Novel Developments of Mobile Sensing Based on the Integration of Microfluidic Devices and Smartphone

PubMed Central

Yang, Ke; Peretz-Soroka, Hagit; Liu, Yong; Lin, Francis

2016-01-01

Portable electronic devices and wireless communication systems enable a broad range of applications such as environmental and food safety monitoring, personalized medicine and healthcare management. Particularly, hybrid smartphone and microfluidic devices provide an integrated solution for the new generation of mobile sensing applications. Such mobile sensing based on microfluidic devices (broadly defined) and smartphones (MS2) offers a mobile laboratory for performing a wide range of bio-chemical detection and analysis functions such as water and food quality analysis, routine health tests and disease diagnosis. MS2 offers significant advantages over traditional platforms in terms of test speed and control, low cost, mobility, ease-of-operation and data management. These improvements put MS2 in a promising position in the fields of interdisciplinary basic and applied research. In particular, MS2 enables applications to remote infield testing, homecare, and healthcare in low-resource areas. The marriage of smartphones and microfluidic devices offers a powerful on-chip operating platform to enable various bio-chemical tests, remote sensing, data analysis and management in a mobile fashion. The implications of such integration are beyond telecommunication and microfluidic-related research and technology development. In this review, we will first provide the general background of microfluidic-based sensing, smartphone-based sensing, and their integration. Then, we will focus on several key application areas of MS2 by systematically reviewing the important literature in each area. We will conclude by discussing our perspectives on the opportunities, issues and future directions of this emerging novel field. PMID:26899264

2009 Biochemical Conversion Platform Review Report

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

Ferrell, John

2009-12-01

This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the U.S. Department of Energy Biomass Program’s Biochemical Conversion platform review meeting, held on April 14-16, 2009, at the Sheraton Denver Downtown, Denver, Colorado.

A novel biochemical platform for fuels and chemicals production from cellulosic biomass

USDA-ARS?s Scientific Manuscript database

The conventional biochemical platform for biofuels production featuring enzymatic hydrolysis involves five key steps: pretreatment, cellulase production, enzymatic hydrolysis, fermentation, and product recovery. Sugars are produced as reactive intermediates for subsequent fermentation to fuels and c...

Optical devices for biochemical sensing in flame hydrolysis deposited glass

NASA Astrophysics Data System (ADS)

Ruano-Lopez, Jesus M.

Previous research in the field of Flame Hydrolysis Deposition (FHD) of glasses has focused on the production of low cost optical devices for the field of telecommunications. The originality of this doctoral research resides in the exploration of this technology in the fabrication of optical bio-chemical sensors, with integrated "Lab-on-a-chip" devices. To achieve this goal, we have combined and applied different microfabrication processes for the manufacture of sensor platforms using FHD. These structures are unique in that they take advantage of the intrinsic benefits of the microfabrication process, such as, miniaturisation and mass production, and combine them with the properties of FHD glass, namely: low loss optical transducing mechanisms, planar technologies and monolithic integration. This thesis demonstrates that FHD is a suitable technology for biosensing and Lab- on-a-Chip applications. The objective is to provide future researchers with the necessary tools to accomplish an integrated analytical system based on FHD. We have designed, fabricated, and successfully tested a FHD miniaturised sensor, which comprised optical and microfluidic circuitry, in the framework of low volume fluorescence assays. For the first time, volumes as low as 570 pL were analysed with a Cyanine-5 fluorophore with a detection limit of 20 pM, or ca. 6000 molecules (+/-3sigma) for this platform. The fabrication of the sensor generated a compilation of processes that were then utilised to produce other possible optical platforms for bio-chemical sensors in FHD, e.g. arrays and microfluidics. The "catalogue" of methods used included new recipes for reactive ion etching, glass deposition and bonding techniques that enabled the development of the microfluidic circuitry, integrated with an optical circuitry. Furthermore, we developed techniques to implement new tasks such as optical signal treatment using integrated optical structures, planar arraying of sensors, a separating element for liquid chromatography, and finally a pumping system for delivering small amounts of liquid along the microfluidic channels. This thesis comprises six chapters. In Chapter 1, an overview of the topic was presented, offering a review of the various fields addressed, as well as a description of the motivation and originality of this work. Chapter 2 describes the processes developed to fabricate an optical sensor, and Chapter 3 assesses its performance. In Chapter 4, integrated optical circuit designs and their fabrication methods, as well as developing and testing of an array of sensors, are presented. The description of a separating element involved in a liquid chromatography system, and the pumping of liquids in a FHD optical device, were addressed in Chapter 5. Finally, Chapter 6 summarised the conclusions and suggested possible future work. Last but not least, the appendix, contains techniques for hybrid integration; recipes for etching of rare earth glasses; as well as instrumentation designs. This research has taken Flame Hydrolysis Deposition technique into the world of optical bio-chemical sensors, creating a bridge between analytical assays and FHD glass. In this respect, the demonstrated flexibility of the technology will enable a variety of configurations to be created and implemented, with the prospect of using the techniques for laboratory-on-a-chip technologies. The work has been patented by the University of Glasgow, for future exploitation in analytical biotechnology and Lab-on-a-Chip.

Integrated electrochemical microsystems for genetic detection of pathogens at the point of care.

PubMed

Hsieh, Kuangwen; Ferguson, B Scott; Eisenstein, Michael; Plaxco, Kevin W; Soh, H Tom

2015-04-21

The capacity to achieve rapid, sensitive, specific, quantitative, and multiplexed genetic detection of pathogens via a robust, portable, point-of-care platform could transform many diagnostic applications. And while contemporary technologies have yet to effectively achieve this goal, the advent of microfluidics provides a potentially viable approach to this end by enabling the integration of sophisticated multistep biochemical assays (e.g., sample preparation, genetic amplification, and quantitative detection) in a monolithic, portable device from relatively small biological samples. Integrated electrochemical sensors offer a particularly promising solution to genetic detection because they do not require optical instrumentation and are readily compatible with both integrated circuit and microfluidic technologies. Nevertheless, the development of generalizable microfluidic electrochemical platforms that integrate sample preparation and amplification as well as quantitative and multiplexed detection remains a challenging and unsolved technical problem. Recognizing this unmet need, we have developed a series of microfluidic electrochemical DNA sensors that have progressively evolved to encompass each of these critical functionalities. For DNA detection, our platforms employ label-free, single-step, and sequence-specific electrochemical DNA (E-DNA) sensors, in which an electrode-bound, redox-reporter-modified DNA "probe" generates a current change after undergoing a hybridization-induced conformational change. After successfully integrating E-DNA sensors into a microfluidic chip format, we subsequently incorporated on-chip genetic amplification techniques including polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) to enable genetic detection at clinically relevant target concentrations. To maximize the potential point-of-care utility of our platforms, we have further integrated sample preparation via immunomagnetic separation, which allowed the detection of influenza virus directly from throat swabs and developed strategies for the multiplexed detection of related bacterial strains from the blood of septic mice. Finally, we developed an alternative electrochemical detection platform based on real-time LAMP, which not is only capable of detecting across a broad dynamic range of target concentrations, but also greatly simplifies quantitative measurement of nucleic acids. These efforts represent considerable progress toward the development of a true sample-in-answer-out platform for genetic detection of pathogens at the point of care. Given the many advantages of these systems, and the growing interest and innovative contributions from researchers in this field, we are optimistic that iterations of these systems will arrive in clinical settings in the foreseeable future.

Integration of biochemical sensors into wearable biomaterial platforms

NASA Astrophysics Data System (ADS)

Jandhyala, Sidhartha; Walper, Scott A.; Cargill, Allison A.; Ozual, Abigail; Daniele, Michael A.

2016-05-01

With rapidly inflating healthcare costs, a limited supply of physicians and an alarming surge in lifestyle diseases, radical changes must be made to improve preventative medicine and ensure a sustainable healthcare system. A compelling solution is to equip the population with wearable health monitors to continuously record representative and actionable physiological data. Herein, we present a preliminary design and evaluation of a biochemical sensor node enabled by a substrate comprised of a nanocellulose thin-film that conforms to the skin and carries a printed sensor element. The nanocellulose layer ensures conformal and biocompatible contact with the skin, while a printed layer provides a high surface-area electrode. While the recognition/transduction element can be exchanged for many different sensing motifs, we utilize the general structure of an electrochemical glucose sensor.

NREL 2012 Achievement of Ethanol Cost Targets: Biochemical Ethanol Fermentation via Dilute-Acid Pretreatment and Enzymatic Hydrolysis of Corn Stover

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

Tao, L.; Schell, D.; Davis, R.

2014-04-01

For the DOE Bioenergy Technologies Office, the annual State of Technology (SOT) assessment is an essential activity for quantifying the benefits of biochemical platform research. This assessment has historically allowed the impact of research progress achieved through targeted Bioenergy Technologies Office funding to be quantified in terms of economic improvements within the context of a fully integrated cellulosic ethanol production process. As such, progress toward the ultimate 2012 goal of demonstrating cost-competitive cellulosic ethanol technology can be tracked. With an assumed feedstock cost for corn stover of $58.50/ton this target has historically been set at $1.41/gal ethanol for conversion costsmore » only (exclusive of feedstock) and $2.15/gal total production cost (inclusive of feedstock) or minimum ethanol selling price (MESP). This year, fully integrated cellulosic ethanol production data generated by National Renewable Energy Laboratory (NREL) researchers in their Integrated Biorefinery Research Facility (IBRF) successfully demonstrated performance commensurate with both the FY 2012 SOT MESP target of $2.15/gal (2007$, $58.50/ton feedstock cost) and the conversion target of $1.41/gal through core research and process improvements in pretreatment, enzymatic hydrolysis, and fermentation.« less

Combinatorial screening of 3D biomaterial properties that promote myofibrogenesis for mesenchymal stromal cell-based heart valve tissue engineering.

PubMed

Usprech, Jenna; Romero, David A; Amon, Cristina H; Simmons, Craig A

2017-08-01

The physical and chemical properties of a biomaterial integrate with soluble cues in the cell microenvironment to direct cell fate and function. Predictable biomaterial-based control of integrated cell responses has been investigated with two-dimensional (2D) screening platforms, but integrated responses in 3D have largely not been explored systematically. To address this need, we developed a screening platform using polyethylene glycol norbornene (PEG-NB) as a model biomaterial with which the polymer wt% (to control elastic modulus) and adhesion peptide types (RGD, DGEA, YIGSR) and densities could be controlled independently and combinatorially in arrays of 3D hydrogels. We applied this platform and regression modeling to identify combinations of biomaterial and soluble biochemical (TGF-β1) factors that best promoted myofibrogenesis of human mesenchymal stromal cells (hMSCs) in order to inform our understanding of regenerative processes for heart valve tissue engineering. In contrast to 2D culture, our screens revealed that soft hydrogels (low PEG-NB wt%) best promoted spread myofibroblastic cells that expressed high levels of α-smooth muscle actin (α-SMA) and collagen type I. High concentrations of RGD enhanced α-SMA expression in the presence of TGF-β1 and cell spreading regardless of whether TGF-β1 was in the culture medium. Strikingly, combinations of peptides that maximized collagen expression depended on the presence or absence of TGF-β1, indicating that biomaterial properties can modulate MSC response to soluble signals. This combination of a 3D biomaterial array screening platform with statistical modeling is broadly applicable to systematically identify combinations of biomaterial and microenvironmental conditions that optimally guide cell responses. We present a novel screening platform and methodology to model and identify how combinations of biomaterial and microenvironmental conditions guide cell phenotypes in 3D. Our approach to systematically identify complex relationships between microenvironmental cues and cell responses enables greater predictive power over cell fate in conditions with interacting material design factors. We demonstrate that this approach not only predicts that mesenchymal stromal cell (MSC) myofibrogenesis is promoted by soft, porous 3D biomaterials, but also generated new insights which demonstrate how biomaterial properties can differentially modulate MSC response to soluble signals. An additional benefit of the process includes utilizing both parametric and non parametric analyses which can demonstrate dominant significant trends as well as subtle interactions between biochemical and biomaterial cues. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Flexible Sensory Platform Based on Oxide-based Neuromorphic Transistors

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Flexible Sensory Platform Based on Oxide-based Neuromorphic Transistors

PubMed Central

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

2015-01-01

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

CHRONIOUS: a wearable platform for monitoring and management of patients with chronic disease.

PubMed

Bellos, Christos; Papadopoulos, Athanassios; Rosso, Roberto; Fotiadis, Dimitrios I

2011-01-01

The CHRONIOUS system has been developed based on an open architecture design that consists of a set of subsystems which interact in order to provide all the needed services to the chronic disease patients. An advanced multi-parametric expert system is being implemented that fuses information effectively from various sources using intelligent techniques. Data are collected by sensors of a body network controlling vital signals while additional tools record dietary habits and plans, drug intake, environmental and biochemical parameters and activity data. The CHRONIOUS platform provides guidelines and standards for the future generations of "chronic disease management systems" and facilitates sophisticated monitoring tools. In addition, an ontological information retrieval system is being delivered satisfying the necessities for up-to-date clinical information of Chronic Obstructive pulmonary disease (COPD) and Chronic Kidney Disease (CKD). Moreover, support tools are being embedded in the system, such as the Mental Tools for the monitoring of patient mental health status. The integrated platform provides real-time patient monitoring and supervision, both indoors and outdoors and represents a generic platform for the management of various chronic diseases.

Recent Advances in Nanobiotechnology and High-Throughput Molecular Techniques for Systems Biomedicine

PubMed Central

Kim, Eung-Sam; Ahn, Eun Hyun; Chung, Euiheon; Kim, Deok-Ho

2013-01-01

Nanotechnology-based tools are beginning to emerge as promising platforms for quantitative high-throughput analysis of live cells and tissues. Despite unprecedented progress made over the last decade, a challenge still lies in integrating emerging nanotechnology-based tools into macroscopic biomedical apparatuses for practical purposes in biomedical sciences. In this review, we discuss the recent advances and limitations in the analysis and control of mechanical, biochemical, fluidic, and optical interactions in the interface areas of nanotechnology-based materials and living cells in both in vitro and in vivo settings. PMID:24258011

Recent advances in nanobiotechnology and high-throughput molecular techniques for systems biomedicine.

PubMed

Kim, Eung-Sam; Ahn, Eun Hyun; Chung, Euiheon; Kim, Deok-Ho

2013-12-01

Nanotechnology-based tools are beginning to emerge as promising platforms for quantitative high-throughput analysis of live cells and tissues. Despite unprecedented progress made over the last decade, a challenge still lies in integrating emerging nanotechnology-based tools into macroscopic biomedical apparatuses for practical purposes in biomedical sciences. In this review, we discuss the recent advances and limitations in the analysis and control of mechanical, biochemical, fluidic, and optical interactions in the interface areas of nanotechnologybased materials and living cells in both in vitro and in vivo settings.

Disruption of SMIM1 causes the Vel− blood type

PubMed Central

Ballif, Bryan A; Helias, Virginie; Peyrard, Thierry; Menanteau, Cécile; Saison, Carole; Lucien, Nicole; Bourgouin, Sébastien; Le Gall, Maude; Cartron, Jean-Pierre; Arnaud, Lionel

2013-01-01

Here, we report the biochemical and genetic basis of the Vel blood group antigen, which has been a vexing mystery for decades, especially as anti-Vel regularly causes severe haemolytic transfusion reactions. The protein carrying the Vel blood group antigen was biochemically purified from red blood cell membranes. Mass spectrometry-based de novo peptide sequencing identified this protein to be small integral membrane protein 1 (SMIM1), a previously uncharacterized single-pass membrane protein. Expression of SMIM1 cDNA in Vel− cultured cells generated anti-Vel cell surface reactivity, confirming that SMIM1 encoded the Vel blood group antigen. A cohort of 70 Vel− individuals was found to be uniformly homozygous for a 17 nucleotide deletion in the coding sequence of SMIM1. The genetic homogeneity of the Vel− blood type, likely having a common origin, facilitated the development of two highly specific DNA-based tests for rapid Vel genotyping, which can be easily integrated into blood group genotyping platforms. These results answer a 60-year-old riddle and provide tools of immediate assistance to all clinicians involved in the care of Vel− patients. PMID:23505126

Integrative Utilization of Microenvironments, Biomaterials and Computational Techniques for Advanced Tissue Engineering.

PubMed

Shamloo, Amir; Mohammadaliha, Negar; Mohseni, Mina

2015-10-20

This review aims to propose the integrative implementation of microfluidic devices, biomaterials, and computational methods that can lead to a significant progress in tissue engineering and regenerative medicine researches. Simultaneous implementation of multiple techniques can be very helpful in addressing biological processes. Providing controllable biochemical and biomechanical cues within artificial extracellular matrix similar to in vivo conditions is crucial in tissue engineering and regenerative medicine researches. Microfluidic devices provide precise spatial and temporal control over cell microenvironment. Moreover, generation of accurate and controllable spatial and temporal gradients of biochemical factors is attainable inside microdevices. Since biomaterials with tunable properties are a worthwhile option to construct artificial extracellular matrix, in vitro platforms that simultaneously utilize natural, synthetic, or engineered biomaterials inside microfluidic devices are phenomenally advantageous to experimental studies in the field of tissue engineering. Additionally, collaboration between experimental and computational methods is a useful way to predict and understand mechanisms responsible for complex biological phenomena. Computational results can be verified by using experimental platforms. Computational methods can also broaden the understanding of the mechanisms behind the biological phenomena observed during experiments. Furthermore, computational methods are powerful tools to optimize the fabrication of microfluidic devices and biomaterials with specific features. Here we present a succinct review of the benefits of microfluidic devices, biomaterial, and computational methods in the case of tissue engineering and regeneration medicine. Furthermore, some breakthroughs in biological phenomena including the neuronal axon development, cancerous cell migration and blood vessel formation via angiogenesis by virtue of the aforementioned approaches are discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

A review of digital microfluidics as portable platforms for lab-on a-chip applications.

PubMed

Samiei, Ehsan; Tabrizian, Maryam; Hoorfar, Mina

2016-07-07

Following the development of microfluidic systems, there has been a high tendency towards developing lab-on-a-chip devices for biochemical applications. A great deal of effort has been devoted to improve and advance these devices with the goal of performing complete sets of biochemical assays on the device and possibly developing portable platforms for point of care applications. Among the different microfluidic systems used for such a purpose, digital microfluidics (DMF) shows high flexibility and capability of performing multiplex and parallel biochemical operations, and hence, has been considered as a suitable candidate for lab-on-a-chip applications. In this review, we discuss the most recent advances in the DMF platforms, and evaluate the feasibility of developing multifunctional packages for performing complete sets of processes of biochemical assays, particularly for point-of-care applications. The progress in the development of DMF systems is reviewed from eight different aspects, including device fabrication, basic fluidic operations, automation, manipulation of biological samples, advanced operations, detection, biological applications, and finally, packaging and portability of the DMF devices. Success in developing the lab-on-a-chip DMF devices will be concluded based on the advances achieved in each of these aspects.

Integrating the glioblastoma microenvironment into engineered experimental models

PubMed Central

Xiao, Weikun; Sohrabi, Alireza; Seidlits, Stephanie K

2017-01-01

Glioblastoma (GBM) is the most lethal cancer originating in the brain. Its high mortality rate has been attributed to therapeutic resistance and rapid, diffuse invasion – both of which are strongly influenced by the unique microenvironment. Thus, there is a need to develop new models that mimic individual microenvironmental features and are able to provide clinically relevant data. Current understanding of the effects of the microenvironment on GBM progression, established experimental models of GBM and recent developments using bioengineered microenvironments as ex vivo experimental platforms that mimic the biochemical and physical properties of GBM tumors are discussed. PMID:28883992

Concise Review: Organ Engineering: Design, Technology, and Integration.

PubMed

Kaushik, Gaurav; Leijten, Jeroen; Khademhosseini, Ali

2017-01-01

Engineering complex tissues and whole organs has the potential to dramatically impact translational medicine in several avenues. Organ engineering is a discipline that integrates biological knowledge of embryological development, anatomy, physiology, and cellular interactions with enabling technologies including biocompatible biomaterials and biofabrication platforms such as three-dimensional bioprinting. When engineering complex tissues and organs, core design principles must be taken into account, such as the structure-function relationship, biochemical signaling, mechanics, gradients, and spatial constraints. Technological advances in biomaterials, biofabrication, and biomedical imaging allow for in vitro control of these factors to recreate in vivo phenomena. Finally, organ engineering emerges as an integration of biological design and technical rigor. An overall workflow for organ engineering and guiding technology to advance biology as well as a perspective on necessary future iterations in the field is discussed. Stem Cells 2017;35:51-60. © 2016 AlphaMed Press.

Seamless integration of dose-response screening and flow chemistry: efficient generation of structure-activity relationship data of β-secretase (BACE1) inhibitors.

PubMed

Werner, Michael; Kuratli, Christoph; Martin, Rainer E; Hochstrasser, Remo; Wechsler, David; Enderle, Thilo; Alanine, Alexander I; Vogel, Horst

2014-02-03

Drug discovery is a multifaceted endeavor encompassing as its core element the generation of structure-activity relationship (SAR) data by repeated chemical synthesis and biological testing of tailored molecules. Herein, we report on the development of a flow-based biochemical assay and its seamless integration into a fully automated system comprising flow chemical synthesis, purification and in-line quantification of compound concentration. This novel synthesis-screening platform enables to obtain SAR data on b-secretase (BACE1) inhibitors at an unprecedented cycle time of only 1 h instead of several days. Full integration and automation of industrial processes have always led to productivity gains and cost reductions, and this work demonstrates how applying these concepts to SAR generation may lead to a more efficient drug discovery process. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Complexity and performance of on-chip biochemical assays

NASA Astrophysics Data System (ADS)

Kopf-Sill, Anne R.; Nikiforov, Theo; Bousse, Luc J.; Nagle, Rob; Parce, J. W.

1997-03-01

The use of microchips for performing biochemical processes has the potential to reduce reagent use and thus assay costs, increase throughput, and automate complex processes. We are building a multifunctional platform that provides sensing and actuation functions for a variety of microchip- based biochemical and analytical processes. Here we describe recent experiments that include on-chip dilution, reagent mixing, reaction, separation, and detection for important classes of biochemical assays. Issues in chip design and control are discussed.

Lessons from (patho)physiological tissue stiffness and their implications for drug screening, drug delivery and regenerative medicine.

PubMed

Chen, Wen Li Kelly; Simmons, Craig A

2011-04-30

Diseased tissues are noted for their compromised mechanical properties, which contribute to organ failure; regeneration entails restoration of tissue structure and thereby functions. Thus, the physical signature of a tissue is closely associated with its biological function. In this review, we consider a mechanics-centric view of disease and regeneration by drawing parallels between in vivo tissue-level observations and corroborative cellular evidence in vitro to demonstrate the importance of the mechanical stiffness of the extracellular matrix in these processes. This is not intended to devalue the importance of biochemical signaling; in fact, as we discuss, many mechanical stiffness-driven processes not only require cooperation with biochemical cues, but they ultimately converge at common signaling cascades to influence cell and tissue function in an integrative manner. The study of how physical and biochemical signals collectively modulate cell function not only brings forth a more holistic understanding of cell (patho)biology, but it also creates opportunities to control material properties to improve culture platforms for research and drug screening and aid in the rationale design of biomaterials for molecular therapy and tissue engineering applications. Copyright © 2011 Elsevier B.V. All rights reserved.

Bacterial cell-free expression technology to in vitro systems engineering and optimization.

PubMed

Caschera, Filippo

2017-06-01

Cell-free expression system is a technology for the synthesis of proteins in vitro . The system is a platform for several bioengineering projects, e.g. cell-free metabolic engineering, evolutionary design of experiments, and synthetic minimal cell construction. Bacterial cell-free protein synthesis system (CFPS) is a robust tool for synthetic biology. The bacteria lysate, the DNA, and the energy module, which are the three optimized sub-systems for in vitro protein synthesis, compose the integrated system. Currently, an optimized E. coli cell-free expression system can produce up to ∼2.3 mg/mL of a fluorescent reporter protein. Herein, I will describe the features of ATP-regeneration systems for in vitro protein synthesis, and I will present a machine-learning experiment for optimizing the protein yield of E. coli cell-free protein synthesis systems. Moreover, I will introduce experiments on the synthesis of a minimal cell using liposomes as dynamic containers, and E. coli cell-free expression system as biochemical platform for metabolism and gene expression. CFPS can be further integrated with other technologies for novel applications in environmental, medical and material science.

2D materials integrated in Si3N4 photonics platform

NASA Astrophysics Data System (ADS)

Faneca, Joaquin; Hogan, Benjamin T.; Torres Alonso, E.; Craciun, Monica; Baldycheva, Anna

2018-02-01

In this paper, we discuss a back-end CMOS fabrication process for the large-scale integration of 2D materials on SOI (siliconon-insulator) platform and present a complete theoretical study of the change in the effective refractive index of 2D materialsenabled silicon nitride waveguide structures. The chemical vapour deposition (CVD) and liquid exfoliation fabrication methods are described for the fabrication of graphene, WS2 and MoS2 thin films. Finite-difference frequency-domain (FDFD) approach and the Transfer Matrix Method were used in order to mathematically describe these structures. The introduction of thin films of 2D material onto Si3N4 waveguide structures allows manipulation of the optical characteristics to a high degree of precision by varying the Fermi-level through the engineering of the number of atomically thin layers or by electrical tuning, for example. Based on the proposed tuning approach, designs of graphene, WS2 and MoS2 enabled Si3N4 micro-ring structures are presented for the visible and NIR range, which demonstrate versatility and desirable properties for a wide range of applications, such as bio-chemical sensing and optical communications.

Microfluidic platform for assessing pancreatic islet functionality through dielectric spectroscopy

PubMed Central

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

2015-01-01

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

Time-resolved SERS for characterizing extracellular vesicles

NASA Astrophysics Data System (ADS)

Rojalin, Tatu; Saari, Heikki; Somersalo, Petter; Laitinen, Saara; Turunen, Mikko; Viitala, Tapani; Wachsmann-Hogiu, Sebastian; Smith, Zachary J.; Yliperttula, Marjo

2017-02-01

The aim of this work is to develop a platform for characterizing extracellular vesicles (EV) by using gold-polymer nanopillar SERS arrays simultaneously circumventing the photoluminescence-related disadvantages of Raman with a time-resolved approach. EVs are rich of biochemical information reporting of, for example, diseased state of the biological system. Currently, straightforward, label-free and fast EV characterization methods with low sample consumption are warranted. In this study, SERS spectra of red blood cell and platelet derived EVs were successfully measured and their biochemical contents analyzed using multivariate data analysis techniques. The developed platform could be conveniently used for EV analytics in general.

RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae

PubMed Central

2010-01-01

Background Root and bulb vegetables (RBV) include carrots, celeriac (root celery), parsnips (Apiaceae), onions, garlic, and leek (Alliaceae)—food crops grown globally and consumed worldwide. Few data analysis platforms are currently available where data collection, annotation and integration initiatives are focused on RBV plant groups. Scientists working on RBV include breeders, geneticists, taxonomists, plant pathologists, and plant physiologists who use genomic data for a wide range of activities including the development of molecular genetic maps, delineation of taxonomic relationships, and investigation of molecular aspects of gene expression in biochemical pathways and disease responses. With genomic data coming from such diverse areas of plant science, availability of a community resource focused on these RBV data types would be of great interest to this scientific community. Description The RoBuST database has been developed to initiate a platform for collecting and organizing genomic information useful for RBV researchers. The current release of RoBuST contains genomics data for 294 Alliaceae and 816 Apiaceae plant species and has the following features: (1) comprehensive sequence annotations of 3663 genes 5959 RNAs, 22,723 ESTs and 11,438 regulatory sequence elements from Apiaceae and Alliaceae plant families; (2) graphical tools for visualization and analysis of sequence data; (3) access to traits, biosynthetic pathways, genetic linkage maps and molecular taxonomy data associated with Alliaceae and Apiaceae plants; and (4) comprehensive plant splice signal repository of 659,369 splice signals collected from 6015 plant species for comparative analysis of plant splicing patterns. Conclusions RoBuST, available at http://robust.genome.com, provides an integrated platform for researchers to effortlessly explore and analyze genomic data associated with root and bulb vegetables. PMID:20691054

Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities.

PubMed

Quo, Chang F; Kaddi, Chanchala; Phan, John H; Zollanvari, Amin; Xu, Mingqing; Wang, May D; Alterovitz, Gil

2012-07-01

Recent advances in high-throughput biotechnologies have led to the rapid growing research interest in reverse engineering of biomolecular systems (REBMS). 'Data-driven' approaches, i.e. data mining, can be used to extract patterns from large volumes of biochemical data at molecular-level resolution while 'design-driven' approaches, i.e. systems modeling, can be used to simulate emergent system properties. Consequently, both data- and design-driven approaches applied to -omic data may lead to novel insights in reverse engineering biological systems that could not be expected before using low-throughput platforms. However, there exist several challenges in this fast growing field of reverse engineering biomolecular systems: (i) to integrate heterogeneous biochemical data for data mining, (ii) to combine top-down and bottom-up approaches for systems modeling and (iii) to validate system models experimentally. In addition to reviewing progress made by the community and opportunities encountered in addressing these challenges, we explore the emerging field of synthetic biology, which is an exciting approach to validate and analyze theoretical system models directly through experimental synthesis, i.e. analysis-by-synthesis. The ultimate goal is to address the present and future challenges in reverse engineering biomolecular systems (REBMS) using integrated workflow of data mining, systems modeling and synthetic biology.

An Intelligent Automation Platform for Rapid Bioprocess Design.

PubMed

Wu, Tianyi; Zhou, Yuhong

2014-08-01

Bioprocess development is very labor intensive, requiring many experiments to characterize each unit operation in the process sequence to achieve product safety and process efficiency. Recent advances in microscale biochemical engineering have led to automated experimentation. A process design workflow is implemented sequentially in which (1) a liquid-handling system performs high-throughput wet lab experiments, (2) standalone analysis devices detect the data, and (3) specific software is used for data analysis and experiment design given the user's inputs. We report an intelligent automation platform that integrates these three activities to enhance the efficiency of such a workflow. A multiagent intelligent architecture has been developed incorporating agent communication to perform the tasks automatically. The key contribution of this work is the automation of data analysis and experiment design and also the ability to generate scripts to run the experiments automatically, allowing the elimination of human involvement. A first-generation prototype has been established and demonstrated through lysozyme precipitation process design. All procedures in the case study have been fully automated through an intelligent automation platform. The realization of automated data analysis and experiment design, and automated script programming for experimental procedures has the potential to increase lab productivity. © 2013 Society for Laboratory Automation and Screening.

An Intelligent Automation Platform for Rapid Bioprocess Design

PubMed Central

Wu, Tianyi

2014-01-01

Bioprocess development is very labor intensive, requiring many experiments to characterize each unit operation in the process sequence to achieve product safety and process efficiency. Recent advances in microscale biochemical engineering have led to automated experimentation. A process design workflow is implemented sequentially in which (1) a liquid-handling system performs high-throughput wet lab experiments, (2) standalone analysis devices detect the data, and (3) specific software is used for data analysis and experiment design given the user’s inputs. We report an intelligent automation platform that integrates these three activities to enhance the efficiency of such a workflow. A multiagent intelligent architecture has been developed incorporating agent communication to perform the tasks automatically. The key contribution of this work is the automation of data analysis and experiment design and also the ability to generate scripts to run the experiments automatically, allowing the elimination of human involvement. A first-generation prototype has been established and demonstrated through lysozyme precipitation process design. All procedures in the case study have been fully automated through an intelligent automation platform. The realization of automated data analysis and experiment design, and automated script programming for experimental procedures has the potential to increase lab productivity. PMID:24088579

HIgh-Q Optical Micro-cavity Resonators as High Sensitive Bio-chemical and Ultrasonic Sensors

NASA Astrophysics Data System (ADS)

Ling, Tao

Optical micro-cavity resonators have quickly emerged in the past few years as a new sensing platform in a wide range of applications, such as bio-chemical molecular detection, environmental monitoring, acoustic and electromagnetic waves detection. In this thesis, we will mainly focus on developing high sensitivity silica micro-tube resonator bio-chemical sensors and high sensitivity polymer micro-ring resonator acoustic sensors. In high sensitivity silica micro-tube resonator bio-chemical sensors part: We first demonstrated a prism coupled silica micro-tube bio-chemical sensing platform to overcome the reliability problem in a fiber coupled thin wall silica micro-tube sensing platform. In refractive index sensing experiment, a unique resonance mode with sensitivity around 600nm/refractive index unit (RIU) has been observed. Surface sensing experiments also have been performed in this platform to detect lipid monolayer, lipid bilayer, electrostatic self assemble layer-by-layer as well as the interaction between the lipid bilayer and proteins. Then a theoretical study on various sensing properties on the silica micro-tube based sensing platform has been realized. Furthermore, we have proposed a coupled cavity system to further enhance the device's sensitivity above 1000nm/RIU. In high sensitivity polymer micro-ring resonator acoustic sensors part: We first presented a simplified fabrication process and realized a polymer microring with a Q factor around 6000. The fabricated device has been used to detect acoustic wave with noise equivalent pressure (NEP) around 230Pa over 1-75MHz frequency rang, which is comparable to state-of-art piezoelectric transducer and the device's frequency response also have been characterized to be up to 90MHz. A new fabrication process combined with resist reflow and thermal oxidation process has been used to improve the Q factor up to 10 5 and the device's NEP has been tested to be around 88Pa over 1-75MHz range. Further improving the device's Q factor has been realized by shifting the device's working wavelength to near-visible wavelength and further reducing the device's sidewall roughness. A record new high Q-˜x105 has been measured and the device's NEP as low as 21Pa has been measured. Furthermore, a smaller size polymer microring device has been developed and fabricated to realize larger angle beam forming applications.

Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B 2 Biosynthesis

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

Barajas, Jesus F.; Zargar, Amin; Pang, Bo

Naturally occurring lactams, such as the polyketide-derived macrolactams, provide a diverse class of natural products that could enhance existing chemically produced lactams. While β-amino acid loading in the fluvirucin B 2 polyketide pathway has been proposed by a previously identified putative biosynthetic gene cluster, biochemical characterization of the complete loading enzymes has not been described. In this paper, we elucidate the complete biosynthetic pathway of the β-amino acid loading pathway in fluvirucin B 2 biosynthesis. We demonstrate the promiscuity of the loading pathway to utilize a range of amino acids and further illustrate the ability to introduce non-native acyl transferasesmore » to selectively transfer β-amino acids onto a PKS loading platform. The results presented here provide a detailed biochemical description of β-amino acid selection and will further aid in future efforts to develop engineered lactam-producing PKS platforms.« less

Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B 2 Biosynthesis

DOE PAGES

Barajas, Jesus F.; Zargar, Amin; Pang, Bo; ...

2018-03-30

Naturally occurring lactams, such as the polyketide-derived macrolactams, provide a diverse class of natural products that could enhance existing chemically produced lactams. While β-amino acid loading in the fluvirucin B 2 polyketide pathway has been proposed by a previously identified putative biosynthetic gene cluster, biochemical characterization of the complete loading enzymes has not been described. In this paper, we elucidate the complete biosynthetic pathway of the β-amino acid loading pathway in fluvirucin B 2 biosynthesis. We demonstrate the promiscuity of the loading pathway to utilize a range of amino acids and further illustrate the ability to introduce non-native acyl transferasesmore » to selectively transfer β-amino acids onto a PKS loading platform. The results presented here provide a detailed biochemical description of β-amino acid selection and will further aid in future efforts to develop engineered lactam-producing PKS platforms.« less

Evaluation of peristaltic micromixers for highly integrated microfluidic systems

PubMed Central

Kim, Duckjong; Rho, Hoon Suk; Jambovane, Sachin; Shin, Soojeong; Hong, Jong Wook

2016-01-01

Microfluidic devices based on the multilayer soft lithography allow accurate manipulation of liquids, handling reagents at the sub-nanoliter level, and performing multiple reactions in parallel processors by adapting micromixers. Here, we have experimentally evaluated and compared several designs of micromixers and operating conditions to find design guidelines for the micromixers. We tested circular, triangular, and rectangular mixing loops and measured mixing performance according to the position and the width of the valves that drive nanoliters of fluids in the micrometer scale mixing loop. We found that the rectangular mixer is best for the applications of highly integrated microfluidic platforms in terms of the mixing performance and the space utilization. This study provides an improved understanding of the flow behaviors inside micromixers and design guidelines for micromixers that are critical to build higher order fluidic systems for the complicated parallel bio/chemical processes on a chip. PMID:27036809

Evaluation of peristaltic micromixers for highly integrated microfluidic systems

NASA Astrophysics Data System (ADS)

Kim, Duckjong; Rho, Hoon Suk; Jambovane, Sachin; Shin, Soojeong; Hong, Jong Wook

2016-03-01

Microfluidic devices based on the multilayer soft lithography allow accurate manipulation of liquids, handling reagents at the sub-nanoliter level, and performing multiple reactions in parallel processors by adapting micromixers. Here, we have experimentally evaluated and compared several designs of micromixers and operating conditions to find design guidelines for the micromixers. We tested circular, triangular, and rectangular mixing loops and measured mixing performance according to the position and the width of the valves that drive nanoliters of fluids in the micrometer scale mixing loop. We found that the rectangular mixer is best for the applications of highly integrated microfluidic platforms in terms of the mixing performance and the space utilization. This study provides an improved understanding of the flow behaviors inside micromixers and design guidelines for micromixers that are critical to build higher order fluidic systems for the complicated parallel bio/chemical processes on a chip.

Cardiomyocytes from human pluripotent stem cells: From laboratory curiosity to industrial biomedical platform.

PubMed

Denning, Chris; Borgdorff, Viola; Crutchley, James; Firth, Karl S A; George, Vinoj; Kalra, Spandan; Kondrashov, Alexander; Hoang, Minh Duc; Mosqueira, Diogo; Patel, Asha; Prodanov, Ljupcho; Rajamohan, Divya; Skarnes, William C; Smith, James G W; Young, Lorraine E

2016-07-01

Cardiomyocytes from human pluripotent stem cells (hPSCs-CMs) could revolutionise biomedicine. Global burden of heart failure will soon reach USD $90bn, while unexpected cardiotoxicity underlies 28% of drug withdrawals. Advances in hPSC isolation, Cas9/CRISPR genome engineering and hPSC-CM differentiation have improved patient care, progressed drugs to clinic and opened a new era in safety pharmacology. Nevertheless, predictive cardiotoxicity using hPSC-CMs contrasts from failure to almost total success. Since this likely relates to cell immaturity, efforts are underway to use biochemical and biophysical cues to improve many of the ~30 structural and functional properties of hPSC-CMs towards those seen in adult CMs. Other developments needed for widespread hPSC-CM utility include subtype specification, cost reduction of large scale differentiation and elimination of the phenotyping bottleneck. This review will consider these factors in the evolution of hPSC-CM technologies, as well as their integration into high content industrial platforms that assess structure, mitochondrial function, electrophysiology, calcium transients and contractility. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Integration of electrochemistry in micro-total analysis systems for biochemical assays: recent developments.

PubMed

Xu, Xiaoli; Zhang, Song; Chen, Hui; Kong, Jilie

2009-11-15

Micro-total analysis systems (microTAS) integrate different analytical operations like sample preparation, separation and detection into a single microfabricated device. With the outstanding advantages of low cost, satisfactory analytical efficiency and flexibility in design, highly integrated and miniaturized devices from the concept of microTAS have gained widespread applications, especially in biochemical assays. Electrochemistry is shown to be quite compatible with microanalytical systems for biochemical assays, because of its attractive merits such as simplicity, rapidity, high sensitivity, reduced power consumption, and sample/reagent economy. This review presents recent developments in the integration of electrochemistry in microdevices for biochemical assays. Ingenious microelectrode design and fabrication methods, and versatility of electrochemical techniques are involved. Practical applications of such integrated microsystem in biochemical assays are focused on in situ analysis, point-of-care testing and portable devices. Electrochemical techniques are apparently suited to microsystems, since easy microfabrication of electrochemical elements and a high degree of integration with multi-analytical functions can be achieved at low cost. Such integrated microsystems will play an increasingly important role for analysis of small volume biochemical samples. Work is in progress toward new microdevice design and applications.

Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions

PubMed Central

Snitkin, Evan S; Dudley, Aimée M; Janse, Daniel M; Wong, Kaisheen; Church, George M; Segrè, Daniel

2008-01-01

Background Understanding the response of complex biochemical networks to genetic perturbations and environmental variability is a fundamental challenge in biology. Integration of high-throughput experimental assays and genome-scale computational methods is likely to produce insight otherwise unreachable, but specific examples of such integration have only begun to be explored. Results In this study, we measured growth phenotypes of 465 Saccharomyces cerevisiae gene deletion mutants under 16 metabolically relevant conditions and integrated them with the corresponding flux balance model predictions. We first used discordance between experimental results and model predictions to guide a stage of experimental refinement, which resulted in a significant improvement in the quality of the experimental data. Next, we used discordance still present in the refined experimental data to assess the reliability of yeast metabolism models under different conditions. In addition to estimating predictive capacity based on growth phenotypes, we sought to explain these discordances by examining predicted flux distributions visualized through a new, freely available platform. This analysis led to insight into the glycerol utilization pathway and the potential effects of metabolic shortcuts on model results. Finally, we used model predictions and experimental data to discriminate between alternative raffinose catabolism routes. Conclusions Our study demonstrates how a new level of integration between high throughput measurements and flux balance model predictions can improve understanding of both experimental and computational results. The added value of a joint analysis is a more reliable platform for specific testing of biological hypotheses, such as the catabolic routes of different carbon sources. PMID:18808699

Integrated chemical/biochemical sample collection, pre-concentration, and analysis on a digital microfluidic lab-on-a-chip platform

NASA Astrophysics Data System (ADS)

Fair, Richard B.; Khlystov, A.; Srinivasan, Vijay; Pamula, Vamsee K.; Weaver, Kathryn N.

2004-12-01

An ideal on-site chemical/biochemical analysis system must be inexpensive, sensitive, fully automated and integrated, reliable, and compatible with a broad range of samples. The advent of digital microfluidic lab-on-a-chip (LoC) technology offers such a detection system due to the advantages in portability, reduction of the volumes of the sample and reagents, faster analysis times, increased automation, low power consumption, compatibility with mass manufacturing, and high throughput. We describe progress towards integrating sample collection onto a digital microfluidic LoC that is a component of a cascade impactor device. The sample collection is performed by impacting airborne particles directly onto the surface of the chip. After the collection phase, the surface of the chip is washed with a micro-droplet of solvent. The droplet will be digitally directed across the impaction surface, dissolving sample constituents. Because of the very small droplet volume used for extraction of the sample from a wide colection area, the resulting solution is realatively concentrated and the analytes can be detected after a very short sampling time (1 min) due to such pre-concentration. After the washing phase, the droplet is mixed with specific reagents that produce colored reaction products. The concentration of the analyte is quantitatively determined by measuring absorption at target wavelengths using a simple light emitting diode and photodiode setup. Specific applications include automatic measurements of major inorganic ions in aerosols, such as sulfate, nitrate and ammonium, with a time resolution of 1 min and a detection limit of 30 nm/m3. We have already demonstrated the detection and quantification of nitroaromatic explosives without integrating the sample collection. Other applications being developed include airborne bioagent detection.

Ultralocalized thermal reactions in subnanoliter droplets-in-air.

PubMed

Salm, Eric; Guevara, Carlos Duarte; Dak, Piyush; Dorvel, Brian Ross; Reddy, Bobby; Alam, Muhammad Ashraf; Bashir, Rashid

2013-02-26

Miniaturized laboratory-on-chip systems promise rapid, sensitive, and multiplexed detection of biological samples for medical diagnostics, drug discovery, and high-throughput screening. Within miniaturized laboratory-on-chips, static and dynamic droplets of fluids in different immiscible media have been used as individual vessels to perform biochemical reactions and confine the products. Approaches to perform localized heating of these individual subnanoliter droplets can allow for new applications that require parallel, time-, and space-multiplex reactions on a single integrated circuit. Our method positions droplets on an array of individual silicon microwave heaters on chip to precisely control the temperature of droplets-in-air, allowing us to perform biochemical reactions, including DNA melting and detection of single base mismatches. We also demonstrate that ssDNA probe molecules can be placed on heaters in solution, dried, and then rehydrated by ssDNA target molecules in droplets for hybridization and detection. This platform enables many applications in droplets including hybridization of low copy number DNA molecules, lysing of single cells, interrogation of ligand-receptor interactions, and rapid temperature cycling for amplification of DNA molecules.

Life Science Research in Outer Space: New Platform Technologies for Low-Cost, Autonomous Small Satellite Missions

NASA Technical Reports Server (NTRS)

Ricco, Antonio J.; Parra, Macarena P.; Niesel, David; McGinnis, Michael; Ehrenfreund, Pascale; Nicholson, Wayne; Mancinelli, Rocco; Piccini, Matthew E.; Beasley, Christopher C.; Timucin, Linda R.;

Integrated Experimental Platforms to Study Blast Injuries: a Bottom-Up Approach

NASA Astrophysics Data System (ADS)

Bo, Chiara

2013-06-01

Developing a cellular and molecular understanding of the nature of traumatic and post-traumatic effects of blast events on live biological samples is critical for improving clinical outcomes.1 To investigate the consequences of pressure waves upon cellular structures and the underlying physiological and biochemical changes, we are using an integrated approach to study the material and biological properties of cells, tissues and organs when subjected to extreme conditions. In particular we have developed a confined Split Hopkinson Pressure Bar (SHPB) system, which allows us to subject cells in suspension or in a monolayer to compression waves of the order of few MPa and duration of hundreds of microseconds.2 The chamber design also enables recovery of the biological samples for cellular and molecular analysis. Specifically, cell survivability, viability, proliferation and morphological changes are investigated post compression for different cell populations. The SHPB platform, coupled with Quasi-Static experiments, is also used to determine stress-strain curves of soft biological tissues under compression at low, medium and high strain rates. Samples are also examined using histological techniques to study macro- and microscopical changes induced by compression waves. Finally, a shock tube has been developed to replicate primary blast damage on organs (i.e. mice lungs) and cell monolayers by generating single or multiple air blast of the order of kPa and few milliseconds duration. This platform allows us to visualize post-traumatic morphological changes at the cellular level as a function of the stimulus pressure and duration as well as biomarker signatures of blast injuries. Adapting and integrating a variety of approaches with different experimental platforms allows us to sample a vast pressure-time space in terms of biological and structural damage that mimic blast injuries and also to determine which physical parameters (peak pressure, stimulus duration, impulse) are contributing to the injury process. Moreover, understanding biological damage following blast events is crucial to developing novel clinical approaches to detect and treat traumatic injury pathologies. This work is supported by he Atomic Weapons Establishment, UK and The Royal British Legion Centre for Blast Injury Studies at Imperial College London, UK

Clinical validation of the CHRONIOUS wearable system in patients with chronic disease.

PubMed

Bellos, Christos; Papadopoulos, Athanassios; Rosso, Roberto; Fotiadis, Dimitrios I

2013-01-01

The CHRONIOUS system defines a powerful and easy to use framework which has been designed to provide services to clinicians and their patients suffering from chronic diseases. The system is composed of a wearable shirt that integrate several body sensors, a portable smart device and a central sub-system that is responsible for the long term storage of the collected patient's data. A multi-parametric expert system is developed for the analysis of the collected data using intelligent algorithms and complex techniques. Apart for the vital signals, dietary habits, drug intake, activity data, environmental and biochemical parameters are recorded. The CHRONIOUS platform is validated through clinical trials in several medical centers and patient's home environments recruiting patients suffering from Chronic Obstructive pulmonary disease (COPD) and Chronic Kidney Disease (CKD) diseases. The clinical trials contribute in improving the system's accuracy, while Pulmonologists and Nephrologists experts utilized the CHRONIOUS platform to evaluate its efficiency and performance. The results of the utilization of the system were very encouraging. The CHRONIOUS system has been proven to be a well-validated real-time patient monitoring and supervision platform, providing a useful tool for the clinician and the patient that would contribute to the more effective management of chronic diseases.

Reductive surface synthesis of gold nanoparticles on silicate glass and their biochemical sensor applicationsa

PubMed Central

Li, M.; Kim, D.-P.; Jeong, G.-Y.; Seo, D.-K.; Park, C.-P.

2012-01-01

Gold nanoparticles (Au NPs) were directly synthesized on the surface of polyvinylsilazane (PVSZ, -[(vinyl)SiH-NH2]-) without use of extra reductive additives. The reductive Si-H functional groups on the surface of cured PVSZ acted as surface bound reducing agents to form gold metal when contacted with an aqueous Au precursor (HAuCl4) solution, leading to formation of Au NPs adhered to silicate glass surface. The Au NPs-silicate platforms were preliminarily tested to detect Rhodamine B (1 μM) by surface enhanced Raman scattering. Furthermore, gold microelectrode obtained by post-chemical plating was used as an integrated amperometric detection element in the polydimethylsilane-glass hybrid microfluidic chip. PMID:24324531

Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast Using CasEMBLR.

PubMed

Jakočiūnas, Tadas; Jensen, Emil D; Jensen, Michael K; Keasling, Jay D

2018-01-01

Genome integration is a vital step for implementing large biochemical pathways to build a stable microbial cell factory. Although traditional strain construction strategies are well established for the model organism Saccharomyces cerevisiae, recent advances in CRISPR/Cas9-mediated genome engineering allow much higher throughput and robustness in terms of strain construction. In this chapter, we describe CasEMBLR, a highly efficient and marker-free genome engineering method for one-step integration of in vivo assembled expression cassettes in multiple genomic sites simultaneously. CasEMBLR capitalizes on the CRISPR/Cas9 technology to generate double-strand breaks in genomic loci, thus prompting native homologous recombination (HR) machinery to integrate exogenously derived homology templates. As proof-of-principle for microbial cell factory development, CasEMBLR was used for one-step assembly and marker-free integration of the carotenoid pathway from 15 exogenously supplied DNA parts into three targeted genomic loci. As a second proof-of-principle, a total of ten DNA parts were assembled and integrated in two genomic loci to construct a tyrosine production strain, and at the same time knocking out two genes. This new method complements and improves the field of genome engineering in S. cerevisiae by providing a more flexible platform for rapid and precise strain building.

Mach-Zehnder Interferometer Biochemical Sensor Based on Silicon-on-Insulator Rib Waveguide with Large Cross Section

PubMed Central

Yuan, Dengpeng; Dong, Ying; Liu, Yujin; Li, Tianjian

2015-01-01

A high-sensitivity Mach-Zehnder interferometer (MZI) biochemical sensing platform based on Silicon-in-insulator (SOI) rib waveguide with large cross section is proposed in this paper. Based on the analyses of the evanescent field intensity, the mode polarization and cross section dimensions of the SOI rib waveguide are optimized through finite difference method (FDM) simulation. To realize high-resolution MZI read-out configuration based on the SOI rib waveguide, medium-filled trenches are employed and their performances are simulated through two-dimensional finite-difference-time domain (2D-FDTD) method. With the fundamental EH-polarized mode of the SOI rib waveguide with a total rib height of 10 μm, an outside rib height of 5 μm and a rib width of 2.5 μm at the operating wavelength of 1550 nm, when the length of the sensitive window in the MZI configuration is 10 mm, a homogeneous sensitivity of 7296.6%/refractive index unit (RIU) is obtained. Supposing the resolutions of the photoelectric detectors connected to the output ports are 0.2%, the MZI sensor can achieve a detection limit of 2.74 × 10−6 RIU. Due to high coupling efficiency of SOI rib waveguide with large cross section with standard single-mode glass optical fiber, the proposed MZI sensing platform can be conveniently integrated with optical fiber communication systems and (opto-) electronic systems, and therefore has the potential to realize remote sensing, in situ real-time detecting, and possible applications in the internet of things. PMID:26343678

Plasmon-enhanced Raman detection of body-fluid components

NASA Astrophysics Data System (ADS)

Matteini, Paolo; Banchelli, Martina; De Angelis, Marella; D'Andrea, Cristiano; Pini, Roberto

2018-02-01

Plasmon-enhanced spectroscopies such as surface-enhanced Raman spectroscopy (SERS) concern the detection of enhanced optical responses of molecules in close proximity to plasmonic structures, which results in a strong increase in sensitivity. Recent advancements in nanofabrication methods have paved the way for a controlled design of tailor-made nanostructures with fine-tuning of their optical and surface properties. Among these, silver nanocubes (AgNCs) represent a convenient choice in SERS owing to intense electromagnetic fields localized at their extremities, which are further intensified in the gap regions between closely spaced nanoparticles. The integration of AgNCs assemblies within an optofluidic platform may confer potential for superior optical investigation due to a molecular enrichment on the plasmonic structures to collect an enhanced photonic response. We developed a novel sensing platform based on an optofluidic system involving assembled silver nanocubes of 50 nm in size for ultrasensitive SERS detection of biomolecules in wet conditions. The proposed system offers the perspective of advanced biochemical and biological characterizations of molecules as well as of effective detection of body fluid components and other molecules of biomedical interest in their own environment.

Energy-based culture medium design for biomanufacturing optimization: A case study in monoclonal antibody production by GS-NS0 cells.

PubMed

Quiroga-Campano, Ana L; Panoskaltsis, Nicki; Mantalaris, Athanasios

2018-03-02

Demand for high-value biologics, a rapidly growing pipeline, and pressure from competition, time-to-market and regulators, necessitate novel biomanufacturing approaches, including Quality by Design (QbD) principles and Process Analytical Technologies (PAT), to facilitate accelerated, efficient and effective process development platforms that ensure consistent product quality and reduced lot-to-lot variability. Herein, QbD and PAT principles were incorporated within an innovative in vitro-in silico integrated framework for upstream process development (UPD). The central component of the UPD framework is a mathematical model that predicts dynamic nutrient uptake and average intracellular ATP content, based on biochemical reaction networks, to quantify and characterize energy metabolism and its adaptive response, metabolic shifts, to maintain ATP homeostasis. The accuracy and flexibility of the model depends on critical cell type/product/clone-specific parameters, which are experimentally estimated. The integrated in vitro-in silico platform and the model's predictive capacity reduced burden, time and expense of experimentation resulting in optimal medium design compared to commercially available culture media (80% amino acid reduction) and a fed-batch feeding strategy that increased productivity by 129%. The framework represents a flexible and efficient tool that transforms, improves and accelerates conventional process development in biomanufacturing with wide applications, including stem cell-based therapies. Copyright © 2018. Published by Elsevier Inc.

Microfluidic Devices for Chemical and Biochemical Analysis in Microgravity

NASA Technical Reports Server (NTRS)

Roman, Gregory T.; Culbertson, Christopher T.; Meyer, Amanda; Ramsey, J. Michael; Gonda, Steven R.

2004-01-01

One often touted benefit of "Lab-on-a-Chip" devices is their potential for use in remote environments. The ultimate remote environment is outer space, and NASA has multiple needs in the area of analytical sensing capability in such an environment. In particular, we are interested in integrating microfluidic devices with NASA bioreactor systems. In such an integrated system, the microfluidic device will serve as a biosensor and be used for both feedback control and for detecting various bioproducts produced by cells cultured in the NASA bioreactors. As a first step in demonstrating the ability of microfluidic devices to operate under the extreme environmental conditions found in outer space, we constructed a portable, battery operated platform for testing under reduced gravity conditions on a NASA KC-135 reduced gravity research aircraft, (AKA "the vomit comet"). The test platform consisted of a microchip, two 0-8kV high voltage power supplies, a high voltage switch, a solid-state diode-pumped green laser, a channel photomultiplier, and an inertial mass measurement unit, all under the control of a laptop computer and powered by 10 D-cell alkaline batteries. Over the course of 4 KC-135 flights, 1817 fast electrophoretic separations of 4 amino acids and/or proteins were performed in a variety of gravitational environments including zero-G, Martian-G, lunar-G, and 2-G. Results from these experiments will be presented and discussed.

An Integrated Qualitative and Quantitative Biochemical Model Learning Framework Using Evolutionary Strategy and Simulated Annealing.

PubMed

Wu, Zujian; Pang, Wei; Coghill, George M

2015-01-01

Both qualitative and quantitative model learning frameworks for biochemical systems have been studied in computational systems biology. In this research, after introducing two forms of pre-defined component patterns to represent biochemical models, we propose an integrative qualitative and quantitative modelling framework for inferring biochemical systems. In the proposed framework, interactions between reactants in the candidate models for a target biochemical system are evolved and eventually identified by the application of a qualitative model learning approach with an evolution strategy. Kinetic rates of the models generated from qualitative model learning are then further optimised by employing a quantitative approach with simulated annealing. Experimental results indicate that our proposed integrative framework is feasible to learn the relationships between biochemical reactants qualitatively and to make the model replicate the behaviours of the target system by optimising the kinetic rates quantitatively. Moreover, potential reactants of a target biochemical system can be discovered by hypothesising complex reactants in the synthetic models. Based on the biochemical models learned from the proposed framework, biologists can further perform experimental study in wet laboratory. In this way, natural biochemical systems can be better understood.

Optical tweezers and multiphoton microscopies integrated photonic tool for mechanical and biochemical cell processes studies

NASA Astrophysics Data System (ADS)

de Thomaz, A. A.; Faustino, W. M.; Fontes, A.; Fernandes, H. P.; Barjas-Castro, M. d. L.; Metze, K.; Giorgio, S.; Barbosa, L. C.; Cesar, C. L.

2007-09-01

The research in biomedical photonics is clearly evolving in the direction of the understanding of biological processes at the cell level. The spatial resolution to accomplish this task practically requires photonics tools. However, an integration of different photonic tools and a multimodal and functional approach will be necessary to access the mechanical and biochemical cell processes. This way we can observe mechanicaly triggered biochemical events or biochemicaly triggered mechanical events, or even observe simultaneously mechanical and biochemical events triggered by other means, e.g. electricaly. One great advantage of the photonic tools is its easiness for integration. Therefore, we developed such integrated tool by incorporating single and double Optical Tweezers with Confocal Single and Multiphoton Microscopies. This system can perform 2-photon excited fluorescence and Second Harmonic Generation microscopies together with optical manipulations. It also can acquire Fluorescence and SHG spectra of specific spots. Force, elasticity and viscosity measurements of stretched membranes can be followed by real time confocal microscopies. Also opticaly trapped living protozoas, such as leishmania amazonensis. Integration with CARS microscopy is under way. We will show several examples of the use of such integrated instrument and its potential to observe mechanical and biochemical processes at cell level.

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

NASA Astrophysics Data System (ADS)

Yong, Xu; Yujin, He

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

Biochemical Conversion Processes of Lignocellulosic Biomass to Fuels and Chemicals - A Review.

PubMed

Brethauer, Simone; Studer, Michael H

2015-01-01

Lignocellulosic biomass - such as wood, agricultural residues or dedicated energy crops - is a promising renewable feedstock for production of fuels and chemicals that is available at large scale at low cost without direct competition for food usage. Its biochemical conversion in a sugar platform biorefinery includes three main unit operations that are illustrated in this review: the physico-chemical pretreatment of the biomass, the enzymatic hydrolysis of the carbohydrates to a fermentable sugar stream by cellulases and finally the fermentation of the sugars by suitable microorganisms to the target molecules. Special emphasis in this review is put on the technology, commercial status and future prospects of the production of second-generation fuel ethanol, as this process has received most research and development efforts so far. Despite significant advances, high enzyme costs are still a hurdle for large scale competitive lignocellulosic ethanol production. This could be overcome by a strategy termed 'consolidated bioprocessing' (CBP), where enzyme production, enzymatic hydrolysis and fermentation is integrated in one step - either by utilizing one genetically engineered superior microorganism or by creating an artificial co-culture. Insight is provided on both CBP strategies for the production of ethanol as well as of advanced fuels and commodity chemicals.

Optofluidic UV-Vis spectrophotometer for online monitoring of photocatalytic reactions

NASA Astrophysics Data System (ADS)

Wang, Ning; Tan, Furui; Zhao, Yu; Tsoi, Chi Chung; Fan, Xudong; Yu, Weixing; Zhang, Xuming

2016-06-01

On-chip integration of optical detection units into the microfluidic systems for online monitoring is highly desirable for many applications and is also well in line with the spirit of optofluidics technology-fusion of optics and microfluidics for advanced functionalities. This paper reports the construction of a UV-Vis spectrophotometer on a microreactor, and demonstrates the online monitoring of the photocatalytic degradations of methylene blue and methyl orange under different flow rates and different pH values by detecting the intensity change and/or the peak shift. The integrated device consists of a TiO2-coated glass substrate, a PDMS micro-sized reaction chamber and two flow cells. By comparing with the results of commercial equipment, we have found that the measuring range and the sensitivity are acceptable, especially when the transmittance is in the range of 0.01-0.9. This integrated optofluidic device can significantly cut down the test time and the sample volume, and would provide a versatile platform for real-time characterization of photochemical performance. Moreover, its online monitoring capability may enable to access the usually hidden information in biochemical reactions like intermediate products, time-dependent processes and reaction kinetics.

