System (ADS)

Macos, Dragan; Solymosi, Andreas

2013-10-01

The software market is dynamically changing: the Internet is going mobile, the software applications are shifting from the desktop hardware onto the mobile devices. The largest markets are the mobile applications for iOS, Android and Windows Phone and for the purpose the typical programming languages include Objective-C, Java and C ♯. The realization of the native applications implies the integration of the developed software into the environments of mentioned mobile operating systems to enable the access to different hardware components of the devices: GPS module, display, GSM module, etc. This paper deals with the definition and possible implementation of an environment for the automatic application generation for multiple mobile platforms. It is based on a DSL for mobile application development, which includes the programming language Scala and a DSL defined in Scala. As part of a multi-stage cross-compiling algorithm, this language is translated into the language of the affected mobile platform. The advantage of our method lies in the expressiveness of the defined language and the transparent source code translation between different languages, which implies, for example, the advantages of debugging and development of the generated code.

Disposable world-to-chip interface for digital microfluidics

DOEpatents

Van Dam, R. Michael; Shah, Gaurav; Keng, Pei-Yuin

2017-05-16

The present disclosure sets forth incorporating microfluidic chips interfaces for use with digital microfluidic processes. Methods and devices according to the present disclosure utilize compact, integrated platforms that interface with a chip upstream and downstream of the reaction, as well as between intermediate reaction steps if needed. In some embodiments these interfaces are automated, including automation of a multiple reagent process. Various reagent delivery systems and methods are also disclosed.

Auditory Modeling for Noisy Speech Recognition.

DTIC Science & Technology

2000-01-01

multiple platforms including PCs, workstations, and DSPs. A prototype version of the SOS process was tested on the Japanese Hiragana language with good...judgment among linguists. American English has 48 phonetic sounds in the ARPABET representation. Hiragana , the Japanese phonetic language, has only 20... Japanese Hiragana ," H.L. Pfister, FL 95, 1995. "State Recognition for Noisy Dynamic Systems," H.L. Pfister, Tech 2005, Chicago, 1995. "Experiences

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

PubMed

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

2017-04-26

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

The iCRISPR platform for rapid genome editing in human pluripotent stem cells.

PubMed

Zhu, Zengrong; González, Federico; Huangfu, Danwei

2014-01-01

Human pluripotent stem cells (hPSCs) have the potential to generate all adult cell types, including rare or inaccessible human cell populations, thus providing a unique platform for disease studies. To realize this promise, it is essential to develop methods for efficient genetic manipulations in hPSCs. Established using TALEN (transcription activator-like effector nuclease) and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) systems, the iCRISPR platform supports a variety of genome-engineering approaches with high efficiencies. Here, we first describe the establishment of the iCRISPR platform through TALEN-mediated targeting of inducible Cas9 expression cassettes into the AAVS1 locus. Next, we provide a series of technical procedures for using iCRISPR to achieve one-step knockout of one or multiple gene(s), "scarless" introduction of precise nucleotide alterations, as well as inducible knockout during hPSC differentiation. We present an optimized workflow, as well as guidelines for the selection of CRISPR targeting sequences and the design of single-stranded DNA (ssDNA) homology-directed DNA repair templates for the introduction of specific nucleotide alterations. We have successfully used these protocols in four different hPSC lines, including human embryonic stem cells and induced pluripotent stem cells. Once the iCRISPR platform is established, clonal lines with desired genetic modifications can be established in as little as 1 month. The methods described here enable a wide range of genome-engineering applications in hPSCs, thus providing a valuable resource for the creation of diverse hPSC-based disease models with superior speed and ease.

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

PubMed Central

2011-01-01

Background Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for high-throughput applications. Cloud computing platforms provide on-demand access to computing infrastructure over the Internet and can be used in combination with custom built virtual machines to distribute pre-packaged with pre-configured software. Results We describe the Cloud Virtual Resource, CloVR, a new desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. In a case study, we demonstrate the use of CloVR to automatically process next-generation sequencing data on multiple cloud computing platforms. Conclusion The CloVR VM and associated architecture lowers the barrier of entry for utilizing complex analysis protocols on both local single- and multi-core computers and cloud systems for high throughput data processing. PMID:21878105

Poly(dimethylsiloxane) microchip-based immunoassay with multiple reaction zones: Toward on-chip multiplex detection platform

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

Shao, Guocheng; Wang, Jun; Li, Zhaohui

2011-09-20

In this work, a poly(dimethylsiloxane) (PDMS) microchip-based immuno-sensing platform with integrated pneumatic micro valves is described. The microchip was fabricated with multiple layer soft lithography technology. By controlling the activation status of corresponding valves, reagent flows in the microchannel network can be well manipulated so that immuno-reactions only take place at designated reaction zones (DRZs). Four DRZs are included in the prototype microchip. Since these DRZs are all isolated from each other by micro valves, cross contamination is prevented. Using the inner surface of the all-PDMS microchannel as immunoassay substrate, on-chip sandwich format solid phase immunoassay was performed to demonstratemore » the feasibility of this immuno-sensing platform. Mouse IgG and fluorescein isothiocyanate (FITC) were used as the model analyte and the signal reporter respectively. Only 10 ul sample is needed for the assay and low detection limit of 5 ng/ml (≈33 pM) was achieved though low-cost polyclonal antibodies were used in our experiment for feasibility study only. The encouraging results from mouse IgG immunoassay proved the feasibility of our microchip design. With slight modification of the assay protocol, the same chip design can be used for multi-target detection and can provide a simple, cost-effective and integrated microchip solution for multiplex immunoassay applications.« less

Multi-source Geospatial Data Analysis with Google Earth Engine

NASA Astrophysics Data System (ADS)

Erickson, T.

2014-12-01

The Google Earth Engine platform is a cloud computing environment for data analysis that combines a public data catalog with a large-scale computational facility optimized for parallel processing of geospatial data. The data catalog is a multi-petabyte archive of georeferenced datasets that include images from Earth observing satellite and airborne sensors (examples: USGS Landsat, NASA MODIS, USDA NAIP), weather and climate datasets, and digital elevation models. Earth Engine supports both a just-in-time computation model that enables real-time preview and debugging during algorithm development for open-ended data exploration, and a batch computation mode for applying algorithms over large spatial and temporal extents. The platform automatically handles many traditionally-onerous data management tasks, such as data format conversion, reprojection, and resampling, which facilitates writing algorithms that combine data from multiple sensors and/or models. Although the primary use of Earth Engine, to date, has been the analysis of large Earth observing satellite datasets, the computational platform is generally applicable to a wide variety of use cases that require large-scale geospatial data analyses. This presentation will focus on how Earth Engine facilitates the analysis of geospatial data streams that originate from multiple separate sources (and often communities) and how it enables collaboration during algorithm development and data exploration. The talk will highlight current projects/analyses that are enabled by this functionality.https://earthengine.google.org

A technical review of flexible endoscopic multitasking platforms.

PubMed

Yeung, Baldwin Po Man; Gourlay, Terence

2012-01-01

Further development of advanced therapeutic endoscopic techniques and natural orifice translumenal endoscopic surgery (NOTES) requires a powerful flexible endoscopic multitasking platform. Medline search was performed to identify literature relating to flexible endoscopic multitasking platform from year 2004-2011 using keywords: Flexible endoscopic multitasking platform, NOTES, Instrumentation, Endoscopic robotic surgery, and specific names of various endoscopic multitasking platforms. Key articles from articles references were reviewed. Flexible multitasking platforms can be classified as either mechanical or robotic. Purely mechanical systems include the dual channel endoscope (DCE) (Olympus), R-Scope (Olympus), the EndoSamurai (Olympus), the ANUBIScope (Karl-Storz), Incisionless Operating Platform (IOP) (USGI), and DDES system (Boston Scientific). Robotic systems include the MASTER system (Nanyang University, Singapore) and the Viacath (Hansen Medical). The DCE, the R-Scope, the EndoSamurai and the ANUBIScope have integrated visual function and instrument manipulation function. The IOP and DDES systems rely on the conventional flexible endoscope for visualization, and instrument manipulation is integrated through the use of a flexible, often lockable, multichannel access device. The advantage of the access device concept is that it allows optics and instrument dissociation. Due to the anatomical constrains of the pharynx, systems are designed to have a diameter of less than 20 mm. All systems are controlled by traction cable system actuated either by hand or by robotic machinery. In a flexible system, this method of actuation inevitably leads to significant hysteresis. This problem will be accentuated with a long endoscope such as that required in performing colonic procedures. Systems often require multiple operators. To date, the DCE, the R-Scope, the IOP, and the Viacath system have data published relating to their application in human. Alternative forms of instrument actuation, camera control and master console ergonomics should be explored to improve instrument precision, sphere of action, size and minimize assistance required. Copyright © 2012 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.

Integrated multi-sensor package (IMSP) for unmanned vehicle operations

NASA Astrophysics Data System (ADS)

Crow, Eddie C.; Reichard, Karl; Rogan, Chris; Callen, Jeff; Seifert, Elwood

2007-10-01

This paper describes recent efforts to develop integrated multi-sensor payloads for small robotic platforms for improved operator situational awareness and ultimately for greater robot autonomy. The focus is on enhancements to perception through integration of electro-optic, acoustic, and other sensors for navigation and inspection. The goals are to provide easier control and operation of the robot through fusion of multiple sensor outputs, to improve interoperability of the sensor payload package across multiple platforms through the use of open standards and architectures, and to reduce integration costs by embedded sensor data processing and fusion within the sensor payload package. The solutions investigated in this project to be discussed include: improved capture, processing and display of sensor data from multiple, non-commensurate sensors; an extensible architecture to support plug and play of integrated sensor packages; built-in health, power and system status monitoring using embedded diagnostics/prognostics; sensor payload integration into standard product forms for optimized size, weight and power; and the use of the open Joint Architecture for Unmanned Systems (JAUS)/ Society of Automotive Engineers (SAE) AS-4 interoperability standard. This project is in its first of three years. This paper will discuss the applicability of each of the solutions in terms of its projected impact to reducing operational time for the robot and teleoperator.

Control system design for the large space systems technology reference platform

NASA Technical Reports Server (NTRS)

Edmunds, R. S.

1982-01-01

Structural models and classical frequency domain control system designs were developed for the large space systems technology (LSST) reference platform which consists of a central bus structure, solar panels, and platform arms on which a variety of experiments may be mounted. It is shown that operation of multiple independently articulated payloads on a single platform presents major problems when subarc second pointing stability is required. Experiment compatibility will be an important operational consideration for systems of this type.

Supplementary immunization activities (SIAs) in South Africa: comprehensive economic evaluation of an integrated child health delivery platform.

PubMed

Verguet, Stéphane; Jassat, Waasila; Bertram, Melanie Y; Tollman, Stephen M; Murray, Christopher J L; Jamison, Dean T; Hofman, Karen J

2013-03-01

Supplementary immunization activity (SIA) campaigns provide children with an additional dose of measles vaccine and deliver other interventions, including vitamin A supplements, deworming medications, and oral polio vaccines. To assess the cost-effectiveness of the full SIA delivery platform in South Africa (SA). We used an epidemiologic cost model to estimate the cost-effectiveness of the 2010 SIA campaign. We used province-level campaign data sourced from the District Health Information System, SA, and from planning records of provincial coordinators of the Expanded Programme on Immunization. The data included the number of children immunized with measles and polio vaccines, the number of children given vitamin A supplements and Albendazole tablets, and costs. The campaign cost $37 million and averted a total of 1,150 deaths (95% uncertainty range: 990-1,360). This ranged from 380 deaths averted in KwaZulu-Natal to 20 deaths averted in the Northern Cape. Vitamin A supplementation alone averted 820 deaths (95% UR: 670-1,040); measles vaccination alone averted 330 deaths (95% UR: 280-370). Incremental cost-effectiveness was $27,100 (95% UR: $18,500-34,400) per death averted nationally, ranging from $11,300 per death averted in the Free State to $91,300 per death averted in the Eastern Cape. Cost-effectiveness of the SIA child health delivery platform varies substantially across SA provinces, and it is substantially more cost-effective when vitamin A supplementation is included in the interventions administered. Cost-effectiveness assessments should consider health system delivery platforms that integrate multiple interventions, and they should be conducted at the sub-national level.

JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals.

PubMed

Rosen, Jebediah; Handy, Kyle; Gillan, André; Smith, Rob

2017-11-06

Despite the ubiquity of mass spectrometry (MS), data processing tools can be surprisingly limited. To date, there is no stand-alone, cross-platform 3-D visualizer for MS data. Available visualization toolkits require large libraries with multiple dependencies and are not well suited for custom MS data processing modules, such as MS storage systems or data processing algorithms. We present JS-MS, a 3-D, modular JavaScript client application for viewing MS data. JS-MS provides several advantages over existing MS viewers, such as a dependency-free, browser-based, one click, cross-platform install and better navigation interfaces. The client includes a modular Java backend with a novel streaming.mzML parser to demonstrate the API-based serving of MS data to the viewer. JS-MS enables custom MS data processing and evaluation by providing fast, 3-D visualization using improved navigation without dependencies. JS-MS is publicly available with a GPLv2 license at github.com/optimusmoose/jsms.

Protein detection using biobarcodes.

PubMed

Müller, Uwe R

2006-10-01

Over the past 50 years the development of assays for the detection of protein analytes has been driven by continuing demands for higher levels of sensitivity and multiplexing. The result has been a progression of sandwich-type immunoassays, starting with simple radioisotopic, colorimetric, or fluorescent labeling systems to include various enzymatic or nanostructure-based signal amplification schemes, with a concomitant sensitivity increase of over 1 million fold. Multiplexing of samples and tests has been enabled by microplate and microarray platforms, respectively, or lately by various molecular barcoding systems. Two different platforms have emerged as the current front-runners by combining a nucleic acid amplification step with the standard two-sided immunoassay. In both, the captured protein analyte is replaced by a multiplicity of oligonucleotides that serve as surrogate targets. One of these platforms employs DNA or RNA polymerases for the amplification step, while detection is by fluorescence. The other is based on gold nanoparticles for both amplification as well as detection. The latter technology, now termed Biobarcode, is completely enzyme-free and offers potentially much higher multiplexing power.

Link prediction in multiplex online social networks

NASA Astrophysics Data System (ADS)

Jalili, Mahdi; Orouskhani, Yasin; Asgari, Milad; Alipourfard, Nazanin; Perc, Matjaž

2017-02-01

Online social networks play a major role in modern societies, and they have shaped the way social relationships evolve. Link prediction in social networks has many potential applications such as recommending new items to users, friendship suggestion and discovering spurious connections. Many real social networks evolve the connections in multiple layers (e.g. multiple social networking platforms). In this article, we study the link prediction problem in multiplex networks. As an example, we consider a multiplex network of Twitter (as a microblogging service) and Foursquare (as a location-based social network). We consider social networks of the same users in these two platforms and develop a meta-path-based algorithm for predicting the links. The connectivity information of the two layers is used to predict the links in Foursquare network. Three classical classifiers (naive Bayes, support vector machines (SVM) and K-nearest neighbour) are used for the classification task. Although the networks are not highly correlated in the layers, our experiments show that including the cross-layer information significantly improves the prediction performance. The SVM classifier results in the best performance with an average accuracy of 89%.

Link prediction in multiplex online social networks.

PubMed

Jalili, Mahdi; Orouskhani, Yasin; Asgari, Milad; Alipourfard, Nazanin; Perc, Matjaž

2017-02-01

Online social networks play a major role in modern societies, and they have shaped the way social relationships evolve. Link prediction in social networks has many potential applications such as recommending new items to users, friendship suggestion and discovering spurious connections. Many real social networks evolve the connections in multiple layers (e.g. multiple social networking platforms). In this article, we study the link prediction problem in multiplex networks. As an example, we consider a multiplex network of Twitter (as a microblogging service) and Foursquare (as a location-based social network). We consider social networks of the same users in these two platforms and develop a meta-path-based algorithm for predicting the links. The connectivity information of the two layers is used to predict the links in Foursquare network. Three classical classifiers (naive Bayes, support vector machines (SVM) and K-nearest neighbour) are used for the classification task. Although the networks are not highly correlated in the layers, our experiments show that including the cross-layer information significantly improves the prediction performance. The SVM classifier results in the best performance with an average accuracy of 89%.

An open source web interface for linking models to infrastructure system databases

NASA Astrophysics Data System (ADS)

Knox, S.; Mohamed, K.; Harou, J. J.; Rheinheimer, D. E.; Medellin-Azuara, J.; Meier, P.; Tilmant, A.; Rosenberg, D. E.

2016-12-01

Models of networked engineered resource systems such as water or energy systems are often built collaboratively with developers from different domains working at different locations. These models can be linked to large scale real world databases, and they are constantly being improved and extended. As the development and application of these models becomes more sophisticated, and the computing power required for simulations and/or optimisations increases, so has the need for online services and tools which enable the efficient development and deployment of these models. Hydra Platform is an open source, web-based data management system, which allows modellers of network-based models to remotely store network topology and associated data in a generalised manner, allowing it to serve multiple disciplines. Hydra Platform uses a web API using JSON to allow external programs (referred to as `Apps') to interact with its stored networks and perform actions such as importing data, running models, or exporting the networks to different formats. Hydra Platform supports multiple users accessing the same network and has a suite of functions for managing users and data. We present ongoing development in Hydra Platform, the Hydra Web User Interface, through which users can collaboratively manage network data and models in a web browser. The web interface allows multiple users to graphically access, edit and share their networks, run apps and view results. Through apps, which are located on the server, the web interface can give users access to external data sources and models without the need to install or configure any software. This also ensures model results can be reproduced by removing platform or version dependence. Managing data and deploying models via the web interface provides a way for multiple modellers to collaboratively manage data, deploy and monitor model runs and analyse results.

Specification Patent Management for Web Application Platform Ecosystem

NASA Astrophysics Data System (ADS)

Fukami, Yoshiaki; Isshiki, Masao; Takeda, Hideaki; Ohmukai, Ikki; Kokuryo, Jiro

Diversified usage of web applications has encouraged disintegration of web platform into management of identification and applications. Users make use of various kinds of data linked to their identity with multiple applications on certain social web platforms such as Facebook or MySpace. There has emerged competition among web application platforms. Platformers can design relationship with developers by controlling patent of their own specification and adopt open technologies developed external organizations. Platformers choose a way to open according to feature of the specification and their position. Patent management of specification come to be a key success factor to build competitive web application platforms. Each way to attract external developers such as standardization, open source has not discussed and analyzed all together.

The Clinical Relevance of Force Platform Measures in Multiple Sclerosis: A Review

PubMed Central

Prosperini, Luca; Pozzilli, Carlo

2013-01-01

Balance impairment and falls are frequent in patients with multiple sclerosis (PwMS), and they may occur even at the earliest stage of the disease and in minimally impaired patients. The introduction of computer-based force platform measures (i.e., static and dynamic posturography) has provided an objective and sensitive tool to document both deficits and improvements in balance. By using more challenging test conditions, force platform measures can also reveal subtle balance disorders undetectable by common clinical scales. Furthermore, posturographic techniques may also allow to reliably identify PwMS who are at risk of accidental falls. Although force platform measures offer several theoretical advantages, only few studies extensively investigated their role in better managing PwMS. Standardised procedures, as well as clinical relevance of changes detected by static or dynamic posturography, are still lacking. In this review, we summarized studies which investigated balance deficit by means of force platform measures, focusing on their ability in detecting patients at high risk of falls and in estimating rehabilitation-induced changes, highlighting the pros and the cons with respect to clinical scales. PMID:23766910

UNIX programmer`s environment and configuration control

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

Arnold, T.R.; Wyatt, P.W.

1993-12-31

A package of UNIX utilities has been developed which unities the advantages of the public domain utility ``imake`` and a configuration control system. The ``imake`` utility is portable It allows a user to make Makefiles on a wide variety of platforms without worrying about the machine-dependent idiosyncracies of the UNIX utility ``make.`` Makefiles are a labor-saving device for compiling and linking complicated programs, and ``imake`` is a labor-saving device for making Makefiles, as well as other useful software (like a program`s internal dependencies on included files). This ``Environment,`` which has been developed around ``imake,`` allows a programmer to manage amore » complicated project consisting of multiple executables which may each link with multiple user-created libraries. The configuration control aspect consists of a directory hierarchy (a baseline) which is mirrored in a developer`s workspace. The workspace includes a minimum of files copied from the baseline; it employs soft links into the baseline wherever possible. The utilities are a multi-tiered suite of Bourne shells to copy or check out sources, check them back in, import new sources (sources which are not in the baseline) and link them appropriately, create new low-level directories and link them, compare with the baseline, update Makefiles with minimal effort, and handle dependencies. The directory hierarchy utilizes a single source repository, which is mirrored in the baseline and in a workspace for a several platform architectures. The system was originally written to support C code on Sun-4`s and RS6000`s. It has now been extended to support FORTRAN as well as C on SGI and Cray YMP platforms as well as Sun-4`s and RS6000`s.« less

Mobile personal health records: an evaluation of features and functionality.

PubMed

Kharrazi, Hadi; Chisholm, Robin; VanNasdale, Dean; Thompson, Benjamin

2012-09-01

To evaluate stand-alone mobile personal health record (mPHR) applications for the three leading cellular phone platforms (iOS, BlackBerry, and Android), assessing each for content, function, security, and marketing characteristics. Nineteen stand-alone mPHR applications (8 for iOS, 5 for BlackBerry, and 6 for Android) were identified and evaluated. Main criteria used to include mPHRs were: operating standalone on a mobile platform; not requiring external connectivity; and covering a wide range of health topics. Selected mPHRs were analyzed considering product characteristics, data elements, and application features. We also reviewed additional features such as marketing tactics. Within and between the different mobile platforms attributes for the mPHR were highly variable. None of the mPHRs contained all attributes included in our evaluation. The top four mPHRs contained 13 of the 14 features omitting only the in-case-of emergency feature. Surprisingly, seven mPHRs lacked basic security measures as important as password protection. The mPHRs were relatively inexpensive: ranging from no cost to $9.99. The mPHR application cost varied in some instances based on whether it supported single or multiple users. Ten mPHRs supported multiple user profiles. Notably, eight mPHRs used scare tactics as marketing strategy. mPHR is an emerging health care technology. The majority of existing mPHR apps is limited by at least one of the attributes considered for this study; however, as the mobile market continues to expand it is likely that more comprehensive mPHRs will be developed in the near future. New advancements in mobile technology can be utilized to enhance mPHRs by long-term patient empowerment features. Marketing strategies for mPHRs should target specific subpopulations and avoid scare tactics. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

The Case for GEO Hosted SSA Payloads

NASA Astrophysics Data System (ADS)

Welsch, C.; Armand, B.; Repp, M.; Robinson, A.

2014-09-01

Space situational awareness (SSA) in the geosynchronous earth orbit (GEO) belt presents unique challenges, and given the national importance and high value of GEO satellites, is increasingly critical as space becomes more congested and contested. Space situational awareness capabilities can serve as an effective deterrent against potential adversaries if they provide accurate, timely, and persistent information and are resilient to the threat environment. This paper will demonstrate how simple optical SSA payloads hosted on GEO commercial and government satellites can complement the SSA mission and data provided by Space-Based Space Surveillance (SBSS) and the Geosynchronous Space Situational Awareness Program (GSSAP). GSSAP is built by Orbital Sciences Corporation and launched on July 28, 2014. Analysis performed for this paper will show how GEO hosted SSA payloads, working in combination with SBSS and GSSAP, can increase persistence and timely coverage of high value assets in the GEO belt. The potential to further increase GEO object identification and tracking accuracy by integrating SSA data from multiple sources across different viewing angles including GEO hosted SSA sources will be addressed. Hosting SSA payloads on GEO platforms also increases SSA mission architecture resiliency as the sensors are by distributed across multiple platforms including commercial platforms. This distributed architecture presents a challenging target for an adversary to attempt to degrade or disable. We will present a viable concept of operations to show how data from hosted SSA sensors could be integrated with SBSS and GSSAP data to present a comprehensive and more accurate data set to users. Lastly, we will present an acquisition approach using commercial practices and building on lessons learned from the Commercially Hosted Infra Red Payload CHIRP to demonstrate the affordability of GEO hosted SSA payloads.

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

PubMed

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

2017-01-01

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

MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data

PubMed Central

Hartler, Jürgen; Thallinger, Gerhard G; Stocker, Gernot; Sturn, Alexander; Burkard, Thomas R; Körner, Erik; Rader, Robert; Schmidt, Andreas; Mechtler, Karl; Trajanoski, Zlatko

2007-01-01

Background The advancements of proteomics technologies have led to a rapid increase in the number, size and rate at which datasets are generated. Managing and extracting valuable information from such datasets requires the use of data management platforms and computational approaches. Results We have developed the MAss SPECTRometry Analysis System (MASPECTRAS), a platform for management and analysis of proteomics LC-MS/MS data. MASPECTRAS is based on the Proteome Experimental Data Repository (PEDRo) relational database schema and follows the guidelines of the Proteomics Standards Initiative (PSI). Analysis modules include: 1) import and parsing of the results from the search engines SEQUEST, Mascot, Spectrum Mill, X! Tandem, and OMSSA; 2) peptide validation, 3) clustering of proteins based on Markov Clustering and multiple alignments; and 4) quantification using the Automated Statistical Analysis of Protein Abundance Ratios algorithm (ASAPRatio). The system provides customizable data retrieval and visualization tools, as well as export to PRoteomics IDEntifications public repository (PRIDE). MASPECTRAS is freely available at Conclusion Given the unique features and the flexibility due to the use of standard software technology, our platform represents significant advance and could be of great interest to the proteomics community. PMID:17567892

Contemporary engagement with social media amongst hernia surgery specialists.

PubMed

Lui, D H; McDonald, J J; de Beaux, A; Tulloh, B; Brady, R R W

2017-08-01

Healthcare professional engagement is increasing. This study aims to identify levels of adoption and engagement of several social media platforms by a large international cohort of hernia surgery specialists. Hernia specialists attending the 38th International Congress of the European Hernia Society were identified. A manual search was then performed on Twitter, ResearchGate, and LinkedIn to identify those who had named accounts. Where accounts were identified, data on markers of utilisation were assessed. 759 surgeons (88.5% male) from 57 countries were identified. 334 surgeons (44%) engaged with a social media platform. 39 (5.1%) had Twitter accounts, 189 (24.9%) had ResearchGate accounts and 265 (34.9%) had LinkedIn accounts. 137 surgeons (18.1%) had accounts on 2 or more social media platforms. There was no gender association with social media account ownership (p > 0.05). Engagement in one social media platform was associated with increased engagement and utilisation on other platforms; LinkedIn users were more likely to have Twitter accounts (p < 0.001) and ResearchGate profiles (p < 0.001). Surgeons on all three SM platforms were more likely to have high markers of engagement across all SM platforms (multiple outcomes, p < 0.05). Geographical variation was noted with UK and South American Surgeons being more likely to be present on Twitter than their counterparts (p = 0.031). The level of engagement with social media amongst Hernia surgeons is similar to other surgical specialities. Geographical variation in SM engagement is seen. Engagement with one SM platform is associated with presence on multiple platforms.

Upgrading well plates using open microfluidic patterning.

PubMed

Berry, Samuel B; Zhang, Tianzi; Day, John H; Su, Xiaojing; Wilson, Ilham Z; Berthier, Erwin; Theberge, Ashleigh B

2017-12-05

Cellular communication between multiple cell types is a ubiquitous process that is responsible for vital physiological responses observed in vivo (e.g., immune response, organ function). Many in vitro coculture strategies have been developed, both in traditional culture and microscale systems, and have shown the potential to recreate some of the physiological behaviors of organs or groups of cells. A fundamental limitation of current systems is the difficulty of reconciling the additional engineering requirements for creating soluble factor signaling systems (e.g., segregated cell culture) with the use of well-characterized materials and platforms that have demonstrated successful results and biocompatibility in assays. We present a new open-microfluidic platform, the Monorail Device, that is placed in any existing well plate or Petri dish and enables patterning of segregated coculture regions, thereby allowing the direct upgrade of monoculture experiments into multiculture assays. Our platform patterns biocompatible hydrogel walls via microfluidic spontaneous capillary flow (SCF) along a rail insert set inside commercially available cultureware, creating customized pipette-accessible cell culture chambers that require fewer cells than standard macroscale culture. Importantly, the device allows the use of native surfaces without additional modification or treatments, while creating permeable dividers for the diffusion of soluble factors. Additionally, the ease of patterning afforded by our platform makes reconfiguration of the culture region as simple as changing the rail insert. We demonstrate the ability of the device to pattern flows on a variety of cell culture surfaces and create hydrogel walls in complex and precise shapes. We characterize the physical parameters that enable a reproducible SCF-driven flow and highlight specialized design features that increase the ease of use of the device and control of the open microfluidic flow. Further, we present the performance of our platform according to useful coculture criteria, including permeability and integrity of our hydrogel walls and surface-sensitive cell culture. Lastly, we show the potential of this type of platform to create modular multikingdom culture systems that can be used to study soluble factor signaling between mammalian cells, bacteria, and fungi, as well as the potential for adaptation of this technology by researchers across multiple fields.

The relational database model and multiple multicenter clinical trials.

PubMed

Blumenstein, B A

1989-12-01

The Southwest Oncology Group (SWOG) chose to use a relational database management system (RDBMS) for the management of data from multiple clinical trials because of the underlying relational model's inherent flexibility and the natural way multiple entity types (patients, studies, and participants) can be accommodated. The tradeoffs to using the relational model as compared to using the hierarchical model include added computing cycles due to deferred data linkages and added procedural complexity due to the necessity of implementing protections against referential integrity violations. The SWOG uses its RDBMS as a platform on which to build data operations software. This data operations software, which is written in a compiled computer language, allows multiple users to simultaneously update the database and is interactive with respect to the detection of conditions requiring action and the presentation of options for dealing with those conditions. The relational model facilitates the development and maintenance of data operations software.

HERMIES-3: A step toward autonomous mobility, manipulation, and perception

NASA Technical Reports Server (NTRS)

Weisbin, C. R.; Burks, B. L.; Einstein, J. R.; Feezell, R. R.; Manges, W. W.; Thompson, D. H.

1989-01-01

HERMIES-III is an autonomous robot comprised of a seven degree-of-freedom (DOF) manipulator designed for human scale tasks, a laser range finder, a sonar array, an omni-directional wheel-driven chassis, multiple cameras, and a dual computer system containing a 16-node hypercube expandable to 128 nodes. The current experimental program involves performance of human-scale tasks (e.g., valve manipulation, use of tools), integration of a dexterous manipulator and platform motion in geometrically complex environments, and effective use of multiple cooperating robots (HERMIES-IIB and HERMIES-III). The environment in which the robots operate has been designed to include multiple valves, pipes, meters, obstacles on the floor, valves occluded from view, and multiple paths of differing navigation complexity. The ongoing research program supports the development of autonomous capability for HERMIES-IIB and III to perform complex navigation and manipulation under time constraints, while dealing with imprecise sensory information.

Multifunctional nanomaterials for advanced molecular imaging and cancer therapy

NASA Astrophysics Data System (ADS)

Subramaniam, Prasad

Nanotechnology offers tremendous potential for use in biomedical applications, including cancer and stem cell imaging, disease diagnosis and drug delivery. The development of nanosystems has aided in understanding the molecular mechanisms of many diseases and permitted the controlled nanoscale manipulation of biological phenomena. In recent years, many studies have focused on the use of several kinds of nanomaterials for cancer and stem cell imaging and also for the delivery of anticancer therapeutics to tumor cells. However, the proper diagnosis and treatment of aggressive tumors such as brain and breast cancer requires highly sensitive diagnostic agents, in addition to the ability to deliver multiple therapeutics using a single platform to the target cells. Addressing these challenges, novel multifunctional nanomaterial-based platforms that incorporate multiple therapeutic and diagnostic agents, with superior molecular imaging and targeting capabilities, has been presented in this work. The initial part of this work presents the development of novel nanomaterials with superior optical properties for efficiently delivering soluble cues such as small interfering RNA (siRNA) into brain cancer cells with minimal toxicity. Specifically, this section details the development of non-toxic quantums dots for the imaging and delivery of siRNA into brain cancer and mesenchymal stem cells, with the hope of using these quantum dots as multiplexed imaging and delivery vehicles. The use of these quantum dots could overcome the toxicity issues associated with the use of conventional quantum dots, enabled the imaging of brain cancer and stem cells with high efficiency and allowed for the delivery of siRNA to knockdown the target oncogene in brain cancer cells. The latter part of this thesis details the development of nanomaterial-based drug delivery platforms for the co-delivery of multiple anticancer drugs to brain tumor cells. In particular, this part of the thesis focuses on the synthesis and use of a biodegradable dendritic polypeptide-based nanocarrier for the delivery of multiple anticancer drugs and siRNA to brain tumor cells. The co-delivery of important anticancer agents using a single platform was shown to increase the efficacy of the drugs manyfold, ensuring the cancer cell-specific delivery and minimizing dose limiting toxicities of the individual drugs. This would be of immense importance when used in vivo.

Comprehensive Method for Culturing Embryonic Dorsal Root Ganglion Neurons for Seahorse Extracellular Flux XF24 Analysis

PubMed Central

Lange, Miranda; Zeng, Yan; Knight, Andrew; Windebank, Anthony; Trushina, Eugenia

2012-01-01

Changes in mitochondrial dynamics and function contribute to progression of multiple neurodegenerative diseases including peripheral neuropathies. The Seahorse Extracellular Flux XF24 analyzer provides a comprehensive assessment of the relative state of glycolytic and aerobic metabolism in live cells making this method instrumental in assessing mitochondrial function. One of the most important steps in the analysis of mitochondrial respiration using the Seahorse XF24 analyzer is plating a uniform monolayer of firmly attached cells. However, culturing of primary dorsal root ganglion (DRG) neurons is associated with multiple challenges, including their propensity to form clumps and detach from the culture plate. This could significantly interfere with proper analysis and interpretation of data. We have tested multiple cell culture parameters including coating substrates, culture medium, XF24 microplate plastics, and plating techniques in order to optimize plating conditions. Here we describe a highly reproducible method to obtain neuron-enriched monolayers of securely attached dissociated primary embryonic (E15) rat DRG neurons suitable for analysis with the Seahorse XF24 platform. PMID:23248613

Comprehensive Method for Culturing Embryonic Dorsal Root Ganglion Neurons for Seahorse Extracellular Flux XF24 Analysis.

PubMed

Lange, Miranda; Zeng, Yan; Knight, Andrew; Windebank, Anthony; Trushina, Eugenia

2012-01-01

Changes in mitochondrial dynamics and function contribute to progression of multiple neurodegenerative diseases including peripheral neuropathies. The Seahorse Extracellular Flux XF24 analyzer provides a comprehensive assessment of the relative state of glycolytic and aerobic metabolism in live cells making this method instrumental in assessing mitochondrial function. One of the most important steps in the analysis of mitochondrial respiration using the Seahorse XF24 analyzer is plating a uniform monolayer of firmly attached cells. However, culturing of primary dorsal root ganglion (DRG) neurons is associated with multiple challenges, including their propensity to form clumps and detach from the culture plate. This could significantly interfere with proper analysis and interpretation of data. We have tested multiple cell culture parameters including coating substrates, culture medium, XF24 microplate plastics, and plating techniques in order to optimize plating conditions. Here we describe a highly reproducible method to obtain neuron-enriched monolayers of securely attached dissociated primary embryonic (E15) rat DRG neurons suitable for analysis with the Seahorse XF24 platform.

Micropillar arrays as a high-throughput screening platform for therapeutics in multiple sclerosis.

PubMed

Mei, Feng; Fancy, Stephen P J; Shen, Yun-An A; Niu, Jianqin; Zhao, Chao; Presley, Bryan; Miao, Edna; Lee, Seonok; Mayoral, Sonia R; Redmond, Stephanie A; Etxeberria, Ainhoa; Xiao, Lan; Franklin, Robin J M; Green, Ari; Hauser, Stephen L; Chan, Jonah R

2014-08-01

Functional screening for compounds that promote remyelination represents a major hurdle in the development of rational therapeutics for multiple sclerosis. Screening for remyelination is problematic, as myelination requires the presence of axons. Standard methods do not resolve cell-autonomous effects and are not suited for high-throughput formats. Here we describe a binary indicant for myelination using micropillar arrays (BIMA). Engineered with conical dimensions, micropillars permit resolution of the extent and length of membrane wrapping from a single two-dimensional image. Confocal imaging acquired from the base to the tip of the pillars allows for detection of concentric wrapping observed as 'rings' of myelin. The platform is formatted in 96-well plates, amenable to semiautomated random acquisition and automated detection and quantification. Upon screening 1,000 bioactive molecules, we identified a cluster of antimuscarinic compounds that enhance oligodendrocyte differentiation and remyelination. Our findings demonstrate a new high-throughput screening platform for potential regenerative therapeutics in multiple sclerosis.

DREAM: Distributed Resources for the Earth System Grid Federation (ESGF) Advanced Management

NASA Astrophysics Data System (ADS)

Williams, D. N.

2015-12-01

The data associated with climate research is often generated, accessed, stored, and analyzed on a mix of unique platforms. The volume, variety, velocity, and veracity of this data creates unique challenges as climate research attempts to move beyond stand-alone platforms to a system that truly integrates dispersed resources. Today, sharing data across multiple facilities is often a challenge due to the large variance in supporting infrastructures. This results in data being accessed and downloaded many times, which requires significant amounts of resources, places a heavy analytic development burden on the end users, and mismanaged resources. Working across U.S. federal agencies, international agencies, and multiple worldwide data centers, and spanning seven international network organizations, the Earth System Grid Federation (ESGF) has begun to solve this problem. Its architecture employs a system of geographically distributed peer nodes that are independently administered yet united by common federation protocols and application programming interfaces. However, significant challenges remain, including workflow provenance, modular and flexible deployment, scalability of a diverse set of computational resources, and more. Expanding on the existing ESGF, the Distributed Resources for the Earth System Grid Federation Advanced Management (DREAM) will ensure that the access, storage, movement, and analysis of the large quantities of data that are processed and produced by diverse science projects can be dynamically distributed with proper resource management. This system will enable data from an infinite number of diverse sources to be organized and accessed from anywhere on any device (including mobile platforms). The approach offers a powerful roadmap for the creation and integration of a unified knowledge base of an entire ecosystem, including its many geophysical, geographical, social, political, agricultural, energy, transportation, and cyber aspects. The resulting aggregation of data combined with analytics services has the potential to generate an informational universe and knowledge system of unprecedented size and value to the scientific community, downstream applications, decision makers, and the public.

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

PubMed

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

2002-10-01

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

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

NASA Astrophysics Data System (ADS)

Demir, I.; Krajewski, W. F.

2012-12-01

Hydroinformatics is a domain of science and technology dealing with the management of information in the field of hydrology (IWA, 2011). There is the need for innovative solutions to the challenges towards open information, integration, and communication in the Internet. This presentation provides an overview of the trends and challenges in the future of hydroinformatics, and demonstrates an information system, Iowa Flood Information System (IFIS), developed within the light of these challenges. The IFIS is a web-based platform developed by the Iowa Flood Center (IFC) to provide access to flood inundation maps, real-time flood conditions, flood forecasts both short-term and seasonal, flood-related data, information and interactive visualizations for communities in Iowa. The key element of the system's architecture is the notion of community. Locations of the communities, those near streams and rivers, define basin boundaries. The IFIS provides community-centric watershed and river characteristics, weather (rainfall) conditions, and streamflow data and visualization tools. Interactive interfaces allow access to inundation maps for different stage and return period values, and flooding scenarios with contributions from multiple rivers. Real-time and historical data of water levels, gauge heights, and rainfall conditions are available in the IFIS by streaming data from automated IFC bridge sensors, USGS stream gauges, NEXRAD radars, and NWS forecasts. 2D and 3D interactive visualizations in the IFIS make the data more understandable to general public. Users are able to filter data sources for their communities and selected rivers. The data and information on IFIS is also accessible through web services and mobile applications. The IFIS is optimized for various browsers and screen sizes to provide access through multiple platforms including tablets and mobile devices. The IFIS includes a rainfall-runoff forecast model to provide a five-day flood risk estimate for more than 1000 communities in Iowa. Multiple view modes in the IFIS accommodate different user types from general public to researchers and decision makers by providing different level of tools and details. River view mode allows users to visualize data from multiple IFC bridge sensors and USGS stream gauges to follow flooding condition along a river. The IFIS will help communities make better-informed decisions on the occurrence of floods, and will alert communities in advance to help minimize damage of floods.

Multifunctional Web Enabled Ocean Sensor Systems for the Monitoring of a Changing Ocean

NASA Astrophysics Data System (ADS)

Pearlman, Jay; Castro, Ayoze; Corrandino, Luigi; del Rio, Joaquin; Delory, Eric; Garello, Rene; Heuermann, Rudinger; Martinez, Enoc; Pearlman, Francoise; Rolin, Jean-Francois; Toma, Daniel; Waldmann, Christoph; Zielinski, Oliver

2016-04-01

As stated in the 2010 "Ostend Declaration", a major challenge in the coming years is the development of a truly integrated and sustainably funded European Ocean Observing System for supporting major policy initiatives such as the Integrated Maritime Policy and the Marine Strategy Framework Directive. This will be achieved with more long-term measurements of key parameters supported by a new generation of sensors whose costs and reliability will enable broad and consistent observations. Within the NeXOS project, a framework including new sensors capabilities and interface software has been put together that embraces the key technical aspects needed to improve the temporal and spatial coverage, resolution and quality of marine observations. The developments include new, low-cost, compact and integrated sensors with multiple functionalities that will allow for the measurements useful for a number of objectives, ranging from more precise monitoring and modeling of the marine environment to an improved assessment of fisheries. The project is entering its third year and will be demonstrating initial capabilities of optical and acoustic sensor prototypes that will become available for a number of platforms. For fisheries management, there is also a series of sensors that support an Ecosystem Approach to Fisheries (EAF). The greatest capabilities for comprehensive operations will occur when these sensors can be integrated into a multisensory capability on a single platform or multiply interconnected and coordinated platforms. Within NeXOS the full processing steps starting from the sensor signal all the way up to distributing collected environmental information will be encapsulated into standardized new state of the art Smart Sensor Interface and Web components to provide both improved integration and a flexible interface for scientists to control sensor operation. The use of the OGC SWE (Sensor Web Enablement) set of standards like OGC PUCK and SensorML at the instrument to platform integration phase will provide standard mechanisms for a truly plug'n'work connection. Through this, NeXOS Instruments will maintain within themselves specific information about how a platform (buoy controller, AUV controller, Observatory controller) has to configure and communicate with the instrument without the platform needing previous knowledge about the instrument. This mechanism is now being evaluated in real platforms like a Slocum Glider from Teledyne Web research, SeaExplorer Glider from Alseamar, Provor Float from NKE, and others including non commercial platforms like Obsea seafloor cabled observatory. The latest developments in the NeXOS sensors and the integration into an observation system will be discussed, addressing demonstration plans both for a variety of platforms and scientific objectives supporting marine management.

Innovative patient care practices using social media.

PubMed

Mattingly, T Joseph

2015-01-01

To characterize the literature on social media applications used to deliver patient care. A search of the literature was conducted on June 11, 2014, using PubMed, MEDLINE, CINAHL, and Communication Abstracts databases for clinical studies between 2004 and 2014. A combination of the search terms "social media" or "Web 2.0" or "online social networking" or "Facebook" or "Twitter" AND "patient care" or "health care" was used. In addition, 42 additional abstracts were retrieved from www.patientslikeme.com for review. Only published, peer-reviewed journal articles were considered and only publications in English were included. The abstracts from this search were reviewed for relevance to Web-based social media platforms being used in patient care activities. A total of 35 articles were included in the review. A majority of the studies published on social media and patient care used cross-sectional designs and were conducted in the United States. Multiple social media applications were studied, but Facebook was the predominant social media tool found. Patient care opportunities for various diseases with social media have been studied. Recurring themes included overcoming barriers, engaging and empowering patients, enhancing research, providing information for health promotion, scratching the surface, and potential pitfalls. Social media have the potential to help patients and practitioners overcome multiple barriers in the delivery of health care. Maintaining patient privacy, security of information shared in the platform, and integrity of information shared are all concerns when using this type of Web application.

Multimedia Information eXchange for I-NET, Inc. at the Kennedy Space Center: A continuing study of the application of worldwideweb technology

NASA Technical Reports Server (NTRS)

Metcalf, David

1995-01-01

Multimedia Information eXchange (MIX) is a multimedia information system that accommodates multiple data types and provides consistency across platforms. Information from all over the world can be accessed quickly and efficiently with the Internet-based system. I-NET's MIX uses the World Wide Web and Mosaic graphical user interface. Mosaic is available on all platforms used at I-NET's Kennedy Space Center (KSC) facilities. Key information system design concepts and benefits are reviewed. The MIX system also defines specific configuration and helper application parameters to ensure consistent operations across the entire organization. Guidelines and procedures for other areas of importance in information systems design are also addressed. Areas include: code of ethics, content, copyright, security, system administration, and support.

Reconfigurable Microfluidic Magnetic Valve Arrays: Towards a Radiotherapy-Compatible Spheroid Culture Platform for the Combinatorial Screening of Cancer Therapies

PubMed Central

Labelle, Frédérique; Wong, Philip

2017-01-01

We introduce here a microfluidic cell culture platform or spheroid culture chamber array (SCCA) that can synthesize, culture, and enable fluorescence imaging of 3D cell aggregates (typically spheroids) directly on-chip while specifying the flow of reagents in each chamber via the use of an array of passive magnetic valves. The SCCA valves demonstrated sufficient resistance to burst (above 100 mBar), including after receiving radiotherapy (RT) doses of up to 8 Gy combined with standard 37 °C incubation for up to 7 days, enabling the simultaneous synthesis of multiple spheroids from different cell lines on the same array. Our results suggest that SCCA would be an asset in drug discovery processes, seeking to identify combinatorial treatments. PMID:28976942

Transoral robotic thyroidectomy: a preclinical feasibility study using the da Vinci Xi platform.

PubMed

Russell, Jonathon O; Noureldine, Salem I; Al Khadem, Mai G; Chaudhary, Hamad A; Day, Andrew T; Kim, Hoon Yub; Tufano, Ralph P; Richmon, Jeremy D

2017-09-01

Transoral thyroid surgery allows the surgeon to conceal incisions within the oral cavity without significantly increasing the amount of required dissection. TORT provides an ideal scarless, midline access to the thyroid gland and bilateral central neck compartments. This approach, however, presents multiple technical challenges. Herein, we present our experience using the latest generation robotic surgical system to accomplish transoral robotic thyroidectomy (TORT). In two human cadavers, the da Vinci Xi surgical system (Intuitive Surgical, Sunnyvale, CA, USA) was used to complete TORT. Total thyroidectomy and bilateral central neck dissection was successfully completed in both cadavers. The da Vinci Xi platform offered several technologic advantages over previous robotic generations including overhead docking, narrower arms, and improved range of motion allowing for improved execution of previously described TORT techniques.

Proactive Time-Rearrangement Scheme for Multi-Radio Collocated Platform

NASA Astrophysics Data System (ADS)

Kim, Chul; Shin, Sang-Heon; Park, Sang Kyu

We present a simple proactive time rearrangement scheme (PATRA) that reduces the interferences from multi-radio devices equipped in one platform and guarantees user-conceived QoS. Simulation results show that the interference among multiple radios in one platform causes severe performance degradation and cannot guarantee the user requested QoS. However, the PATRA can dramatically improve not only the userconceived QoS but also the overall network throughput.