Optofluidic UV-Vis spectrophotometer for online monitoring of photocatalytic reactions

PubMed Central

Wang, Ning; Tan, Furui; Zhao, Yu; Tsoi, Chi Chung; Fan, Xudong; Yu, Weixing; Zhang, Xuming

2016-01-01

On-chip integration of optical detection units into the microfluidic systems for online monitoring is highly desirable for many applications and is also well in line with the spirit of optofluidics technology–fusion of optics and microfluidics for advanced functionalities. This paper reports the construction of a UV-Vis spectrophotometer on a microreactor, and demonstrates the online monitoring of the photocatalytic degradations of methylene blue and methyl orange under different flow rates and different pH values by detecting the intensity change and/or the peak shift. The integrated device consists of a TiO2-coated glass substrate, a PDMS micro-sized reaction chamber and two flow cells. By comparing with the results of commercial equipment, we have found that the measuring range and the sensitivity are acceptable, especially when the transmittance is in the range of 0.01–0.9. This integrated optofluidic device can significantly cut down the test time and the sample volume, and would provide a versatile platform for real-time characterization of photochemical performance. Moreover, its online monitoring capability may enable to access the usually hidden information in biochemical reactions like intermediate products, time-dependent processes and reaction kinetics. PMID:27352840

Optofluidic UV-Vis spectrophotometer for online monitoring of photocatalytic reactions.

PubMed

Wang, Ning; Tan, Furui; Zhao, Yu; Tsoi, Chi Chung; Fan, Xudong; Yu, Weixing; Zhang, Xuming

2016-06-29

On-chip integration of optical detection units into the microfluidic systems for online monitoring is highly desirable for many applications and is also well in line with the spirit of optofluidics technology-fusion of optics and microfluidics for advanced functionalities. This paper reports the construction of a UV-Vis spectrophotometer on a microreactor, and demonstrates the online monitoring of the photocatalytic degradations of methylene blue and methyl orange under different flow rates and different pH values by detecting the intensity change and/or the peak shift. The integrated device consists of a TiO2-coated glass substrate, a PDMS micro-sized reaction chamber and two flow cells. By comparing with the results of commercial equipment, we have found that the measuring range and the sensitivity are acceptable, especially when the transmittance is in the range of 0.01-0.9. This integrated optofluidic device can significantly cut down the test time and the sample volume, and would provide a versatile platform for real-time characterization of photochemical performance. Moreover, its online monitoring capability may enable to access the usually hidden information in biochemical reactions like intermediate products, time-dependent processes and reaction kinetics.

Automated innovative diagnostic, data management and communication tool, for improving malaria vector control in endemic settings.

PubMed

Vontas, John; Mitsakakis, Konstantinos; Zengerle, Roland; Yewhalaw, Delenasaw; Sikaala, Chadwick Haadezu; Etang, Josiane; Fallani, Matteo; Carman, Bill; Müller, Pie; Chouaïbou, Mouhamadou; Coleman, Marlize; Coleman, Michael

2016-01-01

Malaria is a life-threatening disease that caused more than 400,000 deaths in sub-Saharan Africa in 2015. Mass prevention of the disease is best achieved by vector control which heavily relies on the use of insecticides. Monitoring mosquito vector populations is an integral component of control programs and a prerequisite for effective interventions. Several individual methods are used for this task; however, there are obstacles to their uptake, as well as challenges in organizing, interpreting and communicating vector population data. The Horizon 2020 project "DMC-MALVEC" consortium will develop a fully integrated and automated multiplex vector-diagnostic platform (LabDisk) for characterizing mosquito populations in terms of species composition, Plasmodium infections and biochemical insecticide resistance markers. The LabDisk will be interfaced with a Disease Data Management System (DDMS), a custom made data management software which will collate and manage data from routine entomological monitoring activities providing information in a timely fashion based on user needs and in a standardized way. The ResistanceSim, a serious game, a modern ICT platform that uses interactive ways of communicating guidelines and exemplifying good practices of optimal use of interventions in the health sector will also be a key element. The use of the tool will teach operational end users the value of quality data (relevant, timely and accurate) to make informed decisions. The integrated system (LabDisk, DDMS & ResistanceSim) will be evaluated in four malaria endemic countries, representative of the vector control challenges in sub-Saharan Africa, (Cameroon, Ivory Coast, Ethiopia and Zambia), highly representative of malaria settings with different levels of endemicity and vector control challenges, to support informed decision-making in vector control and disease management.

Optical Fiber Sensing Using Quantum Dots

PubMed Central

Jorge, Pedro; Martins, Manuel António; Trindade, Tito; Santos, José Luís; Farahi, Faramarz

2007-01-01

Recent advances in the application of semiconductor nanocrystals, or quantum dots, as biochemical sensors are reviewed. Quantum dots have unique optical properties that make them promising alternatives to traditional dyes in many luminescence based bioanalytical techniques. An overview of the more relevant progresses in the application of quantum dots as biochemical probes is addressed. Special focus will be given to configurations where the sensing dots are incorporated in solid membranes and immobilized in optical fibers or planar waveguide platforms. PMID:28903308

Ras plasma membrane signalling platforms

PubMed Central

2005-01-01

The plasma membrane is a complex, dynamic structure that provides platforms for the assembly of many signal transduction pathways. These platforms have the capacity to impose an additional level of regulation on cell signalling networks. In this review, we will consider specifically how Ras proteins interact with the plasma membrane. The focus will be on recent studies that provide novel spatial and dynamic insights into the micro-environments that different Ras proteins utilize for signal transduction. We will correlate these recent studies suggesting Ras proteins might operate within a heterogeneous plasma membrane with earlier biochemical work on Ras signal transduction. PMID:15954863

Relationship between changes in rat behavior and integral biochemical indexes determined by laser correlation spectroscopy after photothrombosis of the prefrontal cortex.

PubMed

Romanova, G A; Shakova, F M; Kovaleva, O I; Pivovarov, V V; Khlebnikova, N N; Karganov, M Yu

2004-02-01

Experiments on rats showed that Noopept improved retention and retrieval of conditioned passive avoidance response after phototrombosis of the prefrontal cortex (a procedure impairing retention of memory traces). The impairment of mnesic functions was accompanied by changes in integral biochemical indexes of the plasma determined by laser correlation spectroscopy. Treatment of behavioral disorders with Noopepet normalized biochemical indexes.

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

DOEpatents

Jenkins, Chris; Pierson, Lyndon G.

2016-10-25

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

Integrated Micro/nanoengineered Functional Biomaterials for Cell Mechanics and Mechanobiology: A Materials Perspective

PubMed Central

Shao, Yue

2014-01-01

The rapid development of micro/nanoengineered functional biomaterials in the last two decades has empowered materials scientists and bioengineers to precisely control different aspects of the in vitro cell microenvironment. Following a philosophy of reductionism, many studies using synthetic functional biomaterials have revealed instructive roles of individual extracellular biophysical and biochemical cues in regulating cellular behaviors. Development of integrated micro/nanoengineered functional biomaterials to study complex and emergent biological phenomena has also thrived rapidly in recent years, revealing adaptive and integrated cellular behaviors closely relevant to human physiological and pathological conditions. Working at the interface between materials science and engineering, biology, and medicine, we are now at the beginning of a great exploration using micro/nanoengineered functional biomaterials for both fundamental biology study and clinical and biomedical applications such as regenerative medicine and drug screening. In this review, we present an overview of state of the art micro/nanoengineered functional biomaterials that can control precisely individual aspects of cell-microenvironment interactions and highlight them as well-controlled platforms for mechanistic studies of mechano-sensitive and -responsive cellular behaviors and integrative biology research. We also discuss the recent exciting trend where micro/nanoengineered biomaterials are integrated into miniaturized biological and biomimetic systems for dynamic multiparametric microenvironmental control of emergent and integrated cellular behaviors. The impact of integrated micro/nanoengineered functional biomaterials for future in vitro studies of regenerative medicine, cell biology, as well as human development and disease models are discussed. PMID:24339188

Pressure pulse induced-damage in live biological samples

NASA Astrophysics Data System (ADS)

Bo, C.; Balzer, J.; Godfrey, S.; Francois, M.; Saffell, J. L.; Rankin, S. M.; Proud, W. G.; Brown, K. A.

2012-08-01

Developing a cellular and molecular understanding of the nature of traumatic and post-traumatic effects of blast on live biological samples is critical for improving clinical outcomes. To analyze the effects of blast waves upon the cellular structures and the underlying physiological and biochemical changes, we have constructed an experimental platform capable of delivering compression waves, of amplitudes relevant to blast, to cell suspensions in a contained environment. Initial characterization of the system shows that cell cultures can be subjected to high-intensity compression waves up to 15 MPa in pressure and duration of 80 ± 10μs. Studies of mouse mesenchymal stem cells subjected to two different pressure impulses were analysed by cell counting, cell viability assays and microscopic evaluation: the experiments present evidence suggestive of increased levels of damage and loss of cellular integrity compared to uncompressed cell cultures.

Early-branching Gut Fungi Possess A Large, And Comprehensive Array Of Biomass-Degrading Enzymes

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

Solomon, Kevin V.; Haitjema, Charles; Henske, John K.

The fungal kingdom is the source of almost all industrial enzymes in use for lignocellulose bioprocessing. Its more primitive members, however, remain relatively unexploited. We developed a systems-level approach that integrates RNA-Seq, proteomics, phenotype and biochemical studies of relatively unexplored early-branching free-living fungi. Anaerobic gut fungi isolated from herbivores produce a large array of biomass-degrading enzymes that synergistically degrade crude, unpretreated plant biomass, and are competitive with optimized commercial preparations from Aspergillus and Trichoderma. Compared to these model platforms, gut fungal enzymes are unbiased in substrate preference due to a wealth of xylan-degrading enzymes. These enzymes are universally catabolite repressed,more » and are further regulated by a rich landscape of noncoding regulatory RNAs. Furthermore, we identified several promising sequence divergent enzyme candidates for lignocellulosic bioprocessing.« less

Assessment of microbiota:host interactions at the vaginal mucosa interface.

PubMed

Pruski, Pamela; Lewis, Holly V; Lee, Yun S; Marchesi, Julian R; Bennett, Phillip R; Takats, Zoltan; MacIntyre, David A

2018-04-27

There is increasing appreciation of the role that vaginal microbiota play in health and disease throughout a woman's lifespan. This has been driven partly by molecular techniques that enable detailed identification and characterisation of microbial community structures. However, these methods do not enable assessment of the biochemical and immunological interactions between host and vaginal microbiota involved in pathophysiology. This review examines our current knowledge of the relationships that exist between vaginal microbiota and the host at the level of the vaginal mucosal interface. We also consider methodological approaches to microbiomic, immunologic and metabolic profiling that permit assessment of these interactions. Integration of information derived from these platforms brings the potential for biomarker discovery, disease risk stratification and improved understanding of the mechanisms regulating vaginal microbial community dynamics in health and disease. Copyright © 2018 Elsevier Inc. All rights reserved.

Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals.

PubMed

Su, Fei; Xu, Ping

2014-01-29

Microbial strains with high substrate efficiency and excellent environmental tolerance are urgently needed for the production of platform bio-chemicals. Bacillus coagulans has these merits; however, little genetic information is available about this species. Here, we determined the genome sequences of five B. coagulans strains, and used a comparative genomic approach to reconstruct the central carbon metabolism of this species to explain their fermentation features. A novel xylose isomerase in the xylose utilization pathway was identified in these strains. Based on a genome-wide positive selection scan, the selection pressure on amino acid metabolism may have played a significant role in the thermal adaptation. We also researched the immune systems of B. coagulans strains, which provide them with acquired resistance to phages and mobile genetic elements. Our genomic analysis provides comprehensive insights into the genetic characteristics of B. coagulans and paves the way for improving and extending the uses of this species.

Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals

PubMed Central

Su, Fei; Xu, Ping

2014-01-01

Microbial strains with high substrate efficiency and excellent environmental tolerance are urgently needed for the production of platform bio-chemicals. Bacillus coagulans has these merits; however, little genetic information is available about this species. Here, we determined the genome sequences of five B. coagulans strains, and used a comparative genomic approach to reconstruct the central carbon metabolism of this species to explain their fermentation features. A novel xylose isomerase in the xylose utilization pathway was identified in these strains. Based on a genome-wide positive selection scan, the selection pressure on amino acid metabolism may have played a significant role in the thermal adaptation. We also researched the immune systems of B. coagulans strains, which provide them with acquired resistance to phages and mobile genetic elements. Our genomic analysis provides comprehensive insights into the genetic characteristics of B. coagulans and paves the way for improving and extending the uses of this species. PMID:24473268

Nanostructured gold microelectrodes for SERS and EIS measurements by incorporating ZnO nanorod growth with electroplating

PubMed Central

Zong, Xianli; Zhu, Rong; Guo, Xiaoliang

2015-01-01

In this paper, a fine gold nanostructure synthesized on selective planar microelectrodes in micro-chip is realized by using an advanced hybrid fabrication approach incorporating growth of nanorods (NRs) with gold electroplating. By this developed nanostructure, integration of in-situ surface-enhanced Raman spectroscopy (SERS) detection with electrochemical impedance spectroscopy (EIS) measurement for label-free, nondestructive, real-time and rapid monitoring on a single cell has been achieved. Moreover, parameters of Au nanostructures such as size of nanoholes/nanogaps can be controllably adjusted in the fabrication. We have demonstrated a SERS enhancement factor of up to ~2.24 × 106 and double-layer impedance decrease ratio of 90% ~ 95% at low frequency range below 200 kHz by using nanostructured microelectrodes. SERS detection and in-situ EIS measurement of a trapped single cell by using planar microelectrodes are realized to demonstrate the compatibility, multi-functions, high-sensitivity and simplicity of the micro-chip system. This dual function platform integrating SERS and EIS is of great significance in biological, biochemical and biomedical applications. PMID:26558325

A service platform architecture design towards a light integration of heterogeneous systems in the wellbeing domain.

PubMed

Yang, Yaojin; Ahtinen, Aino; Lahteenmaki, Jaakko; Nyman, Petri; Paajanen, Henrik; Peltoniemi, Teijo; Quiroz, Carlos

2007-01-01

System integration is one of the major challenges for building wellbeing or healthcare related information systems. In this paper, we are going to share our experiences on how to design a service platform called Nuadu service platform, for providing integrated services in occupational health promotion and health risk management through two heterogeneous systems. Our design aims for a light integration covering the layers, from data through service up to presentation, while maintaining the integrity of the underlying systems.

Tier-scalable reconnaissance: the challenge of sensor optimization, sensor deployment, sensor fusion, and sensor interoperability

NASA Astrophysics Data System (ADS)

Fink, Wolfgang; George, Thomas; Tarbell, Mark A.

2007-04-01

Robotic reconnaissance operations are called for in extreme environments, not only those such as space, including planetary atmospheres, surfaces, and subsurfaces, but also in potentially hazardous or inaccessible operational areas on Earth, such as mine fields, battlefield environments, enemy occupied territories, terrorist infiltrated environments, or areas that have been exposed to biochemical agents or radiation. Real time reconnaissance enables the identification and characterization of transient events. A fundamentally new mission concept for tier-scalable reconnaissance of operational areas, originated by Fink et al., is aimed at replacing the engineering and safety constrained mission designs of the past. The tier-scalable paradigm integrates multi-tier (orbit atmosphere surface/subsurface) and multi-agent (satellite UAV/blimp surface/subsurface sensing platforms) hierarchical mission architectures, introducing not only mission redundancy and safety, but also enabling and optimizing intelligent, less constrained, and distributed reconnaissance in real time. Given the mass, size, and power constraints faced by such a multi-platform approach, this is an ideal application scenario for a diverse set of MEMS sensors. To support such mission architectures, a high degree of operational autonomy is required. Essential elements of such operational autonomy are: (1) automatic mapping of an operational area from different vantage points (including vehicle health monitoring); (2) automatic feature extraction and target/region-of-interest identification within the mapped operational area; and (3) automatic target prioritization for close-up examination. These requirements imply the optimal deployment of MEMS sensors and sensor platforms, sensor fusion, and sensor interoperability.

Targeting homeostasis in drug delivery using bioresponsive hydrogel microforms.

PubMed

Wilson, A Nolan; Guiseppi-Elie, Anthony

2014-01-30

A drug delivery platform comprising a biocompatible, bioresponsive hydrogel and possessing a covalently tethered peptide-drug conjugate was engineered to achieve stasis, via a closed control loop, of the external biochemical activity of the actuating protease. The delivery platform contains a peptide-drug conjugate covalently tethered to the hydrogel matrix, which in the presence of the appropriate protease, was cleaved and the drug released into the bathing environment. This platform was developed and investigated in silico using a finite element modeling (FEM) approach. Firstly, the primary governing phenomena guiding drug release profiles were investigated, and it was confirmed that under transport-limited conditions, the diffusion of the enzyme within the hydrogel and the coupled enzyme kinetics accurately model the system and are in agreement with published results. Secondly, the FEM model was used to investigate the release of a competitive protease inhibitor, MAG283, via cleavage of Acetyl-Pro-Leu-Gly|Leu-MAG-283 by MMP9 in order to achieve targeted homeostasis of MMP-9 activity, such as in the pathophysiology of chronic wounds, via closed-loop feedback control. The key engineering parameters for the delivery device are the radii of the hydrogel microspheres and the concentration of the peptide-inhibitor conjugate. Homeostatic drug delivery, where the focus turns away from the drug release rate and turns toward achieving targeted control of biochemical activity within a biochemical pathway, is an emerging approach in drug delivery methodologies for which the potential has not yet been fully realized. Copyright © 2013 Elsevier B.V. All rights reserved.

A Strategy to employ coordinated, autonomous Platforms for addressing long-term biochemical observing Tasks

NASA Astrophysics Data System (ADS)

Waldmann, H. C.; Montenegro, S.

2016-02-01

Autonomous platforms get a growing importance for ocean observing tasks in particular to enable long-term observing tasks. Employing the mobility of those platforms allows a targeted investigations of phenomena that up to now are mainly seen from satellite but are lacking detailed scrutiny. As part oft he national funded project ROBEX new operation concepts for mobile platforms are developed in particular a new type of underwater glider with larger payload capacity compared to legacy systems will be developed. First tests in the pool of a aparticular hull shape have led to a better understanding oft he hydrodynamic condition and an optomized hull design was derived from that. The WAVEGLIDER system of Liquid Robotics lends itsself to be used as a communication hub and a platform to track underwater vehicles. Therefore the combination of those systems are currently assessed in regard to a possible operation and its hard- and software implementation. A major issue ist o achieve a coordinated displacement of these completely decoupled systems. Issues on how to mitigate faulty mission runs, coping with low communication bandwidths, and ensuring adequate positioning information about the underwater glider have to be addressed. Robotic concepts known from terrestrial applications like for UAV systems are tested under the more stringent environmental conditions in ocean waters. With this combination of WAVEGLIDER and underwater glider it is planned to carry out long-term missions to investigate biochemical processes in the water column in particular to investigate the particle transport through the water column and the processes resulting from that. Concepts and first results of those tasks will be presented.

Partially reduced graphene oxide based FRET on fiber-optic interferometer for biochemical detection

NASA Astrophysics Data System (ADS)

Yao, B. C.; Wu, Y.; Yu, C. B.; He, J. R.; Rao, Y. J.; Gong, Y.; Fu, F.; Chen, Y. F.; Li, Y. R.

2016-03-01

Fluorescent resonance energy transfer (FRET) with naturally exceptional selectivity is a powerful technique and widely used in chemical and biomedical analysis. However, it is still challenging for conventional FRET to perform as a high sensitivity compact sensor. Here we propose a novel ‘FRET on Fiber’ concept, in which a partially reduced graphene oxide (prGO) film is deposited on a fiber-optic modal interferometer, acting as both the fluorescent quencher for the FRET and the sensitive cladding for optical phase measurement due to refractive index changes in biochemical detection. The target analytes induced fluorescence recovery with good selectivity and optical phase shift with high sensitivity are measured simultaneously. The functionalized prGO film coated on the fiber-optic interferometer shows high sensitivities for the detections of metal ion, dopamine and single-stranded DNA (ssDNA), with detection limits of 1.2 nM, 1.3 μM and 1 pM, respectively. Such a prGO based ‘FRET on fiber’ configuration, bridging the FRET and the fiber-optic sensing technology, may serve as a platform for the realization of series of integrated ‘FRET on Fiber’ sensors for on-line environmental, chemical, and biomedical detection, with excellent compactness, high sensitivity, good selectivity and fast response

Partially reduced graphene oxide based FRET on fiber-optic interferometer for biochemical detection

PubMed Central

Yao, B. C.; Wu, Y.; Yu, C. B.; He, J. R.; Rao, Y. J.; Gong, Y.; Fu, F.; Chen, Y. F.; Li, Y. R.

2016-01-01

Fluorescent resonance energy transfer (FRET) with naturally exceptional selectivity is a powerful technique and widely used in chemical and biomedical analysis. However, it is still challenging for conventional FRET to perform as a high sensitivity compact sensor. Here we propose a novel ‘FRET on Fiber’ concept, in which a partially reduced graphene oxide (prGO) film is deposited on a fiber-optic modal interferometer, acting as both the fluorescent quencher for the FRET and the sensitive cladding for optical phase measurement due to refractive index changes in biochemical detection. The target analytes induced fluorescence recovery with good selectivity and optical phase shift with high sensitivity are measured simultaneously. The functionalized prGO film coated on the fiber-optic interferometer shows high sensitivities for the detections of metal ion, dopamine and single-stranded DNA (ssDNA), with detection limits of 1.2 nM, 1.3 μM and 1 pM, respectively. Such a prGO based ‘FRET on fiber’ configuration, bridging the FRET and the fiber-optic sensing technology, may serve as a platform for the realization of series of integrated ‘FRET on Fiber’ sensors for on-line environmental, chemical, and biomedical detection, with excellent compactness, high sensitivity, good selectivity and fast response PMID:27010752

Genetic and biochemical changes of the serotonergic system in migraine pathobiology.

PubMed

Gasparini, Claudia Francesca; Smith, Robert Anthony; Griffiths, Lyn Robyn

2017-12-01

Migraine is a brain disorder characterized by a piercing headache which affects one side of the head, located mainly at the temples and in the area around the eye. Migraine imparts substantial suffering to the family in addition to the sufferer, particularly as it affects three times more women than men and is most prevalent between the ages of 25 and 45, the years of child rearing. Migraine typically occurs in individuals with a genetic predisposition and is aggravated by specific environmental triggers. Attempts to study the biochemistry of migraine began as early as the 1960s and were primarily directed at serotonin metabolism after an increase of 5-hydroxyindoleacetic acid (5-HIAA), the main metabolite of serotonin was observed in urine of migraineurs. Genetic and biochemical studies have primarily focused on the neurotransmitter serotonin, considering receptor binding, transport and synthesis of serotonin and have investigated serotonergic mediators including enzymes, receptors as well as intermediary metabolites. These studies have been mainly assayed in blood, CSF and urine as the most accessible fluids. More recently PET imaging technology integrated with a metabolomics and a systems biology platform are being applied to study serotonergic biology. The general trend observed is that migraine patients have alterations of neurotransmitter metabolism detected in biological fluids with different biochemistry from controls, however the interpretation of the biological significance of these peripheral changes is unresolved. In this review we present the biology of the serotonergic system and metabolic routes for serotonin and discuss results of biochemical studies with regard to alterations in serotonin in brain, cerebrospinal fluid, saliva, platelets, plasma and urine of migraine patients.

Temperature-programmed natural convection for micromixing and biochemical reaction in a single microfluidic chamber.

PubMed

Kim, Sung-Jin; Wang, Fang; Burns, Mark A; Kurabayashi, Katsuo

2009-06-01

Micromixing is a crucial step for biochemical reactions in microfluidic networks. A critical challenge is that the system containing micromixers needs numerous pumps, chambers, and channels not only for the micromixing but also for the biochemical reactions and detections. Thus, a simple and compatible design of the micromixer element for the system is essential. Here, we propose a simple, yet effective, scheme that enables micromixing and a biochemical reaction in a single microfluidic chamber without using any pumps. We accomplish this process by using natural convection in conjunction with alternating heating of two heaters for efficient micromixing, and by regulating capillarity for sample transport. As a model application, we demonstrate micromixing and subsequent polymerase chain reaction (PCR) for an influenza viral DNA fragment. This process is achieved in a platform of a microfluidic cartridge and a microfabricated heating-instrument with a fast thermal response. Our results will significantly simplify micromixing and a subsequent biochemical reaction that involves reagent heating in microfluidic networks.

High-content screening in microfluidic devices.

PubMed

Cheong, Raymond; Paliwal, Saurabh; Levchenko, Andre

2010-08-01

Miniaturization is the key to advancing the state of the art in high-content screening (HCS) in order to enable dramatic cost savings through reduced usage of expensive biochemical reagents and to enable large-scale screening on primary cells. Microfluidic technology offers the potential to enable HCS to be performed with an unprecedented degree of miniaturization. This perspective highlights a real-world example from the authors’ work of HCS assays implemented in a highly miniaturized microfluidic format. The advantages of this technology are discussed, including cost savings, high-throughput screening on primary cells, improved accuracy, the ability to study complex time-varying stimuli, and ease of automation, integration and scaling. The reader will understand the capabilities of anew microfluidics-based platform for HCS and the advantages it provides over conventional plate-based HCS. Microfluidics technology will drive significant advancements and broader usage and applicability of HCS in drug discovery.

Microfluidics-based integrated airborne pathogen detection systems

NASA Astrophysics Data System (ADS)

Northrup, M. Allen; Alleman-Sposito, Jennifer; Austin, Todd; Devitt, Amy; Fong, Donna; Lin, Phil; Nakao, Brian; Pourahmadi, Farzad; Vinas, Mary; Yuan, Bob

2006-09-01

Microfluidic Systems is focused on building microfluidic platforms that interface front-end mesofluidics to handle real world sample volumes for optimal sensitivity coupled to microfluidic circuitry to process small liquid volumes for complex reagent metering, mixing, and biochemical analysis, particularly for pathogens. MFSI is the prime contractor on two programs for the US Department of Homeland Security: BAND (Bioagent Autonomous Networked Detector) and IBADS (Instantaneous Bio-Aerosol Detection System). The goal of BAND is to develop an autonomous system for monitoring the air for known biological agents. This consists of air collection, sample lysis, sample purification, detection of DNA, RNA, and toxins, and a networked interface to report the results. For IBADS, MFSI is developing the confirmatory device which must verify the presence of a pathogen with 5 minutes of an air collector/trigger sounding an alarm. Instrument designs and biological assay results from both BAND and IBADS will be presented.

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

NASA Astrophysics Data System (ADS)

Shinar, J.; Shinar, R.

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

Integrated micro/nanoengineered functional biomaterials for cell mechanics and mechanobiology: a materials perspective.

PubMed

Shao, Yue; Fu, Jianping

2014-03-12

The rapid development of micro/nanoengineered functional biomaterials in the last two decades has empowered materials scientists and bioengineers to precisely control different aspects of the in vitro cell microenvironment. Following a philosophy of reductionism, many studies using synthetic functional biomaterials have revealed instructive roles of individual extracellular biophysical and biochemical cues in regulating cellular behaviors. Development of integrated micro/nanoengineered functional biomaterials to study complex and emergent biological phenomena has also thrived rapidly in recent years, revealing adaptive and integrated cellular behaviors closely relevant to human physiological and pathological conditions. Working at the interface between materials science and engineering, biology, and medicine, we are now at the beginning of a great exploration using micro/nanoengineered functional biomaterials for both fundamental biology study and clinical and biomedical applications such as regenerative medicine and drug screening. In this review, an overview of state of the art micro/nanoengineered functional biomaterials that can control precisely individual aspects of cell-microenvironment interactions is presented and they are highlighted them as well-controlled platforms for mechanistic studies of mechano-sensitive and -responsive cellular behaviors and integrative biology research. The recent exciting trend where micro/nanoengineered biomaterials are integrated into miniaturized biological and biomimetic systems for dynamic multiparametric microenvironmental control of emergent and integrated cellular behaviors is also discussed. The impact of integrated micro/nanoengineered functional biomaterials for future in vitro studies of regenerative medicine, cell biology, as well as human development and disease models are discussed. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Research on application information system integration platform in medicine manufacturing enterprise.

PubMed

Deng, Wu; Zhao, Huimin; Zou, Li; Li, Yuanyuan; Li, Zhengguang

2012-08-01

Computer and information technology popularizes in the medicine manufacturing enterprise for its potentials in working efficiency and service quality. In allusion to the explosive data and information of application system in current medicine manufacturing enterprise, we desire to propose a novel application information system integration platform in medicine manufacturing enterprise, which based on a combination of RFID technology and SOA, to implement information sharing and alternation. This method exploits the application integration platform across service interface layer to invoke the RFID middleware. The loose coupling in integration solution is realized by Web services. The key techniques in RFID event components and expanded role-based security access mechanism are studied in detail. Finally, a case study is implemented and tested to evidence our understanding on application system integration platform in medicine manufacturing enterprise.

Colloidal core-seeded semiconductor nanorods as fluorescent labels for in-vitro diagnostics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Chan, YinThai

2016-03-01

Colloidal semiconductor nanocrystals are ideal fluorophores for clinical diagnostics, therapeutics, and highly sensitive biochip applications due to their high photostability, size-tunable color of emission and flexible surface chemistry. The relatively recent development of core-seeded semiconductor nanorods showed that the presence of a rod-like shell can confer even more advantageous physicochemical properties than their spherical counterparts, such as large multi-photon absorption cross-sections and facet-specific chemistry that can be exploited to deposit secondary nanoparticles. It may be envisaged that these highly fluorescent nanorods can be integrated with large scale integrated (LSI) microfluidic systems that allow miniaturization and integration of multiple biochemical processes in a single device at the nanoliter scale, resulting in a highly sensitive and automated detection platform. In this talk, I will describe a LSI microfluidic device that integrates RNA extraction, reverse transcription to cDNA, amplification and target pull-down to detect histidine decarboxylase (HDC) gene directly from human white blood cells samples. When anisotropic colloidal semiconductor nanorods (NRs) were used as the fluorescent readout, the detection limit was found to be 0.4 ng of total RNA, which was much lower than that obtained using spherical quantum dots (QDs) or organic dyes. This was attributed to the large action cross-section of NRs and their high probability of target capture in a pull-down detection scheme. The combination of large scale integrated microfluidics with highly fluorescent semiconductor NRs may find widespread utility in point-of-care devices and multi-target diagnostics.

FilmArray, an Automated Nested Multiplex PCR System for Multi-Pathogen Detection: Development and Application to Respiratory Tract Infection

PubMed Central

Poritz, Mark A.; Blaschke, Anne J.; Byington, Carrie L.; Meyers, Lindsay; Nilsson, Kody; Jones, David E.; Thatcher, Stephanie A.; Robbins, Thomas; Lingenfelter, Beth; Amiott, Elizabeth; Herbener, Amy; Daly, Judy; Dobrowolski, Steven F.; Teng, David H. -F.; Ririe, Kirk M.

2011-01-01

The ideal clinical diagnostic system should deliver rapid, sensitive, specific and reproducible results while minimizing the requirements for specialized laboratory facilities and skilled technicians. We describe an integrated diagnostic platform, the “FilmArray”, which fully automates the detection and identification of multiple organisms from a single sample in about one hour. An unprocessed biologic/clinical sample is subjected to nucleic acid purification, reverse transcription, a high-order nested multiplex polymerase chain reaction and amplicon melt curve analysis. Biochemical reactions are enclosed in a disposable pouch, minimizing the PCR contamination risk. FilmArray has the potential to detect greater than 100 different nucleic acid targets at one time. These features make the system well-suited for molecular detection of infectious agents. Validation of the FilmArray technology was achieved through development of a panel of assays capable of identifying 21 common viral and bacterial respiratory pathogens. Initial testing of the system using both cultured organisms and clinical nasal aspirates obtained from children demonstrated an analytical and clinical sensitivity and specificity comparable to existing diagnostic platforms. We demonstrate that automated identification of pathogens from their corresponding target amplicon(s) can be accomplished by analysis of the DNA melting curve of the amplicon. PMID:22039434

System-Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism.

PubMed

Wang, Lei; Sun, Xiaoliang; Weiszmann, Jakob; Weckwerth, Wolfram

2017-01-01

Grapevine is a fruit crop with worldwide economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. This ripening process and production processes define the wine quality. Thus, a thorough understanding of berry ripening is crucial for the prediction of wine quality. For a systemic analysis of grape berry development we applied mass spectrometry based platforms to analyse the metabolome and proteome of Early Campbell at 12 stages covering major developmental phases. Primary metabolites involved in central carbon metabolism, such as sugars, organic acids and amino acids together with various bioactive secondary metabolites like flavonols, flavan-3-ols and anthocyanins were annotated and quantified. At the same time, the proteomic analysis revealed the protein dynamics of the developing grape berries. Multivariate statistical analysis of the integrated metabolomic and proteomic dataset revealed the growth trajectory and corresponding metabolites and proteins contributing most to the specific developmental process. K-means clustering analysis revealed 12 highly specific clusters of co-regulated metabolites and proteins. Granger causality network analysis allowed for the identification of time-shift correlations between metabolite-metabolite, protein- protein and protein-metabolite pairs which is especially interesting for the understanding of developmental processes. The integration of metabolite and protein dynamics with their corresponding biochemical pathways revealed an energy-linked metabolism before veraison with high abundances of amino acids and accumulation of organic acids, followed by protein and secondary metabolite synthesis. Anthocyanins were strongly accumulated after veraison whereas other flavonoids were in higher abundance at early developmental stages and decreased during the grape berry developmental processes. A comparison of the anthocyanin profile of Early Campbell to other cultivars revealed similarities to Concord grape and indicates the strong effect of genetic background on metabolic partitioning in primary and secondary metabolism.

System-Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism

PubMed Central

Wang, Lei; Sun, Xiaoliang; Weiszmann, Jakob; Weckwerth, Wolfram

2017-01-01

Grapevine is a fruit crop with worldwide economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. This ripening process and production processes define the wine quality. Thus, a thorough understanding of berry ripening is crucial for the prediction of wine quality. For a systemic analysis of grape berry development we applied mass spectrometry based platforms to analyse the metabolome and proteome of Early Campbell at 12 stages covering major developmental phases. Primary metabolites involved in central carbon metabolism, such as sugars, organic acids and amino acids together with various bioactive secondary metabolites like flavonols, flavan-3-ols and anthocyanins were annotated and quantified. At the same time, the proteomic analysis revealed the protein dynamics of the developing grape berries. Multivariate statistical analysis of the integrated metabolomic and proteomic dataset revealed the growth trajectory and corresponding metabolites and proteins contributing most to the specific developmental process. K-means clustering analysis revealed 12 highly specific clusters of co-regulated metabolites and proteins. Granger causality network analysis allowed for the identification of time-shift correlations between metabolite-metabolite, protein- protein and protein-metabolite pairs which is especially interesting for the understanding of developmental processes. The integration of metabolite and protein dynamics with their corresponding biochemical pathways revealed an energy-linked metabolism before veraison with high abundances of amino acids and accumulation of organic acids, followed by protein and secondary metabolite synthesis. Anthocyanins were strongly accumulated after veraison whereas other flavonoids were in higher abundance at early developmental stages and decreased during the grape berry developmental processes. A comparison of the anthocyanin profile of Early Campbell to other cultivars revealed similarities to Concord grape and indicates the strong effect of genetic background on metabolic partitioning in primary and secondary metabolism. PMID:28713396

Boutiques: a flexible framework to integrate command-line applications in computing platforms.

PubMed

Glatard, Tristan; Kiar, Gregory; Aumentado-Armstrong, Tristan; Beck, Natacha; Bellec, Pierre; Bernard, Rémi; Bonnet, Axel; Brown, Shawn T; Camarasu-Pop, Sorina; Cervenansky, Frédéric; Das, Samir; Ferreira da Silva, Rafael; Flandin, Guillaume; Girard, Pascal; Gorgolewski, Krzysztof J; Guttmann, Charles R G; Hayot-Sasson, Valérie; Quirion, Pierre-Olivier; Rioux, Pierre; Rousseau, Marc-Étienne; Evans, Alan C

2018-05-01

We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.

VA's Integrated Imaging System on three platforms.

PubMed

Dayhoff, R E; Maloney, D L; Majurski, W J

1992-01-01

The DHCP Integrated Imaging System provides users with integrated patient data including text, image and graphics data. This system has been transferred from its original two screen DOS-based MUMPS platform to an X window workstation and a Microsoft Windows-based workstation. There are differences between these various platforms that impact on software design and on software development strategy. Data structures and conventions were used to isolate hardware, operating system, imaging software, and user-interface differences between platforms in the implementation of functionality for text and image display and interaction. The use of an object-oriented approach greatly increased system portability.

VA's Integrated Imaging System on three platforms.

PubMed Central

Dayhoff, R. E.; Maloney, D. L.; Majurski, W. J.

1992-01-01

The DHCP Integrated Imaging System provides users with integrated patient data including text, image and graphics data. This system has been transferred from its original two screen DOS-based MUMPS platform to an X window workstation and a Microsoft Windows-based workstation. There are differences between these various platforms that impact on software design and on software development strategy. Data structures and conventions were used to isolate hardware, operating system, imaging software, and user-interface differences between platforms in the implementation of functionality for text and image display and interaction. The use of an object-oriented approach greatly increased system portability. PMID:1482983

Label-free optical resonant sensors for biochemical applications

NASA Astrophysics Data System (ADS)

Ciminelli, Caterina; Campanella, Clarissa Martina; Dell'Olio, Francesco; Campanella, Carlo Edoardo; Armenise, Mario Nicola

2013-03-01

For a number of years, the scientific community has been paying growing attention to the monitoring and enhancement of public health and the quality of life through the detection of all dangerous agents for the human body, including gases, proteins, virus, and bacterial agents. When these agents are detected through label-free biochemical sensors, the molecules are not modified structurally or functionally by adding fluorescent or radioactive dyes. This work focuses on label-free optical ring resonator-based configurations suited for bio-chemical sensing, highlighting their physical aspects and specific applications. Resonant wavelength shift and the modal splitting occurring when the analyte interacts with microresonant structures are the two major physical aspects analyzed in this paper. Competitive optical platforms proposed in the literature are also illustrated together with their properties and performance.

FORCEnet Net Centric Architecture - A Standards View

DTIC Science & Technology

2006-06-01

SHARED SERVICES NETWORKING/COMMUNICATIONS STORAGE COMPUTING PLATFORM DATA INTERCHANGE/INTEGRATION DATA MANAGEMENT APPLICATION...R V I C E P L A T F O R M S E R V I C E F R A M E W O R K USER-FACING SERVICES SHARED SERVICES NETWORKING/COMMUNICATIONS STORAGE COMPUTING PLATFORM...E F R A M E W O R K USER-FACING SERVICES SHARED SERVICES NETWORKING/COMMUNICATIONS STORAGE COMPUTING PLATFORM DATA INTERCHANGE/INTEGRATION

Mems: Platform for Large-Scale Integrated Vacuum Electronic Circuits

DTIC Science & Technology

2017-03-20

SECURITY CLASSIFICATION OF: The objective of the LIVEC advanced study project was to develop a platform for large-scale integrated vacuum electronic ...Distribution Unlimited UU UU UU UU 20-03-2017 1-Jul-2014 30-Jun-2015 Final Report: MEMS Platform for Large-Scale Integrated Vacuum Electronic ... Electronic Circuits (LIVEC) Contract No: W911NF-14-C-0093 COR Dr. James Harvey U.S. ARO RTP, NC 27709-2211 Phone: 702-696-2533 e-mail

Introducing WISDEM:An Integrated System Modeling for Wind Turbines and Plant (Presentation)

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

Dykes, K.; Graf, P.; Scott, G.

2015-01-01

The National Wind Technology Center wind energy systems engineering initiative has developed an analysis platform to leverage its research capabilities toward integrating wind energy engineering and cost models across wind plants. This Wind-Plant Integrated System Design & Engineering Model (WISDEM) platform captures the important interactions between various subsystems to achieve a better National Wind Technology Center wind energy systems engineering initiative has developed an analysis platform to leverage its research capabilities toward integrating wind energy engineering and cost models across wind plants. This Wind-Plant Integrated System Design & Engineering Model (WISDEM) platform captures the important interactions between various subsystems tomore » achieve a better understanding of how to improve system-level performance and achieve system-level cost reductions. This work illustrates a few case studies with WISDEM that focus on the design and analysis of wind turbines and plants at different system levels.« less

Boutiques: a flexible framework to integrate command-line applications in computing platforms

PubMed Central

Glatard, Tristan; Kiar, Gregory; Aumentado-Armstrong, Tristan; Beck, Natacha; Bellec, Pierre; Bernard, Rémi; Bonnet, Axel; Brown, Shawn T; Camarasu-Pop, Sorina; Cervenansky, Frédéric; Das, Samir; Ferreira da Silva, Rafael; Flandin, Guillaume; Girard, Pascal; Gorgolewski, Krzysztof J; Guttmann, Charles R G; Hayot-Sasson, Valérie; Quirion, Pierre-Olivier; Rioux, Pierre; Rousseau, Marc-Étienne; Evans, Alan C

2018-01-01

Abstract We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science. PMID:29718199

Aluminum nitride integrated photonics platform for the ultraviolet to visible spectrum.

PubMed

Lu, Tsung-Ju; Fanto, Michael; Choi, Hyeongrak; Thomas, Paul; Steidle, Jeffrey; Mouradian, Sara; Kong, Wei; Zhu, Di; Moon, Hyowon; Berggren, Karl; Kim, Jeehwan; Soltani, Mohammad; Preble, Stefan; Englund, Dirk

2018-04-30

We demonstrate a wide-bandgap semiconductor photonics platform based on nanocrystalline aluminum nitride (AlN) on sapphire. This photonics platform guides light at low loss from the ultraviolet (UV) to the visible spectrum. We measure ring resonators with intrinsic quality factor (Q) exceeding 170,000 at 638 nm and Q >20,000 down to 369.5 nm, which shows a promising path for low-loss integrated photonics in UV and visible spectrum. This platform opens up new possibilities in integrated quantum optics with trapped ions or atom-like color centers in solids, as well as classical applications including nonlinear optics and on-chip UV-spectroscopy.

Bioanalytical and chemical sensors using living taste, olfactory, and neural cells and tissues: a short review.

PubMed

Wu, Chunsheng; Lillehoj, Peter B; Wang, Ping

2015-11-07

Biosensors utilizing living tissues and cells have recently gained significant attention as functional devices for chemical sensing and biochemical analysis. These devices integrate biological components (i.e. single cells, cell networks, tissues) with micro-electro-mechanical systems (MEMS)-based sensors and transducers. Various types of cells and tissues derived from natural and bioengineered sources have been used as recognition and sensing elements, which are generally characterized by high sensitivity and specificity. This review summarizes the state of the art in tissue- and cell-based biosensing platforms with an emphasis on those using taste, olfactory, and neural cells and tissues. Many of these devices employ unique integration strategies and sensing schemes based on sensitive transducers including microelectrode arrays (MEAs), field effect transistors (FETs), and light-addressable potentiometric sensors (LAPSs). Several groups have coupled these hybrid biosensors with microfluidics which offers added benefits of small sample volumes and enhanced automation. While this technology is currently limited to lab settings due to the limited stability of living biological components, further research to enhance their robustness will enable these devices to be employed in field and clinical settings.

Scaling up semi-arid grassland biochemical content from the leaf to the canopy level: challenges and opportunities.

PubMed

He, Yuhong; Mui, Amy

2010-01-01

Remote sensing imagery is being used intensively to estimate the biochemical content of vegetation (e.g., chlorophyll, nitrogen, and lignin) at the leaf level. As a result of our need for vegetation biochemical information and our increasing ability to obtain canopy spectral data, a few techniques have been explored to scale leaf-level biochemical content to the canopy level for forests and crops. However, due to the contribution of non-green materials (i.e., standing dead litter, rock, and bare soil) from canopy spectra in semi-arid grasslands, it is difficult to obtain information about grassland biochemical content from remote sensing data at the canopy level. This paper summarizes available methods used to scale biochemical information from the leaf level to the canopy level and groups these methods into three categories: direct extrapolation, canopy-integrated approach, and inversion of physical models. As for semi-arid heterogeneous grasslands, we conclude that all methods are useful, but none are ideal. It is recommended that future research should explore a systematic upscaling framework which combines spatial pattern analysis, canopy-integrated approach, and modeling methods to retrieve vegetation biochemical content at the canopy level.

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

A droplet-to-digital (D2D) microfluidic device for single cell assays.

PubMed

Shih, Steve C C; Gach, Philip C; Sustarich, Jess; Simmons, Blake A; Adams, Paul D; Singh, Seema; Singh, Anup K

2015-01-07

We have developed a new hybrid droplet-to-digital microfluidic platform (D2D) that integrates droplet-in-channel microfluidics with digital microfluidics (DMF) for performing multi-step assays. This D2D platform combines the strengths of the two formats-droplets-in-channel for facile generation of droplets containing single cells, and DMF for on-demand manipulation of droplets including control of different droplet volumes (pL-μL), creation of a dilution series of ionic liquid (IL), and parallel single cell culturing and analysis for IL toxicity screening. This D2D device also allows for automated analysis that includes a feedback-controlled system for merging and splitting of droplets to add reagents, an integrated Peltier element for parallel cell culture at optimum temperature, and an impedance sensing mechanism to control the flow rate for droplet generation and preventing droplet evaporation. Droplet-in-channel is well-suited for encapsulation of single cells as it allows the careful manipulation of flow rates of aqueous phase containing cells and oil to optimize encapsulation. Once single cell containing droplets are generated, they are transferred to a DMF chip via a capillary where they are merged with droplets containing IL and cultured at 30 °C. The DMF chip, in addition to permitting cell culture and reagent (ionic liquid/salt) addition, also allows recovery of individual droplets for off-chip analysis such as further culturing and measurement of ethanol production. The D2D chip was used to evaluate the effect of IL/salt type (four types: NaOAc, NaCl, [C2mim] [OAc], [C2mim] [Cl]) and concentration (four concentrations: 0, 37.5, 75, 150 mM) on the growth kinetics and ethanol production of yeast and as expected, increasing IL concentration led to lower biomass and ethanol production. Specifically, [C2mim] [OAc] had inhibitory effects on yeast growth at concentrations 75 and 150 mM and significantly reduced their ethanol production compared to cells grown in other ILs/salts. The growth curve trends obtained by D2D matched conventional yeast culturing in microtiter wells, validating the D2D platform. We believe that our approach represents a generic platform for multi-step biochemical assays such as drug screening, digital PCR, enzyme assays, immunoassays and cell-based assays.

Centrifugo-pneumatic valving utilizing dissolvable films.

PubMed

Gorkin, Robert; Nwankire, Charles E; Gaughran, Jennifer; Zhang, Xin; Donohoe, Gerard G; Rook, Martha; O'Kennedy, Richard; Ducrée, Jens

2012-08-21

In this article we introduce a novel technology that utilizes specialized water dissolvable thin films for valving in centrifugal microfluidic systems. In previous work (William Meathrel and Cathy Moritz, IVD Technologies, 2007), dissolvable films (DFs) have been assembled in laminar flow devices to form efficient sacrificial valves where DFs simply open by direct contact with liquid. Here, we build on the original DF valving scheme to leverage sophisticated, merely rotationally actuated vapour barriers and flow control for enabling comprehensive assay integration with low-complexity instrumentation on "lab-on-a-disc" platforms. The advanced sacrificial valving function is achieved by creating an inverted gas-liquid stack upstream of the DF during priming of the system. At low rotational speeds, a pocket of trapped air prevents a surface-tension stabilized liquid plug from wetting the DF membrane. However, high-speed rotation disrupts the metastable gas/liquid interface to wet the DF and thus opens the valve. By judicious choice of the radial position and geometry of the valve, the burst frequency can be tuned over a wide range of rotational speeds nearly 10 times greater than those attained by common capillary burst valves based on hydrophobic constrictions. The broad range of reproducible burst frequencies of the DF valves bears the potential for full integration and automation of comprehensive, multi-step biochemical assay protocols. In this report we demonstrate DF valving, discuss the biocompatibility of using the films, and show a potential sequential valving system including the on-demand release of on-board stored liquid reagents, fast centrifugal sedimentation and vigorous mixing; thus providing a viable basis for use in lab-on-a-disc platforms for point-of-care diagnostics and other life science applications.

The Mouse Heart Attack Research Tool (mHART) 1.0 Database.

PubMed

DeLeon-Pennell, Kristine Y; Iyer, Rugmani Padmanabhan; Ma, Yonggang; Yabluchanskiy, Andriy; Zamilpa, Rogelio; Chiao, Ying Ann; Cannon, Presley; Cates, Courtney; Flynn, Elizabeth R; Halade, Ganesh V; de Castro Bras, Lisandra E; Lindsey, Merry L

2018-05-18

The generation of Big Data has enabled systems-level dissections into the mechanisms of cardiovascular pathology. Integration of genetic, proteomic, and pathophysiological variables across platforms and laboratories fosters discoveries through multidisciplinary investigations and minimizes unnecessary redundancy in research efforts. The Mouse Heart Attack Research Tool (mHART) consolidates a large dataset of over 10 years of experiments from a single laboratory for cardiovascular investigators to generate novel hypotheses and identify new predictive markers of progressive left ventricular remodeling following myocardial infarction (MI) in mice. We designed the mHART REDCap database using our own data to integrate cardiovascular community participation. We generated physiological, biochemical, cellular, and proteomic outputs from plasma and left ventricles obtained from post-MI and no MI (naïve) control groups. We included both male and female mice ranging in age from 3 to 36 months old. After variable collection, data underwent quality assessment for data curation (e.g. eliminate technical errors, check for completeness, remove duplicates, and define terms). Currently, mHART 1.0 contains >888,000 data points and includes results from >2,100 unique mice. Database performance was tested and an example provided to illustrate database utility. This report explains how the first version of the mHART database was established and provides researchers with a standard framework to aid in the integration of their data into our database or in the development of a similar database.

SInCRe—structural interactome computational resource for Mycobacterium tuberculosis

PubMed Central

Metri, Rahul; Hariharaputran, Sridhar; Ramakrishnan, Gayatri; Anand, Praveen; Raghavender, Upadhyayula S.; Ochoa-Montaño, Bernardo; Higueruelo, Alicia P.; Sowdhamini, Ramanathan; Chandra, Nagasuma R.; Blundell, Tom L.; Srinivasan, Narayanaswamy

2015-01-01

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein–protein and protein–small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein–protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host–pathogen protein–protein interactions. Together they provide prerequisites for identification of off-target binding. Database URL: http://proline.biochem.iisc.ernet.in/sincre PMID:26130660

Research Spotlight: The next big thing is actually small.

PubMed

Garcia, Carlos D

2012-07-01

Recent developments in materials, surface modifications, separation schemes, detection systems and associated instrumentation have allowed significant advances in the performance of lab-on-a-chip devices. These devices, also referred to as micro total analysis systems (µTAS), offer great versatility, high throughput, short analysis time, low cost and, more importantly, performance that is comparable to standard bench-top instrumentation. To date, µTAS have demonstrated advantages in a significant number of fields including biochemical, pharmaceutical, military and environmental. Perhaps most importantly, µTAS represent excellent platforms to introduce students to microfabrication and nanotechnology, bridging chemistry with other fields, such as engineering and biology, enabling the integration of various skills and curricular concepts. Considering the advantages of the technology and the potential impact to society, our research program aims to address the need for simpler, more affordable, faster and portable devices to measure biologically active compounds. Specifically, the program is focused on the development and characterization of a series of novel strategies towards the realization of integrated microanalytical devices. One key aspect of our research projects is that the developed analytical strategies must be compatible with each other; therefore, enabling their use in integrated devices. The program combines spectroscopy, surface chemistry, capillary electrophoresis, electrochemical detection and nanomaterials. This article discusses some of the most recent results obtained in two main areas of emphasis: capillary electrophoresis, microchip-capillary electrophoresis, electrochemical detection and interaction of proteins with nanomaterials.

Sharing Health Big Data for Research - A Design by Use Cases: The INSHARE Platform Approach.

PubMed

Bouzillé, Guillaume; Westerlynck, Richard; Defossez, Gautier; Bouslimi, Dalel; Bayat, Sahar; Riou, Christine; Busnel, Yann; Le Guillou, Clara; Cauvin, Jean-Michel; Jacquelinet, Christian; Pladys, Patrick; Oger, Emmanuel; Stindel, Eric; Ingrand, Pierre; Coatrieux, Gouenou; Cuggia, Marc

2017-01-01

Sharing and exploiting Health Big Data (HBD) allow tackling challenges: data protection/governance taking into account legal, ethical, and deontological aspects enables trust, transparent and win-win relationship between researchers, citizens, and data providers. Lack of interoperability: compartmentalized and syntactically/semantica heterogeneous data. INSHARE project using experimental proof of concept explores how recent technologies overcome such issues. Using 6 data providers, platform is designed via 3 steps to: (1) analyze use cases, needs, and requirements; (2) define data sharing governance, secure access to platform; and (3) define platform specifications. Three use cases - from 5 studies and 11 data sources - were analyzed for platform design. Governance derived from SCANNER model was adapted to data sharing. Platform architecture integrates: data repository and hosting, semantic integration services, data processing, aggregate computing, data quality and integrity monitoring, Id linking, multisource query builder, visualization and data export services, data governance, study management service and security including data watermarking.

Photonic Integrated Circuits

NASA Technical Reports Server (NTRS)

Krainak, Michael; Merritt, Scott

2016-01-01

Integrated photonics generally is the integration of multiple lithographically defined photonic and electronic components and devices (e.g. lasers, detectors, waveguides passive structures, modulators, electronic control and optical interconnects) on a single platform with nanometer-scale feature sizes. The development of photonic integrated circuits permits size, weight, power and cost reductions for spacecraft microprocessors, optical communication, processor buses, advanced data processing, and integrated optic science instrument optical systems, subsystems and components. This is particularly critical for small spacecraft platforms. We will give an overview of some NASA applications for integrated photonics.

Integrated testing system FiTest for diagnosis of PCBA

NASA Astrophysics Data System (ADS)

Bogdan, Arkadiusz; Lesniak, Adam

2016-12-01

This article presents the innovative integrated testing system FiTest for automatic, quick inspection of printed circuit board assemblies (PCBA) manufactured in Surface Mount Technology (SMT). Integration of Automatic Optical Inspection (AOI), In-Circuit Tests (ICT) and Functional Circuit Tests (FCT) resulted in universal hardware platform for testing variety of electronic circuits. The platform provides increased test coverage, decreased level of false calls and optimization of test duration. The platform is equipped with powerful algorithms performing tests in a stable and repetitive way and providing effective management of diagnosis.

High-performance silicon photonics technology for telecommunications applications.

PubMed

Yamada, Koji; Tsuchizawa, Tai; Nishi, Hidetaka; Kou, Rai; Hiraki, Tatsurou; Takeda, Kotaro; Fukuda, Hiroshi; Ishikawa, Yasuhiko; Wada, Kazumi; Yamamoto, Tsuyoshi

2014-04-01

By way of a brief review of Si photonics technology, we show that significant improvements in device performance are necessary for practical telecommunications applications. In order to improve device performance in Si photonics, we have developed a Si-Ge-silica monolithic integration platform, on which compact Si-Ge-based modulators/detectors and silica-based high-performance wavelength filters are monolithically integrated. The platform features low-temperature silica film deposition, which cannot damage Si-Ge-based active devices. Using this platform, we have developed various integrated photonic devices for broadband telecommunications applications.

High-performance silicon photonics technology for telecommunications applications

PubMed Central

Yamada, Koji; Tsuchizawa, Tai; Nishi, Hidetaka; Kou, Rai; Hiraki, Tatsurou; Takeda, Kotaro; Fukuda, Hiroshi; Ishikawa, Yasuhiko; Wada, Kazumi; Yamamoto, Tsuyoshi

2014-01-01

By way of a brief review of Si photonics technology, we show that significant improvements in device performance are necessary for practical telecommunications applications. In order to improve device performance in Si photonics, we have developed a Si-Ge-silica monolithic integration platform, on which compact Si-Ge–based modulators/detectors and silica-based high-performance wavelength filters are monolithically integrated. The platform features low-temperature silica film deposition, which cannot damage Si-Ge–based active devices. Using this platform, we have developed various integrated photonic devices for broadband telecommunications applications. PMID:27877659

High-performance silicon photonics technology for telecommunications applications

NASA Astrophysics Data System (ADS)

Yamada, Koji; Tsuchizawa, Tai; Nishi, Hidetaka; Kou, Rai; Hiraki, Tatsurou; Takeda, Kotaro; Fukuda, Hiroshi; Ishikawa, Yasuhiko; Wada, Kazumi; Yamamoto, Tsuyoshi

2014-04-01

By way of a brief review of Si photonics technology, we show that significant improvements in device performance are necessary for practical telecommunications applications. In order to improve device performance in Si photonics, we have developed a Si-Ge-silica monolithic integration platform, on which compact Si-Ge-based modulators/detectors and silica-based high-performance wavelength filters are monolithically integrated. The platform features low-temperature silica film deposition, which cannot damage Si-Ge-based active devices. Using this platform, we have developed various integrated photonic devices for broadband telecommunications applications.

A Barley Efflux Transporter Operates in a Na+-Dependent Manner, as Revealed by a Multidisciplinary Platform[OPEN

PubMed Central

Nagarajan, Yagnesh; Rongala, Jay; Luang, Sukanya; Shadiac, Nadim; Sutton, Tim; Tyerman, Stephen D.; McPhee, Gordon; Voelcker, Nicolas H.; Lee, Jung-Goo

2016-01-01

Plant growth and survival depend upon the activity of membrane transporters that control the movement and distribution of solutes into, around, and out of plants. Although many plant transporters are known, their intrinsic properties make them difficult to study. In barley (Hordeum vulgare), the root anion-permeable transporter Bot1 plays a key role in tolerance to high soil boron, facilitating the efflux of borate from cells. However, its three-dimensional structure is unavailable and the molecular basis of its permeation function is unknown. Using an integrative platform of computational, biophysical, and biochemical tools as well as molecular biology, electrophysiology, and bioinformatics, we provide insight into the origin of transport function of Bot1. An atomistic model, supported by atomic force microscopy measurements, reveals that the protein folds into 13 transmembrane-spanning and five cytoplasmic α-helices. We predict a trimeric assembly of Bot1 and the presence of a Na+ ion binding site, located in the proximity of a pore that conducts anions. Patch-clamp electrophysiology of Bot1 detects Na+-dependent polyvalent anion transport in a Nernstian manner with channel-like characteristics. Using alanine scanning, molecular dynamics simulations, and transport measurements, we show that conductance by Bot1 is abolished by removal of the Na+ ion binding site. Our data enhance the understanding of the permeation functions of Bot1. PMID:26672067

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Integrated protein analysis platform based on column switch recycling size exclusion chromatography, microenzymatic reactor and microRPLC-ESI-MS/MS.

PubMed

Yuan, Huiming; Zhou, Yuan; Zhang, Lihua; Liang, Zhen; Zhang, Yukui

2009-10-30

An integrated platform with the combination of proteins and peptides separation was established via the unit of on-line proteins digestion, by which proteins were in sequence separated by column switch recycling size exclusion chromatography (csrSEC), on-line digested by an immobilized trypsin microreactor, trapped and desalted by two parallel C8 precolumns, separated by microRPLC with the linear gradient of organic modifier concentration, and identified by ESI-MS/MS. A 6-protein mixture, with Mr ranging from 10 kDa to 80 kDa, was used to evaluate the performance of the integrated platform, and all proteins were identified with sequence coverage over 5.67%. Our experimental results demonstrate that such an integrated platform is of advantages such as good time compatibility, high peak capacity, and facile automation, which might be a promising approach for proteome study.

Targeted metabolomics and medication classification data from participants in the ADNI1 cohort.

PubMed

St John-Williams, Lisa; Blach, Colette; Toledo, Jon B; Rotroff, Daniel M; Kim, Sungeun; Klavins, Kristaps; Baillie, Rebecca; Han, Xianlin; Mahmoudiandehkordi, Siamak; Jack, John; Massaro, Tyler J; Lucas, Joseph E; Louie, Gregory; Motsinger-Reif, Alison A; Risacher, Shannon L; Saykin, Andrew J; Kastenmüller, Gabi; Arnold, Matthias; Koal, Therese; Moseley, M Arthur; Mangravite, Lara M; Peters, Mette A; Tenenbaum, Jessica D; Thompson, J Will; Kaddurah-Daouk, Rima

2017-10-17

Alzheimer's disease (AD) is the most common neurodegenerative disease presenting major health and economic challenges that continue to grow. Mechanisms of disease are poorly understood but significant data point to metabolic defects that might contribute to disease pathogenesis. The Alzheimer Disease Metabolomics Consortium (ADMC) in partnership with Alzheimer Disease Neuroimaging Initiative (ADNI) is creating a comprehensive biochemical database for AD. Using targeted and non- targeted metabolomics and lipidomics platforms we are mapping metabolic pathway and network failures across the trajectory of disease. In this report we present quantitative metabolomics data generated on serum from 199 control, 356 mild cognitive impairment and 175 AD subjects enrolled in ADNI1 using AbsoluteIDQ-p180 platform, along with the pipeline for data preprocessing and medication classification for confound correction. The dataset presented here is the first of eight metabolomics datasets being generated for broad biochemical investigation of the AD metabolome. We expect that these collective metabolomics datasets will provide valuable resources for researchers to identify novel molecular mechanisms contributing to AD pathogenesis and disease phenotypes.

Co-fabrication of chitosan and epoxy photoresist to form microwell arrays with permeable hydrogel bottoms

PubMed Central

Ornoff, Douglas M.; Wang, Yuli; Proctor, Angela; Shah, Akash S.; Allbritton, Nancy L.

2015-01-01

Microfabrication technology offers the potential to create biological platforms with customizable patterns and surface chemistries, allowing precise control over the biochemical microenvironment to which a cell or group of cells is exposed. However, most microfabricated platforms grow cells on impermeable surfaces. This report describes the co-fabrication of a micropatterned epoxy photoresist film with a chitosan film to create a freestanding array of permeable, hydrogel-bottomed microwells. These films possess optical properties ideal for microscopy applications, and the chitosan layers are semi-permeable with a molecular exclusion of 9.9 ± 2.1 kDa. By seeding cells into the microwells, overlaying inert mineral oil, and supplying media via the bottom surface, this hybrid film permits cells to be physically isolated from one another but maintained in culture for at least 4 days. Arrays co-fabricated using these materials reduce both large-molecular-weight biochemical crosstalk between cells and mixing of different clonal populations, and will enable high-throughput studies of cellular heterogeneity with increased ability to customize dynamic interrogations compared to materials in currently available technologies. PMID:26447557

Electrochemical Fabrication of Nanostructures on Porous Silicon for Biochemical Sensing Platforms.

PubMed

Ko, Euna; Hwang, Joonki; Kim, Ji Hye; Lee, Joo Heon; Lee, Sung Hwan; Tran, Van-Khue; Chung, Woo Sung; Park, Chan Ho; Choo, Jaebum; Seong, Gi Hun

2016-01-01

We present a method for the electrochemical patterning of gold nanoparticles (AuNPs) or silver nanoparticles (AgNPs) on porous silicon, and explore their applications in: (1) the quantitative analysis of hydroxylamine as a chemical sensing electrode and (2) as a highly sensitive surface-enhanced Raman spectroscopy (SERS) substrate for Rhodamine 6G. For hydroxylamine detection, AuNPs-porous silicon can enhance the electrochemical oxidation of hydroxylamine. The current changed linearly for concentrations ranging from 100 μM to 1.32 mM (R(2) = 0.995), and the detection limit was determined to be as low as 55 μM. When used as SERS substrates, these materials also showed that nanoparticles decorated on porous silicon substrates have more SERS hot spots than those decorated on crystalline silicon substrates, resulting in a larger SERS signal. Moreover, AgNPs-porous silicon provided five-times higher signal compared to AuNPs-porous silicon. From these results, we expect that nanoparticles decorated on porous silicon substrates can be used in various types of biochemical sensing platforms.

Targeted metabolomics and medication classification data from participants in the ADNI1 cohort

PubMed Central

St John-Williams, Lisa; Blach, Colette; Toledo, Jon B.; Rotroff, Daniel M.; Kim, Sungeun; Klavins, Kristaps; Baillie, Rebecca; Han, Xianlin; Mahmoudiandehkordi, Siamak; Jack, John; Massaro, Tyler J.; Lucas, Joseph E.; Louie, Gregory; Motsinger-Reif, Alison A.; Risacher, Shannon L.; Saykin, Andrew J.; Kastenmüller, Gabi; Arnold, Matthias; Koal, Therese; Moseley, M. Arthur; Mangravite, Lara M.; Peters, Mette A.; Tenenbaum, Jessica D.; Thompson, J. Will; Kaddurah-Daouk, Rima

2017-01-01

Alzheimer’s disease (AD) is the most common neurodegenerative disease presenting major health and economic challenges that continue to grow. Mechanisms of disease are poorly understood but significant data point to metabolic defects that might contribute to disease pathogenesis. The Alzheimer Disease Metabolomics Consortium (ADMC) in partnership with Alzheimer Disease Neuroimaging Initiative (ADNI) is creating a comprehensive biochemical database for AD. Using targeted and non- targeted metabolomics and lipidomics platforms we are mapping metabolic pathway and network failures across the trajectory of disease. In this report we present quantitative metabolomics data generated on serum from 199 control, 356 mild cognitive impairment and 175 AD subjects enrolled in ADNI1 using AbsoluteIDQ-p180 platform, along with the pipeline for data preprocessing and medication classification for confound correction. The dataset presented here is the first of eight metabolomics datasets being generated for broad biochemical investigation of the AD metabolome. We expect that these collective metabolomics datasets will provide valuable resources for researchers to identify novel molecular mechanisms contributing to AD pathogenesis and disease phenotypes. PMID:29039849

Prospects for energy recovery during hydrothermal and biological processing of waste biomass.

PubMed

Gerber Van Doren, Léda; Posmanik, Roy; Bicalho, Felipe A; Tester, Jefferson W; Sills, Deborah L

2017-02-01

Thermochemical and biological processes represent promising technologies for converting wet biomasses, such as animal manure, organic waste, or algae, to energy. To convert biomass to energy and bio-chemicals in an economical manner, internal energy recovery should be maximized to reduce the use of external heat and power. In this study, two conversion pathways that couple hydrothermal liquefaction with anaerobic digestion or catalytic hydrothermal gasification were compared. Each of these platforms is followed by two alternative processes for gas utilization: 1) combined heat and power; and 2) combustion in a boiler. Pinch analysis was applied to integrate thermal streams among unit processes and improve the overall system efficiency. A techno-economic analysis was conducted to compare the feasibility of the four modeled scenarios under different market conditions. Our results show that a systems approach designed to recover internal heat and power can reduce external energy demands and increase the overall process sustainability. Copyright © 2016 Elsevier Ltd. All rights reserved.

High content screening in microfluidic devices

PubMed Central

Cheong, Raymond; Paliwal, Saurabh; Levchenko, Andre

2011-01-01

Importance of the field Miniaturization is key to advancing the state-of-the-art in high content screening (HCS), in order to enable dramatic cost savings through reduced usage of expensive biochemical reagents and to enable large-scale screening on primary cells. Microfluidic technology offers the potential to enable HCS to be performed with an unprecedented degree of miniaturization. Areas covered in this review This perspective highlights a real-world example from the authors’ work of HCS assays implemented in a highly miniaturized microfluidic format. Advantages of this technology are discussed, including cost savings, high throughput screening on primary cells, improved accuracy, the ability to study complex time-varying stimuli, and ease of automation, integration, and scaling. What the reader will gain The reader will understand the capabilities of a new microfluidics-based platform for HCS, and the advantages it provides over conventional plate-based HCS. Take home message Microfluidics technology will drive significant advancements and broader usage and applicability of HCS in drug discovery. PMID:21852997

Microfluidic devices for cell cultivation and proliferation

PubMed Central

Tehranirokh, Masoomeh; Kouzani, Abbas Z.; Francis, Paul S.; Kanwar, Jagat R.

2013-01-01

Microfluidic technology provides precise, controlled-environment, cost-effective, compact, integrated, and high-throughput microsystems that are promising substitutes for conventional biological laboratory methods. In recent years, microfluidic cell culture devices have been used for applications such as tissue engineering, diagnostics, drug screening, immunology, cancer studies, stem cell proliferation and differentiation, and neurite guidance. Microfluidic technology allows dynamic cell culture in microperfusion systems to deliver continuous nutrient supplies for long term cell culture. It offers many opportunities to mimic the cell-cell and cell-extracellular matrix interactions of tissues by creating gradient concentrations of biochemical signals such as growth factors, chemokines, and hormones. Other applications of cell cultivation in microfluidic systems include high resolution cell patterning on a modified substrate with adhesive patterns and the reconstruction of complicated tissue architectures. In this review, recent advances in microfluidic platforms for cell culturing and proliferation, for both simple monolayer (2D) cell seeding processes and 3D configurations as accurate models of in vivo conditions, are examined. PMID:24273628

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

PubMed

Swainston, Neil; Batista-Navarro, Riza; Carbonell, Pablo; Dobson, Paul D; Dunstan, Mark; Jervis, Adrian J; Vinaixa, Maria; Williams, Alan R; Ananiadou, Sophia; Faulon, Jean-Loup; Mendes, Pedro; Kell, Douglas B; Scrutton, Nigel S; Breitling, Rainer

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and-crucially-the relationships between them. Such a resource should be extensible, such that newly discovered relationships-for example, those between novel, synthetic enzymes and non-natural products-can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists.

biochem4j: Integrated and extensible biochemical knowledge through graph databases

PubMed Central

Batista-Navarro, Riza; Dunstan, Mark; Jervis, Adrian J.; Vinaixa, Maria; Ananiadou, Sophia; Faulon, Jean-Loup; Kell, Douglas B.

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and–crucially–the relationships between them. Such a resource should be extensible, such that newly discovered relationships–for example, those between novel, synthetic enzymes and non-natural products–can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists. PMID:28708831

Enhancing Mobility: Integrating New Services into Your Library's Mobile Platform to Increase Traffic

ERIC Educational Resources Information Center

Felts, John W., Jr.

2014-01-01

Kimbel Library launched its mobile environment and ran it in full production for several months yet usage patterns were quite low and flat. The library only saw a substantial increase in usage when new, value-added services were integrated into this platform. Upon implementing and integrating discovery services, chat and SMS capabilities, and…

High Level of Integration in Integrated Disease Management Leads to Higher Usage in the e-Vita Study: Self-Management of Chronic Obstructive Pulmonary Disease With Web-Based Platforms in a Parallel Cohort Design

PubMed Central

Verdijk, Noortje A; Kasteleyn, Marise J; Harmans, Lara M; Talboom, Irvin JSH; Numans, Mattijs E; Chavannes, Niels H

2017-01-01

Background Worldwide, nearly 3 million people die of chronic obstructive pulmonary disease (COPD) every year. Integrated disease management (IDM) improves disease-specific quality of life and exercise capacity for people with COPD, but can also reduce hospital admissions and hospital days. Self-management of COPD through eHealth interventions has shown to be an effective method to improve the quality and efficiency of IDM in several settings, but it remains unknown which factors influence usage of eHealth and change in behavior of patients. Objective Our study, e-Vita COPD, compares different levels of integration of Web-based self-management platforms in IDM in three primary care settings. The main aim of this study is to analyze the factors that successfully promote the use of a self-management platform for COPD patients. Methods The e-Vita COPD study compares three different approaches to incorporating eHealth via Web-based self-management platforms into IDM of COPD using a parallel cohort design. Three groups integrated the platforms to different levels. In groups 1 (high integration) and 2 (medium integration), randomization was performed to two levels of personal assistance for patients (high and low assistance); in group 3 there was no integration into disease management (none integration). Every visit to the e-Vita and Zorgdraad COPD Web platforms was tracked objectively by collecting log data (sessions and services). At the first log-in, patients completed a baseline questionnaire. Baseline characteristics were automatically extracted from the log files including age, gender, education level, scores on the Clinical COPD Questionnaire (CCQ), dyspnea scale (MRC), and quality of life questionnaire (EQ5D). To predict the use of the platforms, multiple linear regression analyses for the different independent variables were performed: integration in IDM (high, medium, none), personal assistance for the participants (high vs low), educational level, and self-efficacy level (General Self-Efficacy Scale [GSES]). All analyses were adjusted for age and gender. Results Of the 702 invited COPD patients, 215 (30.6%) registered to a platform. Of the 82 patients in group 1 (high integration IDM), 36 were in group 1A (personal assistance) and 46 in group 1B (low assistance). Of the 96 patients in group 2 (medium integration IDM), 44 were in group 2A (telephone assistance) and 52 in group 2B (low assistance). A total of 37 patients participated in group 3 (no integration IDM). In all, 107 users (49.8%) visited the platform at least once in the 15-month period. The mean number of sessions differed between the three groups (group 1: mean 10.5, SD 1.3; group 2: mean 8.8, SD 1.4; group 3: mean 3.7, SD 1.8; P=.01). The mean number of sessions differed between the high-assistance and low-assistance groups in groups 1 and 2 (high: mean 11.8, SD 1.3; low: mean 6.7, SD 1.4; F1,80=6.55, P=.01). High-assistance participants used more services (mean 45.4, SD 6.2) than low-assistance participants (mean 21.2, SD 6.8; F1,80=6.82, P=.01). No association was found between educational level and usage and between GSES and usage. Conclusions Use of a self-management platform is higher when participants receive adequate personal assistance about how to use the platform. Blended care, where digital health and usual care are integrated, will likely lead to increased use of the online program. Future research should provide additional insights into the preferences of different patient groups. Trial Registration Nederlands Trial Register NTR4098; http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=4098 (Archived by WebCite at http://www.webcitation.org/6qO1hqiJ1) PMID:28566268

Integrated vehicle-based safety systems (IVBSS) : light vehicle platform field operational test data analysis plan.

DOT National Transportation Integrated Search

2009-12-22

This document presents the University of Michigan Transportation Research Institutes plan to : perform analysis of data collected from the light vehicle platform field operational test of the : Integrated Vehicle-Based Safety Systems (IVBSS) progr...

Integrated Proteomic Approaches for Understanding Toxicity of Environmental Chemicals

EPA Science Inventory

To apply quantitative proteomic analysis to the evaluation of toxicity of environmental chemicals, we have developed an integrated proteomic technology platform. This platform has been applied to the analysis of the toxic effects and pathways of many important environmental chemi...

Integrated vehicle-based safety systems (IVBSS) : heavy truck platform field operational test data analysis plan.

DOT National Transportation Integrated Search

2009-11-23

This document presents the University of Michigan Transportation Research Institutes plan to perform : analysis of data collected from the heavy truck platform field operational test of the Integrated Vehicle- : Based Safety Systems (IVBSS) progra...

Development of reactor configurations for an electrofuels platform utilizing genetically modified iron oxidizing bacteria for the reduction of CO2 to biochemicals.

PubMed

Guan, Jingyang; Berlinger, Sarah A; Li, Xiaozheng; Chao, Zhongmou; Sousa E Silva, Victor; Banta, Scott; West, Alan C

2017-03-10

Electrofuels processes are potentially promising platforms for biochemical production from CO 2 using renewable energy. When coupled to solar panels, this approach could avoid the inefficiencies of photosynthesis and there is no competition with food agriculture. In addition, these systems could potentially be used to store intermittent or stranded electricity generated from other renewable sources. Here we develop reactor configurations for continuous electrofuels processes to convert electricity and CO 2 to isobutyric acid (IBA) using genetically modified (GM) chemolithoautotrophic Acidithiobacillus ferrooxidans. These cells oxidize ferrous iron which can be electrochemically reduced. During two weeks of cultivation on ferrous iron, stable cell growth and continuous IBA production from CO 2 were achieved in a process where media was circulated between electrochemical and biochemical rectors. An alternative process with an additional electrochemical cell for accelerated ferrous production was developed, and this system achieved an almost three-fold increase in steady state cell densities, and an almost 4-fold increase in the ferrous iron oxidation rate. Combined, this led to an almost 8-fold increase in the steady state volumetric productivity of IBA up to 0.063±0.012mg/L/h, without a decline in energy efficiency from previous work. Continued development of reactor configurations which can increase the delivery of energy to the genetically modified cells will be required to increase product titers and volumetric productivities. Copyright © 2017 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Yang, Weiqiang; Dong, Yiqiang

2018-05-01

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

CILogon: An Integrated Identity and Access Management Platform for Science

NASA Astrophysics Data System (ADS)

Basney, J.

2016-12-01

When scientists work together, they use web sites and other software to share their ideas and data. To ensure the integrity of their work, these systems require the scientists to log in and verify that they are part of the team working on a particular science problem. Too often, the identity and access verification process is a stumbling block for the scientists. Scientific research projects are forced to invest time and effort into developing and supporting Identity and Access Management (IAM) services, distracting them from the core goals of their research collaboration. CILogon provides an IAM platform that enables scientists to work together to meet their IAM needs more effectively so they can allocate more time and effort to their core mission of scientific research. The CILogon platform enables federated identity management and collaborative organization management. Federated identity management enables researchers to use their home organization identities to access cyberinfrastructure, rather than requiring yet another username and password to log on. Collaborative organization management enables research projects to define user groups for authorization to collaboration platforms (e.g., wikis, mailing lists, and domain applications). CILogon's IAM platform serves the unique needs of research collaborations, namely the need to dynamically form collaboration groups across organizations and countries, sharing access to data, instruments, compute clusters, and other resources to enable scientific discovery. CILogon provides a software-as-a-service platform to ease integration with cyberinfrastructure, while making all software components publicly available under open source licenses to enable re-use. Figure 1 illustrates the components and interfaces of this platform. CILogon has been operational since 2010 and has been used by over 7,000 researchers from more than 170 identity providers to access cyberinfrastructure including Globus, LIGO, Open Science Grid, SeedMe, and XSEDE. The "CILogon 2.0" platform, launched in 2016, adds support for virtual organization (VO) membership management, identity linking, international collaborations, and standard integration protocols, through integration with the Internet2 COmanage collaboration software.

In vivo polymerization and manufacturing of wires and supercapacitors in plants

PubMed Central

Stavrinidou, Eleni; Nilsson, K. Peter R.; Singh, Sandeep Kumar; Franco-Gonzalez, Juan Felipe; Volkov, Anton V.; Jonsson, Magnus P.; Grimoldi, Andrea; Elgland, Mathias; Zozoulenko, Igor V.; Berggren, Magnus

2017-01-01

Electronic plants, e-Plants, are an organic bioelectronic platform that allows electronic interfacing with plants. Recently we have demonstrated plants with augmented electronic functionality. Using the vascular system and organs of a plant, we manufactured organic electronic devices and circuits in vivo, leveraging the internal structure and physiology of the plant as the template, and an integral part of the devices. However, this electronic functionality was only achieved in localized regions, whereas new electronic materials that could be distributed to every part of the plant would provide versatility in device and circuit fabrication and create possibilities for new device concepts. Here we report the synthesis of such a conjugated oligomer that can be distributed and form longer oligomers and polymer in every part of the xylem vascular tissue of a Rosa floribunda cutting, forming long-range conducting wires. The plant’s structure acts as a physical template, whereas the plant’s biochemical response mechanism acts as the catalyst for polymerization. In addition, the oligomer can cross through the veins and enter the apoplastic space in the leaves. Finally, using the plant’s natural architecture we manufacture supercapacitors along the stem. Our results are preludes to autonomous energy systems integrated within plants and distribute interconnected sensor–actuator systems for plant control and optimization. PMID:28242683

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

DOE PAGES

King, Zachary A.; Lu, Justin; Drager, Andreas; ...

2015-10-17

In this study, genome-scale metabolic models are mathematically structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scalemore » metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.« less

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

PubMed Central

King, Zachary A.; Lu, Justin; Dräger, Andreas; Miller, Philip; Federowicz, Stephen; Lerman, Joshua A.; Ebrahim, Ali; Palsson, Bernhard O.; Lewis, Nathan E.

2016-01-01

Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data. PMID:26476456

Smart single-chip gas sensor microsystem

NASA Astrophysics Data System (ADS)

Hagleitner, C.; Hierlemann, A.; Lange, D.; Kummer, A.; Kerness, N.; Brand, O.; Baltes, H.

2001-11-01

Research activity in chemical gas sensing is currently directed towards the search for highly selective (bio)chemical layer materials, and to the design of arrays consisting of different partially selective sensors that permit subsequent pattern recognition and multi-component analysis. Simultaneous use of various transduction platforms has been demonstrated, and the rapid development of integrated-circuit technology has facilitated the fabrication of planar chemical sensors and sensors based on three-dimensional microelectromechanical systems. Complementary metal-oxide silicon processes have previously been used to develop gas sensors based on metal oxides and acoustic-wave-based sensor devices. Here we combine several of these developments to fabricate a smart single-chip chemical microsensor system that incorporates three different transducers (mass-sensitive, capacitive and calorimetric), all of which rely on sensitive polymeric layers to detect airborne volatile organic compounds. Full integration of the microelectronic and micromechanical components on one chip permits control and monitoring of the sensor functions, and enables on-chip signal amplification and conditioning that notably improves the overall sensor performance. The circuitry also includes analog-to-digital converters, and an on-chip interface to transmit the data to off-chip recording units. We expect that our approach will provide a basis for the further development and optimization of gas microsystems.

In vivo polymerization and manufacturing of wires and supercapacitors in plants.

PubMed

Stavrinidou, Eleni; Gabrielsson, Roger; Nilsson, K Peter R; Singh, Sandeep Kumar; Franco-Gonzalez, Juan Felipe; Volkov, Anton V; Jonsson, Magnus P; Grimoldi, Andrea; Elgland, Mathias; Zozoulenko, Igor V; Simon, Daniel T; Berggren, Magnus

2017-03-14

Electronic plants, e -Plants, are an organic bioelectronic platform that allows electronic interfacing with plants. Recently we have demonstrated plants with augmented electronic functionality. Using the vascular system and organs of a plant, we manufactured organic electronic devices and circuits in vivo, leveraging the internal structure and physiology of the plant as the template, and an integral part of the devices. However, this electronic functionality was only achieved in localized regions, whereas new electronic materials that could be distributed to every part of the plant would provide versatility in device and circuit fabrication and create possibilities for new device concepts. Here we report the synthesis of such a conjugated oligomer that can be distributed and form longer oligomers and polymer in every part of the xylem vascular tissue of a Rosa floribunda cutting, forming long-range conducting wires. The plant's structure acts as a physical template, whereas the plant's biochemical response mechanism acts as the catalyst for polymerization. In addition, the oligomer can cross through the veins and enter the apoplastic space in the leaves. Finally, using the plant's natural architecture we manufacture supercapacitors along the stem. Our results are preludes to autonomous energy systems integrated within plants and distribute interconnected sensor-actuator systems for plant control and optimization.

Ultra-Low Loss Waveguides with Application to Photonic Integrated Circuits

NASA Astrophysics Data System (ADS)

Bauters, Jared F.

The integration of photonic components using a planar platform promises advantages in cost, size, weight, and power consumption for optoelectronic systems. Yet, the typical propagation loss of 5-10 dB/m in a planar silica waveguide is nearly five orders-of-magnitude larger than that in low loss optical fibers. For some applications, the miniaturization of the photonic system and resulting smaller propagation lengths from integration are enough to overcome the increase in propagation loss. For other more demanding systems or applications, such as those requiring long optical time delays or high-quality-factor (Q factor) resonators, the high propagation loss can degrade system performance to a degree that trumps the potential advantages offered by integration. Thus, the reduction of planar waveguide propagation loss in a Si3-N4 based waveguide platform is a primary focus of this dissertation. The ultra-low loss stoichiometric Si3-N4 waveguide platform offers the additional advantages of fabrication process stability and repeatability. Yet, active devices such as lasers, amplifiers, and photodetectors have not been monolithically integrated with ultra-low loss waveguides due to the incompatibility of the active and ultra-low loss processing thermal budgets (ultra-low loss waveguides are annealed at temperatures exceeding 1000 °C in order to drive out impurities). So a platform that enables the integration of active devices with the ultra-low losses of the Si3- N4 waveguide platform is this dissertation's second focus. The work enables the future fabrication of sensor, gyroscope, true time delay, and low phase noise oscillator photonic integrated circuits.

Deep subwavelength fourfold rotationally symmetric split-ring-resonator metamaterials for highly sensitive and robust biosensing platform

PubMed Central

Tobing, Landobasa Y. M.; Tjahjana, Liliana; Zhang, Dao Hua; Zhang, Qing; Xiong, Qihua

2013-01-01

Metamaterials provide a good platform for biochemical sensing due to its strong field localization at nanoscale. In this work, we show that electric and magnetic resonant modes in split-ring-resonator (SRR) can be efficiently excited under unpolarized light illumination when the SRRs are arranged in fourfold rotationally symmetric lattice configuration. The fabrication and characterization of deep subwavelength (~λ/15) gold-based SRR structures with resonator size as small as ~ 60 nm are reported with magnetic resonances in Vis-NIR spectrum range. The feasibility for sensing is demonstrated with refractive index sensitivity as high as ~ 636 nm/RIU. PMID:23942416

Framework programmable platform for the advanced software development workstation. Integration mechanism design document

NASA Technical Reports Server (NTRS)

Mayer, Richard J.; Blinn, Thomas M.; Mayer, Paula S. D.; Reddy, Uday; Ackley, Keith; Futrell, Mike

1991-01-01

The Framework Programmable Software Development Platform (FPP) is a project aimed at combining effective tool and data integration mechanisms with a model of the software development process in an intelligent integrated software development environment. Guided by this model, this system development framework will take advantage of an integrated operating environment to automate effectively the management of the software development process so that costly mistakes during the development phase can be eliminated.

European security framework for healthcare.

PubMed

Ruotsalainen, Pekka; Pohjonen, Hanna

2003-01-01

eHealth and telemedicine services are promising business areas in Europe. It is clear that eHealth products and services will be sold and ordered from a distance and over national borderlines in the future. However, there are many barriers to overcome. For both national and pan-European eHealth and telemedicine applications a common security framework is needed. These frameworks set security requirements needed for cross-border eHealth services. The next step is to build a security infrastructure which is independent of technical platforms. Most of the European eHealth platforms are regional or territorial. Some countries are looking for a Public Key Infrastructure, but no large scale solutions do exist in healthcare. There is no clear candidate solution for European-wide interoperable eHealth platform. Gross-platform integration seems to be the most practical integration method at a European level in the short run. The use of Internet as a European integration platform is a promising solution in the long run.

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.

Study on the E-commerce platform based on the agent

NASA Astrophysics Data System (ADS)

Fu, Ruixue; Qin, Lishuan; Gao, Yinmin

2011-10-01

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

Participatory Planning, Monitoring and Evaluation of Multi-Stakeholder Platforms in Integrated Landscape Initiatives.

PubMed

Kusters, Koen; Buck, Louise; de Graaf, Maartje; Minang, Peter; van Oosten, Cora; Zagt, Roderick

2018-07-01

Integrated landscape initiatives typically aim to strengthen landscape governance by developing and facilitating multi-stakeholder platforms. These are institutional coordination mechanisms that enable discussions, negotiations, and joint planning between stakeholders from various sectors in a given landscape. Multi-stakeholder platforms tend to involve complex processes with diverse actors, whose objectives and focus may be subjected to periodic re-evaluation, revision or reform. In this article we propose a participatory method to aid planning, monitoring, and evaluation of such platforms, and we report on experiences from piloting the method in Ghana and Indonesia. The method is comprised of three components. The first can be used to look ahead, identifying priorities for future multi-stakeholder collaboration in the landscape. It is based on the identification of four aspirations that are common across multi-stakeholder platforms in integrated landscape initiatives. The second can be used to look inward. It focuses on the processes within an existing multi-stakeholder platform in order to identify areas for possible improvement. The third can be used to look back, identifying the main outcomes of an existing platform and comparing them to the original objectives. The three components can be implemented together or separately. They can be used to inform planning and adaptive management of the platform, as well as to demonstrate performance and inform the design of new interventions.

Open Targets: a platform for therapeutic target identification and validation

PubMed Central

Koscielny, Gautier; An, Peter; Carvalho-Silva, Denise; Cham, Jennifer A.; Fumis, Luca; Gasparyan, Rippa; Hasan, Samiul; Karamanis, Nikiforos; Maguire, Michael; Papa, Eliseo; Pierleoni, Andrea; Pignatelli, Miguel; Platt, Theo; Rowland, Francis; Wankar, Priyanka; Bento, A. Patrícia; Burdett, Tony; Fabregat, Antonio; Forbes, Simon; Gaulton, Anna; Gonzalez, Cristina Yenyxe; Hermjakob, Henning; Hersey, Anne; Jupe, Steven; Kafkas, Şenay; Keays, Maria; Leroy, Catherine; Lopez, Francisco-Javier; Magarinos, Maria Paula; Malone, James; McEntyre, Johanna; Munoz-Pomer Fuentes, Alfonso; O'Donovan, Claire; Papatheodorou, Irene; Parkinson, Helen; Palka, Barbara; Paschall, Justin; Petryszak, Robert; Pratanwanich, Naruemon; Sarntivijal, Sirarat; Saunders, Gary; Sidiropoulos, Konstantinos; Smith, Thomas; Sondka, Zbyslaw; Stegle, Oliver; Tang, Y. Amy; Turner, Edward; Vaughan, Brendan; Vrousgou, Olga; Watkins, Xavier; Martin, Maria-Jesus; Sanseau, Philippe; Vamathevan, Jessica; Birney, Ewan; Barrett, Jeffrey; Dunham, Ian

2017-01-01

We have designed and developed a data integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases. The platform is designed to support identification and prioritization of biological targets for follow-up. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources. The platform provides either a target-centric workflow to identify diseases that may be associated with a specific target, or a disease-centric workflow to identify targets that may be associated with a specific disease. Users can easily transition between these target- and disease-centric workflows. The Open Targets Validation Platform is accessible at https://www.targetvalidation.org. PMID:27899665

Interfaces and Integration of Medical Image Analysis Frameworks: Challenges and Opportunities.

PubMed

Covington, Kelsie; McCreedy, Evan S; Chen, Min; Carass, Aaron; Aucoin, Nicole; Landman, Bennett A

2010-05-25

Clinical research with medical imaging typically involves large-scale data analysis with interdependent software toolsets tied together in a processing workflow. Numerous, complementary platforms are available, but these are not readily compatible in terms of workflows or data formats. Both image scientists and clinical investigators could benefit from using the framework which is a most natural fit to the specific problem at hand, but pragmatic choices often dictate that a compromise platform is used for collaboration. Manual merging of platforms through carefully tuned scripts has been effective, but exceptionally time consuming and is not feasible for large-scale integration efforts. Hence, the benefits of innovation are constrained by platform dependence. Removing this constraint via integration of algorithms from one framework into another is the focus of this work. We propose and demonstrate a light-weight interface system to expose parameters across platforms and provide seamless integration. In this initial effort, we focus on four platforms Medical Image Analysis and Visualization (MIPAV), Java Image Science Toolkit (JIST), command line tools, and 3D Slicer. We explore three case studies: (1) providing a system for MIPAV to expose internal algorithms and utilize these algorithms within JIST, (2) exposing JIST modules through self-documenting command line interface for inclusion in scripting environments, and (3) detecting and using JIST modules in 3D Slicer. We review the challenges and opportunities for light-weight software integration both within development language (e.g., Java in MIPAV and JIST) and across languages (e.g., C/C++ in 3D Slicer and shell in command line tools).

A MULTILAYER BIOCHEMICAL DRY DEPOSITION MODEL 1. MODEL FORMULATION

EPA Science Inventory

A multilayer biochemical dry deposition model has been developed based on the NOAA Multilayer Model (MLM) to study gaseous exchanges between the soil, plants, and the atmosphere. Most of the parameterizations and submodels have been updated or replaced. The numerical integration ...

Flexible and Stretchable Physical Sensor Integrated Platforms for Wearable Human-Activity Monitoringand Personal Healthcare.

PubMed

Trung, Tran Quang; Lee, Nae-Eung

2016-06-01

Flexible and stretchable physical sensors that can measure and quantify electrical signals generated by human activities are attracting a great deal of attention as they have unique characteristics, such as ultrathinness, low modulus, light weight, high flexibility, and stretchability. These flexible and stretchable physical sensors conformally attached on the surface of organs or skin can provide a new opportunity for human-activity monitoring and personal healthcare. Consequently, in recent years there has been considerable research effort devoted to the development of flexible and stretchable physical sensors to fulfill the requirements of future technology, and much progress has been achieved. Here, the most recent developments of flexible and stretchable physical sensors are described, including temperature, pressure, and strain sensors, and flexible and stretchable sensor-integrated platforms. The latest successful examples of flexible and stretchable physical sensors for the detection of temperature, pressure, and strain, as well as their novel structures, technological innovations, and challenges, are reviewed first. In the next section, recent progress regarding sensor-integrated wearable platforms is overviewed in detail. Some of the latest achievements regarding self-powered sensor-integrated wearable platform technologies are also reviewed. Further research direction and challenges are also proposed to develop a fully sensor-integrated wearable platform for monitoring human activity and personal healthcare in the near future. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa.

PubMed

Nag, Ambarish; Karpinets, Tatiana V; Chang, Christopher H; Bar-Peled, Maor

2012-01-01

Understanding how cellular metabolism works and is regulated requires that the underlying biochemical pathways be adequately represented and integrated with large metabolomic data sets to establish a robust network model. Genetically engineering energy crops to be less recalcitrant to saccharification requires detailed knowledge of plant polysaccharide structures and a thorough understanding of the metabolic pathways involved in forming and regulating cell-wall synthesis. Nucleotide-sugars are building blocks for synthesis of cell wall polysaccharides. The biosynthesis of nucleotide-sugars is catalyzed by a multitude of enzymes that reside in different subcellular organelles, and precise representation of these pathways requires accurate capture of this biological compartmentalization. The lack of simple localization cues in genomic sequence data and annotations however leads to missing compartmentalization information for eukaryotes in automatically generated databases, such as the Pathway-Genome Databases (PGDBs) of the SRI Pathway Tools software that drives much biochemical knowledge representation on the internet. In this report, we provide an informal mechanism using the existing Pathway Tools framework to integrate protein and metabolite sub-cellular localization data with the existing representation of the nucleotide-sugar metabolic pathways in a prototype PGDB for Populus trichocarpa. The enhanced pathway representations have been successfully used to map SNP abundance data to individual nucleotide-sugar biosynthetic genes in the PGDB. The manually curated pathway representations are more conducive to the construction of a computational platform that will allow the simulation of natural and engineered nucleotide-sugar precursor fluxes into specific recalcitrant polysaccharide(s). Database URL: The curated Populus PGDB is available in the BESC public portal at http://cricket.ornl.gov/cgi-bin/beocyc_home.cgi and the nucleotide-sugar biosynthetic pathways can be directly accessed at http://cricket.ornl.gov:1555/PTR/new-image?object=SUGAR-NUCLEOTIDES.

Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa

PubMed Central

Nag, Ambarish; Karpinets, Tatiana V.; Chang, Christopher H.; Bar-Peled, Maor

2012-01-01

Understanding how cellular metabolism works and is regulated requires that the underlying biochemical pathways be adequately represented and integrated with large metabolomic data sets to establish a robust network model. Genetically engineering energy crops to be less recalcitrant to saccharification requires detailed knowledge of plant polysaccharide structures and a thorough understanding of the metabolic pathways involved in forming and regulating cell-wall synthesis. Nucleotide-sugars are building blocks for synthesis of cell wall polysaccharides. The biosynthesis of nucleotide-sugars is catalyzed by a multitude of enzymes that reside in different subcellular organelles, and precise representation of these pathways requires accurate capture of this biological compartmentalization. The lack of simple localization cues in genomic sequence data and annotations however leads to missing compartmentalization information for eukaryotes in automatically generated databases, such as the Pathway-Genome Databases (PGDBs) of the SRI Pathway Tools software that drives much biochemical knowledge representation on the internet. In this report, we provide an informal mechanism using the existing Pathway Tools framework to integrate protein and metabolite sub-cellular localization data with the existing representation of the nucleotide-sugar metabolic pathways in a prototype PGDB for Populus trichocarpa. The enhanced pathway representations have been successfully used to map SNP abundance data to individual nucleotide-sugar biosynthetic genes in the PGDB. The manually curated pathway representations are more conducive to the construction of a computational platform that will allow the simulation of natural and engineered nucleotide-sugar precursor fluxes into specific recalcitrant polysaccharide(s). Database URL: The curated Populus PGDB is available in the BESC public portal at http://cricket.ornl.gov/cgi-bin/beocyc_home.cgi and the nucleotide-sugar biosynthetic pathways can be directly accessed at http://cricket.ornl.gov:1555/PTR/new-image?object=SUGAR-NUCLEOTIDES. PMID:22465851

The Next Big Thing is Actually Small

PubMed Central

Garcia, Carlos D.

2013-01-01

Summary Recent developments in materials, surface modifications, separation schemes, detection systems, and associated instrumentation have allowed significant advances in the performance of lab-on-a-chip devices. These devices, also referred to as micro total analysis systems (µTAS), offer great versatility, high throughput, short analysis time, low cost, and more importantly, performance that is comparable to standard bench-top instrumentation. To date, µTAS have demonstrated advantages in a significant number of fields including biochemical, pharmaceutical, military, and environmental. Perhaps most importantly, µTAS represent excellent platforms to introduce students to microfabrication and nanotechnology, bridging chemistry with other fields such as engineering and biology, enabling the integration of various skills and curricular concepts. Considering the advantages of the technology and the potential impact to society, our research program aims to address the need for simpler, more affordable, faster, and portable devices to measure biologically-active compounds. Specifically, the program is focused on the development and characterization of a series of novel strategies towards the realization of integrated microanalytical devices. One key aspect of our research projects is that the developed analytical strategies must be compatible with each other, therefore enabling their use in integrated devices. The program combines spectroscopy, surface chemistry, capillary electrophoresis, electrochemical detection, and nanomaterials. This article discusses some of the most recent results obtained in two main areas of emphasis: ▪Capillary Electrophoresis, Microchip-CE, Electrochemical Detection, and▪Interaction of Proteins with Nanomaterials PMID:22877217

Progress in Integrative Biomaterial Systems to Approach Three-Dimensional Cell Mechanotransduction

PubMed Central

Zhang, Ying; Liao, Kin; Li, Chuan; Lai, Alvin C.K.; Foo, Ji-Jinn

2017-01-01

Mechanotransduction between cells and the extracellular matrix regulates major cellular functions in physiological and pathological situations. The effect of mechanical cues on biochemical signaling triggered by cell–matrix and cell–cell interactions on model biomimetic surfaces has been extensively investigated by a combination of fabrication, biophysical, and biological methods. To simulate the in vivo physiological microenvironment in vitro, three dimensional (3D) microstructures with tailored bio-functionality have been fabricated on substrates of various materials. However, less attention has been paid to the design of 3D biomaterial systems with geometric variances, such as the possession of precise micro-features and/or bio-sensing elements for probing the mechanical responses of cells to the external microenvironment. Such precisely engineered 3D model experimental platforms pave the way for studying the mechanotransduction of multicellular aggregates under controlled geometric and mechanical parameters. Concurrently with the progress in 3D biomaterial fabrication, cell traction force microscopy (CTFM) developed in the field of cell biophysics has emerged as a highly sensitive technique for probing the mechanical stresses exerted by cells onto the opposing deformable surface. In the current work, we first review the recent advances in the fabrication of 3D micropatterned biomaterials which enable the seamless integration with experimental cell mechanics in a controlled 3D microenvironment. Then, we discuss the role of collective cell–cell interactions in the mechanotransduction of engineered tissue equivalents determined by such integrative biomaterial systems under simulated physiological conditions. PMID:28952551

Citizen Sensors for SHM: Towards a Crowdsourcing Platform

PubMed Central

Ozer, Ekin; Feng, Maria Q.; Feng, Dongming

2015-01-01

This paper presents an innovative structural health monitoring (SHM) platform in terms of how it integrates smartphone sensors, the web, and crowdsourcing. The ubiquity of smartphones has provided an opportunity to create low-cost sensor networks for SHM. Crowdsourcing has given rise to citizen initiatives becoming a vast source of inexpensive, valuable but heterogeneous data. Previously, the authors have investigated the reliability of smartphone accelerometers for vibration-based SHM. This paper takes a step further to integrate mobile sensing and web-based computing for a prospective crowdsourcing-based SHM platform. An iOS application was developed to enable citizens to measure structural vibration and upload the data to a server with smartphones. A web-based platform was developed to collect and process the data automatically and store the processed data, such as modal properties of the structure, for long-term SHM purposes. Finally, the integrated mobile and web-based platforms were tested to collect the low-amplitude ambient vibration data of a bridge structure. Possible sources of uncertainties related to citizens were investigated, including the phone location, coupling conditions, and sampling duration. The field test results showed that the vibration data acquired by smartphones operated by citizens without expertise are useful for identifying structural modal properties with high accuracy. This platform can be further developed into an automated, smart, sustainable, cost-free system for long-term monitoring of structural integrity of spatially distributed urban infrastructure. Citizen Sensors for SHM will be a novel participatory sensing platform in the way that it offers hybrid solutions to transitional crowdsourcing parameters. PMID:26102490

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

PubMed

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

2015-04-21

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

Integrated Microsensors for Autonomous Microrobots

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

ADKINS, DOUGLAS R.; BYRNE, RAYMOND H.; HELLER, EDWIN J.

2003-02-01

This report describes the development of a miniature mobile microrobot device and several microsystems needed to create a miniature microsensor delivery platform. This work was funded under LDRD No.10785, entitled, ''Integrated Microsensors for Autonomous Microrobots''. The approach adopted in this project was to develop a mobile platform, to which would be attached wireless RF remote control and data acquisition in addition to various microsensors. A modular approach was used to produce a versatile microrobot platform and reduce power consumption and physical size.

High Level of Integration in Integrated Disease Management Leads to Higher Usage in the e-Vita Study: Self-Management of Chronic Obstructive Pulmonary Disease With Web-Based Platforms in a Parallel Cohort Design.

PubMed

Talboom-Kamp, Esther Pwa; Verdijk, Noortje A; Kasteleyn, Marise J; Harmans, Lara M; Talboom, Irvin Jsh; Numans, Mattijs E; Chavannes, Niels H

2017-05-31

Worldwide, nearly 3 million people die of chronic obstructive pulmonary disease (COPD) every year. Integrated disease management (IDM) improves disease-specific quality of life and exercise capacity for people with COPD, but can also reduce hospital admissions and hospital days. Self-management of COPD through eHealth interventions has shown to be an effective method to improve the quality and efficiency of IDM in several settings, but it remains unknown which factors influence usage of eHealth and change in behavior of patients. Our study, e-Vita COPD, compares different levels of integration of Web-based self-management platforms in IDM in three primary care settings. The main aim of this study is to analyze the factors that successfully promote the use of a self-management platform for COPD patients. The e-Vita COPD study compares three different approaches to incorporating eHealth via Web-based self-management platforms into IDM of COPD using a parallel cohort design. Three groups integrated the platforms to different levels. In groups 1 (high integration) and 2 (medium integration), randomization was performed to two levels of personal assistance for patients (high and low assistance); in group 3 there was no integration into disease management (none integration). Every visit to the e-Vita and Zorgdraad COPD Web platforms was tracked objectively by collecting log data (sessions and services). At the first log-in, patients completed a baseline questionnaire. Baseline characteristics were automatically extracted from the log files including age, gender, education level, scores on the Clinical COPD Questionnaire (CCQ), dyspnea scale (MRC), and quality of life questionnaire (EQ5D). To predict the use of the platforms, multiple linear regression analyses for the different independent variables were performed: integration in IDM (high, medium, none), personal assistance for the participants (high vs low), educational level, and self-efficacy level (General Self-Efficacy Scale [GSES]). All analyses were adjusted for age and gender. Of the 702 invited COPD patients, 215 (30.6%) registered to a platform. Of the 82 patients in group 1 (high integration IDM), 36 were in group 1A (personal assistance) and 46 in group 1B (low assistance). Of the 96 patients in group 2 (medium integration IDM), 44 were in group 2A (telephone assistance) and 52 in group 2B (low assistance). A total of 37 patients participated in group 3 (no integration IDM). In all, 107 users (49.8%) visited the platform at least once in the 15-month period. The mean number of sessions differed between the three groups (group 1: mean 10.5, SD 1.3; group 2: mean 8.8, SD 1.4; group 3: mean 3.7, SD 1.8; P=.01). The mean number of sessions differed between the high-assistance and low-assistance groups in groups 1 and 2 (high: mean 11.8, SD 1.3; low: mean 6.7, SD 1.4; F1,80=6.55, P=.01). High-assistance participants used more services (mean 45.4, SD 6.2) than low-assistance participants (mean 21.2, SD 6.8; F1,80=6.82, P=.01). No association was found between educational level and usage and between GSES and usage. Use of a self-management platform is higher when participants receive adequate personal assistance about how to use the platform. Blended care, where digital health and usual care are integrated, will likely lead to increased use of the online program. Future research should provide additional insights into the preferences of different patient groups. Nederlands Trial Register NTR4098; http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=4098 (Archived by WebCite at http://www.webcitation.org/6qO1hqiJ1). ©Esther PWA Talboom-Kamp, Noortje A Verdijk, Marise J Kasteleyn, Lara M Harmans, Irvin JSH Talboom, Mattijs E Numans, Niels H Chavannes. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 31.05.2017.

Versatile de novo enzyme activity in capsid proteins from an engineered M13 bacteriophage library.

PubMed

Casey, John P; Barbero, Roberto J; Heldman, Nimrod; Belcher, Angela M

2014-11-26

Biocatalysis has grown rapidly in recent decades as a solution to the evolving demands of industrial chemical processes. Mounting environmental pressures and shifting supply chains underscore the need for novel chemical activities, while rapid biotechnological progress has greatly increased the utility of enzymatic methods. Enzymes, though capable of high catalytic efficiency and remarkable reaction selectivity, still suffer from relative instability, high costs of scaling, and functional inflexibility. Herein, we developed a biochemical platform for engineering de novo semisynthetic enzymes, functionally modular and widely stable, based on the M13 bacteriophage. The hydrolytic bacteriophage described in this paper catalyzes a range of carboxylic esters, is active from 25 to 80 °C, and demonstrates greater efficiency in DMSO than in water. The platform complements biocatalysts with characteristics of heterogeneous catalysis, yielding high-surface area, thermostable biochemical structures readily adaptable to reactions in myriad solvents. As the viral structure ensures semisynthetic enzymes remain linked to the genetic sequences responsible for catalysis, future work will tailor the biocatalysts to high-demand synthetic processes by evolving new activities, utilizing high-throughput screening technology and harnessing M13's multifunctionality.

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

PubMed Central

Bruskiewich, Richard; Senger, Martin; Davenport, Guy; Ruiz, Manuel; Rouard, Mathieu; Hazekamp, Tom; Takeya, Masaru; Doi, Koji; Satoh, Kouji; Costa, Marcos; Simon, Reinhard; Balaji, Jayashree; Akintunde, Akinnola; Mauleon, Ramil; Wanchana, Samart; Shah, Trushar; Anacleto, Mylah; Portugal, Arllet; Ulat, Victor Jun; Thongjuea, Supat; Braak, Kyle; Ritter, Sebastian; Dereeper, Alexis; Skofic, Milko; Rojas, Edwin; Martins, Natalia; Pappas, Georgios; Alamban, Ryan; Almodiel, Roque; Barboza, Lord Hendrix; Detras, Jeffrey; Manansala, Kevin; Mendoza, Michael Jonathan; Morales, Jeffrey; Peralta, Barry; Valerio, Rowena; Zhang, Yi; Gregorio, Sergio; Hermocilla, Joseph; Echavez, Michael; Yap, Jan Michael; Farmer, Andrew; Schiltz, Gary; Lee, Jennifer; Casstevens, Terry; Jaiswal, Pankaj; Meintjes, Ayton; Wilkinson, Mark; Good, Benjamin; Wagner, James; Morris, Jane; Marshall, David; Collins, Anthony; Kikuchi, Shoshi; Metz, Thomas; McLaren, Graham; van Hintum, Theo

2008-01-01

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform; (ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data; (iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making. PMID:18483570

Content Management System for Developing a Virtual Platform for Association of Women's Aid with Lack of Resources

NASA Astrophysics Data System (ADS)

Sainz de Abajo, Beatriz; Flores García, Alberto; García Salcines, Enrique; Burón Fernández, F. Javier; López Coronado, Miguel; de Castro Lozano, Carlos

In this paper we show a Virtual Platform for an Association of Women's Aid called Centro Integral de Ayuda a la Mujer (CIAM). After analyzing different Content Management Systems (CMS) and the benefits that its use would contribute to the development of the Virtual Platform, taking into account the needs and requirements set by CIAM, we have opted for the use of Joomla!. This free CMS, for its characteristics, is the most benefits provided us. The virtual platform design has been developed following customer specifications, to have understood the simplicity and easy handling of the resulting platform. This platform will be integrated into the Web portal that has the Amarex Association and it will be able to be administrates from the CIAM without specific knowledge of programming languages. If new services were necessary, they would be easily implemented, adding new modules and components to perform these services.

Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.

PubMed

Thomas, Philipp; Matuschek, Hannes; Grima, Ramon

2012-01-01

The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA), which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen's system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface. In particular, the present methods allow for quick approximate analysis of time-dependent mean concentrations, variances, covariances and correlations coefficients, which typically outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with direct statistical evaluation and visualization. We showcase iNA's performance by using it to explore the stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network associated with circadian rhythms. The software iNA is freely available as executable binaries for Linux, MacOSX and Microsoft Windows, as well as the full source code under an open source license.

Intrinsic Noise Analyzer: A Software Package for the Exploration of Stochastic Biochemical Kinetics Using the System Size Expansion

PubMed Central

Grima, Ramon

2012-01-01

The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA), which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen’s system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface. In particular, the present methods allow for quick approximate analysis of time-dependent mean concentrations, variances, covariances and correlations coefficients, which typically outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with direct statistical evaluation and visualization. We showcase iNA’s performance by using it to explore the stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network associated with circadian rhythms. The software iNA is freely available as executable binaries for Linux, MacOSX and Microsoft Windows, as well as the full source code under an open source license. PMID:22723865

Integrated Spintronic Platforms for Biomolecular Recognition Detection

NASA Astrophysics Data System (ADS)

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

2008-06-01

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

An integrative top-down and bottom-up qualitative model construction framework for exploration of biochemical systems.

PubMed

Wu, Zujian; Pang, Wei; Coghill, George M

Computational modelling of biochemical systems based on top-down and bottom-up approaches has been well studied over the last decade. In this research, after illustrating how to generate atomic components by a set of given reactants and two user pre-defined component patterns, we propose an integrative top-down and bottom-up modelling approach for stepwise qualitative exploration of interactions among reactants in biochemical systems. Evolution strategy is applied to the top-down modelling approach to compose models, and simulated annealing is employed in the bottom-up modelling approach to explore potential interactions based on models constructed from the top-down modelling process. Both the top-down and bottom-up approaches support stepwise modular addition or subtraction for the model evolution. Experimental results indicate that our modelling approach is feasible to learn the relationships among biochemical reactants qualitatively. In addition, hidden reactants of the target biochemical system can be obtained by generating complex reactants in corresponding composed models. Moreover, qualitatively learned models with inferred reactants and alternative topologies can be used for further web-lab experimental investigations by biologists of interest, which may result in a better understanding of the system.

Accelerating bacterial growth detection and antimicrobial susceptibility assessment in integrated picoliter droplet platform.

PubMed

Kaushik, Aniruddha M; Hsieh, Kuangwen; Chen, Liben; Shin, Dong Jin; Liao, Joseph C; Wang, Tza-Huei

2017-11-15

There remains an urgent need for rapid diagnostic methods that can evaluate antibiotic resistance for pathogenic bacteria in order to deliver targeted antibiotic treatments. Toward this end, we present a rapid and integrated single-cell biosensing platform, termed dropFAST, for bacterial growth detection and antimicrobial susceptibility assessment. DropFAST utilizes a rapid resazurin-based fluorescent growth assay coupled with stochastic confinement of bacteria in 20 pL droplets to detect signal from growing bacteria after 1h incubation, equivalent to 2-3 bacterial replications. Full integration of droplet generation, incubation, and detection into a single, uninterrupted stream also renders this platform uniquely suitable for in-line bacterial phenotypic growth assessment. To illustrate the concept of rapid digital antimicrobial susceptibility assessment, we employ the dropFAST platform to evaluate the antibacterial effect of gentamicin on E. coli growth. Copyright © 2017 Elsevier B.V. All rights reserved.

Compact handheld low-cost biosensor platform for remote health monitoring

NASA Astrophysics Data System (ADS)

Hastanin, J.; Lenaerts, C.; Gailly, P.; Jans, H.; Huang, C.; Lagae, L.; Kokkinos, D.; Fleury-Frenette, K.

2016-04-01

In this paper, we present an original concept of plasmonic-related instrumentation platform dedicated to diagnostic biosensing tests out of the laboratory. The developed instrumental platform includes both disposable one-use microfluidic affinity biochip and compact optical readout device for biochip monitoring involving mobile Internet devices for data processing and communication. The biochip includes both microfluidic and optical coupling structures formed into a single plastic slab. The microfluidic path of the biochip operates in passive capillary pumping mode. In the proof-of-concept prototype, we address specifically the sensing format involving Surface Plasmon Resonance phenomenon. The biochip is plugged in the readout device without the use of an index matching fluid. An essential advantage of the developed biochip is that its implementation involves conventional hot embossing and thin film deposition process, perfectly suited for mass production of low-cost microfluidic biochip for biochemical applications.

New technology for early detection of health threats

NASA Astrophysics Data System (ADS)

Southern, Šárka O.; Lilienthal, Gerald W.

2008-04-01

Governmental agencies charged with protecting the health of the population and agriculture have several main strategic objectives including the detection of harmful agents, the identification of vulnerable biological targets, the prediction of health outcomes and the development of countermeasures. New technologies are urgently needed in several critical areas of bio-chemical defense: economical and minimally invasive biosensors for field use in humans and other species important for agriculture and infrastructure, universal analytical platforms for broad-based, early warnings of threats and technologies guiding the development of countermeasures. A new technology called Stress Response Profiling (SRP) was recently developed by the Gaia Medical Institute. SRP provides a universal analytical platform for monitoring health status based on measurements of physiological stress. The platform is implemented through handheld devices that can be used for noninvasive detection of early-stage health problems. This paper summarizes SRP features, advantages and potential benefits for critical areas of homeland defense.

Strategies to Maximize the Potential of Marine Biomaterials as a Platform for Cell Therapy

PubMed Central

Kim, Hyeongmin; Lee, Jaehwi

2016-01-01

Marine biopolymers have been explored as a promising cell therapy system for efficient cell delivery and tissue engineering. However, the marine biomaterial-based systems themselves have exhibited limited performance in terms of maintenance of cell viability and functions, promotion of cell proliferation and differentiation as well as cell delivery efficiency. Thus, numerous novel strategies have been devised to improve cell therapy outcomes. The strategies include optimization of physical and biochemical properties, provision of stimuli-responsive functions, and design of platforms for efficient cell delivery and tissue engineering. These approaches have demonstrated substantial improvement of therapeutic outcomes in a variety of research settings. In this review, therefore, research progress made with marine biomaterials as a platform for cell therapy is reported along with current research directions to further advance cell therapies as a tool to cure incurable diseases. PMID:26821034

An Integrative Platform for Three-dimensional Quantitative Analysis of Spatially Heterogeneous Metastasis Landscapes

NASA Astrophysics Data System (ADS)

Guldner, Ian H.; Yang, Lin; Cowdrick, Kyle R.; Wang, Qingfei; Alvarez Barrios, Wendy V.; Zellmer, Victoria R.; Zhang, Yizhe; Host, Misha; Liu, Fang; Chen, Danny Z.; Zhang, Siyuan

2016-04-01

Metastatic microenvironments are spatially and compositionally heterogeneous. This seemingly stochastic heterogeneity provides researchers great challenges in elucidating factors that determine metastatic outgrowth. Herein, we develop and implement an integrative platform that will enable researchers to obtain novel insights from intricate metastatic landscapes. Our two-segment platform begins with whole tissue clearing, staining, and imaging to globally delineate metastatic landscape heterogeneity with spatial and molecular resolution. The second segment of our platform applies our custom-developed SMART 3D (Spatial filtering-based background removal and Multi-chAnnel forest classifiers-based 3D ReconsTruction), a multi-faceted image analysis pipeline, permitting quantitative interrogation of functional implications of heterogeneous metastatic landscape constituents, from subcellular features to multicellular structures, within our large three-dimensional (3D) image datasets. Coupling whole tissue imaging of brain metastasis animal models with SMART 3D, we demonstrate the capability of our integrative pipeline to reveal and quantify volumetric and spatial aspects of brain metastasis landscapes, including diverse tumor morphology, heterogeneous proliferative indices, metastasis-associated astrogliosis, and vasculature spatial distribution. Collectively, our study demonstrates the utility of our novel integrative platform to reveal and quantify the global spatial and volumetric characteristics of the 3D metastatic landscape with unparalleled accuracy, opening new opportunities for unbiased investigation of novel biological phenomena in situ.

Integrated nanophotonic frequency shifter on the silicon-organic hybrid (SOH) platform for laser vibrometry

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

Lauermann, M.; Weimann, C.; Palmer, R.

2014-05-27

We demonstrate a waveguide-based frequency shifter on the silicon photonic platform, enabling frequency shifts up to 10 GHz. The device is realized by silicon-organic hybrid (SOH) integration. Temporal shaping of the drive signal allows the suppression of spurious side-modes by more than 23 dB.

Investigating the Nexus of Climate, Energy, Water, and Land at Decision-Relevant Scales: The Platform for Regional Integrated Modeling and Analysis (PRIMA)

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

Kraucunas, Ian P.; Clarke, Leon E.; Dirks, James A.

2015-04-01

The Platform for Regional Integrated Modeling and Analysis (PRIMA) is an innovative modeling system developed at Pacific Northwest National Laboratory (PNNL) to simulate interactions among natural and human systems at scales relevant to regional decision making. PRIMA brings together state-of-the-art models of regional climate, hydrology, agriculture, socioeconomics, and energy systems using a flexible coupling approach. The platform can be customized to inform a variety of complex questions and decisions, such as the integrated evaluation of mitigation and adaptation options across a range of sectors. Research into stakeholder decision support needs underpins the platform's application to regional issues, including uncertainty characterization.more » Ongoing numerical experiments are yielding new insights into the interactions among human and natural systems on regional scales with an initial focus on the energy-land-water nexus in the upper U.S. Midwest. This paper focuses on PRIMA’s functional capabilities and describes some lessons learned to date about integrated regional modeling.« less

Framework Programmable Platform for the Advanced Software Development Workstation: Preliminary system design document

NASA Technical Reports Server (NTRS)

Mayer, Richard J.; Blinn, Thomas M.; Mayer, Paula S. D.; Ackley, Keith A.; Crump, John W., IV; Henderson, Richard; Futrell, Michael T.

1991-01-01

The Framework Programmable Software Development Platform (FPP) is a project aimed at combining effective tool and data integration mechanisms with a model of the software development process in an intelligent integrated software environment. Guided by the model, this system development framework will take advantage of an integrated operating environment to automate effectively the management of the software development process so that costly mistakes during the development phase can be eliminated. The focus here is on the design of components that make up the FPP. These components serve as supporting systems for the Integration Mechanism and the Framework Processor and provide the 'glue' that ties the FPP together. Also discussed are the components that allow the platform to operate in a distributed, heterogeneous environment and to manage the development and evolution of software system artifacts.

A Geospatial Information Grid Framework for Geological Survey.