Two complementary personal medication management applications developed on a common platform: case report.

PubMed

Ross, Stephen E; Johnson, Kevin B; Siek, Katie A; Gordon, Jeffry S; Khan, Danish U; Haverhals, Leah M

2011-07-12

Adverse drug events are a major safety issue in ambulatory care. Improving medication self-management could reduce these adverse events. Researchers have developed medication applications for tethered personal health records (PHRs), but little has been reported about medication applications for interoperable PHRs. Our objective was to develop two complementary personal health applications on a common PHR platform: one to assist children with complex health needs (MyMediHealth), and one to assist older adults in care transitions (Colorado Care Tablet). The applications were developed using a user-centered design approach. The two applications shared a common PHR platform based on a service-oriented architecture. MyMediHealth employed Web and mobile phone user interfaces. Colorado Care Tablet employed a Web interface customized for a tablet PC. We created complementary medication management applications tailored to the needs of distinctly different user groups using common components. Challenges were addressed in multiple areas, including how to encode medication identities, how to incorporate knowledge bases for medication images and consumer health information, how to include supplementary dosing information, how to simplify user interfaces for older adults, and how to support mobile devices for children. These prototypes demonstrate the utility of abstracting PHR data and services (the PHR platform) from applications that can be tailored to meet the needs of diverse patients. Based on the challenges we faced, we provide recommendations on the structure of publicly available knowledge resources and the use of mobile messaging systems for PHR applications.

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

PubMed

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

2010-02-04

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

Blended Learning: An Evolving Praxis

ERIC Educational Resources Information Center

Fogal, Gary G.; Graham, Floyd H., III.; Lavigne, Anthony G.

2014-01-01

TED (Technology Entertainment Design), a collection of regularly updated talks, offers a web-based platform that is easily accessible. This platform affords language learners across multiple proficiency levels an opportunity to develop autonomy and critical thinking skills alongside their second language (L2) development. With an international…

Reconfigurable microfluidic hanging drop network for multi-tissue interaction and analysis.

PubMed

Frey, Olivier; Misun, Patrick M; Fluri, David A; Hengstler, Jan G; Hierlemann, Andreas

2014-06-30

Integration of multiple three-dimensional microtissues into microfluidic networks enables new insights in how different organs or tissues of an organism interact. Here, we present a platform that extends the hanging-drop technology, used for multi-cellular spheroid formation, to multifunctional complex microfluidic networks. Engineered as completely open, 'hanging' microfluidic system at the bottom of a substrate, the platform features high flexibility in microtissue arrangements and interconnections, while fabrication is simple and operation robust. Multiple spheroids of different cell types are formed in parallel on the same platform; the different tissues are then connected in physiological order for multi-tissue experiments through reconfiguration of the fluidic network. Liquid flow is precisely controlled through the hanging drops, which enable nutrient supply, substance dosage and inter-organ metabolic communication. The possibility to perform parallelized microtissue formation on the same chip that is subsequently used for complex multi-tissue experiments renders the developed platform a promising technology for 'body-on-a-chip'-related research.

aGEM: an integrative system for analyzing spatial-temporal gene-expression information

PubMed Central

Jiménez-Lozano, Natalia; Segura, Joan; Macías, José Ramón; Vega, Juanjo; Carazo, José María

2009-01-01

Motivation: The work presented here describes the ‘anatomical Gene-Expression Mapping (aGEM)’ Platform, a development conceived to integrate phenotypic information with the spatial and temporal distributions of genes expressed in the mouse. The aGEM Platform has been built by extending the Distributed Annotation System (DAS) protocol, which was originally designed to share genome annotations over the WWW. DAS is a client-server system in which a single client integrates information from multiple distributed servers. Results: The aGEM Platform provides information to answer three main questions. (i) Which genes are expressed in a given mouse anatomical component? (ii) In which mouse anatomical structures are a given gene or set of genes expressed? And (iii) is there any correlation among these findings? Currently, this Platform includes several well-known mouse resources (EMAGE, GXD and GENSAT), hosting gene-expression data mostly obtained from in situ techniques together with a broad set of image-derived annotations. Availability: The Platform is optimized for Firefox 3.0 and it is accessed through a friendly and intuitive display: http://agem.cnb.csic.es Contact: natalia@cnb.csic.es Supplementary information: Supplementary data are available at http://bioweb.cnb.csic.es/VisualOmics/aGEM/home.html and http://bioweb.cnb.csic.es/VisualOmics/index_VO.html and Bioinformatics online. PMID:19592395

Feasibility of Optimizing Recovery and Reserves from a Mature and Geological Complex Multiple Turbidite Offshore Calif. Reservoir through the Drilling and Completion of a Trilateral Horizontal Well, Class III

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

Pacific Operators Offshore, Inc.

The intent of this project was to increase production and extend the economic life of this mature field through the application of advanced reservoir characterization and drilling technology, demonstrating the efficacy of these technologies to other small operators of aging fields. Two study periods were proposed; the first to include data assimilation and reservoir characterization and the second to drill the demonstration well. The initial study period showed that a single tri-lateral well would not be economically efficient in redevelopment of Carpinteria's multiple deep water turbidite sand reservoirs, and the study was amended to include the drilling of a seriesmore » of horizontal redrills from existing surplus well bores on Pacific Operators' Platform Hogan.« less

A dynamic bead-based microarray for parallel DNA detection

NASA Astrophysics Data System (ADS)

Sochol, R. D.; Casavant, B. P.; Dueck, M. E.; Lee, L. P.; Lin, L.

2011-05-01

A microfluidic system has been designed and constructed by means of micromachining processes to integrate both microfluidic mixing of mobile microbeads and hydrodynamic microbead arraying capabilities on a single chip to simultaneously detect multiple bio-molecules. The prototype system has four parallel reaction chambers, which include microchannels of 18 × 50 µm2 cross-sectional area and a microfluidic mixing section of 22 cm length. Parallel detection of multiple DNA oligonucleotide sequences was achieved via molecular beacon probes immobilized on polystyrene microbeads of 16 µm diameter. Experimental results show quantitative detection of three distinct DNA oligonucleotide sequences from the Hepatitis C viral (HCV) genome with single base-pair mismatch specificity. Our dynamic bead-based microarray offers an effective microfluidic platform to increase parallelization of reactions and improve microbead handling for various biological applications, including bio-molecule detection, medical diagnostics and drug screening.

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

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

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

2009-01-01

The quantitative, simultaneous detection of multiple biomarkers with high sensitivity and specificity is critical for biomedical diagnostics, drug discovery and biomarker characterization [Wilson 2006, Tok 2006, Straub 2005, Joos 2002, Jani 2000]. Detection systems relying on optical signal transduction are, in general, advantageous because they are fast, portable, inexpensive, sensitive, and have the potential for multiplex detection of analytes of interest. However, conventional immunoassays for the detection of biomarkers, such as the Enzyme Linked Immunosorbant Assays (ELISAs) are semi-quantitative, time consuming and insensitive. ELISA assays are also limited by high non-specific binding, especially when used with complex biological samples suchmore » as serum and urine (REF). Organic fluorophores that are commonly used in such applications lack photostability and possess a narrow Stoke's shift that makes simultaneous detection of multiple fluorophores with a single excitation source difficult, thereby restricting their use in multiplex assays. The above limitations with traditional assay platforms have resulted in the increased use of nanotechnology-based tools and techniques in the fields of medical imaging [ref], targeted drug delivery [Caruthers 2007, Liu 2007], and sensing [ref]. One such area of increasing interest is the use of semiconductor quantum dots (QDs) for biomedical research and diagnostics [Gao and Cui 2004, Voura 2004, Michalet 2005, Chan 2002, Jaiswal 2004, Gao 2005, Medintz 2005, So 2006 2006, Wu 2003]. Compared to organic dyes, QDs provide several advantages for use in immunoassay platforms, including broad absorption bands with high extinction coefficients, narrow and symmetric emission bands with high quantum yields, high photostablility, and a large Stokes shift [Michalet 2005, Gu 2002]. These features prompted the use of QDs as probes in biodetection [Michalet 2005, Medintz 2005]. For example, Jaiswal et al. reported long term multiple color imaging of live cells using QD-bioconjugates [Jaiswal 2003]. Gao [Gao 2004] and So [So 2006] have used QDs as probes for in-vivo cancer targeting and imaging. Medintz et al. reported self-assembled QD-based biosensors for detection of analytes based on energy transfer [Medintz 2003]. Others have developed an approach for multiplex optical encoding of biomolecules using QDs [Han 2001]. Immunoassays have also benefited from the advantages of QDs. Recently, dihydrolipoic acid (DHLA) capped-QDs have been attached to antibodies and used as fluorescence reporters in plate-based multiplex immunoassays [Goodman 2004]. However, DHLA-QDs are associated with low quantum efficiency and are unstable at neutral pH. These problems limit the application of this technology to the sensitive detection of biomolecules, especially in complex biological samples. Thus, the development of a rapid, sensitive, quantitative, and specific multiplex platform for the detection of biomarkers in difficult samples remains an elusive target. The goal stated above has applications in many fields including medical diagnostics, biological research, and threat reduction. The current decade alone has seen the development of a need to rapidly and accurately detect potential biological warfare agents. For example, current methods for the detection of anthrax are grossly inadequate for a variety of reasons including long incubation time (5 days from time of exposure to onset of symptoms) and non-specific ('flu-like') symptoms. When five employees of the United State Senate were exposed to B. anthracis in the mail (2001), only one patient had a confirmed diagnosis before death. Since then, sandwich immunoassays using both colorimetric and fluorescence detectors have been developed for key components of the anthrax lethal toxin, namely protective antigen (PA), lethal factor (LF), and the edema factor [Mourez 2001]. While these platforms were successful in assays against anthrax toxins, the sensitivity was poor. Furthermore, no single platform exists for the simultaneous and quantitative detection of multiple components of the B. anthracis toxin. Addressing multiple biomarkers at the same time will increase confidence in a positive result, and may lead to application in the simultaneous detection of anthrax and other biowarfare agents.« less

Space assembly fixtures and aids

NASA Technical Reports Server (NTRS)

Bloom, K. A.; Lillenas, A. N.

1980-01-01

Concepts and requirements for assembly fixtures and aids necessary for the assembly and maintenance of spare platforms were studied. Emphasis was placed on erectable and deployable type structures with the shuttle orbiter as the assembly base. Both single and multiple orbiter flight cases for the platform assembly were considered. Applicable space platform assembly studies were reviewed to provide a data base for establishing the assembly fixture and aids design requirements, assembly constraints, and the development of representative design concepts. Conclusions indicated that fixture requirements will vary with platform size. Larger platforms will require translation relative to the orbiter RMS working volume. The installation of platform payloads and subsystems (e.g., utility distribution) must also be considered in the specification of assembly fixtures and aids.

Geostationary platform systems concepts definition study. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

1980-01-01

The results of a geostationary platform concept analysis are summarized. Mission and payloads definition, concept selection, the requirements of an experimental platform, supporting research and technology, and the Space Transportation System interface requirements are addressed. It is concluded that platforms represent a logical extension of current trends toward larger, more complex, multifrequency satellites. Geostationary platforms offer significant cost savings compared to individual satellites, with the majority of these economies being realized with single Shuttle launched platforms. Further cost savings can be realized, however, by having larger platforms. Platforms accommodating communications equipment that operates at multiple frequencies and which provide larger scale frequency reuse through the use of large aperture multibeam antennas and onboard switching maximize the useful capacity of the orbital arc and frequency spectrum. Projections of market demand indicate that such conservation measures are clearly essential if orderly growth is to be provided for. In addition, it is pointed out that a NASA experimental platform is required to demonstrate the technologies necessary for operational geostationary platforms of the 1990's.

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research.

PubMed

Campagnola, Luke; Kratz, Megan B; Manis, Paul B

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org.

Integrated Display and Simulation for Automatic Dependent Surveillance–Broadcast and Traffic Collision Avoidance System Data Fusion

PubMed Central

Wang, Yanran; Xiao, Gang; Dai, Zhouyun

2017-01-01

Automatic Dependent Surveillance–Broadcast (ADS-B) is the direction of airspace surveillance development. Research analyzing the benefits of Traffic Collision Avoidance System (TCAS) and ADS-B data fusion is almost absent. The paper proposes an ADS-B minimum system from ADS-B In and ADS-B Out. In ADS-B In, a fusion model with a variable sampling Variational Bayesian-Interacting Multiple Model (VSVB-IMM) algorithm is proposed for integrated display and an airspace traffic situation display is developed by using ADS-B information. ADS-B Out includes ADS-B Out transmission based on a simulator platform and an Unmanned Aerial Vehicle (UAV) platform. This paper describes the overall implementation of ADS-B minimum system, including theoretical model design, experimental simulation verification, engineering implementation, results analysis, etc. Simulation and implementation results show that the fused system has better performance than each independent subsystem and it can work well in engineering applications. PMID:29137194

Reducing Health Inequities in the United States: Insights and Recommendations from the National Heart, Lung, and Blood Institute’s Health Inequities Think Tank Meeting

PubMed Central

Sampson, Uchechukwu K.A.; Kaplan, Robert M.; Cooper, Richard S.; Diez Roux, Ana V.; Marks, James S.; Engelgau, Michael M.; Peprah, Emmanuel; Mishoe, Helena; Boulware, L. Ebony; Felix, Kaytura L.; Califf, Robert M.; Flack, John M.; Cooper, Lisa A.; Gracia, J. Nadine; Henderson, Jeffrey A.; Davidson, Karina W.; Krishnan, Jerry A.; Lewis, Tené T.; Sanchez, Eduardo; Luban, Naomi L.; Vaccarino, Viola; Wong, Winston F.; Wright, Jackson T.; Meyers, David; Ogedegbe, Olugbenga G.; Presley-Cantrell, Letitia; Chambers, David A.; Belis, Deshirée; Bennett, Glen C.; Boyington, Josephine E; Creazzo, Tony L.; de Jesus, Janet M.; Krishnamurti, Chitra; Lowden, Mia R.; Punturieri, Antonello; Shero, Susan T.; Young, Neal S.; Zou, Shimian; Mensah, George A.

2016-01-01

The National, Heart, Lung, and Blood Institute convened a Think Tank meeting to obtain insight and recommendations regarding the objectives and design of the next generation of research aimed at reducing health inequities in the United States. The panel recommended several specific actions, including: 1) Embrace broad and inclusive research themes; 2) Develop research platforms that optimize the ability to conduct informative and innovative research, and promote systems science approaches; 3) Develop networks of collaborators and stakeholders, and launch transformative studies that can serve as benchmarks; 4) Optimize the use of new data sources, platforms, and natural experiments; and 5) develop unique transdisciplinary training programs to build research capacity. Confronting health inequities will require engaging multiple disciplines and sectors (including communities), using systems science, and intervening through combinations of individual, family, provider, health system, and community-targeted approaches. Details of the panel’s remarks and recommendations are provided in this report. PMID:27470459

Highly efficient multiple-layer CdS quantum dot sensitized III-V solar cells.

PubMed

Lin, Chien-Chung; Han, Hau-Vei; Chen, Hsin-Chu; Chen, Kuo-Ju; Tsai, Yu-Lin; Lin, Wein-Yi; Kuo, Hao-Chung; Yu, Peichen

2014-02-01

In this review, the concept of utilization of solar spectrum in order to increase the solar cell efficiency is discussed. Among the three mechanisms, down-shifting effect is investigated in detail. Organic dye, rare-earth minerals and quantum dots are three most popular down-shift materials. While the enhancement of solar cell efficiency was not clearly observed in the past, the advances in quantum dot fabrication have brought strong response out of the hybrid platform of a quantum dot solar cell. A multiple layer structure, including PDMS as the isolation layer, is proposed and demonstrated. With the help of pulse spray system, precise control can be achieved and the optimized concentration can be found.

Strategies for Sharing Seismic Data Among Multiple Computer Platforms

NASA Astrophysics Data System (ADS)

Baker, L. M.; Fletcher, J. B.

2001-12-01

Seismic waveform data is readily available from a variety of sources, but it often comes in a distinct, instrument-specific data format. For example, data may be from portable seismographs, such as those made by Refraction Technology or Kinemetrics, from permanent seismograph arrays, such as the USGS Parkfield Dense Array, from public data centers, such as the IRIS Data Center, or from personal communication with other researchers through e-mail or ftp. A computer must be selected to import the data - usually whichever is the most suitable for reading the originating format. However, the computer best suited for a specific analysis may not be the same. When copies of the data are then made for analysis, a proliferation of copies of the same data results, in possibly incompatible, computer-specific formats. In addition, if an error is detected and corrected in one copy, or some other change is made, all the other copies must be updated to preserve their validity. Keeping track of what data is available, where it is located, and which copy is authoritative requires an effort that is easy to neglect. We solve this problem by importing waveform data to a shared network file server that is accessible to all our computers on our campus LAN. We use a Network Appliance file server running Sun's Network File System (NFS) software. Using an NFS client software package on each analysis computer, waveform data can then be read by our MatLab or Fortran applications without first copying the data. Since there is a single copy of the waveform data in a single location, the NFS file system hierarchy provides an implicit complete waveform data catalog and the single copy is inherently authoritative. Another part of our solution is to convert the original data into a blocked-binary format (known historically as USGS DR100 or VFBB format) that is interpreted by MatLab or Fortran library routines available on each computer so that the idiosyncrasies of each machine are not visible to the user. Commercial software packages, such as MatLab, also have the ability to share data in their own formats across multiple computer platforms. Our Fortran applications can create plot files in Adobe PostScript, Illustrator, and Portable Document Format (PDF) formats. Vendor support for reading these files is readily available on multiple computer platforms. We will illustrate by example our strategies for sharing seismic data among our multiple computer platforms, and we will discuss our positive and negative experiences. We will include our solutions for handling the different byte ordering, floating-point formats, and text file ``end-of-line'' conventions on the various computer platforms we use (6 different operating systems on 5 processor architectures).

NSIDC's passive microwave satellite record: The story behind 30 years of data across multiple satellite platforms

NASA Astrophysics Data System (ADS)

Scott, D. J.; Brandt, M.; Savoie, M. H.; Stewart, J. S.

2016-12-01

The National Snow and Ice Data Center (NSIDC) Distributed Active Archive Center (DAAC) has been producing and distributing passive microwave snow and ice data sets from the Special Sensor Microwave Imager (SSM/I) and Special Sensor Microwave Imager/Sounder (SSMIS) for over two decades. Aboard the Defense Meteorological Satellite Program (DMSP) platforms, SSM/I and SSMIS have been operating across eight different orbiting DMSP satellites since 1987, providing an invaluable 30 year record for snow and ice climate data studies. Each sensor has performed within or beyond its expected life cycle, ultimately resulting in a transition across platforms to continue the data record. On occasion the satellites have failed unexpectedly, requiring an unplanned need for science and data management to come together and adjust production code and services to get the data back online in a timely fashion. In recent years, this has become a greater importance as climate blogging sites have increased the visibility of near-real-time passive microwave products to communicate the current changes in the Polar Regions. This presentation summarizes the history and most recent activities surrounding satellite transitions, including the scientific assessment and development required in maintaining a streamlined data record across multiple sensors. In addition, we examine challenges in long-term provenance as well as the considerations and decisions made based on value added products utilizing these data, as well as cryospheric research and general public needs.

Supplementary immunization activities (SIAs) in South Africa: comprehensive economic evaluation of an integrated child health delivery platform

PubMed Central

Verguet, Stéphane; Jassat, Waasila; Bertram, Melanie Y.; Tollman, Stephen M.; Murray, Christopher J. L.; Jamison, Dean T.; Hofman, Karen J.

2013-01-01

Background Supplementary immunization activity (SIA) campaigns provide children with an additional dose of measles vaccine and deliver other interventions, including vitamin A supplements, deworming medications, and oral polio vaccines. Objective To assess the cost-effectiveness of the full SIA delivery platform in South Africa (SA). Design We used an epidemiologic cost model to estimate the cost-effectiveness of the 2010 SIA campaign. We used province-level campaign data sourced from the District Health Information System, SA, and from planning records of provincial coordinators of the Expanded Programme on Immunization. The data included the number of children immunized with measles and polio vaccines, the number of children given vitamin A supplements and Albendazole tablets, and costs. Results The campaign cost $37 million and averted a total of 1,150 deaths (95% uncertainty range: 990–1,360). This ranged from 380 deaths averted in KwaZulu-Natal to 20 deaths averted in the Northern Cape. Vitamin A supplementation alone averted 820 deaths (95% UR: 670–1,040); measles vaccination alone averted 330 deaths (95% UR: 280–370). Incremental cost-effectiveness was $27,100 (95% UR: $18,500–34,400) per death averted nationally, ranging from $11,300 per death averted in the Free State to $91,300 per death averted in the Eastern Cape. Conclusions Cost-effectiveness of the SIA child health delivery platform varies substantially across SA provinces, and it is substantially more cost-effective when vitamin A supplementation is included in the interventions administered. Cost-effectiveness assessments should consider health system delivery platforms that integrate multiple interventions, and they should be conducted at the sub-national level. PMID:23458088

NASA World Wind, Open Source 4D Geospatial Visualization Platform: *.NET & Java* for EDUCATION

NASA Astrophysics Data System (ADS)

Hogan, P.; Kuehnel, F.

2006-12-01

NASA World Wind has only one goal, to provide the maximum opportunity for geospatial information to be experienced, be it education, science, research, business, or government. The benefits to understanding for information delivered in the context of its 4D virtual reality are extraordinary. The NASA World Wind visualization platform is open source and therefore lends itself well to being extended to service *any* requirements, be they proprietary and commercial or simply available. Data accessibility is highly optimized using standard formats including internationally certified open standards (W*S). Although proprietary applications can be built based on World Wind, and proprietary data delivered that leverage World Wind, there is nothing proprietary about the visualization platform itself or the multiple planetary data sets readily available, including global animations of live weather. NASA World Wind is being used by NASA research teams as well as being a formal part of high school and university curriculum. The National Guard uses World Wind for emergency response activities and State governments have incorporated high resolution imagery for GIS management as well as for their cross-agency emergency response activities. The U.S. federal government uses NASA World Wind for a myriad of GIS and security-related issues (NSA, NGA, DOE, FAA, etc.).

NASA World Wind, Open Source 4D Geospatial Visualization Platform: *.NET & Java*

NASA Astrophysics Data System (ADS)

Hogan, P.; Coughlan, J.

2006-12-01

NASA World Wind has only one goal, to provide the maximum opportunity for geospatial information to be experienced, be it education, science, research, business, or government. The benefits to understanding for information delivered in the context of its 4D virtual reality are extraordinary. The NASA World Wind visualization platform is open source and therefore lends itself well to being extended to service *any* requirements, be they proprietary and commercial or simply available. Data accessibility is highly optimized using standard formats including internationally certified open standards (W*S). Although proprietary applications can be built based on World Wind, and proprietary data delivered that leverage World Wind, there is nothing proprietary about the visualization platform itself or the multiple planetary data sets readily available, including global animations of live weather. NASA World Wind is being used by NASA research teams as well as being a formal part of high school and university curriculum. The National Guard uses World Wind for emergency response activities and State governments have incorporated high resolution imagery for GIS management as well as for their cross-agency emergency response activities. The U.S. federal government uses NASA World Wind for a myriad of GIS and security-related issues (NSA, NGA, DOE, FAA, etc.).

MAKING THE WEASELS WILD AGAIN: ENSURING FUTURE AIR DOMINANCE THROUGH EFFECTIVE SEAD TRAINING

DTIC Science & Technology

2016-06-01

both multi-mission design series (MMDS) and joint SEAD training as well as improve the capabilities of its electronic warfare (EW) ranges in order...USAF units to train for multi-mission design series (MMDS) SEAD operations.14 MMDS training includes the use of multiple USAF airborne platforms...not provided SEAD aircrews with either the quantity or quality of training required to conduct effective operations.2 At that time , Major Jon Norman

The Chandra X-ray Center data system: supporting the mission of the Chandra X-ray Observatory

NASA Astrophysics Data System (ADS)

Evans, Janet D.; Cresitello-Dittmar, Mark; Doe, Stephen; Evans, Ian; Fabbiano, Giuseppina; Germain, Gregg; Glotfelty, Kenny; Hall, Diane; Plummer, David; Zografou, Panagoula

2006-06-01

The Chandra X-ray Center Data System provides end-to-end scientific software support for Chandra X-ray Observatory mission operations. The data system includes the following components: (1) observers' science proposal planning tools; (2) science mission planning tools; (3) science data processing, monitoring, and trending pipelines and tools; and (4) data archive and database management. A subset of the science data processing component is ported to multiple platforms and distributed to end-users as a portable data analysis package. Web-based user tools are also available for data archive search and retrieval. We describe the overall architecture of the data system and its component pieces, and consider the design choices and their impacts on maintainability. We discuss the many challenges involved in maintaining a large, mission-critical software system with limited resources. These challenges include managing continually changing software requirements and ensuring the integrity of the data system and resulting data products while being highly responsive to the needs of the project. We describe our use of COTS and OTS software at the subsystem and component levels, our methods for managing multiple release builds, and adapting a large code base to new hardware and software platforms. We review our experiences during the life of the mission so-far, and our approaches for keeping a small, but highly talented, development team engaged during the maintenance phase of a mission.

Large-scale monitoring of shorebird populations using count data and N-mixture models: Black Oystercatcher (Haematopus bachmani) surveys by land and sea

USGS Publications Warehouse

Lyons, James E.; Andrew, Royle J.; Thomas, Susan M.; Elliott-Smith, Elise; Evenson, Joseph R.; Kelly, Elizabeth G.; Milner, Ruth L.; Nysewander, David R.; Andres, Brad A.

2012-01-01

Large-scale monitoring of bird populations is often based on count data collected across spatial scales that may include multiple physiographic regions and habitat types. Monitoring at large spatial scales may require multiple survey platforms (e.g., from boats and land when monitoring coastal species) and multiple survey methods. It becomes especially important to explicitly account for detection probability when analyzing count data that have been collected using multiple survey platforms or methods. We evaluated a new analytical framework, N-mixture models, to estimate actual abundance while accounting for multiple detection biases. During May 2006, we made repeated counts of Black Oystercatchers (Haematopus bachmani) from boats in the Puget Sound area of Washington (n = 55 sites) and from land along the coast of Oregon (n = 56 sites). We used a Bayesian analysis of N-mixture models to (1) assess detection probability as a function of environmental and survey covariates and (2) estimate total Black Oystercatcher abundance during the breeding season in the two regions. Probability of detecting individuals during boat-based surveys was 0.75 (95% credible interval: 0.42–0.91) and was not influenced by tidal stage. Detection probability from surveys conducted on foot was 0.68 (0.39–0.90); the latter was not influenced by fog, wind, or number of observers but was ~35% lower during rain. The estimated population size was 321 birds (262–511) in Washington and 311 (276–382) in Oregon. N-mixture models provide a flexible framework for modeling count data and covariates in large-scale bird monitoring programs designed to understand population change.

A Roadmap for using Agile Development in a Traditional System

NASA Technical Reports Server (NTRS)

Streiffert, Barbara; Starbird, Thomas

2006-01-01

I. Ensemble Development Group: a) Produces activity planning software for in spacecraft; b) Built on Eclipse Rich Client Platform (open source development and runtime software); c) Funded by multiple sources including the Mars Technology Program; d) Incorporated the use of Agile Development. II. Next Generation Uplink Planning System: a) Researches the Activity Planning and Sequencing Subsystem for Mars Science Laboratory (APSS); b) APSS includes Ensemble, Activity Modeling, Constraint Checking, Command Editing and Sequencing tools plus other uplink generation utilities; c) Funded by the Mars Technology Program; d) Integrates all of the tools for APSS.

Methods for open innovation on a genome-design platform associating scientific, commercial, and educational communities in synthetic biology.

PubMed

Toyoda, Tetsuro

2011-01-01

Synthetic biology requires both engineering efficiency and compliance with safety guidelines and ethics. Focusing on the rational construction of biological systems based on engineering principles, synthetic biology depends on a genome-design platform to explore the combinations of multiple biological components or BIO bricks for quickly producing innovative devices. This chapter explains the differences among various platform models and details a methodology for promoting open innovation within the scope of the statutory exemption of patent laws. The detailed platform adopts a centralized evaluation model (CEM), computer-aided design (CAD) bricks, and a freemium model. It is also important for the platform to support the legal aspects of copyrights as well as patent and safety guidelines because intellectual work including DNA sequences designed rationally by human intelligence is basically copyrightable. An informational platform with high traceability, transparency, auditability, and security is required for copyright proof, safety compliance, and incentive management for open innovation in synthetic biology. GenoCon, which we have organized and explained here, is a competition-styled, open-innovation method involving worldwide participants from scientific, commercial, and educational communities that aims to improve the designs of genomic sequences that confer a desired function on an organism. Using only a Web browser, a participating contributor proposes a design expressed with CAD bricks that generate a relevant DNA sequence, which is then experimentally and intensively evaluated by the GenoCon organizers. The CAD bricks that comprise programs and databases as a Semantic Web are developed, executed, shared, reused, and well stocked on the secure Semantic Web platform called the Scientists' Networking System or SciNetS/SciNeS, based on which a CEM research center for synthetic biology and open innovation should be established. Copyright © 2011 Elsevier Inc. All rights reserved.

Defining the ecogeomorphic succession of land building for freshwater, intertidal wetlands in Wax Lake Delta, Louisiana

NASA Astrophysics Data System (ADS)

Olliver, Elizabeth A.; Edmonds, Douglas A.

2017-09-01

Land building in deltaic environments occurs when sediment discharged from a river mouth is deposited subaqueously and transitions to subaerial land. The transition from subaqueous deposition to subaerial land is a critical process that marks the creation of relatively stable land, yet it is unclear what controls the speed and style of this transition. We define how this transition, herein termed the land building succession, varies in time and space for the freshwater, intertidal wetlands in Wax Lake Delta, LA. Using remote sensing and field data we classify land cover into sediment, water, or vegetation classes at maximum and minimum biomass. We see two succession patterns within Wax Lake Delta. Deltaic islands near the apex are initially covered by sediment and open water. Through time, open water and sediment coverage decreases as vegetation coverage increases. On the other hand, distal islands show little sediment exposure through time. In both cases, all deltaic islands become covered with vegetation by 2015. As vegetation colonizes the island, the topography organizes into two platforms vertically separated by ∼0.35 m. The lower, intertidal platform occurs in the island interiors and is commonly inundated by water and dominated by subaqueous or floating vegetation. The upper, subaerial platform occurs along island edges and is dominated by a variety of vegetation species including Salix nigra, Colocasia esculenta, and Polygonum punctatum. It takes an average of ∼10 years for the intertidal platform to transition to the subaerial platform. These two platforms are separated by the tidal range measured in Atchafalaya Bay, and the different vegetation communities occupying each platform suggest they are a manifestation of multiple stable states and arise due to vegetation and sedimentation feedbacks.

The Mars Hopper: a radioisotope powered, impulse driven, long-range, long-lived mobile platform for exploration of Mars

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

Steven D. Howe; Robert C. O'Brien; William Taitano

Planetary exploration mission requirements are becoming more demanding. Due to the increasing cost, the missions that provide mobile platforms that can acquire data at multiple locations are becoming more attractive. Wheeled vehicles such as the MER rovers have proven extremely capable but have very limited range and cannot traverse rugged terrain. Flying vehicles such as balloons and airplanes have been proposed but are problematic due to the very thin atmospheric pressure and the strong, dusty winds present on Mars. The Center for Space Nuclear Research has designed an instrumented platform that can acquire detailed data at hundreds of locations duringmore » its lifetime - a Mars Hopper. The Mars Hopper concept utilizes energy from radioisotopic decay in a manner different from any existing radioisotopic power sources—as a thermal capacitor. By accumulating the heat from radioisotopic decay for long periods, the power of the source can be dramatically increased for short periods. The platform will be able to "hop" from one location to the next every 5-7 days with a separation of 5-10 km per hop. Preliminary designs show a platform that weighs around 52 kgs unfueled which is the condition at deployment. Consequently, several platforms may be deployed on a single launch from Earth. With sufficient lifetime, the entire surface of Mars can be mapped in detail by a couple dozen platforms. In addition, Hoppers can collect samples from all over the planet, including gorges, mountains and crevasses, and deliver them to a central location for eventual pick-up by a Mars Sample Return mission. The status of the Mars Hopper development project at the CSNR is discussed.« less

Dielectrophoretic lab-on-CMOS platform for trapping and manipulation of cells.

PubMed

Park, Kyoungchul; Kabiri, Shideh; Sonkusale, Sameer

2016-02-01

Trapping and manipulation of cells are essential operations in numerous studies in biology and life sciences. We discuss the realization of a Lab-on-a-Chip platform for dielectrophoretic trapping and repositioning of cells and microorganisms on a complementary metal oxide semiconductor (CMOS) technology, which we define here as Lab-on-CMOS (LoC). The LoC platform is based on dielectrophoresis (DEP) which is the force experienced by any dielectric particle including biological entities in non-uniform AC electrical field. DEP force depends on the permittivity of the cells, its size and shape and also on the permittivity of the medium and therefore it enables selective targeting of cells based on their phenotype. In this paper, we address an important matter that of electrode design for DEP for which we propose a three-dimensional (3D) octapole geometry to create highly confined electric fields for trapping and manipulation of cells. Conventional DEP-based platforms are implemented stand-alone on glass, silicon or polymers connected to external infrastructure for electronics and optics, making it bulky and expensive. In this paper, the use of CMOS as a platform provides a pathway to truly miniaturized lab-on-CMOS or LoC platform, where DEP electrodes are designed using built-in multiple metal layers of the CMOS process for effective trapping of cells, with built-in electronics for in-situ impedance monitoring of the cell position. We present electromagnetic simulation results of DEP force for this unique 3D octapole geometry on CMOS. Experimental results with yeast cells validate the design. These preliminary results indicate the promise of using CMOS technology for truly compact miniaturized lab-on-chip platform for cell biotechnology applications.

An Integrated Hydrologic Monitoring Network

NASA Astrophysics Data System (ADS)

Tedesco, L. P.; Baker, M. P.; Hall, B. E.

2004-12-01

Ecological studies depend on the ability to monitor an environment, collect data at appropriate spatial and temporal scales, and analyze that data from the diverse viewpoints of many relevant disciplines. Historically, environmental studies have been conducted by small teams of researchers, usually collecting data by hand at some set but low frequency, and organizing it according to ad hoc, project-specific goals. Recent years have seen dramatic advancement in the ability to gather environmental data remotely and therefore at much higher frequency. We are working to create a dynamic and integrated network of environmental sensors in natural environments to acquire real time data and create tools for visualization appropriate for different audiences to promote scientific exploration. Instrumentation includes an array of water quality and water level sondes and probes distributed throughout three Central Indiana counties. Instrument platforms currently include five river monitoring platforms utilizing YSI water quality and level probes; a lake buoy array that includes three YSI sonde packages monitoring physical, chemical and biological parameters; and over fifteen YSI and Solinist groundwater probes recording both level and water quality. Many sites are providing real-time data and several additional sites are scheduled to be online in the coming months. Visualization of this real time data from remote sensors distributed throughout Central Indiana provides numerous challenges. The benefits of successfully integrating remotely deployed environmental sensors in a post 9-11 world is obvious. We are working to bridge both the extremes associated with the frequency of data collection and the lack of data coordination by creating techniques for data networking and retrieval, and data management, analysis, and visualization capabilities that operate across a range of computing platforms to make this data immediately accessible and useful to a range of interested parties, across multiple disciplines. We are working to integrate multiple data streams into a coherent data base and create applications that allow users to view data from multiple instruments at different sites. Creating visualizations of real time, dynamic data from the everyday world and delivering it via web applications as well as through innovative display spaces will be a key outcome of this program. On-line tools for QA/QC, data queries, graphing, and sensitivity analysis are under development. Our goal is to use the instrumented sites to create analysis and presentation applications to foster a community of learners interested in understanding these ecosystems, and the larger environmental issues that they represent. This broad-based community will include environmental researchers, university faculty in lecture halls, math and science teachers, university and K-12 students, civic leaders, and educators at informal learning centers.

A Platform-Independent Plugin for Navigating Online Radiology Cases.

PubMed

Balkman, Jason D; Awan, Omer A

2016-06-01

Software methods that enable navigation of radiology cases on various digital platforms differ between handheld devices and desktop computers. This has resulted in poor compatibility of online radiology teaching files across mobile smartphones, tablets, and desktop computers. A standardized, platform-independent, or "agnostic" approach for presenting online radiology content was produced in this work by leveraging modern hypertext markup language (HTML) and JavaScript web software technology. We describe the design and evaluation of this software, demonstrate its use across multiple viewing platforms, and make it publicly available as a model for future development efforts.

An ultra low energy biomedical signal processing system operating at near-threshold.

PubMed

Hulzink, J; Konijnenburg, M; Ashouei, M; Breeschoten, A; Berset, T; Huisken, J; Stuyt, J; de Groot, H; Barat, F; David, J; Van Ginderdeuren, J

2011-12-01

This paper presents a voltage-scalable digital signal processing system designed for the use in a wireless sensor node (WSN) for ambulatory monitoring of biomedical signals. To fulfill the requirements of ambulatory monitoring, power consumption, which directly translates to the WSN battery lifetime and size, must be kept as low as possible. The proposed processing platform is an event-driven system with resources to run applications with different degrees of complexity in an energy-aware way. The architecture uses effective system partitioning to enable duty cycling, single instruction multiple data (SIMD) instructions, power gating, voltage scaling, multiple clock domains, multiple voltage domains, and extensive clock gating. It provides an alternative processing platform where the power and performance can be scaled to adapt to the application need. A case study on a continuous wavelet transform (CWT)-based heart-beat detection shows that the platform not only preserves the sensitivity and positive predictivity of the algorithm but also achieves the lowest energy/sample for ElectroCardioGram (ECG) heart-beat detection publicly reported today.

Technologies for Assessment of Motor Disorders in Parkinson’s Disease: A Review

PubMed Central

Oung, Qi Wei; Muthusamy, Hariharan; Lee, Hoi Leong; Basah, Shafriza Nisha; Yaacob, Sazali; Sarillee, Mohamed; Lee, Chia Hau

2015-01-01

Parkinson’s Disease (PD) is characterized as the commonest neurodegenerative illness that gradually degenerates the central nervous system. The goal of this review is to come out with a summary of the recent progress of numerous forms of sensors and systems that are related to diagnosis of PD in the past decades. The paper reviews the substantial researches on the application of technological tools (objective techniques) in the PD field applying different types of sensors proposed by previous researchers. In addition, this also includes the use of clinical tools (subjective techniques) for PD assessments, for instance, patient self-reports, patient diaries and the international gold standard reference scale, Unified Parkinson Disease Rating Scale (UPDRS). Comparative studies and critical descriptions of these approaches have been highlighted in this paper, giving an insight on the current state of the art. It is followed by explaining the merits of the multiple sensor fusion platform compared to single sensor platform for better monitoring progression of PD, and ends with thoughts about the future direction towards the need of multimodal sensor integration platform for the assessment of PD. PMID:26404288

Using digital media to promote kidney disease education.

PubMed

Goldstein, Karen; Briggs, Michael; Oleynik, Veronica; Cullen, Mac; Jones, Jewel; Newman, Eileen; Narva, Andrew

2013-07-01

Health-care providers and patients increasingly turn to the Internet-websites as well as social media platforms-for health-related information and support. Informed by research on audience behaviors and preferences related to digital health information, the National Kidney Disease Education Program (NKDEP) developed a comprehensive and user-friendly digital ecosystem featuring content and platforms relevant for each audience. NKDEP's analysis of website metrics and social media conversation mapping related to CKD revealed gaps and opportunities, informing the development of a digital strategy to position NKDEP as a trustworthy digital source for evidence-based kidney disease information. NKDEP launched a redesigned website (www.nkdep.nih.gov) with enhanced content for multiple audiences as well as a complementary social media presence on Twitter and Facebook serving to drive traffic to the website as well as actively engage target audiences in conversations about kidney disease. The results included improved website metrics and increasing social media engagement among consumers and health-care providers. NKDEP will continue to monitor trends, explore new directions, and work to improve communication across digital platforms. Published by Elsevier Inc.

Investigation of Slosh Dynamics on Flight and Ground Platforms

NASA Astrophysics Data System (ADS)

Vergalla, Michael; Zhou, Ran

The slosh dynamics in cryogenic fuel tanks under microgravity is a problem that severely affects the reliability of spacecraft launching. To investigate slosh dynamics and their effects on space vehicle dynamics three levels of testing are presently in progress. Platforms include a 3-DOF ground testing table, parabolic flights, sounding rockets and finally the International Space Station. Ground tests provide an economically viable platform for investigating rotational, translational, and coupled feed-back modes due to repeatable CNC motions. The parabolic flight campaign has conducted four successful flights aboard multiple aircraft using static and tethered slosh packages. Using the PANTHER II student designed rocket, a slosh package was launched as a payload. Finally with collaboration between Florida Institute of Technology and Massachusetts Institute of Technology SPHERES project, two test sessions investigating feedback using partially and fully filled propellant tanks have been completed aboard the In-ternational Space Station. Motion data from all tests will be input to in house Dynamic Mesh Model to further establish confidence in the versatility and accuracy of the method. The results show that it is necessary to construct additional hardware for slosh studies.

MyDiabetesMyWay

PubMed Central

Wake, Deborah J.; He, Jinzhang; Czesak, Anna Maria; Mughal, Fezan; Cunningham, Scott G.

2016-01-01

MyDiabetesMyWay (MDMW) is an award-wining national electronic personal health record and self-management platform for diabetes patients in Scotland. This platform links multiple national institutional and patient-recorded data sources to provide a unique resource for patient care and self-management. This review considers the current evidence for online interventions in diabetes and discusses these in the context of current and ongoing developments for MDMW. Evaluation of MDMW through patient reported outcomes demonstrates a positive impact on self-management. User feedback has highlighted barriers to uptake and has guided platform evolution from an education resource website to an electronic personal health record now encompassing remote monitoring, communication tools and personalized education links. Challenges in delivering digital interventions for long-term conditions include integration of data between institutional and personal recorded sources to perform big data analytics and facilitating technology use in those with disabilities, low digital literacy, low socioeconomic status and in minority groups. The potential for technology supported health improvement is great, but awareness and adoption by health workers and patients remains a significant barrier. PMID:27162192

Analysis of outcomes in radiation oncology: An integrated computational platform

PubMed Central

Liu, Dezhi; Ajlouni, Munther; Jin, Jian-Yue; Ryu, Samuel; Siddiqui, Farzan; Patel, Anushka; Movsas, Benjamin; Chetty, Indrin J.

2009-01-01

Radiotherapy research and outcome analyses are essential for evaluating new methods of radiation delivery and for assessing the benefits of a given technology on locoregional control and overall survival. In this article, a computational platform is presented to facilitate radiotherapy research and outcome studies in radiation oncology. This computational platform consists of (1) an infrastructural database that stores patient diagnosis, IMRT treatment details, and follow-up information, (2) an interface tool that is used to import and export IMRT plans in DICOM RT and AAPM/RTOG formats from a wide range of planning systems to facilitate reproducible research, (3) a graphical data analysis and programming tool that visualizes all aspects of an IMRT plan including dose, contour, and image data to aid the analysis of treatment plans, and (4) a software package that calculates radiobiological models to evaluate IMRT treatment plans. Given the limited number of general-purpose computational environments for radiotherapy research and outcome studies, this computational platform represents a powerful and convenient tool that is well suited for analyzing dose distributions biologically and correlating them with the delivered radiation dose distributions and other patient-related clinical factors. In addition the database is web-based and accessible by multiple users, facilitating its convenient application and use. PMID:19544785

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

Bioinspired legged-robot based on large deformation of flexible skeleton.

PubMed

Mayyas, Mohammad

2014-11-11

In this article we present STARbot, a bioinspired legged robot capable of multiple locomotion modalities by using large deformation of its skeleton. We construct STARbot by using origami-style folding of flexible laminates. The long-term goal is to provide a robotic platform with maximum mobility on multiple surfaces. This paper particularly studies the quasistatic model of STARbot's leg under different conditions. We describe the large elastic deformation of a leg under external force, payload, and friction by using a set of non-dimensional, nonlinear approximate equations. We developed a test mechanism that models the motion of a leg in STARbot. We augmented several foot shapes and then tested them on soft to rough grounds. Both simulation and experimental findings were in good agreement. We utilized the model to develop several scales of tri and quad STARbot. We demonstrated the capability of these robots to locomote by combining their leg deformations with their foot motions. The combination provided a design platform for an active suspension STARbot with controlled foot locomotion. This included the ability of STARbot to change size, run over obstacles, walk and slide. Furthermore, in this paper we discuss a cost effective manufacturing and production method for manufacturing STARbot.

Modeling and control of flexible space platforms with articulated payloads

NASA Technical Reports Server (NTRS)

Graves, Philip C.; Joshi, Suresh M.

1989-01-01

The first steps in developing a methodology for spacecraft control-structure interaction (CSI) optimization are identification and classification of anticipated missions, and the development of tractable mathematical models in each mission class. A mathematical model of a generic large flexible space platform (LFSP) with multiple independently pointed rigid payloads is considered. The objective is not to develop a general purpose numerical simulation, but rather to develop an analytically tractable mathematical model of such composite systems. The equations of motion for a single payload case are derived, and are linearized about zero steady-state. The resulting model is then extended to include multiple rigid payloads, yielding the desired analytical form. The mathematical models developed clearly show the internal inertial/elastic couplings, and are therefore suitable for analytical and numerical studies. A simple decentralized control law is proposed for fine pointing the payloads and LFSP attitude control, and simulation results are presented for an example problem. The decentralized controller is shown to be adequate for the example problem chosen, but does not, in general, guarantee stability. A centralized dissipative controller is then proposed, requiring a symmetric form of the composite system equations. Such a controller guarantees robust closed loop stability despite unmodeled elastic dynamics and parameter uncertainties.

Cell Culture on MEMS Platforms: A Review

PubMed Central

Ni, Ming; Tong, Wen Hao; Choudhury, Deepak; Rahim, Nur Aida Abdul; Iliescu, Ciprian; Yu, Hanry

2009-01-01

Microfabricated systems provide an excellent platform for the culture of cells, and are an extremely useful tool for the investigation of cellular responses to various stimuli. Advantages offered over traditional methods include cost-effectiveness, controllability, low volume, high resolution, and sensitivity. Both biocompatible and bio-incompatible materials have been developed for use in these applications. Biocompatible materials such as PMMA or PLGA can be used directly for cell culture. However, for bio-incompatible materials such as silicon or PDMS, additional steps need to be taken to render these materials more suitable for cell adhesion and maintenance. This review describes multiple surface modification strategies to improve the biocompatibility of MEMS materials. Basic concepts of cell-biomaterial interactions, such as protein adsorption and cell adhesion are covered. Finally, the applications of these MEMS materials in Tissue Engineering are presented. PMID:20054478

Liquid biopsy genotyping in lung cancer: ready for clinical utility?