PubMed

Wu, Liang; Xue, Lei; Li, Chaoling; Lv, Xia; Chen, Zhanlong; Guo, Mingqiang; Xie, Zhong

2015-01-01

The use of digital information in geological fields is becoming very important. Thus, informatization in geological surveys should not stagnate as a result of the level of data accumulation. The integration and sharing of distributed, multi-source, heterogeneous geological information is an open problem in geological domains. Applications and services use geological spatial data with many features, including being cross-region and cross-domain and requiring real-time updating. As a result of these features, desktop and web-based geographic information systems (GISs) experience difficulties in meeting the demand for geological spatial information. To facilitate the real-time sharing of data and services in distributed environments, a GIS platform that is open, integrative, reconfigurable, reusable and elastic would represent an indispensable tool. The purpose of this paper is to develop a geological cloud-computing platform for integrating and sharing geological information based on a cloud architecture. Thus, the geological cloud-computing platform defines geological ontology semantics; designs a standard geological information framework and a standard resource integration model; builds a peer-to-peer node management mechanism; achieves the description, organization, discovery, computing and integration of the distributed resources; and provides the distributed spatial meta service, the spatial information catalog service, the multi-mode geological data service and the spatial data interoperation service. The geological survey information cloud-computing platform has been implemented, and based on the platform, some geological data services and geological processing services were developed. Furthermore, an iron mine resource forecast and an evaluation service is introduced in this paper.

A Geospatial Information Grid Framework for Geological Survey

PubMed Central

Wu, Liang; Xue, Lei; Li, Chaoling; Lv, Xia; Chen, Zhanlong; Guo, Mingqiang; Xie, Zhong

2015-01-01

The use of digital information in geological fields is becoming very important. Thus, informatization in geological surveys should not stagnate as a result of the level of data accumulation. The integration and sharing of distributed, multi-source, heterogeneous geological information is an open problem in geological domains. Applications and services use geological spatial data with many features, including being cross-region and cross-domain and requiring real-time updating. As a result of these features, desktop and web-based geographic information systems (GISs) experience difficulties in meeting the demand for geological spatial information. To facilitate the real-time sharing of data and services in distributed environments, a GIS platform that is open, integrative, reconfigurable, reusable and elastic would represent an indispensable tool. The purpose of this paper is to develop a geological cloud-computing platform for integrating and sharing geological information based on a cloud architecture. Thus, the geological cloud-computing platform defines geological ontology semantics; designs a standard geological information framework and a standard resource integration model; builds a peer-to-peer node management mechanism; achieves the description, organization, discovery, computing and integration of the distributed resources; and provides the distributed spatial meta service, the spatial information catalog service, the multi-mode geological data service and the spatial data interoperation service. The geological survey information cloud-computing platform has been implemented, and based on the platform, some geological data services and geological processing services were developed. Furthermore, an iron mine resource forecast and an evaluation service is introduced in this paper. PMID:26710255

The research and realization of digital management platform for ultra-precision optical elements within life-cycle

NASA Astrophysics Data System (ADS)

Wang, Juan; Wang, Jian; Li, Lijuan; Zhou, Kun

2014-08-01

In order to solve the information fusion, process integration, collaborative design and manufacturing for ultra-precision optical elements within life-cycle management, this paper presents a digital management platform which is based on product data and business processes by adopting the modern manufacturing technique, information technique and modern management technique. The architecture and system integration of the digital management platform are discussed in this paper. The digital management platform can realize information sharing and interaction for information-flow, control-flow and value-stream from user's needs to offline in life-cycle, and it can also enhance process control, collaborative research and service ability of ultra-precision optical elements.

Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels.

PubMed

Zeng, Yining; Zhao, Shuai; Yang, Shihui; Ding, Shi-You

2014-06-01

A biochemical platform holds the most promising route toward lignocellulosic biofuels, in which polysaccharides are hydrolyzed by cellulase enzymes into simple sugars and fermented to ethanol by microbes. However, these polysaccharides are cross-linked in the plant cell walls with the hydrophobic network of lignin that physically impedes enzymatic deconstruction. A thermochemical pretreatment process is often required to remove or delocalize lignin, which may also generate inhibitors that hamper enzymatic hydrolysis and fermentation. Here we review recent advances in understanding lignin structure in the plant cell walls and the negative roles of lignin in the processes of converting biomass to biofuels. Perspectives and future directions to improve the biomass conversion process are also discussed. Copyright © 2013. Published by Elsevier Ltd.

3D hybrid integrated lasers for silicon photonics

NASA Astrophysics Data System (ADS)

Song, B.; Pinna, S.; Liu, Y.; Megalini, L.; Klamkin, J.

2018-02-01

A novel 3D hybrid integration platform combines group III-V materials and silicon photonics to yield high-performance lasers is presented. This platform is based on flip-chip bonding and vertical optical coupling integration. In this work, indium phosphide (InP) devices with monolithic vertical total internal reflection turning mirrors were bonded to active silicon photonic circuits containing vertical grating couplers. Greater than 2 mW of optical power was coupled into a silicon waveguide from an InP laser. The InP devices can also be bonded directly to the silicon substrate, providing an efficient path for heat dissipation owing to the higher thermal conductance of silicon compared to InP. Lasers realized with this technique demonstrated a thermal impedance as low as 6.2°C/W, allowing for high efficiency and operation at high temperature. InP reflective semiconductor optical amplifiers were also integrated with 3D hybrid integration to form integrated external cavity lasers. These lasers demonstrated a wavelength tuning range of 30 nm, relative intensity noise lower than -135 dB/Hz and laser linewidth of 1.5 MHz. This platform is promising for integration of InP lasers and photonic integrated circuits on silicon photonics.

Metabologenomics of Phaeochromocytoma and Paraganglioma: An Integrated Approach for Personalised Biochemical and Genetic Testing

PubMed Central

Eisenhofer, Graeme; Klink, Barbara; Richter, Susan; Lenders, Jacques WM; Robledo, Mercedes

2017-01-01

The tremendous advances over the past two decades in both clinical genetics and biochemical testing of chromaffin cell tumours have led to new considerations about how these aspects of laboratory medicine can be integrated to improve diagnosis and management of affected patients. With germline mutations in 15 genes now identified to be responsible for over a third of all cases of phaeochromocytomas and paragangliomas, these tumours are recognised to have one of the richest hereditary backgrounds among all neoplasms. Depending on the mutation, tumours show distinct differences in metabolic pathways that relate to or even directly impact clinical presentation. At the same time, there has been improved understanding about how catecholamines are synthesised, stored, secreted and metabolised by chromaffin cell tumours. Although the tumours may not always secrete catecholamines it has become clear that almost all continuously produce and metabolise catecholamines. This has not only fuelled changes in laboratory medicine, but has also assisted in recognition of genotype-biochemical phenotype relationships important for diagnostics and clinical care. In particular, differences in catecholamine and energy pathway metabolomes can guide genetic testing, assist with test interpretation and provide predictions about the nature, behaviour and imaging characteristics of the tumours. Conversely, results of genetic testing are important for guiding how routine biochemical testing should be employed and interpreted in surveillance programmes for at-risk patients. In these ways there are emerging needs for modern laboratory medicine to seamlessly integrate biochemical and genetic testing into the diagnosis and management of patients with chromaffin cell tumours. PMID:29332973

An integrated biotechnology platform for developing sustainable chemical processes.

PubMed

Barton, Nelson R; Burgard, Anthony P; Burk, Mark J; Crater, Jason S; Osterhout, Robin E; Pharkya, Priti; Steer, Brian A; Sun, Jun; Trawick, John D; Van Dien, Stephen J; Yang, Tae Hoon; Yim, Harry

2015-03-01

Genomatica has established an integrated computational/experimental metabolic engineering platform to design, create, and optimize novel high performance organisms and bioprocesses. Here we present our platform and its use to develop E. coli strains for production of the industrial chemical 1,4-butanediol (BDO) from sugars. A series of examples are given to demonstrate how a rational approach to strain engineering, including carefully designed diagnostic experiments, provided critical insights about pathway bottlenecks, byproducts, expression balancing, and commercial robustness, leading to a superior BDO production strain and process.

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

Glyco-Immune Diagnostic Signatures and Therapeutic Targets of Mesothelioma

DTIC Science & Technology

2015-09-01

Immunoprofiles; Robotic Arrayer 16. SECURITY CLASSIFICATION OF: U 17. LIMITATION OF ABSTRACT: UU 18. NUMBER OF PAGES 19 19a. NAME OF RESPONSIBLE...General Comments: This project involved novel technology in which biochemically synthesized glycans were robotically printed on glass slides...glycans and the platform was known as the PGA-400. (Figure 1) A standard robotic technology for printing a large range of aminefunctionalized

Glyco-Immune Diagnostic Signatures and Therapeutic Targets of Mesothelioma

DTIC Science & Technology

2015-09-01

Mesothelioma; Glycan Array; Immunoprofiles; Robotic Arrayer 16. SECURITY CLASSIFICATION OF: U 17. LIMITATION OF ABSTRACT: UU 18. NUMBER OF PAGES 19 19a...PROJECT SUMMARY: General Comments: This project involved novel technology in which biochemically synthesized glycans were robotically printed on glass...include 386 glycans and the platform was known as the PGA-400. (Figure 1) A standard robotic technology for printing a large range of

Finding Common Ground: Use of a Geographically-Framed Landscape Template as an Integrating Platform for an International Education Initiative

ERIC Educational Resources Information Center

Brierley, Gary; Li, Xilai; Qiao, Youming; Huang, He Qing; Wang, Zhaoyin

2018-01-01

This situated case study outlines how a place-based landscape template provided an integrative platform for the environmental arm of a cross-disciplinary international education initiative, the Three Brothers Project, wherein geographers at the University of Auckland worked alongside engineers at Tsinghua University in Beijing to support…

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.

Latent feature decompositions for integrative analysis of multi-platform genomic data

PubMed Central

Gregory, Karl B.; Momin, Amin A.; Coombes, Kevin R.; Baladandayuthapani, Veerabhadran

2015-01-01

Increased availability of multi-platform genomics data on matched samples has sparked research efforts to discover how diverse molecular features interact both within and between platforms. In addition, simultaneous measurements of genetic and epigenetic characteristics illuminate the roles their complex relationships play in disease progression and outcomes. However, integrative methods for diverse genomics data are faced with the challenges of ultra-high dimensionality and the existence of complex interactions both within and between platforms. We propose a novel modeling framework for integrative analysis based on decompositions of the large number of platform-specific features into a smaller number of latent features. Subsequently we build a predictive model for clinical outcomes accounting for both within- and between-platform interactions based on Bayesian model averaging procedures. Principal components, partial least squares and non-negative matrix factorization as well as sparse counterparts of each are used to define the latent features, and the performance of these decompositions is compared both on real and simulated data. The latent feature interactions are shown to preserve interactions between the original features and not only aid prediction but also allow explicit selection of outcome-related features. The methods are motivated by and applied to, a glioblastoma multiforme dataset from The Cancer Genome Atlas to predict patient survival times integrating gene expression, microRNA, copy number and methylation data. For the glioblastoma data, we find a high concordance between our selected prognostic genes and genes with known associations with glioblastoma. In addition, our model discovers several relevant cross-platform interactions such as copy number variation associated gene dosing and epigenetic regulation through promoter methylation. On simulated data, we show that our proposed method successfully incorporates interactions within and between genomic platforms to aid accurate prediction and variable selection. Our methods perform best when principal components are used to define the latent features. PMID:26146492

Wafer-scale integrated micro-supercapacitors on an ultrathin and highly flexible biomedical platform.

PubMed

Maeng, Jimin; Meng, Chuizhou; Irazoqui, Pedro P

2015-02-01

We present wafer-scale integrated micro-supercapacitors on an ultrathin and highly flexible parylene platform, as progress toward sustainably powering biomedical microsystems suitable for implantable and wearable applications. All-solid-state, low-profile (<30 μm), and high-density (up to ~500 μF/mm(2)) micro-supercapacitors are formed on an ultrathin (~20 μm) freestanding parylene film by a wafer-scale parylene packaging process in combination with a polyaniline (PANI) nanowire growth technique assisted by surface plasma treatment. These micro-supercapacitors are highly flexible and shown to be resilient toward flexural stress. Further, direct integration of micro-supercapacitors into a radio frequency (RF) rectifying circuit is achieved on a single parylene platform, yielding a complete RF energy harvesting microsystem. The system discharging rate is shown to improve by ~17 times in the presence of the integrated micro-supercapacitors. This result suggests that the integrated micro-supercapacitor technology described herein is a promising strategy for sustainably powering biomedical microsystems dedicated to implantable and wearable applications.

Integrated liquid-core optical fibers for ultra-efficient nonlinear liquid photonics.

PubMed

Kieu, K; Schneebeli, L; Norwood, R A; Peyghambarian, N

2012-03-26

We have developed a novel integrated platform for liquid photonics based on liquid core optical fiber (LCOF). The platform is created by fusion splicing liquid core optical fiber to standard single-mode optical fiber making it fully integrated and practical - a major challenge that has greatly hindered progress in liquid-photonic applications. As an example, we report here the realization of ultralow threshold Raman generation using an integrated CS₂ filled LCOF pumped with sub-nanosecond pulses at 532 nm and 1064 nm. The measured energy threshold for the Stokes generation is 1nJ, about three orders of magnitude lower than previously reported values in the literature for hydrogen gas, a popular Raman medium. The integrated LCOF platform opens up new possibilities for ultralow power nonlinear optics such as efficient white light generation for displays, mid-IR generation, slow light generation, parametric amplification, all-optical switching and wavelength conversion using liquids that have orders of magnitude larger optical nonlinearities compared with silica glass.

Compact electrochemical sensor system and method for field testing for metals in saliva or other fluids

DOEpatents

Lin, Yuehe; Bennett, Wendy D.; Timchalk, Charles; Thrall, Karla D.

2004-03-02

Microanalytical systems based on a microfluidics/electrochemical detection scheme are described. Individual modules, such as microfabricated piezoelectrically actuated pumps and a microelectrochemical cell were integrated onto portable platforms. This allowed rapid change-out and repair of individual components by incorporating "plug and play" concepts now standard in PC's. Different integration schemes were used for construction of the microanalytical systems based on microfluidics/electrochemical detection. In one scheme, all individual modules were integrated in the surface of the standard microfluidic platform based on a plug-and-play design. Microelectrochemical flow cell which integrated three electrodes based on a wall-jet design was fabricated on polymer substrate. The microelectrochemical flow cell was then plugged directly into the microfluidic platform. Another integration scheme was based on a multilayer lamination method utilizing stacking modules with different functionality to achieve a compact microanalytical device. Application of the microanalytical system for detection of lead in, for example, river water and saliva samples using stripping voltammetry is described.

Biochemical component identification by plasmonic improved whispering gallery mode optical resonance based sensor

NASA Astrophysics Data System (ADS)

Saetchnikov, Vladimir A.; Tcherniavskaia, Elina A.; Saetchnikov, Anton V.; Schweiger, Gustav; Ostendorf, Andreas

2014-05-01

Experimental data on detection and identification of variety of biochemical agents, such as proteins, microelements, antibiotic of different generation etc. in both single and multi component solutions under varied in wide range concentration analyzed on the light scattering parameters of whispering gallery mode optical resonance based sensor are represented. Multiplexing on parameters and components has been realized using developed fluidic sensor cell with fixed in adhesive layer dielectric microspheres and data processing. Biochemical component identification has been performed by developed network analysis techniques. Developed approach is demonstrated to be applicable both for single agent and for multi component biochemical analysis. Novel technique based on optical resonance on microring structures, plasmon resonance and identification tools has been developed. To improve a sensitivity of microring structures microspheres fixed by adhesive had been treated previously by gold nanoparticle solution. Another technique used thin film gold layers deposited on the substrate below adhesive. Both biomolecule and nanoparticle injections caused considerable changes of optical resonance spectra. Plasmonic gold layers under optimized thickness also improve parameters of optical resonance spectra. Biochemical component identification has been also performed by developed network analysis techniques both for single and for multi component solution. So advantages of plasmon enhancing optical microcavity resonance with multiparameter identification tools is used for development of a new platform for ultra sensitive label-free biomedical sensor.

Chapter A7. Section 7.0. Five-Day Biochemical Oxygen Demand

USGS Publications Warehouse

Delzer, Gregory C.; McKenzie, Stuart W.

1999-01-01

The presence of a sufficient concentration of dissolved oxygen is critical to maintaining the aquatic life and aesthetic quality of streams and lakes. Determinng how organic matter affects the concentration of dissolved oxygen (DO) in a stream or lake is integral to water-quality management. The decay of organic matter in water is measured as biochemical or chemical oxygen demand. This report describes the field protocols used by U.S. Geological Survey (USGS) personnel to determine the five-day test for biochemical oxygen demand.

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

PubMed

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

2014-01-01

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

Strategic deployment of CHO expression platforms to deliver Pfizer's Monoclonal Antibody Portfolio.

PubMed

Scarcelli, John J; Shang, Tanya Q; Iskra, Tim; Allen, Martin J; Zhang, Lin

2017-11-01

Development of stable cell lines for expression of large-molecule therapeutics represents a significant portion of the time and effort required to advance a molecule to enabling regulatory toxicology studies and clinical evaluation. Our development strategy employs two different approaches for cell line development based on the needs of a particular project: a random integration approach for projects where high-level expression is critical, and a site-specific integration approach for projects in which speed and reduced employee time spend is a necessity. Here we describe both our random integration and site-specific integration platforms and their applications in support of monoclonal antibody development and production. We also compare product quality attributes of monoclonal antibodies produced with a nonclonal cell pool or clonal cell lines derived from the two platforms. Our data suggests that material source (pools vs. clones) does not significantly alter the examined product quality attributes. Our current practice is to leverage this observation with our site-specific integration platform, where material generated from cell pools is used for an early molecular assessment of a given candidate to make informed decisions around development strategy. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1463-1467, 2017. © 2017 American Institute of Chemical Engineers.

Integrative structure modeling with the Integrative Modeling Platform.

PubMed

Webb, Benjamin; Viswanath, Shruthi; Bonomi, Massimiliano; Pellarin, Riccardo; Greenberg, Charles H; Saltzberg, Daniel; Sali, Andrej

2018-01-01

Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models. Here, we describe our open source software suite for integrative structure modeling, Integrative Modeling Platform (https://integrativemodeling.org), and demonstrate its use. © 2017 The Protein Society.

Measurement of Bacterial Bioluminescence Intensity and Spectrum: Current Physical Techniques and Principles.

PubMed

Jia, Kun; Ionescu, Rodica Elena

2016-01-01

: Bioluminescence is light production by living organisms, which can be observed in numerous marine creatures and some terrestrial invertebrates. More specifically, bacterial bioluminescence is the "cold light" produced and emitted by bacterial cells, including both wild-type luminescent and genetically engineered bacteria. Because of the lively interplay of synthetic biology, microbiology, toxicology, and biophysics, different configurations of whole-cell biosensors based on bacterial bioluminescence have been designed and are widely used in different fields, such as ecotoxicology, food toxicity, and environmental pollution. This chapter first discusses the background of the bioluminescence phenomenon in terms of optical spectrum. Platforms for bacterial bioluminescence detection using various techniques are then introduced, such as a photomultiplier tube, charge-coupled device (CCD) camera, micro-electro-mechanical systems (MEMS), and complementary metal-oxide-semiconductor (CMOS) based integrated circuit. Furthermore, some typical biochemical methods to optimize the analytical performances of bacterial bioluminescent biosensors/assays are reviewed, followed by a presentation of author's recent work concerning the improved sensitivity of a bioluminescent assay for pesticides. Finally, bacterial bioluminescence as implemented in eukaryotic cells, bioluminescent imaging, and cancer cell therapies is discussed.

On-Site Production of Cellulolytic Enzymes by the Sequential Cultivation Method.

PubMed

Farinas, Cristiane S; Florencio, Camila; Badino, Alberto C

2018-01-01

The conversion of renewable lignocellulosic biomass into fuels, chemicals, and high-value materials using the biochemical platform has been considered the most sustainable alternative for the implementation of future biorefineries. However, the high cost of the cellulolytic enzymatic cocktails used in the saccharification step significantly affects the economics of industrial large-scale conversion processes. The on-site production of enzymes, integrated to the biorefinery plant, is being considered as a potential strategy that could be used to reduce costs. In such approach, the microbial production of enzymes can be carried out using the same lignocellulosic biomass as feedstock for fungal development and biofuels production. Most of the microbial cultivation processes for the production of industrial enzymes have been developed using the conventional submerged fermentation. Recently, a sequential solid-state followed by submerged fermentation has been described as a potential alternative cultivation method for cellulolytic enzymes production. This chapter presents the detailed procedure of the sequential cultivation method, which could be employed for the on-site production of the cellulolytic enzymes required to convert lignocellulosic biomass into simple sugars.

Robotic implementation of assays: tissue-nonspecific alkaline phosphatase (TNAP) case study.

PubMed

Chung, Thomas D Y

2013-01-01

Laboratory automation and robotics have "industrialized" the execution and completion of large-scale, enabling high-capacity and high-throughput (100 K-1 MM/day) screening (HTS) campaigns of large "libraries" of compounds (>200 K-2 MM) to complete in a few days or weeks. Critical to the success these HTS campaigns is the ability of a competent assay development team to convert a validated research-grade laboratory "benchtop" assay suitable for manual or semi-automated operations on a few hundreds of compounds into a robust miniaturized (384- or 1,536-well format), well-engineered, scalable, industrialized assay that can be seamlessly implemented on a fully automated, fully integrated robotic screening platform for cost-effective screening of hundreds of thousands of compounds. Here, we provide a review of the theoretical guiding principles and practical considerations necessary to reduce often complex research biology into a "lean manufacturing" engineering endeavor comprising adaption, automation, and implementation of HTS. Furthermore we provide a detailed example specifically for a cell-free in vitro biochemical, enzymatic phosphatase assay for tissue-nonspecific alkaline phosphatase that illustrates these principles and considerations.

Lab-on-a-chip in vitro compartmentalization technologies for protein studies.

PubMed

Zhu, Yonggang; Power, Barbara E

2008-01-01

In vitro compartmentalization (IVC) is a powerful tool for studying protein-protein reactions, due to its high capacity and the versatility of droplet technologies. IVC bridges the gap between chemistry and biology as it enables the incorporation of unnatural amino acids with modifications into biological systems, through protein transcription and translation reactions, in a cell-like microdrop environment. The quest for the ultimate chip for protein studies using IVC is the drive for the development of various microfluidic droplet technologies to enable these unusual biochemical reactions to occur. These techniques have been shown to generate precise microdrops with a controlled size. Various chemical and physical phenomena have been utilized for on-chip manipulation to allow the droplets to be generated, fused, and split. Coupled with detection techniques, droplets can be sorted and selected. These capabilities allow directed protein evolution to be carried out on a microchip. With further technological development of the detection module, factors such as addressable storage, transport and interfacing technologies, could be integrated and thus provide platforms for protein studies with high efficiency and accuracy that conventional laboratories cannot achieve.

Opportunities of CMOS-MEMS integration through LSI foundry and open facility

NASA Astrophysics Data System (ADS)

Mita, Yoshio; Lebrasseur, Eric; Okamoto, Yuki; Marty, Frédéfic; Setoguchi, Ryota; Yamada, Kentaro; Mori, Isao; Morishita, Satoshi; Imai, Yoshiaki; Hosaka, Kota; Hirakawa, Atsushi; Inoue, Shu; Kubota, Masanori; Denoual, Matthieu

2017-06-01

Since the 2000s, several countries have established micro- and nanofabrication platforms for the research and education community as national projects. By combining such platforms with VLSI multichip foundry services, various integrated devices, referred to as “CMOS-MEMS”, can be realized without constructing an entire cleanroom. In this paper, we summarize MEMS-last postprocess schemes for CMOS devices on a bulk silicon wafer as well as on a silicon-on-insulator (SOI) wafer using an open-access cleanroom of the Nanotechnology Platform of MEXT Japan. The integration devices presented in this article are free-standing structures and postprocess isolated LSI devices. Postprocess issues are identified with their solutions, such as the reactive ion etching (RIE) lag for dry release and the impact of the deep RIE (DRIE) postprocess on transistor characteristics. Integration with nonsilicon materials is proposed as one of the future directions.

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

Development of a Web-Enabled Informatics Platform for Manipulation of Gene Expression Data

DTIC Science & Technology

2004-12-01

genomic platforms such as metabolomics and proteomics , and to federated databases for knowledge management. A successful SBIR Phase I completed...measurements that require sophisticated bioinformatic platforms for data archival, management, integration, and analysis if researchers are to derive...web-enabled bioinformatic platform consisting of a Laboratory Information Management System (LIMS), an Analysis Information Management System (AIMS

A fully integrated oven controlled microelectromechanical oscillator -- Part I. Design and fabrication

DOE PAGES

Wojciechowski, Kenneth E.; Baker, Michael S.; Clews, Peggy J.; ...

2015-06-24

Our paper reports the design and fabrication of a fully integrated oven controlled microelectromechanical oscillator (OCMO). This paper begins by describing the limits on oscillator frequency stability imposed by the thermal drift and electronic properties (Q, resistance) of both the resonant tank circuit and feedback electronics required to form an electronic oscillator. An OCMO is presented that takes advantage of high thermal isolation and monolithic integration of both micromechanical resonators and electronic circuitry to thermally stabilize or ovenize all the components that comprise an oscillator. This was achieved by developing a processing technique where both silicon-on-insulator complementary metal-oxide-semiconductor (CMOS) circuitrymore » and piezoelectric aluminum nitride, AlN, micromechanical resonators are placed on a suspended platform within a standard CMOS integrated circuit. Operation at microscale sizes achieves high thermal resistances (~10 °C/mW), and hence thermal stabilization of the oscillators at very low-power levels when compared with the state-of-the-art ovenized crystal oscillators, OCXO. This constant resistance feedback circuit is presented that incorporates on platform resistive heaters and temperature sensors to both measure and stabilize the platform temperature. Moreover, the limits on temperature stability of the OCMO platform and oscillator frequency imposed by the gain of the constant resistance feedback loop, placement of the heater and temperature sensing resistors, as well as platform radiative and convective heat losses are investigated.« less

Information Management Platform for Data Analytics and Aggregation (IMPALA) System Design Document

NASA Technical Reports Server (NTRS)

Carnell, Andrew; Akinyelu, Akinyele

2016-01-01

The System Design document tracks the design activities that are performed to guide the integration, installation, verification, and acceptance testing of the IMPALA Platform. The inputs to the design document are derived from the activities recorded in Tasks 1 through 6 of the Statement of Work (SOW), with the proposed technical solution being the completion of Phase 1-A. With the documentation of the architecture of the IMPALA Platform and the installation steps taken, the SDD will be a living document, capturing the details about capability enhancements and system improvements to the IMPALA Platform to provide users in development of accurate and precise analytical models. The IMPALA Platform infrastructure team, data architecture team, system integration team, security management team, project manager, NASA data scientists and users are the intended audience of this document. The IMPALA Platform is an assembly of commercial-off-the-shelf (COTS) products installed on an Apache-Hadoop platform. User interface details for the COTS products will be sourced from the COTS tools vendor documentation. The SDD is a focused explanation of the inputs, design steps, and projected outcomes of every design activity for the IMPALA Platform through installation and validation.

Complete integrability of information processing by biochemical reactions

PubMed Central

Agliari, Elena; Barra, Adriano; Dello Schiavo, Lorenzo; Moro, Antonio

2016-01-01

Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical kinetics, (anti-)ferromagnetic spin models in statistical mechanics and operational amplifiers/flip-flops in cybernetics. The underlying modeling – based on spin systems – has been proved to be accurate for a wide class of systems matching classical (e.g. Michaelis–Menten, Hill, Adair) scenarios in the infinite-size approximation. However, the current research in biochemical information processing has been focusing on systems involving a relatively small number of units, where this approximation is no longer valid. Here we show that the whole statistical mechanical description of reaction kinetics can be re-formulated via a mechanical analogy – based on completely integrable hydrodynamic-type systems of PDEs – which provides explicit finite-size solutions, matching recently investigated phenomena (e.g. noise-induced cooperativity, stochastic bi-stability, quorum sensing). The resulting picture, successfully tested against a broad spectrum of data, constitutes a neat rationale for a numerically effective and theoretically consistent description of collective behaviors in biochemical reactions. PMID:27812018

Complete integrability of information processing by biochemical reactions

NASA Astrophysics Data System (ADS)

Agliari, Elena; Barra, Adriano; Dello Schiavo, Lorenzo; Moro, Antonio

2016-11-01

Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical kinetics, (anti-)ferromagnetic spin models in statistical mechanics and operational amplifiers/flip-flops in cybernetics. The underlying modeling - based on spin systems - has been proved to be accurate for a wide class of systems matching classical (e.g. Michaelis-Menten, Hill, Adair) scenarios in the infinite-size approximation. However, the current research in biochemical information processing has been focusing on systems involving a relatively small number of units, where this approximation is no longer valid. Here we show that the whole statistical mechanical description of reaction kinetics can be re-formulated via a mechanical analogy - based on completely integrable hydrodynamic-type systems of PDEs - which provides explicit finite-size solutions, matching recently investigated phenomena (e.g. noise-induced cooperativity, stochastic bi-stability, quorum sensing). The resulting picture, successfully tested against a broad spectrum of data, constitutes a neat rationale for a numerically effective and theoretically consistent description of collective behaviors in biochemical reactions.

Complete integrability of information processing by biochemical reactions.

PubMed

Agliari, Elena; Barra, Adriano; Dello Schiavo, Lorenzo; Moro, Antonio

2016-11-04

Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical kinetics, (anti-)ferromagnetic spin models in statistical mechanics and operational amplifiers/flip-flops in cybernetics. The underlying modeling - based on spin systems - has been proved to be accurate for a wide class of systems matching classical (e.g. Michaelis-Menten, Hill, Adair) scenarios in the infinite-size approximation. However, the current research in biochemical information processing has been focusing on systems involving a relatively small number of units, where this approximation is no longer valid. Here we show that the whole statistical mechanical description of reaction kinetics can be re-formulated via a mechanical analogy - based on completely integrable hydrodynamic-type systems of PDEs - which provides explicit finite-size solutions, matching recently investigated phenomena (e.g. noise-induced cooperativity, stochastic bi-stability, quorum sensing). The resulting picture, successfully tested against a broad spectrum of data, constitutes a neat rationale for a numerically effective and theoretically consistent description of collective behaviors in biochemical reactions.

Multi-octave spectral beam combiner on ultra-broadband photonic integrated circuit platform.

PubMed

Stanton, Eric J; Heck, Martijn J R; Bovington, Jock; Spott, Alexander; Bowers, John E

2015-05-04

We present the design of a novel platform that is able to combine optical frequency bands spanning 4.2 octaves from ultraviolet to mid-wave infrared into a single, low M2 output waveguide. We present the design and realization of a key component in this platform that combines the wavelength bands of 350 nm - 1500 nm and 1500 nm - 6500 nm with demonstrated efficiency greater than 90% in near-infrared and mid-wave infrared. The multi-octave spectral beam combiner concept is realized using an integrated platform with silicon nitride waveguides and silicon waveguides. Simulated bandwidth is shown to be over four octaves, and measured bandwidth is shown over two octaves, limited by the availability of sources.

The designing and implementation of PE teaching information resource database based on broadband network

NASA Astrophysics Data System (ADS)

Wang, Jian

2017-01-01

In order to change traditional PE teaching mode and realize the interconnection, interworking and sharing of PE teaching resources, a distance PE teaching platform based on broadband network is designed and PE teaching information resource database is set up. The designing of PE teaching information resource database takes Windows NT 4/2000Server as operating system platform, Microsoft SQL Server 7.0 as RDBMS, and takes NAS technology for data storage and flow technology for video service. The analysis of system designing and implementation shows that the dynamic PE teaching information resource sharing platform based on Web Service can realize loose coupling collaboration, realize dynamic integration and active integration and has good integration, openness and encapsulation. The distance PE teaching platform based on Web Service and the design scheme of PE teaching information resource database can effectively solve and realize the interconnection, interworking and sharing of PE teaching resources and adapt to the informatization development demands of PE teaching.

COBALT: Development of a Platform to Flight Test Lander GN&C Technologies on Suborbital Rockets

NASA Technical Reports Server (NTRS)

Carson, John M., III; Seubert, Carl R.; Amzajerdian, Farzin; Bergh, Chuck; Kourchians, Ara; Restrepo, Carolina I.; Villapando, Carlos Y.; O'Neal, Travis V.; Robertson, Edward A.; Pierrottet, Diego;

Hardware Interface Description for the Integrated Power, Avionics, and Software (iPAS) Space Telecommunications Radio Ssystem (STRS) Radio

NASA Technical Reports Server (NTRS)

Shalkhauser, Mary Jo W.; Roche, Rigoberto

2017-01-01

The Space Telecommunications Radio System (STRS) provides a common, consistent framework for software defined radios (SDRs) to abstract the application software from the radio platform hardware. The STRS standard aims to reduce the cost and risk of using complex, configurable and reprogrammable radio systems across NASA missions. To promote the use of the STRS architecture for future NASA advanced exploration missions, NASA Glenn Research Center (GRC) developed an STRS-compliant SDR on a radio platform used by the Advance Exploration System program at the Johnson Space Center (JSC) in their Integrated Power, Avionics, and Software (iPAS) laboratory. The iPAS STRS Radio was implemented on the Reconfigurable, Intelligently-Adaptive Communication System (RIACS) platform, currently being used for radio development at JSC. The platform consists of a Xilinx ML605 Virtex-6 FPGA board, an Analog Devices FMCOMMS1-EBZ RF transceiver board, and an Embedded PC (Axiomtek eBox 620-110-FL) running the Ubuntu 12.4 operating system. Figure 1 shows the RIACS platform hardware. The result of this development is a very low cost STRS compliant platform that can be used for waveform developments for multiple applications.The purpose of this document is to describe how to develop a new waveform using the RIACS platform and the Very High Speed Integrated Circuits (VHSIC) Hardware Description Language (VHDL) FPGA wrapper code and the STRS implementation on the Axiomtek processor.

Hybrid Integrated Platforms for Silicon Photonics

PubMed Central

Liang, Di; Roelkens, Gunther; Baets, Roel; Bowers, John E.

2010-01-01

A review of recent progress in hybrid integrated platforms for silicon photonics is presented. Integration of III-V semiconductors onto silicon-on-insulator substrates based on two different bonding techniques is compared, one comprising only inorganic materials, the other technique using an organic bonding agent. Issues such as bonding process and mechanism, bonding strength, uniformity, wafer surface requirement, and stress distribution are studied in detail. The application in silicon photonics to realize high-performance active and passive photonic devices on low-cost silicon wafers is discussed. Hybrid integration is believed to be a promising technology in a variety of applications of silicon photonics.

Integration of multisensor hybrid reasoners to support personal autonomy in the smart home.

PubMed

Valero, Miguel Ángel; Bravo, José; Chamizo, Juan Manuel García; López-de-Ipiña, Diego

2014-09-17

The deployment of the Ambient Intelligence (AmI) paradigm requires designing and integrating user-centered smart environments to assist people in their daily life activities. This research paper details an integration and validation of multiple heterogeneous sensors with hybrid reasoners that support decision making in order to monitor personal and environmental data at a smart home in a private way. The results innovate on knowledge-based platforms, distributed sensors, connected objects, accessibility and authentication methods to promote independent living for elderly people. TALISMAN+, the AmI framework deployed, integrates four subsystems in the smart home: (i) a mobile biomedical telemonitoring platform to provide elderly patients with continuous disease management; (ii) an integration middleware that allows context capture from heterogeneous sensors to program environment's reaction; (iii) a vision system for intelligent monitoring of daily activities in the home; and (iv) an ontologies-based integrated reasoning platform to trigger local actions and manage private information in the smart home. The framework was integrated in two real running environments, the UPM Accessible Digital Home and MetalTIC house, and successfully validated by five experts in home care, elderly people and personal autonomy.

Integration of Multisensor Hybrid Reasoners to Support Personal Autonomy in the Smart Home

PubMed Central

Valero, Miguel Ángel; Bravo, José; Chamizo, Juan Manuel García; López-de-Ipiña, Diego

2014-01-01

The deployment of the Ambient Intelligence (AmI) paradigm requires designing and integrating user-centered smart environments to assist people in their daily life activities. This research paper details an integration and validation of multiple heterogeneous sensors with hybrid reasoners that support decision making in order to monitor personal and environmental data at a smart home in a private way. The results innovate on knowledge-based platforms, distributed sensors, connected objects, accessibility and authentication methods to promote independent living for elderly people. TALISMAN+, the AmI framework deployed, integrates four subsystems in the smart home: (i) a mobile biomedical telemonitoring platform to provide elderly patients with continuous disease management; (ii) an integration middleware that allows context capture from heterogeneous sensors to program environment's reaction; (iii) a vision system for intelligent monitoring of daily activities in the home; and (iv) an ontologies-based integrated reasoning platform to trigger local actions and manage private information in the smart home. The framework was integrated in two real running environments, the UPM Accessible Digital Home and MetalTIC house, and successfully validated by five experts in home care, elderly people and personal autonomy. PMID:25232910

Development of an Online Platform to Support the Network of Caregivers of People with Dementia.

PubMed

Verwey, Renée; van Berlo, Miranda; Duymelinck, Saskia; Willard, Sarah; van Rossum, Erik

2016-01-01

In the Netherlands, care technology is used insufficiently to support people with dementia, their family and professional caregivers. In this project we integrate a range of services and applications into an online platform, with the aim to strengthen these networks and to support communication between their members. The prototype of the platform was made in an iterative user centered way. Semi structured (group) interviews were conducted to specify the requirements. The platform consists of 'cubes' with information about dementia (care), video communication options, a calendar and a care plan. The first prototype of the platform was valued by the participants, but privacy matters and registration issues were pointed out when using a shared care plan. Additional applications to monitor health and safety will be integrated in the second prototype. This prototype will be tested on its usability, feasibility and desirability during a pilot study in spring 2016.

ComplexQuant: high-throughput computational pipeline for the global quantitative analysis of endogenous soluble protein complexes using high resolution protein HPLC and precision label-free LC/MS/MS.

PubMed

Wan, Cuihong; Liu, Jian; Fong, Vincent; Lugowski, Andrew; Stoilova, Snejana; Bethune-Waddell, Dylan; Borgeson, Blake; Havugimana, Pierre C; Marcotte, Edward M; Emili, Andrew

2013-04-09

The experimental isolation and characterization of stable multi-protein complexes are essential to understanding the molecular systems biology of a cell. To this end, we have developed a high-throughput proteomic platform for the systematic identification of native protein complexes based on extensive fractionation of soluble protein extracts by multi-bed ion exchange high performance liquid chromatography (IEX-HPLC) combined with exhaustive label-free LC/MS/MS shotgun profiling. To support these studies, we have built a companion data analysis software pipeline, termed ComplexQuant. Proteins present in the hundreds of fractions typically collected per experiment are first identified by exhaustively interrogating MS/MS spectra using multiple database search engines within an integrative probabilistic framework, while accounting for possible post-translation modifications. Protein abundance is then measured across the fractions based on normalized total spectral counts and precursor ion intensities using a dedicated tool, PepQuant. This analysis allows co-complex membership to be inferred based on the similarity of extracted protein co-elution profiles. Each computational step has been optimized for processing large-scale biochemical fractionation datasets, and the reliability of the integrated pipeline has been benchmarked extensively. This article is part of a Special Issue entitled: From protein structures to clinical applications. Copyright © 2012 Elsevier B.V. All rights reserved.

Mitochondria: more than just a powerhouse.

PubMed

McBride, Heidi M; Neuspiel, Margaret; Wasiak, Sylwia

2006-07-25

Pioneering biochemical studies have long forged the concept that the mitochondria are the 'energy powerhouse of the cell'. These studies, combined with the unique evolutionary origin of the mitochondria, led the way to decades of research focusing on the organelle as an essential, yet independent, functional component of the cell. Recently, however, our conceptual view of this isolated organelle has been profoundly altered with the discovery that mitochondria function within an integrated reticulum that is continually remodeled by both fusion and fission events. The identification of a number of proteins that regulate these activities is beginning to provide mechanistic details of mitochondrial membrane remodeling. However, the broader question remains regarding the underlying purpose of mitochondrial dynamics and the translation of these morphological transitions into altered functional output. One hypothesis has been that mitochondrial respiration and metabolism may be spatially and temporally regulated by the architecture and positioning of the organelle. Recent evidence supports and expands this idea by demonstrating that mitochondria are an integral part of multiple cell signaling cascades. Interestingly, proteins such as GTPases, kinases and phosphatases are involved in bi-directional communication between the mitochondrial reticulum and the rest of the cell. These proteins link mitochondrial function and dynamics to the regulation of metabolism, cell-cycle control, development, antiviral responses and cell death. In this review we will highlight the emerging evidence that provides molecular definition to mitochondria as a central platform in the execution of diverse cellular events.

A smartphone controlled handheld microfluidic liquid handling system.

PubMed

Li, Baichen; Li, Lin; Guan, Allan; Dong, Quan; Ruan, Kangcheng; Hu, Ronggui; Li, Zhenyu

2014-10-21

Microfluidics and lab-on-a-chip technologies have made it possible to manipulate small volume liquids with unprecedented resolution, automation and integration. However, most current microfluidic systems still rely on bulky off-chip infrastructures such as compressed pressure sources, syringe pumps and computers to achieve complex liquid manipulation functions. Here, we present a handheld automated microfluidic liquid handling system controlled by a smartphone, which is enabled by combining elastomeric on-chip valves and a compact pneumatic system. As a demonstration, we show that the system can automatically perform all the liquid handling steps of a bead-based HIV1 p24 sandwich immunoassay on a multi-layer PDMS chip without any human intervention. The footprint of the system is 6 × 10.5 × 16.5 cm, and the total weight is 829 g including battery. Powered by a 12.8 V 1500 mAh Li battery, the system consumed 2.2 W on average during the immunoassay and lasted for 8.7 h. This handheld microfluidic liquid handling platform is generally applicable to many biochemical and cell-based assays requiring complex liquid manipulation and sample preparation steps such as FISH, PCR, flow cytometry and nucleic acid sequencing. In particular, the integration of this technology with read-out biosensors may help enable the realization of the long-sought Tricorder-like handheld in vitro diagnostic (IVD) systems.

Advancing Microgrid Research at NREL

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

NREL expanded its microgrid research capabilities at the Energy System Integration Facility (ESIF) with the purchase of a Schweitzer Engineering Laboratories (SEL) microgrid controller, resulting in a more comprehensive microgrid research platform. NREL's microgrid research platform allows manufacturers, utilities, and integrators to develop and evaluate their technology or configuration at full power before implementation - something only possible at a handful of facilities in the world.

Development of an Integrated Process, Modeling and Simulation Platform for Performance-Based Design of Low-Energy and High IEQ Buildings

ERIC Educational Resources Information Center

Chen, Yixing

2013-01-01

The objective of this study was to develop a "Virtual Design Studio (VDS)": a software platform for integrated, coordinated and optimized design of green building systems with low energy consumption, high indoor environmental quality (IEQ), and high level of sustainability. The VDS is intended to assist collaborating architects,…

Department of the Army Justification of Estimates for Fiscal Year 1983 Submitted to Congress February 1982. Part 3 (Weapons & Tracked Combat Vehicles).

DTIC Science & Technology

1982-02-01

of 130 kits for the Fire Support Teem Vehicle, an integrated system platform which will provide under - armor protection for the ground laser locator...procureuent of 495 kits for the Fire Support Team Vehicles, an integrated system platform which will provide under - armor protection for the Ground Laser

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

The mid-IR silicon photonics sensor platform (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kimerling, Lionel; Hu, Juejun; Agarwal, Anuradha M.

2017-02-01

Advances in integrated silicon photonics are enabling highly connected sensor networks that offer sensitivity, selectivity and pattern recognition. Cost, performance and the evolution path of the so-called `Internet of Things' will gate the proliferation of these networks. The wavelength spectral range of 3-8um, commonly known as the mid-IR, is critical to specificity for sensors that identify materials by detection of local vibrational modes, reflectivity and thermal emission. For ubiquitous sensing applications in this regime, the sensors must move from premium to commodity level manufacturing volumes and cost. Scaling performance/cost is critically dependent on establishing a minimum set of platform attributes for point, wearable, and physical sensing. Optical sensors are ideal for non-invasive applications. Optical sensor device physics involves evanescent or intra-cavity structures for applied to concentration, interrogation and photo-catalysis functions. The ultimate utility of a platform is dependent on sample delivery/presentation modalities; system reset, recalibration and maintenance capabilities; and sensitivity and selectivity performance. The attributes and performance of a unified Glass-on-Silicon platform has shown good prospects for heterogeneous integration on materials and devices using a low cost process flow. Integrated, single mode, silicon photonic platforms offer significant performance and cost advantages, but they require discovery and qualification of new materials and process integration schemes for the mid-IR. Waveguide integrated light sources based on rare earth dopants and Ge-pumped frequency combs have promise. Optical resonators and waveguide spirals can enhance sensitivity. PbTe materials are among the best choices for a standard, waveguide integrated photodetector. Chalcogenide glasses are capable of transmitting mid-IR signals with high transparency. Integrated sensor case studies of i) high sensitivity analyte detection in solution; ii) gas sensing in air and iii) on-chip spectrometry provide good insight into the tradeoffs being made en route to ubiquitous sensor deployment in an Internet of Things.

Integrated Power, Avionics, and Software (iPAS) Space Telecommunications Radio System (STRS) Radio User's Guide -- Advanced Exploration Systems (AES)

NASA Technical Reports Server (NTRS)

Roche, Rigoberto; Shalkhauser, Mary Jo Windmille

2017-01-01

The Integrated Power, Avionics and Software (IPAS) software defined radio (SDR) was implemented on the Reconfigurable, Intelligently-Adaptive Communication System (RAICS) platform, for radio development at NASA Johnson Space Center. Software and hardware description language (HDL) code were delivered by NASA Glenn Research Center for use in the IPAS test bed and for development of their own Space Telecommunications Radio System (STRS) waveforms on the RAICS platform. The purpose of this document is to describe how to setup and operate the IPAS STRS Radio platform with its delivered test waveform.

Monolithic integration of a silica AWG and Ge photodiodes on Si photonic platform for one-chip WDM receiver.

PubMed

Nishi, Hidetaka; Tsuchizawa, Tai; Kou, Rai; Shinojima, Hiroyuki; Yamada, Takashi; Kimura, Hideaki; Ishikawa, Yasuhiko; Wada, Kazumi; Yamada, Koji

2012-04-09

On the silicon (Si) photonic platform, we monolithically integrated a silica-based arrayed-waveguide grating (AWG) and germanium (Ge) photodiodes (PDs) using low-temperature fabrication technology. We confirmed demultiplexing by the AWG, optical-electrical signal conversion by Ge PDs, and high-speed signal detection at all channels. In addition, we mounted a multichannel transimpedance amplifier/limiting amplifier (TIA/LA) circuit on the fabricated AWG-PD device using flip-chip bonding technology. The results show the promising potential of our Si photonic platform as a photonics-electronics convergence.

Wolfram technologies as an integrated scalable platform for interactive learning

NASA Astrophysics Data System (ADS)

Kaurov, Vitaliy

2012-02-01

We rely on technology profoundly with the prospect of even greater integration in the future. Well known challenges in education are a technology-inadequate curriculum and many software platforms that are difficult to scale or interconnect. We'll review an integrated technology, much of it free, that addresses these issues for individuals and small schools as well as for universities. Topics include: Mathematica, a programming environment that offers a diverse range of functionality; natural language programming for getting started quickly and accessing data from Wolfram|Alpha; quick and easy construction of interactive courseware and scientific applications; partnering with publishers to create interactive e-textbooks; course assistant apps for mobile platforms; the computable document format (CDF); teacher-student and student-student collaboration on interactive projects and web publishing at the Wolfram Demonstrations site.

Effect of microculture on cell metabolism and biochemistry: do cells get stressed in microchannels?

PubMed

Su, Xiaojing; Theberge, Ashleigh B; January, Craig T; Beebe, David J

2013-02-05

Microfluidics is emerging as a promising platform for cell culture, enabling increased microenvironment control and potential for integrated analysis compared to conventional macroculture systems such as well plates and Petri dishes. To advance the use of microfluidic devices for cell culture, it is necessary to better understand how miniaturization affects cell behavior. In particular, microfluidic devices have significantly higher surface-area-to-volume ratios than conventional platforms, resulting in lower volumes of media per cell, which can lead to cell stress. We investigated cell stress under a variety of culture conditions using three cell lines: parental HEK (human embryonic kidney) cells and transfected HEK cells that stably express wild-type (WT) and mutant (G601S) human ether-a-go-go related gene (hERG) potassium channel protein. These three cell lines provide a unique model system through which to study cell-type-specific responses in microculture because mutant hERG is known to be sensitive to environmental conditions, making its expression a particularly sensitive readout through which to compare macro- and microculture. While expression of WT-hERG was similar in microchannel and well culture, the expression of mutant G601S-hERG was reduced in microchannels. Expression of the endoplasmic reticulum (ER) stress marker immunoglobulin binding protein (BiP) was upregulated in all three cell lines in microculture. Using BiP expression, glucose consumption, and lactate accumulation as readouts we developed methods for reducing ER stress including properly increasing the frequency of media replacement, reducing cell seeding density, and adjusting the serum concentration and buffering capacity of culture medium. Indeed, increasing the buffering capacity of culture medium or frequency of media replacement partially restored the expression of the G601S-hERG in microculture. This work illuminates how biochemical properties of cells differ in macro- and microculture and suggests strategies that can be used to modify cell culture protocols for future studies involving miniaturized culture platforms.

Lectindb: a plant lectin database.

PubMed

Chandra, Nagasuma R; Kumar, Nirmal; Jeyakani, Justin; Singh, Desh Deepak; Gowda, Sharan B; Prathima, M N

2006-10-01

Lectins, a class of carbohydrate-binding proteins, are now widely recognized to play a range of crucial roles in many cell-cell recognition events triggering several important cellular processes. They encompass different members that are diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities, and specificities as well as their larger biological roles and potential applications. It is not surprising, therefore, that the vast amount of experimental data on lectins available in the literature is so diverse, that it becomes difficult and time consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. To achieve an effective use of all the data toward understanding the function and their possible applications, an organization of these seemingly independent data into a common framework is essential. An integrated knowledge base ( Lectindb, http://nscdb.bic.physics.iisc.ernet.in ) together with appropriate analytical tools has therefore been developed initially for plant lectins by collating and integrating diverse data. The database has been implemented using MySQL on a Linux platform and web-enabled using PERL-CGI and Java tools. Data for each lectin pertain to taxonomic, biochemical, domain architecture, molecular sequence, and structural details as well as carbohydrate and hence blood group specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value not only for basic studies in lectin biology but also for basic studies in pursuing several applications in biotechnology, immunology, and clinical practice, using these molecules.

Direct assembling methodologies for high-throughput bioscreening

PubMed Central

Rodríguez-Dévora, Jorge I.; Shi, Zhi-dong; Xu, Tao

2012-01-01

Over the last few decades, high-throughput (HT) bioscreening, a technique that allows rapid screening of biochemical compound libraries against biological targets, has been widely used in drug discovery, stem cell research, development of new biomaterials, and genomics research. To achieve these ambitions, scaffold-free (or direct) assembly of biological entities of interest has become critical. Appropriate assembling methodologies are required to build an efficient HT bioscreening platform. The development of contact and non-contact assembling systems as a practical solution has been driven by a variety of essential attributes of the bioscreening system, such as miniaturization, high throughput, and high precision. The present article reviews recent progress on these assembling technologies utilized for the construction of HT bioscreening platforms. PMID:22021162

The Paris-Sud yeast structural genomics pilot-project: from structure to function.

PubMed

Quevillon-Cheruel, Sophie; Liger, Dominique; Leulliot, Nicolas; Graille, Marc; Poupon, Anne; Li de La Sierra-Gallay, Inès; Zhou, Cong-Zhao; Collinet, Bruno; Janin, Joël; Van Tilbeurgh, Herman

2004-01-01

We present here the outlines and results from our yeast structural genomics (YSG) pilot-project. A lab-scale platform for the systematic production and structure determination is presented. In order to validate this approach, 250 non-membrane proteins of unknown structure were targeted. Strategies and final statistics are evaluated. We finally discuss the opportunity of structural genomics programs to contribute to functional biochemical annotation.

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

PubMed

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

2008-03-01

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

Providing a Platform for Parents? Exploring the Nature of Parental Engagement with School Learning Platforms

ERIC Educational Resources Information Center

Selwyn, N.; Banaji, S.; Hadjithoma-Garstka, C.; Clark, W.

2011-01-01

This paper investigates how schools are supporting parents' involvement with their children's education through the use of "Learning Platform" technologies--i.e. the integrated use of virtual learning environments, management information systems, communications, and other information and resource-sharing technologies. Based on in-depth…

Cloud-Based Speech Technology for Assistive Technology Applications (CloudCAST).

PubMed

Cunningham, Stuart; Green, Phil; Christensen, Heidi; Atria, José Joaquín; Coy, André; Malavasi, Massimiliano; Desideri, Lorenzo; Rudzicz, Frank

2017-01-01

The CloudCAST platform provides a series of speech recognition services that can be integrated into assistive technology applications. The platform and the services provided by the public API are described. Several exemplar applications have been developed to demonstrate the platform to potential developers and users.

Incorporating extrinsic noise into the stochastic simulation of biochemical reactions: A comparison of approaches

NASA Astrophysics Data System (ADS)

Thanh, Vo Hong; Marchetti, Luca; Reali, Federico; Priami, Corrado

2018-02-01

The stochastic simulation algorithm (SSA) has been widely used for simulating biochemical reaction networks. SSA is able to capture the inherently intrinsic noise of the biological system, which is due to the discreteness of species population and to the randomness of their reciprocal interactions. However, SSA does not consider other sources of heterogeneity in biochemical reaction systems, which are referred to as extrinsic noise. Here, we extend two simulation approaches, namely, the integration-based method and the rejection-based method, to take extrinsic noise into account by allowing the reaction propensities to vary in time and state dependent manner. For both methods, new efficient implementations are introduced and their efficiency and applicability to biological models are investigated. Our numerical results suggest that the rejection-based method performs better than the integration-based method when the extrinsic noise is considered.

Waveform Developer's Guide for the Integrated Power, Avionics, and Software (iPAS) Space Telecommunications Radio System (STRS) Radio

NASA Technical Reports Server (NTRS)

Shalkhauser, Mary Jo W.; Roche, Rigoberto

2017-01-01

The Space Telecommunications Radio System (STRS) provides a common, consistent framework for software defined radios (SDRs) to abstract the application software from the radio platform hardware. The STRS standard aims to reduce the cost and risk of using complex, configurable and reprogrammable radio systems across NASA missions. To promote the use of the STRS architecture for future NASA advanced exploration missions, NASA Glenn Research Center (GRC) developed an STRS-compliant SDR on a radio platform used by the Advance Exploration System program at the Johnson Space Center (JSC) in their Integrated Power, Avionics, and Software (iPAS) laboratory. The iPAS STRS Radio was implemented on the Reconfigurable, Intelligently-Adaptive Communication System (RIACS) platform, currently being used for radio development at JSC. The platform consists of a Xilinx(Trademark) ML605 Virtex(Trademark)-6 FPGA board, an Analog Devices FMCOMMS1-EBZ RF transceiver board, and an Embedded PC (Axiomtek(Trademark) eBox 620-110-FL) running the Ubuntu 12.4 operating system. The result of this development is a very low cost STRS compliant platform that can be used for waveform developments for multiple applications. The purpose of this document is to describe how to develop a new waveform using the RIACS platform and the Very High Speed Integrated Circuits (VHSIC) Hardware Description Language (VHDL) FPGA wrapper code and the STRS implementation on the Axiomtek processor.

Design of the Hospital Integrated Information Management System Based on Cloud Platform.

PubMed

Aijing, L; Jin, Y

2015-12-01

At present, the outdated information management style cannot meet the needs of hospital management, and has become the bottleneck of hospital's management and development. In order to improve the integrated management of information, hospitals have increased their investment in integrated information management systems. On account of the lack of reasonable and scientific design, some hospital integrated information management systems have common problems, such as unfriendly interface, poor portability and maintainability, low security and efficiency, lack of interactivity and information sharing. To solve the problem, this paper carries out the research and design of a hospital information management system based on cloud platform, which can realize the optimized integration of hospital information resources and save money.

Optofluidic lasers with a single molecular layer of gain

PubMed Central

Chen, Qiushu; Ritt, Michael; Sivaramakrishnan, Sivaraj; Sun, Yuze; Fan, Xudong

2014-01-01

We achieve optofluidic lasers with a single molecular layer of gain, in which green fluorescent protein, dye-labeled bovine serum albumin, and dye-labeled DNA are respectively used as the gain medium and attached to the surface of a ring resonator via surface immobilization biochemical methods. It is estimated that the surface density of the gain molecules is on the order of 1012/cm2, sufficient for lasing under pulsed optical excitation. It is further shown that the optofluidic laser can be tuned by energy transfer mechanisms through biomolecular interactions. This work not only opens a door to novel photonic devices that can be controlled at the level of a single molecular layer, but also provides a promising sensing platform to analyze biochemical processes at the solid-liquid interface. PMID:25312306

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.

From NHS Choices to the integrated customer service platform.

PubMed

Gann, Bob; Grant, Maria J

2013-03-01

In 2013 the NHS Commissioning Board launches its new integrated customer service platform. The new service utilises the full range of channels (web, telephone, apps etc) to provide access to information to support transparency, participation and transactions. Digital health services have proven benefits in informed choice, shared decision making and patient participation. © 2013 The authors. Health Information and Libraries Journal © 2013 Health Libraries Group.

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

DTIC Science & Technology

2001-10-25

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

Punch Card Programmable Microfluidics

PubMed Central

Korir, George; Prakash, Manu

2015-01-01

Small volume fluid handling in single and multiphase microfluidics provides a promising strategy for efficient bio-chemical assays, low-cost point-of-care diagnostics and new approaches to scientific discoveries. However multiple barriers exist towards low-cost field deployment of programmable microfluidics. Incorporating multiple pumps, mixers and discrete valve based control of nanoliter fluids and droplets in an integrated, programmable manner without additional required external components has remained elusive. Combining the idea of punch card programming with arbitrary fluid control, here we describe a self-contained, hand-crank powered, multiplex and robust programmable microfluidic platform. A paper tape encodes information as a series of punched holes. A mechanical reader/actuator reads these paper tapes and correspondingly executes operations onto a microfluidic chip coupled to the platform in a plug-and-play fashion. Enabled by the complexity of codes that can be represented by a series of holes in punched paper tapes, we demonstrate independent control of 15 on-chip pumps with enhanced mixing, normally-closed valves and a novel on-demand impact-based droplet generator. We demonstrate robustness of operation by encoding a string of characters representing the word “PUNCHCARD MICROFLUIDICS” using the droplet generator. Multiplexing is demonstrated by implementing an example colorimetric water quality assays for pH, ammonia, nitrite and nitrate content in different water samples. With its portable and robust design, low cost and ease-of-use, we envision punch card programmable microfluidics will bring complex control of microfluidic chips into field-based applications in low-resource settings and in the hands of children around the world. PMID:25738834

Punch card programmable microfluidics.

PubMed

Korir, George; Prakash, Manu

2015-01-01

Small volume fluid handling in single and multiphase microfluidics provides a promising strategy for efficient bio-chemical assays, low-cost point-of-care diagnostics and new approaches to scientific discoveries. However multiple barriers exist towards low-cost field deployment of programmable microfluidics. Incorporating multiple pumps, mixers and discrete valve based control of nanoliter fluids and droplets in an integrated, programmable manner without additional required external components has remained elusive. Combining the idea of punch card programming with arbitrary fluid control, here we describe a self-contained, hand-crank powered, multiplex and robust programmable microfluidic platform. A paper tape encodes information as a series of punched holes. A mechanical reader/actuator reads these paper tapes and correspondingly executes operations onto a microfluidic chip coupled to the platform in a plug-and-play fashion. Enabled by the complexity of codes that can be represented by a series of holes in punched paper tapes, we demonstrate independent control of 15 on-chip pumps with enhanced mixing, normally-closed valves and a novel on-demand impact-based droplet generator. We demonstrate robustness of operation by encoding a string of characters representing the word "PUNCHCARD MICROFLUIDICS" using the droplet generator. Multiplexing is demonstrated by implementing an example colorimetric water quality assays for pH, ammonia, nitrite and nitrate content in different water samples. With its portable and robust design, low cost and ease-of-use, we envision punch card programmable microfluidics will bring complex control of microfluidic chips into field-based applications in low-resource settings and in the hands of children around the world.

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.

PubMed

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. This database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

Design distributed simulation platform for vehicle management system

NASA Astrophysics Data System (ADS)

Wen, Zhaodong; Wang, Zhanlin; Qiu, Lihua

2006-11-01

Next generation military aircraft requires the airborne management system high performance. General modules, data integration, high speed data bus and so on are needed to share and manage information of the subsystems efficiently. The subsystems include flight control system, propulsion system, hydraulic power system, environmental control system, fuel management system, electrical power system and so on. The unattached or mixed architecture is changed to integrated architecture. That means the whole airborne system is regarded into one system to manage. So the physical devices are distributed but the system information is integrated and shared. The process function of each subsystem are integrated (including general process modules, dynamic reconfiguration), furthermore, the sensors and the signal processing functions are shared. On the other hand, it is a foundation for power shared. Establish a distributed vehicle management system using 1553B bus and distributed processors which can provide a validation platform for the research of airborne system integrated management. This paper establishes the Vehicle Management System (VMS) simulation platform. Discuss the software and hardware configuration and analyze the communication and fault-tolerant method.

Current and Developing Technologies for Monitoring Agents of Bioterrorism and Biowarfare

PubMed Central

Lim, Daniel V.; Simpson, Joyce M.; Kearns, Elizabeth A.; Kramer, Marianne F.

2005-01-01

Recent events have made public health officials acutely aware of the importance of rapidly and accurately detecting acts of bioterrorism. Because bioterrorism is difficult to predict or prevent, reliable platforms to rapidly detect and identify biothreat agents are important to minimize the spread of these agents and to protect the public health. These platforms must not only be sensitive and specific, but must also be able to accurately detect a variety of pathogens, including modified or previously uncharacterized agents, directly from complex sample matrices. Various commercial tests utilizing biochemical, immunological, nucleic acid, and bioluminescence procedures are currently available to identify biological threat agents. Newer tests have also been developed to identify such agents using aptamers, biochips, evanescent wave biosensors, cantilevers, living cells, and other innovative technologies. This review describes these current and developing technologies and considers challenges to rapid, accurate detection of biothreat agents. Although there is no ideal platform, many of these technologies have proved invaluable for the detection and identification of biothreat agents. PMID:16223949

Label-Free Discovery Array Platform for the Characterization of Glycan Binding Proteins and Glycoproteins.

PubMed

Gray, Christopher J; Sánchez-Ruíz, Antonio; Šardzíková, Ivana; Ahmed, Yassir A; Miller, Rebecca L; Reyes Martinez, Juana E; Pallister, Edward; Huang, Kun; Both, Peter; Hartmann, Mirja; Roberts, Hannah N; Šardzík, Robert; Mandal, Santanu; Turnbull, Jerry E; Eyers, Claire E; Flitsch, Sabine L

2017-04-18

The identification of carbohydrate-protein interactions is central to our understanding of the roles of cell-surface carbohydrates (the glycocalyx), fundamental for cell-recognition events. Therefore, there is a need for fast high-throughput biochemical tools to capture the complexity of these biological interactions. Here, we describe a rapid method for qualitative label-free detection of carbohydrate-protein interactions on arrays of simple synthetic glycans, more complex natural glycosaminoglycans (GAG), and lectins/carbohydrate binding proteins using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The platform can unequivocally identify proteins that are captured from either purified or complex sample mixtures, including biofluids. Identification of proteins bound to the functionalized array is achieved by analyzing either the intact protein mass or, after on-chip proteolytic digestion, the peptide mass fingerprint and/or tandem mass spectrometry of selected peptides, which can yield highly diagnostic sequence information. The platform described here should be a valuable addition to the limited analytical toolbox that is currently available for glycomics.

Framework Programmable Platform for the advanced software development workstation: Framework processor design document

NASA Technical Reports Server (NTRS)

Mayer, Richard J.; Blinn, Thomas M.; Mayer, Paula S. D.; Ackley, Keith A.; Crump, Wes; Sanders, Les

1991-01-01

The design of the Framework Processor (FP) component of the Framework Programmable Software Development Platform (FFP) is described. The FFP is a project aimed at combining effective tool and data integration mechanisms with a model of the software development process in an intelligent integrated software development environment. Guided by the model, this Framework Processor will take advantage of an integrated operating environment to provide automated support for the management and control of the software development process so that costly mistakes during the development phase can be eliminated.

REmote SUpervision to Decrease HospitaLization RaTe. Unified and integrated platform for data collected from devices manufactured by different companies: Design and rationale of the RESULT study.

PubMed

Tajstra, Mateusz; Sokal, Adam; Gwóźdź, Arkadiusz; Wilczek, Marcin; Gacek, Adam; Wojciechowski, Konrad; Gadula-Gacek, Elżbieta; Adamowicz-Czoch, Elżbieta; Chłosta-Niepiekło, Katarzyna; Milewski, Krzysztof; Rozentryt, Piotr; Kalarus, Zbigniew; Gąsior, Mariusz; Poloński, Lech

2017-07-01

The number of patients with heart failure implantable cardiac electronic devices (CIEDs) is growing. Hospitalization rate in this group is very high and generates enormous costs. To avoid the need for hospital treatment, optimized monitoring and follow-up is crucial. Remote monitoring (RM) has been widely put into practice in the management of CIEDs but it may be difficult due to the presence of differences in systems provided by device manufacturers and loss of gathered data in case of device reimplantation. Additionally, conclusions derived from studies about usefulness of RM in clinical practice apply to devices coming only from a single company. An integrated monitoring platform allows for more comprehensive data analysis and interpretation. Therefore, the primary objective of Remote Supervision to Decrease Hospitalization Rate (RESULT) study is to evaluate the impact of RM on the clinical status of patients with ICDs or CRT-Ds using an integrated platform. Six hundred consecutive patients with ICDs or CRT-Ds implanted will be prospectively randomized to either a traditional or RM-based follow-up model. The primary clinical endpoint will be a composite of all-cause mortality or hospitalization for cardiovascular reasons within 12 months after randomization. The primary technical endpoint will be to construct and evaluate a unified and integrated platform for the data collected from RM devices manufactured by different companies. This manuscript describes the design and methodology of the prospective, randomized trial designed to determine whether remote monitoring using an integrated platform for different companies is safe, feasible, and efficacious (ClinicalTrials.gov Identifier: NCT02409225). © 2016 Wiley Periodicals, Inc.

Point-of-Care Quantitative Measure of Glucose-6-Phosphate Dehydrogenase Enzyme Deficiency.

PubMed

Bhutani, Vinod K; Kaplan, Michael; Glader, Bertil; Cotten, Michael; Kleinert, Jairus; Pamula, Vamsee

2015-11-01

Widespread newborn screening on a point-of-care basis could prevent bilirubin neurotoxicity in newborns with glucose-6-phosphate dehydrogenase (G6PD) deficiency. We evaluated a quantitative G6PD assay on a digital microfluidic platform by comparing its performance with standard clinical methods. G6PD activity was measured quantitatively by using digital microfluidic fluorescence and the gold standard fluorescence biochemical test on a convenience sample of 98 discarded blood samples. Twenty-four samples were designated as G6PD deficient. Mean ± SD G6PD activity for normal samples using the digital microfluidic method and the standard method, respectively, was 9.7 ± 2.8 and 11.1 ± 3.0 U/g hemoglobin (Hb), respectively; for G6PD-deficient samples, it was 0.8 ± 0.7 and 1.4 ± 0.9 U/g Hb. Bland-Altman analysis determined a mean difference of -0.96 ± 1.8 U/g Hb between the digital microfluidic fluorescence results and the standard biochemical test results. The lower and upper limits for the digital microfluidic platform were 4.5 to 19.5 U/g Hb for normal samples and 0.2 to 3.7 U/g Hb for G6PD-deficient samples. The lower and upper limits for the Stanford method were 5.5 to 20.7 U/g Hb for normal samples and 0.1 to 2.8 U/g Hb for G6PD-deficient samples. The measured activity discriminated between G6PD-deficient samples and normal samples with no overlap. Pending further validation, a digital microfluidics platform could be an accurate point-of-care screening tool for rapid newborn G6PD screening. Copyright © 2015 by the American Academy of Pediatrics.

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

ERIC Educational Resources Information Center

Barak, Miri; Ziv, Shani

2013-01-01

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

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

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

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

Design and Analysis of a Compact Precision Positioning Platform Integrating Strain Gauges and the Piezoactuator

PubMed Central

Huang, Hu; Zhao, Hongwei; Yang, Zhaojun; Fan, Zunqiang; Wan, Shunguang; Shi, Chengli; Ma, Zhichao

2012-01-01

Miniaturization precision positioning platforms are needed for in situ nanomechanical test applications. This paper proposes a compact precision positioning platform integrating strain gauges and the piezoactuator. Effects of geometric parameters of two parallel plates on Von Mises stress distribution as well as static and dynamic characteristics of the platform were studied by the finite element method. Results of the calibration experiment indicate that the strain gauge sensor has good linearity and its sensitivity is about 0.0468 mV/μm. A closed-loop control system was established to solve the problem of nonlinearity of the platform. Experimental results demonstrate that for the displacement control process, both the displacement increasing portion and the decreasing portion have good linearity, verifying that the control system is available. The developed platform has a compact structure but can realize displacement measurement with the embedded strain gauges, which is useful for the closed-loop control and structure miniaturization of piezo devices. It has potential applications in nanoindentation and nanoscratch tests, especially in the field of in situ nanomechanical testing which requires compact structures. PMID:23012566

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

PubMed

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

2017-01-01

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

An integrated compact airborne multispectral imaging system using embedded computer

NASA Astrophysics Data System (ADS)

Zhang, Yuedong; Wang, Li; Zhang, Xuguo

2015-08-01

An integrated compact airborne multispectral imaging system using embedded computer based control system was developed for small aircraft multispectral imaging application. The multispectral imaging system integrates CMOS camera, filter wheel with eight filters, two-axis stabilized platform, miniature POS (position and orientation system) and embedded computer. The embedded computer has excellent universality and expansibility, and has advantages in volume and weight for airborne platform, so it can meet the requirements of control system of the integrated airborne multispectral imaging system. The embedded computer controls the camera parameters setting, filter wheel and stabilized platform working, image and POS data acquisition, and stores the image and data. The airborne multispectral imaging system can connect peripheral device use the ports of the embedded computer, so the system operation and the stored image data management are easy. This airborne multispectral imaging system has advantages of small volume, multi-function, and good expansibility. The imaging experiment results show that this system has potential for multispectral remote sensing in applications such as resource investigation and environmental monitoring.

The Integrity bare-metal stent made by continuous sinusoid technology.

PubMed

Turco, Mark A

2011-05-01

The Integrity Coronary Stent System (Medtronic Vascular, CA, USA) is a low-profile, open-cell, cobalt-chromium-alloy advanced bare-metal iteration of the well-known Driver/Micro-Driver Coronary Stent System (Medtronic Vascular). The Integrity stent is made with a process called continuous sinusoid technology. This process allows stent construction via wrapping a single thin strand of wire around a mandrel in a sinusoid configuration, with laser fusion of adjacent crowns. The wire-forming process and fusion pattern provide the stent with a continuous preferential bending plane, intended to allow easier access to, and smoother tracking within, distal and tortuous vessels while radial strength is maintained. Continuous sinusoid technology represents innovation in the design of stent platforms and will provide a future stent platform for newer technology, including drug-eluting stent platforms, drug-filled stents and core wire stents.

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

PubMed

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

2017-05-01

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

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

NASA Astrophysics Data System (ADS)

Hu, Zunyu

2018-04-01

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

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.

Monolithically Integrated InGaAs Nanowires on 3D Structured Silicon-on-Insulator as a New Platform for Full Optical Links.

PubMed

Kim, Hyunseok; Farrell, Alan C; Senanayake, Pradeep; Lee, Wook-Jae; Huffaker, Diana L

2016-03-09

Monolithically integrated III-V semiconductors on a silicon-on-insulator (SOI) platform can be used as a building block for energy-efficient on-chip optical links. Epitaxial growth of III-V semiconductors on silicon, however, has been challenged by the large mismatches in lattice constants and thermal expansion coefficients between epitaxial layers and silicon substrates. Here, we demonstrate for the first time the monolithic integration of InGaAs nanowires on the SOI platform and its feasibility for photonics and optoelectronic applications. InGaAs nanowires are grown not only on a planar SOI layer but also on a 3D structured SOI layer by catalyst-free metal-organic chemical vapor deposition. The precise positioning of nanowires on 3D structures, including waveguides and gratings, reveals the versatility and practicality of the proposed platform. Photoluminescence measurements exhibit that the composition of ternary InGaAs nanowires grown on the SOI layer has wide tunability covering all telecommunication wavelengths from 1.2 to 1.8 μm. We also show that the emission from an optically pumped single nanowire is effectively coupled and transmitted through an SOI waveguide, explicitly showing that this work lays the foundation for a new platform toward energy-efficient optical links.

Integration of the virtual model of a Stewart platform with the avatar of a vehicle in a virtual reality

NASA Astrophysics Data System (ADS)

Herbuś, K.; Ociepka, P.

2016-08-01

The development of methods of computer aided design and engineering allows conducting virtual tests, among others concerning motion simulation of technical means. The paper presents a method of integrating an object in the form of a virtual model of a Stewart platform with an avatar of a vehicle moving in a virtual environment. The area of the problem includes issues related to the problem of fidelity of mapping the work of the analyzed technical mean. The main object of investigations is a 3D model of a Stewart platform, which is a subsystem of the simulator designated for driving learning for disabled persons. The analyzed model of the platform, prepared for motion simulation, was created in the “Motion Simulation” module of a CAD/CAE class system Siemens PLM NX. Whereas the virtual environment, in which the moves the avatar of the passenger car, was elaborated in a VR class system EON Studio. The element integrating both of the mentioned software environments is a developed application that reads information from the virtual reality (VR) concerning the current position of the car avatar. Then, basing on the accepted algorithm, it sends control signals to respective joints of the model of the Stewart platform (CAD).

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

PubMed Central

2014-01-01

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

REopt: A Platform for Energy System Integration and Optimization: Preprint

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

Simpkins, T.; Cutler, D.; Anderson, K.

2014-08-01

REopt is NREL's energy planning platform offering concurrent, multi-technology integration and optimization capabilities to help clients meet their cost savings and energy performance goals. The REopt platform provides techno-economic decision-support analysis throughout the energy planning process, from agency-level screening and macro planning to project development to energy asset operation. REopt employs an integrated approach to optimizing a site?s energy costs by considering electricity and thermal consumption, resource availability, complex tariff structures including time-of-use, demand and sell-back rates, incentives, net-metering, and interconnection limits. Formulated as a mixed integer linear program, REopt recommends an optimally-sized mix of conventional and renewable energy, andmore » energy storage technologies; estimates the net present value associated with implementing those technologies; and provides the cost-optimal dispatch strategy for operating them at maximum economic efficiency. The REopt platform can be customized to address a variety of energy optimization scenarios including policy, microgrid, and operational energy applications. This paper presents the REopt techno-economic model along with two examples of recently completed analysis projects.« less

Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein

NASA Technical Reports Server (NTRS)

Gaucher, Eric A.; Miyamoto, Michael M.; Benner, Steven A.

2003-01-01

The Leptin protein is central to the regulation of energy metabolism in mammals. By integrating evolutionary, structural, and biochemical information, a surface segment, outside of its known receptor contacts, is predicted as a second interaction site that may help to further define its roles in energy balance and its functional differences between humans and other mammals.

Supporting Crop Loss Insurance Policy of Indonesia through Rice Yield Modelling and Forecasting

NASA Astrophysics Data System (ADS)

van Verseveld, Willem; Weerts, Albrecht; Trambauer, Patricia; de Vries, Sander; Conijn, Sjaak; van Valkengoed, Eric; Hoekman, Dirk; Grondard, Nicolas; Hengsdijk, Huib; Schrevel, Aart; Vlasbloem, Pieter; Klauser, Dominik

2017-04-01

The Government of Indonesia has decided on a crop insurance policy to assist Indonesia's farmers and to boost food security. To support the Indonesian government, the G4INDO project (www.g4indo.org) is developing/constructing an integrated platform implemented in the Delft-FEWS forecasting system (Werner et al., 2013). The integrated platform brings together remote sensed data (both visible and radar) and hydrologic, crop and reservoir modelling and forecasting to improve the modelling and forecasting of rice yield. The hydrological model (wflow_sbm), crop model (wflow_lintul) and reservoir models (RTC-Tools) are coupled on time stepping basis in the OpenStreams framework (see https://github.com/openstreams/wflow) and deployed in the integrated platform to support seasonal forecasting of water availability and crop yield. First we will show the general idea about the G4INDO project, the integrated platform (including Sentinel 1 & 2 data) followed by first (reforecast) results of the coupled models for predicting water availability and crop yield in the Brantas catchment in Java, Indonesia. Werner, M., Schellekens, J., Gijsbers, P., Van Dijk, M., Van den Akker, O. and Heynert K, 2013. The Delft-FEWS flow forecasting system, Environmental Modelling & Software; 40:65-77. DOI: 10.1016/j.envsoft.2012.07.010.

Automated microfluidic platform of bead-based electrochemical immunosensor integrated with bioreactor for continual monitoring of cell secreted biomarkers

NASA Astrophysics Data System (ADS)

Riahi, Reza; Shaegh, Seyed Ali Mousavi; Ghaderi, Masoumeh; Zhang, Yu Shrike; Shin, Su Ryon; Aleman, Julio; Massa, Solange; Kim, Duckjin; Dokmeci, Mehmet Remzi; Khademhosseini, Ali

2016-04-01

There is an increasing interest in developing microfluidic bioreactors and organs-on-a-chip platforms combined with sensing capabilities for continual monitoring of cell-secreted biomarkers. Conventional approaches such as ELISA and mass spectroscopy cannot satisfy the needs of continual monitoring as they are labor-intensive and not easily integrable with low-volume bioreactors. This paper reports on the development of an automated microfluidic bead-based electrochemical immunosensor for in-line measurement of cell-secreted biomarkers. For the operation of the multi-use immunosensor, disposable magnetic microbeads were used to immobilize biomarker-recognition molecules. Microvalves were further integrated in the microfluidic immunosensor chip to achieve programmable operations of the immunoassay including bead loading and unloading, binding, washing, and electrochemical sensing. The platform allowed convenient integration of the immunosensor with liver-on-chips to carry out continual quantification of biomarkers secreted from hepatocytes. Transferrin and albumin productions were monitored during a 5-day hepatotoxicity assessment in which human primary hepatocytes cultured in the bioreactor were treated with acetaminophen. Taken together, our unique microfluidic immunosensor provides a new platform for in-line detection of biomarkers in low volumes and long-term in vitro assessments of cellular functions in microfluidic bioreactors and organs-on-chips.

Automated microfluidic platform of bead-based electrochemical immunosensor integrated with bioreactor for continual monitoring of cell secreted biomarkers

PubMed Central

Riahi, Reza; Shaegh, Seyed Ali Mousavi; Ghaderi, Masoumeh; Zhang, Yu Shrike; Shin, Su Ryon; Aleman, Julio; Massa, Solange; Kim, Duckjin; Dokmeci, Mehmet Remzi; Khademhosseini, Ali

2016-01-01

There is an increasing interest in developing microfluidic bioreactors and organs-on-a-chip platforms combined with sensing capabilities for continual monitoring of cell-secreted biomarkers. Conventional approaches such as ELISA and mass spectroscopy cannot satisfy the needs of continual monitoring as they are labor-intensive and not easily integrable with low-volume bioreactors. This paper reports on the development of an automated microfluidic bead-based electrochemical immunosensor for in-line measurement of cell-secreted biomarkers. For the operation of the multi-use immunosensor, disposable magnetic microbeads were used to immobilize biomarker-recognition molecules. Microvalves were further integrated in the microfluidic immunosensor chip to achieve programmable operations of the immunoassay including bead loading and unloading, binding, washing, and electrochemical sensing. The platform allowed convenient integration of the immunosensor with liver-on-chips to carry out continual quantification of biomarkers secreted from hepatocytes. Transferrin and albumin productions were monitored during a 5-day hepatotoxicity assessment in which human primary hepatocytes cultured in the bioreactor were treated with acetaminophen. Taken together, our unique microfluidic immunosensor provides a new platform for in-line detection of biomarkers in low volumes and long-term in vitro assessments of cellular functions in microfluidic bioreactors and organs-on-chips. PMID:27098564

Integrating cell on chip—Novel waveguide platform employing ultra-long optical paths

NASA Astrophysics Data System (ADS)

Fohrmann, Lena Simone; Sommer, Gerrit; Pitruzzello, Giampaolo; Krauss, Thomas F.; Petrov, Alexander Yu.; Eich, Manfred

2017-09-01

Optical waveguides are the most fundamental building blocks of integrated optical circuits. They are extremely well understood, yet there is still room for surprises. Here, we introduce a novel 2D waveguide platform which affords a strong interaction of the evanescent tail of a guided optical wave with an external medium while only employing a very small geometrical footprint. The key feature of the platform is its ability to integrate the ultra-long path lengths by combining low propagation losses in a silicon slab with multiple reflections of the guided wave from photonic crystal (PhC) mirrors. With a reflectivity of 99.1% of our tailored PhC-mirrors, we achieve interaction paths of 25 cm within an area of less than 10 mm2. This corresponds to 0.17 dB/cm effective propagation which is much lower than the state-of-the-art loss of approximately 1 dB/cm of single mode silicon channel waveguides. In contrast to conventional waveguides, our 2D-approach leads to a decay of the guided wave power only inversely proportional to the optical path length. This entirely different characteristic is the major advantage of the 2D integrating cell waveguide platform over the conventional channel waveguide concepts that obey the Beer-Lambert law.

Design of the Hospital Integrated Information Management System Based on Cloud Platform

PubMed Central

Aijing, L; Jin, Y

2015-01-01

ABSTRACT At present, the outdated information management style cannot meet the needs of hospital management, and has become the bottleneck of hospital's management and development. In order to improve the integrated management of information, hospitals have increased their investment in integrated information management systems. On account of the lack of reasonable and scientific design, some hospital integrated information management systems have common problems, such as unfriendly interface, poor portability and maintainability, low security and efficiency, lack of interactivity and information sharing. To solve the problem, this paper carries out the research and design of a hospital information management system based on cloud platform, which can realize the optimized integration of hospital information resources and save money. PMID:27399033

Computational toxicology using the OpenTox application programming interface and Bioclipse

PubMed Central

2011-01-01

Background Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications. Findings This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources. Conclusions A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers. PMID:22075173

EPOS Thematic Core Service ANTHROPOGENIC HAZARDS (TCS AH) - development of e-research platform

NASA Astrophysics Data System (ADS)

Orlecka-Sikora, Beata

2017-04-01

TCS AH is based on IS-EPOS Platform. The Platform facilitates research on anthropogenic hazards and is available online, free of charge https://tcs.ah-epos.eu/. The Platform is a final product of the IS-EPOS project, founded by the national programme - POIG - which was implemented in 2013-2015 (POIG.02.03.00-14-090/13-00). The platform is a result of a joint work of scientific community and industrial partners. Currently, the development of TCS AH is carried under EPOS IP project (H2020-INFRADEV-1-2015-1, INFRADEV-3-2015). Platform is an open virtual access point for researchers and Ph. D. students interested in anthropogenic seismicity and related hazards. This environment is designed to ensure a researcher the maximum possible liberty for experimentation by providing a virtual laboratory, in which the researcher can design own processing streams and process the data integrated on the platform. TCS AH integrates: data and specific high-level services. Data gathered in the so-called "episodes", comprehensively describing a geophysical process, induced or triggered by human technological activity, which, under certain circumstances can become hazardous for people, infrastructure and the environment. 7 sets of seismic, geological and technological data were made available on the Platform. The data come from Poland, Germany, UK and Vietnam, and refer to underground mining, reservoir impoundment, shale gas exploitation and geothermal energy production. The next at least 19 new episodes related to conventional hydrocarbon extraction, reservoir treatment, underground mining and geothermal energy production are being integrated within the framework of EPOS IP project. The heterogeneous multi-disciplinary data (seismic, displacement, geomechanical data, production data etc.) are transformed to unified structures to form integrated and validated datasets. To deal with this various data the problem-oriented services were designed and implemented. The particular attention devoted to methods analyzing correlations between technology, geophysical response and resulting hazard was stressed out in service preparation. TCS AH contains a number of computing and data visualization services, which give opportunity to make graphical presentations of the available data. Further development of the Platform, except integration of at least new episodes of all types of anthropogenic hazards, will be covering gradually implementation of new services. TCS AH platform is open for the whole research community. The platform is also designated to be used in research projects, eg. it serves "Shale gas exploration and exploitation induced risks (SHEER)" project (Horizon 2020, call LCE 16-2014). In addition, it is also meant to serve the public sector expert knowledge and background information. In order to fulfill this aim the services for outreach, dissemination & communication will be implemented. TCS AH was used as a teaching tool in Ph. D. students education within IG PAS seismology course for Ph. D. candidates, Interdisciplinary Polar Studies as well as in several workshops for Polish and international students. Additionally, the platform is also used within educational project ERIS (Exploitation of Research results In School practice) aimed for junior high and high schools, funded with support from the European Commission within ERASMUS+ Programme.

Improving Satellite Compatible Microdevices to Study Biology in Space

NASA Technical Reports Server (NTRS)

Kalkus, Trevor; Snyder, Jessica; Paulino-Lima, Ivan; Rothschild, Lynn

2017-01-01

The technology for biology in space lags far behind the gold standard for biological experiments on Earth. To remedy this disparity, the Rothschild lab works on proof of concept, prototyping, and developing of new sensors and devices to further the capabilities of biology research on satellites. One such device is the PowerCell Payload System. One goal for synthetic biology in aiding space travel and colonization is to genetically engineer living cells to produce biochemicals in space. However, such farming in space presupposes bacteria retain their functionality post-launch, bombarded by radiation, and without the 1G of Earth. Our questions is, does a co-culture of cyanobacteria and protein-synthesizing bacteria produce Earth-like yields of target proteins? Is the yield sensitive to variable gravitational forces? To answer these questions, a PowerCell Payload System will spend 1 year aboard the German Aerospace Center's Euglena and Combined Regenerative Organic-food Production In Space (Eu:CROPIS) mission satellite. The PowerCell system is a pair of two 48-well microfluidic cards, each well seeded with bacteria. The system integrates fluidic, thermal, optical, electronic, and control systems to germinate bacteria spores, then measure the protein synthesized for comparison to parallel experiments conducted on the Earth. In developing the PowerCell Payload, we gained insight into the shortcomings of biology experiments on satellites. To address these issues, we have started three new prototyping projects: 1) The development of an extremely stable and radiation resistant cell-free system, allowing for the construction of proteins utilizing only cell components instead of living cells. This can be lyophilized on a substrate, like paper. (2) Using paper as a microfluidic platform that is flexible, stable, cheap, and wicking. The capillary action eliminates the need for pumps, reducing volume, mass, and potential failing points. Electrodes can be printed on the paper to sense for biochemicals. (3) Developing a modular, semi-autonomous microfluidic device that can be easily adapted for a variety of common biological experiments. This versatility will allow for quicker and cheaper experimentation. These improvements to satellite experiment platforms have the potential to radically increase the return from NASA's biological and field studies with reduced development time, mass, and cost with increased robustness data and interpretation.

CSDC: a nationwide screening platform for stroke control and prevention in China.

PubMed

Jinghui Yu; Huajian Mao; Mei Li; Dan Ye; Dongsheng Zhao

2016-08-01

As a leading cause of severe disability and death, stroke places an enormous burden on Chinese society. A nationwide stroke screening platform called CSDC (China Stoke Data Center) has been built to support the national stroke prevention program and stroke clinical research since 2011. This platform is composed of a data integration system and a big data analysis system. The data integration system is used to collect information on risk factors, diagnosis history, treatment, and sociodemographic characteristics and stroke patients' EMR. The big data analysis system support decision making of stroke control and prevention, clinical evaluation and research. In this paper, the design and implementation of CSDC are illustrated, and some application results are presented. This platform is expected to provide rich data and powerful tool support for stroke control and prevention in China.

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.

Low-loss compact multilayer silicon nitride platform for 3D photonic integrated circuits.

PubMed

Shang, Kuanping; Pathak, Shibnath; Guan, Binbin; Liu, Guangyao; Yoo, S J B

2015-08-10

We design, fabricate, and demonstrate a silicon nitride (Si(3)N(4)) multilayer platform optimized for low-loss and compact multilayer photonic integrated circuits. The designed platform, with 200 nm thick waveguide core and 700 nm interlayer gap, is compatible for active thermal tuning and applicable to realizing compact photonic devices such as arrayed waveguide gratings (AWGs). We achieve ultra-low loss vertical couplers with 0.01 dB coupling loss, multilayer crossing loss of 0.167 dB at 90° crossing angle, 50 μm bending radius, 100 × 2 μm(2) footprint, lateral misalignment tolerance up to 400 nm, and less than -52 dB interlayer crosstalk at 1550 nm wavelength. Based on the designed platform, we demonstrate a 27 × 32 × 2 multilayer star coupler.

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.

The Mobile Aircraft Maintenance Office Concept from a Wide Area Perspective

DTIC Science & Technology

2003-03-01

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

Can the Integration of a PLE in an E-Portfolio Platform Improve Generic Competences?

ERIC Educational Resources Information Center

Galván-Fernández, Cristina; Rubio-Hurtado, María José; Martínez-Olmo, Francesc; Rodríguez-Illera, José Luis

2017-01-01

The study analyzes the improvement in generic competences through e-portfolio/PLE platform and didactic planning. The new version of the platform, Digital Folder, contains utilities for students and teachers and some PLE components that help the learning process through e-portfolios. Didactic planning is compared for students from the University…

Microfluidic in-channel multi-electrode platform for neurotransmitter sensing

NASA Astrophysics Data System (ADS)

Kara, A.; Mathault, J.; Reitz, A.; Boisvert, M.; Tessier, F.; Greener, J.; Miled, A.

2016-03-01

In this project we present a microfluidic platform with in-channel micro-electrodes for in situ screening of bio/chemical samples through a lab-on-chip system. We used a novel method to incorporate electrochemical sensors array (16x20) connected to a PCB, which opens the way for imaging applications. A 200 μm height microfluidic channel was bonded to electrochemical sensors. The micro-channel contains 3 inlets used to introduce phosphate buffer saline (PBS), ferrocynide and neurotransmitters. The flow rate was controlled through automated micro-pumps. A multiplexer was used to scan electrodes and perform individual cyclic voltammograms by a custom potentiostat. The behavior of the system was linear in terms of variation of current versus concentration. It was used to detect the neurotransmitters serotonin, dopamine and glutamate.

Payao: a community platform for SBML pathway model curation

PubMed Central

Matsuoka, Yukiko; Ghosh, Samik; Kikuchi, Norihiro; Kitano, Hiroaki

2010-01-01

Summary: Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation. The system combines Web 2.0 technologies and online model visualization functions to enable a collaborative community to annotate and curate biological models. Payao reads the models in Systems Biology Markup Language format, displays them with CellDesigner, a process diagram editor, which complies with the Systems Biology Graphical Notation, and provides an interface for model enrichment (adding tags and comments to the models) for the access-controlled community members. Availability and implementation: Freely available for model curation service at http://www.payaologue.org. Web site implemented in Seaser Framework 2.0 with S2Flex2, MySQL 5.0 and Tomcat 5.5, with all major browsers supported. Contact: kitano@sbi.jp PMID:20371497

Understanding sequence similarity and framework analysis between centromere proteins using computational biology.

PubMed

Doss, C George Priya; Chakrabarty, Chiranjib; Debajyoti, C; Debottam, S

2014-11-01

Certain mysteries pointing toward their recruitment pathways, cell cycle regulation mechanisms, spindle checkpoint assembly, and chromosome segregation process are considered the centre of attraction in cancer research. In modern times, with the established databases, ranges of computational platforms have provided a platform to examine almost all the physiological and biochemical evidences in disease-associated phenotypes. Using existing computational methods, we have utilized the amino acid residues to understand the similarity within the evolutionary variance of different associated centromere proteins. This study related to sequence similarity, protein-protein networking, co-expression analysis, and evolutionary trajectory of centromere proteins will speed up the understanding about centromere biology and will create a road map for upcoming researchers who are initiating their work of clinical sequencing using centromere proteins.

Integrated long-range UAV/UGV collaborative target tracking

NASA Astrophysics Data System (ADS)

Moseley, Mark B.; Grocholsky, Benjamin P.; Cheung, Carol; Singh, Sanjiv

2009-05-01

Coordinated operations between unmanned air and ground assets allow leveraging of multi-domain sensing and increase opportunities for improving line of sight communications. While numerous military missions would benefit from coordinated UAV-UGV operations, foundational capabilities that integrate stove-piped tactical systems and share available sensor data are required and not yet available. iRobot, AeroVironment, and Carnegie Mellon University are working together, partially SBIR-funded through ARDEC's small unit network lethality initiative, to develop collaborative capabilities for surveillance, targeting, and improved communications based on PackBot UGV and Raven UAV platforms. We integrate newly available technologies into computational, vision, and communications payloads and develop sensing algorithms to support vision-based target tracking. We first simulated and then applied onto real tactical platforms an implementation of Decentralized Data Fusion, a novel technique for fusing track estimates from PackBot and Raven platforms for a moving target in an open environment. In addition, system integration with AeroVironment's Digital Data Link onto both air and ground platforms has extended our capabilities in communications range to operate the PackBot as well as in increased video and data throughput. The system is brought together through a unified Operator Control Unit (OCU) for the PackBot and Raven that provides simultaneous waypoint navigation and traditional teleoperation. We also present several recent capability accomplishments toward PackBot-Raven coordinated operations, including single OCU display design and operation, early target track results, and Digital Data Link integration efforts, as well as our near-term capability goals.

Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont

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

Tauzin, Alexandra S.; Kwiatkowski, Kurt J.; Orlovsky, Nicole I.

Polysaccharide utilization loci (PUL) within the genomes of resident human gutBacteroidetesare central to the metabolism of the otherwise indigestible complex carbohydrates known as “dietary fiber.” However, functional characterization of PUL lags significantly behind sequencing efforts, which limits physiological understanding of the human-bacterial symbiosis. In particular, the molecular basis of complex polysaccharide recognition, an essential prerequisite to hydrolysis by cell surface glycosidases and subsequent metabolism, is generally poorly understood. Here, we present the biochemical, structural, and reverse genetic characterization of two unique cell surface glycan-binding proteins (SGBPs) encoded by a xyloglucan utilization locus (XyGUL) fromBacteroides ovatus, which are integral to growthmore » on this key dietary vegetable polysaccharide. Biochemical analysis reveals that these outer membrane-anchored proteins are in fact exquisitely specific for the highly branched xyloglucan (XyG) polysaccharide. The crystal structure of SGBP-A, a SusD homolog, with a bound XyG tetradecasaccharide reveals an extended carbohydrate-binding platform that primarily relies on recognition of the β-glucan backbone. The unique, tetra-modular structure of SGBP-B is comprised of tandem Ig-like folds, with XyG binding mediated at the distal C-terminal domain. Despite displaying similar affinities for XyG, reverse-genetic analysis reveals that SGBP-B is only required for the efficient capture of smaller oligosaccharides, whereas the presence of SGBP-A is more critical than its carbohydrate-binding ability for growth on XyG. Finally, together, these data demonstrate that SGBP-A and SGBP-B play complementary, specialized roles in carbohydrate capture byB. ovatusand elaborate a model of how vegetable xyloglucans are accessed by theBacteroidetes.« less

Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont

DOE PAGES

Tauzin, Alexandra S.; Kwiatkowski, Kurt J.; Orlovsky, Nicole I.; ...

2016-04-26

Polysaccharide utilization loci (PUL) within the genomes of resident human gutBacteroidetesare central to the metabolism of the otherwise indigestible complex carbohydrates known as “dietary fiber.” However, functional characterization of PUL lags significantly behind sequencing efforts, which limits physiological understanding of the human-bacterial symbiosis. In particular, the molecular basis of complex polysaccharide recognition, an essential prerequisite to hydrolysis by cell surface glycosidases and subsequent metabolism, is generally poorly understood. Here, we present the biochemical, structural, and reverse genetic characterization of two unique cell surface glycan-binding proteins (SGBPs) encoded by a xyloglucan utilization locus (XyGUL) fromBacteroides ovatus, which are integral to growthmore » on this key dietary vegetable polysaccharide. Biochemical analysis reveals that these outer membrane-anchored proteins are in fact exquisitely specific for the highly branched xyloglucan (XyG) polysaccharide. The crystal structure of SGBP-A, a SusD homolog, with a bound XyG tetradecasaccharide reveals an extended carbohydrate-binding platform that primarily relies on recognition of the β-glucan backbone. The unique, tetra-modular structure of SGBP-B is comprised of tandem Ig-like folds, with XyG binding mediated at the distal C-terminal domain. Despite displaying similar affinities for XyG, reverse-genetic analysis reveals that SGBP-B is only required for the efficient capture of smaller oligosaccharides, whereas the presence of SGBP-A is more critical than its carbohydrate-binding ability for growth on XyG. Finally, together, these data demonstrate that SGBP-A and SGBP-B play complementary, specialized roles in carbohydrate capture byB. ovatusand elaborate a model of how vegetable xyloglucans are accessed by theBacteroidetes.« less

Operational Monitoring and Forecasting in Regional Seas: the Aegean Sea example

NASA Astrophysics Data System (ADS)

Nittis, K.; Perivoliotis, L.; Zervakis, V.; Papadopoulos, A.; Tziavos, C.

2003-04-01

The increasing economic activities in the coastal zone and the associated pressure on the marine environment have raised the interest on monitoring systems able to provide supporting information for its effective management and protection. Such an integrated monitoring, forecasting and information system is being developed during the past years in the Aegean Sea. Its main component is the POSEIDON network that provides real-time data for meteorological and surface oceanographic parameters (waves, currents, hydrological and biochemical data) from 11 fixed oceanographic buoys. The numerical forecasting system is composed by an ETA atmospheric model, a WAM wave model and a POM hydrodynamic model that provide every day 72 hours forecasts. The system is operational since May 2000 and its products are published through Internet while a sub-set is also available through cellular telephony. New type of observing platforms will be available in the near future through a number of EU funded research projects. The Mediterranean Moored Multi-sensor Array (M3A) that was developed for the needs of the Mediterranean Forecasting System and was tested during 2000-2001 will be operational in 2004 during the MFSTEP project. The M3A system incorporates sensors for optical and chemical measurements (Oxygen, Turbidity, Chlorophyll-a, Nutrients and PAR) in the euphotic zone (0-100m) together with sensors for physical parameters (Temperature, Salinity, Current speed and direction) at the 0-500m layer. A Ferry-Box system will also operate during 2004 in the southern Aegean Sea, providing surface data for physical and bio-chemical properties. The ongoing modeling efforts include coupling with larger scale circulation models of the Mediterranean, high-resolution downscaling to coastal areas of the Aegean Sea and development of multi-variate data assimilation methods.

Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont

PubMed Central

Tauzin, Alexandra S.; Kwiatkowski, Kurt J.; Orlovsky, Nicole I.; Smith, Christopher J.; Creagh, A. Louise; Haynes, Charles A.; Wawrzak, Zdzislaw

2016-01-01

ABSTRACT Polysaccharide utilization loci (PUL) within the genomes of resident human gut Bacteroidetes are central to the metabolism of the otherwise indigestible complex carbohydrates known as “dietary fiber.” However, functional characterization of PUL lags significantly behind sequencing efforts, which limits physiological understanding of the human-bacterial symbiosis. In particular, the molecular basis of complex polysaccharide recognition, an essential prerequisite to hydrolysis by cell surface glycosidases and subsequent metabolism, is generally poorly understood. Here, we present the biochemical, structural, and reverse genetic characterization of two unique cell surface glycan-binding proteins (SGBPs) encoded by a xyloglucan utilization locus (XyGUL) from Bacteroides ovatus, which are integral to growth on this key dietary vegetable polysaccharide. Biochemical analysis reveals that these outer membrane-anchored proteins are in fact exquisitely specific for the highly branched xyloglucan (XyG) polysaccharide. The crystal structure of SGBP-A, a SusD homolog, with a bound XyG tetradecasaccharide reveals an extended carbohydrate-binding platform that primarily relies on recognition of the β-glucan backbone. The unique, tetra-modular structure of SGBP-B is comprised of tandem Ig-like folds, with XyG binding mediated at the distal C-terminal domain. Despite displaying similar affinities for XyG, reverse-genetic analysis reveals that SGBP-B is only required for the efficient capture of smaller oligosaccharides, whereas the presence of SGBP-A is more critical than its carbohydrate-binding ability for growth on XyG. Together, these data demonstrate that SGBP-A and SGBP-B play complementary, specialized roles in carbohydrate capture by B. ovatus and elaborate a model of how vegetable xyloglucans are accessed by the Bacteroidetes. PMID:27118585

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.

PubMed

Nogales, Juan; Palsson, Bernhard Ø; Thiele, Ines

2008-09-16

Pseudomonas putida is the best studied pollutant degradative bacteria and is harnessed by industrial biotechnology to synthesize fine chemicals. Since the publication of P. putida KT2440's genome, some in silico analyses of its metabolic and biotechnology capacities have been published. However, global understanding of the capabilities of P. putida KT2440 requires the construction of a metabolic model that enables the integration of classical experimental data along with genomic and high-throughput data. The constraint-based reconstruction and analysis (COBRA) approach has been successfully used to build and analyze in silico genome-scale metabolic reconstructions. We present a genome-scale reconstruction of P. putida KT2440's metabolism, iJN746, which was constructed based on genomic, biochemical, and physiological information. This manually-curated reconstruction accounts for 746 genes, 950 reactions, and 911 metabolites. iJN746 captures biotechnologically relevant pathways, including polyhydroxyalkanoate synthesis and catabolic pathways of aromatic compounds (e.g., toluene, benzoate, phenylacetate, nicotinate), not described in other metabolic reconstructions or biochemical databases. The predictive potential of iJN746 was validated using experimental data including growth performance and gene deletion studies. Furthermore, in silico growth on toluene was found to be oxygen-limited, suggesting the existence of oxygen-efficient pathways not yet annotated in P. putida's genome. Moreover, we evaluated the production efficiency of polyhydroxyalkanoates from various carbon sources and found fatty acids as the most prominent candidates, as expected. Here we presented the first genome-scale reconstruction of P. putida, a biotechnologically interesting all-surrounder. Taken together, this work illustrates the utility of iJN746 as i) a knowledge-base, ii) a discovery tool, and iii) an engineering platform to explore P. putida's potential in bioremediation and bioplastic production.

A fully-integrated aptamer-based affinity assay platform for monitoring astronaut health in space.

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

Yang, Xianbin; Durland, Ross H.; Hecht, Ariel H.

2010-07-01

Here we demonstrate the suitability of robust nucleic acid affinity reagents in an integrated point-of-care diagnostic platform for monitoring proteomic biomarkers indicative of astronaut health in spaceflight applications. A model thioaptamer targeting nuclear factor-kappa B (NF-{kappa}B) is evaluated in an on-chip electrophoretic gel-shift assay for human serum. Key steps of (i) mixing sample with the aptamer, (ii) buffer exchange, and (iii) preconcentration of sample were successfully integrated upstream of fluorescence-based detection. Challenges due to (i) nonspecific interactions with serum, and (ii) preconcentration at a nanoporous membrane are discussed and successfully resolved to yield a robust, rapid, and fully-integrated diagnostic system.

Microfabricated Nickel Based Sensors for Hostile and High Pressure Environments

NASA Astrophysics Data System (ADS)

Holt, Christopher Michael Bjustrom

This thesis outlines the development of two platforms for integrating microfabricated sensors with high pressure feedthroughs for application in hostile high temperature high pressure environments. An application in oil well production logging is explored and two sensors were implemented with these platforms for application in an oil well. The first platform developed involved microfabrication directly onto a cut and polished high pressure feedthrough. This technique enables a system that is more robust than the wire bonded silicon die technique used for MEMS integration in pressure sensors. Removing wire bonds from the traditional MEMS package allows for direct interface of a microfabricated sensor with a hostile high pressure fluid environment which is not currently possible. During the development of this platform key performance metrics included pressure testing to 70MPa and temperature cycling from 20°C to 200°C. This platform enables electronics integration with a variety of microfabricated electrical and thermal based sensors which can be immersed within the oil well environment. The second platform enabled free space fabrication of nickel microfabricated devices onto an array of pins using a thick tin sacrificial layer. This technique allowed microfabrication of metal MEMS that are released by distances of 1cm from their substrate. This method is quite flexible and allows for fabrication to be done on any pin array substrate regardless of surface quality. Being able to place released MEMS sensors directly onto traditional style circuit boards, ceramic circuit boards, electrical connectors, ribbon cables, pin headers, or high pressure feedthroughs greatly improves the variety of possible applications and reduces fabrication costs. These two platforms were then used to fabricate thermal conductivity sensors that showed excellent performance for distinguishing between oil, water, and gas phases. Testing was conducted at various flow rates and performance of the released platform was shown to be better than the performance seen in the anchored sensors while both platforms were significantly better than a simply fabricated wrapped wire sensor. The anchored platform was also used to demonstrate a traditional capacitance based fluid dielectric sensor which was found to work similarly to conventional commercial capacitance probes while being significantly smaller in size.

[Ginseng prescription rules and molecular mechanism in treating coronary heart disease based on data mining and integrative pharmacology].

PubMed

Li, Sen; Tang, Shi-Huan; Liu, Jin-Ling; Su, Jin; He, Fu-Yuan

2018-04-01

The ancient dragon Materia Medica, Compendium of Materia Medica and other works recorded that the main effect of ginseng is tonifying qi. It is reported that the main active ingredient of ginseng is ginsenoside. Modern studies have found that ginseng mono saponins are effective for cardiovascular related diseases. This paper preliminary clarified the efficacy of traditional ginseng-nourishing qi and cardiovascular disease through the traditional Chinese medicine (TCM) inheritance auxiliary platform and integration platform of association of pharmacology. With the help of TCM inheritance auxiliary platform-analysis of "Chinese medicine database", Chinese medicine treatment of modern diseases that ginseng rules, so the traditional effect associated with modern medicine and pharmacology; application integration platform enrichment analysis on the target of drug and gene function, metabolic pathway, to further explore the molecular mechanism of ginseng in the treatment of coronary heart disease, aimed at mining the molecular mechanism of ginseng in the treatment of coronary heart disease. Chinese medicine containing ginseng 307 prescriptions, 87 kinds of disease indications, western medicine disease Chinese medicine therapy for ginseng main coronary heart disease; analysis of molecular mechanism of ginseng pharmacology integration platform for the treatment of coronary heart disease. Ginsenosides（Ra₁, Ra₂, Rb₁, Rb₂, Rg₁, Ro) bind these targets, PRKAA1, PRKAA2, NDUFA4, COX5B, UQCRC1, affect chemokines, non-alcoholic fatty liver, gonadotropin, carbon metabolism, glucose metabolism and other pathways to treat coronary heart disease indirectly. The molecular mechanism of Panax ginseng's multi-component, multi-target and synergistic action is preliminarily elucidated in this paper. Copyright© by the Chinese Pharmaceutical Association.

Electrical Power Subsystem Integration and Test for the NPS Solar Cell Array Tester CubeSat

DTIC Science & Technology

2010-12-01

Earth’s Gravitational Constant MCU Microcontroller Unit MPPT Maximum Power Point Tracker NiCr Nickel Chromium NPS Naval Postgraduate School P...new testing platform was designed, built, and used to conduct integrated testing on CubeSat Kit (CSK) compatible devices. The power budgets and...acceptance test results obtained from the testing platform were used with a solar array power generation simulation, and a battery state of charge

CVN 78 Gerald R. Ford Class Nuclear Aircraft Carrier (CVN 78)

DTIC Science & Technology

2013-12-01

Capabil... -Follow-on Ship (CVN 79) DAB Program Review - • Start Construction - • Delivery .-:K IOT &E IOT &E Start .-:41 IOT &E Complete e(41 Follow-on...Ship (CVN 80) DAB Program Review -Platform-Level Integration D ... ....., Milestone C .. EMALS EMALS Delivery (with Ship) .-:o; IOC ..:<! IOT ...E IOT &E Start ..:<! IOT &E Complete -· Platform-Level Integration .. ...:<! CVN 78 Milestones SAR Baseline Dev Est Current APB Development

Hybrid Integrated Si/SiN Platforms for Wideband Optical Processing

DTIC Science & Technology

2017-05-08

material platform for integrated photonic applications." IEEE Photonics Journal, vol. 6, no.6 (2014). [8] E. Timurdogan, C . Agaskar, J . Sun, E...Sparacin, J . Michel, M. A. Beals, and L. C . Kimerling, DISTRIBUTION A: Distribution approved for public release. 24 “Demonstration of a...Brasch, J . D. Jost, C . Y. Wang, N. M. Kondratiev, M. L. Gorodetsky, and T. J . Kippenberg, “Temporal solitons in optical microresonators,” Nature

An automated synthesis-purification-sample-management platform for the accelerated generation of pharmaceutical candidates.

PubMed

Sutherland, J David; Tu, Noah P; Nemcek, Thomas A; Searle, Philip A; Hochlowski, Jill E; Djuric, Stevan W; Pan, Jeffrey Y

2014-04-01

A flexible and integrated flow-chemistry-synthesis-purification compound-generation and sample-management platform has been developed to accelerate the production of small-molecule organic-compound drug candidates in pharmaceutical research. Central to the integrated system is a Mitsubishi robot, which hands off samples throughout the process to the next station, including synthesis and purification, sample dispensing for purity and quantification analysis, dry-down, and aliquot generation.

Analyzing Cyber-Physical Threats on Robotic Platforms.

PubMed

Ahmad Yousef, Khalil M; AlMajali, Anas; Ghalyon, Salah Abu; Dweik, Waleed; Mohd, Bassam J

2018-05-21

Robots are increasingly involved in our daily lives. Fundamental to robots are the communication link (or stream) and the applications that connect the robots to their clients or users. Such communication link and applications are usually supported through client/server network connection. This networking system is amenable of being attacked and vulnerable to the security threats. Ensuring security and privacy for robotic platforms is thus critical, as failures and attacks could have devastating consequences. In this paper, we examine several cyber-physical security threats that are unique to the robotic platforms; specifically the communication link and the applications. Threats target integrity, availability and confidential security requirements of the robotic platforms, which use MobileEyes/arnlServer client/server applications. A robot attack tool (RAT) was developed to perform specific security attacks. An impact-oriented approach was adopted to analyze the assessment results of the attacks. Tests and experiments of attacks were conducted in simulation environment and physically on the robot. The simulation environment was based on MobileSim; a software tool for simulating, debugging and experimenting on MobileRobots/ActivMedia platforms and their environments. The robot platform PeopleBot TM was used for physical experiments. The analysis and testing results show that certain attacks were successful at breaching the robot security. Integrity attacks modified commands and manipulated the robot behavior. Availability attacks were able to cause Denial-of-Service (DoS) and the robot was not responsive to MobileEyes commands. Integrity and availability attacks caused sensitive information on the robot to be hijacked. To mitigate security threats, we provide possible mitigation techniques and suggestions to raise awareness of threats on the robotic platforms, especially when the robots are involved in critical missions or applications.

Analyzing Cyber-Physical Threats on Robotic Platforms †

PubMed Central

2018-01-01

Robots are increasingly involved in our daily lives. Fundamental to robots are the communication link (or stream) and the applications that connect the robots to their clients or users. Such communication link and applications are usually supported through client/server network connection. This networking system is amenable of being attacked and vulnerable to the security threats. Ensuring security and privacy for robotic platforms is thus critical, as failures and attacks could have devastating consequences. In this paper, we examine several cyber-physical security threats that are unique to the robotic platforms; specifically the communication link and the applications. Threats target integrity, availability and confidential security requirements of the robotic platforms, which use MobileEyes/arnlServer client/server applications. A robot attack tool (RAT) was developed to perform specific security attacks. An impact-oriented approach was adopted to analyze the assessment results of the attacks. Tests and experiments of attacks were conducted in simulation environment and physically on the robot. The simulation environment was based on MobileSim; a software tool for simulating, debugging and experimenting on MobileRobots/ActivMedia platforms and their environments. The robot platform PeopleBotTM was used for physical experiments. The analysis and testing results show that certain attacks were successful at breaching the robot security. Integrity attacks modified commands and manipulated the robot behavior. Availability attacks were able to cause Denial-of-Service (DoS) and the robot was not responsive to MobileEyes commands. Integrity and availability attacks caused sensitive information on the robot to be hijacked. To mitigate security threats, we provide possible mitigation techniques and suggestions to raise awareness of threats on the robotic platforms, especially when the robots are involved in critical missions or applications. PMID:29883403

A Distributed Amplifier System for Bilayer Lipid Membrane (BLM) Arrays With Noise and Individual Offset Cancellation.

PubMed

Crescentini, Marco; Thei, Frederico; Bennati, Marco; Saha, Shimul; de Planque, Maurits R R; Morgan, Hywel; Tartagni, Marco

2015-06-01

Lipid bilayer membrane (BLM) arrays are required for high throughput analysis, for example drug screening or advanced DNA sequencing. Complex microfluidic devices are being developed but these are restricted in terms of array size and structure or have integrated electronic sensing with limited noise performance. We present a compact and scalable multichannel electrophysiology platform based on a hybrid approach that combines integrated state-of-the-art microelectronics with low-cost disposable fluidics providing a platform for high-quality parallel single ion channel recording. Specifically, we have developed a new integrated circuit amplifier based on a novel noise cancellation scheme that eliminates flicker noise derived from devices under test and amplifiers. The system is demonstrated through the simultaneous recording of ion channel activity from eight bilayer membranes. The platform is scalable and could be extended to much larger array sizes, limited only by electronic data decimation and communication capabilities.

Smooth integral sliding mode controller for the position control of Stewart platform.

PubMed

Kumar P, Ramesh; Chalanga, Asif; Bandyopadhyay, B

2015-09-01

This paper proposes the application of a new algorithm for the position control of a Stewart platform. The conventional integral sliding mode controller is a combination of nominal control and discontinuous feedback control hence the overall control is discontinuous in nature. The discontinuity in the feedback control is undesirable for practical applications due to chattering which causes the wear and tear of the mechanical actuators. In this paper the existing integral sliding mode control law for systems with matched disturbances is modified by replacing the discontinuous part by a continuous modified twisting control. This proposed controller is continuous in nature due to the combinations of two continuous controls. The desired position of the platform has been achieved using the proposed controller even in the presence of matched disturbances. The effectiveness of the proposed controller has been proved with the simulation results. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Vertical integration of high-Q silicon nitride microresonators into silicon-on-insulator platform.

PubMed

Li, Qing; Eftekhar, Ali A; Sodagar, Majid; Xia, Zhixuan; Atabaki, Amir H; Adibi, Ali

2013-07-29

We demonstrate a vertical integration of high-Q silicon nitride microresonators into the silicon-on-insulator platform for applications at the telecommunication wavelengths. Low-loss silicon nitride films with a thickness of 400 nm are successfully grown, enabling compact silicon nitride microresonators with ultra-high intrinsic Qs (~ 6 × 10(6) for 60 μm radius and ~ 2 × 10(7) for 240 μm radius). The coupling between the silicon nitride microresonator and the underneath silicon waveguide is based on evanescent coupling with silicon dioxide as buffer. Selective coupling to a desired radial mode of the silicon nitride microresonator is also achievable using a pulley coupling scheme. In this work, a 60-μm-radius silicon nitride microresonator has been successfully integrated into the silicon-on-insulator platform, showing a single-mode operation with an intrinsic Q of 2 × 10(6).

Controls-Structures Interaction (CSI) technology program summary. Earth orbiting platforms program area of the space platforms technology program

NASA Technical Reports Server (NTRS)

Newsom, Jerry R.

1991-01-01

Control-Structures Interaction (CSI) technology embraces the understanding of the interaction between the spacecraft structure and the control system, and the creation and validation of concepts, techniques, and tools, for enabling the interdisciplinary design of an integrated structure and control system, rather than the integration of a structural design and a control system design. The goal of this program is to develop validated CSI technology for integrated design/analysis and qualification of large flexible space systems and precision space structures. A description of the CSI technology program is presented.

Cultivating engineering innovation ability based on optoelectronic experimental platform

NASA Astrophysics Data System (ADS)

Li, Dangjuan; Wu, Shenjiang

2017-08-01

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

Geostationary platform systems concepts definition study. Volume 2: Technical, book 3

NASA Technical Reports Server (NTRS)

1980-01-01

The supporting research and technology, and space demonstrations required to support the 1990s operational geostationary platforms are identified. Also the requirements on and interfaces with the Space Transportation System hardware elements supporting the geostationary platform program, including the shuttle, orbital transfer vehicles, teleoperator, etc., are investigated to provide integrated support requirements. Finally, a preliminary evaluation of the practicability and capabilities of an experimental platform from the standpoint of technology, schedule, and cost is given.

Colombia a Source of Cacao Genetic Diversity As Revealed by the Population Structure Analysis of Germplasm Bank of Theobroma cacao L.

PubMed

Osorio-Guarín, Jaime A; Berdugo-Cely, Jhon; Coronado, Roberto Antonio; Zapata, Yeny Patricia; Quintero, Constanza; Gallego-Sánchez, Gerardo; Yockteng, Roxana

2017-01-01

Beans of the species Theobroma cacao L., also known as cacao, are the raw material to produce chocolate. Colombian cacao has been classified as a fine flavor cacao that represents the 5% of cacao world's production. Colombian genetic resources from this species are conserved in ex situ and in-field germplasm banks, since T. cacao has recalcitrant seeds to desication and long-term storage. Currently, the collection of T. cacao of the Colombian Corporation of Agricultural Research (CORPOICA) has approximately 700 germplasm accessions. We conducted a molecular analysis of Corpoica's cacao collection and a morphological characterization of some accessions with the goal to study its genetic diversity and population structure and, to select interesting accessions for the cacao's breeding program. Phenotypic evaluation was performed based on 18 morphological traits and 4 biochemical traits. PCA analysis of morphological traits explained 60.6% of the total variation in seven components and 100% of the total variation of biochemical traits in four components, grouping the collection in 4 clusters for both variables. We explored 565 accessions from Corpoica's germplasm and 252 accessions from reference populations using 96 single nucleotide polymorphism (SNP) molecular markers. Molecular patterns of cacao Corpoica's collection were obtained amplifying specific alleles in a Fluidigm platform that used integrated circuits of fluids. Corpoica's collection showed highest genetic diversity [Expected Heterozygosity ( H E = 0.314), Observed Heterozygosity ( H O = 0.353)] that is reduced when reference populations were included in the dataset ( H E = 0.294, H O = 0.261). The collection was divided into four clusters based on population structure analysis. Cacao accessions from distinct groups showed some taxonomic concordance and reflected their geographic origins. For instance, accessions classified as Criollo were clearly differentiated in one group and we identified two new Colombian genetic groups. Using a number of allelic variations based on 87 SNP markers and 22 different morphological/biochemical traits, a core collection with a total of 232 accessions was selected as a primary genetic resource for cacao breeders.

Colombia a Source of Cacao Genetic Diversity As Revealed by the Population Structure Analysis of Germplasm Bank of Theobroma cacao L.

PubMed Central

Osorio-Guarín, Jaime A.; Berdugo-Cely, Jhon; Coronado, Roberto Antonio; Zapata, Yeny Patricia; Quintero, Constanza; Gallego-Sánchez, Gerardo; Yockteng, Roxana

2017-01-01

Beans of the species Theobroma cacao L., also known as cacao, are the raw material to produce chocolate. Colombian cacao has been classified as a fine flavor cacao that represents the 5% of cacao world’s production. Colombian genetic resources from this species are conserved in ex situ and in-field germplasm banks, since T. cacao has recalcitrant seeds to desication and long-term storage. Currently, the collection of T. cacao of the Colombian Corporation of Agricultural Research (CORPOICA) has approximately 700 germplasm accessions. We conducted a molecular analysis of Corpoica’s cacao collection and a morphological characterization of some accessions with the goal to study its genetic diversity and population structure and, to select interesting accessions for the cacao’s breeding program. Phenotypic evaluation was performed based on 18 morphological traits and 4 biochemical traits. PCA analysis of morphological traits explained 60.6% of the total variation in seven components and 100% of the total variation of biochemical traits in four components, grouping the collection in 4 clusters for both variables. We explored 565 accessions from Corpoica’s germplasm and 252 accessions from reference populations using 96 single nucleotide polymorphism (SNP) molecular markers. Molecular patterns of cacao Corpoica’s collection were obtained amplifying specific alleles in a Fluidigm platform that used integrated circuits of fluids. Corpoica’s collection showed highest genetic diversity [Expected Heterozygosity (HE = 0.314), Observed Heterozygosity (HO = 0.353)] that is reduced when reference populations were included in the dataset (HE = 0.294, HO = 0.261). The collection was divided into four clusters based on population structure analysis. Cacao accessions from distinct groups showed some taxonomic concordance and reflected their geographic origins. For instance, accessions classified as Criollo were clearly differentiated in one group and we identified two new Colombian genetic groups. Using a number of allelic variations based on 87 SNP markers and 22 different morphological/biochemical traits, a core collection with a total of 232 accessions was selected as a primary genetic resource for cacao breeders. PMID:29209353

A collaborative visual analytics suite for protein folding research.