PubMed

Huang, Wei-Lun; Chen, Yi-Lin; Yang, Szu-Chun; Ho, Chung-Liang; Wei, Fang; Wong, David T; Su, Wu-Chou; Lin, Chien-Chung

2017-03-14

Liquid biopsy is a blood test that detects evidence of cancer cells or tumor DNA in the circulation. Despite complicated collection methods and the requirement for technique-dependent platforms, it has generated substantial interest due, in part, to its potential to detect driver oncogenes such as epidermal growth factor receptor (EGFR) mutants in lung cancer. This technology is advancing rapidly and is being incorporated into numerous EGFR tyrosine kinase inhibitor (EGFR-TKI) development programs. It appears ready for integration into clinical care. Recent studies have demonstrated that biological fluids such as saliva and urine can also be used for detecting EGFR mutant DNA through application other user-friendly techniques. This review focuses on the clinical application of liquid biopsies to lung cancer genotyping, including EGFR and other targets of genotype-directed therapy and compares multiple platforms used for liquid biopsy.

Fiber Bragg grating sensor interrogators on chip: challenges and opportunities

NASA Astrophysics Data System (ADS)

Marin, Yisbel; Nannipieri, Tiziano; Oton, Claudio J.; Di Pasquale, Fabrizio

2017-04-01

In this paper we present an overview of the current efforts towards integration of Fiber Bragg Grating (FBG) sensor interrogators. Different photonic integration platforms will be discussed, including monolithic planar lightwave circuit technology, silicon on insulator (SOI), indium phosphide (InP) and gallium arsenide (GaAs) material platforms. Also various possible techniques for wavelength metering and methods for FBG multiplexing will be discussed and compared in terms of resolution, dynamic performance, multiplexing capabilities and reliability. The use of linear filters, array waveguide gratings (AWG) as multiple linear filters and AWG based centroid signal processing techniques will be addressed as well as interrogation techniques based on tunable micro-ring resonators and Mach-Zehnder interferometers (MZI) for phase sensitive detection. The paper will also discuss the challenges and perspectives of photonic integration to address the increasing requirements of several industrial applications.

Optical sensing of analytes in aqueous solutions with a multiple surface-plasmon-polariton-wave platform

PubMed Central

Swiontek, Stephen E.; Pulsifer, Drew P.; Lakhtakia, Akhlesh

2013-01-01

The commonly used optical sensor based on surface plasmon-polariton wave phenomenon can sense just one chemical, because only one SPP wave can be guided by the interface of a metal and a dielectric material contained in the sensor. Multiple analytes could be detected and/or the sensing reliability for a single analyte could be enhanced, if multiple SPP-wave modes could be excited on a single metal/dielectric interface. For that to happen, the partnering dielectric material must be periodically non-homogeneous. Using a chiral sculptured thin film (CSTF) as that material in a SPP-wave platform, we show that the angular locations of multiple SPP-wave modes shift when the void regions of the CSTF are infiltrated with a fluid. The sensitivities realized in the proof-of-concept experiments are comparable to state-of-research values. PMID:23474988

pytc: Open-Source Python Software for Global Analyses of Isothermal Titration Calorimetry Data.

PubMed

Duvvuri, Hiranmayi; Wheeler, Lucas C; Harms, Michael J

2018-05-08

Here we describe pytc, an open-source Python package for global fits of thermodynamic models to multiple isothermal titration calorimetry experiments. Key features include simplicity, the ability to implement new thermodynamic models, a robust maximum likelihood fitter, a fast Bayesian Markov-Chain Monte Carlo sampler, rigorous implementation, extensive documentation, and full cross-platform compatibility. pytc fitting can be done using an application program interface or via a graphical user interface. It is available for download at https://github.com/harmslab/pytc .

Architectures and methodologies for future deployment of multi-site Zettabyte-Exascale data handling platforms

NASA Astrophysics Data System (ADS)

Acín, V.; Bird, I.; Boccali, T.; Cancio, G.; Collier, I. P.; Corney, D.; Delaunay, B.; Delfino, M.; dell'Agnello, L.; Flix, J.; Fuhrmann, P.; Gasthuber, M.; Gülzow, V.; Heiss, A.; Lamanna, G.; Macchi, P.-E.; Maggi, M.; Matthews, B.; Neissner, C.; Nief, J.-Y.; Porto, M. C.; Sansum, A.; Schulz, M.; Shiers, J.

2015-12-01

Several scientific fields, including Astrophysics, Astroparticle Physics, Cosmology, Nuclear and Particle Physics, and Research with Photons, are estimating that by the 2020 decade they will require data handling systems with data volumes approaching the Zettabyte distributed amongst as many as 1018 individually addressable data objects (Zettabyte-Exascale systems). It may be convenient or necessary to deploy such systems using multiple physical sites. This paper describes the findings of a working group composed of experts from several

MONO FOR CROSS-PLATFORM CONTROL SYSTEM ENVIRONMENT

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

Nishimura, Hiroshi; Timossi, Chris

2006-10-19

Mono is an independent implementation of the .NET Frameworkby Novell that runs on multiple operating systems (including Windows,Linux and Macintosh) and allows any .NET compatible application to rununmodified. For instance Mono can run programs with graphical userinterfaces (GUI) developed with the C# language on Windows with VisualStudio (a full port of WinForm for Mono is in progress). We present theresults of tests we performed to evaluate the portability of our controlssystem .NET applications from MS Windows to Linux.

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.

High-speed multiple sequence alignment on a reconfigurable platform.

PubMed

Oliver, Tim; Schmidt, Bertil; Maskell, Douglas; Nathan, Darran; Clemens, Ralf

2006-01-01

Progressive alignment is a widely used approach to compute multiple sequence alignments (MSAs). However, aligning several hundred sequences by popular progressive alignment tools requires hours on sequential computers. Due to the rapid growth of sequence databases biologists have to compute MSAs in a far shorter time. In this paper we present a new approach to MSA on reconfigurable hardware platforms to gain high performance at low cost. We have constructed a linear systolic array to perform pairwise sequence distance computations using dynamic programming. This results in an implementation with significant runtime savings on a standard FPGA.

Research in Evaluation Methods for Data Fusion-Capable Tactical Platforms and Distributed Multi-platform Systems in Electronic Warfare and Information-Warfare Related Missions

DTIC Science & Technology

2009-02-01

They support their launches until both outside reds are killed or until second shots are needed. In the baseline scenario shown, US2 achieves 2 kills ...red 5/6 kills . The SUT gate multiplication factor was 5 and 15. The PE gate multiplication factors of 3 and 5, PE designs for Vogel and Hungarian... ploughed in various sections of this land by splitting it into sub plots came to be known as the subplot factor. Such a design is used only when there

MetaCoMET: a web platform for discovery and visualization of the core microbiome

USDA-ARS?s Scientific Manuscript database

A key component of the analysis of microbiome datasets is the identification of OTUs shared between multiple experimental conditions, commonly referred to as the core microbiome. Results: We present a web platform named MetaCoMET that enables the discovery and visualization of the core microbiome an...

A Multimodal Deep Log-Based User Experience (UX) Platform for UX Evaluation

PubMed Central

Ali Khan, Wajahat; Hur, Taeho; Muhammad Bilal, Hafiz Syed; Ul Hassan, Anees; Lee, Sungyoung

2018-01-01

The user experience (UX) is an emerging field in user research and design, and the development of UX evaluation methods presents a challenge for both researchers and practitioners. Different UX evaluation methods have been developed to extract accurate UX data. Among UX evaluation methods, the mixed-method approach of triangulation has gained importance. It provides more accurate and precise information about the user while interacting with the product. However, this approach requires skilled UX researchers and developers to integrate multiple devices, synchronize them, analyze the data, and ultimately produce an informed decision. In this paper, a method and system for measuring the overall UX over time using a triangulation method are proposed. The proposed platform incorporates observational and physiological measurements in addition to traditional ones. The platform reduces the subjective bias and validates the user’s perceptions, which are measured by different sensors through objectification of the subjective nature of the user in the UX assessment. The platform additionally offers plug-and-play support for different devices and powerful analytics for obtaining insight on the UX in terms of multiple participants. PMID:29783712

A Multimodal Deep Log-Based User Experience (UX) Platform for UX Evaluation.

PubMed

Hussain, Jamil; Khan, Wajahat Ali; Hur, Taeho; Bilal, Hafiz Syed Muhammad; Bang, Jaehun; Hassan, Anees Ul; Afzal, Muhammad; Lee, Sungyoung

2018-05-18

The user experience (UX) is an emerging field in user research and design, and the development of UX evaluation methods presents a challenge for both researchers and practitioners. Different UX evaluation methods have been developed to extract accurate UX data. Among UX evaluation methods, the mixed-method approach of triangulation has gained importance. It provides more accurate and precise information about the user while interacting with the product. However, this approach requires skilled UX researchers and developers to integrate multiple devices, synchronize them, analyze the data, and ultimately produce an informed decision. In this paper, a method and system for measuring the overall UX over time using a triangulation method are proposed. The proposed platform incorporates observational and physiological measurements in addition to traditional ones. The platform reduces the subjective bias and validates the user's perceptions, which are measured by different sensors through objectification of the subjective nature of the user in the UX assessment. The platform additionally offers plug-and-play support for different devices and powerful analytics for obtaining insight on the UX in terms of multiple participants.

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

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.

Universal SaaS platform of internet of things for real-time monitoring

NASA Astrophysics Data System (ADS)

Liu, Tongke; Wu, Gang

2018-04-01

Real-time monitoring service, as a member of the IoT (Internet of Things) service, has a wide range application scenario. To support rapid construction and deployment of applications and avoid repetitive development works in these processes, this paper designs and develops a universal SaaS platform of IoT for real-time monitoring. Evaluation shows that this platform can provide SaaS service to multiple tenants and achieve high real-time performance under the situation of large amount of device access.

Portable Biomarker Detection with Magnetic Nanotags

PubMed Central

Hall, Drew A.; Wang, Shan X.; Murmann, Boris; Gaster, Richard S.

2012-01-01

This paper presents a hand-held, portable biosensor platform for quantitative biomarker measurement. By combining magnetic nanoparticle (MNP) tags with giant magnetoresistive (GMR) spin-valve sensors, the hand-held platform achieves highly sensitive (picomolar) and specific biomarker detection in less than 20 minutes. The rapid analysis and potential low cost make this technology ideal for point-of-care (POC) diagnostics. Furthermore, this platform is able to detect multiple biomarkers simultaneously in a single assay, creating a promising diagnostic tool for a vast number of applications. PMID:22495252

Perioperative and ICU Healthcare Analytics within a Veterans Integrated System Network: a Qualitative Gap Analysis.

PubMed

Mudumbai, Seshadri; Ayer, Ferenc; Stefanko, Jerry

2017-08-01

Health care facilities are implementing analytics platforms as a way to document quality of care. However, few gap analyses exist on platforms specifically designed for patients treated in the Operating Room, Post-Anesthesia Care Unit, and Intensive Care Unit (ICU). As part of a quality improvement effort, we undertook a gap analysis of an existing analytics platform within the Veterans Healthcare Administration. The objectives were to identify themes associated with 1) current clinical use cases and stakeholder needs; 2) information flow and pain points; and 3) recommendations for future analytics development. Methods consisted of semi-structured interviews in 2 phases with a diverse set (n = 9) of support personnel and end users from five facilities across a Veterans Integrated Service Network. Phase 1 identified underlying needs and previous experiences with the analytics platform across various roles and operational responsibilities. Phase 2 validated preliminary feedback, lessons learned, and recommendations for improvement. Emerging themes suggested that the existing system met a small pool of national reporting requirements. However, pain points were identified with accessing data in several information system silos and performing multiple manual validation steps of data content. Notable recommendations included enhancing systems integration to create "one-stop shopping" for data, and developing a capability to perform trends analysis. Our gap analysis suggests that analytics platforms designed for surgical and ICU patients should employ approaches similar to those being used for primary care patients.

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

Design of sensor node platform for wireless biomedical sensor networks.

PubMed

Xijun, Chen; -H Meng, Max; Hongliang, Ren

2005-01-01

Design of low-cost, miniature, lightweight, ultra low-power, flexible sensor platform capable of customization and seamless integration into a wireless biomedical sensor network(WBSN) for health monitoring applications presents one of the most challenging tasks. In this paper, we propose a WBSN node platform featuring an ultra low-power microcontroller, an IEEE 802.15.4 compatible transceiver, and a flexible expansion connector. The proposed solution promises a cost-effective, flexible platform that allows easy customization, energy-efficient computation and communication. The development of a common platform for multiple physical sensors will increase reuse and alleviate costs of transition to a new generation of sensors. As a case study, we present an implementation of an ECG (Electrocardiogram) sensor.

jsc2018m000314_Spinning_Science_Multi-use_Variable-g_Platform_Arrives_at_the_Space_Station-MP4

NASA Image and Video Library

2018-05-09

Spinning Science: Multi-use Variable-g Platform Arrives at the Space Station --- The Multi-use Variable-gravity Platform (MVP) Validation mission will install and test the MVP, a new hardware platform developed and owned by Techshot Inc., on the International Space Station (ISS). Though the MVP is designed for research with many different kinds of organisms and cell types, this validation mission will focus on Drosophila melanogaster, more commonly known as the fruit fly. This platform will be especially important for fruit fly research, as it will allow researchers to study larger sample sizes of Drosophila melanogaster than in other previous hardware utilizing centrifuges and it will be able to support fly colonies for multiple generations.

NDSI products system based on Hadoop platform

NASA Astrophysics Data System (ADS)

Zhou, Yan; Jiang, He; Yang, Xiaoxia; Geng, Erhui

2015-12-01

Snow is solid state of water resources on earth, and plays an important role in human life. Satellite remote sensing is significant in snow extraction with the advantages of cyclical, macro, comprehensiveness, objectivity, timeliness. With the continuous development of remote sensing technology, remote sensing data access to the trend of multiple platforms, multiple sensors and multiple perspectives. At the same time, in view of the remote sensing data of compute-intensive applications demand increase gradually. However, current the producing system of remote sensing products is in a serial mode, and this kind of production system is used for professional remote sensing researchers mostly, and production systems achieving automatic or semi-automatic production are relatively less. Facing massive remote sensing data, the traditional serial mode producing system with its low efficiency has been difficult to meet the requirements of mass data timely and efficient processing. In order to effectively improve the production efficiency of NDSI products, meet the demand of large-scale remote sensing data processed timely and efficiently, this paper build NDSI products production system based on Hadoop platform, and the system mainly includes the remote sensing image management module, NDSI production module, and system service module. Main research contents and results including: (1)The remote sensing image management module: includes image import and image metadata management two parts. Import mass basis IRS images and NDSI product images (the system performing the production task output) into HDFS file system; At the same time, read the corresponding orbit ranks number, maximum/minimum longitude and latitude, product date, HDFS storage path, Hadoop task ID (NDSI products), and other metadata information, and then create thumbnails, and unique ID number for each record distribution, import it into base/product image metadata database. (2)NDSI production module: includes the index calculation, production tasks submission and monitoring two parts. Read HDF images related to production task in the form of a byte stream, and use Beam library to parse image byte stream to the form of Product; Use MapReduce distributed framework to perform production tasks, at the same time monitoring task status; When the production task complete, calls remote sensing image management module to store NDSI products. (3)System service module: includes both image search and DNSI products download. To image metadata attributes described in JSON format, return to the image sequence ID existing in the HDFS file system; For the given MapReduce task ID, package several task output NDSI products into ZIP format file, and return to the download link (4)System evaluation: download massive remote sensing data and use the system to process it to get the NDSI products testing the performance, and the result shows that the system has high extendibility, strong fault tolerance, fast production speed, and the image processing results with high accuracy.

Satellite communications provisions on NASA Ames instrumented aircraft platforms for Earth science research/applications

NASA Technical Reports Server (NTRS)

Shameson, L.; Brass, J. A.; Hanratty, J. J.; Roberts, A. C.; Wegener, S. S.

1995-01-01

Earth science activities at NASA Ames are research in atmospheric and ecosystem science, development of remote sensing and in situ sampling instruments, and their integration into scientific research platform aircraft. The use of satellite communications can greatly extend the capability of these agency research platform aircraft. Current projects and plans involve satellite links on the Perseus UAV and the ER-2 via TDRSS and a proposed experiment on the NASA Advanced Communications Technology Satellite. Provisions for data links on the Perseus research platform, via TDRSS S-band multiple access service, have been developed and are being tested. Test flights at Dryden are planned to demonstrate successful end-to-end data transfer. A Unisys Corp. airborne satcom STARLink system is being integrated into an Ames ER-2 aircraft. This equipment will support multiple data rates up to 43 Mb/s each via the TDRS S Ku-band single access service. The first flight mission for this high-rate link is planned for August 1995. Ames and JPL have proposed an ACTS experiment to use real-time satellite communications to improve wildfire research campaigns. Researchers and fire management teams making use of instrumented aircraft platforms at a prescribed burn site will be able to communicate with experts at Ames, the U.S. Forest Service, and emergency response agencies.

Mobile Sensor Technologies Being Developed

NASA Technical Reports Server (NTRS)

Greer, Lawrence C.; Oberle, Lawrence G.

2003-01-01

The NASA Glenn Research Center is developing small mobile platforms for sensor placement, as well as methods for communicating between roving platforms and a central command location. The first part of this project is to use commercially available equipment to miniaturize an existing sensor platform. We developed a five-circuit-board suite, with an average board size of 1.5 by 3 cm. Shown in the preceding photograph, this suite provides all motor control, direction finding, and communications capabilities for a 27- by 21- by 40-mm prototype mobile platform. The second part of the project is to provide communications between mobile platforms, and also between multiple platforms and a central command location. This is accomplished with a low-power network labeled "SPAN," Sensor Platform Area Network, a local area network made up of proximity elements. In practice, these proximity elements are composed of fixed- and mobile-sensor-laden science packages that communicate to each other via radiofrequency links. Data in the network will be shared by a central command location that will pass information into and out of the network through its access to a backbone element. The result will be a protocol portable to general purpose microcontrollers satisfying a host of sensor networking tasks. This network will enter the gap somewhere between television remotes and Bluetooth but, unlike 802.15.4, will not specify a physical layer, thus allowing for many data rates over optical, acoustical, radiofrequency, hardwire, or other media. Since the protocol will exist as portable C-code, developers may be able to embed it in a host of microcontrollers from commercial to space grade and, of course, to design it into ASICs. Unlike in 802.15.4, the nodes will relate to each other as peers. A demonstration of this protocol using the two test bed platforms was recently held. Two NASA modified, commercially available, mobile platforms communicated and shared data with each other and a central command location. Web-based control and interrogation of similar mobile sensor platforms have also been demonstrated. Expected applications of this technology include robotic planetary exploration, astronaut-to-equipment communication, and remote aerospace engine inspections.

A Standard Platform for Testing and Comparison of MDAO Architectures

NASA Technical Reports Server (NTRS)

Gray, Justin S.; Moore, Kenneth T.; Hearn, Tristan A.; Naylor, Bret A.

2012-01-01

The Multidisciplinary Design Analysis and Optimization (MDAO) community has developed a multitude of algorithms and techniques, called architectures, for performing optimizations on complex engineering systems which involve coupling between multiple discipline analyses. These architectures seek to efficiently handle optimizations with computationally expensive analyses including multiple disciplines. We propose a new testing procedure that can provide a quantitative and qualitative means of comparison among architectures. The proposed test procedure is implemented within the open source framework, OpenMDAO, and comparative results are presented for five well-known architectures: MDF, IDF, CO, BLISS, and BLISS-2000. We also demonstrate how using open source soft- ware development methods can allow the MDAO community to submit new problems and architectures to keep the test suite relevant.

An update on MS Nurse PROfessional, an ongoing project of the European Multiple Sclerosis Platform.

PubMed

Winslow, Anne

2016-12-01

Within the multidisciplinary team required to manage people with multiple sclerosis (MS) effectively, the nurse is the central component of coordinated care and support. A 2009 survey led by the European Multiple Sclerosis Platform, an umbrella organization of national MS associations, identified variance and disparity across Europe in the nursing care of MS patients. This led to development of MS Nurse PROfessional, a continuing medical education-accredited modular online learning program endorsed and approved by leading international nursing and professional groups, and people with MS, as a tool to support the evolving role of the European MS nurse. Analysis of participant experience and nurse practice to date has been overwhelmingly positive. Expansion of MS Nurse PRO is underway or planned for future.

Data integration: Combined imaging and electrophysiology data in the cloud.

PubMed

Kini, Lohith G; Davis, Kathryn A; Wagenaar, Joost B

2016-01-01

There has been an increasing effort to correlate electrophysiology data with imaging in patients with refractory epilepsy over recent years. IEEG.org provides a free-access, rapidly growing archive of imaging data combined with electrophysiology data and patient metadata. It currently contains over 1200 human and animal datasets, with multiple data modalities associated with each dataset (neuroimaging, EEG, EKG, de-identified clinical and experimental data, etc.). The platform is developed around the concept that scientific data sharing requires a flexible platform that allows sharing of data from multiple file formats. IEEG.org provides high- and low-level access to the data in addition to providing an environment in which domain experts can find, visualize, and analyze data in an intuitive manner. Here, we present a summary of the current infrastructure of the platform, available datasets and goals for the near future. Copyright © 2015 Elsevier Inc. All rights reserved.

Data integration: Combined Imaging and Electrophysiology data in the cloud

PubMed Central

Kini, Lohith G.; Davis, Kathryn A.; Wagenaar, Joost B.

2015-01-01

There has been an increasing effort to correlate electrophysiology data with imaging in patients with refractory epilepsy over recent years. IEEG.org provides a free-access, rapidly growing archive of imaging data combined with electrophysiology data and patient metadata. It currently contains over 1200 human and animal datasets, with multiple data modalities associated with each dataset (neuroimaging, EEG, EKG, de-identified clinical and experimental data, etc.). The platform is developed around the concept that scientific data sharing requires a flexible platform that allows sharing of data from multiple file-formats. IEEG.org provides high and low-level access to the data in addition to providing an environment in which domain experts can find, visualize, and analyze data in an intuitive manner. Here, we present a summary of the current infrastructure of the platform, available datasets and goals for the near future. PMID:26044858

A Framework for the Generation and Dissemination of Drop Size Distribution (DSD) Characteristics Using Multiple Platforms

NASA Technical Reports Server (NTRS)

Wolf, David B.; Tokay, Ali; Petersen, Walt; Williams, Christopher; Gatlin, Patrick; Wingo, Mathew

2010-01-01

Proper characterization of the precipitation drop size distribution (DSD) is integral to providing realistic and accurate space- and ground-based precipitation retrievals. Current technology allows for the development of DSD products from a variety of platforms, including disdrometers, vertical profilers and dual-polarization radars. Up to now, however, the dissemination or availability of such products has been limited to individual sites and/or field campaigns, in a variety of formats, often using inconsistent algorithms for computing the integral DSD parameters, such as the median- and mass-weighted drop diameter, total number concentration, liquid water content, rain rate, etc. We propose to develop a framework for the generation and dissemination of DSD characteristic products using a unified structure, capable of handling the myriad collection of disdrometers, profilers, and dual-polarization radar data currently available and to be collected during several upcoming GPM Ground Validation field campaigns. This DSD super-structure paradigm is an adaptation of the radar super-structure developed for NASA s Radar Software Library (RSL) and RSL_in_IDL. The goal is to provide the DSD products in a well-documented format, most likely NetCDF, along with tools to ingest and analyze the products. In so doing, we can develop a robust archive of DSD products from multiple sites and platforms, which should greatly benefit the development and validation of precipitation retrieval algorithms for GPM and other precipitation missions. An outline of this proposed framework will be provided as well as a discussion of the algorithms used to calculate the DSD parameters.

Sequential glycan profiling at single cell level with the microfluidic lab-in-a-trench platform: a new era in experimental cell biology.

PubMed

O'Connell, Tríona M; King, Damien; Dixit, Chandra K; O'Connor, Brendan; Walls, Dermot; Ducrée, Jens

2014-09-21

It is now widely recognised that the earliest changes that occur on a cell when it is stressed or becoming diseased are alterations in its surface glycosylation. Current state-of-the-art technologies in glycoanalysis include mass spectrometry, protein microarray formats, techniques in cytometry and more recently, glyco-quantitative polymerase chain reaction (Glyco-qPCR). Techniques for the glycoprofiling of the surfaces of single cells are either limited to the analysis of large cell populations or are unable to handle multiple and/or sequential probing. Here, we report a novel approach of single live cell glycoprofiling enabled by the microfluidic "Lab-in-a-Trench" (LiaT) platform for performing capture and retention of cells, along with shear-free reagent loading and washing. The significant technical improvement on state-of-the-art is the demonstration of consecutive, spatio-temporally profiling of glycans on a single cell by sequential elution of the previous lectin probe using their corresponding free sugar. We have qualitatively analysed glycan density on the surface of individual cells. This has allowed us to qualitatively co-localise the observed glycans. This approach enables exhaustive glycoprofiling and glycan mapping on the surface of individual live cells with multiple lectins. The possibility of sequentially profiling glycans on cells will be a powerful new tool to add to current glycoanalytical techniques. The LiaT platform will enable cell biologists to perform many high sensitivity assays and also will also make a significant impact on biomarker research.

Convergence Is Real

ERIC Educational Resources Information Center

Enyeart, Mike; Staman, E. Michael; Valdes, Jose J., Jr.

2007-01-01

The concept of convergence has evolved significantly during recent years. Today, "convergence" refers to the integration of the communications and computing resources and services that seamlessly traverse multiple infrastructures and deliver content to multiple platforms or appliances. Convergence is real. Those in higher education, and especially…

SWATShare- A Platform for Collaborative Hydrology Research and Education with Cyber-enabled Sharing, Running and Visualization of SWAT Models

NASA Astrophysics Data System (ADS)

Rajib, M. A.; Merwade, V.; Song, C.; Zhao, L.; Kim, I. L.; Zhe, S.

2014-12-01

Setting up of any hydrologic model requires a large amount of efforts including compilation of all the data, creation of input files, calibration and validation. Given the amount of efforts involved, it is possible that models for a watershed get created multiple times by multiple groups or organizations to accomplish different research, educational or policy goals. To reduce the duplication of efforts and enable collaboration among different groups or organizations around an already existing hydrology model, a platform is needed where anyone can search for existing models, perform simple scenario analysis and visualize model results. The creator and users of a model on such a platform can then collaborate to accomplish new research or educational objectives. From this perspective, a prototype cyber-infrastructure (CI), called SWATShare, is developed for sharing, running and visualizing Soil Water Assessment Tool (SWAT) models in an interactive GIS-enabled web environment. Users can utilize SWATShare to publish or upload their own models, search and download existing SWAT models developed by others, run simulations including calibration using high performance resources provided by XSEDE and Cloud. Besides running and sharing, SWATShare hosts a novel spatio-temporal visualization system for SWAT model outputs. In temporal scale, the system creates time-series plots for all the hydrology and water quality variables available along the reach as well as in watershed-level. In spatial scale, the system can dynamically generate sub-basin level thematic maps for any variable at any user-defined date or date range; and thereby, allowing users to run animations or download the data for subsequent analyses. In addition to research, SWATShare can also be used within a classroom setting as an educational tool for modeling and comparing the hydrologic processes under different geographic and climatic settings. SWATShare is publicly available at https://www.water-hub.org/swatshare.

Social media in radiology: early trends in Twitter microblogging at radiology's largest international meeting.

PubMed

Hawkins, C Matthew; Duszak, Richard; Rawson, James V

2014-04-01

Twitter is a social media microblogging platform that allows rapid exchange of information between individuals. Despite its widespread acceptance and use at various other medical specialty meetings, there are no published data evaluating its use at radiology meetings. The purpose of this study is to quantitatively and qualitatively evaluate the use of Twitter as a microblogging platform at recent RSNA annual meetings. Twitter activity meta-data tagged with official meeting hashtags #RSNA11 and #RSNA12 were collected and analyzed. Multiple metrics were evaluated, including daily and hourly Twitter activity, frequency of microblogging activity over time, characteristics of the 100 most active Twitter users at each meeting, characteristics of meeting-related tweets, and the geographic origin of meeting microbloggers. The use of Twitter microblogging increased by at least 30% by all identifiable meaningful metrics between the 2011 and 2012 RSNA annual meetings, including total tweets, tweets per day, activity of the most active microbloggers, and total number of microbloggers. Similar increases were observed in numbers of North American and international microbloggers. Markedly increased use of the Twitter microblogging platform at recent RSNA annual meetings demonstrates the potential to leverage this technology to engage meeting attendees, improve scientific sessions, and promote improved collaboration at national radiology meetings. Copyright © 2014 American College of Radiology. Published by Elsevier Inc. All rights reserved.

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

PubMed

Tyanova, Stefka; Temu, Tikira; Cox, Juergen

2016-12-01

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

Seasonal and Inter-annual Phenological Varibility is Greatest in Low-Arctic and Wet Sites Across the North Slope of Alaska as Observed from Multiple Remote Sensing Platforms

NASA Astrophysics Data System (ADS)

Vargas, S. A., Jr.; Andresen, C. G.; May, J. L.; Oberbauer, S. F.; Hollister, R. D.; Tweedie, C. E.

2017-12-01

The Arctic is experiencing among the most dramatic impacts from climate variability on the planet. Arctic plant phenology has been identified as an ideal indicator of climate change impacts and provides great insight into seasonal and inter-annual vegetative trends and their responses to such changes. Traditionally, phenology has been quantified using satellite-based systems and plot-level observations but each approach presents limitations especially in high latitude regions. Mid-scale systems (e.g. automated sensor platforms and trams) have shown to provide alternative, and in most cases, cheaper solutions with comparable results to those acquired traditionally. This study contributes to the US Arctic Observing Network (AON) and assesses the effectiveness of using digital images acquired from pheno-cams, a kite aerial photography (KAP) system, and plot-level images (PLI) in their capacity to assess phenological variability (e.g. snow melt, greening and end-of-season) for dominant vegetation communities present at two sites in both Utqiagvik and Atqasuk, Alaska, namely the Mobile Instrumented Sensor Platform (MISP) and the Circum-arctic Active Layer Monitoring (CALM) grids. RGB indices (e.g. GEI and %G) acquired from these methods were compared to the normalized difference vegetation index (NDVI) calculated from multispectral ground-based reflectance measurements, which has been identified and used as a proxy of primary productivity across multiple ecosystems including the Arctic. The 5 years of growing season data collected generally resulted with stronger Pearson's correlations between indices located in plots containing higher soil moisture versus those that were drier. Future studies will extend platform inter-comparison to the satellite level by scaling trends to MODIS land surface products. Trends documented thus far, however, suggest that the long-term changes in satellite NDVI for these study areas, could be a direct response from wet tundra landscapes.

Microfluidic platform for multiplexed detection in single cells and methods thereof

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

Wu, Meiye; Singh, Anup K.

The present invention relates to a microfluidic device and platform configured to conduct multiplexed analysis within the device. In particular, the device allows multiple targets to be detected on a single-cell level. Also provided are methods of performing multiplexed analyses to detect one or more target nucleic acids, proteins, and post-translational modifications.

A Novel Wiki-Based Remote Laboratory Platform for Engineering Education

ERIC Educational Resources Information Center

Wang, Ning; Chen, Xuemin; Lan, Qianlong; Song, Gangbing; Parsaei, Hamid R.; Ho, Siu-Chun

2017-01-01

With the unprecedented growth of e-learning, more and more new IT technologies are used to develop e-learning tools. As one of the most common forms of social computing, Wiki technology has been used to develop the collaborative and cooperative learning platform to support multiple users learning online effectively. In this paper, we propose a new…

MeDICi Software Superglue for Data Analysis Pipelines

ScienceCinema

Ian Gorton

2017-12-09

The Middleware for Data-Intensive Computing (MeDICi) Integration Framework is an integrated middleware platform developed to solve data analysis and processing needs of scientists across many domains. MeDICi is scalable, easily modified, and robust to multiple languages, protocols, and hardware platforms, and in use today by PNNL scientists for bioinformatics, power grid failure analysis, and text analysis.

Remote observations of reentering spacecraft including the space shuttle orbiter

NASA Astrophysics Data System (ADS)

Horvath, Thomas J.; Cagle, Melinda F.; Grinstead, Jay H.; Gibson, David M.

Flight measurement is a critical phase in development, validation and certification processes of technologies destined for future civilian and military operational capabilities. This paper focuses on several recent NASA-sponsored remote observations that have provided unique engineering and scientific insights of reentry vehicle flight phenomenology and performance that could not necessarily be obtained with more traditional instrumentation methods such as onboard discrete surface sensors. The missions highlighted include multiple spatially-resolved infrared observations of the NASA Space Shuttle Orbiter during hypersonic reentry from 2009 to 2011, and emission spectroscopy of comparatively small-sized sample return capsules returning from exploration missions. Emphasis has been placed upon identifying the challenges associated with these remote sensing missions with focus on end-to-end aspects that include the initial science objective, selection of the appropriate imaging platform and instrumentation suite, target flight path analysis and acquisition strategy, pre-mission simulations to optimize sensor configuration, logistics and communications during the actual observation. Explored are collaborative opportunities and technology investments required to develop a next-generation quantitative imaging system (i.e., an intelligent sensor and platform) with greater capability, which could more affordably support cross cutting civilian and military flight test needs.

Remote Observations of Reentering Spacecraft Including the Space Shuttle Orbiter

NASA Technical Reports Server (NTRS)

Horvath, Thomas J.; Cagle, Melinda F.; Grinstead, jay H.; Gibson, David

2013-01-01

Flight measurement is a critical phase in development, validation and certification processes of technologies destined for future civilian and military operational capabilities. This paper focuses on several recent NASA-sponsored remote observations that have provided unique engineering and scientific insights of reentry vehicle flight phenomenology and performance that could not necessarily be obtained with more traditional instrumentation methods such as onboard discrete surface sensors. The missions highlighted include multiple spatially-resolved infrared observations of the NASA Space Shuttle Orbiter during hypersonic reentry from 2009 to 2011, and emission spectroscopy of comparatively small-sized sample return capsules returning from exploration missions. Emphasis has been placed upon identifying the challenges associated with these remote sensing missions with focus on end-to-end aspects that include the initial science objective, selection of the appropriate imaging platform and instrumentation suite, target flight path analysis and acquisition strategy, pre-mission simulations to optimize sensor configuration, logistics and communications during the actual observation. Explored are collaborative opportunities and technology investments required to develop a next-generation quantitative imaging system (i.e., an intelligent sensor and platform) with greater capability, which could more affordably support cross cutting civilian and military flight test needs.

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research

PubMed Central

Campagnola, Luke; Kratz, Megan B.; Manis, Paul B.

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org. PMID:24523692

Flexible imaging payload for real-time fluorescent biological imaging in parabolic, suborbital and space analog environments

NASA Astrophysics Data System (ADS)

Bamsey, Matthew T.; Paul, Anna-Lisa; Graham, Thomas; Ferl, Robert J.

2014-10-01

Fluorescent imaging offers the ability to monitor biological functions, in this case biological responses to space-related environments. For plants, fluorescent imaging can include general health indicators such as chlorophyll fluorescence as well as specific metabolic indicators such as engineered fluorescent reporters. This paper describes the Flex Imager a fluorescent imaging payload designed for Middeck Locker deployment and now tested on multiple flight and flight-related platforms. The Flex Imager and associated payload elements have been developed with a focus on 'flexibility' allowing for multiple imaging modalities and change-out of individual imaging or control components in the field. The imaging platform is contained within the standard Middeck Locker spaceflight form factor, with components affixed to a baseplate that permits easy rearrangement and fine adjustment of components. The Flex Imager utilizes standard software packages to simplify operation, operator training, and evaluation by flight provider flight test engineers, or by researchers processing the raw data. Images are obtained using a commercial cooled CCD image sensor, with light-emitting diodes for excitation and a suite of filters that allow biological samples to be imaged over wavelength bands of interest. Although baselined for the monitoring of green fluorescent protein and chlorophyll fluorescence from Arabidopsis samples, the Flex Imager payload permits imaging of any biological sample contained within a standard 10 cm by 10 cm square Petri plate. A sample holder was developed to secure sample plates under different flight profiles while permitting sample change-out should crewed operations be possible. In addition to crew-directed imaging, autonomous or telemetric operation of the payload is also a viable operational mode. An infrared camera has also been integrated into the Flex Imager payload to allow concurrent fluorescent and thermal imaging of samples. The Flex Imager has been utilized to assess, in real-time, the response of plants to novel environments including various spaceflight analogs, including several parabolic flight environments as well as hypobaric plant growth chambers. Basic performance results obtained under these operational environments, as well as laboratory-based tests are described. The Flex Imager has also been designed to be compatible with emerging suborbital platforms.

Robotic intelligence kernel

DOEpatents

Bruemmer, David J [Idaho Falls, ID

2009-11-17

A robot platform includes perceptors, locomotors, and a system controller. The system controller executes a robot intelligence kernel (RIK) that includes a multi-level architecture and a dynamic autonomy structure. The multi-level architecture includes a robot behavior level for defining robot behaviors, that incorporate robot attributes and a cognitive level for defining conduct modules that blend an adaptive interaction between predefined decision functions and the robot behaviors. The dynamic autonomy structure is configured for modifying a transaction capacity between an operator intervention and a robot initiative and may include multiple levels with at least a teleoperation mode configured to maximize the operator intervention and minimize the robot initiative and an autonomous mode configured to minimize the operator intervention and maximize the robot initiative. Within the RIK at least the cognitive level includes the dynamic autonomy structure.

Liquid biopsy genotyping in lung cancer: ready for clinical utility?

PubMed Central

Ho, Chung-Liang; Wei, Fang; Wong, David T.; Su, Wu-Chou; Lin, Chien-Chung

2017-01-01

Liquid biopsy is a blood test that detects evidence of cancer cells or tumor DNA in the circulation. Despite complicated collection methods and the requirement for technique-dependent platforms, it has generated substantial interest due, in part, to its potential to detect driver oncogenes such as epidermal growth factor receptor (EGFR) mutants in lung cancer. This technology is advancing rapidly and is being incorporated into numerous EGFR tyrosine kinase inhibitor (EGFR-TKI) development programs. It appears ready for integration into clinical care. Recent studies have demonstrated that biological fluids such as saliva and urine can also be used for detecting EGFR mutant DNA through application other user-friendly techniques. This review focuses on the clinical application of liquid biopsies to lung cancer genotyping, including EGFR and other targets of genotype-directed therapy and compares multiple platforms used for liquid biopsy. PMID:28099915

Introduction

NASA Astrophysics Data System (ADS)

Gaskin, J. A.; Smith, I. S.; Jones, W. V.

In 1783, the Montgolfier brothers ushered in a new era of transportation and exploration when they used hot air to drive an un-tethered balloon to an altitude of 2 km. Made of sackcloth and held together with cords, this balloon challenged the way we thought about human travel, and it has since evolved into a robust platform for performing novel science and testing new technologies. Today, high-altitude balloons regularly reach altitudes of 40 km, and they can support payloads that weigh more than 3000 kg. Long-duration balloons can currently support mission durations lasting 55 days, and developing balloon technologies (i.e. Super-Pressure Balloons) are expected to extend that duration to 100 days or longer; competing with satellite payloads. This relatively inexpensive platform supports a broad range of science payloads, spanning multiple disciplines (astrophysics, heliophysics, planetary and earth science). Applications extending beyond traditional science include testing new technologies for eventual space-based application and stratospheric airships for planetary applications.

Parallel Domain Decomposition Formulation and Software for Large-Scale Sparse Symmetrical/Unsymmetrical Aeroacoustic Applications

NASA Technical Reports Server (NTRS)

Nguyen, D. T.; Watson, Willie R. (Technical Monitor)

2005-01-01

The overall objectives of this research work are to formulate and validate efficient parallel algorithms, and to efficiently design/implement computer software for solving large-scale acoustic problems, arised from the unified frameworks of the finite element procedures. The adopted parallel Finite Element (FE) Domain Decomposition (DD) procedures should fully take advantages of multiple processing capabilities offered by most modern high performance computing platforms for efficient parallel computation. To achieve this objective. the formulation needs to integrate efficient sparse (and dense) assembly techniques, hybrid (or mixed) direct and iterative equation solvers, proper pre-conditioned strategies, unrolling strategies, and effective processors' communicating schemes. Finally, the numerical performance of the developed parallel finite element procedures will be evaluated by solving series of structural, and acoustic (symmetrical and un-symmetrical) problems (in different computing platforms). Comparisons with existing "commercialized" and/or "public domain" software are also included, whenever possible.

Communication architecture for large geostationary platforms

NASA Technical Reports Server (NTRS)

Bond, F. E.

1979-01-01

Large platforms have been proposed for supporting multipurpose communication payloads to exploit economy of scale, reduce congestion in the geostationary orbit, provide interconnectivity between diverse earth stations, and obtain significant frequency reuse with large multibeam antennas. This paper addresses a specific system design, starting with traffic projections in the next two decades and discussing tradeoffs and design approaches for major components including: antennas, transponders, and switches. Other issues explored are selection of frequency bands, modulation, multiple access, switching methods, and techniques for servicing areas with nonuniform traffic demands. Three-major services are considered: a high-volume trunking system, a direct-to-user system, and a broadcast system for video distribution and similar functions. Estimates of payload weight and d.c. power requirements are presented. Other subjects treated are: considerations of equipment layout for servicing by an orbit transfer vehicle, mechanical stability requirements for the large antennas, and reliability aspects of the large number of transponders employed.

Photonic integrated circuits based on sampled-grating distributed-Bragg-reflector lasers

NASA Astrophysics Data System (ADS)

Barton, Jonathon S.; Skogen, Erik J.; Masanovic, Milan L.; Raring, James; Sysak, Matt N.; Johansson, Leif; DenBaars, Steven P.; Coldren, Larry A.

2003-07-01

The Sampled-Grating Distributed-Bragg-Reflector laser(SGDBR) provides wide tunability (>40nm), and high output power (>10mW). Driven by the demand for network reconfigurability and ease of implementation, the SGDBR has moved from the research lab to be commercially viable in the marketplace. The SGDBR is most often implemented using an offset-quantum well epitaxial structure in which the quantum wells are etched off in the passive sections. Alternatively, quantum well intermixing has been used recently to achieve the same goal - resulting in improved optical gain and the potential for multiple bandgaps along the device structure. These epitaxial "platforms" provide the basis for more exotic opto-electronic device functionality exhibiting low chirp for digital applications and enhanced linearity for analog applications. This talk will cover state-of-the-art opto-electronic devices based on the SGDBR platform including: integrated Mach-Zehnder modulators, and integrated electro-absorption modulators.

xQTL workbench: a scalable web environment for multi-level QTL analysis.

PubMed

Arends, Danny; van der Velde, K Joeri; Prins, Pjotr; Broman, Karl W; Möller, Steffen; Jansen, Ritsert C; Swertz, Morris A

2012-04-01

xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator. xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. m.a.swertz@rug.nl.

xQTL workbench: a scalable web environment for multi-level QTL analysis

PubMed Central

Arends, Danny; van der Velde, K. Joeri; Prins, Pjotr; Broman, Karl W.; Möller, Steffen; Jansen, Ritsert C.; Swertz, Morris A.

2012-01-01

Summary: xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator. Availability: xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. Contact: m.a.swertz@rug.nl PMID:22308096

The use of multiple “Omic” platforms to evaluate the effects of endocrine disrupting compounds in small fish species

EPA Science Inventory

Linking molecular changes at multiple levels of biological organization using “omic” methods provides highly complimentary, “data-dense” information for predicting outcomes for organisms exposed to environmental contaminants. However, performing separate ...

Power in the loop real time simulation platform for renewable energy generation

NASA Astrophysics Data System (ADS)

Li, Yang; Shi, Wenhui; Zhang, Xing; He, Guoqing

2018-02-01

Nowadays, a large scale of renewable energy sources has been connecting to power system and the real time simulation platform is widely used to carry out research on integration control algorithm, power system stability etc. Compared to traditional pure digital simulation and hardware in the loop simulation, power in the loop simulation has higher accuracy and degree of reliability. In this paper, a power in the loop analog digital hybrid simulation platform has been built and it can be used not only for the single generation unit connecting to grid, but also for multiple new energy generation units connecting to grid. A wind generator inertia control experiment was carried out on the platform. The structure of the inertia control platform was researched and the results verify that the platform is up to need for renewable power in the loop real time simulation.

Implementing Audio Digital Feedback Loop Using the National Instruments RIO System

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

Huang, G.; Byrd, J. M.

2006-11-20

Development of system for high precision RF distribution and laser synchronization at Berkeley Lab has been ongoing for several years. Successful operation of these systems requires multiple audio bandwidth feedback loops running at relatively high gains. Stable operation of the feedback loops requires careful design of the feedback transfer function. To allow for flexible and compact implementation, we have developed digital feedback loops on the National Instruments Reconfigurable Input/Output (RIO) platform. This platform uses an FPGA and multiple I/Os that can provide eight parallel channels running different filters. We present the design and preliminary experimental results of this system.

Scalable and massively parallel Monte Carlo photon transport simulations for heterogeneous computing platforms

NASA Astrophysics Data System (ADS)

Yu, Leiming; Nina-Paravecino, Fanny; Kaeli, David; Fang, Qianqian

2018-01-01

We present a highly scalable Monte Carlo (MC) three-dimensional photon transport simulation platform designed for heterogeneous computing systems. Through the development of a massively parallel MC algorithm using the Open Computing Language framework, this research extends our existing graphics processing unit (GPU)-accelerated MC technique to a highly scalable vendor-independent heterogeneous computing environment, achieving significantly improved performance and software portability. A number of parallel computing techniques are investigated to achieve portable performance over a wide range of computing hardware. Furthermore, multiple thread-level and device-level load-balancing strategies are developed to obtain efficient simulations using multiple central processing units and GPUs.

Regional satellite systems - Required or redundant

NASA Astrophysics Data System (ADS)

Filep, R.

1981-09-01

It is shown that the development of such regional satellite systems as the Arab League's Arabsat, the South American Aseta, and the ASEAN nations' Palapa II, will be redundant if Intelsat moves ahead with its expanded service options with multiple frequency and beam configurations. Attention is given to direct broadcast satellite systems and the geostationary platform concept, which would incorporate C-band high-volume trunking, meteorological data relay, interplatform link, and Ku-band TV distribution and could be constructed in orbit by the Space Shuttle. The platform concept offers antenna reflectors that could be utilized by many 'feeds' or multiple-phase arrays, permitting frequency reuse many hundreds of times over.

GEMS Project: A Platform to Investigate Multiple Sclerosis Risk

PubMed Central

Xia, Zongqi; White, Charles C.; Owen, Emily K.; Von Korff, Alina; Clarkson, Sarah R.; McCabe, Cristin A.; Cimpean, Maria; Winn, Phoebe A.; Hoesing, Ashley; Steele, Sonya U.; Cortese, Irene C. M.; Chitnis, Tanuja; Weiner, Howard L.; Reich, Daniel S.; Chibnik, Lori B.; De Jager, Philip L.

2015-01-01

The Genes and Environment in Multiple Sclerosis (GEMS) project establishes a platform to investigate the events leading to MS in at-risk individuals. It has recruited 2,632 first-degree relatives from across the USA. Using an integrated genetic and environmental risk score, we identified subjects with twice the MS risk when compared to the average family member, and we report an initial incidence rate in these subjects that is 30 times greater than that of sporadic MS. We discuss the feasibility of large-scale studies of asymptomatic at-risk subjects that leverage modern tools of subject recruitment to execute collaborative projects. PMID:26583565

Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment

PubMed Central

2013-01-01

Citizen science games such as Galaxy Zoo, Foldit, and Phylo aim to harness the intelligence and processing power generated by crowds of online gamers to solve scientific problems. However, the selection of the data to be analyzed through these games is under the exclusive control of the game designers, and so are the results produced by gamers. Here, we introduce Open-Phylo, a freely accessible crowd-computing platform that enables any scientist to enter our system and use crowds of gamers to assist computer programs in solving one of the most fundamental problems in genomics: the multiple sequence alignment problem. PMID:24148814

Fully distributed monitoring architecture supporting multiple trackees and trackers in indoor mobile asset management application.