PubMed

Harvey, William; Park, In-Hee; Rübel, Oliver; Pascucci, Valerio; Bremer, Peer-Timo; Li, Chenglong; Wang, Yusu

2014-09-01

Molecular dynamics (MD) simulation is a crucial tool for understanding principles behind important biochemical processes such as protein folding and molecular interaction. With the rapidly increasing power of modern computers, large-scale MD simulation experiments can be performed regularly, generating huge amounts of MD data. An important question is how to analyze and interpret such massive and complex data. One of the (many) challenges involved in analyzing MD simulation data computationally is the high-dimensionality of such data. Given a massive collection of molecular conformations, researchers typically need to rely on their expertise and prior domain knowledge in order to retrieve certain conformations of interest. It is not easy to make and test hypotheses as the data set as a whole is somewhat "invisible" due to its high dimensionality. In other words, it is hard to directly access and examine individual conformations from a sea of molecular structures, and to further explore the entire data set. There is also no easy and convenient way to obtain a global view of the data or its various modalities of biochemical information. To this end, we present an interactive, collaborative visual analytics tool for exploring massive, high-dimensional molecular dynamics simulation data sets. The most important utility of our tool is to provide a platform where researchers can easily and effectively navigate through the otherwise "invisible" simulation data sets, exploring and examining molecular conformations both as a whole and at individual levels. The visualization is based on the concept of a topological landscape, which is a 2D terrain metaphor preserving certain topological and geometric properties of the high dimensional protein energy landscape. In addition to facilitating easy exploration of conformations, this 2D terrain metaphor also provides a platform where researchers can visualize and analyze various properties (such as contact density) overlayed on the top of the 2D terrain. Finally, the software provides a collaborative environment where multiple researchers can assemble observations and biochemical events into storyboards and share them in real time over the Internet via a client-server architecture. The software is written in Scala and runs on the cross-platform Java Virtual Machine. Binaries and source code are available at http://www.aylasoftware.org and have been released under the GNU General Public License. Copyright © 2014 Elsevier Inc. All rights reserved.

OTEC platform configuration and integration study. Volume I. Systems engineering and integration. Final report

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

None

1978-04-01

The economic success of an Ocean Thermal Energy Conversion (OTEC) system is highly dependent on a platform which provides adequate support for the power system, accommodates reliably the cold water pipe, and is most cost effective. The results of a study conducted for the Department of Energy to assess six generic types of platforms to determine the most satisfactory platform for severl potential sites are presented. The six platform configurations are ship, circular barge, semi-submersible, Tuned Sphere, submersible, and spar. These represent directional and symmetric types of platforms which operate on the surface, at the interface, and submerged. The fivemore » sites for this study were primarily New Orleans, Keahole Point (Hawaii), Brazil, and secondarily Key West and Puerto Rico. Electrical transmission of energy by submarine cable is the planned form of energy transmission for all sites except Brazil, where chemical conversion is to be the method of transmission. This study is devoted to the platform (or ocean systems) of the OTEC plant which is chiefly comprised of the hull and structure, the seawater system, the position control system, and miscellaneous support/assembly systems. The principal elements in the work breakdown structure for the commercial plants are presented. The assessment of the six platform configurations was conducted utilizing a baseline plan (100-MW(e) (Net)) and site (New Orleans) with variations from the baseline to cover the range of interested platforms and sites.« less

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

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application.

PubMed

Hanwell, Marcus D; de Jong, Wibe A; Harris, Christopher J

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction-connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web-going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.

Surface-Enhanced Raman Spectroscopy for Staphylococcus aureus DNA Detection by Using Surface-Enhanced Raman Scattering Tag on Au Film Over Nanosphere Substrate.

PubMed

Chen, Jian; Wang, Jun-Feng; Wu, Xue-Zhong; Rong, Zhen; Dong, Pei-Tao; Xiao, Rui

2018-06-01

We developed a high-performance surface-enhanced Raman scattering (SERS) sensing platform that can be used for specific and sensitive DNA detection. The SERS platform combines the advantages of Au film over nanosphere (AuFON) substrate and Ag@PATP@SiO2 SERS tag. SERS tag-on-AuFON is a sensing system that operates by the self-assembly of SERS tag onto an AuFON substrate in the presence of target DNAs. The SERS signals can be dramatically enhanced by the formation of "hot spots" in the interstices between the assembled nanostructures, as confirmed by finite-difference time-domain (FDTD) simulation. As a new sensing platform, SERS tag-on-AuFON was utilized to detect Staphylococcus aureus (S. aureus) DNA with a limit of detection at 1 nM. A linear relationship was also observed between the SERS intensity at Raman peak 1439 cm-1 and the logarithm of target DNA concentrations ranging from 1 μM to 1 nM. Besides, the sensing platform showed good homogeneity, with a relative standard deviation of about 1%. The sensitive SERS platform created in this study is a promising tool for detecting trace biochemical molecules because of its relatively simple and effective fabrication procedure, high sensitivity, and high reproducibility of the SERS effect.

Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform.

PubMed

Moutsatsos, Ioannis K; Hossain, Imtiaz; Agarinis, Claudia; Harbinski, Fred; Abraham, Yann; Dobler, Luc; Zhang, Xian; Wilson, Christopher J; Jenkins, Jeremy L; Holway, Nicholas; Tallarico, John; Parker, Christian N

2017-03-01

High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community.

Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform

PubMed Central

Moutsatsos, Ioannis K.; Hossain, Imtiaz; Agarinis, Claudia; Harbinski, Fred; Abraham, Yann; Dobler, Luc; Zhang, Xian; Wilson, Christopher J.; Jenkins, Jeremy L.; Holway, Nicholas; Tallarico, John; Parker, Christian N.

2016-01-01

High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an “off-the-shelf,” open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community. PMID:27899692

The planning coordinator: A design architecture for autonomous error recovery and on-line planning of intelligent tasks

NASA Technical Reports Server (NTRS)

Farah, Jeffrey J.

1992-01-01

Developing a robust, task level, error recovery and on-line planning architecture is an open research area. There is previously published work on both error recovery and on-line planning; however, none incorporates error recovery and on-line planning into one integrated platform. The integration of these two functionalities requires an architecture that possesses the following characteristics. The architecture must provide for the inclusion of new information without the destruction of existing information. The architecture must provide for the relating of pieces of information, old and new, to one another in a non-trivial rather than trivial manner (e.g., object one is related to object two under the following constraints, versus, yes, they are related; no, they are not related). Finally, the architecture must be not only a stand alone architecture, but also one that can be easily integrated as a supplement to some existing architecture. This thesis proposal addresses architectural development. Its intent is to integrate error recovery and on-line planning onto a single, integrated, multi-processor platform. This intelligent x-autonomous platform, called the Planning Coordinator, will be used initially to supplement existing x-autonomous systems and eventually replace them.

Integrated Kerr comb-based reconfigurable transversal differentiator for microwave photonic signal processing

NASA Astrophysics Data System (ADS)

Xu, Xingyuan; Wu, Jiayang; Shoeiby, Mehrdad; Nguyen, Thach G.; Chu, Sai T.; Little, Brent E.; Morandotti, Roberto; Mitchell, Arnan; Moss, David J.

2018-01-01

An arbitrary-order intensity differentiator for high-order microwave signal differentiation is proposed and experimentally demonstrated on a versatile transversal microwave photonic signal processing platform based on integrated Kerr combs. With a CMOS-compatible nonlinear micro-ring resonator, high quality Kerr combs with broad bandwidth and large frequency spacings are generated, enabling a larger number of taps and an increased Nyquist zone. By programming and shaping individual comb lines' power, calculated tap weights are realized, thus achieving a versatile microwave photonic signal processing platform. Arbitrary-order intensity differentiation is demonstrated on the platform. The RF responses are experimentally characterized, and systems demonstrations for Gaussian input signals are also performed.

Optofluidic platforms based on surface-enhanced Raman scattering.

PubMed

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

2010-05-01

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

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.

Development of deployable structures for large space platform systems, volume 1

NASA Technical Reports Server (NTRS)

1982-01-01

Generic deployable spacecraft configurations and deployable platform systems concepts were identified. Sizing, building block concepts, orbiter packaging, thermal analysis, cost analysis, and mass properties analysis as related to platform systems integration are considered. Technology needs are examined and the major criteria used in concept selection are delineated. Requirements for deployable habitat modules, tunnels, and OTV hangars are considered.

Development of deployable structures for large space platform systems, part 1

NASA Technical Reports Server (NTRS)

Cox, R. L.; Nelson, R. A.

1982-01-01

Eight deployable platform design objectives were established: autodeploy/retract; fully integrated utilities; configuration variability; versatile payload and subsystem interfaces; structural and packing efficiency; 1986 technology readiness; minimum EVA/RMS; and Shuttle operational compatibility.

An in vitro synthetic biology platform for the industrial biomanufacturing of myo-inositol from starch.

PubMed

You, Chun; Shi, Ting; Li, Yunjie; Han, Pingping; Zhou, Xigui; Zhang, Yi-Heng Percival

2017-08-01

Myo-Inositol (vitamin B8) is widely used in the drug, cosmetic, and food & feed industries. Here, we present an in vitro non-fermentative enzymatic pathway that converts starch to inositol in one vessel. This in vitro pathway is comprised of four enzymes that operate without ATP or NAD + supplementation. All enzyme BioBricks are carefully selected from hyperthermophilic microorganisms, that is, alpha-glucan phosphorylase from Thermotoga maritima, phosphoglucomutase from Thermococcus kodakarensis, inositol 1-phosphate synthase from Archaeoglobus fulgidus, and inositol monophosphatase from T. maritima. They were expressed efficiently in high-density fermentation of Escherichia coli BL21(DE3) and easily purified by heat treatment. The four-enzyme pathway supplemented with two other hyperthermophilic enzymes (i.e., 4-α-glucanotransferase from Thermococcus litoralis and isoamylase from Sulfolobus tokodaii) converts branched or linear starch to inositol, accomplishing a very high product yield of 98.9 ± 1.8% wt./wt. This in vitro (aeration-free) biomanufacturing has been successfully operated on 20,000-L reactors. Less costly inositol would be widely added in heath food, low-end soft drink, and animal feed, and may be converted to other value-added biochemicals (e.g., glucarate). This biochemical is the first product manufactured by the in vitro synthetic biology platform on an industrial scale. Biotechnol. Bioeng. 2017;114: 1855-1864. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Infrared Microspectroscopy: A Multiple-Screening Platform for Investigating Single-Cell Biochemical Perturbations upon Prion Infection

PubMed Central

2011-01-01

Prion diseases are a group of fatal neurodegenerative disorders characterized by the accumulation of prions in the central nervous system. The pathogenic prion (PrPSc) possesses the capability to convert the host-encoded cellular isoform of the prion protein, PrPC, into nascent PrPSc. The present work aims at providing novel insight into cellular response upon prion infection evidenced by synchrotron radiation infrared microspectroscopy (SR-IRMS). This non-invasive, label-free analytical technique was employed to investigate the biochemical perturbations undergone by prion infected mouse hypothalamic GT1-1 cells at the cellular and subcellular level. A decrement in total cellular protein content upon prion infection was identified by infrared (IR) whole-cell spectra and validated by bicinchoninic acid assay and single-cell volume analysis by atomic force microscopy (AFM). Hierarchical cluster analysis (HCA) of IR data discriminated between infected and uninfected cells and allowed to deduce an increment of lysosomal bodies within the cytoplasm of infected GT1-1 cells, a hypothesis further confirmed by SR-IRMS at subcellular spatial resolution and fluorescent microscopy. The purpose of this work, therefore, consists of proposing IRMS as a powerful multiscreening platform, drawing on the synergy with conventional biological assays and microscopy techniques in order to increase the accuracy of investigations performed at the single-cell level. PMID:22778865

Infrared microspectroscopy: a multiple-screening platform for investigating single-cell biochemical perturbations upon prion infection.

PubMed

Didonna, Alessandro; Vaccari, Lisa; Bek, Alpan; Legname, Giuseppe

2011-03-16

Prion diseases are a group of fatal neurodegenerative disorders characterized by the accumulation of prions in the central nervous system. The pathogenic prion (PrP(Sc)) possesses the capability to convert the host-encoded cellular isoform of the prion protein, PrP(C), into nascent PrP(Sc). The present work aims at providing novel insight into cellular response upon prion infection evidenced by synchrotron radiation infrared microspectroscopy (SR-IRMS). This non-invasive, label-free analytical technique was employed to investigate the biochemical perturbations undergone by prion infected mouse hypothalamic GT1-1 cells at the cellular and subcellular level. A decrement in total cellular protein content upon prion infection was identified by infrared (IR) whole-cell spectra and validated by bicinchoninic acid assay and single-cell volume analysis by atomic force microscopy (AFM). Hierarchical cluster analysis (HCA) of IR data discriminated between infected and uninfected cells and allowed to deduce an increment of lysosomal bodies within the cytoplasm of infected GT1-1 cells, a hypothesis further confirmed by SR-IRMS at subcellular spatial resolution and fluorescent microscopy. The purpose of this work, therefore, consists of proposing IRMS as a powerful multiscreening platform, drawing on the synergy with conventional biological assays and microscopy techniques in order to increase the accuracy of investigations performed at the single-cell level.

Microfluidic Lab-on-a-Chip Platforms: Requirements, Characteristics and Applications

NASA Astrophysics Data System (ADS)

Mark, D.; Haeberle, S.; Roth, G.; Von Stetten, F.; Zengerle, R.

This review summarizes recent developments in microfluidic platform approaches. In contrast to isolated application-specific solutions, a microfluidic platform provides a set of fluidic unit operations, which are designed for easy combination within a well-defined fabrication technology. This allows the implementation of different application-specific (bio-) chemical processes, automated by microfluidic process integration [1]. A brief introduction into technical advances, major market segments and promising applications is followed by a detailed characterization of different microfluidic platforms, comprising a short definition, the functional principle, microfluidic unit operations, application examples as well as strengths and limitations. The microfluidic platforms in focus are lateral flow tests, linear actuated devices, pressure driven laminar flow, microfluidic large scale integration, segmented flow microfluidics, centrifugal microfluidics, electro-kinetics, electrowetting, surface acoustic waves, and systems for massively parallel analysis. The review concludes with the attempt to provide a selection scheme for microfluidic platforms which is based on their characteristics according to key requirements of different applications and market segments. Applied selection criteria comprise portability, costs of instrument and disposable, sample throughput, number of parameters per sample, reagent consumption, precision, diversity of microfluidic unit operations and the flexibility in programming different liquid handling protocols.

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

PubMed

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

2015-11-10

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

Smart adaptable system for older adults' Daily Life Activities Management - The ABLE platform.

PubMed

Giokas, Kostas; Anastasiou, Athanasios; Tsirmpas, Charalampos; Koutsouri, Georgia; Koutsouris, Dimitris; Iliopoulou, Dimitra

2014-01-01

In this paper we propose a system (ABLE) that will act as the main platform for a number of low-cost, mature technologies that will be integrated in order to create a dynamically adaptive Daily Life Activities Management environment in order to facilitate the everyday life of senior (but not exclusively) citizens at home. While the main target group of ABLE's users is the ageing population its use can be extended to all people that are vulnerable or atypical in body, intellect or emotions and are categorized by society as disabled. The classes of assistive products that are well defined in the international standard, ISO9999 such as assistive products for personal medical treatment, personal care and protection, communication, information and reaction and for personal mobility, will be easily incorporated in our proposed platform. Furthermore, our platform could integrate and implement the above classes under several service models that will be analyzed further.

Smart Sensor Systems for Aerospace Applications: From Sensor Development to Application Testing

NASA Technical Reports Server (NTRS)

Hunter, G. W.; Xu, J. C.; Dungan, L. K.; Ward, B. J.; Rowe, S.; Williams, J.; Makel, D. B.; Liu, C. C.; Chang, C. W.

2008-01-01

The application of Smart Sensor Systems for aerospace applications is a multidisciplinary process consisting of sensor element development, element integration into Smart Sensor hardware, and testing of the resulting sensor systems in application environments. This paper provides a cross-section of these activities for multiple aerospace applications illustrating the technology challenges involved. The development and application testing topics discussed are: 1) The broadening of sensitivity and operational range of silicon carbide (SiC) Schottky gas sensor elements; 2) Integration of fire detection sensor technology into a "Lick and Stick" Smart Sensor hardware platform for Crew Exploration Vehicle applications; 3) Extended testing for zirconia based oxygen sensors in the basic "Lick and Stick" platform for environmental monitoring applications. It is concluded that that both core sensor platform technology and a basic hardware platform can enhance the viability of implementing smart sensor systems in aerospace applications.

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

NASA Astrophysics Data System (ADS)

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

1996-05-01

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

Chip-scale sensor system integration for portable health monitoring.

PubMed

Jokerst, Nan M; Brooke, Martin A; Cho, Sang-Yeon; Shang, Allan B

2007-12-01

The revolution in integrated circuits over the past 50 yr has produced inexpensive computing and communications systems that are powerful and portable. The technologies for these integrated chip-scale sensing systems, which will be miniature, lightweight, and portable, are emerging with the integration of sensors with electronics, optical systems, micromachines, microfluidics, and the integration of chemical and biological materials (soft/wet material integration with traditional dry/hard semiconductor materials). Hence, we stand at a threshold for health monitoring technology that promises to provide wearable biochemical sensing systems that are comfortable, inauspicious, wireless, and battery-operated, yet that continuously monitor health status, and can transmit compressed data signals at regular intervals, or alarm conditions immediately. In this paper, we explore recent results in chip-scale sensor integration technology for health monitoring. The development of inexpensive chip-scale biochemical optical sensors, such as microresonators, that are customizable for high sensitivity coupled with rapid prototyping will be discussed. Ground-breaking work in the integration of chip-scale optical systems to support these optical sensors will be highlighted, and the development of inexpensive Si complementary metal-oxide semiconductor circuitry (which makes up the vast majority of computational systems today) for signal processing and wireless communication with local receivers that lie directly on the chip-scale sensor head itself will be examined.

Turbine blade and non-integral platform with pin attachment

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

Campbell, Christian X; Eng, Darryl; Marra, John J

Platforms (36, 38) span between turbine blades (23, 24, 25) on a disk (32). Each platform may be individually mounted to the disk by a pin attachment (42). Each platform (36) may have a rotationally rearward edge portion (50) that underlies a forward portion (45) of the adjacent platform (38). This limits centrifugal bending of the rearward portion of the platform, and provides coolant sealing. The rotationally forward edge (44A, 44B) of the platform overlies a seal element (51) on the pressure side (28) of the forwardly adjacent blade, and does not underlie a shelf on that blade. The pinmore » attachment allows radial mounting of each platform onto the disk via tilting (60) of the platform during mounting to provide mounting clearance for the rotationally rearward edge portion (50). This facilitates quick platform replacement without blade removal.« less

Turbine blade and non-integral platform with pin attachment

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

Campbell, Christian Xavier; Eng, Darryl; Marra, John J.

2016-08-02

Platforms (36, 38) span between turbine blades (23, 24, 25) on a disk (32). Each platform may be individually mounted to the disk by a pin attachment (42). Each platform (36) may have a rotationally rearward edge portion (50) that underlies a forward portion (45) of the adjacent platform (38). This limits centrifugal bending of the rearward portion of the platform, and provides coolant sealing. The rotationally forward edge (44A, 44B) of the platform overlies a seal element (51) on the pressure side (28) of the forwardly adjacent blade, and does not underlie a shelf on that blade. The pinmore » attachment allows radial mounting of each platform onto the disk via tilting (60) of the platform during mounting to provide mounting clearance for the rotationally rearward edge portion (50). This facilitates quick platform replacement without blade removal.« less

Improved prediction of biochemical recurrence after radical prostatectomy by genetic polymorphisms.

PubMed

Morote, Juan; Del Amo, Jokin; Borque, Angel; Ars, Elisabet; Hernández, Carlos; Herranz, Felipe; Arruza, Antonio; Llarena, Roberto; Planas, Jacques; Viso, María J; Palou, Joan; Raventós, Carles X; Tejedor, Diego; Artieda, Marta; Simón, Laureano; Martínez, Antonio; Rioja, Luis A

2010-08-01

Single nucleotide polymorphisms are inherited genetic variations that can predispose or protect individuals against clinical events. We hypothesized that single nucleotide polymorphism profiling may improve the prediction of biochemical recurrence after radical prostatectomy. We performed a retrospective, multi-institutional study of 703 patients treated with radical prostatectomy for clinically localized prostate cancer who had at least 5 years of followup after surgery. All patients were genotyped for 83 prostate cancer related single nucleotide polymorphisms using a low density oligonucleotide microarray. Baseline clinicopathological variables and single nucleotide polymorphisms were analyzed to predict biochemical recurrence within 5 years using stepwise logistic regression. Discrimination was measured by ROC curve AUC, specificity, sensitivity, predictive values, net reclassification improvement and integrated discrimination index. The overall biochemical recurrence rate was 35%. The model with the best fit combined 8 covariates, including the 5 clinicopathological variables prostate specific antigen, Gleason score, pathological stage, lymph node involvement and margin status, and 3 single nucleotide polymorphisms at the KLK2, SULT1A1 and TLR4 genes. Model predictive power was defined by 80% positive predictive value, 74% negative predictive value and an AUC of 0.78. The model based on clinicopathological variables plus single nucleotide polymorphisms showed significant improvement over the model without single nucleotide polymorphisms, as indicated by 23.3% net reclassification improvement (p = 0.003), integrated discrimination index (p <0.001) and likelihood ratio test (p <0.001). Internal validation proved model robustness (bootstrap corrected AUC 0.78, range 0.74 to 0.82). The calibration plot showed close agreement between biochemical recurrence observed and predicted probabilities. Predicting biochemical recurrence after radical prostatectomy based on clinicopathological data can be significantly improved by including patient genetic information. Copyright (c) 2010 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Fundamentals of microfluidic cell culture in controlled microenvironments†

PubMed Central

Young, Edmond W. K.; Beebe, David J.

2010-01-01

Microfluidics has the potential to revolutionize the way we approach cell biology research. The dimensions of microfluidic channels are well suited to the physical scale of biological cells, and the many advantages of microfluidics make it an attractive platform for new techniques in biology. One of the key benefits of microfluidics for basic biology is the ability to control parameters of the cell microenvironment at relevant length and time scales. Considerable progress has been made in the design and use of novel microfluidic devices for culturing cells and for subsequent treatment and analysis. With the recent pace of scientific discovery, it is becoming increasingly important to evaluate existing tools and techniques, and to synthesize fundamental concepts that would further improve the efficiency of biological research at the microscale. This tutorial review integrates fundamental principles from cell biology and local microenvironments with cell culture techniques and concepts in microfluidics. Culturing cells in microscale environments requires knowledge of multiple disciplines including physics, biochemistry, and engineering. We discuss basic concepts related to the physical and biochemical microenvironments of the cell, physicochemical properties of that microenvironment, cell culture techniques, and practical knowledge of microfluidic device design and operation. We also discuss the most recent advances in microfluidic cell culture and their implications on the future of the field. The goal is to guide new and interested researchers to the important areas and challenges facing the scientific community as we strive toward full integration of microfluidics with biology. PMID:20179823

Miniaturized devices towards an integrated lab-on-a-chip platform for DNA diagnostics

NASA Astrophysics Data System (ADS)

Kaprou, G.; Papadakis, G.; Kokkoris, G.; Papadopoulos, V.; Kefala, I.; Papageorgiou, D.; Gizeli, E.; Tserepi, A.

2015-06-01

Microfluidics is an emerging technology enabling the development of Lab-on-a-chip (LOC) systems for clinical diagnostics, drug discovery and screening, food safety and environmental analysis. LOC systems integrate and scale down one or several laboratory functions on a single chip of a few mm2 to cm2 in size, and account for many advantages on biochemical analyses, such as low sample and reagent consumption, low cost, reduced analysis time, portability and point-of-need compatibility. Currently, available nucleic acid diagnostic tests take advantage of Polymerase Chain Reaction (PCR) that allows exponential amplification of portions of nucleic acid sequences that can be used as indicators for the identification of various diseases. Here, we present a comparison between static chamber and continuous flow miniaturized PCR devices, in terms of energy consumption for devices fabricated on the same material stack, with identical sample volume and channel dimensions. The comparison is implemented by a computational study coupling heat transfer in both solid and fluid, mass conservation of species, and joule heating. Based on the conclusions of this study, we develop low-cost and fast DNA amplification devices for both PCR and isothermal amplification, and we implement them in the detection of mutations related to breast cancer. The devices are fabricated by mass production amenable technologies on printed circuit board (PCB) substrates, where copper facilitates the incorporation of on-chip microheaters, defining the thermal zones necessary for PCR or isothermal amplification methods.

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

The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes.

PubMed

Smith, Adam Alexander Thil; Belda, Eugeni; Viari, Alain; Medigue, Claudine; Vallenet, David

2012-05-01

Of all biochemically characterized metabolic reactions formalized by the IUBMB, over one out of four have yet to be associated with a nucleic or protein sequence, i.e. are sequence-orphan enzymatic activities. Few bioinformatics annotation tools are able to propose candidate genes for such activities by exploiting context-dependent rather than sequence-dependent data, and none are readily accessible and propose result integration across multiple genomes. Here, we present CanOE (Candidate genes for Orphan Enzymes), a four-step bioinformatics strategy that proposes ranked candidate genes for sequence-orphan enzymatic activities (or orphan enzymes for short). The first step locates "genomic metabolons", i.e. groups of co-localized genes coding proteins catalyzing reactions linked by shared metabolites, in one genome at a time. These metabolons can be particularly helpful for aiding bioanalysts to visualize relevant metabolic data. In the second step, they are used to generate candidate associations between un-annotated genes and gene-less reactions. The third step integrates these gene-reaction associations over several genomes using gene families, and summarizes the strength of family-reaction associations by several scores. In the final step, these scores are used to rank members of gene families which are proposed for metabolic reactions. These associations are of particular interest when the metabolic reaction is a sequence-orphan enzymatic activity. Our strategy found over 60,000 genomic metabolons in more than 1,000 prokaryote organisms from the MicroScope platform, generating candidate genes for many metabolic reactions, of which more than 70 distinct orphan reactions. A computational validation of the approach is discussed. Finally, we present a case study on the anaerobic allantoin degradation pathway in Escherichia coli K-12.

Omics Approaches for Understanding Grapevine Berry Development: Regulatory Networks Associated with Endogenous Processes and Environmental Responses

PubMed Central

Serrano, Alejandra; Espinoza, Carmen; Armijo, Grace; Inostroza-Blancheteau, Claudio; Poblete, Evelyn; Meyer-Regueiro, Carlos; Arce, Anibal; Parada, Francisca; Santibáñez, Claudia; Arce-Johnson, Patricio

2017-01-01

Grapevine fruit development is a dynamic process that can be divided into three stages: formation (I), lag (II), and ripening (III), in which physiological and biochemical changes occur, leading to cell differentiation and accumulation of different solutes. These stages can be positively or negatively affected by multiple environmental factors. During the last decade, efforts have been made to understand berry development from a global perspective. Special attention has been paid to transcriptional and metabolic networks associated with the control of grape berry development, and how external factors affect the ripening process. In this review, we focus on the integration of global approaches, including proteomics, metabolomics, and especially transcriptomics, to understand grape berry development. Several aspects will be considered, including seed development and the production of seedless fruits; veraison, at which anthocyanin accumulation begins in the berry skin of colored varieties; and hormonal regulation of berry development and signaling throughout ripening, focusing on the transcriptional regulation of hormone receptors, protein kinases, and genes related to secondary messenger sensing. Finally, berry responses to different environmental factors, including abiotic (temperature, water-related stress and UV-B radiation) and biotic (fungi and viruses) stresses, and how they can significantly modify both, development and composition of vine fruit, will be discussed. Until now, advances have been made due to the application of Omics tools at different molecular levels. However, the potential of these technologies should not be limited to the study of single-level questions; instead, data obtained by these platforms should be integrated to unravel the molecular aspects of grapevine development. Therefore, the current challenge is the generation of new tools that integrate large-scale data to assess new questions in this field, and to support agronomical practices. PMID:28936215

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.

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.

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

PubMed

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

2010-01-13

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

Genomics Portals: integrative web-platform for mining genomics data

PubMed Central

2010-01-01

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

Distributed and Modular CAN-Based Architecture for Hardware Control and Sensor Data Integration

PubMed Central

Losada, Diego P.; Fernández, Joaquín L.; Paz, Enrique; Sanz, Rafael

2017-01-01

In this article, we present a CAN-based (Controller Area Network) distributed system to integrate sensors, actuators and hardware controllers in a mobile robot platform. With this work, we provide a robust, simple, flexible and open system to make hardware elements or subsystems communicate, that can be applied to different robots or mobile platforms. Hardware modules can be connected to or disconnected from the CAN bus while the system is working. It has been tested in our mobile robot Rato, based on a RWI (Real World Interface) mobile platform, to replace the old sensor and motor controllers. It has also been used in the design of two new robots: BellBot and WatchBot. Currently, our hardware integration architecture supports different sensors, actuators and control subsystems, such as motor controllers and inertial measurement units. The integration architecture was tested and compared with other solutions through a performance analysis of relevant parameters such as transmission efficiency and bandwidth usage. The results conclude that the proposed solution implements a lightweight communication protocol for mobile robot applications that avoids transmission delays and overhead. PMID:28467381

Distributed and Modular CAN-Based Architecture for Hardware Control and Sensor Data Integration.

PubMed

Losada, Diego P; Fernández, Joaquín L; Paz, Enrique; Sanz, Rafael

2017-05-03

In this article, we present a CAN-based (Controller Area Network) distributed system to integrate sensors, actuators and hardware controllers in a mobile robot platform. With this work, we provide a robust, simple, flexible and open system to make hardware elements or subsystems communicate, that can be applied to different robots or mobile platforms. Hardware modules can be connected to or disconnected from the CAN bus while the system is working. It has been tested in our mobile robot Rato, based on a RWI (Real World Interface) mobile platform, to replace the old sensor and motor controllers. It has also been used in the design of two new robots: BellBot and WatchBot. Currently, our hardware integration architecture supports different sensors, actuators and control subsystems, such as motor controllers and inertial measurement units. The integration architecture was tested and compared with other solutions through a performance analysis of relevant parameters such as transmission efficiency and bandwidth usage. The results conclude that the proposed solution implements a lightweight communication protocol for mobile robot applications that avoids transmission delays and overhead.

Investigation of Tumor Cell Behaviors on a Vascular Microenvironment-Mimicking Microfluidic Chip

PubMed Central

Huang, Rong; Zheng, Wenfu; Liu, Wenwen; Zhang, Wei; Long, Yunze; Jiang, Xingyu

2015-01-01

The extravasation of tumor cells is a key event in tumor metastasis. However, the mechanism underlying tumor cell extravasation remains unknown, mainly hindered by obstacles from the lack of complexity of biological tissues in conventional cell culture, and the costliness and ethical issues of in vivo experiments. Thus, a cheap, time and labor saving, and most of all, vascular microenvironment-mimicking research model is desirable. Herein, we report a microfluidic chip-based tumor extravasation research model which is capable of simultaneously simulating both mechanical and biochemical microenvironments of human vascular systems and analyzing their synergistic effects on the tumor extravasation. Under different mechanical conditions of the vascular system, the tumor cells (HeLa cells) had the highest viability and adhesion activity in the microenvironment of the capillary. The integrity of endothelial cells (ECs) monolayer was destroyed by tumor necrosis factor-α (TNF-α) in a hemodynamic background, which facilitated the tumor cell adhesion, this situation was recovered by the administration of platinum nanoparticles (Pt-NPs). This model bridges the gap between cell culture and animal experiments and is a promising platform for studying tumor behaviors in the vascular system. PMID:26631692

Wearables in Medicine.

PubMed

Yetisen, Ali K; Martinez-Hurtado, Juan Leonardo; Ünal, Barış; Khademhosseini, Ali; Butt, Haider

2018-06-11

Wearables as medical technologies are becoming an integral part of personal analytics, measuring physical status, recording physiological parameters, or informing schedule for medication. These continuously evolving technology platforms do not only promise to help people pursue a healthier life style, but also provide continuous medical data for actively tracking metabolic status, diagnosis, and treatment. Advances in the miniaturization of flexible electronics, electrochemical biosensors, microfluidics, and artificial intelligence algorithms have led to wearable devices that can generate real-time medical data within the Internet of things. These flexible devices can be configured to make conformal contact with epidermal, ocular, intracochlear, and dental interfaces to collect biochemical or electrophysiological signals. This article discusses consumer trends in wearable electronics, commercial and emerging devices, and fabrication methods. It also reviews real-time monitoring of vital signs using biosensors, stimuli-responsive materials for drug delivery, and closed-loop theranostic systems. It covers future challenges in augmented, virtual, and mixed reality, communication modes, energy management, displays, conformity, and data safety. The development of patient-oriented wearable technologies and their incorporation in randomized clinical trials will facilitate the design of safe and effective approaches. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Cost-Effective Fluorescence Mini-Microscope with Adjustable Magnifications for Biomedical Applications

PubMed Central

Zhang, Yu Shrike; Ribas, João; Nadhman, Akhtar; Aleman, Julio; Selimović, Šeila; Lesher-Perez, Sasha Cai; Wang, Ting; Manoharan, Vijayan; Shin, Su-Ryon; Damilano, Alessia; Annabi, Nasim; Dokmeci, Mehmet Remzi; Takayama, Shuichi; Khademhosseini, Ali

2015-01-01

We have designed and fabricated a miniature microscope from off-the-shelf components and webcam, with built-in fluorescence capability for biomedical applications. The mini-microscope was able to detect both biochemical parameters such as cell/tissue viability (e.g. Live/Dead assay), and biophysical properties of the microenvironment such as oxygen levels in microfabricated tissues based on an oxygen-sensitive fluorescent dye. This mini-microscope has adjustable magnifications from 8-60X, achieves a resolution as high as <2 μm, and possesses a long working distance of 4.5 mm (at a magnification of 8X). The mini-microscope was able to chronologically monitor cell migration and analyze beating of microfluidic liver and cardiac bioreactors in real time, respectively. The mini-microscope system is cheap, and its modularity allows convenient integration with a wide variety of pre-existing platforms including but not limited to, cell culture plates, microfluidic devices, and organs-on-a-chip systems. Therefore, we envision its widespread applications in cell biology, tissue engineering, biosensing, microfluidics, and organs-on-chips, which can potentially replace conventional bench-top microscopy where long-term in situ and large-scale imaging/analysis is required. PMID:26282117

A cost-effective fluorescence mini-microscope for biomedical applications.

PubMed

Zhang, Yu Shrike; Ribas, João; Nadhman, Akhtar; Aleman, Julio; Selimović, Šeila; Lesher-Perez, Sasha Cai; Wang, Ting; Manoharan, Vijayan; Shin, Su-Ryon; Damilano, Alessia; Annabi, Nasim; Dokmeci, Mehmet Remzi; Takayama, Shuichi; Khademhosseini, Ali

2015-01-01

We have designed and fabricated a miniature microscope from off-the-shelf components and a webcam, with built-in fluorescence capability for biomedical applications. The mini-microscope was able to detect both biochemical parameters, such as cell/tissue viability (e.g. live/dead assay), and biophysical properties of the microenvironment such as oxygen levels in microfabricated tissues based on an oxygen-sensitive fluorescent dye. This mini-microscope has adjustable magnifications from 8-60×, achieves a resolution as high as <2 μm, and possesses a long working distance of 4.5 mm (at a magnification of 8×). The mini-microscope was able to chronologically monitor cell migration and analyze beating of microfluidic liver and cardiac bioreactors in real time, respectively. The mini-microscope system is cheap, and its modularity allows convenient integration with a wide variety of pre-existing platforms including, but not limited to, cell culture plates, microfluidic devices, and organs-on-a-chip systems. Therefore, we envision its widespread application in cell biology, tissue engineering, biosensing, microfluidics, and organs-on-chips, which can potentially replace conventional bench-top microscopy where long-term in situ and large-scale imaging/analysis is required.

Feasibility Study on a Microwave-Based Sensor for Measuring Hydration Level Using Human Skin Models

PubMed Central

Brendtke, Rico; Wiehl, Michael; Groeber, Florian; Schwarz, Thomas; Walles, Heike; Hansmann, Jan

2016-01-01

Tissue dehydration results in three major types of exsiccosis—hyper-, hypo-, or isonatraemia. All three types entail alterations of salt concentrations leading to impaired biochemical processes, and can finally cause severe morbidity. The aim of our study was to demonstrate the feasibility of a microwave-based sensor technology for the non-invasive measurement of the hydration status. Electromagnetic waves at high frequencies interact with molecules, especially water. Hence, if a sample contains free water molecules, this can be detected in a reflected microwave signal. To develop the sensor system, human three-dimensional skin equivalents were instituted as a standardized test platform mimicking reproducible exsiccosis scenarios. Therefore, skin equivalents with a specific hydration and density of matrix components were generated and microwave measurements were performed. Hydration-specific spectra allowed deriving the hydration state of the skin models. A further advantage of the skin equivalents was the characterization of the impact of distinct skin components on the measured signals to investigate mechanisms of signal generation. The results demonstrate the feasibility of a non-invasive microwave-based hydration sensor technology. The sensor bears potential to be integrated in a wearable medical device for personal health monitoring. PMID:27046226

Feasibility Study on a Microwave-Based Sensor for Measuring Hydration Level Using Human Skin Models.

PubMed

Brendtke, Rico; Wiehl, Michael; Groeber, Florian; Schwarz, Thomas; Walles, Heike; Hansmann, Jan

2016-01-01

Tissue dehydration results in three major types of exsiccosis--hyper-, hypo-, or isonatraemia. All three types entail alterations of salt concentrations leading to impaired biochemical processes, and can finally cause severe morbidity. The aim of our study was to demonstrate the feasibility of a microwave-based sensor technology for the non-invasive measurement of the hydration status. Electromagnetic waves at high frequencies interact with molecules, especially water. Hence, if a sample contains free water molecules, this can be detected in a reflected microwave signal. To develop the sensor system, human three-dimensional skin equivalents were instituted as a standardized test platform mimicking reproducible exsiccosis scenarios. Therefore, skin equivalents with a specific hydration and density of matrix components were generated and microwave measurements were performed. Hydration-specific spectra allowed deriving the hydration state of the skin models. A further advantage of the skin equivalents was the characterization of the impact of distinct skin components on the measured signals to investigate mechanisms of signal generation. The results demonstrate the feasibility of a non-invasive microwave-based hydration sensor technology. The sensor bears potential to be integrated in a wearable medical device for personal health monitoring.

Metabonomics of ageing - Towards understanding metabolism of a long and healthy life.

PubMed

Martin, Francois-Pierre J; Montoliu, Ivan; Kussmann, Martin

2017-07-01

Systems biology approaches have been increasingly employed in clinical studies to enhance our understanding of the role of genetics, environmental factors and their interactions on nutritional, health and disease status. Amongst the new omics technologies, metabonomics has emerged as a robust platform to capture metabolic and nutritional requirements by enabling, in a minimally invasive fashion, the monitoring of a wide range of biochemical compounds. Their variations reflect comprehensively the various molecular regulatory processes, which are tightly controlled and under the influence of genetics, diet, gut microbiota and other environmental factors. They are providing key insights into complex metabolic phenomena as well as into differences and specificities at individual and population level. The aim of this review is to evaluate promising metabolic insights towards understanding metabolism of a long and healthy life from pre-clinical and clinical metabonomics studies. We will also discuss analytical approaches to enable data integration, with an emphasis on the longitudinal component. Herein, we will illustrate current examples, challenges and perspectives in the applications of metabonomics monitoring and modelling approaches in the context of healthy ageing research. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

RNA–protein binding kinetics in an automated microfluidic reactor

PubMed Central

Ridgeway, William K.; Seitaridou, Effrosyni; Phillips, Rob; Williamson, James R.

2009-01-01

Microfluidic chips can automate biochemical assays on the nanoliter scale, which is of considerable utility for RNA–protein binding reactions that would otherwise require large quantities of proteins. Unfortunately, complex reactions involving multiple reactants cannot be prepared in current microfluidic mixer designs, nor is investigation of long-time scale reactions possible. Here, a microfluidic ‘Riboreactor’ has been designed and constructed to facilitate the study of kinetics of RNA–protein complex formation over long time scales. With computer automation, the reactor can prepare binding reactions from any combination of eight reagents, and is optimized to monitor long reaction times. By integrating a two-photon microscope into the microfluidic platform, 5-nl reactions can be observed for longer than 1000 s with single-molecule sensitivity and negligible photobleaching. Using the Riboreactor, RNA–protein binding reactions with a fragment of the bacterial 30S ribosome were prepared in a fully automated fashion and binding rates were consistent with rates obtained from conventional assays. The microfluidic chip successfully combines automation, low sample consumption, ultra-sensitive fluorescence detection and a high degree of reproducibility. The chip should be able to probe complex reaction networks describing the assembly of large multicomponent RNPs such as the ribosome. PMID:19759214

Remote sensing of key grassland nutrients using hyperspectral techniques in KwaZulu-Natal, South Africa

NASA Astrophysics Data System (ADS)

Singh, Leeth; Mutanga, Onisimo; Mafongoya, Paramu; Peerbhay, Kabir

2017-07-01

The concentration of forage fiber content is critical in explaining the palatability of forage quality for livestock grazers in tropical grasslands. Traditional methods of determining forage fiber content are usually time consuming, costly, and require specialized laboratory analysis. With the potential of remote sensing technologies, determination of key fiber attributes can be made more accurately. This study aims to determine the effectiveness of known absorption wavelengths for detecting forage fiber biochemicals, neutral detergent fiber, acid detergent fiber, and lignin using hyperspectral data. Hyperspectral reflectance spectral measurements (350 to 2500 nm) of grass were collected and implemented within the random forest (RF) ensemble. Results show successful correlations between the known absorption features and the biochemicals with coefficients of determination (R2) ranging from 0.57 to 0.81 and root mean square errors ranging from 6.97 to 3.03 g/kg. In comparison, using the entire dataset, the study identified additional wavelengths for detecting fiber biochemicals, which contributes to the accurate determination of forage quality in a grassland environment. Overall, the results showed that hyperspectral remote sensing in conjunction with the competent RF ensemble could discriminate each key biochemical evaluated. This study shows the potential to upscale the methodology to a space-borne multispectral platform with similar spectral configurations for an accurate and cost effective mapping analysis of forage quality.

Antioxidant power as biochemical endpoint in bread for screening and early managing quality and toxicant-related safety anomalies in food production.

PubMed

Dragone, Roberto; Ermilov, Laura; Grasso, Gerardo; Maggioni, Silvia; Mantovani, Alberto; Frazzoli, Chiara

2016-08-01

Flaxseeds are both a food ingredient and a natural source of antioxidants (e.g. lignans, PUFAs) and pro-oxidant contaminants (e.g. cadmium): the variable mixture of anti- and pro-oxidant substances may impact on the redox homeostasis of flaxseed-enriched foods. The antioxidant power is studied here as biochemical activity of flaxseeds in white wheat bread and as endpoint for possible screening of anomalous variations of bioactive mixtures (antioxidants vs. prooxidants) in food matrices. A bioprobe assay based on the superoxide dismutase (SOD) enzyme (6 channels of the multiprobe bioelectronic platform BEST) was performed on white wheat bread with and without flaxseeds. Nine BEST channels were simultaneously used for validation and monitoring of measuring conditions (temperature, pH, conductivity). Findings were compared with quantitative analysis of antioxidants and pro-oxidant contaminants. Organic and aqueous extracts of both bread types were examined in parallel. The SOD-probe detected the difference in antioxidant power given by 10% flaxseed, thus supporting the use of antioxidant power detected by bioenzymatic screening as sensitive biochemical endpoint. Mixtures of bioactive molecules in foods generate biochemical activities that can be monitored as time-effective indicators of invariability, which is pivotal in the daily control of anomalies in food production and therefore in the protection of consumers' health. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optofluidic plasmonic onchip nanosensor array for biodetection

NASA Astrophysics Data System (ADS)

Huang, Min

Surface plasmon resonance (SPR) sensing has been demonstrated in the past decade to be the gold standard technique for biochemical interaction analysis, and plays an important role in drug discovery and biomedical research. The technique circumvents the need of fluorescence/radioactive tagging or enzymatic detection, enables ultrasensitive remote sensing, and quantitatively monitors bio-interaction in real time. Although SPR has these attractive features that can satisfy most research/clinic requirements, there still exist problems that limit its applications. First, the reflection geometry of the prism coupling scheme adds limitations for high throughput screening application. Additionally, SPR instrumentations are bulky and not suitable for point-of-care settings. Moreover, the SPR sensor is embedded in conventional micro-fluidic cells, in which the sensor performance is limited by inefficient analyte transport. Suspended plasmonic nanohole array (PNA) offers an opportunity to overcome these limitations. A collinear excitation/collection coupling scheme combined with the small footprint of PNA provides unique platform for multiplexing and system minimization. The suspended nanohole structure also offers a unique configuration to integrate nano-photonics with nano-fluidics. This thesis focuses on developing a lab-on-a-chip PNA platform for point-of-care bio-detection. To achieve this, we first demonstrate that the figure-of-merit of our PNA sensor surpasses that of the prism coupled SPR. We also show that the ultrasensitive label-free PNA sensor is able to directly detect intact viruses from biological media at clinically relevant concentrations with little sample preparation. We then present a plasmonic microarray with over one million PNA sensors on a microscope slide for high throughput screening applications. A dual-color filter imaging method is introduced to increase the accuracy, reliability, and signal-to-noise ratio in a highly multiplexed manner. Finally, we present a nanoplasmonic-nanofluidic platform enabling active delivery of analyte to the sensor. Sensor response time is reduced by an order of magnitude compared to the conventional flow scheme. A dynamic range spanning 5 orders of magnitude from 103 to 107 particles/mL is shown on this platform corresponding to analyte concentration sufficient for clinical applications. The proposed approach opens up opportunities of a lab-on-a-chip bio-detection system for drug screening, disease diagnostic as well as clinic studies.

A Robust Cooling Platform for NIS Junction Refrigeration and sub-Kelvin Cryogenic Systems

NASA Astrophysics Data System (ADS)

Wilson, B.; Atlas, M.; Lowell, P.; Moyerman, S.; Stebor, N.; Ullom, J.; Keating, B.

2014-08-01

Recent advances in Normal metal-insulator-superconductor (NIS) tunnel junctions (Clark et al. Appl Phys Lett 86: 173508, 2005, Appl Phys Lett 84: 4, 2004) have proven these devices to be a viable technology for sub-Kelvin refrigeration. NIS junction coolers, coupled to a separate cold stage, provide a flexible platform for cooling a wide range of user-supplied payloads. Recently, a stage was cooled from 290 to 256 mK (Lowell et al. Appl Phys Lett 102: 082601 2013), but further mechanical and electrical improvements are necessary for the stage to reach its full potential. We have designed and built a new Kevlar suspended cooling platform for NIS junction refrigeration that is both lightweight and well thermally isolated; the calculated parasitic loading is pW from 300 to 100 mK. The platform is structurally rigid with a measured deflection of 25 m under a 2.5 kg load and has an integrated mechanical heat switch driven by a superconducting stepper motor with thermal conductivity G W/K at 300 mK. An integrated radiation shield limits thermal loading and a modular platform accommodates enough junctions to provide nanowatts of continuous cooling power. The compact stage size of 7.6 cm 8.6 cm 4.8 cm and overall radiation shield size of 8.9 cm 10.0 cm 7.0 cm along with minimal electrical power requirements allow easy integration into a range of cryostats. We present the design, construction, and performance of this cooling platform as well as projections for coupling to arrays of NIS junctions and other future applications.

Development and Characteristics of a Mobile, Semi-Autonomous Floating Platform for in situ Lake Measurements

NASA Astrophysics Data System (ADS)

Barry, D.; Lemmin, U.; Le Dantec, N.; Zulliger, L.; Rusterholz, M.; Bolay, M.; Rossier, J.; Kangur, K.

2013-12-01

In the development of sustainable management strategies of lakes more insight into their physical, chemical and ecological dynamics is needed. Field data obtained from various types of sensors with adequate spatial and temporal sampling rate are essential to understand better the processes that govern fluxes and pathways of water masses and transported compounds, whether for model validation or for monitoring purposes. One advantage of unmanned platforms is that they limit the disturbances typically affecting the quality of data collected on small vessels, including perturbations caused by movements of onboard crew. We have developed a mobile, semi-autonomous floating platform with 8 h power autonomy using a 5 m long by 2.5 m wide catamaran. Our approach focused on modularity and high payload capacity in order to accommodate a large number of sensors both in terms of electronic (power and data) and mechanical constraints of integration. Software architecture and onboard electronics use National Instruments technology to simplify and standardize integration of sensors, actuators and communication. Piecewise-movable deck sections allow optimizing platform stability depending on the payload. The entire system is controlled by a remote computer located on an accompanying vessel and connected via a wireless link with a range of over 1 km. Real-time transmission of GPS-stamped measurements allows immediate modifications in the survey plan if needed. The displacement of the platform is semi-autonomous, with the options of either autopilot mode following a pre-planned course specified by waypoints or remote manual control from the accompanying vessel. Maintenance of permanent control over the platform displacement is required for safety reasons with respect to other users of the lake. Currently, the sensor payload comprises an array of fast temperature probes, a bottom-tracking ADCP and atmospheric sensors including a radiometer. A towed CTD with additional water quality sensors operated from a remotely controlled winch is presently being integrated. Field tests have shown that the platform is reliable, capable of collecting long transects of 2D lake and collocated atmospheric boundary layer data and adaptable to integrate new sensors.

Improving Marine Ecosystem Models with Biochemical Tracers

NASA Astrophysics Data System (ADS)

Pethybridge, Heidi R.; Choy, C. Anela; Polovina, Jeffrey J.; Fulton, Elizabeth A.

2018-01-01

Empirical data on food web dynamics and predator-prey interactions underpin ecosystem models, which are increasingly used to support strategic management of marine resources. These data have traditionally derived from stomach content analysis, but new and complementary forms of ecological data are increasingly available from biochemical tracer techniques. Extensive opportunities exist to improve the empirical robustness of ecosystem models through the incorporation of biochemical tracer data and derived indices, an area that is rapidly expanding because of advances in analytical developments and sophisticated statistical techniques. Here, we explore the trophic information required by ecosystem model frameworks (species, individual, and size based) and match them to the most commonly used biochemical tracers (bulk tissue and compound-specific stable isotopes, fatty acids, and trace elements). Key quantitative parameters derived from biochemical tracers include estimates of diet composition, niche width, and trophic position. Biochemical tracers also provide powerful insight into the spatial and temporal variability of food web structure and the characterization of dominant basal and microbial food web groups. A major challenge in incorporating biochemical tracer data into ecosystem models is scale and data type mismatches, which can be overcome with greater knowledge exchange and numerical approaches that transform, integrate, and visualize data.

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.

20170312 - Computer Simulation of Developmental ...

EPA Pesticide Factsheets

Rationale: Recent progress in systems toxicology and synthetic biology have paved the way to new thinking about in vitro/in silico modeling of developmental processes and toxicities, both for embryological and reproductive impacts. Novel in vitro platforms such as 3D organotypic culture models, engineered microscale tissues and complex microphysiological systems (MPS), together with computational models and computer simulation of tissue dynamics, lend themselves to a integrated testing strategies for predictive toxicology. As these emergent methodologies continue to evolve, they must be integrally tied to maternal/fetal physiology and toxicity of the developing individual across early lifestage transitions, from fertilization to birth, through puberty and beyond. Scope: This symposium will focus on how the novel technology platforms can help now and in the future, with in vitro/in silico modeling of complex biological systems for developmental and reproductive toxicity issues, and translating systems models into integrative testing strategies. The symposium is based on three main organizing principles: (1) that novel in vitro platforms with human cells configured in nascent tissue architectures with a native microphysiological environments yield mechanistic understanding of developmental and reproductive impacts of drug/chemical exposures; (2) that novel in silico platforms with high-throughput screening (HTS) data, biologically-inspired computational models of

Computer Simulation of Developmental Processes and ...

EPA Pesticide Factsheets

Rationale: Recent progress in systems toxicology and synthetic biology have paved the way to new thinking about in vitro/in silico modeling of developmental processes and toxicities, both for embryological and reproductive impacts. Novel in vitro platforms such as 3D organotypic culture models, engineered microscale tissues and complex microphysiological systems (MPS), together with computational models and computer simulation of tissue dynamics, lend themselves to a integrated testing strategies for predictive toxicology. As these emergent methodologies continue to evolve, they must be integrally tied to maternal/fetal physiology and toxicity of the developing individual across early lifestage transitions, from fertilization to birth, through puberty and beyond. Scope: This symposium will focus on how the novel technology platforms can help now and in the future, with in vitro/in silico modeling of complex biological systems for developmental and reproductive toxicity issues, and translating systems models into integrative testing strategies. The symposium is based on three main organizing principles: (1) that novel in vitro platforms with human cells configured in nascent tissue architectures with a native microphysiological environments yield mechanistic understanding of developmental and reproductive impacts of drug/chemical exposures; (2) that novel in silico platforms with high-throughput screening (HTS) data, biologically-inspired computational models of

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.

The Development of GIS Educational Resources Sharing among Central Taiwan Universities

NASA Astrophysics Data System (ADS)

Chou, T.-Y.; Yeh, M.-L.; Lai, Y.-C.

2011-09-01

Using GIS in the classroom enhance students' computer skills and explore the range of knowledge. The paper highlights GIS integration on e-learning platform and introduces a variety of abundant educational resources. This research project will demonstrate tools for e-learning environment and delivers some case studies for learning interaction from Central Taiwan Universities. Feng Chia University (FCU) obtained a remarkable academic project subsidized by Ministry of Education and developed e-learning platform for excellence in teaching/learning programs among Central Taiwan's universities. The aim of the project is to integrate the educational resources of 13 universities in central Taiwan. FCU is serving as the hub of Center University. To overcome the problem of distance, e-platforms have been established to create experiences with collaboration enhanced learning. The e-platforms provide coordination of web service access among the educational community and deliver GIS educational resources. Most of GIS related courses cover the development of GIS, principles of cartography, spatial data analysis and overlaying, terrain analysis, buffer analysis, 3D GIS application, Remote Sensing, GPS technology, and WebGIS, MobileGIS, ArcGIS manipulation. In each GIS case study, students have been taught to know geographic meaning, collect spatial data and then use ArcGIS software to analyze spatial data. On one of e-Learning platforms provide lesson plans and presentation slides. Students can learn Arc GIS online. As they analyze spatial data, they can connect to GIS hub to get data they need including satellite images, aerial photos, and vector data. Moreover, e-learning platforms provide solutions and resources. Different levels of image scales have been integrated into the systems. Multi-scale spatial development and analyses in Central Taiwan integrate academic research resources among CTTLRC partners. Thus, establish decision-making support mechanism in teaching and learning. Accelerate communication, cooperation and sharing among academic units

IIIV/Si Nanoscale Lasers and Their Integration with Silicon Photonics

NASA Astrophysics Data System (ADS)

Bondarenko, Olesya

The rapidly evolving global information infrastructure requires ever faster data transfer within computer networks and stations. Integrated chip scale photonics can pave the way to accelerated signal manipulation and boost bandwidth capacity of optical interconnects in a compact and ergonomic arrangement. A key building block for integrated photonic circuits is an on-chip laser. In this dissertation we explore ways to reduce the physical footprint of semiconductor lasers and make them suitable for high density integration on silicon, a standard material platform for today's integrated circuits. We demonstrated the first room temperature metalo-dielectric nanolaser, sub-wavelength in all three dimensions. Next, we demonstrated a nanolaser on silicon, showing the feasibility of its integration with this platform. We also designed and realized an ultracompact feedback laser with edge-emitting structure, amenable for in-plane coupling with a standard silicon waveguide. Finally, we discuss the challenges and propose solutions for improvement of the device performance and practicality.

Ontology driven integration platform for clinical and translational research

PubMed Central

Mirhaji, Parsa; Zhu, Min; Vagnoni, Mattew; Bernstam, Elmer V; Zhang, Jiajie; Smith, Jack W

2009-01-01

Semantic Web technologies offer a promising framework for integration of disparate biomedical data. In this paper we present the semantic information integration platform under development at the Center for Clinical and Translational Sciences (CCTS) at the University of Texas Health Science Center at Houston (UTHSC-H) as part of our Clinical and Translational Science Award (CTSA) program. We utilize the Semantic Web technologies not only for integrating, repurposing and classification of multi-source clinical data, but also to construct a distributed environment for information sharing, and collaboration online. Service Oriented Architecture (SOA) is used to modularize and distribute reusable services in a dynamic and distributed environment. Components of the semantic solution and its overall architecture are described. PMID:19208190

SOCRAT Platform Design: A Web Architecture for Interactive Visual Analytics Applications

PubMed Central

Kalinin, Alexandr A.; Palanimalai, Selvam; Dinov, Ivo D.

2018-01-01

The modern web is a successful platform for large scale interactive web applications, including visualizations. However, there are no established design principles for building complex visual analytics (VA) web applications that could efficiently integrate visualizations with data management, computational transformation, hypothesis testing, and knowledge discovery. This imposes a time-consuming design and development process on many researchers and developers. To address these challenges, we consider the design requirements for the development of a module-based VA system architecture, adopting existing practices of large scale web application development. We present the preliminary design and implementation of an open-source platform for Statistics Online Computational Resource Analytical Toolbox (SOCRAT). This platform defines: (1) a specification for an architecture for building VA applications with multi-level modularity, and (2) methods for optimizing module interaction, re-usage, and extension. To demonstrate how this platform can be used to integrate a number of data management, interactive visualization, and analysis tools, we implement an example application for simple VA tasks including raw data input and representation, interactive visualization and analysis. PMID:29630069

Portable Microfluidic Integrated Plasmonic Platform for Pathogen Detection

PubMed Central

Tokel, Onur; Yildiz, Umit Hakan; Inci, Fatih; Durmus, Naside Gozde; Ekiz, Okan Oner; Turker, Burak; Cetin, Can; Rao, Shruthi; Sridhar, Kaushik; Natarajan, Nalini; Shafiee, Hadi; Dana, Aykutlu; Demirci, Utkan

2015-01-01

Timely detection of infectious agents is critical in early diagnosis and treatment of infectious diseases. Conventional pathogen detection methods, such as enzyme linked immunosorbent assay (ELISA), culturing or polymerase chain reaction (PCR) require long assay times, and complex and expensive instruments, which are not adaptable to point-of-care (POC) needs at resource-constrained as well as primary care settings. Therefore, there is an unmet need to develop simple, rapid, and accurate methods for detection of pathogens at the POC. Here, we present a portable, multiplex, inexpensive microfluidic-integrated surface plasmon resonance (SPR) platform that detects and quantifies bacteria, i.e., Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) rapidly. The platform presented reliable capture and detection of E. coli at concentrations ranging from ~105 to 3.2 × 107 CFUs/mL in phosphate buffered saline (PBS) and peritoneal dialysis (PD) fluid. The multiplexing and specificity capability of the platform was also tested with S. aureus samples. The presented platform technology could potentially be applicable to capture and detect other pathogens at the POC and primary care settings. PMID:25801042

SOCRAT Platform Design: A Web Architecture for Interactive Visual Analytics Applications.

PubMed

Kalinin, Alexandr A; Palanimalai, Selvam; Dinov, Ivo D

2017-04-01

The modern web is a successful platform for large scale interactive web applications, including visualizations. However, there are no established design principles for building complex visual analytics (VA) web applications that could efficiently integrate visualizations with data management, computational transformation, hypothesis testing, and knowledge discovery. This imposes a time-consuming design and development process on many researchers and developers. To address these challenges, we consider the design requirements for the development of a module-based VA system architecture, adopting existing practices of large scale web application development. We present the preliminary design and implementation of an open-source platform for Statistics Online Computational Resource Analytical Toolbox (SOCRAT). This platform defines: (1) a specification for an architecture for building VA applications with multi-level modularity, and (2) methods for optimizing module interaction, re-usage, and extension. To demonstrate how this platform can be used to integrate a number of data management, interactive visualization, and analysis tools, we implement an example application for simple VA tasks including raw data input and representation, interactive visualization and analysis.

A Ubiquitous Sensor Network Platform for Integrating Smart Devices into the Semantic Sensor Web

PubMed Central

de Vera, David Díaz Pardo; Izquierdo, Álvaro Sigüenza; Vercher, Jesús Bernat; Gómez, Luis Alfonso Hernández

2014-01-01

Ongoing Sensor Web developments make a growing amount of heterogeneous sensor data available to smart devices. This is generating an increasing demand for homogeneous mechanisms to access, publish and share real-world information. This paper discusses, first, an architectural solution based on Next Generation Networks: a pilot Telco Ubiquitous Sensor Network (USN) Platform that embeds several OGC® Sensor Web services. This platform has already been deployed in large scale projects. Second, the USN-Platform is extended to explore a first approach to Semantic Sensor Web principles and technologies, so that smart devices can access Sensor Web data, allowing them also to share richer (semantically interpreted) information. An experimental scenario is presented: a smart car that consumes and produces real-world information which is integrated into the Semantic Sensor Web through a Telco USN-Platform. Performance tests revealed that observation publishing times with our experimental system were well within limits compatible with the adequate operation of smart safety assistance systems in vehicles. On the other hand, response times for complex queries on large repositories may be inappropriate for rapid reaction needs. PMID:24945678

DoctorEye: A clinically driven multifunctional platform, for accurate processing of tumors in medical images.

PubMed

Skounakis, Emmanouil; Farmaki, Christina; Sakkalis, Vangelis; Roniotis, Alexandros; Banitsas, Konstantinos; Graf, Norbert; Marias, Konstantinos

2010-01-01

This paper presents a novel, open access interactive platform for 3D medical image analysis, simulation and visualization, focusing in oncology images. The platform was developed through constant interaction and feedback from expert clinicians integrating a thorough analysis of their requirements while having an ultimate goal of assisting in accurately delineating tumors. It allows clinicians not only to work with a large number of 3D tomographic datasets but also to efficiently annotate multiple regions of interest in the same session. Manual and semi-automatic segmentation techniques combined with integrated correction tools assist in the quick and refined delineation of tumors while different users can add different components related to oncology such as tumor growth and simulation algorithms for improving therapy planning. The platform has been tested by different users and over large number of heterogeneous tomographic datasets to ensure stability, usability, extensibility and robustness with promising results. the platform, a manual and tutorial videos are available at: http://biomodeling.ics.forth.gr. it is free to use under the GNU General Public License.

A ubiquitous sensor network platform for integrating smart devices into the semantic sensor web.

PubMed

de Vera, David Díaz Pardo; Izquierdo, Alvaro Sigüenza; Vercher, Jesús Bernat; Hernández Gómez, Luis Alfonso

2014-06-18

Ongoing Sensor Web developments make a growing amount of heterogeneous sensor data available to smart devices. This is generating an increasing demand for homogeneous mechanisms to access, publish and share real-world information. This paper discusses, first, an architectural solution based on Next Generation Networks: a pilot Telco Ubiquitous Sensor Network (USN) Platform that embeds several OGC® Sensor Web services. This platform has already been deployed in large scale projects. Second, the USN-Platform is extended to explore a first approach to Semantic Sensor Web principles and technologies, so that smart devices can access Sensor Web data, allowing them also to share richer (semantically interpreted) information. An experimental scenario is presented: a smart car that consumes and produces real-world information which is integrated into the Semantic Sensor Web through a Telco USN-Platform. Performance tests revealed that observation publishing times with our experimental system were well within limits compatible with the adequate operation of smart safety assistance systems in vehicles. On the other hand, response times for complex queries on large repositories may be inappropriate for rapid reaction needs.

Wearable Platform for Real-time Monitoring of Sodium in Sweat.

PubMed

McCaul, Margaret; Porter, Adam; Barrett, Ruairi; White, Paddy; Stroiescu, Florien; Wallace, Gordon; Diamond, Dermot

2018-06-19

A fully integrated and wearable platform for harvesting and analysing sweat sodium concentration in real time during exercise has been developed and tested. The platform was largely produced using 3D printing, which greatly simplifies fabrication and operation compared to previous versions generated with traditional production techniques. The 3D printed platform doubles the capacity of the sample storage reservoir to about 1.3 ml, reduces the assembly time and provides simple and precise component alignment and contact of the integrated solid-state ion-selective and reference electrodes with the sorbent material. The sampling flowrate in the device can be controlled by introducing threads to enhance wicking of sweat from the skin, across the electrodes to the storage area. The platform was characterised in the lab and in exercise trials over a period of about 60 minutes continuous monitoring. Sweat sodium concentration was found to rise initially to approximately 17 mM and decline gradually over the period of the trial to about 11-12 mM. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integrated Design and Implementation of Embedded Control Systems with Scilab

PubMed Central

Ma, Longhua; Xia, Feng; Peng, Zhe

2008-01-01

Embedded systems are playing an increasingly important role in control engineering. Despite their popularity, embedded systems are generally subject to resource constraints and it is therefore difficult to build complex control systems on embedded platforms. Traditionally, the design and implementation of control systems are often separated, which causes the development of embedded control systems to be highly time-consuming and costly. To address these problems, this paper presents a low-cost, reusable, reconfigurable platform that enables integrated design and implementation of embedded control systems. To minimize the cost, free and open source software packages such as Linux and Scilab are used. Scilab is ported to the embedded ARM-Linux system. The drivers for interfacing Scilab with several communication protocols including serial, Ethernet, and Modbus are developed. Experiments are conducted to test the developed embedded platform. The use of Scilab enables implementation of complex control algorithms on embedded platforms. With the developed platform, it is possible to perform all phases of the development cycle of embedded control systems in a unified environment, thus facilitating the reduction of development time and cost. PMID:27873827

Integrated Design and Implementation of Embedded Control Systems with Scilab.

PubMed

Ma, Longhua; Xia, Feng; Peng, Zhe

2008-09-05

Embedded systems are playing an increasingly important role in control engineering. Despite their popularity, embedded systems are generally subject to resource constraints and it is therefore difficult to build complex control systems on embedded platforms. Traditionally, the design and implementation of control systems are often separated, which causes the development of embedded control systems to be highly timeconsuming and costly. To address these problems, this paper presents a low-cost, reusable, reconfigurable platform that enables integrated design and implementation of embedded control systems. To minimize the cost, free and open source software packages such as Linux and Scilab are used. Scilab is ported to the embedded ARM-Linux system. The drivers for interfacing Scilab with several communication protocols including serial, Ethernet, and Modbus are developed. Experiments are conducted to test the developed embedded platform. The use of Scilab enables implementation of complex control algorithms on embedded platforms. With the developed platform, it is possible to perform all phases of the development cycle of embedded control systems in a unified environment, thus facilitating the reduction of development time and cost.

Surface presentation of biochemical cues for stem cell expansion - Spatial distribution of growth factors and self-assembly of extracellular matrix

NASA Astrophysics Data System (ADS)

Liu, Xingyu

Despite its great potential applications to stem cell technology and tissue engineering, matrix presentation of biochemical cues such as growth factors and extracellular matrix (ECM) components remains undefined. This is largely due to the difficulty in preserving the bioactivities of signaling molecules and in controlling the spatial distribution, cellular accessibility, molecular orientation and intermolecular assembly of the biochemical cues. This dissertation comprises of two parts that focuses on understanding surface presentation of a growth factor and ECM components, respectively. This dissertation addresses two fundamental questions in stem cell biology using two biomaterials platforms. How does nanoscale distribution of growth factor impact signaling activation and cellular behaviors of adult neural stem cells? How does ECM self-assembly impact human embryonic stem cell survival and proliferation? The first question was addressed by the design of a novel quantitative platform that allows the control of FGF-2 molecular presentation locally as either monomers or clusters when tethered to a polymeric substrate. This substrate-tethered FGF-2 enables a switch-like signaling activation in response to dose titration of FGF-2. This is in contrast to a continuous MAPK activation pattern elicited by soluble FGF-2. Consequently, cell proliferation, and spreading were also consistent with this FGF-2 does-response pattern. We demonstrated that the combination of FGF-2 concentration and its cluster size, rather than concentration alone, serves as the determinants to govern its biological effect on neural stem cells. The second part of this dissertation was inspired by the challenge that hESCs have extremely low clonal efficiency and hESC survival is critically dependent on cell substrate adhesion. We postulated that ECM integrity is a critical factor in preventing hESC anchorage-dependent apoptosis, and that the matrix for feeder-free culture need to be properly assembled in order to mimic the stem cell niche in vivo. First, we established assays that allow high-throughput quantification of hESC proliferation and ECM deposition. Human ESC survival was found to be highly sensitive to ECM assembly, and was improved by at least 20 times on substrates with well-assembled ECM. ECM polymerization alone improves clonal efficiency by at least 20 fold, from less than 0.1% to be 3-5%. This ratio is further improved to greater than 35% when combined with ROCK inhibitor, suggesting ECM polymerization underlines another critical factor in dictating hESC survival and growth. Given that many important signaling molecules including growth factors and extracellular matrix are highly enriched and restricted at the stem cell niche, we anticipate that our investigation into these questions provides better insight into the physiological roles of the stem cell niche components, and helps us to rationally direct stem cell fates in future stem cell-based therapeutic interventions.

Integrated sample-to-detection chip for nucleic acid test assays.

PubMed

Prakash, R; Pabbaraju, K; Wong, S; Tellier, R; Kaler, K V I S

2016-06-01

Nucleic acid based diagnostic techniques are routinely used for the detection of infectious agents. Most of these assays rely on nucleic acid extraction platforms for the extraction and purification of nucleic acids and a separate real-time PCR platform for quantitative nucleic acid amplification tests (NATs). Several microfluidic lab on chip (LOC) technologies have been developed, where mechanical and chemical methods are used for the extraction and purification of nucleic acids. Microfluidic technologies have also been effectively utilized for chip based real-time PCR assays. However, there are few examples of microfluidic systems which have successfully integrated these two key processes. In this study, we have implemented an electro-actuation based LOC micro-device that leverages multi-frequency actuation of samples and reagents droplets for chip based nucleic acid extraction and real-time, reverse transcription (RT) PCR (qRT-PCR) amplification from clinical samples. Our prototype micro-device combines chemical lysis with electric field assisted isolation of nucleic acid in a four channel parallel processing scheme. Furthermore, a four channel parallel qRT-PCR amplification and detection assay is integrated to deliver the sample-to-detection NAT chip. The NAT chip combines dielectrophoresis and electrostatic/electrowetting actuation methods with resistive micro-heaters and temperature sensors to perform chip based integrated NATs. The two chip modules have been validated using different panels of clinical samples and their performance compared with standard platforms. This study has established that our integrated NAT chip system has a sensitivity and specificity comparable to that of the standard platforms while providing up to 10 fold reduction in sample/reagent volumes.

Smart Cities Intelligence System (SMACiSYS) Integrating Sensor Web with Spatial Data Infrastructures (sensdi)

NASA Astrophysics Data System (ADS)

Bhattacharya, D.; Painho, M.

2017-09-01

The paper endeavours to enhance the Sensor Web with crucial geospatial analysis capabilities through integration with Spatial Data Infrastructure. The objective is development of automated smart cities intelligence system (SMACiSYS) with sensor-web access (SENSDI) utilizing geomatics for sustainable societies. There has been a need to develop automated integrated system to categorize events and issue information that reaches users directly. At present, no web-enabled information system exists which can disseminate messages after events evaluation in real time. Research work formalizes a notion of an integrated, independent, generalized, and automated geo-event analysing system making use of geo-spatial data under popular usage platform. Integrating Sensor Web With Spatial Data Infrastructures (SENSDI) aims to extend SDIs with sensor web enablement, converging geospatial and built infrastructure, and implement test cases with sensor data and SDI. The other benefit, conversely, is the expansion of spatial data infrastructure to utilize sensor web, dynamically and in real time for smart applications that smarter cities demand nowadays. Hence, SENSDI augments existing smart cities platforms utilizing sensor web and spatial information achieved by coupling pairs of otherwise disjoint interfaces and APIs formulated by Open Geospatial Consortium (OGC) keeping entire platform open access and open source. SENSDI is based on Geonode, QGIS and Java, that bind most of the functionalities of Internet, sensor web and nowadays Internet of Things superseding Internet of Sensors as well. In a nutshell, the project delivers a generalized real-time accessible and analysable platform for sensing the environment and mapping the captured information for optimal decision-making and societal benefit.

Virtual health platform for medical tourism purposes.

PubMed

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

2008-01-01

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

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

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

Quintana, John P.

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

From WSN towards WoT: Open API Scheme Based on oneM2M Platforms.

PubMed

Kim, Jaeho; Choi, Sung-Chan; Ahn, Il-Yeup; Sung, Nak-Myoung; Yun, Jaeseok

2016-10-06

Conventional computing systems have been able to be integrated into daily objects and connected to each other due to advances in computing and network technologies, such as wireless sensor networks (WSNs), forming a global network infrastructure, called the Internet of Things (IoT). To support the interconnection and interoperability between heterogeneous IoT systems, the availability of standardized, open application programming interfaces (APIs) is one of the key features of common software platforms for IoT devices, gateways, and servers. In this paper, we present a standardized way of extending previously-existing WSNs towards IoT systems, building the world of the Web of Things (WoT). Based on the oneM2M software platforms developed in the previous project, we introduce a well-designed open API scheme and device-specific thing adaptation software (TAS) enabling WSN elements, such as a wireless sensor node, to be accessed in a standardized way on a global scale. Three pilot services are implemented (i.e., a WiFi-enabled smart flowerpot, voice-based control for ZigBee-connected home appliances, and WiFi-connected AR.Drone control) to demonstrate the practical usability of the open API scheme and TAS modules. Full details on the method of integrating WSN elements into three example systems are described at the programming code level, which is expected to help future researchers in integrating their WSN systems in IoT platforms, such as oneM2M. We hope that the flexibly-deployable, easily-reusable common open API scheme and TAS-based integration method working with the oneM2M platforms will help the conventional WSNs in diverse industries evolve into the emerging WoT solutions.

Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach.

PubMed

Liang, Muxuan; Li, Zhizhong; Chen, Ting; Zeng, Jianyang

2015-01-01

Identification of cancer subtypes plays an important role in revealing useful insights into disease pathogenesis and advancing personalized therapy. The recent development of high-throughput sequencing technologies has enabled the rapid collection of multi-platform genomic data (e.g., gene expression, miRNA expression, and DNA methylation) for the same set of tumor samples. Although numerous integrative clustering approaches have been developed to analyze cancer data, few of them are particularly designed to exploit both deep intrinsic statistical properties of each input modality and complex cross-modality correlations among multi-platform input data. In this paper, we propose a new machine learning model, called multimodal deep belief network (DBN), to cluster cancer patients from multi-platform observation data. In our integrative clustering framework, relationships among inherent features of each single modality are first encoded into multiple layers of hidden variables, and then a joint latent model is employed to fuse common features derived from multiple input modalities. A practical learning algorithm, called contrastive divergence (CD), is applied to infer the parameters of our multimodal DBN model in an unsupervised manner. Tests on two available cancer datasets show that our integrative data analysis approach can effectively extract a unified representation of latent features to capture both intra- and cross-modality correlations, and identify meaningful disease subtypes from multi-platform cancer data. In addition, our approach can identify key genes and miRNAs that may play distinct roles in the pathogenesis of different cancer subtypes. Among those key miRNAs, we found that the expression level of miR-29a is highly correlated with survival time in ovarian cancer patients. These results indicate that our multimodal DBN based data analysis approach may have practical applications in cancer pathogenesis studies and provide useful guidelines for personalized cancer therapy.

From WSN towards WoT: Open API Scheme Based on oneM2M Platforms

PubMed Central

Kim, Jaeho; Choi, Sung-Chan; Ahn, Il-Yeup; Sung, Nak-Myoung; Yun, Jaeseok

2016-01-01

Conventional computing systems have been able to be integrated into daily objects and connected to each other due to advances in computing and network technologies, such as wireless sensor networks (WSNs), forming a global network infrastructure, called the Internet of Things (IoT). To support the interconnection and interoperability between heterogeneous IoT systems, the availability of standardized, open application programming interfaces (APIs) is one of the key features of common software platforms for IoT devices, gateways, and servers. In this paper, we present a standardized way of extending previously-existing WSNs towards IoT systems, building the world of the Web of Things (WoT). Based on the oneM2M software platforms developed in the previous project, we introduce a well-designed open API scheme and device-specific thing adaptation software (TAS) enabling WSN elements, such as a wireless sensor node, to be accessed in a standardized way on a global scale. Three pilot services are implemented (i.e., a WiFi-enabled smart flowerpot, voice-based control for ZigBee-connected home appliances, and WiFi-connected AR.Drone control) to demonstrate the practical usability of the open API scheme and TAS modules. Full details on the method of integrating WSN elements into three example systems are described at the programming code level, which is expected to help future researchers in integrating their WSN systems in IoT platforms, such as oneM2M. We hope that the flexibly-deployable, easily-reusable common open API scheme and TAS-based integration method working with the oneM2M platforms will help the conventional WSNs in diverse industries evolve into the emerging WoT solutions. PMID:27782058

Framework Programmable Platform for the Advanced Software Development Workstation (FPP/ASDW). Demonstration framework document. Volume 1: Concepts and activity descriptions

NASA Technical Reports Server (NTRS)

Mayer, Richard J.; Blinn, Thomas M.; Dewitte, Paul S.; Crump, John W.; Ackley, Keith A.

1992-01-01

The Framework Programmable Software Development Platform (FPP) is a project aimed at effectively combining tool and data integration mechanisms with a model of the software development process to provide an intelligent integrated software development environment. Guided by the model, this system development framework will take advantage of an integrated operating environment to automate effectively the management of the software development process so that costly mistakes during the development phase can be eliminated. The Advanced Software Development Workstation (ASDW) program is conducting research into development of advanced technologies for Computer Aided Software Engineering (CASE).

SERVIR-Africa: Developing an Integrated Platform for Floods Disaster Management in Africa

NASA Technical Reports Server (NTRS)

Macharia, Daniel; Korme, Tesfaye; Policelli, Fritz; Irwin, Dan; Adler, Bob; Hong, Yang

2010-01-01

SERVIR-Africa is an ambitious regional visualization and monitoring system that integrates remotely sensed data with predictive models and field-based data to monitor ecological processes and respond to natural disasters. It aims addressing societal benefits including floods and turning data into actionable information for decision-makers. Floods are exogenous disasters that affect many parts of Africa, probably second only to drought in terms of social-economic losses. This paper looks at SERVIR-Africa's approach to floods disaster management through establishment of an integrated platform, floods prediction models, post-event flood mapping and monitoring as well as flood maps dissemination in support of flood disaster management.

Developing a Customized Perfusion Bioreactor Prototype with Controlled Positional Variability in Oxygen Partial Pressure for Bone and Cartilage Tissue Engineering.

PubMed

Lee, Poh Soo; Eckert, Hagen; Hess, Ricarda; Gelinsky, Michael; Rancourt, Derrick; Krawetz, Roman; Cuniberti, Gianaurelio; Scharnweber, Dieter

2017-05-01

Skeletal development is a multistep process that involves the complex interplay of multiple cell types at different stages of development. Besides biochemical and physical cues, oxygen tension also plays a pivotal role in influencing cell fate during skeletal development. At physiological conditions, bone cells generally reside in a relatively oxygenated environment whereas chondrocytes reside in a hypoxic environment. However, it is technically challenging to achieve such defined, yet diverse oxygen distribution on traditional in vitro cultivation platforms. Instead, engineered osteochondral constructs are commonly cultivated in a homogeneous, stable environment. In this study, we describe a customized perfusion bioreactor having stable positional variability in oxygen tension at defined regions. Further, engineered collagen constructs were coaxed into adopting the shape and dimensions of defined cultivation platforms that were precasted in 1.5% agarose bedding. After cultivating murine embryonic stem cells that were embedded in collagen constructs for 50 days, mineralized constructs of specific dimensions and a stable structural integrity were achieved. The end-products, specifically constructs cultivated without chondroitin sulfate A (CSA), showed a significant increase in mechanical stiffness compared with their initial gel-like constructs. More importantly, the localization of osteochondral cell types was specific and corresponded to the oxygen tension gradient generated in the bioreactor. In addition, CSA in complementary with low oxygen tension was also found to be a potent inducer of chondrogenesis in this system. In summary, we have demonstrated a customized perfusion bioreactor prototype that is capable of generating a more dynamic, yet specific cultivation environment that could support propagation of multiple osteochondral lineages within a single engineered construct in vitro. Our system opens up new possibilities for in vitro research on human skeletal development.

Studying the rapid bioconversion of lignocellulosic sugars into ethanol using high cell density fermentations with cell recycle

PubMed Central

2014-01-01

Background The Rapid Bioconversion with Integrated recycle Technology (RaBIT) process reduces capital costs, processing times, and biocatalyst cost for biochemical conversion of cellulosic biomass to biofuels by reducing total bioprocessing time (enzymatic hydrolysis plus fermentation) to 48 h, increasing biofuel productivity (g/L/h) twofold, and recycling biocatalysts (enzymes and microbes) to the next cycle. To achieve these results, RaBIT utilizes 24-h high cell density fermentations along with cell recycling to solve the slow/incomplete xylose fermentation issue, which is critical for lignocellulosic biofuel fermentations. Previous studies utilizing similar fermentation conditions showed a decrease in xylose consumption when recycling cells into the next fermentation cycle. Eliminating this decrease is critical for RaBIT process effectiveness for high cycle counts. Results Nine different engineered microbial strains (including Saccharomyces cerevisiae strains, Scheffersomyces (Pichia) stipitis strains, Zymomonas mobilis 8b, and Escherichia coli KO11) were tested under RaBIT platform fermentations to determine their suitability for this platform. Fermentation conditions were then optimized for S. cerevisiae GLBRCY128. Three different nutrient sources (corn steep liquor, yeast extract, and wheat germ) were evaluated to improve xylose consumption by recycled cells. Capacitance readings were used to accurately measure viable cell mass profiles over five cycles. Conclusion The results showed that not all strains are capable of effectively performing the RaBIT process. Acceptable performance is largely correlated to the specific xylose consumption rate. Corn steep liquor was found to reduce the deleterious impacts of cell recycle and improve specific xylose consumption rates. The viable cell mass profiles indicated that reduction in specific xylose consumption rate, not a drop in viable cell mass, was the main cause for decreasing xylose consumption. PMID:24847379

Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application.

PubMed

Rahman, Mahabubur; Watabe, Hiroshi

2018-05-01

Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management. As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built. The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development. MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid achievement in cancer diagnosis and therapeutics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Reversible thermo-pneumatic valves on centrifugal microfluidic platforms.

PubMed

Aeinehvand, Mohammad Mahdi; Ibrahim, Fatimah; Harun, Sulaiman Wadi; Kazemzadeh, Amin; Rothan, Hussin A; Yusof, Rohana; Madou, Marc

2015-08-21

Centrifugal microfluidic systems utilize a conventional spindle motor to automate parallel biochemical assays on a single microfluidic disk. The integration of complex, sequential microfluidic procedures on these platforms relies on robust valving techniques that allow for the precise control and manipulation of fluid flow. The ability of valves to consistently return to their former conditions after each actuation plays a significant role in the real-time manipulation of fluidic operations. In this paper, we introduce an active valving technique that operates based on the deflection of a latex film with the potential for real-time flow manipulation in a wide range of operational spinning speeds. The reversible thermo-pneumatic valve (RTPV) seals or reopens an inlet when a trapped air volume is heated or cooled, respectively. The RTPV is a gas-impermeable valve composed of an air chamber enclosed by a latex membrane and a specially designed liquid transition chamber that enables the efficient usage of the applied thermal energy. Inputting thermo-pneumatic (TP) energy into the air chamber deflects the membrane into the liquid transition chamber against an inlet, sealing it and thus preventing fluid flow. From this point, a centrifugal pressure higher than the induced TP pressure in the air chamber reopens the fluid pathway. The behaviour of this newly introduced reversible valving system on a microfluidic disk is studied experimentally and theoretically over a range of rotational frequencies from 700 RPM to 2500 RPM. Furthermore, adding a physical component (e.g., a hemispherical rubber element) to induce initial flow resistance shifts the operational range of rotational frequencies of the RTPV to more than 6000 RPM. An analytical solution for the cooling of a heated RTPV on a spinning disk is also presented, which highlights the need for the future development of time-programmable RTPVs. Moreover, the reversibility and gas impermeability of the RTPV in the microfluidic networks are validated on a microfluidic disk designed for performing liquid circulation. Finally, an array of RTPVs is integrated into a microfluidic cartridge to enable sequential aliquoting for the conversion of dengue virus RNA to cDNA and the preparation of PCR reaction mixtures.

In-situ Testing of the EHT High Gain and Frequency Ultra-Stable Integrators

NASA Astrophysics Data System (ADS)

Miller, Kenneth; Ziemba, Timothy; Prager, James; Slobodov, Ilia; Lotz, Dan

2014-10-01

Eagle Harbor Technologies (EHT) has developed a long-pulse integrator that exceeds the ITER specification for integration error and pulse duration. During the Phase I program, EHT improved the RPPL short-pulse integrators, added a fast digital reset, and demonstrated that the new integrators exceed the ITER integration error and pulse duration requirements. In Phase II, EHT developed Field Programmable Gate Array (FPGA) software that allows for integrator control and real-time signal digitization and processing. In the second year of Phase II, the EHT integrator will be tested at a validation platform experiment (HIT-SI) and tokamak (DIII-D). In the Phase IIB program, EHT will continue development of the EHT integrator to reduce overall cost per channel. EHT will test lower cost components, move to surface mount components, and add an onboard Field Programmable Gate Array and data acquisition to produce a stand-alone system with lower cost per channel and increased the channel density. EHT will test the Phase IIB integrator at a validation platform experiment (HIT-SI) and tokamak (DIII-D). Work supported by the DOE under Contract Number (DE-SC0006281).

Generation and precise control of dynamic biochemical gradients for cellular assays

NASA Astrophysics Data System (ADS)

Saka, Yasushi; MacPherson, Murray; Giuraniuc, Claudiu V.

2017-03-01

Spatial gradients of diffusible signalling molecules play crucial roles in controlling diverse cellular behaviour such as cell differentiation, tissue patterning and chemotaxis. In this paper, we report the design and testing of a microfluidic device for diffusion-based gradient generation for cellular assays. A unique channel design of the device eliminates cross-flow between the source and sink channels, thereby stabilizing gradients by passive diffusion. The platform also enables quick and flexible control of chemical concentration that makes highly dynamic gradients in diffusion chambers. A model with the first approximation of diffusion and surface adsorption of molecules recapitulates the experimentally observed gradients. Budding yeast cells cultured in a gradient of a chemical inducer expressed a reporter fluorescence protein in a concentration-dependent manner. This microfluidic platform serves as a versatile prototype applicable to a broad range of biomedical investigations.

Canine model of crush syndrome established by a digital crush injury device platform

PubMed Central

Song, Jie; Ding, Hui; Fan, Hao-Jun; Dong, Wen-Long; Sun, Zhen-Xing; Hou, Shi-Ke

2015-01-01

Objective: To establish a canine model of crush syndrome (CS). Methods: A total of 16 healthy adult female Beagle dogs were randomly divided into the control group (n=8) and the experimental group (n=8). The crush injury was created in the left hind leg of each dog in the experimental group. Results: The biochemical indexes in the experimental group changed significantly compared to the values before extrusion. And they were also significantly different from the values of the control group. The glomerular capillary dilation, renal tubular epithelial cell degeneration, and renal interstitial lymphocytic infiltration were found in the kidneys. Conclusion: The canine CS model established by the digital crush injury device platform was successful according with the diagnosis of CS. It is good for the investigation of the CS mechanism and treatment using this model. PMID:26261489

Energizing eukaryotic cell-free protein synthesis with glucose metabolism.

PubMed

Anderson, Mark J; Stark, Jessica C; Hodgman, C Eric; Jewett, Michael C

2015-07-08

Eukaryotic cell-free protein synthesis (CFPS) is limited by the dependence on costly high-energy phosphate compounds and exogenous enzymes to power protein synthesis (e.g., creatine phosphate and creatine kinase, CrP/CrK). Here, we report the ability to use glucose as a secondary energy substrate to regenerate ATP in a Saccharomyces cerevisiae crude extract CFPS platform. We observed synthesis of 3.64±0.35 μg mL(-1) active luciferase in batch reactions with 16 mM glucose and 25 mM phosphate, resulting in a 16% increase in relative protein yield (μg protein/$ reagents) compared to the CrP/CrK system. Our demonstration provides the foundation for development of cost-effective eukaryotic CFPS platforms. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Nanomechanical recognition of prognostic biomarker suPAR with DVD-ROM optical technology.

PubMed

Bache, Michael; Bosco, Filippo G; Brøgger, Anna L; Frøhling, Kasper B; Alstrøm, Tommy Sonne; Hwu, En-Te; Chen, Ching-Hsiu; Eugen-Olsen, Jesper; Hwang, Ing-Shouh; Boisen, Anja

2013-11-08

In this work the use of a high-throughput nanomechanical detection system based on a DVD-ROM optical drive and cantilever sensors is presented for the detection of urokinase plasminogen activator receptor inflammatory biomarker (uPAR). Several large scale studies have linked elevated levels of soluble uPAR (suPAR) to infectious diseases, such as HIV, and certain types of cancer. Using hundreds of cantilevers and a DVD-based platform, cantilever deflection response from antibody-antigen recognition is investigated as a function of suPAR concentration. The goal is to provide a cheap and portable detection platform which can carry valuable prognostic information. In order to optimize the cantilever response the antibody immobilization and unspecific binding are initially characterized using quartz crystal microbalance technology. Also, the choice of antibody is explored in order to generate the largest surface stress on the cantilevers, thus increasing the signal. Using optimized experimental conditions the lowest detectable suPAR concentration is currently around 5 nM. The results reveal promising research strategies for the implementation of specific biochemical assays in a portable and high-throughput microsensor-based detection platform.

Conformational Response of 30S-bound IF3 to A-Site Binders Streptomycin and Kanamycin

PubMed Central

Chulluncuy, Roberto; Espiche, Carlos; Nakamoto, Jose Alberto; Fabbretti, Attilio; Milón, Pohl

2016-01-01

Aminoglycoside antibiotics are widely used to treat infectious diseases. Among them, streptomycin and kanamycin (and derivatives) are of importance to battle multidrug-resistant (MDR) Mycobacterium tuberculosis. Both drugs bind the small ribosomal subunit (30S) and inhibit protein synthesis. Genetic, structural, and biochemical studies indicate that local and long-range conformational rearrangements of the 30S subunit account for this inhibition. Here, we use intramolecular FRET between the C- and N-terminus domains of the flexible IF3 to monitor real-time perturbations of their binding sites on the 30S platform. Steady and pre-steady state binding experiments show that both aminoglycosides bring IF3 domains apart, promoting an elongated state of the factor. Binding of Initiation Factor IF1 triggers closure of IF3 bound to the 30S complex, while both aminoglycosides revert the IF1-dependent conformation. Our results uncover dynamic perturbations across the 30S subunit, from the A-site to the platform, and suggest that both aminoglycosides could interfere with prokaryotic translation initiation by modulating the interaction between IF3 domains with the 30S platform. PMID:27983590

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

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

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE PAGES

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

Microfluidic platform for detection and quantification of magnetic markers

NASA Astrophysics Data System (ADS)

Kokkinis, Georgios; Cardoso, Susana; Giouroudi, Ioanna

2017-05-01

This paper reports on a microfluidic platform with an integrated spin valve giant magneto-resistance (GMR) sensor used for the detection and quantification of single magnetic micromarkers. A microfluidic channel containing the magnetic fluid, microconductors (MCs) for collection of the magnetic markers and a spin valve GMR sensor for detecting the presence of their magnetic stray field were integrated on a single chip. The results show that the sensor is capable of detecting a single magnetic marker with 2.8 μm diameter.

Recent developments using TowerJazz SiGe BiCMOS platform for mmWave and THz applications

NASA Astrophysics Data System (ADS)

Kar-Roy, Arjun; Howard, David; Preisler, Edward J.; Racanelli, Marco

2013-05-01

In this paper, we report on the highest speed 240GHz/340GHz FT/FMAX NPN which is now available for product designs in the SBC18H4 process variant of TowerJazz's mature 0.18μm SBC18 silicon germanium (SiGe) BiCMOS technology platform. NFMIN of ~2dB at 50GHz has been obtained with these NPNs. We also describe the integration of earlier generation NPNs with FT/FMAX of 240GHz/280GHz into SBC13H3, a 0.13μm SiGe BiCMOS technology platform. Next, we detail the integration of the deep silicon via (DSV), through silicon via (TSV), high-resistivity substrate, sub-field stitching and hybrid-stitching capability into the 0.18μm SBC18 technology platform to enable higher performance and highly integrated product designs. The integration of SBC18H3 into a thick-film SOI substrate, with essentially unchanged FT and FMAX, is also described. We also report on recent circuit demonstrations using the SBC18H3 platform: (1) a 4-element phased-array 70-100GHz broadband transmit and receive chip with flat saturated power greater than 5dBm and conversion gain of 33dB; (2) a fully integrated W-band 9-element phase-controllable array with responsivity of 800MV/W and receiver NETD is 0.45K with 20ms integration time; (3) a 16-element 4x4 phased-array transmitter with scanning in both the E- and H-planes with maximum EIRP of 23-25 dBm at 100-110GHz; (4) a power efficient 200GHz VCO with -7.25dBm output power and tuning range of 3.5%; and (5) a 320GHz 16-element imaging receiver array with responsivity of 18KV/W at 315GHz, a 3dB bandwidth of 25GHz and a low NEP of 34pW/Hz1/2. Wafer-scale large-die implementation of the phased-arrays and mmWave imagers using stitching in TowerJazz SBC18 process are also discussed.

Digitized molecular diagnostics: reading disk-based bioassays with standard computer drives.

PubMed

Li, Yunchao; Ou, Lily M L; Yu, Hua-Zhong

2008-11-01

We report herein a digital signal readout protocol for screening disk-based bioassays with standard optical drives of ordinary desktop/notebook computers. Three different types of biochemical recognition reactions (biotin-streptavidin binding, DNA hybridization, and protein-protein interaction) were performed directly on a compact disk in a line array format with the help of microfluidic channel plates. Being well-correlated with the optical darkness of the binding sites (after signal enhancement by gold nanoparticle-promoted autometallography), the reading error levels of prerecorded audio files can serve as a quantitative measure of biochemical interaction. This novel readout protocol is about 1 order of magnitude more sensitive than fluorescence labeling/scanning and has the capability of examining multiplex microassays on the same disk. Because no modification to either hardware or software is needed, it promises a platform technology for rapid, low-cost, and high-throughput point-of-care biomedical diagnostics.

The underlying pathway structure of biochemical reaction networks

PubMed Central

Schilling, Christophe H.; Palsson, Bernhard O.

1998-01-01

Bioinformatics is yielding extensive, and in some cases complete, genetic and biochemical information about individual cell types and cellular processes, providing the composition of living cells and the molecular structure of its components. These components together perform integrated cellular functions that now need to be analyzed. In particular, the functional definition of biochemical pathways and their role in the context of the whole cell is lacking. In this study, we show how the mass balance constraints that govern the function of biochemical reaction networks lead to the translation of this problem into the realm of linear algebra. The functional capabilities of biochemical reaction networks, and thus the choices that cells can make, are reflected in the null space of their stoichiometric matrix. The null space is spanned by a finite number of basis vectors. We present an algorithm for the synthesis of a set of basis vectors for spanning the null space of the stoichiometric matrix, in which these basis vectors represent the underlying biochemical pathways that are fundamental to the corresponding biochemical reaction network. In other words, all possible flux distributions achievable by a defined set of biochemical reactions are represented by a linear combination of these basis pathways. These basis pathways thus represent the underlying pathway structure of the defined biochemical reaction network. This development is significant from a fundamental and conceptual standpoint because it yields a holistic definition of biochemical pathways in contrast to definitions that have arisen from the historical development of our knowledge about biochemical processes. Additionally, this new conceptual framework will be important in defining, characterizing, and studying biochemical pathways from the rapidly growing information on cellular function. PMID:9539712

Serious games for upper limb rehabilitation: a systematic review.

PubMed

Proença, João Pedro; Quaresma, Cláudia; Vieira, Pedro

2018-01-01

The aim of this research is to carry out a systematic review of the use of technological gaming platforms with serious games in the upper limb rehabilitation of patients with neuromotor disorders. Through a systematic review, the first two authors defined the inclusion criteria and extracted the data, resulting in 38 studies collected from B-On, PubMed and Medline. Ninety-two per cent of the selected articles were published since 2010. This review documents 35 different gaming platforms types. Twenty-one of the 38 articles included in this review conducted a clinical trial and of those only eight report improvements in the target population following the use of the games and platforms. This review concludes that a new paradigm is emerging in the rehabilitation field, characterized by the systematic use of technological gaming platforms with serious games in/for rehabilitation. The use of this approach seems to be beneficial. However, to facilitate the full integration of these platforms, it is necessary to conduct more research in this area, explore new approaches and carry out in-depth clinical studies into the benefits of these platforms. Implications for rehabilitation This review states that the use serious games and gaming platforms for upper limb rehabilitation are starting a new paradigm in the rehabilitation. For a full integration of this technologies in the rehabilitation field more studies are needed.

Breast cancer diagnosis: Imaging techniques and biochemical markers.

PubMed

Jafari, Seyed Hamed; Saadatpour, Zahra; Salmaninejad, Arash; Momeni, Fatemeh; Mokhtari, Mojgan; Nahand, Javid Sadri; Rahmati, Majid; Mirzaei, Hamed; Kianmehr, Mojtaba

2018-07-01

Breast cancer is a complex disease which is found as the second cause of cancer-associated death among women. Accumulating of evidence indicated that various factors (i.e., gentical and envirmental factors) could be associated with initiation and progression of breast cancer. Diagnosis of breast cancer patients in early stages is one of important aspects of breast cancer treatment. Among of various diagnosis platforms, imaging techniques are main diagnosis approaches which could provide valuable data on patients with breast cancer. It has been showed that various imaging techniques such as mammography, magnetic resonance imaging (MRI), positron-emission tomography (PET), Computed tomography (CT), and single-photon emission computed tomography (SPECT) could be used for diagnosis and monitoring patients with breast cancer in various stages. Beside, imaging techniques, utilization of biochemical biomarkers such as proteins, DNAs, mRNAs, and microRNAs could be employed as new diagnosis and therapeutic tools for patients with breast cancer. Here, we summarized various imaging techniques and biochemical biomarkers could be utilized as diagnosis of patients with breast cancer. Moreover, we highlighted microRNAs and exosomes as new diagnosis and therapeutic biomarkers for monitoring patients with breast cancer. © 2017 Wiley Periodicals, Inc.

Design and Application of Sensors for Chemical Cytometry.

PubMed

Vickerman, Brianna M; Anttila, Matthew M; Petersen, Brae V; Allbritton, Nancy L; Lawrence, David S

2018-02-08

The bulk cell population response to a stimulus, be it a growth factor or a cytotoxic agent, neglects the cell-to-cell variability that can serve as a friend or as a foe in human biology. Biochemical variations among closely related cells furnish the basis for the adaptability of the immune system but also act as the root cause of resistance to chemotherapy by tumors. Consequently, the ability to probe for the presence of key biochemical variables at the single-cell level is now recognized to be of significant biological and biomedical impact. Chemical cytometry has emerged as an ultrasensitive single-cell platform with the flexibility to measure an array of cellular components, ranging from metabolite concentrations to enzyme activities. We briefly review the various chemical cytometry strategies, including recent advances in reporter design, probe and metabolite separation, and detection instrumentation. We also describe strategies for improving intracellular delivery, biochemical specificity, metabolic stability, and detection sensitivity of probes. Recent applications of these strategies to small molecules, lipids, proteins, and other analytes are discussed. Finally, we assess the current scope and limitations of chemical cytometry and discuss areas for future development to meet the needs of single-cell research.

The Doktabörse - an innovative online platform for research projects at the medical faculty of the LMU Munich.

PubMed

Nicolai, Leo; Gradel, Maximilian; Antón, Sofia; Pander, Tanja; Kalb, Anke; Köhler, Lisa; Fischer, Martin R; Dimitriadis, Konstantinos; von der Borch, Philip

2017-01-01

Introduction: One of the most important extracurricular aspects of medical studies in Germany is a research thesis completed by most students. This research project often times conveys relevant competencies for the physician's role as scientist. Nevertheless, the choice of the right project remains a challenge. Reasons for this are among others, missing structures for a comprehensive overview of research groups and their respective projects. Description of the project: We developed the online platform Doktabörse as an online marketplace for doctoral research projects. The platform enables authorized researchers to create working groups and upload, deactivate and change research projects within their institute. For interested students, a front end with integrated search function displays these projects in a structured and well-arranged way. In parallel, the Doktabörse provides for a comprehensive overview of research at the medical faculty. We evaluated Researchers' and students' use of the platform. Results: 96,6% of students participating in the evaluation (n=400) were in favor of a centralized research platform at the medical faculty. The platform grew at a steady pace and included 120 research groups in June 2016. The students appreciated the structure and design of the Doktabörse. Two thirds of all uploaded projects matched successfully with doctoral students via the platform and over 94% of researchers stated that they did not need technical assistance with uploading projects and handling the platform. Discussion : The Doktabörse represents an innovative and well accepted platform for doctoral research projects. The platform is perceived positively by researchers and students alike. However, students criticized limited extent and timeliness of offered projects. In addition, the platform serves as databank of research at the medical faculty of the LMU Munich. The future potential of this platform is to provide for an integrated management solution of doctoral thesis projects, possibly beyond the medical field and faculty.

A Model Incorporating Some of the Mechanical and Biochemical Factors Underlying Clot Formation and Dissolution in Flowing Blood

DOE PAGES

Anand, M.; Rajagopal, K.; Rajagopal, K. R.

2003-01-01

Multiple interacting mechanisms control the formation and dissolution of clots to maintain blood in a state of delicate balance. In addition to a myriad of biochemical reactions, rheological factors also play a crucial role in modulating the response of blood to external stimuli. To date, a comprehensive model for clot formation and dissolution, that takes into account the biochemical, medical and rheological factors, has not been put into place, the existing models emphasizing either one or the other of the factors. In this paper, after discussing the various biochemical, physiologic and rheological factors at some length, we develop a modelmore » for clot formation and dissolution that incorporates many of the relevant crucial factors that have a bearing on the problem. The model, though just a first step towards understanding a complex phenomenon, goes further than previous models in integrating the biochemical, physiologic and rheological factors that come into play.« less

Integrating MPI and deduplication engines: a software architecture roadmap.

PubMed

Baksi, Dibyendu

2009-03-01

The objective of this paper is to clarify the major concepts related to architecture and design of patient identity management software systems so that an implementor looking to solve a specific integration problem in the context of a Master Patient Index (MPI) and a deduplication engine can address the relevant issues. The ideas presented are illustrated in the context of a reference use case from Integrating the Health Enterprise Patient Identifier Cross-referencing (IHE PIX) profile. Sound software engineering principles using the latest design paradigm of model driven architecture (MDA) are applied to define different views of the architecture. The main contribution of the paper is a clear software architecture roadmap for implementors of patient identity management systems. Conceptual design in terms of static and dynamic views of the interfaces is provided as an example of platform independent model. This makes the roadmap applicable to any specific solutions of MPI, deduplication library or software platform. Stakeholders in need of integration of MPIs and deduplication engines can evaluate vendor specific solutions and software platform technologies in terms of fundamental concepts and can make informed decisions that preserve investment. This also allows freedom from vendor lock-in and the ability to kick-start integration efforts based on a solid architecture.

Passive and electro-optic polymer photonics and InP electronics integration

NASA Astrophysics Data System (ADS)

Zhang, Z.; Katopodis, V.; Groumas, P.; Konczykowska, A.; Dupuy, J.-.; Beretta, A.; Dede, A.; Miller, E.; Choi, J. H.; Harati, P.; Jorge, F.; Nodjiadjim, V.; Dinu, R.; Cangini, G.; Vannucci, A.; Felipe, D.; Maese-Novo, A.; Keil, N.; Bach, H.-.; Schell, Martin; Avramopoulos, H.; Kouloumentas, Ch.

2015-05-01

Hybrid photonic integration allows individual components to be developed at their best-suited material platforms without sacrificing the overall performance. In the past few years a polymer-enabled hybrid integration platform has been established, comprising 1) EO polymers for constructing low-complexity and low-cost Mach-Zehnder modulators (MZMs) with extremely high modulation bandwidth; 2) InP components for light sources, detectors, and high-speed electronics including MUX drivers and DEMUX circuits; 3) Ceramic (AIN) RF board that links the electronic signals within the package. On this platform, advanced optoelectronic modules have been demonstrated, including serial 100 Gb/s [1] and 2x100 Gb/s [2] optical transmitters, but also 400 Gb/s optoelectronic interfaces for intra-data center networks [3]. To expand the device functionalities to an unprecedented level and at the same time improve the integration compatibility with diversified active / passive photonic components, we have added a passive polymer-based photonic board (polyboard) as the 4th material system. This passive polyboard allows for low-cost fabrication of single-mode waveguide networks, enables fast and convenient integration of various thin-film elements (TFEs) to control the light polarization, and provides efficient thermo-optic elements (TOEs) for wavelength tuning, light amplitude regulation and light-path switching.

Development of fast wireless detection system for fixed offshore platform

NASA Astrophysics Data System (ADS)

Li, Zhigang; Yu, Yan; Jiao, Dong; Wang, Jie; Li, Zhirui; Ou, Jinping

2011-04-01

Offshore platforms' security is concerned since in 1950s and 1960s, and in the early 1980s some important specifications and standards are built, and all these provide technical basis of fixed platform design, construction, installation and evaluation. With the condition that more and more platforms are in serving over age, the research about the evaluation and detection technology of offshore platform has been a hotspot, especially underwater detection, and assessment method based on the finite element calculation. For fixed platform structure detection, conventional NDT methods, such as eddy current, magnetic powder, permeate, X-ray and ultrasonic, etc, are generally used. These techniques are more mature, intuitive, but underwater detection needs underwater robot, the necessary supporting tools of auxiliary equipment, and trained professional team, thus resources and cost used are considerable, installation time of test equipment is long. This project presents a new kind of fast wireless detection and damage diagnosis system for fixed offshore platform using wireless sensor networks, that is, wireless sensor nodes can be put quickly on the offshore platform, detect offshore platform structure global status by wireless communication, and then make diagnosis. This system is operated simply, suitable for offshore platform integrity states rapid assessment. The designed system consists in intelligence acquisition equipment and 8 wireless collection nodes, the whole system has 64 collection channels, namely every wireless collection node has eight 16-bit accuracy of A/D channels. Wireless collection node, integrated with vibration sensing unit, embedded low-power micro-processing unit, wireless transceiver unit, large-capacity power unit, and GPS time synchronization unit, can finish the functions such as vibration data collection, initial analysis, data storage, data wireless transmission. Intelligence acquisition equipment, integrated with high-performance computation unit, wireless transceiver unit, mobile power unit and embedded data analysis software, can totally control multi-wireless collection nodes, receive and analyze data, parameter identification. Data is transmitted at the 2.4GHz wireless communication channel, every sensing data channel in charge of data transmission is in a stable frequency band, control channel responsible for the control of power parameters is in a public frequency band. The test is initially conducted for the designed system, experimental results show that the system has good application prospects and practical value with fast arrangement, high sampling rate, high resolution, capacity of low frequency detection.

Synchronised integrated online e-health profiles.

PubMed

Liang, Jian; Iannella, Renato; Sahama, Tony

2011-01-01

Web-based social networking applications have become increasingly important in recent years. The current applications in the healthcare sphere can support the health management, but to date there is no patient-controlled integrator. This paper proposes a platform called Multiple Profile Manager (MPM) that enables a user to create and manage an integrated profile that can be shared across numerous social network sites. Moreover, it is able to facilitate the collection of personal healthcare data, which makes a contribution to the development of public health informatics. Here we want to illustrate how patients and physicians can be benefited from enabling the platform for online social network sites. The MPM simplifies the management of patients' profiles and allows health professionals to obtain a more complete picture of the patients' background so that they can provide better health care. To do so, we demonstrate a prototype of the platform and describe its protocol specification, which is an XMPP (Extensible Messaging and Presence Protocol) [1] extension, for sharing and synchronising profile data (vCard²) between different social networks.

IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform.

PubMed

Lee, Tae-Rim; Ahn, Jin Mo; Kim, Gyuhee; Kim, Sangsoo

2017-12-01

Next-generation sequencing (NGS) technology has become a trend in the genomics research area. There are many software programs and automated pipelines to analyze NGS data, which can ease the pain for traditional scientists who are not familiar with computer programming. However, downstream analyses, such as finding differentially expressed genes or visualizing linkage disequilibrium maps and genome-wide association study (GWAS) data, still remain a challenge. Here, we introduce a dockerized web application written in R using the Shiny platform to visualize pre-analyzed RNA sequencing and GWAS data. In addition, we have integrated a genome browser based on the JBrowse platform and an automated intermediate parsing process required for custom track construction, so that users can easily build and navigate their personal genome tracks with in-house datasets. This application will help scientists perform series of downstream analyses and obtain a more integrative understanding about various types of genomic data by interactively visualizing them with customizable options.

Run Environment and Data Management for Earth System Models

NASA Astrophysics Data System (ADS)

Widmann, H.; Lautenschlager, M.; Fast, I.; Legutke, S.

2009-04-01

The Integrating Model and Data Infrastructure (IMDI) developed and maintained by the Model and Data Group (M&D) comprises the Standard Compile Environment (SCE) and the Standard Run Environment (SRE). The IMDI software has a modular design, which allows to combine and couple a suite of model components and as well to execute the tasks independently and on various platforms. Furthermore the modular structure enables the extension to new model combinations and new platforms. The SRE presented here enables the configuration and performance of earth system model experiments from model integration up to storage and visualization of data. We focus on recently implemented tasks such as synchronous data base filling, graphical monitoring and automatic generation of meta data in XML forms during run time. As well we address the capability to run experiments in heterogeneous IT environments with different computing systems for model integration, data processing and storage. These features are demonstrated for model configurations and on platforms used in current or upcoming projects, e.g. MILLENNIUM or IPCC AR5.

Handheld Microneedle-Based Electrolyte Sensing Platform.

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

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

2015-11-01

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

Multiple wavelength silicon photonic 200 mm R+D platform for 25Gb/s and above applications

NASA Astrophysics Data System (ADS)

Szelag, B.; Blampey, B.; Ferrotti, T.; Reboud, V.; Hassan, K.; Malhouitre, S.; Grand, G.; Fowler, D.; Brision, S.; Bria, T.; Rabillé, G.; Brianceau, P.; Hartmann, J. M.; Hugues, V.; Myko, A.; Elleboode, F.; Gays, F.; Fédéli, J. M.; Kopp, C.

2016-05-01

A silicon photonics platform that uses a CMOS foundry line is described. Fabrication process is following a modular integration scheme which leads to a flexible platform, allowing different device combinations. A complete device library is demonstrated for 1310 nm applications with state of the art performances. A PDK which includes specific photonic features and which is compatible with commercial EDA tools has been developed allowing an MPW shuttle service. Finally platform evolutions such as device offer extension to 1550 nm or new process modules introduction are presented.

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

DOE PAGES

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

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

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

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

PubMed Central

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

2016-01-01

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

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.

A Prospective Trial of Intensity Modulated Radiation Therapy (IMRT) Incorporating a Simultaneous Integrated Boost for Prostate Cancer: Long-term Outcomes Compared With Standard Image Guided IMRT

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

Schild, Michael H.; Schild, Steven E., E-mail: sschild@mayo.edu; Wong, William W.

Purpose: This report describes the long-term outcomes of a prospective trial of intensity modulated radiation therapy (IMRT), integrating a {sup 111}In capromab pendetide (ProstaScint) scan-directed simultaneous integrated boost (SIB) for localized prostate cancer. Methods and Materials: Seventy-one patients with T1N0M0 to T4N0M0 prostate cancer were enrolled, and their ProstaScint and pelvic computed tomography scans were coregistered for treatment planning. The entire prostate received 75.6 Gy in 42 fractions with IMRT, whereas regions of increased uptake on ProstaScint scans received 82 Gy as an SIB. Patients with intermediate- and high-risk disease also received 6 months and 12 months of adjuvant hormonal therapy, respectively. Results: The studymore » enrolled 31 low-, 30 intermediate-, and 10 high-risk patients. The median follow-up was 120 months (range, 24-150 months). The 10-year biochemical control rates were 85% for the entire cohort and 84%, 84%, and 90% for patients with low-, intermediate-, and high-risk disease, respectively. The 10-year survival rate of the entire cohort was 69%. Pretreatment prostate-specific antigen level >10 ng/mL and boost volume of >10% of the prostate volume were significantly associated with poorer biochemical control and survival. The outcomes were compared with those of a cohort of 302 patients treated similarly but without the SIB and followed up for a median of 91 months (range, 6-138 months). The 5- and 10-year biochemical control rates were 86% and 61%, respectively, in patients without the SIB compared with 94% and 85%, respectively, in patients in this trial who received the SIB (P=.02). The cohort that received an SIB did not have increased toxicity. Conclusions: The described IMRT strategy, integrating multiple imaging modalities to administer 75.6 Gy to the entire prostate with a boost dose of 82 Gy, was feasible. The addition of the SIB was associated with greater biochemical control but not toxicity. Modern imaging technology can be used to locally intensify the dose to tumors and spare normal tissues, producing very favorable long-term biochemical disease control.« less

A compact multi-trap optical tweezer system based on CD-ROM technologies

NASA Astrophysics Data System (ADS)

McMenamin, T.; Lee, W. M.

2017-08-01

We implemented an integrated time sharing multiple optical trapping system through the synchronisation of high speed voice coil scanning lens and laser pulsing. The integration is achieved by using commonly available optical pickup unit (OPU) that exists inside optical drives. Scanning frequencies of up to 2 kHz were showed to achieve arbitrary distribution of optical traps within the one-dimensional scan range of the voice coil motor. The functions of the system were demonstrated by the imaging and trapping of 1 μm particles and giant unilamellar vesicles (GUVs). The new device circumvents existing bulky laser scanning systems (4f lens systems) with an integrated laser and lens steering platform that can be integrated on a variety of microscopy platforms (confocal, lightsheet, darkfield).

A Integrated Service Platform for Remote Sensing Image 3D Interpretation and Draughting based on HTML5

NASA Astrophysics Data System (ADS)

LIU, Yiping; XU, Qing; ZhANG, Heng; LV, Liang; LU, Wanjie; WANG, Dandi

2016-11-01

The purpose of this paper is to solve the problems of the traditional single system for interpretation and draughting such as inconsistent standards, single function, dependence on plug-ins, closed system and low integration level. On the basis of the comprehensive analysis of the target elements composition, map representation and similar system features, a 3D interpretation and draughting integrated service platform for multi-source, multi-scale and multi-resolution geospatial objects is established based on HTML5 and WebGL, which not only integrates object recognition, access, retrieval, three-dimensional display and test evaluation but also achieves collection, transfer, storage, refreshing and maintenance of data about Geospatial Objects and shows value in certain prospects and potential for growth.

Comparison of biochemical compositions of phytoplankton during spring and fall seasons in the northern East/Japan Sea

NASA Astrophysics Data System (ADS)

Kang, Jae Joong; Joo, HuiTae; Lee, Jae Hyung; Lee, Jang Han; Lee, Ho Won; Lee, Dabin; Kang, Chang Keun; Yun, Mi Sun; Lee, Sang Heon

2017-09-01

The East/Japan Sea (EJS) where is surrounded by the Korean peninsula, the Japanese islands, and the Russian coast has been experiencing a large change in physicochemical properties. Based on biochemical composition analysis (carbohydrates, proteins, and lipids), the current qualitative status of phytoplankton was identified in the northern EJS from two different sampling seasons (fall and spring in 2012 and 2015, respectively). The average chlorophyll-a (chl-a) concentration integrated from the euphotic depths was significantly higher in 2015 (99.3 ± 69.2 mg m-2) than 2012 (21.5 ± 6.7 mg m-2). Large phytoplankton (> 2 μm) were predominant in 2015 accounting for 64.5 ± 19.7% whereas small-size phytoplankton (0.7-2 μm) were dominant (49.1 ± 17.5%) in 2012. The biochemical compositions of phytoplankton were predominated by lipids (42.6 ± 7.8%) in 2012 whereas carbohydrate composition largely contributed (53.2 ± 11.7%) to the total biochemical composition in 2015, which is mainly due to different nutrient availabilities and growth stages. Interestingly, the averaged FM concentrations and calorific values for phytoplankton based on the biochemical compositions had similar values between the two years, although the integrated chl-a concentrations were substantially different between 2012 and 2015. In terms of different cell sizes of phytoplankton, we found that small phytoplankton assimilate more FM and calorific energy per unit of chl-a concentration than total phytoplankton. Our results are meaningful for the understanding of future marine ecosystems where small phytoplankton will become dominant at a scenario of ongoing warmer oceans.

Effect of whole-body vibration training on body composition, exercise performance and biochemical responses in middle-aged mice.

PubMed

Lin, Ching-I; Huang, Wen-Ching; Chen, Wen-Chyuan; Kan, Nai-Wen; Wei, Li; Chiu, Yen-Shuo; Huang, Chi-Chang

2015-09-01

Whole-body vibration (WBV) is a well-known light-resistance exercise by automatic adaptations to rapid and repeated oscillations from a vibrating platform, which is also a simple and convenient exercise for older adults. However, the potential benefits of WBV on aging-associated changes in body composition, exercise performance, and fatigue are currently unclear. The objective of the study is to investigate the beneficial effects of WBV training on body composition, exercise performance, and physical fatigue-related and biochemical responses in middle-aged mice. In total, 24 male C57BL/6 mice aged 15 months old were randomly divided into 3 groups (n=8 per group): sedentary control (SC), relatively low-frequency WBV (5.6 Hz, 2 mm, 0.13 g) (LV), and relatively high-frequency WBV (13 Hz, 2 mm, 0.68 g) (HV). Mice in the LV and HV groups were placed inside a vibration platform and vibrated at different frequencies and fixed amplitude (2 mm) for 15 min, 5 days/week for 4 weeks. Exercise performance, core temperature and anti-fatigue function were evaluated by forelimb grip strength and levels of serum lactate, ammonia, glucose, and creatine kinase (CK) after a 15-min swimming exercise, as were changes in body composition and biochemical variables at the end of the experiment. Relative muscle and brown adipose tissue weight (%) was significantly higher for the HV than SC mice, but relative liver weight (%) was lower. On trend analysis, WBV increased grip strength, aerobic endurance and core temperature in mice. As well, serum lactate, ammonia and CK levels were dose-dependently decreased with vibration frequency after the swimming test. Fasting serum levels of albumin and total protein were increased and serum levels of alkaline phosphatase and creatinine decreased dose-dependently with vibration frequency. Moreover, WBV training improved the age-related abnormal morphology of skeletal muscle, liver and kidney tissues. Therefore, it could improve exercise performance and ameliorate fatigue and prevent senescence-associated biochemical and pathological alterations in middle-aged mice. WBV training may be an effective intervention for health promotion in the aging population. The detailed molecular mechanism of how WBV training regulates anti-aging activity warrants further functional studies. Copyright © 2015 Elsevier Inc. All rights reserved.