PubMed

Jeong, Seol Young; Jo, Hyeong Gon; Kang, Soon Ju

2014-03-21

A tracking service like asset management is essential in a dynamic hospital environment consisting of numerous mobile assets (e.g., wheelchairs or infusion pumps) that are continuously relocated throughout a hospital. The tracking service is accomplished based on the key technologies of an indoor location-based service (LBS), such as locating and monitoring multiple mobile targets inside a building in real time. An indoor LBS such as a tracking service entails numerous resource lookups being requested concurrently and frequently from several locations, as well as a network infrastructure requiring support for high scalability in indoor environments. A traditional centralized architecture needs to maintain a geographic map of the entire building or complex in its central server, which can cause low scalability and traffic congestion. This paper presents a self-organizing and fully distributed indoor mobile asset management (MAM) platform, and proposes an architecture for multiple trackees (such as mobile assets) and trackers based on the proposed distributed platform in real time. In order to verify the suggested platform, scalability performance according to increases in the number of concurrent lookups was evaluated in a real test bed. Tracking latency and traffic load ratio in the proposed tracking architecture was also evaluated.

Design, Analysis, Hybrid Testing and Orientation Control of a Floating Platform with Counter-Rotating Vertical-Axis Wind Turbines

NASA Astrophysics Data System (ADS)

Kanner, Samuel Adam Chinman

The design and operation of two counter-rotating vertical-axis wind turbines on a floating, semi-submersible platform is studied. The technology, called the Multiple Integrated and Synchronized Turbines (MIST) platform has the potential to reduce the cost of offshore wind energy per unit of installed capacity. Attached to the platform are closely-spaced, counter-rotating turbines, which can achieve a higher power density per planform area because of synergistic interaction effects. The purpose of the research is to control the orientation of the platform and rotational speeds of the turbines by modifying the energy absorbed by each of the generators of the turbines. To analyze the various aspects of the platform and wind turbines, the analysis is drawn from the fields of hydrodynamics, electromagnetics, aerodynamics and control theory. To study the hydrodynamics of the floating platform in incident monochromatic waves, potential theory is utilized, taking into account the slow-drift yaw motion of the platform. Steady, second-order moments that are spatially dependent (i.e., dependent on the platform's yaw orientation relative to the incident waves) are given special attention since there are no natural restoring yaw moment. The aerodynamics of the counter-rotating turbines are studied in collaboration with researchers at the UC Berkeley Mathematics Department using a high-order, implicit, large-eddy simulation. An element flipping technique is utilized to extend the method to a domain with counter-rotating turbines and the effects from the closely-spaced turbines is compared with existing experimental data. Hybrid testing techniques on a model platform are utilized to prove the controllability of the platform in lieu of a wind-wave tank. A 1:82 model-scale floating platform is fabricated and tested at the UC Berkeley Physical-Model Testing Facility. The vertical-axis wind turbines are simulated by spinning, controllable actuators that can be updated in real-time of the model scale. Under certain wind and wave headings, it is possible to control the orientation of the platform in regular waves to maximize the power output from the turbines. A time-domain numerical simulation tool is able to confirm some of the experimental findings, taking into account the decoupled properties of the slow-drift hydrodynamics and wind turbine aerodynamics. Future platform designs are discussed, including the French-based, pre-commercial design from Nenuphar Wind, called the TwinFloat, which is closely related to concepts examined in the thesis.

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

In support of complex water-resource sustainability projects in the Great Basin region of the United States, Earth Knowledge, Inc. has developed several web-based data management and analysis platforms that have been used by its scientists, clients, and public to facilitate information exchanges, collaborations, and decision making. These platforms support accurate water-resource decision-making by combining second-generation internet (Web 2.0) technologies with traditional 2D GIS and web-based 2D and 3D mapping systems such as Google Maps, and Google Earth. Most data management and analysis systems use traditional software systems to address the data needs and usage behavior of the scientific community. In contrast, these platforms employ more accessible open-source and “off-the-shelf” consumer-oriented, hosted web-services. They exploit familiar software tools using industry standard protocols, formats, and APIs to discover, process, fuse, and visualize earth, engineering, and social science datasets. Thus, they respond to the information needs and web-interface expectations of both subject-matter experts and the public. Because the platforms continue to gather and store all the contributions of their broad-spectrum of users, each new assessment leverages the data, information, and expertise derived from previous investigations. In the last year, Earth Knowledge completed a conceptual system design and feasibility study for a platform, which has a Knowledge Portal providing access to users wishing to retrieve information or knowledge developed by the science enterprise and a Collaboration Environment Module, a framework that links the user-access functions to a Technical Core supporting technical and scientific analyses including Data Management, Analysis and Modeling, and Decision Management, and to essential system administrative functions within an Administrative Module. The over-riding technical challenge is the design and development of a single technical platform that is accessed through a flexible series of knowledge portal and collaboration environment styles reflecting the information needs and user expectations of a diverse community of users. Recent investigations have defined the information needs and expectations of the major end-users and also have reviewed and assessed a wide variety of modern web-based technologies. Combining these efforts produced design specifications and recommendations for the selection and integration of web- and client-based tools. When fully developed, the resulting platform will: -Support new, advanced information systems and decision environments that take full advantage of multiple data sources and platforms; -Provide a distribution network tailored to the timely delivery of products to a broad range of users that are needed to support applications in disaster management, resource management, energy, and urban sustainability; -Establish new integrated multiple-user requirements and knowledge databases that support researchers and promote infusion of successful technologies into existing processes; and -Develop new decision support strategies and presentation methodologies for applied earth science applications to reduce risk, cost, and time.

Monitoring system including an electronic sensor platform and an interrogation transceiver

DOEpatents

Kinzel, Robert L.; Sheets, Larry R.

2003-09-23

A wireless monitoring system suitable for a wide range of remote data collection applications. The system includes at least one Electronic Sensor Platform (ESP), an Interrogator Transceiver (IT) and a general purpose host computer. The ESP functions as a remote data collector from a number of digital and analog sensors located therein. The host computer provides for data logging, testing, demonstration, installation checkout, and troubleshooting of the system. The IT transmits signals from one or more ESP's to the host computer to the ESP's. The IT host computer may be powered by a common power supply, and each ESP is individually powered by a battery. This monitoring system has an extremely low power consumption which allows remote operation of the ESP for long periods; provides authenticated message traffic over a wireless network; utilizes state-of-health and tamper sensors to ensure that the ESP is secure and undamaged; has robust housing of the ESP suitable for use in radiation environments; and is low in cost. With one base station (host computer and interrogator transceiver), multiple ESP's may be controlled at a single monitoring site.

Integrated genome browser: visual analytics platform for genomics.

PubMed

Freese, Nowlan H; Norris, David C; Loraine, Ann E

2016-07-15

Genome browsers that support fast navigation through vast datasets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser. Here we describe multiple updates to IGB, including all-new capabilities to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of datasets from RNA-Seq, ChIP-Seq and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related datasets. To facilitate this, we enhanced IGB's ability to consume data from diverse sources, including Galaxy, Distributed Annotation and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data. IGB is open source and is freely available from http://bioviz.org/igb aloraine@uncc.edu. © The Author 2016. Published by Oxford University Press.

The COMET Sleep Research Platform.

PubMed

Nichols, Deborah A; DeSalvo, Steven; Miller, Richard A; Jónsson, Darrell; Griffin, Kara S; Hyde, Pamela R; Walsh, James K; Kushida, Clete A

2014-01-01

The Comparative Outcomes Management with Electronic Data Technology (COMET) platform is extensible and designed for facilitating multicenter electronic clinical research. Our research goals were the following: (1) to conduct a comparative effectiveness trial (CET) for two obstructive sleep apnea treatments-positive airway pressure versus oral appliance therapy; and (2) to establish a new electronic network infrastructure that would support this study and other clinical research studies. The COMET platform was created to satisfy the needs of CET with a focus on creating a platform that provides comprehensive toolsets, multisite collaboration, and end-to-end data management. The platform also provides medical researchers the ability to visualize and interpret data using business intelligence (BI) tools. COMET is a research platform that is scalable and extensible, and which, in a future version, can accommodate big data sets and enable efficient and effective research across multiple studies and medical specialties. The COMET platform components were designed for an eventual move to a cloud computing infrastructure that enhances sustainability, overall cost effectiveness, and return on investment.

The COMET Sleep Research Platform

PubMed Central

Nichols, Deborah A.; DeSalvo, Steven; Miller, Richard A.; Jónsson, Darrell; Griffin, Kara S.; Hyde, Pamela R.; Walsh, James K.; Kushida, Clete A.

2014-01-01

Introduction: The Comparative Outcomes Management with Electronic Data Technology (COMET) platform is extensible and designed for facilitating multicenter electronic clinical research. Background: Our research goals were the following: (1) to conduct a comparative effectiveness trial (CET) for two obstructive sleep apnea treatments—positive airway pressure versus oral appliance therapy; and (2) to establish a new electronic network infrastructure that would support this study and other clinical research studies. Discussion: The COMET platform was created to satisfy the needs of CET with a focus on creating a platform that provides comprehensive toolsets, multisite collaboration, and end-to-end data management. The platform also provides medical researchers the ability to visualize and interpret data using business intelligence (BI) tools. Conclusion: COMET is a research platform that is scalable and extensible, and which, in a future version, can accommodate big data sets and enable efficient and effective research across multiple studies and medical specialties. The COMET platform components were designed for an eventual move to a cloud computing infrastructure that enhances sustainability, overall cost effectiveness, and return on investment. PMID:25848590

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

PubMed

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

2016-03-15

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

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

Jia, Feng

The main objective of this project is to design novel nano-structured carriers and strategies to co-localize multiple enzymes to mimic the functionalities of MECs. In order to achieve this goal, distinct approaches for enzyme co-localization were developed and evaluated. Specifically, we investigated different polymeric nano-carriers, both flexible and rigid, as platforms for co-localization, as well as distinct enzyme attachment techniques using model enzyme systems using glucose oxidase and horseradish peroxidase to control the spatial arrangement of the multiple enzymes on the nanocarriers. This platform technology can be potentially used to co-localize various enzyme systems and its broad applicability will bemore » tested using the sclareol biosynthesis process to control the formation of products through the formation of MECs with multiple enzymes NgCPS and sSsSS to regulate the pathway of reactive intermediate to enhance the final product conversion rate.« less

First aircraft test results of a compact, low cost hyperspectral imager for earth observation from space

NASA Astrophysics Data System (ADS)

de Goeij, B. T. G.; Otter, G. C. J.; van Wakeren, J. M. O.; Veefkind, J. P.; Vlemmix, T.; Ge, X.; Levelt, P. F.; Dirks, B. P. F.; Toet, P. M.; van der Wal, L. F.; Jansen, R.

2017-09-01

In recent years TNO has investigated and developed different innovative opto-mechanical designs to realize advanced spectrometers for space applications in a more compact and cost-effective manner. This offers multiple advantages: a compact instrument can be flown on a much smaller platform or as add-on on a larger platform; a low-cost instrument opens up the possibility to fly multiple instruments in a satellite constellation, improving both global coverage and temporal sampling (e.g. multiple overpasses per day to study diurnal processes); in this way a constellation of low-cost instruments may provide added value to the larger scientific and operational satellite missions (e.g. the Copernicus Sentinel missions); a small, lightweight spectrometer can easily be mounted on a small aircraft or high-altitude UAV (offering high spatial resolution).

Insight: An ontology-based integrated database and analysis platform for epilepsy self-management research.

PubMed

Sahoo, Satya S; Ramesh, Priya; Welter, Elisabeth; Bukach, Ashley; Valdez, Joshua; Tatsuoka, Curtis; Bamps, Yvan; Stoll, Shelley; Jobst, Barbara C; Sajatovic, Martha

2016-10-01

We present Insight as an integrated database and analysis platform for epilepsy self-management research as part of the national Managing Epilepsy Well Network. Insight is the only available informatics platform for accessing and analyzing integrated data from multiple epilepsy self-management research studies with several new data management features and user-friendly functionalities. The features of Insight include, (1) use of Common Data Elements defined by members of the research community and an epilepsy domain ontology for data integration and querying, (2) visualization tools to support real time exploration of data distribution across research studies, and (3) an interactive visual query interface for provenance-enabled research cohort identification. The Insight platform contains data from five completed epilepsy self-management research studies covering various categories of data, including depression, quality of life, seizure frequency, and socioeconomic information. The data represents over 400 participants with 7552 data points. The Insight data exploration and cohort identification query interface has been developed using Ruby on Rails Web technology and open source Web Ontology Language Application Programming Interface to support ontology-based reasoning. We have developed an efficient ontology management module that automatically updates the ontology mappings each time a new version of the Epilepsy and Seizure Ontology is released. The Insight platform features a Role-based Access Control module to authenticate and effectively manage user access to different research studies. User access to Insight is managed by the Managing Epilepsy Well Network database steering committee consisting of representatives of all current collaborating centers of the Managing Epilepsy Well Network. New research studies are being continuously added to the Insight database and the size as well as the unique coverage of the dataset allows investigators to conduct aggregate data analysis that will inform the next generation of epilepsy self-management studies. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

PubMed

Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

2018-06-01

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

Use of ultrasonic array method for positioning multiple partial discharge sources in transformer oil.

PubMed

Xie, Qing; Tao, Junhan; Wang, Yongqiang; Geng, Jianghai; Cheng, Shuyi; Lü, Fangcheng

2014-08-01

Fast and accurate positioning of partial discharge (PD) sources in transformer oil is very important for the safe, stable operation of power systems because it allows timely elimination of insulation faults. There is usually more than one PD source once an insulation fault occurs in the transformer oil. This study, which has both theoretical and practical significance, proposes a method of identifying multiple PD sources in the transformer oil. The method combines the two-sided correlation transformation algorithm in the broadband signal focusing and the modified Gerschgorin disk estimator. The method of classification of multiple signals is used to determine the directions of arrival of signals from multiple PD sources. The ultrasonic array positioning method is based on the multi-platform direction finding and the global optimization searching. Both the 4 × 4 square planar ultrasonic sensor array and the ultrasonic array detection platform are built to test the method of identifying and positioning multiple PD sources. The obtained results verify the validity and the engineering practicability of this method.

Multifunctional picoliter droplet manipulation platform and its application in single cell analysis.

PubMed

Gu, Shu-Qing; Zhang, Yun-Xia; Zhu, Ying; Du, Wen-Bin; Yao, Bo; Fang, Qun

2011-10-01

We developed an automated and multifunctional microfluidic platform based on DropLab to perform flexible generation and complex manipulations of picoliter-scale droplets. Multiple manipulations including precise droplet generation, sequential reagent merging, and multistep solid-phase extraction for picoliter-scale droplets could be achieved in the present platform. The system precision in generating picoliter-scale droplets was significantly improved by minimizing the thermo-induced fluctuation of flow rate. A novel droplet fusion technique based on the difference of droplet interfacial tensions was developed without the need of special microchannel networks or external devices. It enabled sequential addition of reagents to droplets on demand for multistep reactions. We also developed an effective picoliter-scale droplet splitting technique with magnetic actuation. The difficulty in phase separation of magnetic beads from picoliter-scale droplets due to the high interfacial tension was overcome using ferromagnetic particles to carry the magnetic beads to pass through the phase interface. With this technique, multistep solid-phase extraction was achieved among picoliter-scale droplets. The present platform had the ability to perform complex multistep manipulations to picoliter-scale droplets, which is particularly required for single cell analysis. Its utility and potentials in single cell analysis were preliminarily demonstrated in achieving high-efficiency single-cell encapsulation, enzyme activity assay at the single cell level, and especially, single cell DNA purification based on solid-phase extraction.

Suspension arrays based on nanoparticle-encoded microspheres for high-throughput multiplexed detection

PubMed Central

Leng, Yuankui

2017-01-01

Spectrometrically or optically encoded microsphere based suspension array technology (SAT) is applicable to the high-throughput, simultaneous detection of multiple analytes within a small, single sample volume. Thanks to the rapid development of nanotechnology, tremendous progress has been made in the multiplexed detecting capability, sensitivity, and photostability of suspension arrays. In this review, we first focus on the current stock of nanoparticle-based barcodes as well as the manufacturing technologies required for their production. We then move on to discuss all existing barcode-based bioanalysis patterns, including the various labels used in suspension arrays, label-free platforms, signal amplification methods, and fluorescence resonance energy transfer (FRET)-based platforms. We then introduce automatic platforms for suspension arrays that use superparamagnetic nanoparticle-based microspheres. Finally, we summarize the current challenges and their proposed solutions, which are centered on improving encoding capacities, alternative probe possibilities, nonspecificity suppression, directional immobilization, and “point of care” platforms. Throughout this review, we aim to provide a comprehensive guide for the design of suspension arrays, with the goal of improving their performance in areas such as multiplexing capacity, throughput, sensitivity, and cost effectiveness. We hope that our summary on the state-of-the-art development of these arrays, our commentary on future challenges, and some proposed avenues for further advances will help drive the development of suspension array technology and its related fields. PMID:26021602

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

Introduction - We present a point of departure architecture for prospecting for Lunar Resources from an Exploration Platform at the Earth - Moon Lagrange points. Included in our study are launch vehicle, cis-lunar transportation architecture, habitat requirements and utilization, lander/rover concepts and sample return. Different transfer design techniques can be explored by mission designers, testing various propulsive systems, maneuvers, rendezvous, and other in-space and surface operations. Understanding the availability of high and low energy trajectory transfer options opens up the possibility of exploring the human and logistics support mission design space and deriving solutions never before contemplated. For sample return missions from the lunar surface, low-energy transfers could be utilized between EML platform and the surface as well as return of samples to EML-based spacecraft. Human Habitation at the Exploration Platform - Telerobotic and telepresence capabilities are considered by the agency to be "grand challenges" for space technology. While human visits to the lunar surface provide optimal opportunities for field geologic exploration, on-orbit telerobotics may provide attractive early opportunities for geologic exploration, resource prospecting, and other precursor activities in advance of human exploration campaigns and ISRU processing. The Exploration Platform provides a perfect port for a small lander which could be refueled and used for multiple missions including sample return. The EVA and robotic capabilities of the EML Exploration Platform allow the lander to be serviced both internally and externally, based on operational requirements. The placement of the platform at an EML point allows the lander to access any site on the lunar surface, thus providing the global lunar surface access that is commonly understood to be required in order to enable a robust lunar exploration program. Designing the sample return lander for low-energy trajectories would reduce the overall mass and potentially increase the sample return mass. The Initial Lunar Mission -Building upon Apollo sample investigations, the recent results of the LRO/LCROSS, international missions such as Chandrayaan-1, and legacy missions including Lunar Prospector, and Clementine, among the most important science and exploration goals is surface prospecting for lunar resources and to provide ground truth for orbital observations. Being able to constrain resource production potential will allow us to estimate the prospect for reducing the size of payloads launched from Earth required for Solar System exploration. Flight opportunities for something like the NASA RESOLVE instrument suite to areas of high science and exploration interest could be used to refine and improve future Exploration architectures, reducing the outlays required for cis-lunar operations. Summary - EML points are excellent for placement of a semi-permanent human-tended Exploration Platform both in the near term, while providing important infrastructure and deep-space experience that will be built upon to gradually increase long-term operational capabilities.

Effects of Platform Design on the Customer Experience in an Online Solar PV Marketplace

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

OShaughnessy, Eric J; Margolis, Robert M; Leibowicz, Benjamin

Residential solar photovoltaic (PV) customers are increasingly buying PV systems in online marketplaces, where customers can compare multiple quotes from several installers on quote platforms. In this study, we use data from an online marketplace to explore how quote platform design affects customer experiences. We analyze how four design changes affected customer experiences in terms of factors such as prices. We find that three of the four design changes are associated with statistically significant and robust price reductions, even though none of the changes were implemented specifically to reduce prices. The results suggest that even seemingly small platform design changesmore » can affect PV customer experiences in online marketplaces.« less

Building a national Infection Intelligence Platform to improve antimicrobial stewardship and drive better patient outcomes: the Scottish experience.

PubMed

Bennie, Marion; Malcolm, William; Marwick, Charis A; Kavanagh, Kimberley; Sneddon, Jean; Nathwani, Dilip

2017-10-01

The better use of new and emerging data streams to understand the epidemiology of infectious disease and to inform and evaluate antimicrobial stewardship improvement programmes is paramount in the global fight against antimicrobial resistance. To create a national informatics platform that synergizes the wealth of disjointed, infection-related health data, building an intelligence capability that allows rapid enquiry, generation of new knowledge and feedback to clinicians and policy makers. A multi-stakeholder community, led by the Scottish Antimicrobial Prescribing Group, secured government funding to deliver a national programme of work centred on three key aspects: (i) technical platform development with record linkage capability across multiple datasets; (ii) a proportionate governance approach to enhance responsiveness; and (iii) generation of new evidence to guide clinical practice. The National Health Service Scotland Infection Intelligence Platform (IIP) is now hosted within the national health data repository to assure resilience and sustainability. New technical solutions include simplified 'data views' of complex, linked datasets and embedded statistical programs to enhance capability. These developments have enabled responsiveness, flexibility and robustness in conducting population-based studies including a focus on intended and unintended effects of antimicrobial stewardship interventions and quantification of infection risk factors and clinical outcomes. We have completed the build and test phase of IIP, overcoming the technical and governance challenges, and produced new capability in infection informatics, generating new evidence for improved clinical practice. This provides a foundation for expansion and opportunity for global collaborations. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

NiftyNet: a deep-learning platform for medical imaging.

PubMed

Gibson, Eli; Li, Wenqi; Sudre, Carole; Fidon, Lucas; Shakir, Dzhoshkun I; Wang, Guotai; Eaton-Rosen, Zach; Gray, Robert; Doel, Tom; Hu, Yipeng; Whyntie, Tom; Nachev, Parashkev; Modat, Marc; Barratt, Dean C; Ourselin, Sébastien; Cardoso, M Jorge; Vercauteren, Tom

2018-05-01

Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this domain of application requires substantial implementation effort. Consequently, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups. This work presents the open-source NiftyNet platform for deep learning in medical imaging. The ambition of NiftyNet is to accelerate and simplify the development of these solutions, and to provide a common mechanism for disseminating research outputs for the community to use, adapt and build upon. The NiftyNet infrastructure provides a modular deep-learning pipeline for a range of medical imaging applications including segmentation, regression, image generation and representation learning applications. Components of the NiftyNet pipeline including data loading, data augmentation, network architectures, loss functions and evaluation metrics are tailored to, and take advantage of, the idiosyncracies of medical image analysis and computer-assisted intervention. NiftyNet is built on the TensorFlow framework and supports features such as TensorBoard visualization of 2D and 3D images and computational graphs by default. We present three illustrative medical image analysis applications built using NiftyNet infrastructure: (1) segmentation of multiple abdominal organs from computed tomography; (2) image regression to predict computed tomography attenuation maps from brain magnetic resonance images; and (3) generation of simulated ultrasound images for specified anatomical poses. The NiftyNet infrastructure enables researchers to rapidly develop and distribute deep learning solutions for segmentation, regression, image generation and representation learning applications, or extend the platform to new applications. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Implementation and Evaluation of a Fully Automated Multiplex Real-Time PCR Assay on the BD Max Platform to Detect and Differentiate Herpesviridae from Cerebrospinal Fluids

PubMed Central

Köller, Thomas; Kurze, Daniel; Lange, Mirjam; Scherdin, Martin; Podbielski, Andreas; Warnke, Philipp

2016-01-01

A fully automated multiplex real-time PCR assay—including a sample process control and a plasmid based positive control—for the detection and differentiation of herpes simplex virus 1 (HSV1), herpes simplex virus 2 (HSV2) and varicella-zoster virus (VZV) from cerebrospinal fluids (CSF) was developed on the BD Max platform. Performance was compared to an established accredited multiplex real time PCR protocol utilizing the easyMAG and the LightCycler 480/II, both very common devices in viral molecular diagnostics. For clinical validation, 123 CSF specimens and 40 reference samples from national interlaboratory comparisons were examined with both methods, resulting in 97.6% and 100% concordance for CSF and reference samples, respectively. Utilizing the BD Max platform revealed sensitivities of 173 (CI 95%, 88–258) copies/ml for HSV1, 171 (CI 95%, 148–194) copies/ml for HSV2 and 84 (CI 95%, 5–163) copies/ml for VZV. Cross reactivity could be excluded by checking 25 common viral, bacterial and fungal human pathogens. Workflow analyses displayed shorter test duration as well as remarkable fewer and easier preparation steps with the potential to reduce error rates occurring when manually assessing patient samples. This protocol allows for a fully automated PCR assay on the BD Max platform for the simultaneously detection of herpesviridae from CSF specimens. Singular or multiple infections due to HSV1, HSV2 and VZV can reliably be differentiated with good sensitivities. Control parameters are included within the assay, thereby rendering its suitability for current quality management requirements. PMID:27092772

Recent developments in OLED-based chemical and biological sensors

NASA Astrophysics Data System (ADS)

Shinar, Joseph; Zhou, Zhaoqun; Cai, Yuankun; Shinar, Ruth

2007-09-01

Recent developments in the structurally integrated OLED-based platform of luminescent chemical and biological sensors are reviewed. In this platform, an array of OLED pixels, which is structurally integrated with the sensing elements, is used as the photoluminescence (PL) excitation source. The structural integration is achieved by fabricating the OLED array and the sensing element on opposite sides of a common glass substrate or on two glass substrates that are attached back-to-back. As it does not require optical fibers, lens, or mirrors, it results in a uniquely simple, low-cost, and potentially rugged geometry. The recent developments on this platform include the following: (1) Enhancing the performance of gas-phase and dissolved oxygen sensors. This is achieved by (a) incorporating high-dielectric TiO II nanoparticles in the oxygen-sensitive Pt and Pd octaethylporphyrin (PtOEP and PdOEP, respectively)- doped polystyrene (PS) sensor films, and (b) embedding the oxygen-sensitive dyes in a matrix of polymer blends such as PS:polydimethylsiloxane (PDMS). (2) Developing sensor arrays for simultaneous detection of multiple serum analytes, including oxygen, glucose, lactate, and alcohol. The sensing element for each analyte consists of a PtOEP-doped PS oxygen sensor, and a solution containing the oxidase enzyme specific to the analyte. Each sensing element is coupled to two individually addressable OLED pixels and a Si photodiode photodetector (PD). (3) Enhancing the integration of the platform, whereby a PD array is also structurally integrated with the OLED array and sensing elements. This enhanced integration is achieved by fabricating an array of amorphous or nanocrystalline Si-based PDs, followed by fabrication of the OLED pixels in the gaps between these Si PDs.

Driving platform for OLED lighting investigations

NASA Astrophysics Data System (ADS)

Vogel, Uwe; Elgner, Andreas; Kreye, Daniel; Amelung, Jörg; Scholles, Michael

2006-08-01

OLED technology may be excellently suitable for lighting applications by combining high efficiency, cost effective manufacturing and the use of low cost materials. Certain issues remain to be solved so far, including OLED brightness, color, lifetime, large area uniformity and encapsulation. Another aspect, that might be capable in addressing some of the mentioned issues, is OLED lighting electrical driving. We report on the design of a driving platform for OLED lighting test panels or substrates. It is intended for being a test environment for lighting substrates as well as demonstration/presentation environment. It is based on a 128-channel passive-matrix driver/controller ASIC OC2. Its key component is an MSP430-compatible 16-bit micro-controller core including embedded Flash memory (program), EEPROM (parameter), and RAM (data memory). A significant feature of the device is an electronic approach for improving the lifetime/uniformity behavior of connected OLED. The embedded micro-controller is the key to the high versatility of OC2, since by firmware modification it can be adapted to various applications and conditions. Here its application for an OLED lighting driving platform is presented. Major features of this platform are PC-control mode (via USB interface), stand-alone mode (no external control necessary, just power supply), on-board OLED panel parameter storage, flat geometry of OLED lighting panel carrier (board), AC and DC driving regimes, adjustable reverse voltage, dedicated user SW (PC/Windows-based), sub-tile patterning and single sub-tile control, combination of multiple channels for increasing driving current. This publication contains results of the project "High Brightness OLEDs for ICT & Next Generation Lighting Applications" (OLLA), funded by the European Commission.

Composite airfoil assembly

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

Garcia-Crespo, Andres Jose

A composite blade assembly for mounting on a turbine wheel includes a ceramic airfoil and an airfoil platform. The ceramic airfoil is formed with an airfoil portion, a blade shank portion and a blade dovetail tang. The metal platform includes a platform shank and a radially inner platform dovetail. The ceramic airfoil is captured within the metal platform, such that in use, the ceramic airfoil is held within the turbine wheel independent of the metal platform.

SERS diagnostic platforms, methods and systems microarrays, biosensors and biochips

DOEpatents

Vo-Dinh, Tuan [Knoxville, TN

2007-09-11

A Raman integrated sensor system for the detection of targets including biotargets includes at least one sampling platform, at least one receptor probe disposed on the sampling platform, and an integrated circuit detector system communicably connected to the receptor. The sampling platform is preferably a Raman active surface-enhanced scattering (SERS) platform, wherein the Raman sensor is a SERS sensor. The receptors can include at least one protein receptor and at least one nucleic acid receptor.

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...

A Versatile Integrated Ambient Ionization Source Platform.

PubMed

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

2018-04-30

The pursuit of high-throughput sample analysis from complex matrix demands development of multiple ionization techniques with complementary specialties. A versatile integrated ambient ionization source (iAmIS) platform is proposed in this work, based on the idea of integrating multiple functions, enhancing the efficiency of current ionization techniques, extending the applications, and decreasing the cost of the instrument. The design of the iAmIS platform combines flowing atmospheric pressure afterglow (FAPA) source/direct analysis in real time (DART), dielectric barrier discharge ionization (DBDI)/low-temperature plasma (LTP), desorption electrospray ionization (DESI), and laser desorption (LD) technique. All individual and combined ionization modes can be easily attained by modulating parameters. In particular, the FAPA/DART&DESI mode can realize the detection of polar and nonpolar compounds at the same time with two different ionization mechanisms: proton transfer and charge transfer. The introduction of LD contributes to the mass spectrometry imaging and the surface-assisted laser desorption (SALDI) under ambient condition. Compared with other individual or multi-mode ion source, the iAmIS platform provides the flexibility of choosing different ionization modes, broadens the scope of the analyte detection, and facilitates the analysis of complex samples. Graphical abstract ᅟ.

A Versatile Integrated Ambient Ionization Source Platform

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Novel peptide-based platform for the dual presentation of biologically active peptide motifs on biomaterials.

PubMed

Mas-Moruno, Carlos; Fraioli, Roberta; Albericio, Fernando; Manero, José María; Gil, F Javier

2014-05-14

Biofunctionalization of metallic materials with cell adhesive molecules derived from the extracellular matrix is a feasible approach to improve cell-material interactions and enhance the biointegration of implant materials (e.g., osseointegration of bone implants). However, classical biomimetic strategies may prove insufficient to elicit complex and multiple biological signals required in the processes of tissue regeneration. Thus, newer strategies are focusing on installing multifunctionality on biomaterials. In this work, we introduce a novel peptide-based divalent platform with the capacity to simultaneously present distinct bioactive peptide motifs in a chemically controlled fashion. As a proof of concept, the integrin-binding sequences RGD and PHSRN were selected and introduced in the platform. The biofunctionalization of titanium with this platform showed a positive trend towards increased numbers of cell attachment, and statistically higher values of spreading and proliferation of osteoblast-like cells compared to control noncoated samples. Moreover, it displayed statistically comparable or improved cell responses compared to samples coated with the single peptides or with an equimolar mixture of the two motifs. Osteoblast-like cells produced higher levels of alkaline phosphatase on surfaces functionalized with the platform than on control titanium; however, these values were not statistically significant. This study demonstrates that these peptidic structures are versatile tools to convey multiple biofunctionality to biomaterials in a chemically defined manner.

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

PubMed

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

2016-11-15

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

Collaboration-Centred Cities through Urban Apps Based on Open and User-Generated Data

PubMed Central

Aguilera, Unai; López-de-Ipiña, Diego; Pérez, Jorge

2016-01-01

This paper describes the IES Cities platform conceived to streamline the development of urban apps that combine heterogeneous datasets provided by diverse entities, namely, government, citizens, sensor infrastructure and other information data sources. This work pursues the challenge of achieving effective citizen collaboration by empowering them to prosume urban data across time. Particularly, this paper focuses on the query mapper; a key component of the IES Cities platform devised to democratize the development of open data-based mobile urban apps. This component allows developers not only to use available data, but also to contribute to existing datasets with the execution of SQL sentences. In addition, the component allows developers to create ad hoc storages for their applications, publishable as new datasets accessible by other consumers. As multiple users could be contributing and using a dataset, our solution also provides a data level permission mechanism to control how the platform manages the access to its datasets. We have evaluated the advantages brought forward by IES Cities from the developers’ perspective by describing an exemplary urban app created on top of it. In addition, we include an evaluation of the main functionalities of the query mapper. PMID:27376300

Collaboration-Centred Cities through Urban Apps Based on Open and User-Generated Data.

PubMed

Aguilera, Unai; López-de-Ipiña, Diego; Pérez, Jorge

2016-07-01

This paper describes the IES Cities platform conceived to streamline the development of urban apps that combine heterogeneous datasets provided by diverse entities, namely, government, citizens, sensor infrastructure and other information data sources. This work pursues the challenge of achieving effective citizen collaboration by empowering them to prosume urban data across time. Particularly, this paper focuses on the query mapper; a key component of the IES Cities platform devised to democratize the development of open data-based mobile urban apps. This component allows developers not only to use available data, but also to contribute to existing datasets with the execution of SQL sentences. In addition, the component allows developers to create ad hoc storages for their applications, publishable as new datasets accessible by other consumers. As multiple users could be contributing and using a dataset, our solution also provides a data level permission mechanism to control how the platform manages the access to its datasets. We have evaluated the advantages brought forward by IES Cities from the developers' perspective by describing an exemplary urban app created on top of it. In addition, we include an evaluation of the main functionalities of the query mapper.

In Situ Localized Growth of Ordered Metal Oxide Hollow Sphere Array on Microheater Platform for Sensitive, Ultra-Fast Gas Sensing.

PubMed

Rao, Ameya; Long, Hu; Harley-Trochimczyk, Anna; Pham, Thang; Zettl, Alex; Carraro, Carlo; Maboudian, Roya

2017-01-25

A simple and versatile strategy is presented for the localized on-chip synthesis of an ordered metal oxide hollow sphere array directly on a low power microheater platform to form a closely integrated miniaturized gas sensor. Selective microheater surface modification through fluorinated monolayer self-assembly and its subsequent microheater-induced thermal decomposition enables the position-controlled deposition of an ordered two-dimensional colloidal sphere array, which serves as a sacrificial template for metal oxide growth via homogeneous chemical precipitation; this strategy ensures control in both the morphology and placement of the sensing material on only the active heated area of the microheater platform, providing a major advantage over other methods of presynthesized nanomaterial integration via suspension coating or printing. A fabricated tin oxide hollow sphere-based sensor shows high sensitivity (6.5 ppb detection limit) and selectivity toward formaldehyde, and extremely fast response (1.8 s) and recovery (5.4 s) times. This flexible and scalable method can be used to fabricate high performance miniaturized gas sensors with a variety of hollow nanostructured metal oxides for a range of applications, including combining multiple metal oxides for superior sensitivity and tunable selectivity.

Multi-agent-based bio-network for systems biology: protein-protein interaction network as an example.

PubMed

Ren, Li-Hong; Ding, Yong-Sheng; Shen, Yi-Zhen; Zhang, Xiang-Feng

2008-10-01

Recently, a collective effort from multiple research areas has been made to understand biological systems at the system level. This research requires the ability to simulate particular biological systems as cells, organs, organisms, and communities. In this paper, a novel bio-network simulation platform is proposed for system biology studies by combining agent approaches. We consider a biological system as a set of active computational components interacting with each other and with an external environment. Then, we propose a bio-network platform for simulating the behaviors of biological systems and modelling them in terms of bio-entities and society-entities. As a demonstration, we discuss how a protein-protein interaction (PPI) network can be seen as a society of autonomous interactive components. From interactions among small PPI networks, a large PPI network can emerge that has a remarkable ability to accomplish a complex function or task. We also simulate the evolution of the PPI networks by using the bio-operators of the bio-entities. Based on the proposed approach, various simulators with different functions can be embedded in the simulation platform, and further research can be done from design to development, including complexity validation of the biological system.

GRAPE: a graphical pipeline environment for image analysis in adaptive magnetic resonance imaging.

PubMed

Gabr, Refaat E; Tefera, Getaneh B; Allen, William J; Pednekar, Amol S; Narayana, Ponnada A

2017-03-01

We present a platform, GRAphical Pipeline Environment (GRAPE), to facilitate the development of patient-adaptive magnetic resonance imaging (MRI) protocols. GRAPE is an open-source project implemented in the Qt C++ framework to enable graphical creation, execution, and debugging of real-time image analysis algorithms integrated with the MRI scanner. The platform provides the tools and infrastructure to design new algorithms, and build and execute an array of image analysis routines, and provides a mechanism to include existing analysis libraries, all within a graphical environment. The application of GRAPE is demonstrated in multiple MRI applications, and the software is described in detail for both the user and the developer. GRAPE was successfully used to implement and execute three applications in MRI of the brain, performed on a 3.0-T MRI scanner: (i) a multi-parametric pipeline for segmenting the brain tissue and detecting lesions in multiple sclerosis (MS), (ii) patient-specific optimization of the 3D fluid-attenuated inversion recovery MRI scan parameters to enhance the contrast of brain lesions in MS, and (iii) an algebraic image method for combining two MR images for improved lesion contrast. GRAPE allows graphical development and execution of image analysis algorithms for inline, real-time, and adaptive MRI applications.

New strategies for SHM based on a multichannel wireless AE node

NASA Astrophysics Data System (ADS)

Godinez-Azcuaga, Valery; Ley, Obdulia

2014-03-01

This paper discusses the development of an Acoustic Emission (AE) wireless node and its application for SHM (Structural Health Monitoring). The instrument development was planned for applications monitoring steel and concrete bridges components. The final product, now commercially available, is a sensor node which includes multiple sensing elements, on board signal processing and analysis capabilities, signal conditioning electronics, power management circuits, wireless data transmission element and energy harvesting unit. The sensing elements are capable of functioning in both passive and active modes, while the multiple parametric inputs are available for connecting various sensor types to measure external characteristics affecting the performance of the structure under monitoring. The output of all these sensors are combined and analyzed at the node in order to minimize the data transmission rate, which consumes significant amount of power. Power management circuits are used to reduce the data collection intervals through selective data acquisition strategies and minimize the sensor node power consumption. This instrument, known as the 1284, is an excellent platform to deploy SHM in the original bridge applications, but initial prototypes has shown significant potential in monitoring composite wind turbine blades and composites mockups of Unmanned Autonomous Vehicles (UAV) components; currently we are working to extend the use of this system to fields such as coal flow, power transformer, and off-shore platform monitoring.

Identification of species by multiplex analysis of variable-length sequences

PubMed Central

Pereira, Filipe; Carneiro, João; Matthiesen, Rune; van Asch, Barbara; Pinto, Nádia; Gusmão, Leonor; Amorim, António

2010-01-01

The quest for a universal and efficient method of identifying species has been a longstanding challenge in biology. Here, we show that accurate identification of species in all domains of life can be accomplished by multiplex analysis of variable-length sequences containing multiple insertion/deletion variants. The new method, called SPInDel, is able to discriminate 93.3% of eukaryotic species from 18 taxonomic groups. We also demonstrate that the identification of prokaryotic and viral species with numeric profiles of fragment lengths is generally straightforward. A computational platform is presented to facilitate the planning of projects and includes a large data set with nearly 1800 numeric profiles for species in all domains of life (1556 for eukaryotes, 105 for prokaryotes and 130 for viruses). Finally, a SPInDel profiling kit for discrimination of 10 mammalian species was successfully validated on highly processed food products with species mixtures and proved to be easily adaptable to multiple screening procedures routinely used in molecular biology laboratories. These results suggest that SPInDel is a reliable and cost-effective method for broad-spectrum species identification that is appropriate for use in suboptimal samples and is amenable to different high-throughput genotyping platforms without the need for DNA sequencing. PMID:20923781

Conjugated Polymer Nanoparticles for the Amplified Detection of Nitro-explosive Picric Acid on Multiple Platforms.

PubMed

Malik, Akhtar Hussain; Hussain, Sameer; Kalita, Anamika; Iyer, Parameswar Krishnan

2015-12-09

Spontaneously formed conjugated polymer nanoparticles (CPNs) or polymer dots displayed remarkable fluorescence response toward nitroexplosive-picric acid (PA) in multiple environments including 100% aqueous media, solid support using portable paper strips and vapor phase detection via two terminal device. This new cationic conjugated polyelectrolyte (CPE) poly(3,3'-((2-phenyl-9H-fluorene-9,9-diyl)bis(hexane-6,1-diyl))bis(1-methyl-1H-imidazol-3-ium)bromide) (PFMI) was synthesized by Suzuki coupling polymerization followed by post functionalization method without employing any hectic purification technique. Highest quenching constant value (K(sv)) of 1.12 × 10(8) M(-1) and a very low detection limit of 30.9 pM/7.07 ppt were obtained exclusively for PA in 100% aqueous environment which is rare and unique for any CPE/CPNs. Contact mode detection of PA was also performed using simple, cost-effective and portable fluorescent paper strips for achieving on-site detection. Furthermore, the two terminal sensor device fabricated with nanoparticles of PFMI (PFMI-NPs) provides an exceptional and unprecedented platform for the vapor mode detection of PA under ambient conditions. The mechanism for the ultrasensitivity of PFMI-NPs probe to detect PA is attributed to the "molecular-wire effect", electrostatic interaction, photoinduced electron transfer (PET), and possible resonance energy transfer (RET).

Sample Acquisition and Handling System from a Remote Platform

NASA Technical Reports Server (NTRS)

Badescu, Mircea; Sherrit, Stewart; Jones, Jack A.

2011-01-01

A system has been developed to acquire and handle samples from a suspended remote platform. The system includes a penetrator, a penetrator deployment mechanism, and a sample handler. A gravity-driven harpoon sampler was used for the system, but other solutions can be used to supply the penetration energy, such as pyrotechnic, pressurized gas, or springs. The deployment mechanism includes a line that is attached to the penetrator, a spool for reeling in the line, and a line engagement control mechanism. The penetrator has removable tips that can collect liquid, ice, or solid samples. The handling mechanism consists of a carousel that can store a series of identical or different tips, assist in penetrator reconfiguration for multiple sample acquisition, and deliver the sample to a series of instruments for analysis. The carousel sample handling system was combined with a brassboard reeling mechanism and a penetrator with removable tips. It can attach the removable tip to the penetrator, release and retrieve the penetrator, remove the tip, and present it to multiple instrument stations. The penetrator can be remotely deployed from an aerobot, penetrate and collect the sample, and be retrieved with the sample to the aerobot. The penetrator with removable tips includes sample interrogation windows and a sample retainment spring for unconsolidated samples. The line engagement motor can be used to control the penetrator release and reeling engagement, and to evenly distribute the line on the spool by rocking between left and right ends of the spool. When the arm with the guiding ring is aligned with the spool axis, the line is free to unwind from the spool without rotating the spool. When the arm is perpendicular to the spool axis, the line can move only if the spool rotates.

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

Rashid, A.; Nygaard, C.

The use of concrete in marine environment has gained tremendous popularity in the past decade and is continued to be a very popular material for marine industry in the world today. It has a very diversified use from large offshore platforms and floating structures in the North Sea, Canada and South America to offshore loading terminals and junction platforms in shallow waters in the marshes of southern Louisiana in the Gulf of Mexico. Also, precast concrete sections are extensively used all over the world in the construction of marine structures. Because of their large variety of shapes and sizes, theymore » can be tailored to fit multiple applications in marine environment. The added quality control in the fabrication yard and the ease of installation by lifting makes them a very attractive option. The use of precast concrete sections is gaining a lot of popularity in South America. A lot of fabrication yards are manufacturing these sections locally. There are hundreds of offshore concrete platforms utilizing these sections in Lake Maracaibo, Venezuela. The paper discusses the use of concrete for offshore structures including floaters. It describes some general concepts and advantages to be gained by the use of concrete (precast and cast-in-place) in marine environment. It also discusses some general design considerations required for the use of different types of precast concrete sections that can be utilized for oil and gas platforms and loading terminals. Lastly the paper describes some typical examples of concrete platforms built out of concrete piles, precast concrete girders and beam sections and concrete decking.« less

Turbulence Measurements from Compliant Moorings - Part I: Motion Characterization

DOE PAGES

Harding, Samuel; Kilcher, Levi; Thomson, Jim

2017-06-20

High-fidelity measurements of turbulence in the ocean have long been challenging to collect, in particular in the middle of the water column. In response, a measurement technique has been developed to deploy an Acoustic Doppler Velocimeter (ADV) to mid-water locations on a compliant mooring. A variety of instrumentation platforms have been deployed as part of this work with a range of dynamic motion characteristics. The platforms discussed herein include the streamlined StableMoor™ buoy (SMB), the Tidal Turbulence Mooring (TTM) system based on a conventional 0.9 m spherical buoy, and a 100 lb sounding weight suspended from the stern of amore » research vessel. The ADV head motion is computed from inertial motion sensors integrated into an ADV, and the spectra of these signals are investigated to quantify the motion of each platform. The SMB with a single ADV head mounted on the nose provided the most stable platform for the measurement of tidal turbulence in the inertial sub-range for flow speeds exceeding 1:0 ms -1. The modification of the SMB with a transverse wing configuration for multiple ADVs showed a similar frequency response to the nose configuration in the horizontal plane but with large contamination in the vertical direction as a result of platform roll. While the ADV motion on the TTM was significant in the horizontal directions, the vertical motion of this configuration was the most stable of all configurations tested. The sounding weight measurements showed the greatest motion at the ADV head but are likely to be influenced by both prop-wash and vessel motion.« less

Immunocontraception: Filamentous Bacteriophage as a Platform for Vaccine Development.

PubMed

Samoylova, Tatiana I; Braden, Timothy D; Spencer, Jennifer A; Bartol, Frank F

2017-11-20

Population control of domestic, wild, invasive, and captive animal species is a global issue of importance to public health, animal welfare and the economy. There is pressing need for effective, safe, and inexpensive contraceptive technologies to address this problem. Contraceptive vaccines, designed to stimulate the immune system in order to block critical reproductive events and suppress fertility, may provide a solution. Filamentous bacteriophages can be used as platforms for development of such vaccines. In this review authors highlight structural and immunogenic properties of filamentous phages, and discuss applications of phage-peptide vaccines for advancement of immunocontraception technology in animals. Phages can be engineered to display fusion (non-phage) peptides as coat proteins. Such modifications can be accomplished via genetic manipulation of phage DNA, or by chemical conjugation of synthetic peptides to phage surface proteins. Phage fusions with antigenic determinants induce humoral as well as cell-mediated immune responses in animals, making them attractive as vaccines. Additional advantages of the phage platform include environmental stability, low cost, and safety for immunized animals and those administering the vaccines. Filamentous phages are viable platforms for vaccine development that can be engineered with molecular and organismal specificity. Phage-based vaccines can be produced in abundance at low cost, are environmentally stable, and are immunogenic when administered via multiple routes. These features are essential for a contraceptive vaccine to be operationally practical in animal applications. Adaptability of the phage platform also makes it attractive for design of human immunocontraceptive agents. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Immunocontraception: Filamentous Bacteriophage as a Platform for Vaccine Development

PubMed Central

Samoylova, Tatiana I.; Braden, Timothy D.; Spencer, Jennifer A.; Bartol, Frank F.

2017-01-01

Background: Population control of domestic, wild, invasive, and captive animal species is a global issue of importance to public health, animal welfare and the economy. There is pressing need for effective, safe, and inexpensive contraceptive technologies to ad-dress this problem. Contraceptive vaccines, designed to stimulate the immune system in order to block critical reproductive events and suppress fertility, may provide a solution. Fil-amentous bacteriophages can be used as platforms for development of such vaccines. Objective: In this review authors highlight structural and immunogenic properties of fila-mentous phages, and discuss applications of phage-peptide vaccines for advancement of immunocontraception technology in animals. Results: Phages can be engineered to display fusion (non-phage) peptides as coat proteins. Such modifications can be accomplished via genetic manipulation of phage DNA, or by chemical conjugation of synthetic peptides to phage surface proteins. Phage fusions with antigenic determinants induce humoral as well as cell-mediated immune responses in ani-mals, making them attractive as vaccines. Additional advantages of the phage platform include environmental stability, low cost, and safety for immunized animals and those ad-ministering the vaccines. Conclusion: Filamentous phages are viable platforms for vaccine development that can be engineered with molecular and organismal specificity. Phage-based vaccines can be pro-duced in abundance at low cost, are environmentally stable, and are immunogenic when administered via multiple routes. These features are essential for a contraceptive vaccine to be operationally practical in animal applications. Adaptability of the phage platform also makes it attractive for design of human immunocontraceptive agents. PMID:28901276

Roel Verhaak, Ph.D., Presents the Somatic Genomic Landscape of Glioblastoma - TCGA

Cancer.gov

Diffuse lower grade gliomas (LGGs) are infiltrative neoplasms of the central nervous system that include astrocytoma, oligodendroglioma and oligo-astrocytoma histologies of grades II and III. Roel G.W. Verhaak, Ph.D., presents a comprehensive analysis of 293 LGGs using multiple advanced genomic, transcriptomic and proteomic platforms from The Cancer Genome Atlas to provide a deeper understanding of the molecular features of this group of neoplasms, to classify them in a clinically-relevant manner, and to provide a public resource that identifies potential targets for emerging therapies.

External Contamination Environment at ISS Included: Selected Results from Payloads Contamination Mapping Delivery 3 Package

NASA Technical Reports Server (NTRS)

Olsen, Randy; Huang, Alvin; Steagall, Courtney; Kohl, Nathaniel; Koontz, Steve; Worthy, Erica

2017-01-01

The International Space Station is the largest and most complex on-orbit platform for space science utilization in low Earth orbit. Multiple sites for external payloads, with exposure to the associated natural and induced environments, are available to support a variety of space science utilization objectives. Contamination is one of the induced environments that can impact performance, mission success and science utilization on the vehicle. The ISS has been designed, built and integrated with strict contamination requirements to provide low levels of induced contamination on external payload assets.

Engineering topological phases in the Luttinger semimetal α -Sn

NASA Astrophysics Data System (ADS)

Zhang, Dongqin; Wang, Huaiqiang; Ruan, Jiawei; Yao, Ge; Zhang, Haijun

2018-05-01

α -Sn is well known as a typical Luttinger semimetal with a quadratic band touching at the Γ point. Based on the effective k .p analysis as well as first-principles calculations, we demonstrate that multiple topological phases with a rich diagram, including topological insulator, Dirac semimetal, and Weyl semimetal phases, can be induced and engineered in α -Sn by external strains, magnetic fields, and circularly polarized light (CPL). Intriguingly, not only the conventional type-I Weyl nodes but also type-II Weyl nodes and double-Weyl nodes can be generated directly from the quadratic semimetal by applying a magnetic field or CPL. Our results apply equally well to other Luttinger semimetals with similar crystal and electronic structures, and thus open an avenue for realizing and engineering multiple topological phases on a versatile platform.

Multiple-Targeted Graphene-based Nanocarrier for Intracellular Imaging of mRNAs

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

Wang, Ying; Li, Zhaohui; Liu, Misha

Simultaneous detection and imaging of multiple intracellular messenger RNA (mRNAs) hold great significant for early cancer diagnostics and preventive medicine development. Herein, we propose a multiple-targeted graphene oxide (GO) nanocarrier that can simultaneously detect and image different type mRNAs in living cells. First of all, in vitro detection of multiple targets have been realized successfully based on the multiple-targeted GO nanocarrier with linear relationship ranging from 3 nM to 200 nM, as well as sensitive detection limit of 1.84 nM for manganese superoxide dismutase (Mn-SOD) mRNA and 2.45 nM for β-actin mRNA. Additionally, this nanosensing platform composed of fluorescent labeledmore » single strand DNA probes and GO nanocarrier can identify Mn-SOD mRNA and endogenous mRNA of β-actin in living cancer cells, showing rapid response, high specificity, nuclease stability, and good biocompatibility during the cell imaging. Thirdly, changes of the expression levels of mRNA in living cells before or after the drug treatment can be monitored successfully. By using multiple ssDNA as probes and GO nanocarrier as the cellular delivery cargo, the proposed simultaneous multiple-targeted sensing platform will be of great potential as a powerful tool for intracellular trafficking process from basic research to clinical diagnosis.« less

Next-generation sequencing library preparation method for identification of RNA viruses on the Ion Torrent Sequencing Platform.

PubMed

Chen, Guiqian; Qiu, Yuan; Zhuang, Qingye; Wang, Suchun; Wang, Tong; Chen, Jiming; Wang, Kaicheng

2018-05-09

Next generation sequencing (NGS) is a powerful tool for the characterization, discovery, and molecular identification of RNA viruses. There were multiple NGS library preparation methods published for strand-specific RNA-seq, but some methods are not suitable for identifying and characterizing RNA viruses. In this study, we report a NGS library preparation method to identify RNA viruses using the Ion Torrent PGM platform. The NGS sequencing adapters were directly inserted into the sequencing library through reverse transcription and polymerase chain reaction, without fragmentation and ligation of nucleic acids. The results show that this method is simple to perform, able to identify multiple species of RNA viruses in clinical samples.

A Virtual Radial Arm Maze for the Study of Multiple Memory Systems in a Functional Magnetic Resonance Imaging Environment

PubMed Central

Xu, Dongrong; Hao, Xuejun; Wang, Zhishun; Duan, Yunsuo; Liu, Feng; Marsh, Rachel; Yu, Shan; Peterson, Bradley S.

2015-01-01

An increasing number of functional brain imaging studies are employing computer-based virtual reality (VR) to study changes in brain activity during the performance of high-level psychological and cognitive tasks. We report the development of a VR radial arm maze that adapts for human use in a scanning environment with the same general experimental design of behavioral tasks as that has been used with remarkable effectiveness for the study of multiple memory systems in rodents. The software platform is independent of specific computer hardware and operating systems, as we aim to provide shared access to this technology by the research community. We hope that doing so will provide greater standardization of software platform and study paradigm that will reduce variability and improve the comparability of findings across studies. We report the details of the design and implementation of this platform and provide information for downloading of the system for demonstration and research applications. PMID:26366052

Design and testing of a multi-sensor pedestrian location and navigation platform.

PubMed

Morrison, Aiden; Renaudin, Valérie; Bancroft, Jared B; Lachapelle, Gérard

2012-01-01

Navigation and location technologies are continually advancing, allowing ever higher accuracies and operation under ever more challenging conditions. The development of such technologies requires the rapid evaluation of a large number of sensors and related utilization strategies. The integration of Global Navigation Satellite Systems (GNSSs) such as the Global Positioning System (GPS) with accelerometers, gyros, barometers, magnetometers and other sensors is allowing for novel applications, but is hindered by the difficulties to test and compare integrated solutions using multiple sensor sets. In order to achieve compatibility and flexibility in terms of multiple sensors, an advanced adaptable platform is required. This paper describes the design and testing of the NavCube, a multi-sensor navigation, location and timing platform. The system provides a research tool for pedestrian navigation, location and body motion analysis in an unobtrusive form factor that enables in situ data collections with minimal gait and posture impact. Testing and examples of applications of the NavCube are provided.

Attitude control for on-orbit servicing spacecraft using hybrid actuator

NASA Astrophysics Data System (ADS)

Wu, Yunhua; Han, Feng; Zheng, Mohong; He, Mengjie; Chen, Zhiming; Hua, Bing; Wang, Feng

2018-03-01

On-orbit servicing is one of the research hotspots of space missions. A small satellite equipped with multiple robotic manipulators is expected to carry out device replacement task for target large spacecraft. Attitude hyperstable control of a small satellite platform under rotations of the manipulators is a challenging problem. A hybrid momentum exchanging actuator consists of Control Moment Gyro (CMG) and Reaction Wheel (RW) is proposed to tackle the above issue, due to its huge amount of momentum storage capacity of the CMG and high control accuracy of the RW, in which the CMG produces large command torque while the RW offers additional control degrees. The constructed dynamic model of the servicing satellite advises that it's feasible for attitude hyperstable control of the platform with arbitrary manipulators through compensating the disturbance generated by rapid rotation of the manipulators. Then, null motion between the CMG and RW is exploited to drive the system to the expected target with favorable performance, and to overcome the CMG inherent geometric singularity and RW saturation. Simulations with different initial situations, including CMG hyperbolic and elliptic singularities and RW saturation, are executed. Compared to the scenarios where the CMG or RW fails stabilizing the platform, large control torque, precise control effect and escape of singularity are guaranteed by the introduced hybrid actuator, CMGRW (CMGRW refers to the hybrid momentum exchanging devices in this paper, consisting of 4 CMGs in classical pyramid cluster and 3 RWs in an orthogonal group (specific description can been found in Section 4)). The feasible performance of the satellite, CMG and RW under large disturbance demonstrates that the control architecture proposed is capable of attitude control for on-orbit servicing satellite with multiple robotic manipulators.

Considerations in evaluating potential socioeconomic impacts of offshore platform decommissioning in California.

PubMed

Kruse, Sarah A; Bernstein, Brock; Scholz, Astrid J

2015-10-01

The 27 oil and gas platforms offshore southern California will eventually reach the end of their useful lifetimes (estimated between 2015 and 2030) and will be decommissioned. Current state and federal laws and regulations allow for alternative uses in lieu of the complete removal required in existing leases. Any decommissioning pathway will create a complex mix of costs, benefits, opportunities, and constraints for multiple user groups. To assist the California Natural Resources Agency in understanding these issues, we evaluated the potential socioeconomic impacts of the 2 most likely options: complete removal and partial removal of the structure to 85 feet below the waterline with the remaining structure left in place as an artificial reef-generally defined as a manmade structure with some properties that mimic a natural reef. We estimated impacts on commercial fishing, commercial shipping, recreational fishing, nonconsumptive boating, and nonconsumptive SCUBA diving. Available data supported quantitative estimates for some impacts, semiquantitative estimates for others, and only qualitative approximations of the direction of impact for still others. Even qualitative estimates of the direction of impacts and of user groups' likely preferred options have been useful to the public and decision makers and provided valuable input to the project's integrative decision model. Uncertainty surrounds even qualitative estimates of the likely direction of impact where interactions between multiple impacts could occur or where user groups include subsets that would experience the same option differently. In addition, we were unable to quantify effects on ecosystem value and on the larger regional ecosystem, because of data gaps on the population sizes and dynamics of key species and the uncertainty surrounding the contribution of platforms to available hard substrate and related natural populations offshore southern California. © 2015 SETAC.

Web-based reactive transport modeling using PFLOTRAN

NASA Astrophysics Data System (ADS)

Zhou, H.; Karra, S.; Lichtner, P. C.; Versteeg, R.; Zhang, Y.

2017-12-01

Actionable understanding of system behavior in the subsurface is required for a wide spectrum of societal and engineering needs by both commercial firms and government entities and academia. These needs include, for example, water resource management, precision agriculture, contaminant remediation, unconventional energy production, CO2 sequestration monitoring, and climate studies. Such understanding requires the ability to numerically model various coupled processes that occur across different temporal and spatial scales as well as multiple physical domains (reservoirs - overburden, surface-subsurface, groundwater-surface water, saturated-unsaturated zone). Currently, this ability is typically met through an in-house approach where computational resources, model expertise, and data for model parameterization are brought together to meet modeling needs. However, such an approach has multiple drawbacks which limit the application of high-end reactive transport codes such as the Department of Energy funded[?] PFLOTRAN code. In addition, while many end users have a need for the capabilities provided by high-end reactive transport codes, they do not have the expertise - nor the time required to obtain the expertise - to effectively use these codes. We have developed and are actively enhancing a cloud-based software platform through which diverse users are able to easily configure, execute, visualize, share, and interpret PFLOTRAN models. This platform consists of a web application and available on-demand HPC computational infrastructure. The web application consists of (1) a browser-based graphical user interface which allows users to configure models and visualize results interactively, and (2) a central server with back-end relational databases which hold configuration, data, modeling results, and Python scripts for model configuration, and (3) a HPC environment for on-demand model execution. We will discuss lessons learned in the development of this platform, the rationale for different interfaces, implementation choices, as well as the planned path forward.

Education and Public Outreach at The Pavilion Lake Research Project: Fusion of Science and Education using Web 2.0

NASA Astrophysics Data System (ADS)

Cowie, B. R.; Lim, D. S.; Pendery, R.; Laval, B.; Slater, G. F.; Brady, A. L.; Dearing, W. L.; Downs, M.; Forrest, A.; Lees, D. S.; Lind, R. A.; Marinova, M.; Reid, D.; Seibert, M. A.; Shepard, R.; Williams, D.

2009-12-01

The Pavilion Lake Research Project (PLRP) is an international multi-disciplinary science and exploration effort to explain the origin and preservation potential of freshwater microbialites in Pavilion Lake, British Columbia, Canada. Using multiple exploration platforms including one person DeepWorker submersibles, Autonomous Underwater Vehicles, and SCUBA divers, the PLRP acts as an analogue research site for conducting science in extreme environments, such as the Moon or Mars. In 2009, the PLRP integrated several Web 2.0 technologies to provide a pilot-scale Education and Public Outreach (EPO) program targeting the internet savvy generation. The seamless integration of multiple technologies including Google Earth, Wordpress, Youtube, Twitter and Facebook, facilitated the rapid distribution of exciting and accessible science and exploration information over multiple channels. Field updates, science reports, and multimedia including videos, interactive maps, and immersive visualization were rapidly available through multiple social media channels, partly due to the ease of integration of these multiple technologies. Additionally, the successful application of videoconferencing via a readily available technology (Skype) has greatly increased the capacity of our team to conduct real-time education and public outreach from remote locations. The improved communication afforded by Web 2.0 has increased the quality of EPO provided by the PLRP, and has enabled a higher level of interaction between the science team and the community at large. Feedback from these online interactions suggest that remote communication via Web 2.0 technologies were effective tools for increasing public discourse and awareness of the science and exploration activity at Pavilion Lake.

ASSISTments Dataset from Multiple Randomized Controlled Experiments

ERIC Educational Resources Information Center

Selent, Douglas; Patikorn, Thanaporn; Heffernan, Neil

2016-01-01

In this paper, we present a dataset consisting of data generated from 22 previously and currently running randomized controlled experiments inside the ASSISTments online learning platform. This dataset provides data mining opportunities for researchers to analyze ASSISTments data in a convenient format across multiple experiments at the same time.…

Distinguishing Schemes and Tasks in Children's Development of Multiplicative Reasoning

ERIC Educational Resources Information Center

Tzur, Ron; Johnson, Heather L.; McClintock, Evan; Kenney, Rachael H.; Xin, Yan P.; Si, Luo; Woordward, Jerry; Hord, Casey; Jin, Xianyan

2013-01-01

We present a synthesis of findings from constructivist teaching experiments regarding six schemes children construct for reasoning multiplicatively and tasks to promote them. We provide a task-generating platform game, depictions of each scheme, and supporting tasks. Tasks must be distinguished from children's thinking, and learning situations…

Considering IIOT and security for the DoD

NASA Astrophysics Data System (ADS)

Klawon, Kevin; Gold, Josh; Bachman, Kristen; Landoll, Darren

2016-05-01

The Internet of Things (IoT) has come of age and domestic and industrial devices are all "smart". But how can they be universally classified and queried? How do we know that the underlying architecture is secure enough to deploy on a defense network? By leverage existing platforms designed for interoperability, extensibility, and security that can manage data across multiple domains and runs on any platform.

Army Communicator. Volume 36, Number 2, Summer 2011

DTIC Science & Technology

2011-06-01

Portal was utilized to provide an integrated platform for visualization of operational data derived from the CIDNE SIGACT database. Content staging...information across multiple platforms and services. Preliminary efforts during my tour were underway with SIGACT web services that allow data ...all content and data in a CM system, and the CM system itself, is fully protected against accidental deletion or corruption. Conclusion As we

Lab-on-a-Chip Proteomic Assays for Psychiatric Disorders.

PubMed

Peter, Harald; Wienke, Julia; Guest, Paul C; Bistolas, Nikitas; Bier, Frank F

2017-01-01

Lab-on-a-chip assays allow rapid identification of multiple parameters on an automated user-friendly platform. Here we describe a fully automated multiplex immunoassay and readout in less than 15 min using the Fraunhofer in vitro diagnostics (ivD) platform to enable inexpensive point-of-care profiling of sera or a single drop of blood from patients with various diseases such as psychiatric disorders.

Optimizing the Army’s Aerial Reconnaissance and Surveillance Asset Mix via the Joint Platform Allocation Tool (JPAT)

DTIC Science & Technology

2013-08-01

OF FIGURES Figure 1. Three example systems composed of platforms P1, P2, and P3, and sensors SN1, SN2 , SN3, and SN4...sensors SN1, SN2 , SN3, and SN4. 4 Figure 2. An example configuration consisting of equipment derived from multiple systems. At times, it may be

WOGEN. Work Order Generation Macros for Word Perfect 6.X for Windows

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

Grenz, G.

Included are three general WP macros (two independent and one multiple) and a template used at the Test Reactor Area (TRA) for the generation of the Work Orders (WO`s) used to perform corrective and preventative maintenance, as well as modifications of existing systems and installation of new systems. They incorporate facility specific requirements as well as selected federal/state orders. These macros are used to generate a WP document which is then converted into ASCII text for import to the maintenance software. Currently we are using MCRS but should be compatible with other platforms such as Passport. Reference the included filemore » Wogen.txt for installation and usage instructions.« less

Work Order Generation Macros for Word Perfect 6.X for Windows

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

Grenz, Gordon G.

Included are three general WP macros (two independent and one multiple) and a template used at the Test Reactor Area (TRA) for the generation of the Work Orders (WO's) used to perform corrective and preventative maintenance, as well as modifications of existing systems and installation of new systems. They incorporate facility specific requirements as well as selected federal/state orders. These macros are used to generate a WP document which is then converted into ASCII text for import to the maintenance software. Currently we are using MCRS but should be compatible with other platforms such as Passport. Reference the included filemore » Wogen.txt for installation and usage instructions.« less

Transactive Systems Simulation and Valuation Platform Trial Analysis

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

Widergren, Steven E.; Hammerstrom, Donald J.; Huang, Qiuhua

Transactive energy systems use principles of value to coordinate responsive supply and demand in energy systems. Work continues within the Transactive Systems Program, which is funded by the U.S. Department of Energy at Pacific Northwest National Laboratory, to understand the value of, understand the theory behind, and simulate the behaviors of transactive energy systems. This report summarizes recent advances made by this program. The main capability advances include a more comprehensive valuation model, including recommended documentation that should make valuation studies of all sorts more transparent, definition of economic metrics with which transactive mechanisms can be evaluated, and multiple improvementsmore » to the time-simulation environment that is being used to evaluate transactive scenarios.« less

Virtual Systems Pharmacology (ViSP) software for simulation from mechanistic systems-level models.

PubMed

Ermakov, Sergey; Forster, Peter; Pagidala, Jyotsna; Miladinov, Marko; Wang, Albert; Baillie, Rebecca; Bartlett, Derek; Reed, Mike; Leil, Tarek A

2014-01-01

Multiple software programs are available for designing and running large scale system-level pharmacology models used in the drug development process. Depending on the problem, scientists may be forced to use several modeling tools that could increase model development time, IT costs and so on. Therefore, it is desirable to have a single platform that allows setting up and running large-scale simulations for the models that have been developed with different modeling tools. We developed a workflow and a software platform in which a model file is compiled into a self-contained executable that is no longer dependent on the software that was used to create the model. At the same time the full model specifics is preserved by presenting all model parameters as input parameters for the executable. This platform was implemented as a model agnostic, therapeutic area agnostic and web-based application with a database back-end that can be used to configure, manage and execute large-scale simulations for multiple models by multiple users. The user interface is designed to be easily configurable to reflect the specifics of the model and the user's particular needs and the back-end database has been implemented to store and manage all aspects of the systems, such as Models, Virtual Patients, User Interface Settings, and Results. The platform can be adapted and deployed on an existing cluster or cloud computing environment. Its use was demonstrated with a metabolic disease systems pharmacology model that simulates the effects of two antidiabetic drugs, metformin and fasiglifam, in type 2 diabetes mellitus patients.

Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics.

PubMed

Inci, Fatih; Filippini, Chiara; Baday, Murat; Ozen, Mehmet Ozgun; Calamak, Semih; Durmus, Naside Gozde; Wang, ShuQi; Hanhauser, Emily; Hobbs, Kristen S; Juillard, Franceline; Kuang, Ping Ping; Vetter, Michael L; Carocci, Margot; Yamamoto, Hidemi S; Takagi, Yuko; Yildiz, Umit Hakan; Akin, Demir; Wesemann, Duane R; Singhal, Amit; Yang, Priscilla L; Nibert, Max L; Fichorova, Raina N; Lau, Daryl T-Y; Henrich, Timothy J; Kaye, Kenneth M; Schachter, Steven C; Kuritzkes, Daniel R; Steinmetz, Lars M; Gambhir, Sanjiv S; Davis, Ronald W; Demirci, Utkan

2015-08-11

Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. In practice, these barriers prevent broad applications in clinics and at patients' homes. Here, we demonstrate the nanoplasmonic electrical field-enhanced resonating device (NE(2)RD), which addresses all these impediments on a single platform. The NE(2)RD employs an immunodetection assay to capture biotargets, and precisely measures spectral color changes by their wavelength and extinction intensity shifts in nanoparticles without prior sample labeling or preprocessing. We present through multiple examples, a label-free, quantitative, portable, multitarget platform by rapidly detecting various protein biomarkers, drugs, protein allergens, bacteria, eukaryotic cells, and distinct viruses. The linear dynamic range of NE(2)RD is five orders of magnitude broader than ELISA, with a sensitivity down to 400 fg/mL This range and sensitivity are achieved by self-assembling gold nanoparticles to generate hot spots on a 3D-oriented substrate for ultrasensitive measurements. We demonstrate that this precise platform handles multiple clinical samples such as whole blood, serum, and saliva without sample preprocessing under diverse conditions of temperature, pH, and ionic strength. The NE(2)RD's broad dynamic range, detection limit, and portability integrated with a disposable fluidic chip have broad applications, potentially enabling the transition toward precision medicine at the point-of-care or primary care settings and at patients' homes.

Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics

PubMed Central

Inci, Fatih; Filippini, Chiara; Ozen, Mehmet Ozgun; Calamak, Semih; Durmus, Naside Gozde; Wang, ShuQi; Hanhauser, Emily; Hobbs, Kristen S.; Juillard, Franceline; Kuang, Ping Ping; Vetter, Michael L.; Carocci, Margot; Yamamoto, Hidemi S.; Takagi, Yuko; Yildiz, Umit Hakan; Akin, Demir; Wesemann, Duane R.; Singhal, Amit; Yang, Priscilla L.; Nibert, Max L.; Fichorova, Raina N.; Lau, Daryl T.-Y.; Henrich, Timothy J.; Kaye, Kenneth M.; Schachter, Steven C.; Kuritzkes, Daniel R.; Steinmetz, Lars M.; Gambhir, Sanjiv S.; Davis, Ronald W.; Demirci, Utkan

2015-01-01

Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. In practice, these barriers prevent broad applications in clinics and at patients’ homes. Here, we demonstrate the nanoplasmonic electrical field-enhanced resonating device (NE2RD), which addresses all these impediments on a single platform. The NE2RD employs an immunodetection assay to capture biotargets, and precisely measures spectral color changes by their wavelength and extinction intensity shifts in nanoparticles without prior sample labeling or preprocessing. We present through multiple examples, a label-free, quantitative, portable, multitarget platform by rapidly detecting various protein biomarkers, drugs, protein allergens, bacteria, eukaryotic cells, and distinct viruses. The linear dynamic range of NE2RD is five orders of magnitude broader than ELISA, with a sensitivity down to 400 fg/mL This range and sensitivity are achieved by self-assembling gold nanoparticles to generate hot spots on a 3D-oriented substrate for ultrasensitive measurements. We demonstrate that this precise platform handles multiple clinical samples such as whole blood, serum, and saliva without sample preprocessing under diverse conditions of temperature, pH, and ionic strength. The NE2RD’s broad dynamic range, detection limit, and portability integrated with a disposable fluidic chip have broad applications, potentially enabling the transition toward precision medicine at the point-of-care or primary care settings and at patients’ homes. PMID:26195743

Virtual Systems Pharmacology (ViSP) software for simulation from mechanistic systems-level models

PubMed Central

Ermakov, Sergey; Forster, Peter; Pagidala, Jyotsna; Miladinov, Marko; Wang, Albert; Baillie, Rebecca; Bartlett, Derek; Reed, Mike; Leil, Tarek A.

2014-01-01

Multiple software programs are available for designing and running large scale system-level pharmacology models used in the drug development process. Depending on the problem, scientists may be forced to use several modeling tools that could increase model development time, IT costs and so on. Therefore, it is desirable to have a single platform that allows setting up and running large-scale simulations for the models that have been developed with different modeling tools. We developed a workflow and a software platform in which a model file is compiled into a self-contained executable that is no longer dependent on the software that was used to create the model. At the same time the full model specifics is preserved by presenting all model parameters as input parameters for the executable. This platform was implemented as a model agnostic, therapeutic area agnostic and web-based application with a database back-end that can be used to configure, manage and execute large-scale simulations for multiple models by multiple users. The user interface is designed to be easily configurable to reflect the specifics of the model and the user's particular needs and the back-end database has been implemented to store and manage all aspects of the systems, such as Models, Virtual Patients, User Interface Settings, and Results. The platform can be adapted and deployed on an existing cluster or cloud computing environment. Its use was demonstrated with a metabolic disease systems pharmacology model that simulates the effects of two antidiabetic drugs, metformin and fasiglifam, in type 2 diabetes mellitus patients. PMID:25374542

Development of automated high throughput single molecular microfluidic detection platform for signal transduction analysis

NASA Astrophysics Data System (ADS)

Huang, Po-Jung; Baghbani Kordmahale, Sina; Chou, Chao-Kai; Yamaguchi, Hirohito; Hung, Mien-Chie; Kameoka, Jun

2016-03-01

Signal transductions including multiple protein post-translational modifications (PTM), protein-protein interactions (PPI), and protein-nucleic acid interaction (PNI) play critical roles for cell proliferation and differentiation that are directly related to the cancer biology. Traditional methods, like mass spectrometry, immunoprecipitation, fluorescence resonance energy transfer, and fluorescence correlation spectroscopy require a large amount of sample and long processing time. "microchannel for multiple-parameter analysis of proteins in single-complex (mMAPS)"we proposed can reduce the process time and sample volume because this system is composed by microfluidic channels, fluorescence microscopy, and computerized data analysis. In this paper, we will present an automated mMAPS including integrated microfluidic device, automated stage and electrical relay for high-throughput clinical screening. Based on this result, we estimated that this automated detection system will be able to screen approximately 150 patient samples in a 24-hour period, providing a practical application to analyze tissue samples in a clinical setting.

NASA Operation IceBridge Flies Into the Classroom!

NASA Astrophysics Data System (ADS)

Kane, M.

2017-12-01

Field research opportunities for educators is leveraged as an invaluable tool to increase public engagement in climate research and the geosciences. We investigate the influence of educator's authentic fieldwork by highlighting the post-field impacts of a PolarTREC Teacher who participated in two campaigns, including NASA Operation IceBridge campaign over Antarctica in 2016. NASA's Operation IceBridge has hosted PolarTREC teachers since 2012, welcoming five teachers aboard multiple flights over the Arctic and one over Antarctica. The continuity of teacher inclusion in Operation IceBridge campaigns has facilitated a platform for collaborative curriculum development and revision, integration of National Snow and Ice Data Center (NSIDC) data into multiple classrooms, and given us a means whereby students can interact with science team members. I present impacts to my teaching and classrooms as I grapple with "Big Data" to allow students to work directly with lidar and radar data, I examine public outreach impacts through analytics from virtual networking tools including social media, NASA's Mission Tools Suite for Education, and field blog interactions.

A Paper-Based Device for Performing Loop-Mediated Isothermal Amplification with Real-Time Simultaneous Detection of Multiple DNA Targets.

PubMed

Seok, Youngung; Joung, Hyou-Arm; Byun, Ju-Young; Jeon, Hyo-Sung; Shin, Su Jeong; Kim, Sanghyo; Shin, Young-Beom; Han, Hyung Soo; Kim, Min-Gon

2017-01-01

Paper-based diagnostic devices have many advantages as a one of the multiple diagnostic test platforms for point-of-care (POC) testing because they have simplicity, portability, and cost-effectiveness. However, despite high sensitivity and specificity of nucleic acid testing (NAT), the development of NAT based on a paper platform has not progressed as much as the others because various specific conditions for nucleic acid amplification reactions such as pH, buffer components, and temperature, inhibitions from technical differences of paper-based device. Here, we propose a paper-based device for performing loop-mediated isothermal amplification (LAMP) with real-time simultaneous detection of multiple DNA targets. We determined the optimal chemical components to enable dry conditions for the LAMP reaction without lyophilization or other techniques. We also devised the simple paper device structure by sequentially stacking functional layers, and employed a newly discovered property of hydroxynaphthol blue fluorescence to analyze real-time LAMP signals in the paper device. This proposed platform allowed analysis of three different meningitis DNA samples in a single device with single-step operation. This LAMP-based multiple diagnostic device has potential for real-time analysis with quantitative detection of 10 2 -10 5 copies of genomic DNA. Furthermore, we propose the transformation of DNA amplification devices to a simple and affordable paper system approach with great potential for realizing a paper-based NAT system for POC testing.

A Paper-Based Device for Performing Loop-Mediated Isothermal Amplification with Real-Time Simultaneous Detection of Multiple DNA Targets

PubMed Central

Seok, Youngung; Joung, Hyou-Arm; Byun, Ju-Young; Jeon, Hyo-Sung; Shin, Su Jeong; Kim, Sanghyo; Shin, Young-Beom; Han, Hyung Soo; Kim, Min-Gon

2017-01-01

Paper-based diagnostic devices have many advantages as a one of the multiple diagnostic test platforms for point-of-care (POC) testing because they have simplicity, portability, and cost-effectiveness. However, despite high sensitivity and specificity of nucleic acid testing (NAT), the development of NAT based on a paper platform has not progressed as much as the others because various specific conditions for nucleic acid amplification reactions such as pH, buffer components, and temperature, inhibitions from technical differences of paper-based device. Here, we propose a paper-based device for performing loop-mediated isothermal amplification (LAMP) with real-time simultaneous detection of multiple DNA targets. We determined the optimal chemical components to enable dry conditions for the LAMP reaction without lyophilization or other techniques. We also devised the simple paper device structure by sequentially stacking functional layers, and employed a newly discovered property of hydroxynaphthol blue fluorescence to analyze real-time LAMP signals in the paper device. This proposed platform allowed analysis of three different meningitis DNA samples in a single device with single-step operation. This LAMP-based multiple diagnostic device has potential for real-time analysis with quantitative detection of 102-105 copies of genomic DNA. Furthermore, we propose the transformation of DNA amplification devices to a simple and affordable paper system approach with great potential for realizing a paper-based NAT system for POC testing. PMID:28740546

Fully Distributed Monitoring Architecture Supporting Multiple Trackees and Trackers in Indoor Mobile Asset Management Application

PubMed Central

Jeong, Seol Young; Jo, Hyeong Gon; Kang, Soon Ju

2014-01-01

A tracking service like asset management is essential in a dynamic hospital environment consisting of numerous mobile assets (e.g., wheelchairs or infusion pumps) that are continuously relocated throughout a hospital. The tracking service is accomplished based on the key technologies of an indoor location-based service (LBS), such as locating and monitoring multiple mobile targets inside a building in real time. An indoor LBS such as a tracking service entails numerous resource lookups being requested concurrently and frequently from several locations, as well as a network infrastructure requiring support for high scalability in indoor environments. A traditional centralized architecture needs to maintain a geographic map of the entire building or complex in its central server, which can cause low scalability and traffic congestion. This paper presents a self-organizing and fully distributed indoor mobile asset management (MAM) platform, and proposes an architecture for multiple trackees (such as mobile assets) and trackers based on the proposed distributed platform in real time. In order to verify the suggested platform, scalability performance according to increases in the number of concurrent lookups was evaluated in a real test bed. Tracking latency and traffic load ratio in the proposed tracking architecture was also evaluated. PMID:24662407

Parallel Agent-Based Simulations on Clusters of GPUs and Multi-Core Processors

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

Aaby, Brandon G; Perumalla, Kalyan S; Seal, Sudip K

2010-01-01

An effective latency-hiding mechanism is presented in the parallelization of agent-based model simulations (ABMS) with millions of agents. The mechanism is designed to accommodate the hierarchical organization as well as heterogeneity of current state-of-the-art parallel computing platforms. We use it to explore the computation vs. communication trade-off continuum available with the deep computational and memory hierarchies of extant platforms and present a novel analytical model of the tradeoff. We describe our implementation and report preliminary performance results on two distinct parallel platforms suitable for ABMS: CUDA threads on multiple, networked graphical processing units (GPUs), and pthreads on multi-core processors. Messagemore » Passing Interface (MPI) is used for inter-GPU as well as inter-socket communication on a cluster of multiple GPUs and multi-core processors. Results indicate the benefits of our latency-hiding scheme, delivering as much as over 100-fold improvement in runtime for certain benchmark ABMS application scenarios with several million agents. This speed improvement is obtained on our system that is already two to three orders of magnitude faster on one GPU than an equivalent CPU-based execution in a popular simulator in Java. Thus, the overall execution of our current work is over four orders of magnitude faster when executed on multiple GPUs.« less

Factors affecting the abundance of selected fishes near oil and gas platforms in the northern Gulf of Mexico

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

Stanley, D.R.; Wilson, C.A.

1991-01-01

A logbook program was initiated to determine the relative abundance of selected fish species around oil and gas platforms off the Louisiana coast. Logbooks were maintained by 55 anglers and 10 charterboat operators from March 1987 to March 1988. A total of 36,839 fish were caught representing over 46 different species. Principal component analysis (PCA) grouped the seventeen most abundant species into reef fish, pelagic fish, bluefish-red drum, Atlantic croaker-silver/sand seatrout, and cobia-shark-blue runner associations. Multiple regression analyses were used to compare PCA groupings to physical platform, temporal, geological, and angler characteristic variables and their interactions. Reef fish, Atlantic croaker,more » and silver/sand seatrout abundances were highest near large, structurally complex platforms in relatively deep water. High spotted seatrout abundances were correlated with small, unmanned oil and gas platforms in shallow water. Pelagic fish, bluefish, red drum, cobia, and shark abundances were not related to the physical parameters of the platforms.« less

Differential white cell count by centrifugal microfluidics.

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

Sommer, Gregory Jon; Tentori, Augusto M.; Schaff, Ulrich Y.

We present a method for counting white blood cells that is uniquely compatible with centrifugation based microfluidics. Blood is deposited on top of one or more layers of density media within a microfluidic disk. Spinning the disk causes the cell populations within whole blood to settle through the media, reaching an equilibrium based on the density of each cell type. Separation and fluorescence measurement of cell types stained with a DNA dye is demonstrated using this technique. The integrated signal from bands of fluorescent microspheres is shown to be proportional to their initial concentration in suspension. Among the current generationmore » of medical diagnostics are devices based on the principle of centrifuging a CD sized disk functionalized with microfluidics. These portable 'lab on a disk' devices are capable of conducting multiple assays directly from a blood sample, embodied by platforms developed by Gyros, Samsung, and Abaxis. [1,2] However, no centrifugal platform to date includes a differential white blood cell count, which is an important metric complimentary to diagnostic assays. Measuring the differential white blood cell count (the relative fraction of granulocytes, lymphocytes, and monocytes) is a standard medical diagnostic technique useful for identifying sepsis, leukemia, AIDS, radiation exposure, and a host of other conditions that affect the immune system. Several methods exist for measuring the relative white blood cell count including flow cytometry, electrical impedance, and visual identification from a stained drop of blood under a microscope. However, none of these methods is easily incorporated into a centrifugal microfluidic diagnostic platform.« less

NextGen Technologies on the FAA's Standard Terminal Automation Replacement System

NASA Technical Reports Server (NTRS)

Witzberger, Kevin; Swenson, Harry; Martin, Lynne; Lin, Melody; Cheng, Jinn-Hwei

2014-01-01

This paper describes the integration, evaluation, and results from a high-fidelity human-in-the-loop (HITL) simulation of key NASA Air Traffic Management Technology Demonstration - 1 (ATD- 1) technologies implemented in an enhanced version of the FAA's Standard Terminal Automation Replacement System (STARS) platform. These ATD-1 technologies include: (1) a NASA enhanced version of the FAA's Time-Based Flow Management, (2) a NASA ground-based automation technology known as controller-managed spacing (CMS), and (3) a NASA advanced avionics airborne technology known as flight-deck interval management (FIM). These ATD-1 technologies have been extensively tested in large-scale HITL simulations using general-purpose workstations to study air transportation technologies. These general purpose workstations perform multiple functions and are collectively referred to as the Multi-Aircraft Control System (MACS). Researchers at NASA Ames Research Center and Raytheon collaborated to augment the STARS platform by including CMS and FIM advisory tools to validate the feasibility of integrating these automation enhancements into the current FAA automation infrastructure. NASA Ames acquired three STARS terminal controller workstations, and then integrated the ATD-1 technologies. HITL simulations were conducted to evaluate the ATD-1 technologies when using the STARS platform. These results were compared with the results obtained when the ATD-1 technologies were tested in the MACS environment. Results collected from the numerical data show acceptably minor differences, and, together with the subjective controller questionnaires showing a trend towards preferring STARS, validate the ATD-1/STARS integration.

High-Resolution Inflorescence Phenotyping Using a Novel Image-Analysis Pipeline, PANorama1[W][OPEN

PubMed Central

Crowell, Samuel; Falcão, Alexandre X.; Shah, Ankur; Wilson, Zachary; Greenberg, Anthony J.; McCouch, Susan R.

2014-01-01

Variation in inflorescence development is an important target of selection for numerous crop species, including many members of the Poaceae (grasses). In Asian rice (Oryza sativa), inflorescence (panicle) architecture is correlated with yield and grain-quality traits. However, many rice breeders continue to use composite phenotypes in selection pipelines, because measuring complex, branched panicles requires a significant investment of resources. We developed an open-source phenotyping platform, PANorama, which measures multiple architectural and branching phenotypes from images simultaneously. PANorama automatically extracts skeletons from images, allows users to subdivide axes into individual internodes, and thresholds away structures, such as awns, that normally interfere with accurate panicle phenotyping. PANorama represents an improvement in both efficiency and accuracy over existing panicle imaging platforms, and flexible implementation makes PANorama capable of measuring a range of organs from other plant species. Using high-resolution phenotypes, a mapping population of recombinant inbred lines, and a dense single-nucleotide polymorphism data set, we identify, to our knowledge, the largest number of quantitative trait loci (QTLs) for panicle traits ever reported in a single study. Several areas of the genome show pleiotropic clusters of panicle QTLs, including a region near the rice Green Revolution gene SEMIDWARF1. We also confirm that multiple panicle phenotypes are distinctly different among a small collection of diverse rice varieties. Taken together, these results suggest that clusters of small-effect QTLs may be responsible for varietal or subpopulation-specific panicle traits, representing a significant opportunity for rice breeders selecting for yield performance across different genetic backgrounds. PMID:24696519

The Changing Role of Data Stewardship in Creating Trustworthy, Interdisciplinary High Performance Data Platforms for the Future.

NASA Astrophysics Data System (ADS)

Richards, C. J.; Evans, B. J. K.; Wyborn, L. A.; Wang, J.; Trenham, C. E.; Druken, K. A.

2016-12-01

The Australian National Computational Infrastructure (NCI) has ingested over 10PB of national and international environmental, Earth systems science and geophysics reference data onto a single platform to advance high performance data (HPD) techniques that enable interdisciplinary Data-intensive Science. Improved Data Stewardship is critical to evolve both data and data services that support the increasing need for programmatic usability and that prioritises interoperability rather than just traditional data download or portal access. A data platform designed for programmatic access requires quality checked collections that better utilise interoperable data formats and standards. Achieving this involves strategies to meet both the technical and `social' challenges. Aggregating datasets used by different communities and organisations requires satisfying multiple use cases for the broader research community, whilst addressing existing BAU requirements. For NCI, this requires working with data stewards to manage the process of replicating data to the common platform, community representatives and developers to confirm their requirements, and with international peers to better enable globally integrated data communities. It is particularly important to engage with representatives from each community who can work collaboratively to a common goal, as well as capture their community needs, apply quality assurance, determine any barriers to change and to understand priorities. This is critical when managing the aggregation of data collections from multiple producers with different levels of stewardship maturity, technologies and standards, and where organisational barriers can impact the transformation to interoperable and performant data access. To facilitate the management, development and operation of the HPD platform, NCI coordinates technical and domain committees made up of user representatives, data stewards and informatics experts to provide a forum to discuss, learn and advise NCI's management. This experience has been a useful collaboration and suggests that in the age of interdisciplinary HPD research, Data Stewardship is evolving from a focus on the needs of a single community to one which helps balance priorities and navigates change for multiple communities.

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.

Parallel and Preemptable Dynamically Dimensioned Search Algorithms for Single and Multi-objective Optimization in Water Resources

NASA Astrophysics Data System (ADS)

Tolson, B.; Matott, L. S.; Gaffoor, T. A.; Asadzadeh, M.; Shafii, M.; Pomorski, P.; Xu, X.; Jahanpour, M.; Razavi, S.; Haghnegahdar, A.; Craig, J. R.

2015-12-01

We introduce asynchronous parallel implementations of the Dynamically Dimensioned Search (DDS) family of algorithms including DDS, discrete DDS, PA-DDS and DDS-AU. These parallel algorithms are unique from most existing parallel optimization algorithms in the water resources field in that parallel DDS is asynchronous and does not require an entire population (set of candidate solutions) to be evaluated before generating and then sending a new candidate solution for evaluation. One key advance in this study is developing the first parallel PA-DDS multi-objective optimization algorithm. The other key advance is enhancing the computational efficiency of solving optimization problems (such as model calibration) by combining a parallel optimization algorithm with the deterministic model pre-emption concept. These two efficiency techniques can only be combined because of the asynchronous nature of parallel DDS. Model pre-emption functions to terminate simulation model runs early, prior to completely simulating the model calibration period for example, when intermediate results indicate the candidate solution is so poor that it will definitely have no influence on the generation of further candidate solutions. The computational savings of deterministic model preemption available in serial implementations of population-based algorithms (e.g., PSO) disappear in synchronous parallel implementations as these algorithms. In addition to the key advances above, we implement the algorithms across a range of computation platforms (Windows and Unix-based operating systems from multi-core desktops to a supercomputer system) and package these for future modellers within a model-independent calibration software package called Ostrich as well as MATLAB versions. Results across multiple platforms and multiple case studies (from 4 to 64 processors) demonstrate the vast improvement over serial DDS-based algorithms and highlight the important role model pre-emption plays in the performance of parallel, pre-emptable DDS algorithms. Case studies include single- and multiple-objective optimization problems in water resources model calibration and in many cases linear or near linear speedups are observed.

Soft Somatosensitive Actuators via Embedded 3D Printing.

PubMed

Truby, Ryan L; Wehner, Michael; Grosskopf, Abigail K; Vogt, Daniel M; Uzel, Sebastien G M; Wood, Robert J; Lewis, Jennifer A

2018-04-01

Humans possess manual dexterity, motor skills, and other physical abilities that rely on feedback provided by the somatosensory system. Herein, a method is reported for creating soft somatosensitive actuators (SSAs) via embedded 3D printing, which are innervated with multiple conductive features that simultaneously enable haptic, proprioceptive, and thermoceptive sensing. This novel manufacturing approach enables the seamless integration of multiple ionically conductive and fluidic features within elastomeric matrices to produce SSAs with the desired bioinspired sensing and actuation capabilities. Each printed sensor is composed of an ionically conductive gel that exhibits both long-term stability and hysteresis-free performance. As an exemplar, multiple SSAs are combined into a soft robotic gripper that provides proprioceptive and haptic feedback via embedded curvature, inflation, and contact sensors, including deep and fine touch contact sensors. The multimaterial manufacturing platform enables complex sensing motifs to be easily integrated into soft actuating systems, which is a necessary step toward closed-loop feedback control of soft robots, machines, and haptic devices. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A visualization tool to support decision making in environmental and biological planning

USGS Publications Warehouse

Romañach, Stephanie S.; McKelvy, James M.; Conzelmann, Craig; Suir, Kevin J.

2014-01-01

Large-scale ecosystem management involves consideration of many factors for informed decision making. The EverVIEW Data Viewer is a cross-platform desktop decision support tool to help decision makers compare simulation model outputs from competing plans for restoring Florida's Greater Everglades. The integration of NetCDF metadata conventions into EverVIEW allows end-users from multiple institutions within and beyond the Everglades restoration community to share information and tools. Our development process incorporates continuous interaction with targeted end-users for increased likelihood of adoption. One of EverVIEW's signature features is side-by-side map panels, which can be used to simultaneously compare species or habitat impacts from alternative restoration plans. Other features include examination of potential restoration plan impacts across multiple geographic or tabular displays, and animation through time. As a result of an iterative, standards-driven approach, EverVIEW is relevant to large-scale planning beyond Florida, and is used in multiple biological planning efforts in the United States.

KeyWare: an open wireless distributed computing environment

NASA Astrophysics Data System (ADS)

Shpantzer, Isaac; Schoenfeld, Larry; Grindahl, Merv; Kelman, Vladimir

1995-12-01

Deployment of distributed applications in the wireless domain lack equivalent tools, methodologies, architectures, and network management that exist in LAN based applications. A wireless distributed computing environment (KeyWareTM) based on intelligent agents within a multiple client multiple server scheme was developed to resolve this problem. KeyWare renders concurrent application services to wireline and wireless client nodes encapsulated in multiple paradigms such as message delivery, database access, e-mail, and file transfer. These services and paradigms are optimized to cope with temporal and spatial radio coverage, high latency, limited throughput and transmission costs. A unified network management paradigm for both wireless and wireline facilitates seamless extensions of LAN- based management tools to include wireless nodes. A set of object oriented tools and methodologies enables direct asynchronous invocation of agent-based services supplemented by tool-sets matched to supported KeyWare paradigms. The open architecture embodiment of KeyWare enables a wide selection of client node computing platforms, operating systems, transport protocols, radio modems and infrastructures while maintaining application portability.

The role of sustained observations in tracking impacts of environmental change on marine biodiversity and ecosystems

PubMed Central

Mieszkowska, N.; Sugden, H.; Firth, L. B.; Hawkins, S. J.

2014-01-01

Marine biodiversity currently faces unprecedented threats from multiple pressures arising from human activities. Global drivers such as climate change and ocean acidification interact with regional eutrophication, exploitation of commercial fish stocks and localized pressures including pollution, coastal development and the extraction of aggregates and fuel, causing alteration and degradation of habitats and communities. Segregating natural from anthropogenically induced change in marine ecosystems requires long-term, sustained observations of marine biota. In this review, we outline the history of biological recording in the coastal and shelf seas of the UK and Ireland and highlight where sustained observations have contributed new understanding of how anthropogenic activities have impacted on marine biodiversity. The contributions of sustained observations, from those collected at observatories, single station platforms and multiple-site programmes to the emergent field of multiple stressor impacts research, are discussed, along with implications for management and sustainable governance of marine resources in an era of unprecedented use of the marine environment. PMID:25157190

Diversity Performance Analysis on Multiple HAP Networks.

PubMed

Dong, Feihong; Li, Min; Gong, Xiangwu; Li, Hongjun; Gao, Fengyue

2015-06-30

One of the main design challenges in wireless sensor networks (WSNs) is achieving a high-data-rate transmission for individual sensor devices. The high altitude platform (HAP) is an important communication relay platform for WSNs and next-generation wireless networks. Multiple-input multiple-output (MIMO) techniques provide the diversity and multiplexing gain, which can improve the network performance effectively. In this paper, a virtual MIMO (V-MIMO) model is proposed by networking multiple HAPs with the concept of multiple assets in view (MAV). In a shadowed Rician fading channel, the diversity performance is investigated. The probability density function (PDF) and cumulative distribution function (CDF) of the received signal-to-noise ratio (SNR) are derived. In addition, the average symbol error rate (ASER) with BPSK and QPSK is given for the V-MIMO model. The system capacity is studied for both perfect channel state information (CSI) and unknown CSI individually. The ergodic capacity with various SNR and Rician factors for different network configurations is also analyzed. The simulation results validate the effectiveness of the performance analysis. It is shown that the performance of the HAPs network in WSNs can be significantly improved by utilizing the MAV to achieve overlapping coverage, with the help of the V-MIMO techniques.

The BioExtract Server: a web-based bioinformatic workflow platform

PubMed Central

Lushbough, Carol M.; Jennewein, Douglas M.; Brendel, Volker P.

2011-01-01

The BioExtract Server (bioextract.org) is an open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. PMID:21546552

Exploring Google Earth Engine platform for big data processing: classification of multi-temporal satellite imagery for crop mapping

NASA Astrophysics Data System (ADS)

Shelestov, Andrii; Lavreniuk, Mykola; Kussul, Nataliia; Novikov, Alexei; Skakun, Sergii

2017-02-01

Many applied problems arising in agricultural monitoring and food security require reliable crop maps at national or global scale. Large scale crop mapping requires processing and management of large amount of heterogeneous satellite imagery acquired by various sensors that consequently leads to a “Big Data” problem. The main objective of this study is to explore efficiency of using the Google Earth Engine (GEE) platform when classifying multi-temporal satellite imagery with potential to apply the platform for a larger scale (e.g. country level) and multiple sensors (e.g. Landsat-8 and Sentinel-2). In particular, multiple state-of-the-art classifiers available in the GEE platform are compared to produce a high resolution (30 m) crop classification map for a large territory ( 28,100 km2 and 1.0 M ha of cropland). Though this study does not involve large volumes of data, it does address efficiency of the GEE platform to effectively execute complex workflows of satellite data processing required with large scale applications such as crop mapping. The study discusses strengths and weaknesses of classifiers, assesses accuracies that can be achieved with different classifiers for the Ukrainian landscape, and compares them to the benchmark classifier using a neural network approach that was developed in our previous studies. The study is carried out for the Joint Experiment of Crop Assessment and Monitoring (JECAM) test site in Ukraine covering the Kyiv region (North of Ukraine) in 2013. We found that Google Earth Engine (GEE) provides very good performance in terms of enabling access to the remote sensing products through the cloud platform and providing pre-processing; however, in terms of classification accuracy, the neural network based approach outperformed support vector machine (SVM), decision tree and random forest classifiers available in GEE.

Measuring What Matters

DTIC Science & Technology

2014-11-18

multiple platforms were forced to be reset and Forbes.com and its WordPress platform were taken offline several times over 2 days. Forbes has focused...does not enter h1s credentials on the subsequent login page Returning to his blog, WordPress prompts him to log in again. Almost immediately...again compromise the WordPress super-administrator account and deface six Forbes blog pages with the phrase "Hacked By The Syrian Electronic Army

KSC-08pd1244

NASA Image and Video Library

2008-05-02

CAPE CANAVERAL, Fla. -- Artist's rendering of the empty Constellation Program's mobile launcher platform planned for the Ares I rocket. 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.

KSC-08pd1245

NASA Image and Video Library

2008-05-02

CAPE CANAVERAL, Fla. -- Artist's rendering of the Constellation Program's mobile launcher platform with an Ares I rocket attached. 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.

Multicore Architectures for Multiple Independent Levels of Security Applications

DTIC Science & Technology

2012-09-01

to bolster the MILS effort. However, current MILS operating systems are not designed for multi-core platforms. They do not have the hardware support...current MILS operating systems are not designed for multi‐core platforms. They do not have the hardware support to ensure that the separation...the availability of information at different security classification levels while increasing the overall security of the computing system . Due to the

The Science of a Sundae: Using the Principle of Colligative Properties in Food Science Outreach Activities for Middle and High School Students

ERIC Educational Resources Information Center

Wickware, Carmen L.; Day, Charles T.C.; Adams, Michael; Orta-Ramirez, Alicia; Snyder, Abigail B.

2017-01-01

The opportunities for outreach activities for professionals and academics in food science are extensive, as too are the range of participants' experience levels and platforms for delivery. Here, we present a set of activities that are readily adaptable for a range of students (ages 10 to 18) in multiple platforms (demonstration table and hands-on…

We-Measure: Toward a low-cost portable posturography for patients with multiple sclerosis using the commercial Wii balance board.

PubMed

Castelli, Letizia; Stocchi, Luca; Patrignani, Maurizio; Sellitto, Giovanni; Giuliani, Manuela; Prosperini, Luca

2015-12-15

This study was aimed at investigating whether postural sway measures derived from a standard force platform were similar to those generated by a custom-written software ("We-Measure") acquiring and processing data from a commercial Nintendo balance board (BB). For this purpose, 90 patients with multiple sclerosis (MS) and 50 healthy controls (HC) were tested in a single-day session with a reference standard force platform and a BB-based system. Despite its acceptable between-device agreement (tested by visual evaluation of Bland-Altman plot), the low-cost BB-based system tended to overestimate postural sway when compared to the reference standard force platform in both MS and HC groups (on average +30% and +54%, respectively). Between-device reliability was just adequate (MS: 66%, HC: 47%), while test-retest reliability was excellent (MS: 84%, HC: 88%). Concurrent validity evaluation showed similar performance between the reference standard force platform and the BB-based system in discriminating fallers and non-fallers among patients with MS. All these findings may encourage the use of this balance board-based new device in longitudinal study, rather than in cross-sectional design, thus providing a potential useful tool for multicenter settings. Copyright © 2015 Elsevier B.V. All rights reserved.

B-CAN: a resource sharing platform to improve the operation, visualization and integrated analysis of TCGA breast cancer data.

PubMed

Wen, Can-Hong; Ou, Shao-Min; Guo, Xiao-Bo; Liu, Chen-Feng; Shen, Yan-Bo; You, Na; Cai, Wei-Hong; Shen, Wen-Jun; Wang, Xue-Qin; Tan, Hai-Zhu

2017-12-12

Breast cancer is a high-risk heterogeneous disease with myriad subtypes and complicated biological features. The Cancer Genome Atlas (TCGA) breast cancer database provides researchers with the large-scale genome and clinical data via web portals and FTP services. Researchers are able to gain new insights into their related fields, and evaluate experimental discoveries with TCGA. However, it is difficult for researchers who have little experience with database and bioinformatics to access and operate on because of TCGA's complex data format and diverse files. For ease of use, we build the breast cancer (B-CAN) platform, which enables data customization, data visualization, and private data center. The B-CAN platform runs on Apache server and interacts with the backstage of MySQL database by PHP. Users can customize data based on their needs by combining tables from original TCGA database and selecting variables from each table. The private data center is applicable for private data and two types of customized data. A key feature of the B-CAN is that it provides single table display and multiple table display. Customized data with one barcode corresponding to many records and processed customized data are allowed in Multiple Tables Display. The B-CAN is an intuitive and high-efficient data-sharing platform.

Blade platform seal for ceramic/metal rotor assembly

DOEpatents

Wertz, John L.

1982-01-01

A combination ceramic and metal turbine rotor for use in high temperature gas turbine engines includes a metal rotor disc having a rim with a plurality of circumferentially spaced blade root retention slots therein to receive a plurality of ceramic blades, each including side platform segments thereon and a dovetail configured root slidably received in one of the slots. Adjacent ones of the platform segments including edge portions thereon closely spaced when the blades are assembled to form expansion gaps in an annular flow surface for gas passage through the blades and wherein the assembly further includes a plurality of unitary seal members on the rotor connected to its rim and each including a plurality of spaced, axially extending, flexible fingers that underlie and conform to the edge portions of the platform segments and which are operative at turbine operating temperatures and speeds to distribute loading on the platform segments as the fingers are seated against the underside of the blade platforms to seal the gaps without undesirably stressing thin web ceramic sections of the platform.

Predicting Droplet Formation on Centrifugal Microfluidic Platforms

NASA Astrophysics Data System (ADS)

Moebius, Jacob Alfred

Centrifugal microfluidics is a widely known research tool for biological sample and water quality analysis. Currently, the standard equipment used for such diagnostic applications include slow, bulky machines controlled by multiple operators. These machines can be condensed into a smaller, faster benchtop sample-to-answer system. Sample processing is an important step taken to extract, isolate, and convert biological factors, such as nucleic acids or proteins, from a raw sample to an analyzable solution. Volume definition is one such step. The focus of this thesis is the development of a model predicting monodispersed droplet formation and the application of droplets as a technique for volume definition. First, a background of droplet microfluidic platforms is presented, along with current biological analysis technologies and the advantages of integrating such technologies onto microfluidic platforms. Second, background and theories of centrifugal microfluidics is given, followed by theories relevant to droplet emulsions. Third, fabrication techniques for centrifugal microfluidic designs are discussed. Finally, the development of a model for predicting droplet formation on the centrifugal microfluidic platform are presented for the rest of the thesis. Predicting droplet formation analytically based on the volumetric flow rates of the continuous and dispersed phases, the ratios of these two flow rates, and the interfacial tension between the continuous and dispersed phases presented many challenges, which will be discussed in this work. Experimental validation was completed using continuous phase solutions of different interfacial tensions. To conclude, prospective applications are discussed with expected challenges.

Development of Real Time PCR Using Novel Genomic Target for Detection of Multiple Salmonella Serovars from Milk and Chickens

USDA-ARS?s Scientific Manuscript database

Background: A highly sensitive and specific novel genomic and plasmid target-based PCR platform was developed to detect multiple Salmonella serovars (S. Heidelberg, S. Dublin, S. Hadar, S. Kentucky and S. Enteritidis). Through extensive genome mining of protein databases of these serovars and compar...

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

USDA-ARS?s Scientific Manuscript database

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 i...

Task Description Language

NASA Technical Reports Server (NTRS)

Simmons, Reid; Apfelbaum, David

2005-01-01

Task Description Language (TDL) is an extension of the C++ programming language that enables programmers to quickly and easily write complex, concurrent computer programs for controlling real-time autonomous systems, including robots and spacecraft. TDL is based on earlier work (circa 1984 through 1989) on the Task Control Architecture (TCA). TDL provides syntactic support for hierarchical task-level control functions, including task decomposition, synchronization, execution monitoring, and exception handling. A Java-language-based compiler transforms TDL programs into pure C++ code that includes calls to a platform-independent task-control-management (TCM) library. TDL has been used to control and coordinate multiple heterogeneous robots in projects sponsored by NASA and the Defense Advanced Research Projects Agency (DARPA). It has also been used in Brazil to control an autonomous airship and in Canada to control a robotic manipulator.

Probabilistic Multi-Sensor Fusion Based Indoor Positioning System on a Mobile Device

PubMed Central

He, Xiang; Aloi, Daniel N.; Li, Jia

2015-01-01

Nowadays, smart mobile devices include more and more sensors on board, such as motion sensors (accelerometer, gyroscope, magnetometer), wireless signal strength indicators (WiFi, Bluetooth, Zigbee), and visual sensors (LiDAR, camera). People have developed various indoor positioning techniques based on these sensors. In this paper, the probabilistic fusion of multiple sensors is investigated in a hidden Markov model (HMM) framework for mobile-device user-positioning. We propose a graph structure to store the model constructed by multiple sensors during the offline training phase, and a multimodal particle filter to seamlessly fuse the information during the online tracking phase. Based on our algorithm, we develop an indoor positioning system on the iOS platform. The experiments carried out in a typical indoor environment have shown promising results for our proposed algorithm and system design. PMID:26694387

Probabilistic Multi-Sensor Fusion Based Indoor Positioning System on a Mobile Device.

PubMed

He, Xiang; Aloi, Daniel N; Li, Jia

2015-12-14

Nowadays, smart mobile devices include more and more sensors on board, such as motion sensors (accelerometer, gyroscope, magnetometer), wireless signal strength indicators (WiFi, Bluetooth, Zigbee), and visual sensors (LiDAR, camera). People have developed various indoor positioning techniques based on these sensors. In this paper, the probabilistic fusion of multiple sensors is investigated in a hidden Markov model (HMM) framework for mobile-device user-positioning. We propose a graph structure to store the model constructed by multiple sensors during the offline training phase, and a multimodal particle filter to seamlessly fuse the information during the online tracking phase. Based on our algorithm, we develop an indoor positioning system on the iOS platform. The experiments carried out in a typical indoor environment have shown promising results for our proposed algorithm and system design.

Designing Dendrimer and Miktoarm Polymer Based Multi-Tasking Nanocarriers for Efficient Medical Therapy.

PubMed

Sharma, Anjali; Kakkar, Ashok

2015-09-17

To address current complex health problems, there has been an increasing demand for smart nanocarriers that could perform multiple complimentary biological tasks with high efficacy. This has provoked the design of tailor made nanocarriers, and the scientific community has made tremendous effort in meeting daunting challenges associated with synthetically articulating multiple functions into a single scaffold. Branched and hyper-branched macromolecular architectures have offered opportunities in enabling carriers with capabilities including location, delivery, imaging etc. Development of simple and versatile synthetic methodologies for these nanomaterials has been the key in diversifying macromolecule based medical therapy and treatment. This review highlights the advancement from conventional "only one function" to multifunctional nanomedicine. It is achieved by synthetic elaboration of multivalent platforms in miktoarm polymers and dendrimers by physical encapsulation, covalent linking and combinations thereof.

System for damping vibrations in a turbine

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

Roberts, III, Herbert Chidsey; Johnson, Curtis Alan; Taxacher, Glenn Curtis

2015-11-24

A system for damping vibrations in a turbine includes a first rotating blade having a first ceramic airfoil, a first ceramic platform connected to the first ceramic airfoil, and a first root connected to the first ceramic platform. A second rotating blade adjacent to the first rotating blade includes a second ceramic airfoil, a second ceramic platform connected to the second ceramic airfoil, and a second root connected to the second ceramic platform. A non-metallic platform damper has a first position in simultaneous contact with the first and second ceramic platforms.

Application of the CometChip platform to assess DNA damage in field-collected blood samples from turtles.

PubMed

Sykora, Peter; Chiari, Ylenia; Heaton, Andrew; Moreno, Nickolas; Glaberman, Scott; Sobol, Robert W

2018-05-01

DNA damage has been linked to genomic instability and the progressive breakdown of cellular and organismal homeostasis, leading to the onset of disease and reduced longevity. Insults to DNA from endogenous sources include base deamination, base hydrolysis, base alkylation, and metabolism-induced oxidative damage that can lead to single-strand and double-strand DNA breaks. Alternatively, exposure to environmental pollutants, radiation or ultra-violet light, can also contribute to exogenously derived DNA damage. We previously validated a novel, high through-put approach to measure levels of DNA damage in cultured mammalian cells. This new CometChip Platform builds on the classical single cell gel electrophoresis or comet methodology used extensively in environmental toxicology and molecular biology. We asked whether the CometChip Platform could be used to measure DNA damage in samples derived from environmental field studies. To this end, we determined that nucleated erythrocytes from multiple species of turtle could be successfully evaluated in the CometChip Platform to quantify levels of DNA damage. In total, we compared levels of DNA damage in 40 animals from two species: the box turtle (Terrapene carolina) and the red-eared slider (Trachemys scripta elegans). Endogenous levels of DNA damage were identical between the two species, yet we did discover some sex-linked differences and changes in DNA damage accumulation. Based on these results, we confirm that the CometChip Platform allows for the measurement of DNA damage in a large number of samples quickly and accurately, and is particularly adaptable to environmental studies using field-collected samples. Environ. Mol. Mutagen. 59:322-333, 2018. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

New Tools for New Missions - Unmanned Aircraft Systems Offer Exciting Capabilities

NASA Astrophysics Data System (ADS)

Bland, G.; Miles, T.; Pieri, D. C.; Coronado, P. L.; Fladeland, M. M.; Diaz, J. A.; Cione, J.; Maslanik, J. A.; Roman, M. O.; de Boer, G.; Argrow, B. M.; Novara, J.; Stachura, M.; Neal, D.; Moisan, J. R.

2015-12-01

There are numerous emerging possibilities for utilizing unmanned aircraft systems (UAS) to investigate a variety of natural hazards, both for prediction and analysis of specific events. Additionally, quick response capabilities will provide affordable, low risk support for emergency management teams. NASA's partnerships with commercial, university and other government agency teams are bringing new capabilities to research and emergency management communities. New technology platforms and instrument systems are gaining momentum for stand-off remote sensing observations, as well as penetration and detailed in-situ examination of natural and anthropogenic phenomena. Several pioneering investigations have provided the foundation for this development, including NASA projects with Aerosonde, Dragon Eye, and SIERRA platforms. With miniaturized instrument and platform technologies, these experiments demonstrated that previously unobtainable observations may significantly aid in the understanding, prediction, and assessment of natural hazards such as storms, volcanic eruptions, floods, and the potential impact of environmental changes. Remote sensing observations of storms and fires have also been successfully demonstrated through NASA's efforts with larger UAS such as the Global Hawk and Ikhana platforms. The future may unfold with new high altitude and/or long endurance capabilities, in some cases with less size and costs as payload capacity requirements are reduced through further miniaturization, and alternatively with expanded instrumentation and mission profiles. Several new platforms and instrument development projects are underway that will enable affordable, quick response observations. Additionally, distributed measurements that will provide near-simultaneous coverage at multiple locations will be possible - an exciting new mission concept that will greatly aid many observation scenarios. Partnerships with industry, academia, and other government agencies are all making significant contributions to these new capabilities.

OpenAQ: A Platform to Aggregate and Freely Share Global Air Quality Data

NASA Astrophysics Data System (ADS)

Hasenkopf, C. A.; Flasher, J. C.; Veerman, O.; DeWitt, H. L.

2015-12-01

Thousands of ground-based air quality monitors around the world publicly publish real-time air quality data; however, researchers and the public do not have access to this information in the ways most useful to them. Often, air quality data are posted on obscure websites showing only current values, are programmatically inaccessible, and/or are in inconsistent data formats across sites. Yet, historical and programmatic access to such a global dataset would be transformative to several scientific fields, from epidemiology to low-cost sensor technologies to estimates of ground-level aerosol by satellite retrievals. To increase accessibility and standardize this disparate dataset, we have built OpenAQ, an innovative, open platform created by a group of scientists and open data programmers. The source code for the platform is viewable at github.com/openaq. Currently, we are aggregating, storing, and making publicly available real-time air quality data (PM2.5, PM10, SO2, NO2, and O3) via an Application Program Interface (API). We will present the OpenAQ platform, which currently has the following specific capabilities: A continuous ingest mechanism for some of the most polluted cities, generalizable to more sources An API providing data-querying, including ability to filter by location, measurement type and value and date, as well as custom sort options A generalized, chart-based visualization tool to explore data accessible via the API At this stage, we are seeking wider participation and input from multiple research communities in expanding our data retrieval sites, standardizing our protocols, receiving feedback on quality issues, and creating tools that can be built on top of this open platform.

User localization in complex environments by multimodal combination of GPS, WiFi, RFID, and pedometer technologies.

PubMed

Dao, Trung-Kien; Nguyen, Hung-Long; Pham, Thanh-Thuy; Castelli, Eric; Nguyen, Viet-Tung; Nguyen, Dinh-Van

2014-01-01

Many user localization technologies and methods have been proposed for either indoor or outdoor environments. However, each technology has its own drawbacks. Recently, many researches and designs have been proposed to build a combination of multiple localization technologies system which can provide higher precision results and solve the limitation in each localization technology alone. In this paper, a conceptual design of a general localization platform using combination of multiple localization technologies is introduced. The combination is realized by dividing spaces into grid points. To demonstrate this platform, a system with GPS, RFID, WiFi, and pedometer technologies is established. Experiment results show that the accuracy and availability are improved in comparison with each technology individually.

User Localization in Complex Environments by Multimodal Combination of GPS, WiFi, RFID, and Pedometer Technologies

PubMed Central

Dao, Trung-Kien; Nguyen, Hung-Long; Pham, Thanh-Thuy; Nguyen, Viet-Tung; Nguyen, Dinh-Van

2014-01-01

Many user localization technologies and methods have been proposed for either indoor or outdoor environments. However, each technology has its own drawbacks. Recently, many researches and designs have been proposed to build a combination of multiple localization technologies system which can provide higher precision results and solve the limitation in each localization technology alone. In this paper, a conceptual design of a general localization platform using combination of multiple localization technologies is introduced. The combination is realized by dividing spaces into grid points. To demonstrate this platform, a system with GPS, RFID, WiFi, and pedometer technologies is established. Experiment results show that the accuracy and availability are improved in comparison with each technology individually. PMID:25147866

Impaired neurosteroid synthesis in multiple sclerosis

PubMed Central

Noorbakhsh, Farshid; Ellestad, Kristofor K.; Maingat, Ferdinand; Warren, Kenneth G.; Han, May H.; Steinman, Lawrence; Baker, Glen B.

2011-01-01

High-throughput technologies have led to advances in the recognition of disease pathways and their underlying mechanisms. To investigate the impact of micro-RNAs on the disease process in multiple sclerosis, a prototypic inflammatory neurological disorder, we examined cerebral white matter from patients with or without the disease by micro-RNA profiling, together with confirmatory reverse transcription–polymerase chain reaction analysis, immunoblotting and gas chromatography-mass spectrometry. These observations were verified using the in vivo multiple sclerosis model, experimental autoimmune encephalomyelitis. Brains of patients with or without multiple sclerosis demonstrated differential expression of multiple micro-RNAs, but expression of three neurosteroid synthesis enzyme-specific micro-RNAs (miR-338, miR-155 and miR-491) showed a bias towards induction in patients with multiple sclerosis (P < 0.05). Analysis of the neurosteroidogenic pathways targeted by micro-RNAs revealed suppression of enzyme transcript and protein levels in the white matter of patients with multiple sclerosis (P < 0.05). This was confirmed by firefly/Renilla luciferase micro-RNA target knockdown experiments (P < 0.05) and detection of specific micro-RNAs by in situ hybridization in the brains of patients with or without multiple sclerosis. Levels of important neurosteroids, including allopregnanolone, were suppressed in the white matter of patients with multiple sclerosis (P < 0.05). Induction of the murine micro-RNAs, miR-338 and miR-155, accompanied by diminished expression of neurosteroidogenic enzymes and allopregnanolone, was also observed in the brains of mice with experimental autoimmune encephalomyelitis (P < 0.05). Allopregnanolone treatment of the experimental autoimmune encephalomyelitis mouse model limited the associated neuropathology, including neuroinflammation, myelin and axonal injury and reduced neurobehavioral deficits (P < 0.05). These multi-platform studies point to impaired neurosteroidogenesis in both multiple sclerosis and experimental autoimmune encephalomyelitis. The findings also indicate that allopregnanolone and perhaps other neurosteroid-like compounds might represent potential biomarkers or therapies for multiple sclerosis. PMID:21908875

Multiplatform Mission Planning and Operations Simulation Environment for Adaptive Remote Sensors

NASA Astrophysics Data System (ADS)

Smith, G.; Ball, C.; O'Brien, A.; Johnson, J. T.

2017-12-01

We report on the design and development of mission simulator libraries to support the emerging field of adaptive remote sensors. We will outline the current state of the art in adaptive sensing, provide analysis of how the current approach to performing observing system simulation experiments (OSSEs) must be changed to enable adaptive sensors for remote sensing, and present an architecture to enable their inclusion in future OSSEs.The growing potential of sensors capable of real-time adaptation of their operational parameters calls for a new class of mission planning and simulation tools. Existing simulation tools used in OSSEs assume a fixed set of sensor parameters in terms of observation geometry, frequencies used, resolution, or observation time, which allows simplifications to be made in the simulation and allows sensor observation errors to be characterized a priori. Adaptive sensors may vary these parameters depending on the details of the scene observed, so that sensor performance is not simple to model without conducting OSSE simulations that include sensor adaptation in response to varying observational environment. Adaptive sensors are of significance to resource-constrained, small satellite platforms because they enable the management of power and data volumes while providing methods for multiple sensors to collaborate.The new class of OSSEs required to utilize adaptive sensors located on multiple platforms must answer the question: If the physical act of sensing has a cost, how does the system determine if the science value of a measurement is worth the cost and how should that cost be shared among the collaborating sensors?Here we propose to answer this question using an architecture structured around three modules: ADAPT, MANAGE and COLLABORATE. The ADAPT module is a set of routines to facilitate modeling of adaptive sensors, the MANAGE module will implement a set of routines to facilitate simulations of sensor resource management when power and data volume are constrained, and the COLLABORATE module will support simulations of coordination among multiple platforms with adaptive sensors. When used together these modules will for a simulation OSSEs that can enable both the design of adaptive algorithms to support remote sensing and the prediction of the sensor performance.

Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS).

PubMed

Abbatiello, Susan E; Mani, D R; Schilling, Birgit; Maclean, Brendan; Zimmerman, Lisa J; Feng, Xingdong; Cusack, Michael P; Sedransk, Nell; Hall, Steven C; Addona, Terri; Allen, Simon; Dodder, Nathan G; Ghosh, Mousumi; Held, Jason M; Hedrick, Victoria; Inerowicz, H Dorota; Jackson, Angela; Keshishian, Hasmik; Kim, Jong Won; Lyssand, John S; Riley, C Paige; Rudnick, Paul; Sadowski, Pawel; Shaddox, Kent; Smith, Derek; Tomazela, Daniela; Wahlander, Asa; Waldemarson, Sofia; Whitwell, Corbin A; You, Jinsam; Zhang, Shucha; Kinsinger, Christopher R; Mesri, Mehdi; Rodriguez, Henry; Borchers, Christoph H; Buck, Charles; Fisher, Susan J; Gibson, Bradford W; Liebler, Daniel; Maccoss, Michael; Neubert, Thomas A; Paulovich, Amanda; Regnier, Fred; Skates, Steven J; Tempst, Paul; Wang, Mu; Carr, Steven A

2013-09-01

Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation <0.15, peak width coefficient of variation <0.15, standard deviation of RT <0.15 min (9 s), and the RT drift <0.5min (30 s). The deleterious effect of a marginally performing LC-SID-MRM-MS system on the limit of quantification (LOQ) in targeted quantitative assays illustrates the use and need for a SSP to establish robust and reliable system performance. Use of a SSP helps to ensure that analyte quantification measurements can be replicated with good precision within and across multiple laboratories and should facilitate more widespread use of MRM-MS technology by the basic biomedical and clinical laboratory research communities.

Design, Implementation and Multisite Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in Liquid Chromatography-Multiple Reaction Monitoring-MS (LC-MRM-MS)*

PubMed Central

Abbatiello, Susan E.; Mani, D. R.; Schilling, Birgit; MacLean, Brendan; Zimmerman, Lisa J.; Feng, Xingdong; Cusack, Michael P.; Sedransk, Nell; Hall, Steven C.; Addona, Terri; Allen, Simon; Dodder, Nathan G.; Ghosh, Mousumi; Held, Jason M.; Hedrick, Victoria; Inerowicz, H. Dorota; Jackson, Angela; Keshishian, Hasmik; Kim, Jong Won; Lyssand, John S.; Riley, C. Paige; Rudnick, Paul; Sadowski, Pawel; Shaddox, Kent; Smith, Derek; Tomazela, Daniela; Wahlander, Asa; Waldemarson, Sofia; Whitwell, Corbin A.; You, Jinsam; Zhang, Shucha; Kinsinger, Christopher R.; Mesri, Mehdi; Rodriguez, Henry; Borchers, Christoph H.; Buck, Charles; Fisher, Susan J.; Gibson, Bradford W.; Liebler, Daniel; MacCoss, Michael; Neubert, Thomas A.; Paulovich, Amanda; Regnier, Fred; Skates, Steven J.; Tempst, Paul; Wang, Mu; Carr, Steven A.

2013-01-01

Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation <0.15, peak width coefficient of variation <0.15, standard deviation of RT <0.15 min (9 s), and the RT drift <0.5min (30 s). The deleterious effect of a marginally performing LC-SID-MRM-MS system on the limit of quantification (LOQ) in targeted quantitative assays illustrates the use and need for a SSP to establish robust and reliable system performance. Use of a SSP helps to ensure that analyte quantification measurements can be replicated with good precision within and across multiple laboratories and should facilitate more widespread use of MRM-MS technology by the basic biomedical and clinical laboratory research communities. PMID:23689285

A LabVIEW®-based software for the control of the AUTORAD platform: a fully automated multisequential flow injection analysis Lab-on-Valve (MSFIA-LOV) system for radiochemical analysis.

PubMed

Barbesi, Donato; Vicente Vilas, Víctor; Millet, Sylvain; Sandow, Miguel; Colle, Jean-Yves; Aldave de Las Heras, Laura

2017-01-01

A LabVIEW ® -based software for the control of the fully automated multi-sequential flow injection analysis Lab-on-Valve (MSFIA-LOV) platform AutoRAD performing radiochemical analysis is described. The analytical platform interfaces an Arduino ® -based device triggering multiple detectors providing a flexible and fit for purpose choice of detection systems. The different analytical devices are interfaced to the PC running LabVIEW ® VI software using USB and RS232 interfaces, both for sending commands and receiving confirmation or error responses. The AUTORAD platform has been successfully applied for the chemical separation and determination of Sr, an important fission product pertinent to nuclear waste.

Design and Calibration of a Flowfield Survey Rake for Inlet Flight Research

NASA Technical Reports Server (NTRS)

Flynn, Darin C.; Ratnayake, Nalin A.; Frederick, Michael

2009-01-01

The Propulsion Flight Test Fixture at the NASA Dryden Flight Research Center is a unique test platform available for use on NASA's F-15B aircraft, tail number 836, as a modular host for a variety of aerodynamics and propulsion research. For future flight data from this platform to be valid, more information must be gathered concerning the quality of the airflow underneath the body of the F-15B at various flight conditions, especially supersonic conditions. The flow angularity and Mach number must be known at multiple locations on any test article interface plane for measurement data at these locations to be valid. To determine this prerequisite information, flight data will be gathered in the Rake Airflow Gauge Experiment using a custom-designed flowfield rake to probe the airflow underneath the F-15B at the desired flight conditions. This paper addresses the design considerations of the rake and probe assembly, including the loads and stress analysis using analytical methods, computational fluid dynamics, and finite element analysis. It also details the flow calibration procedure, including the completed wind-tunnel test and posttest data reduction, calibration verification, and preparation for flight-testing.

WMS Server 2.0

NASA Technical Reports Server (NTRS)

Plesea, Lucian; Wood, James F.

2012-01-01

This software is a simple, yet flexible server of raster map products, compliant with the Open Geospatial Consortium (OGC) Web Map Service (WMS) 1.1.1 protocol. The server is a full implementation of the OGC WMS 1.1.1 as a fastCGI client and using Geospatial Data Abstraction Library (GDAL) for data access. The server can operate in a proxy mode, where all or part of the WMS requests are done on a back server. The server has explicit support for a colocated tiled WMS, including rapid response of black (no-data) requests. It generates JPEG and PNG images, including 16-bit PNG. The GDAL back-end support allows great flexibility on the data access. The server is a port to a Linux/GDAL platform from the original IRIX/IL platform. It is simpler to configure and use, and depending on the storage format used, it has better performance than other available implementations. The WMS server 2.0 is a high-performance WMS implementation due to the fastCGI architecture. The use of GDAL data back end allows for great flexibility. The configuration is relatively simple, based on a single XML file. It provides scaling and cropping, as well as blending of multiple layers based on layer transparency.

CFGP: a web-based, comparative fungal genomics platform.

PubMed

Park, Jongsun; Park, Bongsoo; Jung, Kyongyong; Jang, Suwang; Yu, Kwangyul; Choi, Jaeyoung; Kong, Sunghyung; Park, Jaejin; Kim, Seryun; Kim, Hyojeong; Kim, Soonok; Kim, Jihyun F; Blair, Jaime E; Lee, Kwangwon; Kang, Seogchan; Lee, Yong-Hwan

2008-01-01

Since the completion of the Saccharomyces cerevisiae genome sequencing project in 1996, the genomes of over 80 fungal species have been sequenced or are currently being sequenced. Resulting data provide opportunities for studying and comparing fungal biology and evolution at the genome level. To support such studies, the Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr), a web-based multifunctional informatics workbench, was developed. The CFGP comprises three layers, including the basal layer, middleware and the user interface. The data warehouse in the basal layer contains standardized genome sequences of 65 fungal species. The middleware processes queries via six analysis tools, including BLAST, ClustalW, InterProScan, SignalP 3.0, PSORT II and a newly developed tool named BLASTMatrix. The BLASTMatrix permits the identification and visualization of genes homologous to a query across multiple species. The Data-driven User Interface (DUI) of the CFGP was built on a new concept of pre-collecting data and post-executing analysis instead of the 'fill-in-the-form-and-press-SUBMIT' user interfaces utilized by most bioinformatics sites. A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI.

ARMOUR - A Rice miRNA: mRNA Interaction Resource.

PubMed

Sanan-Mishra, Neeti; Tripathi, Anita; Goswami, Kavita; Shukla, Rohit N; Vasudevan, Madavan; Goswami, Hitesh

2018-01-01

ARMOUR was developed as A Rice miRNA:mRNA interaction resource. This informative and interactive database includes the experimentally validated expression profiles of miRNAs under different developmental and abiotic stress conditions across seven Indian rice cultivars. This comprehensive database covers 689 known and 1664 predicted novel miRNAs and their expression profiles in more than 38 different tissues or conditions along with their predicted/known target transcripts. The understanding of miRNA:mRNA interactome in regulation of functional cellular machinery is supported by the sequence information of the mature and hairpin structures. ARMOUR provides flexibility to users in querying the database using multiple ways like known gene identifiers, gene ontology identifiers, KEGG identifiers and also allows on the fly fold change analysis and sequence search query with inbuilt BLAST algorithm. ARMOUR database provides a cohesive platform for novel and mature miRNAs and their expression in different experimental conditions and allows searching for their interacting mRNA targets, GO annotation and their involvement in various biological pathways. The ARMOUR database includes a provision for adding more experimental data from users, with an aim to develop it as a platform for sharing and comparing experimental data contributed by research groups working on rice.

Earth observing system. Output data products and input requirements, version 2.0. Volume 1: Instrument data product characteristics

NASA Technical Reports Server (NTRS)

Lu, Yun-Chi; Chang, Hyo Duck; Krupp, Brian; Kumar, Ravindra; Swaroop, Anand

1992-01-01

Information on Earth Observing System (EOS) output data products and input data requirements that has been compiled by the Science Processing Support Office (SPSO) at GSFC is presented. Since Version 1.0 of the SPSO Report was released in August 1991, there have been significant changes in the EOS program. In anticipation of a likely budget cut for the EOS Project, NASA HQ restructured the EOS program. An initial program consisting of two large platforms was replaced by plans for multiple, smaller platforms, and some EOS instruments were either deselected or descoped. Updated payload information reflecting the restructured EOS program superseding the August 1991 version of the SPSO report is included. This report has been expanded to cover information on non-EOS data products, and consists of three volumes (Volumes 1, 2, and 3). Volume 1 provides information on instrument outputs and input requirements. Volume 2 is devoted to Interdisciplinary Science (IDS) outputs and input requirements, including the 'best' and 'alternative' match analysis. Volume 3 provides information about retrieval algorithms, non-EOS input requirements of instrument teams and IDS investigators, and availability of non-EOS data products at seven primary Distributed Active Archive Centers (DAAC's).

Burried MIS 5 abrasion platforms in the Bay of Koper (Gulf of Trieste, Northern Adriatic) confirm long-term subsidence of the Northern Adriatic region

NASA Astrophysics Data System (ADS)

Trobec, Ana; Šmuc, Andrej; Poglajen, Sašo; Vrabec, Marko

2016-04-01

The youngest seafloor sediments of the Gulf of Trieste (Northern Adriatic) are represented by an up to several 100 meters thick succession of Pliocene to Quaternary continental and shallow-marine deposits recording numerous transgressive-regressive cycles. These sediments are separated from older lithologies (mainly Eocene flysch) by an erosional unconformity. Previous geophysical campaigns conducted in the Italian part of the Gulf of Trieste revealed a complex undulating morphology of the unconformity characterised by numerous morphological steps in the flysch appearing between 40 and 200 m below sea level. From correlation with onshore well data from the Friuli and Veneto area it is assumed that the highest system of these unconformities located at approximately 40 mbsl represents a marine abrasion platform formed during the MIS 5 period sea-level highstand. We present the first observations of these abrasion platforms in the Bay of Koper in the southern (Slovenian) part of the Gulf of Trieste. A series of perpendicular sub-bottom sonar profiles with a spacing of 250-500 meters was acquired in the Bay of Koper between 2009 and 2012 with the Innomar parametric sediment echo sounder SES-2000. Along the northern coast of the bay several acoustic facies were resolved, including the top erosional unconformity surface of the flysch. On this surface we located platforms at 35 ms (platform A), 40 ms (platform B) and 50 ms (platform C) of two-way-travel time. The top of abrasion platform B coincides with the top of a sediment progradational wedge which overlies abrasion platform C. No progradational wedge is developed at the top of platform A. Due to signal attenuation and multiples sub-bottom profiles could not be interpreted below 53 ms TWT time. We used a sound velocity of 1650 m/s for the time to depth conversion, which places the platforms at the depth of 28, 33 and 41 mbsl, respectively. Assuming that the abrasion platforms are a remnant of the MIS 5 highstand, this implies an average subsidence rate of the area between 0.28 and 0.38 mm/year, which agrees with previously published data for the Gulf of Trieste. This new dataset demonstrates that the Bay of Koper was connected to the Adriatic Sea approximately 125.000 ky ago during the MIS 5 sea-level highstand. Together with marine abrasion platforms and well data previously documented in the northeastern part of the Gulf of Trieste and well data from the northwestern part of the gulf our data corroborates the long-term subsidence of the Northern Adriatic region.

Activity-Based Protein Profiling of Organophosphorus and Thiocarbamate Pesticides Reveals Multiple Serine Hydrolase Targets in Mouse Brain

PubMed Central

NOMURA, DANIEL K.; CASIDA, JOHN E.

2010-01-01

Organophosphorus (OP) and thiocarbamate (TC) agrochemicals are used worldwide as insecticides, herbicides, and fungicides, but their safety assessment in terms of potential off-targets remains incomplete. In this study, we used a chemoproteomic platform, termed activity-based protein profiling, to broadly define serine hydrolase targets in mouse brain of a panel of 29 OP and TC pesticides. Among the secondary targets identified, enzymes involved in degradation of endocannabinoid signaling lipids, monoacylglycerol lipase and fatty acid amide hydrolase, were inhibited by several OP and TC pesticides. Blockade of these two enzymes led to elevations in brain endocannabinoid levels and dysregulated brain arachidonate metabolism. Other secondary targets include enzymes thought to also play important roles in the nervous system and unannotated proteins. This study reveals a multitude of secondary targets for OP and TC pesticides and underscores the utility of chemoproteomic platforms in gaining insights into biochemical pathways that are perturbed by these toxicants. PMID:21341672

Offshore Hydrokinetic Energy Conversion for Onshore Power Generation

NASA Technical Reports Server (NTRS)

Jones, Jack A.; Chao, Yi

2009-01-01

Design comparisons have been performed for a number of different tidal energy systems, including a fully submerged, horizontal-axis electro-turbine system, similar to Verdant Tidal Turbines in New York's East River, a platform-based Marine Current Turbine, now operating in Northern Ireland's Strangford Narrows, and the Rotech Lunar Energy system, to be installed off the South Korean Coast. A fourth type of tidal energy system studied is a novel JPL/Caltech hydraulic energy transfer system that uses submerged turbine blades which are mechanically attached to adjacent high-pressure pumps, instead of to adjacent electrical turbines. The generated highpressure water streams are combined and transferred to an onshore hydroelectric plant by means of a closed-cycle pipeline. The hydraulic energy transfer system was found to be cost competitive, and it allows all electronics to be placed onshore, thus greatly reducing maintenance costs and corrosion problems. It also eliminates the expenses of conditioning and transferring multiple offshore power lines and of building offshore platforms embedded in the sea floor.

Speech to Text Translation for Malay Language

NASA Astrophysics Data System (ADS)

Al-khulaidi, Rami Ali; Akmeliawati, Rini

2017-11-01

The speech recognition system is a front end and a back-end process that receives an audio signal uttered by a speaker and converts it into a text transcription. The speech system can be used in several fields including: therapeutic technology, education, social robotics and computer entertainments. In most cases in control tasks, which is the purpose of proposing our system, wherein the speed of performance and response concern as the system should integrate with other controlling platforms such as in voiced controlled robots. Therefore, the need for flexible platforms, that can be easily edited to jibe with functionality of the surroundings, came to the scene; unlike other software programs that require recording audios and multiple training for every entry such as MATLAB and Phoenix. In this paper, a speech recognition system for Malay language is implemented using Microsoft Visual Studio C#. 90 (ninety) Malay phrases were tested by 10 (ten) speakers from both genders in different contexts. The result shows that the overall accuracy (calculated from Confusion Matrix) is satisfactory as it is 92.69%.

Optimization of sparse matrix-vector multiplication on emerging multicore platforms

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

Williams, Samuel; Oliker, Leonid; Vuduc, Richard

2007-01-01

We are witnessing a dramatic change in computer architecture due to the multicore paradigm shift, as every electronic device from cell phones to supercomputers confronts parallelism of unprecedented scale. To fully unleash the potential of these systems, the HPC community must develop multicore specific optimization methodologies for important scientific computations. In this work, we examine sparse matrix-vector multiply (SpMV) - one of the most heavily used kernels in scientific computing - across a broad spectrum of multicore designs. Our experimental platform includes the homogeneous AMD dual-core and Intel quad-core designs, the heterogeneous STI Cell, as well as the first scientificmore » study of the highly multithreaded Sun Niagara2. We present several optimization strategies especially effective for the multicore environment, and demonstrate significant performance improvements compared to existing state-of-the-art serial and parallel SpMV implementations. Additionally, we present key insights into the architectural tradeoffs of leading multicore design strategies, in the context of demanding memory-bound numerical algorithms.« less

Introduction (Special Issue on Scientific Balloon Capabilities and Instrumentation)

NASA Technical Reports Server (NTRS)

Gaskin, Jessica A.; Smith, I. S.; Jones, W. V.

2014-01-01

In 1783, the Montgolfier brothers ushered in a new era of transportation and exploration when they used hot air to drive an un-tethered balloon to an altitude of 2 km. Made of sackcloth and held together with cords, this balloon challenged the way we thought about human travel, and it has since evolved into a robust platform for performing novel science and testing new technologies. Today, high-altitude balloons regularly reach altitudes of 40 km, and they can support payloads that weigh more than 3,000 kg. Long-duration balloons can currently support mission durations lasting 55 days, and developing balloon technologies (i.e. Super-Pressure Balloons) are expected to extend that duration to 100 days or longer; competing with satellite payloads. This relatively inexpensive platform supports a broad range of science payloads, spanning multiple disciplines (astrophysics, heliophysics, planetary and earth science.) Applications extending beyond traditional science include testing new technologies for eventual space-based application and stratospheric airships for planetary applications.

Performance Analysis, Design Considerations, and Applications of Extreme-Scale In Situ Infrastructures

DOE PAGES

Ayachit, Utkarsh; Bauer, Andrew; Duque, Earl P. N.; ...

2016-11-01

A key trend facing extreme-scale computational science is the widening gap between computational and I/O rates, and the challenge that follows is how to best gain insight from simulation data when it is increasingly impractical to save it to persistent storage for subsequent visual exploration and analysis. One approach to this challenge is centered around the idea of in situ processing, where visualization and analysis processing is performed while data is still resident in memory. Our paper examines several key design and performance issues related to the idea of in situ processing at extreme scale on modern platforms: Scalability, overhead,more » performance measurement and analysis, comparison and contrast with a traditional post hoc approach, and interfacing with simulation codes. We illustrate these principles in practice with studies, conducted on large-scale HPC platforms, that include a miniapplication and multiple science application codes, one of which demonstrates in situ methods in use at greater than 1M-way concurrency.« less

From sequencer to supercomputer: an automatic pipeline for managing and processing next generation sequencing data.

PubMed

Camerlengo, Terry; Ozer, Hatice Gulcin; Onti-Srinivasan, Raghuram; Yan, Pearlly; Huang, Tim; Parvin, Jeffrey; Huang, Kun

2012-01-01

Next Generation Sequencing is highly resource intensive. NGS Tasks related to data processing, management and analysis require high-end computing servers or even clusters. Additionally, processing NGS experiments requires suitable storage space and significant manual interaction. At The Ohio State University's Biomedical Informatics Shared Resource, we designed and implemented a scalable architecture to address the challenges associated with the resource intensive nature of NGS secondary analysis built around Illumina Genome Analyzer II sequencers and Illumina's Gerald data processing pipeline. The software infrastructure includes a distributed computing platform consisting of a LIMS called QUEST (http://bisr.osumc.edu), an Automation Server, a computer cluster for processing NGS pipelines, and a network attached storage device expandable up to 40TB. The system has been architected to scale to multiple sequencers without requiring additional computing or labor resources. This platform provides demonstrates how to manage and automate NGS experiments in an institutional or core facility setting.

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.

Evolving Educational Techniques in Surgical Training.

PubMed

Evans, Charity H; Schenarts, Kimberly D

2016-02-01

Training competent and professional surgeons efficiently and effectively requires innovation and modernization of educational methods. Today's medical learner is quite adept at using multiple platforms to gain information, providing surgical educators with numerous innovative avenues to promote learning. With the growth of technology, and the restriction of work hours in surgical education, there has been an increase in use of simulation, including virtual reality, robotics, telemedicine, and gaming. The use of simulation has shifted the learning of basic surgical skills to the laboratory, reserving limited time in the operating room for the acquisition of complex surgical skills". Copyright © 2016 Elsevier Inc. All rights reserved.

vvtools v. 1.0

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

Drake, Richard R.

Vvtools is a suite of testing tools, with a focus on reproducible verification and validation. They are written in pure Python, and contain a test harness and an automated process management tool. Users of vvtools can develop suites of verification and validation tests and run them on small to large high performance computing resources in an automated and reproducible way. The test harness enables complex processes to be performed in each test and even supports a one-level parent/child dependency between tests. It includes a built in capability to manage workloads requiring multiple processors and platforms that use batch queueing systems.

SAbPred: a structure-based antibody prediction server

PubMed Central

Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo; Marks, Claire; Nowak, Jaroslaw; Regep, Cristian; Georges, Guy; Kelm, Sebastian; Popovic, Bojana; Deane, Charlotte M.

2016-01-01

SAbPred is a server that makes predictions of the properties of antibodies focusing on their structures. Antibody informatics tools can help improve our understanding of immune responses to disease and aid in the design and engineering of therapeutic molecules. SAbPred is a single platform containing multiple applications which can: number and align sequences; automatically generate antibody variable fragment homology models; annotate such models with estimated accuracy alongside sequence and structural properties including potential developability issues; predict paratope residues; and predict epitope patches on protein antigens. The server is available at http://opig.stats.ox.ac.uk/webapps/sabpred. PMID:27131379

Global change technology architecture trade study

NASA Technical Reports Server (NTRS)

Garrett, L. Bernard (Editor); Hypes, Warren D. (Editor); Wright, Robert L. (Editor)

1991-01-01

Described here is an architecture trade study conducted by the Langley Research Center to develop a representative mix of advanced space science instrumentation, spacecraft, and mission orbits to assist in the technology selection processes. The analyses concentrated on the highest priority classes of global change measurements which are the global climate changes. Issues addressed in the tradeoffs includes assessments of the economics of scale of large platforms with multiple instruments relative to smaller spacecraft; the influences of current and possible future launch vehicles on payload sizes, and on-orbit assembly decisions; and the respective roles of low-Earth versus geostationary Earth orbiting systems.

Multi-Robot Assembly Strategies and Metrics.

PubMed

Marvel, Jeremy A; Bostelman, Roger; Falco, Joe

2018-02-01

We present a survey of multi-robot assembly applications and methods and describe trends and general insights into the multi-robot assembly problem for industrial applications. We focus on fixtureless assembly strategies featuring two or more robotic systems. Such robotic systems include industrial robot arms, dexterous robotic hands, and autonomous mobile platforms, such as automated guided vehicles. In this survey, we identify the types of assemblies that are enabled by utilizing multiple robots, the algorithms that synchronize the motions of the robots to complete the assembly operations, and the metrics used to assess the quality and performance of the assemblies.

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

Karr, T.J.

The SAR energy-aperture product limit is extended to multi-beam SARS, Spotlight and moving spotlight SARS. This fundamental limit bounds the tradeoff between energy and antenna size. The kinematic relations between design variables such as platform speed, pulse repetition frequency, beam width and area rate are analyzed in a unified framework applicable to a wide variety of SARs including strip maps, spotlights, vermer arrays and multi-beam SARS, both scanning and swept-beam. Then the energy-aperture product limit is derived from the signal-to noise requirement and the kinematic constraints. The derivation clarifies impact of multiple beams and spotlighting on SAR performance.

Opportunities and Challenges of Digital Technology for HIV Treatment and Prevention.

PubMed

Simoni, Jane M; Kutner, Bryan A; Horvath, Keith J

2015-12-01

Novel eHealth interventions are creating exciting opportunities for health promotion along the continuum of HIV care and prevention. Reviews of recent work indicate the use of multiple platforms (e.g., smartphones, social media), with trends toward individualized approaches and real-time assessments. However, the field needs more rigorous investigations to provide evidence of long-term impact on clinical indicators and should expand its targets beyond men who have sex with men and medication adherence. Challenges to the field include working within restricted funding timelines and disseminating eHealth interventions to those most in need.

Multi-Robot Assembly Strategies and Metrics

PubMed Central

MARVEL, JEREMY A.; BOSTELMAN, ROGER; FALCO, JOE

2018-01-01

We present a survey of multi-robot assembly applications and methods and describe trends and general insights into the multi-robot assembly problem for industrial applications. We focus on fixtureless assembly strategies featuring two or more robotic systems. Such robotic systems include industrial robot arms, dexterous robotic hands, and autonomous mobile platforms, such as automated guided vehicles. In this survey, we identify the types of assemblies that are enabled by utilizing multiple robots, the algorithms that synchronize the motions of the robots to complete the assembly operations, and the metrics used to assess the quality and performance of the assemblies. PMID:29497234

Targeted proteomics guided by label-free global proteome analysis in saliva reveal transition signatures from health to periodontal disease.

PubMed

Bostanci, Nagihan; Selevsek, Nathalie; Wolski, Witold; Grossmann, Jonas; Bao, Kai; Wahlander, Asa; Trachsel, Christian; Schlapbach, Ralph; Özturk, Veli Özgen; Afacan, Beral; Emingil, Gulnur; Belibasakis, Georgios N

2018-04-02

Periodontal diseases are among the most prevalent worldwide, but largely silent, chronic diseases. They affect the tooth-supporting tissues with multiple ramifications on life quality. Their early diagnosis is still challenging, due to lack of appropriate molecular diagnostic methods. Saliva offers a non-invasively collectable reservoir of clinically relevant biomarkers, which, if utilized efficiently, could facilitate early diagnosis and monitoring of ongoing disease. Despite several novel protein markers being recently enlisted by discovery proteomics, their routine diagnostic application is hampered by the lack of validation platforms that allow for rapid, accurate and simultaneous quantification of multiple proteins in large cohorts. We carried out a pipeline of two proteomic platforms; firstly, we applied open ended label-free quantitative (LFQ) proteomics for discovery in saliva (n=67, health, gingivitis, and periodontitis), followed by selected-reaction monitoring (SRM)-targeted proteomics for validation in an independent cohort (n=82). The LFQ platform led to the discovery of 119 proteins with at least two-fold significant difference between health and disease. The 65 proteins chosen for the subsequent SRM platform included 50 related proteins derived from the significantly enriched processes of the LFQ data, 11 from literature-mining, and four house-keeping ones. Among those, 60 were reproducibly quantifiable proteins (92% success rate), represented by a total of 143 peptides. Machine-learning modeling led to a narrowed-down panel of five proteins of high predictive value for periodontal diseases (higher in disease: Matrix metalloproteinase-9, Ras-related protein-1, Actin-related protein 2/3 complex subunit 5; lower in disease: Clusterin, Deleted in Malignant Brain Tumors 1), with maximum area under the receiver operating curve >0.97. This panel enriches the pool of credible clinical biomarker candidates for diagnostic assay development. Yet, the quantum leap brought in periodontal diagnostics by this study lies in the introduction of the well established discovery-through-verification pipeline for periodontal biomarker discovery and validation in further periodontal patient cohorts. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Cloud computing geospatial application for water resources based on free and open source software and open standards - a prototype

NASA Astrophysics Data System (ADS)

Delipetrev, Blagoj

2016-04-01

Presently, most of the existing software is desktop-based, designed to work on a single computer, which represents a major limitation in many ways, starting from limited computer processing, storage power, accessibility, availability, etc. The only feasible solution lies in the web and cloud. This abstract presents research and development of a cloud computing geospatial application for water resources based on free and open source software and open standards using hybrid deployment model of public - private cloud, running on two separate virtual machines (VMs). The first one (VM1) is running on Amazon web services (AWS) and the second one (VM2) is running on a Xen cloud platform. The presented cloud application is developed using free and open source software, open standards and prototype code. The cloud application presents a framework how to develop specialized cloud geospatial application that needs only a web browser to be used. This cloud application is the ultimate collaboration geospatial platform because multiple users across the globe with internet connection and browser can jointly model geospatial objects, enter attribute data and information, execute algorithms, and visualize results. The presented cloud application is: available all the time, accessible from everywhere, it is scalable, works in a distributed computer environment, it creates a real-time multiuser collaboration platform, the programing languages code and components are interoperable, and it is flexible in including additional components. The cloud geospatial application is implemented as a specialized water resources application with three web services for 1) data infrastructure (DI), 2) support for water resources modelling (WRM), 3) user management. The web services are running on two VMs that are communicating over the internet providing services to users. The application was tested on the Zletovica river basin case study with concurrent multiple users. The application is a state-of-the-art cloud geospatial collaboration platform. The presented solution is a prototype and can be used as a foundation for developing of any specialized cloud geospatial applications. Further research will be focused on distributing the cloud application on additional VMs, testing the scalability and availability of services.

Future of antibody purification.

PubMed

Low, Duncan; O'Leary, Rhona; Pujar, Narahari S

2007-03-15

Antibody purification seems to be safely ensconced in a platform, now well-established by way of multiple commercialized antibody processes. However, natural evolution compels us to peer into the future. This is driven not only by a large, projected increase in the number of antibody therapies, but also by dramatic improvements in upstream productivity, and process economics. Although disruptive technologies have yet escaped downstream processes, evolution of the so-called platform is already evident in antibody processes in late-stage development. Here we perform a wide survey of technologies that are competing to be part of that platform, and provide our [inherently dangerous] assessment of those that have the most promise.

SU-E-T-157: CARMEN: A MatLab-Based Research Platform for Monte Carlo Treatment Planning (MCTP) and Customized System for Planning Evaluation

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

Baeza, J.A.; Ureba, A.; Jimenez-Ortega, E.

Purpose: Although there exist several radiotherapy research platforms, such as: CERR, the most widely used and referenced; SlicerRT, which allows treatment plan comparison from various sources; and MMCTP, a full MCTP system; it is still needed a full MCTP toolset that provides users complete control of calculation grids, interpolation methods and filters in order to “fairly” compare results from different TPSs, supporting verification with experimental measurements. Methods: This work presents CARMEN, a MatLab-based platform including multicore and GPGPU accelerated functions for loading RT data; designing treatment plans; and evaluating dose matrices and experimental data.CARMEN supports anatomic and functional imaging inmore » DICOM format, as well as RTSTRUCT, RTPLAN and RTDOSE. Besides, it contains numerous tools to accomplish the MCTP process, managing egs4phant and phase space files.CARMEN planning mode assist in designing IMRT, VMAT and MERT treatments via both inverse and direct optimization. The evaluation mode contains a comprehensive toolset (e.g. 2D/3D gamma evaluation, difference matrices, profiles, DVH, etc.) to compare datasets from commercial TPS, MC simulations (i.e. 3ddose) and radiochromic film in a user-controlled manner. Results: CARMEN has been validated against commercial RTPs and well-established evaluation tools, showing coherent behavior of its multiple algorithms. Furthermore, CARMEN platform has been used to generate competitive complex treatment that has been published in comparative studies. Conclusion: A new research oriented MCTP platform with a customized validation toolset has been presented. Despite of being coded with a high-level programming language, CARMEN is agile due to the use of parallel algorithms. The wide-spread use of MatLab provides straightforward access to CARMEN’s algorithms to most researchers. Similarly, our platform can benefit from the MatLab community scientific developments as filters, registration algorithms etc. Finally, CARMEN arises the importance of grid and filtering control in treatment plan comparison.« less

Bird interactions with offshore oil and gas platforms: review of impacts and monitoring techniques.

PubMed

Ronconi, Robert A; Allard, Karel A; Taylor, Philip D

2015-01-01

Thousands of oil and gas platforms are currently operating in offshore waters globally, and this industry is expected to expand in coming decades. Although the potential environmental impacts of offshore oil and gas activities are widely recognized, there is limited understanding of their impacts on migratory and resident birds. A literature review identified 24 studies and reports of bird-platform interactions, most being qualitative and half having been peer-reviewed. The most frequently observed effect, for seabirds and landbirds, is attraction and sometimes collisions associated with lights and flares; episodic events have caused the deaths of hundreds or even thousands of birds. Though typically unpredictable, anecdotally, it is known that poor weather, such as fog, precipitation and low cloud cover, can exacerbate the effect of nocturnal attraction to lights, especially when coincidental with bird migrations. Other effects include provision of foraging and roosting opportunities, increased exposure to oil and hazardous environments, increased exposure to predators, or repulsion from feeding sites. Current approaches to monitoring birds at offshore platforms have focused on observer-based methods which can offer species-level bird identification, quantify seasonal patterns of relative abundance and distribution, and document avian mortality events and underlying factors. Observer-based monitoring is time-intensive, limited in spatial and temporal coverage, and suffers without clear protocols and when not conducted by trained, independent observers. These difficulties are exacerbated because deleterious bird-platform interaction is episodic and likely requires the coincidence of multiple factors (e.g., darkness, cloud, fog, rain conditions, occurrence of birds in vicinity). Collectively, these considerations suggest a need to implement supplemental systems for monitoring bird activities around offshore platforms. Instrument-based approaches, such as radar, cameras, acoustic recordings, and telemetry, hold promise for continuous monitoring. Recommendations are provided for a rigorous and comprehensive monitoring approach within an adaptive management framework. Copyright © 2014 Elsevier Ltd. All rights reserved.

Synthesis of Cesium Lead Halide Perovskite Nanocrystals in a Droplet-Based Microfluidic Platform: Fast Parametric Space Mapping.

PubMed

Lignos, Ioannis; Stavrakis, Stavros; Nedelcu, Georgian; Protesescu, Loredana; deMello, Andrew J; Kovalenko, Maksym V

2016-03-09

Prior to this work, fully inorganic nanocrystals of cesium lead halide perovskite (CsPbX3, X = Br, I, Cl and Cl/Br and Br/I mixed halide systems), exhibiting bright and tunable photoluminescence, have been synthesized using conventional batch (flask-based) reactions. Unfortunately, our understanding of the parameters governing the formation of these nanocrystals is still very limited due to extremely fast reaction kinetics and multiple variables involved in ion-metathesis-based synthesis of such multinary halide systems. Herein, we report the use of a droplet-based microfluidic platform for the synthesis of CsPbX3 nanocrystals. The combination of online photoluminescence and absorption measurements and the fast mixing of reagents within such a platform allows the rigorous and rapid mapping of the reaction parameters, including molar ratios of Cs, Pb, and halide precursors, reaction temperatures, and reaction times. This translates into enormous savings in reagent usage and screening times when compared to analogous batch synthetic approaches. The early-stage insight into the mechanism of nucleation of metal halide nanocrystals suggests similarities with multinary metal chalcogenide systems, albeit with much faster reaction kinetics in the case of halides. Furthermore, we show that microfluidics-optimized synthesis parameters are also directly transferrable to the conventional flask-based reaction.

Smartphone-Based Food Diagnostic Technologies: A Review.

PubMed

Rateni, Giovanni; Dario, Paolo; Cavallo, Filippo

2017-06-20

A new generation of mobile sensing approaches offers significant advantages over traditional platforms in terms of test speed, control, low cost, ease-of-operation, and data management, and requires minimal equipment and user involvement. The marriage of novel sensing technologies with cellphones enables the development of powerful lab-on-smartphone platforms for many important applications including medical diagnosis, environmental monitoring, and food safety analysis. This paper reviews the recent advancements and developments in the field of smartphone-based food diagnostic technologies, with an emphasis on custom modules to enhance smartphone sensing capabilities. These devices typically comprise multiple components such as detectors, sample processors, disposable chips, batteries and software, which are integrated with a commercial smartphone. One of the most important aspects of developing these systems is the integration of these components onto a compact and lightweight platform that requires minimal power. To date, researchers have demonstrated several promising approaches employing various sensing techniques and device configurations. We aim to provide a systematic classification according to the detection strategy, providing a critical discussion of strengths and weaknesses. We have also extended the analysis to the food scanning devices that are increasingly populating the Internet of Things (IoT) market, demonstrating how this field is indeed promising, as the research outputs are quickly capitalized on new start-up companies.

Smartphone-Based Food Diagnostic Technologies: A Review

PubMed Central

Rateni, Giovanni; Dario, Paolo; Cavallo, Filippo

2017-01-01

A new generation of mobile sensing approaches offers significant advantages over traditional platforms in terms of test speed, control, low cost, ease-of-operation, and data management, and requires minimal equipment and user involvement. The marriage of novel sensing technologies with cellphones enables the development of powerful lab-on-smartphone platforms for many important applications including medical diagnosis, environmental monitoring, and food safety analysis. This paper reviews the recent advancements and developments in the field of smartphone-based food diagnostic technologies, with an emphasis on custom modules to enhance smartphone sensing capabilities. These devices typically comprise multiple components such as detectors, sample processors, disposable chips, batteries and software, which are integrated with a commercial smartphone. One of the most important aspects of developing these systems is the integration of these components onto a compact and lightweight platform that requires minimal power. To date, researchers have demonstrated several promising approaches employing various sensing techniques and device configurations. We aim to provide a systematic classification according to the detection strategy, providing a critical discussion of strengths and weaknesses. We have also extended the analysis to the food scanning devices that are increasingly populating the Internet of Things (IoT) market, demonstrating how this field is indeed promising, as the research outputs are quickly capitalized on new start-up companies. PMID:28632188

MSiReader: an open-source interface to view and analyze high resolving power MS imaging files on Matlab platform.

PubMed

Robichaud, Guillaume; Garrard, Kenneth P; Barry, Jeremy A; Muddiman, David C

2013-05-01

During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform

NASA Astrophysics Data System (ADS)

Robichaud, Guillaume; Garrard, Kenneth P.; Barry, Jeremy A.; Muddiman, David C.

2013-05-01

During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

INFORM Lab: a testbed for high-level information fusion and resource management

NASA Astrophysics Data System (ADS)

Valin, Pierre; Guitouni, Adel; Bossé, Eloi; Wehn, Hans; Happe, Jens

2011-05-01

DRDC Valcartier and MDA have created an advanced simulation testbed for the purpose of evaluating the effectiveness of Network Enabled Operations in a Coastal Wide Area Surveillance situation, with algorithms provided by several universities. This INFORM Lab testbed allows experimenting with high-level distributed information fusion, dynamic resource management and configuration management, given multiple constraints on the resources and their communications networks. This paper describes the architecture of INFORM Lab, the essential concepts of goals and situation evidence, a selected set of algorithms for distributed information fusion and dynamic resource management, as well as auto-configurable information fusion architectures. The testbed provides general services which include a multilayer plug-and-play architecture, and a general multi-agent framework based on John Boyd's OODA loop. The testbed's performance is demonstrated on 2 types of scenarios/vignettes for 1) cooperative search-and-rescue efforts, and 2) a noncooperative smuggling scenario involving many target ships and various methods of deceit. For each mission, an appropriate subset of Canadian airborne and naval platforms are dispatched to collect situation evidence, which is fused, and then used to modify the platform trajectories for the most efficient collection of further situation evidence. These platforms are fusion nodes which obey a Command and Control node hierarchy.

antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers.

PubMed

Blin, Kai; Medema, Marnix H; Kazempour, Daniyal; Fischbach, Michael A; Breitling, Rainer; Takano, Eriko; Weber, Tilmann

2013-07-01

Microbial secondary metabolites are a potent source of antibiotics and other pharmaceuticals. Genome mining of their biosynthetic gene clusters has become a key method to accelerate their identification and characterization. In 2011, we developed antiSMASH, a web-based analysis platform that automates this process. Here, we present the highly improved antiSMASH 2.0 release, available at http://antismash.secondarymetabolites.org/. For the new version, antiSMASH was entirely re-designed using a plug-and-play concept that allows easy integration of novel predictor or output modules. antiSMASH 2.0 now supports input of multiple related sequences simultaneously (multi-FASTA/GenBank/EMBL), which allows the analysis of draft genomes comprising multiple contigs. Moreover, direct analysis of protein sequences is now possible. antiSMASH 2.0 has also been equipped with the capacity to detect additional classes of secondary metabolites, including oligosaccharide antibiotics, phenazines, thiopeptides, homo-serine lactones, phosphonates and furans. The algorithm for predicting the core structure of the cluster end product is now also covering lantipeptides, in addition to polyketides and non-ribosomal peptides. The antiSMASH ClusterBlast functionality has been extended to identify sub-clusters involved in the biosynthesis of specific chemical building blocks. The new features currently make antiSMASH 2.0 the most comprehensive resource for identifying and analyzing novel secondary metabolite biosynthetic pathways in microorganisms.

A microfabricated platform with hydrogel arrays for 3D mechanical stimulation of cells.

PubMed

Liu, Haijiao; Usprech, Jenna; Sun, Yu; Simmons, Craig A

2016-04-01

Cellular microenvironments present cells with multiple stimuli, including not only soluble biochemical and insoluble matrix cues but also mechanical factors. Biomaterial array platforms have been used to combinatorially and efficiently probe and define two-dimensional (2D) and 3D microenvironmental cues to guide cell functions for tissue engineering applications. However, there are few examples of array platforms that include dynamic mechanical forces, particularly to enable stretching of 3D cell-seeded biomaterials, which is relevant to engineering connective and cardiovascular tissues. Here we present a deformable membrane platform that enables 3D dynamic mechanical stretch of arrayed biomaterial constructs. Cell-seeded polyethylene glycol norbornene (PEG-NB) hydrogels were bound to miniaturized deformable membranes via a thiol-ene reaction with off-stoichiometry thiol-ene based polydimethylsiloxane (OSTE-PDMS) as the membrane material. Bonding to OSTE-PDMS enabled the 3D hydrogel microconstructs to be cyclically deformed and stretched by the membrane. As a first demonstration, human mesenchymal stromal cells (MSCs) embedded in PEG-NB were stretched for several days. They were found to be viable, spread in the 3D hydrogels, and exhibited a contractile myofibroblast phenotype when exposed to dynamic 3D mechanical deformation. This platform, which is readily scalable to larger arrays, enables systematic interrogation of the relationships between combinations of 3D mechanobiological cues and cellular responses, and thus has the potential to identify strategies to predictably control the construction of functional engineered tissues. Current high-throughput biomaterial screening approaches fail to consider the effects of dynamic mechanical stimulation, despite its importance in a wide variety of regenerative medicine applications. To meet this need, we developed a deformable membrane platform that enables 3D dynamic stretch of arrayed biomaterial constructs. Our approach combines microtechnologies fabricated with off-stoichiometry thiol-ene based polydimethylsiloxane membranes that can covalently bond cell-seeded polyethylene glycol norbornene 3D hydrogels, a model biomaterial with tunable adhesive, elastic and degradation characteristics. As a first demonstration, we show that human mesenchymal stromal cells embedded in hydrogels and subjected to dynamic mechanical stimulation undergo myofibroblast differentiation. This system is readily scaled up to larger arrays, and will enable systematic and efficient screening of combinations of 3D mechanobiological and biomaterial cues on cell fate and function. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Extending the BEAGLE library to a multi-FPGA platform.

PubMed

Jin, Zheming; Bakos, Jason D

2013-01-19

Maximum Likelihood (ML)-based phylogenetic inference using Felsenstein's pruning algorithm is a standard method for estimating the evolutionary relationships amongst a set of species based on DNA sequence data, and is used in popular applications such as RAxML, PHYLIP, GARLI, BEAST, and MrBayes. The Phylogenetic Likelihood Function (PLF) and its associated scaling and normalization steps comprise the computational kernel for these tools. These computations are data intensive but contain fine grain parallelism that can be exploited by coprocessor architectures such as FPGAs and GPUs. A general purpose API called BEAGLE has recently been developed that includes optimized implementations of Felsenstein's pruning algorithm for various data parallel architectures. In this paper, we extend the BEAGLE API to a multiple Field Programmable Gate Array (FPGA)-based platform called the Convey HC-1. The core calculation of our implementation, which includes both the phylogenetic likelihood function (PLF) and the tree likelihood calculation, has an arithmetic intensity of 130 floating-point operations per 64 bytes of I/O, or 2.03 ops/byte. Its performance can thus be calculated as a function of the host platform's peak memory bandwidth and the implementation's memory efficiency, as 2.03 × peak bandwidth × memory efficiency. Our FPGA-based platform has a peak bandwidth of 76.8 GB/s and our implementation achieves a memory efficiency of approximately 50%, which gives an average throughput of 78 Gflops. This represents a ~40X speedup when compared with BEAGLE's CPU implementation on a dual Xeon 5520 and 3X speedup versus BEAGLE's GPU implementation on a Tesla T10 GPU for very large data sizes. The power consumption is 92 W, yielding a power efficiency of 1.7 Gflops per Watt. The use of data parallel architectures to achieve high performance for likelihood-based phylogenetic inference requires high memory bandwidth and a design methodology that emphasizes high memory efficiency. To achieve this objective, we integrated 32 pipelined processing elements (PEs) across four FPGAs. For the design of each PE, we developed a specialized synthesis tool to generate a floating-point pipeline with resource and throughput constraints to match the target platform. We have found that using low-latency floating-point operators can significantly reduce FPGA area and still meet timing requirement on the target platform. We found that this design methodology can achieve performance that exceeds that of a GPU-based coprocessor.

Integrating Multiple Autonomous Underwater Vessels, Surface Vessels and Aircraft into Oceanographic Research Vessel Operations

NASA Astrophysics Data System (ADS)

McGillivary, P. A.; Borges de Sousa, J.; Martins, R.; Rajan, K.

2012-12-01

Autonomous platforms are increasingly used as components of Integrated Ocean Observing Systems and oceanographic research cruises. Systems deployed can include gliders or propeller-driven autonomous underwater vessels (AUVs), autonomous surface vessels (ASVs), and unmanned aircraft systems (UAS). Prior field campaigns have demonstrated successful communication, sensor data fusion and visualization for studies using gliders and AUVs. However, additional requirements exist for incorporating ASVs and UASs into ship operations. For these systems to be optimally integrated into research vessel data management and operational planning systems involves addressing three key issues: real-time field data availability, platform coordination, and data archiving for later analysis. A fleet of AUVs, ASVs and UAS deployed from a research vessel is best operated as a system integrated with the ship, provided communications among them can be sustained. For this purpose, Disruptive Tolerant Networking (DTN) software protocols for operation in communication-challenged environments help ensure reliable high-bandwidth communications. Additionally, system components need to have considerable onboard autonomy, namely adaptive sampling capabilities using their own onboard sensor data stream analysis. We discuss Oceanographic Decision Support System (ODSS) software currently used for situational awareness and planning onshore, and in the near future event detection and response will be coordinated among multiple vehicles. Results from recent field studies from oceanographic research vessels using AUVs, ASVs and UAS, including the Rapid Environmental Picture (REP-12) cruise, are presented describing methods and results for use of multi-vehicle communication and deliberative control networks, adaptive sampling with single and multiple platforms, issues relating to data management and archiving, and finally challenges that remain in addressing these technological issues. Significantly, the use of UAS on oceanographic research vessels is just beginning. We report on several initial field efforts which demonstrated that UAS improve spatial and temporal mapping of ocean features, as well as monitoring marine mammal populations, ocean color, sea ice and wave fields and air-sea gas exchange. These studies however also confirm the challenges for shipboard computer systems ingesting and archiving UAS high resolution video, SAR and lidar data. We describe the successful inclusion of DTN communications for: 1) passing video data between two UAS or a UAS and ship; 2) for inclusion of ASVs as communication nodes for AUVs; as well as, 3) enabling extension of adaptive sampling software from AUVs and ASVs to include UAS. In conclusion, we describe how autonomous sampling systems may be best integrated into shipboard oceanographic vessel research to provide new and more comprehensive time-space ocean and atmospheric data collection that is important not only for scientific study, but also for sustainable ocean management, including emergency response capabilities. The recent examples of such integrated studies highlighted confirm ocean and atmospheric studies can more cost-effectively pursued, and in some cases only accomplished, by combining underwater, surface and aircraft autonomous systems with research vessel operations.

Miniature fiber optic spectrometer-based quantitative fluorescence resonance energy transfer measurement in single living cells.

PubMed

Chai, Liuying; Zhang, Jianwei; Zhang, Lili; Chen, Tongsheng

2015-03-01

Spectral measurement of fluorescence resonance energy transfer (FRET), spFRET, is a widely used FRET quantification method in living cells today. We set up a spectrometer-microscope platform that consists of a miniature fiber optic spectrometer and a widefield fluorescence microscope for the spectral measurement of absolute FRET efficiency (E) and acceptor-to-donor concentration ratio (R(C)) in single living cells. The microscope was used for guiding cells and the spectra were simultaneously detected by the miniature fiber optic spectrometer. Moreover, our platform has independent excitation and emission controllers, so different excitations can share the same emission channel. In addition, we developed a modified spectral FRET quantification method (mlux-FRET) for the multiple donors and multiple acceptors FRET construct (mD∼nA) sample, and we also developed a spectra-based 2-channel acceptor-sensitized FRET quantification method (spE-FRET). We implemented these modified FRET quantification methods on our platform to measure the absolute E and R(C) values of tandem constructs with different acceptor/donor stoichiometries in single living Huh-7 cells.

Dynamic modal estimation using instrumental variables

NASA Technical Reports Server (NTRS)

Salzwedel, H.

1980-01-01

A method to determine the modes of dynamical systems is described. The inputs and outputs of a system are Fourier transformed and averaged to reduce the error level. An instrumental variable method that estimates modal parameters from multiple correlations between responses of single input, multiple output systems is applied to estimate aircraft, spacecraft, and off-shore platform modal parameters.

Development of High Data Rate Acoustic Multiple-Input/Multiple-Output Modems

DTIC Science & Technology

2015-09-30

communication capabilities of underwater platforms and facilitate real-time adaptive operations in the ocean. OBJECTIVES The ...signaling at the transmitter and low-complexity time reversal processing at the receiver. APPROACH Underwater acoustic (UWA) communication is useful...digital communications in shallow water environments. The advancement has direct impacts on defense appliations since underwater acoustic modems

Organization of Functional Postural Responses Following Perturbations in Multiple Directions in Elderly Fallers Standing Quietly

ERIC Educational Resources Information Center

Matjacic, Zlatko; Sok, David; Jakovljevic, Miroljub; Cikajlo, Imre

2013-01-01

The objective of the study was to assess functional postural responses by analyzing the center-of-pressure trajectories resulting from perturbations delivered in multiple directions to elderly fallers. Ten elderly individuals were standing quietly on two force platforms while an apparatus delivered controlled perturbations at the level of pelvis…

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

Multifunctional cell-culture platform for aligned cell sheet monitoring, transfer printing, and therapy.

PubMed

Kim, Seok Joo; Cho, Hye Rim; Cho, Kyoung Won; Qiao, Shutao; Rhim, Jung Soo; Soh, Min; Kim, Taeho; Choi, Moon Kee; Choi, Changsoon; Park, Inhyuk; Hwang, Nathaniel S; Hyeon, Taeghwan; Choi, Seung Hong; Lu, Nanshu; Kim, Dae-Hyeong

2015-03-24

While several functional platforms for cell culturing have been proposed for cell sheet engineering, a soft integrated system enabling in vitro physiological monitoring of aligned cells prior to their in vivo applications in tissue regeneration has not been reported. Here, we present a multifunctional, soft cell-culture platform equipped with ultrathin stretchable nanomembrane sensors and graphene-nanoribbon cell aligners, whose system modulus is matched with target tissues. This multifunctional platform is capable of aligning plated cells and in situ monitoring of cellular physiological characteristics during proliferation and differentiation. In addition, it is successfully applied as an in vitro muscle-on-a-chip testing platform. Finally, a simple but high-yield transfer printing mechanism is proposed to deliver cell sheets for scaffold-free, localized cell therapy in vivo. The muscle-mimicking stiffness of the platform allows the high-yield transfer printing of multiple cell sheets and results in successful therapies in diseased animal models. Expansion of current results to stem cells will provide unique opportunities for emerging classes of tissue engineering and cell therapy technologies.

Organ-On-A-Chip Platforms: A Convergence of Advanced Materials, Cells, and Microscale Technologies.

PubMed

Ahadian, Samad; Civitarese, Robert; Bannerman, Dawn; Mohammadi, Mohammad Hossein; Lu, Rick; Wang, Erika; Davenport-Huyer, Locke; Lai, Ben; Zhang, Boyang; Zhao, Yimu; Mandla, Serena; Korolj, Anastasia; Radisic, Milica

2018-01-01

Significant advances in biomaterials, stem cell biology, and microscale technologies have enabled the fabrication of biologically relevant tissues and organs. Such tissues and organs, referred to as organ-on-a-chip (OOC) platforms, have emerged as a powerful tool in tissue analysis and disease modeling for biological and pharmacological applications. A variety of biomaterials are used in tissue fabrication providing multiple biological, structural, and mechanical cues in the regulation of cell behavior and tissue morphogenesis. Cells derived from humans enable the fabrication of personalized OOC platforms. Microscale technologies are specifically helpful in providing physiological microenvironments for tissues and organs. In this review, biomaterials, cells, and microscale technologies are described as essential components to construct OOC platforms. The latest developments in OOC platforms (e.g., liver, skeletal muscle, cardiac, cancer, lung, skin, bone, and brain) are then discussed as functional tools in simulating human physiology and metabolism. Future perspectives and major challenges in the development of OOC platforms toward accelerating clinical studies of drug discovery are finally highlighted. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Collaborative Procurement Initiative

EPA Pesticide Factsheets

GPP's Clean Energy Collaborative Procurement Initiative provides a platform for deploying clean energy technologies across multiple government and educational organizations for maximum impact on installed solar system capacity and local economic activity.

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

NASA Astrophysics Data System (ADS)

Liang, Zhixue; Wang, Shui

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

Diversity Performance Analysis on Multiple HAP Networks

PubMed Central

Dong, Feihong; Li, Min; Gong, Xiangwu; Li, Hongjun; Gao, Fengyue

2015-01-01

One of the main design challenges in wireless sensor networks (WSNs) is achieving a high-data-rate transmission for individual sensor devices. The high altitude platform (HAP) is an important communication relay platform for WSNs and next-generation wireless networks. Multiple-input multiple-output (MIMO) techniques provide the diversity and multiplexing gain, which can improve the network performance effectively. In this paper, a virtual MIMO (V-MIMO) model is proposed by networking multiple HAPs with the concept of multiple assets in view (MAV). In a shadowed Rician fading channel, the diversity performance is investigated. The probability density function (PDF) and cumulative distribution function (CDF) of the received signal-to-noise ratio (SNR) are derived. In addition, the average symbol error rate (ASER) with BPSK and QPSK is given for the V-MIMO model. The system capacity is studied for both perfect channel state information (CSI) and unknown CSI individually. The ergodic capacity with various SNR and Rician factors for different network configurations is also analyzed. The simulation results validate the effectiveness of the performance analysis. It is shown that the performance of the HAPs network in WSNs can be significantly improved by utilizing the MAV to achieve overlapping coverage, with the help of the V-MIMO techniques. PMID:26134102

An analytical platform for cumulative impact assessment based on multiple futures: the impact of petroleum drilling and forest harvesting on moose (Alces alces) and marten (Martes americana) habitats in northeastern British Columbia.

PubMed

Strimbu, Bogdan; Innes, John

2011-07-01

The combined influence on the environment of all projects occurring in a single area is evaluated through cumulative impact assessments (CIA), which consider the consequences of multiple projects, each insignificant on its own, yet important when evaluated collectively. Traditionally, future human activities are included in CIA using an analytical platform, commonly based on complex models that supply precise predictions but with reduced accuracy. To compensate for the lack of accuracy in current CIA approaches, we propose a shift in the paradigm governing CIA. The paradigm shift involves a change in the focus of CIA investigations from the detailed analysis of one unlikely future to the identification of the patterns describing multiple potential future changes in the environment. To illustrate the approach, a set of 144 possible and equally likely futures were developed that aimed to identify the potential impacts of forest harvesting and petroleum drilling on the habitat suitability of moose and marten in northeast British Columbia, Canada. The evolution of two measures of habitat suitability (average habitat suitability index and surface of the stands with habitat suitability index >0.5) revealed that the human activities could induce cycles in the habitat dynamics of moose and marten. The planning period of 100 years was separated into three distinct periods following a sinusoidal pattern (i.e., increase - constant - decrease in the habitat suitability measures). The attributes that could induce significant changes in the assessment of environment are the choice of harvesting age and species. Copyright © 2011 Elsevier Ltd. All rights reserved.

Design of the SLAC RCE Platform: A General Purpose ATCA Based Data Acquisition System

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

Herbst, R.; Claus, R.; Freytag, M.

2015-01-23

The SLAC RCE platform is a general purpose clustered data acquisition system implemented on a custom ATCA compliant blade, called the Cluster On Board (COB). The core of the system is the Reconfigurable Cluster Element (RCE), which is a system-on-chip design based upon the Xilinx Zynq family of FPGAs, mounted on custom COB daughter-boards. The Zynq architecture couples a dual core ARM Cortex A9 based processor with a high performance 28nm FPGA. The RCE has 12 external general purpose bi-directional high speed links, each supporting serial rates of up to 12Gbps. 8 RCE nodes are included on a COB, eachmore » with a 10Gbps connection to an on-board 24-port Ethernet switch integrated circuit. The COB is designed to be used with a standard full-mesh ATCA backplane allowing multiple RCE nodes to be tightly interconnected with minimal interconnect latency. Multiple shelves can be clustered using the front panel 10-gbps connections. The COB also supports local and inter-blade timing and trigger distribution. An experiment specific Rear Transition Module adapts the 96 high speed serial links to specific experiments and allows an experiment-specific timing and busy feedback connection. This coupling of processors with a high performance FPGA fabric in a low latency, multiple node cluster allows high speed data processing that can be easily adapted to any physics experiment. RTEMS and Linux are both ported to the module. The RCE has been used or is the baseline for several current and proposed experiments (LCLS, HPS, LSST, ATLAS-CSC, LBNE, DarkSide, ILC-SiD, etc).« less

Common aero vehicle autonomous reentry trajectory optimization satisfying waypoint and no-fly zone constraints

NASA Astrophysics Data System (ADS)

Jorris, Timothy R.

2007-12-01

To support the Air Force's Global Reach concept, a Common Aero Vehicle is being designed to support the Global Strike mission. "Waypoints" are specified for reconnaissance or multiple payload deployments and "no-fly zones" are specified for geopolitical restrictions or threat avoidance. Due to time critical targets and multiple scenario analysis, an autonomous solution is preferred over a time-intensive, manually iterative one. Thus, a real-time or near real-time autonomous trajectory optimization technique is presented to minimize the flight time, satisfy terminal and intermediate constraints, and remain within the specified vehicle heating and control limitations. This research uses the Hypersonic Cruise Vehicle (HCV) as a simplified two-dimensional platform to compare multiple solution techniques. The solution techniques include a unique geometric approach developed herein, a derived analytical dynamic optimization technique, and a rapidly emerging collocation numerical approach. This up-and-coming numerical technique is a direct solution method involving discretization then dualization, with pseudospectral methods and nonlinear programming used to converge to the optimal solution. This numerical approach is applied to the Common Aero Vehicle (CAV) as the test platform for the full three-dimensional reentry trajectory optimization problem. The culmination of this research is the verification of the optimality of this proposed numerical technique, as shown for both the two-dimensional and three-dimensional models. Additionally, user implementation strategies are presented to improve accuracy and enhance solution convergence. Thus, the contributions of this research are the geometric approach, the user implementation strategies, and the determination and verification of a numerical solution technique for the optimal reentry trajectory problem that minimizes time to target while satisfying vehicle dynamics and control limitation, and heating, waypoint, and no-fly zone constraints.

StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform.

PubMed

Zheng, Wenning; Tan, Tze King; Paterson, Ian C; Mutha, Naresh V R; Siow, Cheuk Chuen; Tan, Shi Yang; Old, Lesley A; Jakubovics, Nicholas S; Choo, Siew Woh

2016-01-01

The oral streptococci are spherical Gram-positive bacteria categorized under the phylum Firmicutes which are among the most common causative agents of bacterial infective endocarditis (IE) and are also important agents in septicaemia in neutropenic patients. The Streptococcus mitis group is comprised of 13 species including some of the most common human oral colonizers such as S. mitis, S. oralis, S. sanguinis and S. gordonii as well as species such as S. tigurinus, S. oligofermentans and S. australis that have only recently been classified and are poorly understood at present. We present StreptoBase, which provides a specialized free resource focusing on the genomic analyses of oral species from the mitis group. It currently hosts 104 S. mitis group genomes including 27 novel mitis group strains that we sequenced using the high throughput Illumina HiSeq technology platform, and provides a comprehensive set of genome sequences for analyses, particularly comparative analyses and visualization of both cross-species and cross-strain characteristics of S. mitis group bacteria. StreptoBase incorporates sophisticated in-house designed bioinformatics web tools such as Pairwise Genome Comparison (PGC) tool and Pathogenomic Profiling Tool (PathoProT), which facilitate comparative pathogenomics analysis of Streptococcus strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different S. mitis group bacteria and putative virulence genes profile across multiple streptococcal strains. In conclusion, StreptoBase offers access to a range of streptococci genomic resources as well as analysis tools and will be an invaluable platform to accelerate research in streptococci. Database URL: http://streptococcus.um.edu.my.

Tissue Engineering Platforms to Replicate the Tumor Microenvironment of Multiple Myeloma.

PubMed

Zhang, Wenting; Lee, Woo Y; Zilberberg, Jenny

2017-01-01

We described here the manufacturing and implementation of two prototype perfusion culture devices designed primarily for the cultivation of difficult-to-preserve primary patient-derived multiple myeloma cells (MMC). The first device consists of an osteoblast (OSB)-derived 3D tissue scaffold constructed in a perfused microfluidic environment. The second platform is a 96-well plate-modified perfusion culture device that can be utilized to reconstruct several tissue and tumor microenvironments utilizing both primary human and murine cells. This culture device was designed and fabricated specifically to: (1) enable the preservation of primary MMC for downstream use in biological studies and chemosensitivity analyses and, (2) provide a high-throughput format that is compatible with plate readers specifically seeing that this system is built on an industry standard 96-well tissue culture plate.

EverVIEW: a visualization platform for hydrologic and Earth science gridded data

USGS Publications Warehouse

Romañach, Stephanie S.; McKelvy, James M.; Suir, Kevin J.; Conzelmann, Craig

2015-01-01

The EverVIEW Data Viewer is a cross-platform desktop application that combines and builds upon multiple open source libraries to help users to explore spatially-explicit gridded data stored in Network Common Data Form (NetCDF). Datasets are displayed across multiple side-by-side geographic or tabular displays, showing colorized overlays on an Earth globe or grid cell values, respectively. Time-series datasets can be animated to see how water surface elevation changes through time or how habitat suitability for a particular species might change over time under a given scenario. Initially targeted toward Florida's Everglades restoration planning, EverVIEW has been flexible enough to address the varied needs of large-scale planning beyond Florida, and is currently being used in biological planning efforts nationally and internationally.

Covering Chemical Diversity of Genetically-Modified Tomatoes Using Metabolomics for Objective Substantial Equivalence Assessment

PubMed Central

Hirai, Tadayoshi; Oikawa, Akira; Matsuda, Fumio; Fukushima, Atsushi; Arita, Masanori; Watanabe, Shin; Yano, Megumu; Hiwasa-Tanase, Kyoko; Ezura, Hiroshi; Saito, Kazuki

2011-01-01

As metabolomics can provide a biochemical snapshot of an organism's phenotype it is a promising approach for charting the unintended effects of genetic modification. A critical obstacle for this application is the inherently limited metabolomic coverage of any single analytical platform. We propose using multiple analytical platforms for the direct acquisition of an interpretable data set of estimable chemical diversity. As an example, we report an application of our multi-platform approach that assesses the substantial equivalence of tomatoes over-expressing the taste-modifying protein miraculin. In combination, the chosen platforms detected compounds that represent 86% of the estimated chemical diversity of the metabolites listed in the LycoCyc database. Following a proof-of-safety approach, we show that % had an acceptable range of variation while simultaneously indicating a reproducible transformation-related metabolic signature. We conclude that multi-platform metabolomics is an approach that is both sensitive and robust and that it constitutes a good starting point for characterizing genetically modified organisms. PMID:21359231

Development of an Autonomous, Dual Chamber Bioreactor for the Growth of 3-Dimensional Epithelial-Stromal Tissues in Microgravity

NASA Technical Reports Server (NTRS)

Patel, Zarana S.; Wettergreen, Matthew A.; Huff, Janice L.

2014-01-01

We are developing a novel, autonomous bioreactor that can provide for the growth and maintenance in microgravity of 3-D organotypic epithelial-stromal cultures that require an air-liquid interface. These complex 3-D tissue models accurately represent the morphological features, differentiation markers, and growth characteristics observed in normal human epithelial tissues, including the skin, esophagus, lung, breast, pancreas, and colon. However, because of their precise and complex culture requirements, including that of an air-liquid interface, these 3-D models have yet to be utilized for life sciences research aboard the International Space Station. The development of a bioreactor for these cultures will provide the capability to perform biological research on the ISS using these realistic, tissue-like human epithelial-stromal cell models and will contribute significantly to advances in fundamental space biology research on questions regarding microgravity effects on normal tissue development, aging, cancer, and other disease processes. It will also allow for the study of how combined stressors, such as microgravity with radiation and nutritional deficiencies, affect multiple biological processes and will provide a platform for conducting countermeasure investigations on the ISS without the use of animal models. The technology will be autonomous and consist of a cell culture chamber that provides for air-liquid, liquid-liquid, and liquid-air exchanges within the chambers while maintaining the growth and development of the biological samples. The bioreactor will support multiple tissue types and its modular design will provide for incorporation of add-on capabilities such as microfluidics drug delivery, media sampling, and in situ biomarker analysis. Preliminary flight testing of the hardware will be conducted on a parabolic platform through NASA's Flight Opportunities Program.

Evaluating Precipitation Observed in Complex Terrain During GPM Field Campaigns with the SIMBA Data-Fusion Tool

NASA Astrophysics Data System (ADS)

Wingo, S. M.; Petersen, W. A.; Gatlin, P. N.; Marks, D. A.; Wolff, D. B.; Pabla, C. S.

2017-12-01

The versatile SIMBA (System for Integrating Multi-platform data to Build the Atmospheric column) precipitation data-fusion framework produces an atmospheric column data product with multi-platform observations set into a common 3-D grid, affording an efficient starting point for multi-sensor comparisons and analysis that can be applied to any region. Supported data sources include: ground-based scanning and profiling radars (S-, X-, Ku-, K-, and Ka-band), multiple types of disdrometers and rain gauges, the GPM Core Observatory's Microwave Imager (GMI, 10-183 GHz) and Dual-frequency Precipitation Radar (DPR, Ka/Ku-band), as well as thermodynamic soundings and the Multi-Radar/Multi-Sensor QPE product. SIMBA column data files provide a unique way to evaluate the complete vertical profile of precipitation. Two post-launch (GPM Core in orbit) field campaigns focused on different facets of the GPM mission: the Olympic Mountains Experiment (OLYMPEX) was geared toward winter season (November-February) precipitation in Pacific frontal systems and their transition from the coastal to mountainous terrain of northwest Washington, while the Integrated Precipitation and Hydrology Experiment (IPHEx) sampled warm season (April-June) precipitation and supported hydrologic applications in the southern Appalachians and eastern North Carolina. Both campaigns included multiple orographic precipitation enhancement episodes. SIMBA column products generated for select OLYMPEX and IPHEx events will be used to evaluate spatial variability and vertical profiles of precipitation and drop size distribution parameters derived and/or observed by space- and ground-based sensors. Results will provide a cursory view of how well the space-based measurements represent what is observed from the ground below and an indication to how the terrain in both regions impacts the characteristics of precipitation within the column and reaching the ground.

How smartphones are changing the face of mobile and participatory healthcare: an overview, with example from eCAALYX.

PubMed

Boulos, Maged N Kamel; Wheeler, Steve; Tavares, Carlos; Jones, Ray

2011-04-05

The latest generation of smartphones are increasingly viewed as handheld computers rather than as phones, due to their powerful on-board computing capability, capacious memories, large screens and open operating systems that encourage application development. This paper provides a brief state-of-the-art overview of health and healthcare smartphone apps (applications) on the market today, including emerging trends and market uptake. Platforms available today include Android, Apple iOS, RIM BlackBerry, Symbian, and Windows (Windows Mobile 6.x and the emerging Windows Phone 7 platform). The paper covers apps targeting both laypersons/patients and healthcare professionals in various scenarios, e.g., health, fitness and lifestyle education and management apps; ambient assisted living apps; continuing professional education tools; and apps for public health surveillance. Among the surveyed apps are those assisting in chronic disease management, whether as standalone apps or part of a BAN (Body Area Network) and remote server configuration. We describe in detail the development of a smartphone app within eCAALYX (Enhanced Complete Ambient Assisted Living Experiment, 2009-2012), an EU-funded project for older people with multiple chronic conditions. The eCAALYX Android smartphone app receives input from a BAN (a patient-wearable smart garment with wireless health sensors) and the GPS (Global Positioning System) location sensor in the smartphone, and communicates over the Internet with a remote server accessible by healthcare professionals who are in charge of the remote monitoring and management of the older patient with multiple chronic conditions. Finally, we briefly discuss barriers to adoption of health and healthcare smartphone apps (e.g., cost, network bandwidth and battery power efficiency, usability, privacy issues, etc.), as well as some workarounds to mitigate those barriers.

Evaluating Precipitation Observed in Complex Terrain During GPM Field Campaigns with the SIMBA Data-Fusion Tool

NASA Astrophysics Data System (ADS)

Wingo, S. M.; Petersen, W. A.; Gatlin, P. N.; Marks, D. A.; Wolff, D. B.; Pabla, C. S.

2016-12-01

The versatile SIMBA (System for Integrating Multi-platform data to Build the Atmospheric column) precipitation data-fusion framework produces an atmospheric column data product with multi-platform observations set into a common 3-D grid, affording an efficient starting point for multi-sensor comparisons and analysis that can be applied to any region. Supported data sources include: ground-based scanning and profiling radars (S-, X-, Ku-, K-, and Ka-band), multiple types of disdrometers and rain gauges, the GPM Core Observatory's Microwave Imager (GMI, 10-183 GHz) and Dual-frequency Precipitation Radar (DPR, Ka/Ku-band), as well as thermodynamic soundings and the Multi-Radar/Multi-Sensor QPE product. SIMBA column data files provide a unique way to evaluate the complete vertical profile of precipitation. Two post-launch (GPM Core in orbit) field campaigns focused on different facets of the GPM mission: the Olympic Mountains Experiment (OLYMPEX) was geared toward winter season (November-February) precipitation in Pacific frontal systems and their transition from the coastal to mountainous terrain of northwest Washington, while the Integrated Precipitation and Hydrology Experiment (IPHEx) sampled warm season (April-June) precipitation and supported hydrologic applications in the southern Appalachians and eastern North Carolina. Both campaigns included multiple orographic precipitation enhancement episodes. SIMBA column products generated for select OLYMPEX and IPHEx events will be used to evaluate spatial variability and vertical profiles of precipitation and drop size distribution parameters derived and/or observed by space- and ground-based sensors. Results will provide a cursory view of how well the space-based measurements represent what is observed from the ground below and an indication to how the terrain in both regions impacts the characteristics of precipitation within the column and reaching the ground.

How smartphones are changing the face of mobile and participatory healthcare: an overview, with example from eCAALYX

PubMed Central

2011-01-01

The latest generation of smartphones are increasingly viewed as handheld computers rather than as phones, due to their powerful on-board computing capability, capacious memories, large screens and open operating systems that encourage application development. This paper provides a brief state-of-the-art overview of health and healthcare smartphone apps (applications) on the market today, including emerging trends and market uptake. Platforms available today include Android, Apple iOS, RIM BlackBerry, Symbian, and Windows (Windows Mobile 6.x and the emerging Windows Phone 7 platform). The paper covers apps targeting both laypersons/patients and healthcare professionals in various scenarios, e.g., health, fitness and lifestyle education and management apps; ambient assisted living apps; continuing professional education tools; and apps for public health surveillance. Among the surveyed apps are those assisting in chronic disease management, whether as standalone apps or part of a BAN (Body Area Network) and remote server configuration. We describe in detail the development of a smartphone app within eCAALYX (Enhanced Complete Ambient Assisted Living Experiment, 2009-2012), an EU-funded project for older people with multiple chronic conditions. The eCAALYX Android smartphone app receives input from a BAN (a patient-wearable smart garment with wireless health sensors) and the GPS (Global Positioning System) location sensor in the smartphone, and communicates over the Internet with a remote server accessible by healthcare professionals who are in charge of the remote monitoring and management of the older patient with multiple chronic conditions. Finally, we briefly discuss barriers to adoption of health and healthcare smartphone apps (e.g., cost, network bandwidth and battery power efficiency, usability, privacy issues, etc.), as well as some workarounds to mitigate those barriers. PMID:21466669

A multi-reference filtered-x-Newton narrowband algorithm for active isolation of vibration and experimental investigations

NASA Astrophysics Data System (ADS)

Wang, Chun-yu; He, Lin; Li, Yan; Shuai, Chang-geng

2018-01-01

In engineering applications, ship machinery vibration may be induced by multiple rotational machines sharing a common vibration isolation platform and operating at the same time, and multiple sinusoidal components may be excited. These components may be located at frequencies with large differences or at very close frequencies. A multi-reference filtered-x Newton narrowband (MRFx-Newton) algorithm is proposed to control these multiple sinusoidal components in an MIMO (multiple input and multiple output) system, especially for those located at very close frequencies. The proposed MRFx-Newton algorithm can decouple and suppress multiple sinusoidal components located in the same narrow frequency band even though such components cannot be separated from each other by a narrowband-pass filter. Like the Fx-Newton algorithm, good real-time performance is also achieved by the faster convergence speed brought by the 2nd-order inverse secondary-path filter in the time domain. Experiments are also conducted to verify the feasibility and test the performance of the proposed algorithm installed in an active-passive vibration isolation system in suppressing the vibration excited by an artificial source and air compressor/s. The results show that the proposed algorithm not only has comparable convergence rate as the Fx-Newton algorithm but also has better real-time performance and robustness than the Fx-Newton algorithm in active control of the vibration induced by multiple sound sources/rotational machines working on a shared platform.

Surviving sepsis--a 3D integrative educational simulator.

PubMed

Ježek, Filip; Tribula, Martin; Kulhánek, Tomáš; Mateják, Marek; Privitzer, Pavol; Šilar, Jan; Kofránek, Jiří; Lhotská, Lenka

2015-08-01

Computer technology offers greater educational possibilities, notably simulation and virtual reality. This paper presents a technology which serves to integrate multiple modalities, namely 3D virtual reality, node-based simulator, Physiomodel explorer and explanatory physiological simulators employing Modelica language and Unity3D platform. This emerging tool chain should allow the authors to concentrate more on educational content instead of application development. The technology is demonstrated through Surviving sepsis educational scenario, targeted on Microsoft Windows Store platform.

Constructing Cost-Effective and Targetable ICS Honeypots Suited for Production Networks

DTIC Science & Technology

2015-03-26

introducing Honeyd+ has a marginal impact on performance. Notable findings are that the Raspberry Pi is the preferred hosting platform for the EtherNet/IP... Raspberry Pi or Gumstix, which is a low-cost approach to replicating multiple decoys. One hidden drawback to low- interaction honeypots is the extensive time...EtherNet/IP industrial protocol. Honeyd+ is hosted on a low-cost computing platform ( Raspberry Pi running Raspbian, approximately $50) and a high-cost

Study on the application of mobile internet cloud computing platform

NASA Astrophysics Data System (ADS)

Gong, Songchun; Fu, Songyin; Chen, Zheng

2012-04-01

The innovative development of computer technology promotes the application of the cloud computing platform, which actually is the substitution and exchange of a sort of resource service models and meets the needs of users on the utilization of different resources after changes and adjustments of multiple aspects. "Cloud computing" owns advantages in many aspects which not merely reduce the difficulties to apply the operating system and also make it easy for users to search, acquire and process the resources. In accordance with this point, the author takes the management of digital libraries as the research focus in this paper, and analyzes the key technologies of the mobile internet cloud computing platform in the operation process. The popularization and promotion of computer technology drive people to create the digital library models, and its core idea is to strengthen the optimal management of the library resource information through computers and construct an inquiry and search platform with high performance, allowing the users to access to the necessary information resources at any time. However, the cloud computing is able to promote the computations within the computers to distribute in a large number of distributed computers, and hence implement the connection service of multiple computers. The digital libraries, as a typical representative of the applications of the cloud computing, can be used to carry out an analysis on the key technologies of the cloud computing.

B-CAN: a resource sharing platform to improve the operation, visualization and integrated analysis of TCGA breast cancer data

PubMed Central

Wen, Can-Hong; Ou, Shao-Min; Guo, Xiao-Bo; Liu, Chen-Feng; Shen, Yan-Bo; You, Na; Cai, Wei-Hong; Shen, Wen-Jun; Wang, Xue-Qin; Tan, Hai-Zhu

2017-01-01

Breast cancer is a high-risk heterogeneous disease with myriad subtypes and complicated biological features. The Cancer Genome Atlas (TCGA) breast cancer database provides researchers with the large-scale genome and clinical data via web portals and FTP services. Researchers are able to gain new insights into their related fields, and evaluate experimental discoveries with TCGA. However, it is difficult for researchers who have little experience with database and bioinformatics to access and operate on because of TCGA’s complex data format and diverse files. For ease of use, we build the breast cancer (B-CAN) platform, which enables data customization, data visualization, and private data center. The B-CAN platform runs on Apache server and interacts with the backstage of MySQL database by PHP. Users can customize data based on their needs by combining tables from original TCGA database and selecting variables from each table. The private data center is applicable for private data and two types of customized data. A key feature of the B-CAN is that it provides single table display and multiple table display. Customized data with one barcode corresponding to many records and processed customized data are allowed in Multiple Tables Display. The B-CAN is an intuitive and high-efficient data-sharing platform. PMID:29312567

Efficient exploration of pan-cancer networks by generalized covariance selection and interactive web content

PubMed Central

Kling, Teresia; Johansson, Patrik; Sanchez, José; Marinescu, Voichita D.; Jörnsten, Rebecka; Nelander, Sven

2015-01-01

Statistical network modeling techniques are increasingly important tools to analyze cancer genomics data. However, current tools and resources are not designed to work across multiple diagnoses and technical platforms, thus limiting their applicability to comprehensive pan-cancer datasets such as The Cancer Genome Atlas (TCGA). To address this, we describe a new data driven modeling method, based on generalized Sparse Inverse Covariance Selection (SICS). The method integrates genetic, epigenetic and transcriptional data from multiple cancers, to define links that are present in multiple cancers, a subset of cancers, or a single cancer. It is shown to be statistically robust and effective at detecting direct pathway links in data from TCGA. To facilitate interpretation of the results, we introduce a publicly accessible tool (cancerlandscapes.org), in which the derived networks are explored as interactive web content, linked to several pathway and pharmacological databases. To evaluate the performance of the method, we constructed a model for eight TCGA cancers, using data from 3900 patients. The model rediscovered known mechanisms and contained interesting predictions. Possible applications include prediction of regulatory relationships, comparison of network modules across multiple forms of cancer and identification of drug targets. PMID:25953855

Designing an effective vaccine to prevent Epstein-Barr virus-associated diseases: challenges and opportunities.

PubMed

Dasari, Vijayendra; Bhatt, Kunal H; Smith, Corey; Khanna, Rajiv

2017-04-01

Epstein-Barr virus (EBV) is a ubiquitous herpesvirus associated with a number of clinical manifestations. Primary EBV infection in young adolescents often manifests as acute infectious mononucleosis and latent infection is associated with multiple lymphoid and epithelial cancers and autoimmune disorders, particularly multiple sclerosis. Areas covered: Over the last decade, our understanding of pathogenesis and immune regulation of EBV-associated diseases has provided an important platform for the development of novel vaccine formulations. In this review, we discuss developmental strategies for prophylactic and therapeutic EBV vaccines which have been assessed in preclinical and clinical settings. Expert commentary: Major roadblocks in EBV vaccine development include no precise understanding of the clinical correlates of protection, uncertainty about adjuvant selection and the unavailability of appropriate animal models. Recent development of new EBV vaccine formulations provides exciting opportunities for the formal clinical assessment of novel formulations.

E-learning: controlling costs and increasing value.

PubMed

Walsh, Kieran

2015-04-01

E-learning now accounts for a substantial proportion of medical education provision. This progress has required significant investment and this investment has in turn come under increasing scrutiny so that the costs of e-learning may be controlled and its returns maximised. There are multiple methods by which the costs of e-learning can be controlled and its returns maximised. This short paper reviews some of those methods that are likely to be most effective and that are likely to save costs without compromising quality. Methods might include accessing free or low-cost resources from elsewhere; create short learning resources that will work on multiple devices; using open source platforms to host content; using in-house faculty to create content; sharing resources between institutions; and promoting resources to ensure high usage. Whatever methods are used to control costs or increase value, it is most important to evaluate the impact of these methods.

AXARM: An Extensible Remote Assistance and Monitoring Tool for ND Telerehabilitation

NASA Astrophysics Data System (ADS)

Bueno, Antonio; Marzo, Jose L.; Vallejo, Xavier

AXARM is a multimedia tool for rehabilitation specialists that allow remote assistance and monitoring of patients activities. This tool is the evolution of the work done in 2005-06 between the BCDS research group of UdG and the Multiple Sclerosis Foundation (FEM in Spanish) in Girona under the TRiEM project. Multiple Sclerosis (MS) is a neurodegenerative disease (ND) that can provoke significant exhaustion in patients even just by going to the medical centre for rehabilitation or regular checking visits. The tool presented in this paper allows the medical staff to remotely carry on patient consults and activities from their home, minimizing the displacements to medical consulting. AXARM has a hybrid P2P architecture and consists essentially of a cross-platform videoconference system, with audio/video recording capabilities. The system can easily be extended to include new capabilities like, among others, asynchronous activities whose result can later be analyzed by the medical personnel.

Microbial Monitoring of Pathogens by Comparing Multiple Real-Time PCR Platforms for Potential Space Applications

NASA Technical Reports Server (NTRS)

Birmele, Michele

2012-01-01

The International Space Station (ISS) is a closed environment wih rotations of crew and equipment each introducing their own microbial flora making it necessary to monitor the air, surfaces, and water for microbial contamination. Current microbial monitoring includes labor and time intensive methods to enumerate total bacterial and fungal cells with limited characterization during in-flight testing. Although this culture-based method has been sufficient for monitoring the ISS, future long duration missions will need to perform more comprehensive characterization in-flight, since sample return and ground characterization may not be available. A workshop was held in 2011 at the Johnson Space Center to discuss alternative methodologies and technologies suitable for microbial monitoring for these longterm exploration missions where molecular-based methodologies, such as polymerase chain reaction (PCR), were recommended. In response, a multi-center (Marshall Space Flight Center, Johnson Space Center, Jet Propulsion Laboratory, and Kennedy Space Center) collaborative research effort was initiated to explore novel commercial-off-the-shelf hardware options for spaceflight environmental monitoring. The goal was to evaluate quantitative/semi-quantitative PCR approaches to space applications for low cost in-flight rapid identification of microorganisms affecting crew safety. The initial phase of this project identified commercially available platforms that could be minimally modified to perform nominally in microgravity followed by proof-of-concept testing on the highest qualifying candidates with a universally available test organism, Salmonella enterica. The platforms evaluated during proof-of-concept testing included the iCubate 2.0(TradeMark) (iCubate, Huntsville, AL), RAZOR EX (BioFire Diagnostics; Salt Lake City, Utah) and SmartCycler(TradeMark) (Cepheid; Sunnyvale, CA). The analysis identified two potential technologies (iCubate 2.0 and RAZOR EX) that were able to perform sample-to-answer testing with cell sample concentrations between SO to 400 cells. In addition, the commercial systems were evaluated for initial flight safety and readiness, sample concentration needs were reviewed, and a competitive procurement of commercially available platforms was initiated.

Paleaostress/strain study and its implications for the geodynamic history of the Jabal Akhdar Dome (Oman)

NASA Astrophysics Data System (ADS)

Scharf, Andreas; Amrouch, Khalid; Mattern, Frank

2016-04-01

Field observations, including oolite-, styolite, fracture analyses combined with laboratory measurements using calcite twin analysis show a ductile-to-brittle multiple-phase deformation history of the Arabian carbonate platform, ranging from Late Cretaceous to Neogene times. The Arabian carbonate platform, belonging to a passive continental margin since the Late Permian, was the site of the obduction of Tethyan oceanic lithosphere (Semail Ophiolite) during the Late Cretaceous, caused by the northward drift of Africa (Hanna, 1995). After or during the obduction, large parts of the entire nape pile composed of the Arabian platform and the Hawasina/Semail nappes, where folded and exhumed. This led to the exhumation of the Jabal Akhdar Dome. Our oolite samples from the Jabal Akhdar Dome and from below the ophiolite thrust reveal the strain ellipsoid related to the obduction. This strain ellipsoid shows components of pure and simple shear. In the latter case the longest axes of the strain ellipsoid are parallelly oriented to the direction of obduction (NE to SW), which is in good agreement with the direction of obduction as depicted by Hacker et al. (1996) for the study area. The pure-shear component (flattening) is interpreted to be a result of the overburden of the up to 7 km thick oceanic lithosphere. The oolites that are located approximately 200 m below the ophiolite thrust contact provide evidence for ductile deformation during the Late Cretaceous. These results are compared with strain and stress tensors obtained from styolites, calcite twins and fracture analyses, derived from the uppermost part of the Arabian platform of the Jabal Akhdar Dome. Our results show a complex and detailed structural deformation of the post-obduction history of the Jabal Akhdar Dome, including its folding and exhumation. Hanna, S. (1995) Field guide to the Geology of Oman. Ruwi (Historical Association of Oman. 178 pp. Hacker, B.R., Mosenfelder, J.L. & Gnos, E. (1996) Rapid emplacement of the Oman ophiolite: Thermal and geochronological constraints. Tectonics, 15(6), 1230-1247.

Current test results for the Athena radar responsive tag

NASA Astrophysics Data System (ADS)

Ormesher, Richard C.; Martinez, Ana; Plummer, Kenneth W.; Erlandson, David; Delaware, Sheri; Clark, David R.

2006-05-01

Sandia National Laboratories has teamed with General Atomics and Sierra Monolithics to develop the Athena tag for the Army's Radar Tag Engagement (RaTE) program. The radar-responsive Athena tag can be used for Blue Force tracking and Combat Identification (CID) as well as data collection, identification, and geolocation applications. The Athena tag is small (~4.5" x 2.4" x 4.2"), battery-powered, and has an integral antenna. Once remotely activated by a Synthetic Aperture Radar (SAR) or Moving Target Indicator (MTI) radar, the tag transponds modulated pulses to the radar at a low transmit power. The Athena tag can operate Ku-band and X-band airborne SAR and MTI radars. This paper presents results from current tag development testing activities. Topics covered include recent field tests results from the AN/APY-8 Lynx, F16/APG-66, and F15E/APG-63 V(1) radars and other Fire Control radars. Results show that the Athena tag successfully works with multiple radar platforms, in multiple radar modes, and for multiple applications. Radar-responsive tags such as Athena have numerous applications in military and government arenas. Military applications include battlefield situational awareness, combat identification, targeting, personnel recovery, and unattended ground sensors. Government applications exist in nonproliferation, counter-drug, search-and-rescue, and land-mapping activities.

Circular Bioassay Platforms for Applications in Microwave-Accelerated Techniques.

PubMed

Mohammed, Muzaffer; Clement, Travis C; Aslan, Kadir

2014-12-02

In this paper, we present the design of four different circular bioassay platforms, which are suitable for homogeneous microwave heating, using theoretical calculations (i.e., COMSOL™ multiphysics software). Circular bioassay platforms are constructed from poly(methyl methacrylate) (PMMA) for optical transparency between 400-800 nm, has multiple sample capacity (12, 16, 19 and 21 wells) and modified with silver nanoparticle films (SNFs) to be used in microwave-accelerated bioassays (MABs). In addition, a small monomode microwave cavity, which can be operated with an external microwave generator (100 W), for use with the bioassay platforms in MABs is also developed. Our design parameters for the circular bioassay platforms and monomode microwave cavity during microwave heating were: (i) temperature profiles, (ii) electric field distributions, (iii) location of the circular bioassay platforms inside the microwave cavity, and (iv) design and number of wells on the circular bioassay platforms. We have also carried out additional simulations to assess the use of circular bioassay platforms in a conventional kitchen microwave oven (e.g., 900 W). Our results show that the location of the circular bioassay platforms in the microwave cavity was predicted to have a significant effect on the homogeneous heating of these platforms. The 21-well circular bioassay platform design in our monomode microwave cavity was predicted to offer a homogeneous heating pattern, where inter-well temperature was observed to be in between 23.72-24.13°C and intra-well temperature difference was less than 0.21°C for 60 seconds of microwave heating, which was also verified experimentally.

Circular Bioassay Platforms for Applications in Microwave-Accelerated Techniques

PubMed Central

Mohammed, Muzaffer; Clement, Travis C.; Aslan, Kadir

2014-01-01

In this paper, we present the design of four different circular bioassay platforms, which are suitable for homogeneous microwave heating, using theoretical calculations (i.e., COMSOL™ multiphysics software). Circular bioassay platforms are constructed from poly(methyl methacrylate) (PMMA) for optical transparency between 400–800 nm, has multiple sample capacity (12, 16, 19 and 21 wells) and modified with silver nanoparticle films (SNFs) to be used in microwave-accelerated bioassays (MABs). In addition, a small monomode microwave cavity, which can be operated with an external microwave generator (100 W), for use with the bioassay platforms in MABs is also developed. Our design parameters for the circular bioassay platforms and monomode microwave cavity during microwave heating were: (i) temperature profiles, (ii) electric field distributions, (iii) location of the circular bioassay platforms inside the microwave cavity, and (iv) design and number of wells on the circular bioassay platforms. We have also carried out additional simulations to assess the use of circular bioassay platforms in a conventional kitchen microwave oven (e.g., 900 W). Our results show that the location of the circular bioassay platforms in the microwave cavity was predicted to have a significant effect on the homogeneous heating of these platforms. The 21-well circular bioassay platform design in our monomode microwave cavity was predicted to offer a homogeneous heating pattern, where inter-well temperature was observed to be in between 23.72–24.13°C and intra-well temperature difference was less than 0.21°C for 60 seconds of microwave heating, which was also verified experimentally. PMID:25568813

Parallel k-means++ for Multiple Shared-Memory Architectures

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

Mackey, Patrick S.; Lewis, Robert R.

2016-09-22

In recent years k-means++ has become a popular initialization technique for improved k-means clustering. To date, most of the work done to improve its performance has involved parallelizing algorithms that are only approximations of k-means++. In this paper we present a parallelization of the exact k-means++ algorithm, with a proof of its correctness. We develop implementations for three distinct shared-memory architectures: multicore CPU, high performance GPU, and the massively multithreaded Cray XMT platform. We demonstrate the scalability of the algorithm on each platform. In addition we present a visual approach for showing which platform performed k-means++ the fastest for varyingmore » data sizes.« less

Gas diffusion as a new fluidic unit operation for centrifugal microfluidic platforms.

PubMed

Ymbern, Oriol; Sández, Natàlia; Calvo-López, Antonio; Puyol, Mar; Alonso-Chamarro, Julian

2014-03-07

A centrifugal microfluidic platform prototype with an integrated membrane for gas diffusion is presented for the first time. The centrifugal platform allows multiple and parallel analysis on a single disk and integrates at least ten independent microfluidic subunits, which allow both calibration and sample determination. It is constructed with a polymeric substrate material and it is designed to perform colorimetric determinations by the use of a simple miniaturized optical detection system. The determination of three different analytes, sulfur dioxide, nitrite and carbon dioxide, is carried out as a proof of concept of a versatile microfluidic system for the determination of analytes which involve a gas diffusion separation step during the analytical procedure.

Simultaneous detection of multiple DNA targets by integrating dual-color graphene quantum dot nanoprobes and carbon nanotubes.

PubMed

Qian, Zhaosheng; Shan, Xiaoyue; Chai, Lujing; Chen, Jianrong; Feng, Hui

2014-12-01

Simultaneous detection of multiple DNA targets was achieved based on a biocompatible graphene quantum dots (GQDs) and carbon nanotubes (CNTs) platform through spontaneous assembly between dual-color GQD-based probes and CNTs and subsequently self-recognition between DNA probes and targets. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

UGV Interoperability Profile (IOP) Communications Profile, Version 0

DTIC Science & Technology

2011-12-21

some UGV systems employ Orthogonal Frequency Division Multiplexing ( OFDM ) or Coded Orthogonal Frequency Division Multiplexing (COFDM) waveforms which...other portions of the IOP. Attribute Paragraph Title Values Waveform 3.3 Air Interface/ Waveform OFDM , COFDM, DDL, CDL, None OCU to Platform...Sight MANET Mobile Ad-hoc Network Mbps Megabits per second MC/PM Master Controller/ Payload Manager MHz Megahertz MIMO Multiple Input Multiple

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 Network for Standardized Ocean Color Validation Measurements

NASA Technical Reports Server (NTRS)

Zibordi, Giuseppe; Holben, Brent; Hooker, Stanford; Melin, Frederic; Berthon, Jean-Francois; Slutsker, Ilya; Giles, David; Vandemark, Doug; Feng, Hui; Rutledge, Ken;

Low Cost Real Time Autonomous Remote Monitoring Platform

NASA Astrophysics Data System (ADS)

Rodríguez, J. R.; Maldonado, P. M.; Pierson, J. J.; Harris, L.

2016-02-01

Environmental scientists have a need for gathering multiple parameters during specific time periods to answer their research questions. Most available monitoring systems are very expensive and closed systems, which limits the potential to scale up research projects. We developed a low cost, autonomous, real-time monitoring platform that is both open hardware/software and easy to build, deploy, manage and maintain. The hardware is built with off-the-shelf components and a credit card sized computer called Raspberry Pi, running an open source operating (Raspbian). The system runs off a set of batteries and a solar panel, which makes it ideal for remote locations. The software is divided into three parts: 1) a framework for abstracting the sensors (initializing, pooling and communications) designed in python and using a fully object-oriented design, making it easy for new sensor to be added with minimal code changes, 2) a web front end for managing the entire system, 3) a data store (database) framework for local and remote data retrieval and reporting services. Connectivity to the system can be accomplished through a Wi-Fi or cellular Internet connection. Scientists are being forced to do more with less, in response our platform will provide them with a flexible system that can improve the process of data gathering with an accessible, modular, low-cost, and efficient monitoring system. Currently, we have the required permits from the Department of Natural Resources in Puerto Rico to deploy the platform at the Laguna Grande Bioluminescence Lagoon in Fajardo, PR. This station will include probes for pH, DO, Conductivity and water temperature.

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data

PubMed Central

2016-01-01

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app. PMID:27302480

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data.

PubMed

Riffle, Michael; Jaschob, Daniel; Zelter, Alex; Davis, Trisha N

2016-08-05

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app .

Paradoxical resistance of multiple myeloma to proteasome inhibitors by decreased levels of 19S proteasomal subunits

PubMed Central

Acosta-Alvear, Diego; Cho, Min Y; Wild, Thomas; Buchholz, Tonia J; Lerner, Alana G; Simakova, Olga; Hahn, Jamie; Korde, Neha; Landgren, Ola; Maric, Irina; Choudhary, Chunaram; Walter, Peter; Weissman, Jonathan S; Kampmann, Martin

2015-01-01

Hallmarks of cancer, including rapid growth and aneuploidy, can result in non-oncogene addiction to the proteostasis network that can be exploited clinically. The defining example is the exquisite sensitivity of multiple myeloma (MM) to 20S proteasome inhibitors, such as carfilzomib. However, MM patients invariably acquire resistance to these drugs. Using a next-generation shRNA platform, we found that proteostasis factors, including chaperones and stress-response regulators, controlled the response to carfilzomib. Paradoxically, 19S proteasome regulator knockdown induced resistance to carfilzomib in MM and non-MM cells. 19S subunit knockdown did not affect the activity of the 20S subunits targeted by carfilzomib nor their inhibition by the drug, suggesting an alternative mechanism, such as the selective accumulation of protective factors. In MM patients, lower 19S levels predicted a diminished response to carfilzomib-based therapies. Together, our findings suggest that an understanding of network rewiring can inform development of new combination therapies to overcome drug resistance. DOI: http://dx.doi.org/10.7554/eLife.08153.001 PMID:26327694

Estimation of Genetic Relationships Between Individuals Across Cohorts and Platforms: Application to Childhood Height.

PubMed

Fedko, Iryna O; Hottenga, Jouke-Jan; Medina-Gomez, Carolina; Pappa, Irene; van Beijsterveldt, Catharina E M; Ehli, Erik A; Davies, Gareth E; Rivadeneira, Fernando; Tiemeier, Henning; Swertz, Morris A; Middeldorp, Christel M; Bartels, Meike; Boomsma, Dorret I

2015-09-01

Combining genotype data across cohorts increases power to estimate the heritability due to common single nucleotide polymorphisms (SNPs), based on analyzing a Genetic Relationship Matrix (GRM). However, the combination of SNP data across multiple cohorts may lead to stratification, when for example, different genotyping platforms are used. In the current study, we address issues of combining SNP data from different cohorts, the Netherlands Twin Register (NTR) and the Generation R (GENR) study. Both cohorts include children of Northern European Dutch background (N = 3102 + 2826, respectively) who were genotyped on different platforms. We explore imputation and phasing as a tool and compare three GRM-building strategies, when data from two cohorts are (1) just combined, (2) pre-combined and cross-platform imputed and (3) cross-platform imputed and post-combined. We test these three strategies with data on childhood height for unrelated individuals (N = 3124, average age 6.7 years) to explore their effect on SNP-heritability estimates and compare results to those obtained from the independent studies. All combination strategies result in SNP-heritability estimates with a standard error smaller than those of the independent studies. We did not observe significant difference in estimates of SNP-heritability based on various cross-platform imputed GRMs. SNP-heritability of childhood height was on average estimated as 0.50 (SE = 0.10). Introducing cohort as a covariate resulted in ≈2 % drop. Principal components (PCs) adjustment resulted in SNP-heritability estimates of about 0.39 (SE = 0.11). Strikingly, we did not find significant difference between cross-platform imputed and combined GRMs. All estimates were significant regardless the use of PCs adjustment. Based on these analyses we conclude that imputation with a reference set helps to increase power to estimate SNP-heritability by combining cohorts of the same ethnicity genotyped on different platforms. However, important factors should be taken into account such as remaining cohort stratification after imputation and/or phenotypic heterogeneity between and within cohorts. Whether one should use imputation, or just combine the genotype data, depends on the number of overlapping SNPs in relation to the total number of genotyped SNPs for both cohorts, and their ability to tag all the genetic variance related to the specific trait of interest.

CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment.

PubMed

Chen, Xi; Wang, Chen; Tang, Shanjiang; Yu, Ce; Zou, Quan

2017-06-24

The multiple sequence alignment (MSA) is a classic and powerful technique for sequence analysis in bioinformatics. With the rapid growth of biological datasets, MSA parallelization becomes necessary to keep its running time in an acceptable level. Although there are a lot of work on MSA problems, their approaches are either insufficient or contain some implicit assumptions that limit the generality of usage. First, the information of users' sequences, including the sizes of datasets and the lengths of sequences, can be of arbitrary values and are generally unknown before submitted, which are unfortunately ignored by previous work. Second, the center star strategy is suited for aligning similar sequences. But its first stage, center sequence selection, is highly time-consuming and requires further optimization. Moreover, given the heterogeneous CPU/GPU platform, prior studies consider the MSA parallelization on GPU devices only, making the CPUs idle during the computation. Co-run computation, however, can maximize the utilization of the computing resources by enabling the workload computation on both CPU and GPU simultaneously. This paper presents CMSA, a robust and efficient MSA system for large-scale datasets on the heterogeneous CPU/GPU platform. It performs and optimizes multiple sequence alignment automatically for users' submitted sequences without any assumptions. CMSA adopts the co-run computation model so that both CPU and GPU devices are fully utilized. Moreover, CMSA proposes an improved center star strategy that reduces the time complexity of its center sequence selection process from O(mn 2 ) to O(mn). The experimental results show that CMSA achieves an up to 11× speedup and outperforms the state-of-the-art software. CMSA focuses on the multiple similar RNA/DNA sequence alignment and proposes a novel bitmap based algorithm to improve the center star strategy. We can conclude that harvesting the high performance of modern GPU is a promising approach to accelerate multiple sequence alignment. Besides, adopting the co-run computation model can maximize the entire system utilization significantly. The source code is available at https://github.com/wangvsa/CMSA .

A quantitative model of application slow-down in multi-resource shared systems

DOE PAGES

Lim, Seung-Hwan; Kim, Youngjae

2016-12-26

Scheduling multiple jobs onto a platform enhances system utilization by sharing resources. The benefits from higher resource utilization include reduced cost to construct, operate, and maintain a system, which often include energy consumption. Maximizing these benefits comes at a price-resource contention among jobs increases job completion time. In this study, we analyze slow-downs of jobs due to contention for multiple resources in a system; referred to as dilation factor. We observe that multiple-resource contention creates non-linear dilation factors of jobs. From this observation, we establish a general quantitative model for dilation factors of jobs in multi-resource systems. A job ismore » characterized by a vector-valued loading statistics and dilation factors of a job set are given by a quadratic function of their loading vectors. We demonstrate how to systematically characterize a job, maintain the data structure to calculate the dilation factor (loading matrix), and calculate the dilation factor of each job. We validate the accuracy of the model with multiple processes running on a native Linux server, virtualized servers, and with multiple MapReduce workloads co-scheduled in a cluster. Evaluation with measured data shows that the D-factor model has an error margin of less than 16%. We extended the D-factor model to capture the slow-down of applications when multiple identical resources exist such as multi-core environments and multi-disks environments. Finally, validation results of the extended D-factor model with HPC checkpoint applications on the parallel file systems show that D-factor accurately captures the slow down of concurrent applications in such environments.« less

A quantitative model of application slow-down in multi-resource shared systems

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

Lim, Seung-Hwan; Kim, Youngjae

Scheduling multiple jobs onto a platform enhances system utilization by sharing resources. The benefits from higher resource utilization include reduced cost to construct, operate, and maintain a system, which often include energy consumption. Maximizing these benefits comes at a price-resource contention among jobs increases job completion time. In this study, we analyze slow-downs of jobs due to contention for multiple resources in a system; referred to as dilation factor. We observe that multiple-resource contention creates non-linear dilation factors of jobs. From this observation, we establish a general quantitative model for dilation factors of jobs in multi-resource systems. A job ismore » characterized by a vector-valued loading statistics and dilation factors of a job set are given by a quadratic function of their loading vectors. We demonstrate how to systematically characterize a job, maintain the data structure to calculate the dilation factor (loading matrix), and calculate the dilation factor of each job. We validate the accuracy of the model with multiple processes running on a native Linux server, virtualized servers, and with multiple MapReduce workloads co-scheduled in a cluster. Evaluation with measured data shows that the D-factor model has an error margin of less than 16%. We extended the D-factor model to capture the slow-down of applications when multiple identical resources exist such as multi-core environments and multi-disks environments. Finally, validation results of the extended D-factor model with HPC checkpoint applications on the parallel file systems show that D-factor accurately captures the slow down of concurrent applications in such environments.« less

Mechanically latchable tiltable platform for forming micromirrors and micromirror arrays

DOEpatents

Garcia, Ernest J [Albuquerque, NM; Polosky, Marc A [Tijeras, NM; Sleefe, Gerard E [Cedar Crest, NM

2006-12-12

A microelectromechanical (MEM) apparatus is disclosed which includes a platform that can be electrostatically tilted from being parallel to a substrate on which the platform to being tilted at an angle of 1 20 degrees with respect to the substrate. Once the platform has been tilted to a maximum angle of tilt, the platform can be locked in position using an electrostatically-operable latching mechanism which engages a tab protruding below the platform. The platform has a light-reflective upper surface which can be optionally coated to provide an enhanced reflectivity and form a micromirror. An array of such micromirrors can be formed on a common substrate for applications including optical switching (e.g. for fiber optic communications), optical information processing, image projection displays or non-volatile optical memories.

Users, Uses, and Effects of Social Media in Dietetic Practice: Scoping Review of the Quantitative and Qualitative Evidence.

PubMed

Dumas, Audrée-Anne; Lapointe, Annie; Desroches, Sophie

2018-02-20

Social media platforms are increasingly used by registered dietitians (RDs) to improve knowledge translation and exchange in nutrition. However, a thorough understanding of social media in dietetic practice is lacking. The objective of this study was to map and summarize the evidence about the users, uses, and effects of social media in dietetic practice to identify gaps in the literature and inform future research by using a scoping review methodology. Stages for conducting the scoping review included the following: (1) identifying the research question; (2) identifying relevant studies through a comprehensive multidatabase and gray literature search strategy; (3) selecting eligible studies; (4) charting the data; and (5) collating, summarizing, and reporting results for dissemination. Finally, knowledge users (RDs working for dietetic professional associations and public health organizations) were involved in each review stage to generate practical findings. Of the 47 included studies, 34 were intervention studies, 4 were descriptive studies, 2 were content analysis studies, and 7 were expert opinion papers in dietetic practice. Discussion forums were the most frequent social media platform evaluated (n=19), followed by blogs (n=13) and social networking sites (n=10). Most studies targeted overweight and obese or healthy users, with adult populations being most studied. Social media platforms were used to deliver content as part of larger multiple component interventions for weight management. Among intervention studies using a control group with no exposition to social media, we identified positive, neutral, and mixed effects of social media for outcomes related to users' health behaviors and status (eg, dietary intakes and body weight), participation rates, and professional knowledge. Factors associated with the characteristics of the specific social media, such as ease of use, a design for quick access to desired information, and concurrent reminders of use, were perceived as the main facilitators to the use of social media in dietetic practice, followed to a lesser extent by interactions with an RD and social support from fellow users. Barriers to social media use were mostly related to complicated access to the site and time issues. Research on social media in dietetic practice is at its infancy, but it is growing fast. So far, this field of research has targeted few social media platforms, most of which were assessed in multiple-component interventions for weight management among overweight or obese adults. Trials isolating the effects and mechanisms of action of specific social media platforms are needed to draw conclusions regarding the effectiveness of those tools to support dietetic practice. Future studies should address barriers and facilitators related to the use of social media written by RDs and should explore how to make these tools useful for RDs to reach health consumers to improve health through diet. ©Audrée-Anne Dumas, Annie Lapointe, Sophie Desroches. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 20.02.2018.

Users, Uses, and Effects of Social Media in Dietetic Practice: Scoping Review of the Quantitative and Qualitative Evidence

PubMed Central

2018-01-01

Background Social media platforms are increasingly used by registered dietitians (RDs) to improve knowledge translation and exchange in nutrition. However, a thorough understanding of social media in dietetic practice is lacking. Objective The objective of this study was to map and summarize the evidence about the users, uses, and effects of social media in dietetic practice to identify gaps in the literature and inform future research by using a scoping review methodology. Methods Stages for conducting the scoping review included the following: (1) identifying the research question; (2) identifying relevant studies through a comprehensive multidatabase and gray literature search strategy; (3) selecting eligible studies; (4) charting the data; and (5) collating, summarizing, and reporting results for dissemination. Finally, knowledge users (RDs working for dietetic professional associations and public health organizations) were involved in each review stage to generate practical findings. Results Of the 47 included studies, 34 were intervention studies, 4 were descriptive studies, 2 were content analysis studies, and 7 were expert opinion papers in dietetic practice. Discussion forums were the most frequent social media platform evaluated (n=19), followed by blogs (n=13) and social networking sites (n=10). Most studies targeted overweight and obese or healthy users, with adult populations being most studied. Social media platforms were used to deliver content as part of larger multiple component interventions for weight management. Among intervention studies using a control group with no exposition to social media, we identified positive, neutral, and mixed effects of social media for outcomes related to users’ health behaviors and status (eg, dietary intakes and body weight), participation rates, and professional knowledge. Factors associated with the characteristics of the specific social media, such as ease of use, a design for quick access to desired information, and concurrent reminders of use, were perceived as the main facilitators to the use of social media in dietetic practice, followed to a lesser extent by interactions with an RD and social support from fellow users. Barriers to social media use were mostly related to complicated access to the site and time issues. Conclusions Research on social media in dietetic practice is at its infancy, but it is growing fast. So far, this field of research has targeted few social media platforms, most of which were assessed in multiple-component interventions for weight management among overweight or obese adults. Trials isolating the effects and mechanisms of action of specific social media platforms are needed to draw conclusions regarding the effectiveness of those tools to support dietetic practice. Future studies should address barriers and facilitators related to the use of social media written by RDs and should explore how to make these tools useful for RDs to reach health consumers to improve health through diet. PMID:29463487

A Universal and Robust Integrated Platform for the Scalable Production of Human Cardiomyocytes From Pluripotent Stem Cells.

PubMed

Fonoudi, Hananeh; Ansari, Hassan; Abbasalizadeh, Saeed; Larijani, Mehran Rezaei; Kiani, Sahar; Hashemizadeh, Shiva; Zarchi, Ali Sharifi; Bosman, Alexis; Blue, Gillian M; Pahlavan, Sara; Perry, Matthew; Orr, Yishay; Mayorchak, Yaroslav; Vandenberg, Jamie; Talkhabi, Mahmood; Winlaw, David S; Harvey, Richard P; Aghdami, Nasser; Baharvand, Hossein

2015-12-01

Recent advances in the generation of cardiomyocytes (CMs) from human pluripotent stem cells (hPSCs), in conjunction with the promising outcomes from preclinical and clinical studies, have raised new hopes for cardiac cell therapy. We report the development of a scalable, robust, and integrated differentiation platform for large-scale production of hPSC-CM aggregates in a stirred suspension bioreactor as a single-unit operation. Precise modulation of the differentiation process by small molecule activation of WNT signaling, followed by inactivation of transforming growth factor-β and WNT signaling and activation of sonic hedgehog signaling in hPSCs as size-controlled aggregates led to the generation of approximately 100% beating CM spheroids containing virtually pure (∼90%) CMs in 10 days. Moreover, the developed differentiation strategy was universal, as demonstrated by testing multiple hPSC lines (5 human embryonic stem cell and 4 human inducible PSC lines) without cell sorting or selection. The produced hPSC-CMs successfully expressed canonical lineage-specific markers and showed high functionality, as demonstrated by microelectrode array and electrophysiology tests. This robust and universal platform could become a valuable tool for the mass production of functional hPSC-CMs as a prerequisite for realizing their promising potential for therapeutic and industrial applications, including drug discovery and toxicity assays. Recent advances in the generation of cardiomyocytes (CMs) from human pluripotent stem cells (hPSCs) and the development of novel cell therapy strategies using hPSC-CMs (e.g., cardiac patches) in conjunction with promising preclinical and clinical studies, have raised new hopes for patients with end-stage cardiovascular disease, which remains the leading cause of morbidity and mortality globally. In this study, a simplified, scalable, robust, and integrated differentiation platform was developed to generate clinical grade hPSC-CMs as cell aggregates under chemically defined culture conditions. This approach resulted in approximately 100% beating CM spheroids with virtually pure (∼90%) functional cardiomyocytes in 10 days from multiple hPSC lines. This universal and robust bioprocessing platform can provide sufficient numbers of hPSC-CMs for companies developing regenerative medicine technologies to rescue, replace, and help repair damaged heart tissues and for pharmaceutical companies developing advanced biologics and drugs for regeneration of lost heart tissue using high-throughput technologies. It is believed that this technology can expedite clinical progress in these areas to achieve a meaningful impact on improving clinical outcomes, cost of care, and quality of life for those patients disabled and experiencing heart disease. ©AlphaMed Press.

A Universal and Robust Integrated Platform for the Scalable Production of Human Cardiomyocytes From Pluripotent Stem Cells

PubMed Central

Fonoudi, Hananeh; Ansari, Hassan; Abbasalizadeh, Saeed; Larijani, Mehran Rezaei; Kiani, Sahar; Hashemizadeh, Shiva; Zarchi, Ali Sharifi; Bosman, Alexis; Blue, Gillian M.; Pahlavan, Sara; Perry, Matthew; Orr, Yishay; Mayorchak, Yaroslav; Vandenberg, Jamie; Talkhabi, Mahmood; Winlaw, David S.; Harvey, Richard P.; Aghdami, Nasser

2015-01-01

Recent advances in the generation of cardiomyocytes (CMs) from human pluripotent stem cells (hPSCs), in conjunction with the promising outcomes from preclinical and clinical studies, have raised new hopes for cardiac cell therapy. We report the development of a scalable, robust, and integrated differentiation platform for large-scale production of hPSC-CM aggregates in a stirred suspension bioreactor as a single-unit operation. Precise modulation of the differentiation process by small molecule activation of WNT signaling, followed by inactivation of transforming growth factor-β and WNT signaling and activation of sonic hedgehog signaling in hPSCs as size-controlled aggregates led to the generation of approximately 100% beating CM spheroids containing virtually pure (∼90%) CMs in 10 days. Moreover, the developed differentiation strategy was universal, as demonstrated by testing multiple hPSC lines (5 human embryonic stem cell and 4 human inducible PSC lines) without cell sorting or selection. The produced hPSC-CMs successfully expressed canonical lineage-specific markers and showed high functionality, as demonstrated by microelectrode array and electrophysiology tests. This robust and universal platform could become a valuable tool for the mass production of functional hPSC-CMs as a prerequisite for realizing their promising potential for therapeutic and industrial applications, including drug discovery and toxicity assays. Significance Recent advances in the generation of cardiomyocytes (CMs) from human pluripotent stem cells (hPSCs) and the development of novel cell therapy strategies using hPSC-CMs (e.g., cardiac patches) in conjunction with promising preclinical and clinical studies, have raised new hopes for patients with end-stage cardiovascular disease, which remains the leading cause of morbidity and mortality globally. In this study, a simplified, scalable, robust, and integrated differentiation platform was developed to generate clinical grade hPSC-CMs as cell aggregates under chemically defined culture conditions. This approach resulted in approximately 100% beating CM spheroids with virtually pure (∼90%) functional cardiomyocytes in 10 days from multiple hPSC lines. This universal and robust bioprocessing platform can provide sufficient numbers of hPSC-CMs for companies developing regenerative medicine technologies to rescue, replace, and help repair damaged heart tissues and for pharmaceutical companies developing advanced biologics and drugs for regeneration of lost heart tissue using high-throughput technologies. It is believed that this technology can expedite clinical progress in these areas to achieve a meaningful impact on improving clinical outcomes, cost of care, and quality of life for those patients disabled and experiencing heart disease. PMID:26511653