Integrating Neglected Tropical Disease and Immunization Programs: The Experiences of the Tanzanian Ministry of Health

PubMed Central

Mwingira, Upendo John; Means, Arianna Rubin; Chikawe, Maria; Kilembe, Bernard; Lyimo, Dafrossa; Crowley, Kathryn; Rusibamayila, Neema; Nshala, Andreas; Mphuru, Alex

2016-01-01

Global health practitioners are increasingly advocating for the integration of community-based health-care platforms as a strategy for increasing the coverage of programs, encouraging program efficiency, and promoting universal health-care goals. To leverage the strengths of compatible programs and avoid geographic and temporal duplications in efforts, the Tanzanian Ministry of Health and Social Welfare coordinated immunization and neglected tropical disease programs for the first time in 2014. Specifically, a measles and rubella supplementary vaccine campaign, mass drug administration (MDA) of ivermectin and albendazole, and Vitamin A were provisionally integrated into a shared community-based delivery platform. Over 21 million people were targeted by the integrated campaign, with the immunization program and MDA program reaching 97% and 93% of targeted individuals, respectively. The purpose of this short report is to share the Tanzanian experience of launching and managing this integrated campaign with key stakeholders. PMID:27246449

Integration of genetically modified virus-like-particles with an optical resonator for selective bio-detection

NASA Astrophysics Data System (ADS)

Fan, X. Z.; Naves, L.; Siwak, N. P.; Brown, A.; Culver, J.; Ghodssi, R.

2015-05-01

A novel virus-like particle (TMV-VLP) receptor layer has been integrated with an optical microdisk resonator transducer for biosensing applications. This bioreceptor layer is functionalized with selective peptides that encode unique recognition affinities. Integration of bioreceptors with sensor platforms is very challenging due their very different compatibility regimes. The TMV-VLP nanoreceptor exhibits integration robustness, including the ability for self-assembly along with traditional top-down microfabrication processes. An optical microdisk resonator has been functionalized for antibody binding with this receptor, demonstrating resonant wavelength shifts of (Δλo) of 0.79 nm and 5.95 nm after primary antibody binding and enzyme-linked immunosorbent assay (ELISA), respectively, illustrating label-free sensing of this bonding event. This demonstration of label-free sensing with genetically engineered TMV-VLP shows the flexibility and utility of this receptor coating when considering integration with other existing transducer platforms.

Airborne Platforms for Emergency Communications and Reconnaissance in Domestic Disaster Response

DTIC Science & Technology

2010-04-01

primarily focused in the areas of tourism , port operations, and educational services. 3 Telecommunications are foundational in our nation’s...concerted effort to successfully integrate these airborne platforms into domestic disaster response operations must be undertaken, or we are doomed to

Green farming systems for the Southeast USA using manure-to-energy conversion platforms

USDA-ARS?s Scientific Manuscript database

Livestock operations in the Southeastern USA are faced with implementing holistic solutions to address effective manure treatment through efficient energy management and safeguarding of supporting natural resources. By integrating waste-to-energy conversion platforms, future green farming systems ca...

System Architecture Development for Energy and Water Infrastructure Data Management and Geovisual Analytics

NASA Astrophysics Data System (ADS)

Berres, A.; Karthik, R.; Nugent, P.; Sorokine, A.; Myers, A.; Pang, H.

2017-12-01

Building an integrated data infrastructure that can meet the needs of a sustainable energy-water resource management requires a robust data management and geovisual analytics platform, capable of cross-domain scientific discovery and knowledge generation. Such a platform can facilitate the investigation of diverse complex research and policy questions for emerging priorities in Energy-Water Nexus (EWN) science areas. Using advanced data analytics, machine learning techniques, multi-dimensional statistical tools, and interactive geovisualization components, such a multi-layered federated platform is being developed, the Energy-Water Nexus Knowledge Discovery Framework (EWN-KDF). This platform utilizes several enterprise-grade software design concepts and standards such as extensible service-oriented architecture, open standard protocols, event-driven programming model, enterprise service bus, and adaptive user interfaces to provide a strategic value to the integrative computational and data infrastructure. EWN-KDF is built on the Compute and Data Environment for Science (CADES) environment in Oak Ridge National Laboratory (ORNL).

Minilaparoscopic hysterectomy made easy: first report on alternative instrumentation and new integrated energy platform.

PubMed

Ng, Ying Woo; Lim, Li Min; Fong, Yoke Fai

2014-05-01

Minilaparoscopy is an attractive approach for hysterectomy due to advantages such as reduced morbidities and enhanced cosmesis. However, it has not been popularized due to the lack of suitable instruments and high technical demand. We aim to highlight the first case of minilaparoscopic hysterectomy reported in Asia and the use of a new integrated energy platform, Thunderbeat. We would like to propose an alternative method of instrumentation, so as to improve the feasibility and safety of minilaparoscopic hysterectomy. The first minilaparoscopic hysterectomy in Singapore was successfully completed using the alternative instrumentation and new energy platform. There was no conversion or complication during the surgery. The patient recovered uneventfully. To our knowledge, this is the first report on the use of such alternative instrumentation. This approach in instrumentation and the new energy platform will improve the feasibility and speed of the surgery and ensure safety in our patients. © 2014 The Authors. Journal of Obstetrics and Gynaecology Research © 2014 Japan Society of Obstetrics and Gynecology.

ePix: a class of architectures for second generation LCLS cameras

DOE PAGES

Dragone, A.; Caragiulo, P.; Markovic, B.; ...

2014-03-31

ePix is a novel class of ASIC architectures, based on a common platform, optimized to build modular scalable detectors for LCLS. The platform architecture is composed of a random access analog matrix of pixel with global shutter, fast parallel column readout, and dedicated sigma-delta analog-to-digital converters per column. It also implements a dedicated control interface and all the required support electronics to perform configuration, calibration and readout of the matrix. Based on this platform a class of front-end ASICs and several camera modules, meeting different requirements, can be developed by designing specific pixel architectures. This approach reduces development time andmore » expands the possibility of integration of detector modules with different size, shape or functionality in the same camera. The ePix platform is currently under development together with the first two integrating pixel architectures: ePix100 dedicated to ultra low noise applications and ePix10k for high dynamic range applications.« less

GIS Application System Design Applied to Information Monitoring

NASA Astrophysics Data System (ADS)

Qun, Zhou; Yujin, Yuan; Yuena, Kang

Natural environment information management system involves on-line instrument monitoring, data communications, database establishment, information management software development and so on. Its core lies in collecting effective and reliable environmental information, increasing utilization rate and sharing degree of environment information by advanced information technology, and maximizingly providing timely and scientific foundation for environmental monitoring and management. This thesis adopts C# plug-in application development and uses a set of complete embedded GIS component libraries and tools libraries provided by GIS Engine to finish the core of plug-in GIS application framework, namely, the design and implementation of framework host program and each functional plug-in, as well as the design and implementation of plug-in GIS application framework platform. This thesis adopts the advantages of development technique of dynamic plug-in loading configuration, quickly establishes GIS application by visualized component collaborative modeling and realizes GIS application integration. The developed platform is applicable to any application integration related to GIS application (ESRI platform) and can be as basis development platform of GIS application development.

Bringing eCare platforms to the market.

PubMed

Vannieuwenborg, Frederic; Van der Auwermeulen, Thomas; Van Ooteghem, Jan; Jacobs, An; Verbugge, Sofie; Colle, Didier

2017-09-01

Due to changes in the demographic situation of most Western European countries, interest in Information and Communication Technologies (ICT)-supported care services is growing fast. eCare services that foster better care information exchange, social involvement, lifestyle monitoring services, etc., offered via ICT platforms, integrated in the homes of the elderly are believed to be cost-effective. Additionally, they could lead to an increased quality of life of both care receiver and (in)formal caregiver. Currently, adoption and integration of these eCare platforms (eCPs) is slowed down by several barriers such as unclear added value, a lack of regulations, or lack of sustainable financial models. In this work, the added value of eCPs is identified for the several involved key actors such as the care receiver, the (in)formal care providers, and the home care organizations. In a second step, several go-to-market strategies are formulated. Because the gap between the current way of providing home care and providing home care supported by a fully integrated eCP seems too big to bridge in one effort, a migration path is provided for stepwise integration and adoption of eCPs in the current way of home care provisioning.

Co-integrating plasmonics with Si3N4 photonics towards a generic CMOS compatible PIC platform for high-sensitivity multi-channel biosensors: the H2020 PlasmoFab approach (Conference Presentation)

NASA Astrophysics Data System (ADS)

Tsiokos, Dimitris M.; Dabos, George; Ketzaki, Dimitra; Weeber, Jean-Claude; Markey, Laurent; Dereux, Alain; Giesecke, Anna Lena; Porschatis, Caroline; Chmielak, Bartos; Wahlbrink, Thorsten; Rochracher, Karl; Pleros, Nikos

2017-05-01

Silicon photonics meet most fabrication requirements of standard CMOS process lines encompassing the photonics-electronics consolidation vision. Despite this remarkable progress, further miniaturization of PICs for common integration with electronics and for increasing PIC functional density is bounded by the inherent diffraction limit of light imposed by optical waveguides. Instead, Surface Plasmon Polariton (SPP) waveguides can guide light at sub-wavelength scales at the metal surface providing unique light-matter interaction properties, exploiting at the same time their metallic nature to naturally integrate with electronics in high-performance ASPICs. In this article, we demonstrate the main goals of the recently introduced H2020 project PlasmoFab towards addressing the ever increasing needs for low energy, small size and high performance mass manufactured PICs by developing a revolutionary yet CMOS-compatible fabrication platform for seamless co-integration of plasmonics with photonic and supporting electronic. We demonstrate recent advances on the hosting SiN photonic hosting platform reporting on low-loss passive SiN waveguide and Grating Coupler circuits for both the TM and TE polarization states. We also present experimental results of plasmonic gold thin-film and hybrid slot waveguide configurations that can allow for high-sensitivity sensing, providing also the ongoing activities towards replacing gold with Cu, Al or TiN metal in order to yield the same functionality over a CMOS metallic structure. Finally, the first experimental results on the co-integrated SiN+plasmonic platform are demonstrated, concluding to an initial theoretical performance analysis of the CMOS plasmo-photonic biosensor that has the potential to allow for sensitivities beyond 150000nm/RIU.

Web-based visual analysis for high-throughput genomics

PubMed Central

2013-01-01

Background Visualization plays an essential role in genomics research by making it possible to observe correlations and trends in large datasets as well as communicate findings to others. Visual analysis, which combines visualization with analysis tools to enable seamless use of both approaches for scientific investigation, offers a powerful method for performing complex genomic analyses. However, there are numerous challenges that arise when creating rich, interactive Web-based visualizations/visual analysis applications for high-throughput genomics. These challenges include managing data flow from Web server to Web browser, integrating analysis tools and visualizations, and sharing visualizations with colleagues. Results We have created a platform simplifies the creation of Web-based visualization/visual analysis applications for high-throughput genomics. This platform provides components that make it simple to efficiently query very large datasets, draw common representations of genomic data, integrate with analysis tools, and share or publish fully interactive visualizations. Using this platform, we have created a Circos-style genome-wide viewer, a generic scatter plot for correlation analysis, an interactive phylogenetic tree, a scalable genome browser for next-generation sequencing data, and an application for systematically exploring tool parameter spaces to find good parameter values. All visualizations are interactive and fully customizable. The platform is integrated with the Galaxy (http://galaxyproject.org) genomics workbench, making it easy to integrate new visual applications into Galaxy. Conclusions Visualization and visual analysis play an important role in high-throughput genomics experiments, and approaches are needed to make it easier to create applications for these activities. Our framework provides a foundation for creating Web-based visualizations and integrating them into Galaxy. Finally, the visualizations we have created using the framework are useful tools for high-throughput genomics experiments. PMID:23758618

SAW-Based Phononic Crystal Microfluidic Sensor—Microscale Realization of Velocimetry Approaches for Integrated Analytical Platform Applications

PubMed Central

Lucklum, Ralf; Zubtsov, Mikhail; Schmidt, Marc-Peter; Mukhin, Nikolay V.; Hirsch, Soeren

2017-01-01

The current work demonstrates a novel surface acoustic wave (SAW) based phononic crystal sensor approach that allows the integration of a velocimetry-based sensor concept into single chip integrated solutions, such as Lab-on-a-Chip devices. The introduced sensor platform merges advantages of ultrasonic velocimetry analytic systems and a microacoustic sensor approach. It is based on the analysis of structural resonances in a periodic composite arrangement of microfluidic channels confined within a liquid analyte. Completed theoretical and experimental investigations show the ability to utilize periodic structure localized modes for the detection of volumetric properties of liquids and prove the efficacy of the proposed sensor concept. PMID:28946609

An Approach to Integrate a Space-Time GIS Data Model with High Performance Computers

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

Wang, Dali; Zhao, Ziliang; Shaw, Shih-Lung

2011-01-01

In this paper, we describe an approach to integrate a Space-Time GIS data model on a high performance computing platform. The Space-Time GIS data model has been developed on a desktop computing environment. We use the Space-Time GIS data model to generate GIS module, which organizes a series of remote sensing data. We are in the process of porting the GIS module into an HPC environment, in which the GIS modules handle large dataset directly via parallel file system. Although it is an ongoing project, authors hope this effort can inspire further discussions on the integration of GIS on highmore » performance computing platforms.« less

SAW-Based Phononic Crystal Microfluidic Sensor-Microscale Realization of Velocimetry Approaches for Integrated Analytical Platform Applications.

PubMed

Oseev, Aleksandr; Lucklum, Ralf; Zubtsov, Mikhail; Schmidt, Marc-Peter; Mukhin, Nikolay V; Hirsch, Soeren

2017-09-23

The current work demonstrates a novel surface acoustic wave (SAW) based phononic crystal sensor approach that allows the integration of a velocimetry-based sensor concept into single chip integrated solutions, such as Lab-on-a-Chip devices. The introduced sensor platform merges advantages of ultrasonic velocimetry analytic systems and a microacoustic sensor approach. It is based on the analysis of structural resonances in a periodic composite arrangement of microfluidic channels confined within a liquid analyte. Completed theoretical and experimental investigations show the ability to utilize periodic structure localized modes for the detection of volumetric properties of liquids and prove the efficacy of the proposed sensor concept.

Silicon-nanomembrane-based photonic crystal nanostructures for chip-integrated open sensor systems

NASA Astrophysics Data System (ADS)

Chakravarty, Swapnajit; Lai, Wei-Cheng; Zou, Yi; Lin, Cheyun; Wang, Xiaolong; Chen, Ray T.

2011-11-01

We experimentally demonstrate two devices on the photonic crystal platform for chip-integrated optical absorption spectroscopy and chip-integrated biomolecular microarray assays. Infrared optical absorption spectroscopy and biomolecular assays based on conjugate-specific binding principles represent two dominant sensing mechanisms for a wide spectrum of applications in environmental pollution sensing in air and water, chem-bio agents and explosives detection for national security, microbial contamination sensing in food and beverages to name a few. The easy scalability of photonic crystal devices to any wavelength ensures that the sensing principles hold across a wide electromagnetic spectrum. Silicon, the workhorse of the electronics industry, is an ideal platform for the above optical sensing applications.

Fourier transform spectrometer controller for partitioned architectures

NASA Astrophysics Data System (ADS)

Tamas-Selicean, D.; Keymeulen, D.; Berisford, D.; Carlson, R.; Hand, K.; Pop, P.; Wadsworth, W.; Levy, R.

The current trend in spacecraft computing is to integrate applications of different criticality levels on the same platform using no separation. This approach increases the complexity of the development, verification and integration processes, with an impact on the whole system life cycle. Researchers at ESA and NASA advocated for the use of partitioned architecture to reduce this complexity. Partitioned architectures rely on platform mechanisms to provide robust temporal and spatial separation between applications. Such architectures have been successfully implemented in several industries, such as avionics and automotive. In this paper we investigate the challenges of developing and the benefits of integrating a scientific instrument, namely a Fourier Transform Spectrometer, in such a partitioned architecture.

The application of a Web-geographic information system for improving urban water cycle modelling.

PubMed

Mair, M; Mikovits, C; Sengthaler, M; Schöpf, M; Kinzel, H; Urich, C; Kleidorfer, M; Sitzenfrei, R; Rauch, W

2014-01-01

Research in urban water management has experienced a transition from traditional model applications to modelling water cycles as an integrated part of urban areas. This includes the interlinking of models of many research areas (e.g. urban development, socio-economy, urban water management). The integration and simulation is realized in newly developed frameworks (e.g. DynaMind and OpenMI) and often assumes a high knowledge in programming. This work presents a Web based urban water management modelling platform which simplifies the setup and usage of complex integrated models. The platform is demonstrated with a small application example on a case study within the Alpine region. The used model is a DynaMind model benchmarking the impact of newly connected catchments on the flooding behaviour of an existing combined sewer system. As a result the workflow of the user within a Web browser is demonstrated and benchmark results are shown. The presented platform hides implementation specific aspects behind Web services based technologies such that the user can focus on his main aim, which is urban water management modelling and benchmarking. Moreover, this platform offers a centralized data management, automatic software updates and access to high performance computers accessible with desktop computers and mobile devices.

A Versatile Microfluidic Device for Automating Synthetic Biology.

PubMed

Shih, Steve C C; Goyal, Garima; Kim, Peter W; Koutsoubelis, Nicolas; Keasling, Jay D; Adams, Paul D; Hillson, Nathan J; Singh, Anup K

2015-10-16

New microbes are being engineered that contain the genetic circuitry, metabolic pathways, and other cellular functions required for a wide range of applications such as producing biofuels, biobased chemicals, and pharmaceuticals. Although currently available tools are useful in improving the synthetic biology process, further improvements in physical automation would help to lower the barrier of entry into this field. We present an innovative microfluidic platform for assembling DNA fragments with 10× lower volumes (compared to that of current microfluidic platforms) and with integrated region-specific temperature control and on-chip transformation. Integration of these steps minimizes the loss of reagents and products compared to that with conventional methods, which require multiple pipetting steps. For assembling DNA fragments, we implemented three commonly used DNA assembly protocols on our microfluidic device: Golden Gate assembly, Gibson assembly, and yeast assembly (i.e., TAR cloning, DNA Assembler). We demonstrate the utility of these methods by assembling two combinatorial libraries of 16 plasmids each. Each DNA plasmid is transformed into Escherichia coli or Saccharomyces cerevisiae using on-chip electroporation and further sequenced to verify the assembly. We anticipate that this platform will enable new research that can integrate this automated microfluidic platform to generate large combinatorial libraries of plasmids and will help to expedite the overall synthetic biology process.

Transference of CALIPER pediatric reference intervals to biochemical assays on the Roche cobas 6000 and the Roche Modular P.

PubMed

Higgins, Victoria; Chan, Man Khun; Nieuwesteeg, Michelle; Hoffman, Barry R; Bromberg, Irvin L; Gornall, Doug; Randell, Edward; Adeli, Khosrow

2016-01-01

The Canadian Laboratory Initiative on Pediatric Reference Intervals (CALIPER) has recently established pediatric age- and sex-specific reference intervals for over 85 biochemical markers on the Abbott Architect system. Previously, CALIPER reference intervals for several biochemical markers were successfully transferred from Abbott assays to Roche, Beckman, Ortho, and Siemens assays. This study further broadens the CALIPER database by performing transference and verification for 52 biochemical assays on the Roche cobas 6000 and the Roche Modular P. Using CLSI C28-A3 and EP9-A2 guidelines, transference of the CALIPER reference intervals was attempted for 16 assays on the Roche cobas 6000 and 36 on the Modular P. Calculated reference intervals were further verified using 100 healthy CALIPER samples. Most assays showed strong correlation between assay systems and were transferable from Abbott to the Roche cobas 6000 (81%) and the Modular P (86%). Bicarbonate and magnesium were not transferable on either system and calcium and prealbumin were not transferable to the Modular P. Of the transferable analytes, 62% and 61% were verified on the cobas 6000 and the Modular P, respectively. This study extends the utility of the CALIPER database to two additional analytical systems, which facilitates the broad application of CALIPER reference intervals at pediatric centers utilizing Roche biochemical assays. Transference studies across different analytical platforms can later be collectively analyzed in an attempt to develop common reference intervals across all clinical chemistry instruments to harmonize laboratory test interpretation in diagnosis and monitoring of pediatric disease. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Nanocomposites in Multifuntional Structures for Spacecraft Platforms

NASA Astrophysics Data System (ADS)

Marcos, J.; Mendizabal, M.; Elizetxea, C.; Florez, S.; Atxaga, G.; Del Olmo, E.

2012-07-01

The integration of functionalities as electrical, thermal, power or radiation shielding inside carrier electronic boxes, solar panels or platform structures allows reducing weight, volume, and harness for spacecraft. The multifunctional structures represent an advanced design approach for space components and subsystems. The development of such multifunctional structures aims the re-engineering traditional metallic structures by composites in space, which request to provide specific solutions for thermal conductivity, EMI-EMC, radiation shielding and integration. The use of nanomaterials as CNF and nano-adds to reinforce composite structures allows obtaining local solutions for improving electrical conductivity, thermal conductivity and radiation shielding. The paper summarises the results obtained in of three investigations conducted by Tecnalia based on carbon nanofillers for improving electro-thermal characteristics of spacecraft platform, electronic substrates and electronics boxes respectively.

Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes.

PubMed

Margaria, Tiziana; Kubczak, Christian; Steffen, Bernhard

2008-04-25

With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms for an LC/MS analysis of FAAH gene knockout. Bio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution. As a service definition and provisioning platform, Bio-jETI has the potential to become a core technology in interdisciplinary service orchestration and technology transfer. Domain experts, like biologists not trained in computer science, directly define complex service orchestrations as process models and use efficient and complex bioinformatics tools in a simple and intuitive way.

Radiation and scattering from printed antennas on cylindrically conformal platforms

NASA Technical Reports Server (NTRS)

Kempel, Leo C.; Volakis, John L.; Bindiganavale, Sunil

1994-01-01

The goal was to develop suitable methods and software for the analysis of antennas on cylindrical coated and uncoated platforms. Specifically, the finite element boundary integral and finite element ABC methods were employed successfully and associated software were developed for the analysis and design of wraparound and discrete cavity-backed arrays situated on cylindrical platforms. This work led to the successful implementation of analysis software for such antennas. Developments which played a role in this respect are the efficient implementation of the 3D Green's function for a metallic cylinder, the incorporation of the fast Fourier transform in computing the matrix-vector products executed in the solver of the finite element-boundary integral system, and the development of a new absorbing boundary condition for terminating the finite element mesh on cylindrical surfaces.

pH measurements of FET-based (bio)chemical sensors using portable measurement system.

PubMed

Voitsekhivska, T; Zorgiebel, F; Suthau, E; Wolter, K-J; Bock, K; Cuniberti, G

2015-01-01

In this study we demonstrate the sensing capabilities of a portable multiplex measurement system for FET-based (bio)chemical sensors with an integrated microfluidic interface. We therefore conducted pH measurements with Silicon Nanoribbon FET-based Sensors using different measurement procedures that are suitable for various applications. We have shown multiplexed measurements in aqueous medium for three different modes that are mutually specialized in fast data acquisition (constant drain current), calibration-less sensing (constant gate voltage) and in providing full information content (sweeping mode). Our system therefore allows surface charge sensing for a wide range of applications and is easily adaptable for multiplexed sensing with novel FET-based (bio)chemical sensors.

Exploration of graphene oxide as an intelligent platform for cancer vaccines

NASA Astrophysics Data System (ADS)

Yue, Hua; Wei, Wei; Gu, Zonglin; Ni, Dezhi; Luo, Nana; Yang, Zaixing; Zhao, Lin; Garate, Jose Antonio; Zhou, Ruhong; Su, Zhiguo; Ma, Guanghui

2015-11-01

We explored an intelligent vaccine system via facile approaches using both experimental and theoretical techniques based on the two-dimensional graphene oxide (GO). Without extra addition of bio/chemical stimulators, the microsized GO imparted various immune activation tactics to improve the antigen immunogenicity. A high antigen adsorption was acquired, and the mechanism was revealed to be a combination of electrostatic, hydrophobic, and π-π stacking interactions. The ``folding GO'' acted as a cytokine self-producer and antigen reservoir and showed a particular autophagy, which efficiently promoted the activation of antigen presenting cells (APCs) and subsequent antigen cross-presentation. Such a ``One but All'' modality thus induced a high level of anti-tumor responses in a programmable way and resulted in efficient tumor regression in vivo. This work may shed light on the potential use of a new dimensional nano-platform in the development of high-performance cancer vaccines.We explored an intelligent vaccine system via facile approaches using both experimental and theoretical techniques based on the two-dimensional graphene oxide (GO). Without extra addition of bio/chemical stimulators, the microsized GO imparted various immune activation tactics to improve the antigen immunogenicity. A high antigen adsorption was acquired, and the mechanism was revealed to be a combination of electrostatic, hydrophobic, and π-π stacking interactions. The ``folding GO'' acted as a cytokine self-producer and antigen reservoir and showed a particular autophagy, which efficiently promoted the activation of antigen presenting cells (APCs) and subsequent antigen cross-presentation. Such a ``One but All'' modality thus induced a high level of anti-tumor responses in a programmable way and resulted in efficient tumor regression in vivo. This work may shed light on the potential use of a new dimensional nano-platform in the development of high-performance cancer vaccines. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04986e

Posterior Approach to Kidney Dissection: An Old Surgical Approach for Integrated Medical Curricula

ERIC Educational Resources Information Center

Daly, Frank J.; Bolender, David L.; Jain, Deepali; Uyeda, Sheryl; Hoagland, Todd M.

2015-01-01

Integrated medical curricular changes are altering the historical regional anatomy approach to abdominal dissection. The renal system is linked physiologically and biochemically to the cardiovascular and respiratory systems; yet, anatomists often approach the urinary system as part of the abdomen and pelvic regions. As part of an integrated…

Process and information integration via hypermedia

NASA Technical Reports Server (NTRS)

Hammen, David G.; Labasse, Daniel L.; Myers, Robert M.

1990-01-01

Success stories for advanced automation prototypes abound in the literature but the deployments of practical large systems are few in number. There are several factors that militate against the maturation of such prototypes into products. Here, the integration of advanced automation software into large systems is discussed. Advanced automation systems tend to be specific applications that need to be integrated and aggregated into larger systems. Systems integration can be achieved by providing expert user-developers with verified tools to efficiently create small systems that interface to large systems through standard interfaces. The use of hypermedia as such a tool in the context of the ground control centers that support Shuttle and space station operations is explored. Hypermedia can be an integrating platform for data, conventional software, and advanced automation software, enabling data integration through the display of diverse types of information and through the creation of associative links between chunks of information. Further, hypermedia enables process integration through graphical invoking of system functions. Through analysis and examples, researchers illustrate how diverse information and processing paradigms can be integrated into a single software platform.

Direct Electron Transfer of Enzymes in a Biologically Assembled Conductive Nanomesh Enzyme Platform.

PubMed

Lee, Seung-Woo; Lee, Ki-Young; Song, Yong-Won; Choi, Won Kook; Chang, Joonyeon; Yi, Hyunjung

2016-02-24

Nondestructive assembly of a nanostructured enzyme platform is developed in combination of the specific biomolecular attraction and electrostatic coupling for highly efficient direct electron transfer (DET) of enzymes with unprecedented applicability and versatility. The biologically assembled conductive nanomesh enzyme platform enables DET-based flexible integrated biosensors and DET of eight different enzyme with various catalytic activities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Future Directions for Astronomical Image Display

NASA Technical Reports Server (NTRS)

Mandel, Eric

2000-01-01

In the "Future Directions for Astronomical Image Displav" project, the Smithsonian Astrophysical Observatory (SAO) and the National Optical Astronomy Observatories (NOAO) evolved our existing image display program into fully extensible. cross-platform image display software. We also devised messaging software to support integration of image display into astronomical analysis systems. Finally, we migrated our software from reliance on Unix and the X Window System to a platform-independent architecture that utilizes the cross-platform Tcl/Tk technology.

Efficient Sensor Integration on Platforms (NeXOS)

NASA Astrophysics Data System (ADS)

Memè, S.; Delory, E.; Del Rio, J.; Jirka, S.; Toma, D. M.; Martinez, E.; Frommhold, L.; Barrera, C.; Pearlman, J.

2016-12-01

In-situ ocean observing platforms provide power and information transmission capability to sensors. Ocean observing platforms can be mobile, such as ships, autonomous underwater vehicles, drifters and profilers, or fixed, such as buoys, moorings and cabled observatories. The process of integrating sensors on platforms can imply substantial engineering time and resources. Constraints range from stringent mechanical constraints to proprietary communication and control firmware. In NeXOS, the implementation of a PUCK plug and play capability is being done with applications to multiple sensors and platforms. This is complemented with a sensor web enablement that addresses the flow of information from sensor to user. Open standards are being tested in order to assess their costs and benefits in existing and future observing systems. Part of the testing implied open-source coding and hardware prototyping of specific control devices in particular for closed commercial platforms where firmware upgrading is not straightforward or possible without prior agreements or service fees. Some platform manufacturers such as European companies ALSEAMAR[1] and NKE Instruments [2] are currently upgrading their control and communication firmware as part of their activities in NeXOS. The sensor development companies Sensorlab[3] SMID[4] and TRIOS [5]upgraded their firmware with this plug and play functionality. Other industrial players in Europe and the US have been sent NeXOS sensors emulators to test the new protocol on their platforms. We are currently demonstrating that with little effort, it is also possible to have such middleware implemented on very low-cost compact computers such as the open Raspberry Pi[6], and have a full end-to-end interoperable communication path from sensor to user with sensor plug and play capability. The result is an increase in sensor integration cost-efficiency and the demonstration will be used to highlight the benefit to users and ocean observatory operators. [1] http://www.alseamar-alcen.com [2] http://www.nke-instrumentation.com [3] http://sensorlab.es [4] http://www.smidtechnology.it/ [5] http://www.trios.de/en/products/ [6] Raspberry Pi is a trademark of the Raspberry Pi Foundation

Physical constraints on biological integral control design for homeostasis and sensory adaptation.

PubMed

Ang, Jordan; McMillen, David R

2013-01-22

Synthetic biology includes an effort to use design-based approaches to create novel controllers, biological systems aimed at regulating the output of other biological processes. The design of such controllers can be guided by results from control theory, including the strategy of integral feedback control, which is central to regulation, sensory adaptation, and long-term robustness. Realization of integral control in a synthetic network is an attractive prospect, but the nature of biochemical networks can make the implementation of even basic control structures challenging. Here we present a study of the general challenges and important constraints that will arise in efforts to engineer biological integral feedback controllers or to analyze existing natural systems. Constraints arise from the need to identify target output values that the combined process-plus-controller system can reach, and to ensure that the controller implements a good approximation of integral feedback control. These constraints depend on mild assumptions about the shape of input-output relationships in the biological components, and thus will apply to a variety of biochemical systems. We summarize our results as a set of variable constraints intended to provide guidance for the design or analysis of a working biological integral feedback controller. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Exploring infrared neural stimulation with multimodal nonlinear imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Adams, Wilson R.; Mahadevan-Jansen, Anita

2017-02-01

Infrared neural stimulation (INS) provides optical control of neural excitability using near to mid-infrared (mid-IR) light, which allows for spatially selective, artifact-free excitation without the introduction of exogenous agents or genetic modification. Although neural excitability is mediated by a transient temperature increase due to water absorption of IR energy, the molecular nature of IR excitability in neural tissue remains unknown. Current research suggests that transient changes in local tissue temperature give rise to a myriad of cellular responses that have been individually attributed to IR mediated excitability. To further elucidate the underlying biophysical mechanisms, we have begun work towards employing a novel multimodal nonlinear imaging platform to probe the molecular underpinnings of INS. Our imaging system performs coherent anti-Stokes Raman scattering (CARS), stimulated Raman scattering (SRS), two-photon excitation fluorescence (TPEF), second-harmonic generation (SHG) and thermal imaging into a single platform that allows for unprecedented co-registration of thermal and biochemical information in real-time. Here, we present our work leveraging CARS and SRS in acute thalamocortical brain slice preparations. We observe the evolution of lipid and protein-specific Raman bands during INS and electrically evoked activity in real-time. Combined with two-photon fluorescence and second harmonic generation, we offer insight to cellular metabolism and membrane dynamics during INS. Thermal imaging allows for the coregistration of acquired biochemical information with temperature information. Our work previews the versatility and capabilities of coherent Raman imaging combined with multiphoton imaging to observe biophysical phenomena for neuroscience applications.

Modelling and Forecasting of Rice Yield in support of Crop Insurance

NASA Astrophysics Data System (ADS)

Weerts, A.; van Verseveld, W.; Trambauer, P.; de Vries, S.; Conijn, S.; van Valkengoed, E.; Hoekman, D.; Hengsdijk, H.; Schrevel, A.

2016-12-01

The Government of Indonesia has embarked on a policy to bring crop insurance to all of Indonesia's farmers. To support the Indonesian government, the G4INDO project (www.g4indo.org) is developing/constructing an integrated platform for judging and handling insurance claims. The platform consists of bringing together remote sensed data (both visible and radar) and hydrologic and crop modelling and forecasting to improve predictions in one forecasting platform (i.e. Delft-FEWS, Werner et al., 2013). The hydrological model and crop model (LINTUL) are coupled on time stepping basis in the OpenStreams framework (see https://github.com/openstreams/wflow) and deployed in a Delft-FEWS forecasting platform to support seasonal forecasting of water availability and crop yield. First we will show the general idea about the project, the integrated platform (including Sentinel 1 & 2 data) followed by first (reforecast) results of the coupled models for predicting water availability and crop yield in the Brantas catchment in Java, Indonesia. Werner, M., Schellekens, J., Gijsbers, P., Van Dijk, M., Van den Akker, O. and Heynert K, 2013. The Delft-FEWS flow forecasting system, Environmental Modelling & Software; 40:65-77. DOI: 10.1016/j.envsoft.2012.07.010 .

Educational process in modern climatology within the web-GIS platform "Climate"

NASA Astrophysics Data System (ADS)

Gordova, Yulia; Gorbatenko, Valentina; Gordov, Evgeny; Martynova, Yulia; Okladnikov, Igor; Titov, Alexander; Shulgina, Tamara

2013-04-01

These days, common to all scientific fields the problem of training of scientists in the environmental sciences is exacerbated by the need to develop new computational and information technology skills in distributed multi-disciplinary teams. To address this and other pressing problems of Earth system sciences, software infrastructure for information support of integrated research in the geosciences was created based on modern information and computational technologies and a software and hardware platform "Climate» (http://climate.scert.ru/) was developed. In addition to the direct analysis of geophysical data archives, the platform is aimed at teaching the basics of the study of changes in regional climate. The educational component of the platform includes a series of lectures on climate, environmental and meteorological modeling and laboratory work cycles on the basics of analysis of current and potential future regional climate change using Siberia territory as an example. The educational process within the Platform is implemented using the distance learning system Moodle (www.moodle.org). This work is partially supported by the Ministry of education and science of the Russian Federation (contract #8345), SB RAS project VIII.80.2.1, RFBR grant #11-05-01190a, and integrated project SB RAS #131.

Comprehensive, comprehensible, distributed and intelligent databases: current status.

PubMed

Frishman, D; Heumann, K; Lesk, A; Mewes, H W

1998-01-01

It is only a matter of time until a user will see not many but one integrated database of information for molecular biology. Is this true? Is it a good thing? Why will it happen? Where are we now? What developments are fostering and what developments are impeding progress towards this end? A list of WWW resources devoted to database issues in molecular biology is available at http://www.mips.biochem.mpg.de frishman@mips.biochem.mpg.de

Undergraduate Laboratory Module for Implementing ELISA on the High Performance Microfluidic Platform

ERIC Educational Resources Information Center

Giri, Basant; Peesara, Ravichander R.; Yanagisawa, Naoki; Dutta, Debashis

2015-01-01

Implementing enzyme-linked immunosorbent assays (ELISA) in microchannels offers several advantages over its traditional microtiter plate-based format, including a reduced sample volume requirement, shorter incubation period, and greater sensitivity. Moreover, microfluidic ELISA platforms are inexpensive to fabricate and allow integration of…

Next Generation Proton Beam Writing: A Platform Technology for Nanowire Integration

DTIC Science & Technology

2010-06-01

Final Report AOARD 09-4020 Next Generation Proton Beam Writing: a platform technology for Nanowire Integration JA van Kan1, AA Bettiol1, T...PBW with a finely focused 2 MeV beam was used to write holes in a matrix of thick PMMA . A G-G developer was used to develop the PMMA patterns. The...solution. The deposition speed was about 1 μm of plated Au in every 5 min. When a sufficient thickness of Au had been deposited, the PMMA around the

Integration of Personalized Healthcare Pathways in an ICT Platform for Diabetes Managements: A Small-Scale Exploratory Study.

PubMed

Fico, Giuseppe; Fioravanti, Alessio; Arredondo, Maria Teresa; Gorman, Joe; Diazzi, Chiara; Arcuri, Giovanni; Conti, Claudio; Pirini, Giampiero

2016-01-01

The availability of new tools able to support patient monitoring and personalized care may substantially improve the quality of chronic disease management. A personalized healthcare pathway (PHP) has been developed for diabetes disease management and integrated into an information and communication technology system to accomplish a shift from organization-centered care to patient-centered care. A small-scale exploratory study was conducted to test the platform. Preliminary results are presented that shed light on how the PHP influences system usage and performance outcomes.

A Point-of-Need infrared mediated PCR platform with compatible lateral flow strip for HPV detection.

PubMed

Liu, Wenjia; Zhang, Mingfang; Liu, Xiaoyan; Sharma, Alok; Ding, Xianting

2017-10-15

With the increasing need of monitoring the epidemiology of serious infectious diseases, food hygiene, food additives and pesticide residues, it is urgent to develop portable, easy-to-use, inexpensive and rapid molecular diagnostic tools. Herein, we demonstrate a prototype of IR mediated Conducting Oil and CarbOn Nanotube circUlaTing PCR (IR-COCONUT PCR) platform for nucleic acid amplification. The presented platform offers a new solution for miniaturized PCR instruments with non-contact heaters by using conducting oil and carbon nanotube as a medium in IR mediated PCR. This novel platform offers accurate and flexible control of temperature through the integration of PID (proportional-integral-derivative) algorithms to manipulate the duty cycle of the voltage signals of IR LED and a peristaltic pump. The ramping rate of the introduced platform in current study is 1.5°C/s for heating speed and -2.0°C/s for cooling speed. This platform fulfills 30 thermal cycles within 50min which is a match to the conventional bench-top PCR thermo cyclers. For demonstration purpose, human papillomavirus (HPV) patient cervical swab specimens were examined. Downstream lateral flow strip (LFS) was also developed to quantity the PCR products from the IR-COCONUT PCR device within 25min. This PCR platform together with the compatible LFS shows great potential for in-field and Point-of-Need (PoN) testing of genetic or contagious diseases. Copyright © 2017 Elsevier B.V. All rights reserved.

In-vitro nanodiagnostic platform through nanoparticles and DNA-RNA nanotechnology.

PubMed

Chan, Ki; Ng, Tzi Bun

2015-04-01

Nanocomposites containing nanoparticles or nanostructured domains exhibit an even higher degree of material complexity that leads to an extremely high variability of nanostructured materials. This review introduces analytical concepts and techniques for nanomaterials and derives recommendations for a qualified selection of characterization techniques for specific types of samples, and focuses the characterization of nanoparticles and their agglomerates or aggregates. In addition, DNA nanotechnology and the more recent newcomer RNA nanotechnology have achieved almost an advanced status among nanotechnology researchers¸ therefore, the core features, potential, and significant challenges of DNA nanotechnology are also highlighted as a new discipline. Moreover, nanobiochips made by nanomaterials are rapidly emerging as a new paradigm in the area of large-scale biochemical analysis. The use of nanoscale components enables higher precision in diagnostics while considerably reducing the cost of the platform that leads this review to explore the use of nanoparticles, nanomaterials, and other bionanotechnologies for its application to nanodiagnostics in-vitro.

Microfluidics for cell-based high throughput screening platforms - A review.

PubMed

Du, Guansheng; Fang, Qun; den Toonder, Jaap M J

2016-01-15

In the last decades, the basic techniques of microfluidics for the study of cells such as cell culture, cell separation, and cell lysis, have been well developed. Based on cell handling techniques, microfluidics has been widely applied in the field of PCR (Polymerase Chain Reaction), immunoassays, organ-on-chip, stem cell research, and analysis and identification of circulating tumor cells. As a major step in drug discovery, high-throughput screening allows rapid analysis of thousands of chemical, biochemical, genetic or pharmacological tests in parallel. In this review, we summarize the application of microfluidics in cell-based high throughput screening. The screening methods mentioned in this paper include approaches using the perfusion flow mode, the droplet mode, and the microarray mode. We also discuss the future development of microfluidic based high throughput screening platform for drug discovery. Copyright © 2015 Elsevier B.V. All rights reserved.

Cell illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2011-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

Nucleic acid programmable protein array a just-in-time multiplexed protein expression and purification platform.

PubMed

Qiu, Ji; LaBaer, Joshua

2011-01-01

Systematic study of proteins requires the availability of thousands of proteins in functional format. However, traditional recombinant protein expression and purification methods have many drawbacks for such study at the proteome level. We have developed an innovative in situ protein expression and capture system, namely NAPPA (nucleic acid programmable protein array), where C-terminal tagged proteins are expressed using an in vitro expression system and efficiently captured/purified by antitag antibodies coprinted at each spot. The NAPPA technology presented in this chapter enable researchers to produce and display fresh proteins just in time in a multiplexed high-throughput fashion and utilize them for various downstream biochemical researches of interest. This platform could revolutionize the field of functional proteomics with it ability to produce thousands of spatially separated proteins in high density with narrow dynamic rand of protein concentrations, reproducibly and functionally. Copyright © 2011 Elsevier Inc. All rights reserved.

Cell Illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2010-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

Egg Yolk Lecithin: A Biochemical Laboratory Project

ERIC Educational Resources Information Center

White, Bernard J.; And Others

1974-01-01

Describes an undergraduate laboratory project involving lecithin which integrates two general aspects of lipid methodology: chromatographic techniques and use of enzymes specificity to obtain structural information. (Author/SLH)

High-density stretchable microelectrode arrays: An integrated technology platform for neural and muscular surface interfacing

NASA Astrophysics Data System (ADS)

Guo, Liang

2011-12-01

Numerous applications in neuroscience research and neural prosthetics, such as retinal prostheses, spinal-cord surface stimulation for prosthetics, electrocorticogram (ECoG) recording for epilepsy detection, etc., involve electrical interaction with soft excitable tissues using a surface stimulation and/or recording approach. These applications require an interface that is able to set up electrical communications with a high throughput between electronics and the excitable tissue and that can dynamically conform to the shape of the soft tissue. Being a compliant and biocompatible material with mechanical impedance close to that of soft tissues, polydimethylsiloxane (PDMS) offers excellent potential as the substrate material for such neural interfaces. However, fabrication of electrical functionalities on PDMS has long been very challenging. This thesis work has successfully overcome many challenges associated with PDMS-based microfabrication and achieved an integrated technology platform for PDMS-based stretchable microelectrode arrays (sMEAs). This platform features a set of technological advances: (1) we have fabricated uniform current density profile microelectrodes as small as 10 mum in diameter; (2) we have patterned high-resolution (feature as small as 10 mum), high-density (pitch as small as 20 mum) thin-film gold interconnects on PDMS substrate; (3) we have developed a multilayer wiring interconnect technology within the PDMS substrate to further boost the achievable integration density of such sMEA; and (4) we have invented a bonding technology---via-bonding---to facilitate high-resolution, high-density integration of the sMEA with integrated circuits (ICs) to form a compact implant. Taken together, this platform provides a high-resolution, high-density integrated system solution for neural and muscular surface interfacing. sMEAs of example designs are evaluated through in vitro and in vivo experimentations on their biocompatibility, surface conformability, and surface recording/stimulation capabilities, with a focus on epimysial (i.e. on the surface of muscle) applications. Finally, as an example medical application, we investigate a prosthesis for unilateral vocal cord paralysis (UVCP) based on simultaneous multichannel epimysial recording and stimulation.

Tele-Supervised Adaptive Ocean Sensor Fleet

NASA Technical Reports Server (NTRS)

Lefes, Alberto; Podnar, Gregg W.; Dolan, John M.; Hosler, Jeffrey C.; Ames, Troy J.

2009-01-01

The Tele-supervised Adaptive Ocean Sensor Fleet (TAOSF) is a multi-robot science exploration architecture and system that uses a group of robotic boats (the Ocean-Atmosphere Sensor Integration System, or OASIS) to enable in-situ study of ocean surface and subsurface characteristics and the dynamics of such ocean phenomena as coastal pollutants, oil spills, hurricanes, or harmful algal blooms (HABs). The OASIS boats are extended- deployment, autonomous ocean surface vehicles. The TAOSF architecture provides an integrated approach to multi-vehicle coordination and sliding human-vehicle autonomy. One feature of TAOSF is the adaptive re-planning of the activities of the OASIS vessels based on sensor input ( smart sensing) and sensorial coordination among multiple assets. The architecture also incorporates Web-based communications that permit control of the assets over long distances and the sharing of data with remote experts. Autonomous hazard and assistance detection allows the automatic identification of hazards that require human intervention to ensure the safety and integrity of the robotic vehicles, or of science data that require human interpretation and response. Also, the architecture is designed for science analysis of acquired data in order to perform an initial onboard assessment of the presence of specific science signatures of immediate interest. TAOSF integrates and extends five subsystems developed by the participating institutions: Emergent Space Tech - nol ogies, Wallops Flight Facility, NASA s Goddard Space Flight Center (GSFC), Carnegie Mellon University, and Jet Propulsion Laboratory (JPL). The OASIS Autonomous Surface Vehicle (ASV) system, which includes the vessels as well as the land-based control and communications infrastructure developed for them, controls the hardware of each platform (sensors, actuators, etc.), and also provides a low-level waypoint navigation capability. The Multi-Platform Simulation Environment from GSFC is a surrogate for the OASIS ASV system and allows for independent development and testing of higher-level software components. The Platform Communicator acts as a proxy for both actual and simulated platforms. It translates platform-independent messages from the higher control systems to the device-dependent communication protocols. This enables the higher-level control systems to interact identically with heterogeneous actual or simulated platforms.

Design of Smart Multi-Functional Integrated Aviation Photoelectric Payload

NASA Astrophysics Data System (ADS)

Zhang, X.

2018-04-01

To coordinate with the small UAV at reconnaissance mission, we've developed a smart multi-functional integrated aviation photoelectric payload. The payload weighs only 1kg, and has a two-axis stabilized platform with visible task payload, infrared task payload, laser pointers and video tracker. The photoelectric payload could complete the reconnaissance tasks above the target area (including visible and infrared). Because of its light weight, small size, full-featured, high integrated, the constraints of the UAV platform carrying the payload will be reduced a lot, which helps the payload suit for more extensive using occasions. So all users of this type of smart multi-functional integrated aviation photoelectric payload will do better works on completion of the ground to better pinpoint targets, artillery calibration, assessment of observe strike damage, customs officials and other tasks.

A discussion for integrating INSPIRE with volunteered geographic information (VGI) and the vision for a global spatial-based platform

NASA Astrophysics Data System (ADS)

Demetriou, Demetris; Campagna, Michele; Racetin, Ivana; Konecny, Milan

2017-09-01

INSPIRE is the EU's authoritative Spatial Data Infrastructure (SDI) in which each Member State provides access to their spatial data across a wide spectrum of data themes to support policy making. In contrast, Volunteered Geographic Information (VGI) is one type of user-generated geographic information where volunteers use the web and mobile devices to create, assemble and disseminate spatial information. There are similarities and differences between SDIs and VGI initiatives, as well as advantages and disadvantages. Thus, the integration of these two data sources will enhance what is offered to end users to facilitate decision makers and the wider community regarding solving complex spatial problems, managing emergency situations and getting useful information for peoples' daily activities. Although some efforts towards this direction have been arisen, several key issues need to be considered and resolved. Further to this integration, the vision is the development of a global integrated GIS platform, which extends the capabilities of a typical data-hub by embedding on-line spatial and non-spatial applications, to deliver both static and dynamic outputs to support planning and decision making. In this context, this paper discusses the challenges of integrating INSPIRE with VGI and outlines a generic framework towards creating a global integrated web-based GIS platform. The tremendous high speed evolution of the Web and Geospatial technologies suggest that this "super" global Geo-system is not far away.

Fluidics platform and method for sample preparation

DOEpatents

Benner, Henry W.; Dzenitis, John M.

2016-06-21

Provided herein are fluidics platforms and related methods for performing integrated sample collection and solid-phase extraction of a target component of the sample all in one tube. The fluidics platform comprises a pump, particles for solid-phase extraction and a particle-holding means. The method comprises contacting the sample with one or more reagents in a pump, coupling a particle-holding means to the pump and expelling the waste out of the pump while the particle-holding means retains the particles inside the pump. The fluidics platform and methods herein described allow solid-phase extraction without pipetting and centrifugation.

Test Platforms for Model-Based Flight Research

NASA Astrophysics Data System (ADS)

Dorobantu, Andrei

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

Should biomedical research be like Airbnb?

PubMed

Bonazzi, Vivien R; Bourne, Philip E

2017-04-01

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

Should biomedical research be like Airbnb?

PubMed Central

Bonazzi, Vivien R.

2017-01-01

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

Cloud Based Web 3d GIS Taiwan Platform

NASA Astrophysics Data System (ADS)

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

2011-09-01

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

Creation of an Integrated Environment to Supply e-Learning Platforms with Office Automation Features

ERIC Educational Resources Information Center

Palumbo, Emilio; Verga, Francesca

2015-01-01

Over the last years great efforts have been made within the University environment to implement e-learning technologies in the standard educational practice. These learning technologies distribute online educational multimedia contents through technological platforms. Even though specific e-learning tools for technical disciplines were already…

Perspectives on Blended Learning through the On-Line Platform, LabLessons, for Chemistry

ERIC Educational Resources Information Center

Jihad, Teeba; Klementowicz, Edward; Gryczka, Patrick; Sharrock, Chappel; Maxfield, MacRae; Lee, Yongjun; Montclare, Jin Kim

2018-01-01

The effectiveness of blended learning was evaluated through the integration of an online chemistry platform, LabLessons. Two modules, "Formation of Hydrogen" and "Titration," were designed by college mentors alongside classroom chemistry teachers to engage and allow high school students to better comprehend these scientific…

An Integrated Library Platform: Wales' Approach to Delivering Digital Information and Resources Nationally

ERIC Educational Resources Information Center

Bevan, Paul; Tyler, Alyson

2009-01-01

Purpose: This paper aims to outline the developments and strategies employed to supply online library services in Wales through a national platform: library.wales.org These services include: the "Cat Cymru" cross-catalogue search, centrally procured subscription resources and local library microsites. Design/methodology/approach: The…

KDE Bioscience: platform for bioinformatics analysis workflows.

PubMed

Lu, Qiang; Hao, Pei; Curcin, Vasa; He, Weizhong; Li, Yuan-Yuan; Luo, Qing-Ming; Guo, Yi-Ke; Li, Yi-Xue

2006-08-01

Bioinformatics is a dynamic research area in which a large number of algorithms and programs have been developed rapidly and independently without much consideration so far of the need for standardization. The lack of such common standards combined with unfriendly interfaces make it difficult for biologists to learn how to use these tools and to translate the data formats from one to another. Consequently, the construction of an integrative bioinformatics platform to facilitate biologists' research is an urgent and challenging task. KDE Bioscience is a java-based software platform that collects a variety of bioinformatics tools and provides a workflow mechanism to integrate them. Nucleotide and protein sequences from local flat files, web sites, and relational databases can be entered, annotated, and aligned. Several home-made or 3rd-party viewers are built-in to provide visualization of annotations or alignments. KDE Bioscience can also be deployed in client-server mode where simultaneous execution of the same workflow is supported for multiple users. Moreover, workflows can be published as web pages that can be executed from a web browser. The power of KDE Bioscience comes from the integrated algorithms and data sources. With its generic workflow mechanism other novel calculations and simulations can be integrated to augment the current sequence analysis functions. Because of this flexible and extensible architecture, KDE Bioscience makes an ideal integrated informatics environment for future bioinformatics or systems biology research.

Technology for the future - Long range planning for space technology development

NASA Technical Reports Server (NTRS)

Collier, Lisa D.; Breckenridge, Roger A.; Llewellyn, Charles P.

1992-01-01

NASA's Office of Aeronautics and Space Technology (OAST) has begun the definition of an Integrated Technology Plan for the civilian space program which guides long-term technology development for space platforms, in light of continuing marker research and other planning data. OAST has conferred particular responsibility for future candidate space mission evaluations and platform performance requirement projections to NASA-Langley. An implementation plan is devised which is amenable to periodic space-platform technology updates.

Silicon Nitride Photonic Integration Platforms for Visible, Near-Infrared and Mid-Infrared Applications

PubMed Central

Micó, Gloria; Pastor, Daniel; Pérez, Daniel; Doménech, José David; Fernández, Juan; Baños, Rocío; Alemany, Rubén; Sánchez, Ana M.; Cirera, Josep M.; Mas, Roser

2017-01-01

Silicon nitride photonics is on the rise owing to the broadband nature of the material, allowing applications of biophotonics, tele/datacom, optical signal processing and sensing, from visible, through near to mid-infrared wavelengths. In this paper, a review of the state of the art of silicon nitride strip waveguide platforms is provided, alongside the experimental results on the development of a versatile 300 nm guiding film height silicon nitride platform. PMID:28895906

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

PubMed

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

2015-01-01

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

Progress in Open-World, Integrative, Collaborative Science Data Platforms (Invited)

NASA Astrophysics Data System (ADS)

Fox, P. A.

2013-12-01

As collaborative, or network science spreads into more Earth and space science fields, both the participants and their funders have expressed a very strong desire for highly functional data and information capabilities that are a) easy to use, b) integrated in a variety of ways, c) leverage prior investments and keep pace with rapid technical change, and d) are not expensive or time-consuming to build or maintain. In response, and based on our accumulated experience over the last decade and a maturing of several key technical approaches, we have adapted, extended, and integrated several open source applications and frameworks that handle major portions of functionality for these platforms. At minimum, these functions include: an object-type repository, collaboration tools, an ability to identify and manage all key entities in the platform, and an integrated portal to manage diverse content and applications, with varied access levels and privacy options. At a conceptual level, science networks (even small ones) deal with people, and many intellectual artifacts produced or consumed in research, organizational and/our outreach activities, as well as the relations among them. Increasingly these networks are modeled as knowledge networks, i.e. graphs with named and typed relations among the 'nodes'. Nodes can be people, organizations, datasets, events, presentations, publications, videos, meetings, reports, groups, and more. In this heterogeneous ecosystem, it is also important to use a set of common informatics approaches to co-design and co-evolve the needed science data platforms based on what real people want to use them for. In this contribution, we present our methods and results for information modeling, adapting, integrating and evolving a networked data science and information architecture based on several open source technologies (Drupal, VIVO, the Comprehensive Knowledge Archive Network; CKAN, and the Global Handle System; GHS). In particular we present both the instantiation of this data platform for the Deep Carbon Observatory, including key functional and non-functional attributes, how the smart mediation among the components is modeled and managed, and discuss its general applicability.

CompatPM: enabling energy efficient multimedia workloads for distributed mobile platforms

NASA Astrophysics Data System (ADS)

Nathuji, Ripal; O'Hara, Keith J.; Schwan, Karsten; Balch, Tucker

2007-01-01

The computation and communication abilities of modern platforms are enabling increasingly capable cooperative distributed mobile systems. An example is distributed multimedia processing of sensor data in robots deployed for search and rescue, where a system manager can exploit the application's cooperative nature to optimize the distribution of roles and tasks in order to successfully accomplish the mission. Because of limited battery capacities, a critical task a manager must perform is online energy management. While support for power management has become common for the components that populate mobile platforms, what is lacking is integration and explicit coordination across the different management actions performed in a variety of system layers. This papers develops an integration approach for distributed multimedia applications, where a global manager specifies both a power operating point and a workload for a node to execute. Surprisingly, when jointly considering power and QoS, experimental evaluations show that using a simple deadline-driven approach to assigning frequencies can be non-optimal. These trends are further affected by certain characteristics of underlying power management mechanisms, which in our research, are identified as groupings that classify component power management as "compatible" (VFC) or "incompatible" (VFI) with voltage and frequency scaling. We build on these findings to develop CompatPM, a vertically integrated control strategy for power management in distributed mobile systems. Experimental evaluations of CompatPM indicate average energy improvements of 8% when platform resources are managed jointly rather than independently, demonstrating that previous attempts to maximize battery life by simply minimizing frequency are inappropriate from a platform-level perspective.

Supporting Building Portfolio Investment and Policy Decision Making through an Integrated Building Utility Data Platform

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

Aziz, Azizan; Lasternas, Bertrand; Alschuler, Elena

The American Recovery and Reinvestment Act stimulus funding of 2009 for smart grid projects resulted in the tripling of smart meters deployment. In 2012, the Green Button initiative provided utility customers with access to their real-time1 energy usage. The availability of finely granular data provides an enormous potential for energy data analytics and energy benchmarking. The sheer volume of time-series utility data from a large number of buildings also poses challenges in data collection, quality control, and database management for rigorous and meaningful analyses. In this paper, we will describe a building portfolio-level data analytics tool for operational optimization, businessmore » investment and policy assessment using 15-minute to monthly intervals utility data. The analytics tool is developed on top of the U.S. Department of Energy’s Standard Energy Efficiency Data (SEED) platform, an open source software application that manages energy performance data of large groups of buildings. To support the significantly large volume of granular interval data, we integrated a parallel time-series database to the existing relational database. The time-series database improves on the current utility data input, focusing on real-time data collection, storage, analytics and data quality control. The fully integrated data platform supports APIs for utility apps development by third party software developers. These apps will provide actionable intelligence for building owners and facilities managers. Unlike a commercial system, this platform is an open source platform funded by the U.S. Government, accessible to the public, researchers and other developers, to support initiatives in reducing building energy consumption.« less

Integrative multi-platform meta-analysis of gene expression profiles in pancreatic ductal adenocarcinoma patients for identifying novel diagnostic biomarkers.

PubMed

Irigoyen, Antonio; Jimenez-Luna, Cristina; Benavides, Manuel; Caba, Octavio; Gallego, Javier; Ortuño, Francisco Manuel; Guillen-Ponce, Carmen; Rojas, Ignacio; Aranda, Enrique; Torres, Carolina; Prados, Jose

2018-01-01

Applying differentially expressed genes (DEGs) to identify feasible biomarkers in diseases can be a hard task when working with heterogeneous datasets. Expression data are strongly influenced by technology, sample preparation processes, and/or labeling methods. The proliferation of different microarray platforms for measuring gene expression increases the need to develop models able to compare their results, especially when different technologies can lead to signal values that vary greatly. Integrative meta-analysis can significantly improve the reliability and robustness of DEG detection. The objective of this work was to develop an integrative approach for identifying potential cancer biomarkers by integrating gene expression data from two different platforms. Pancreatic ductal adenocarcinoma (PDAC), where there is an urgent need to find new biomarkers due its late diagnosis, is an ideal candidate for testing this technology. Expression data from two different datasets, namely Affymetrix and Illumina (18 and 36 PDAC patients, respectively), as well as from 18 healthy controls, was used for this study. A meta-analysis based on an empirical Bayesian methodology (ComBat) was then proposed to integrate these datasets. DEGs were finally identified from the integrated data by using the statistical programming language R. After our integrative meta-analysis, 5 genes were commonly identified within the individual analyses of the independent datasets. Also, 28 novel genes that were not reported by the individual analyses ('gained' genes) were also discovered. Several of these gained genes have been already related to other gastroenterological tumors. The proposed integrative meta-analysis has revealed novel DEGs that may play an important role in PDAC and could be potential biomarkers for diagnosing the disease.

Multifunctional System-on-Glass for Lab-on-Chip applications.

PubMed

Petrucci, G; Caputo, D; Lovecchio, N; Costantini, F; Legnini, I; Bozzoni, I; Nascetti, A; de Cesare, G

2017-07-15

Lab-on-Chip are miniaturized systems able to perform biomolecular analysis in shorter time and with lower reagent consumption than a standard laboratory. Their miniaturization interferes with the multiple functions that the biochemical procedures require. In order to address this issue, our paper presents, for the first time, the integration on a single glass substrate of different thin film technologies in order to develop a multifunctional platform suitable for on-chip thermal treatments and on-chip detection of biomolecules. The proposed System on-Glass hosts thin metal films acting as heating sources; hydrogenated amorphous silicon diodes acting both as temperature sensors to monitor the temperature distribution and photosensors for the on-chip detection and a ground plane ensuring that the heater operation does not affect the photodiode currents. The sequence of the technological steps, the deposition temperatures of the thin films and the parameters of the photolithographic processes have been optimized in order to overcome all the issues of the technological integration. The device has been designed, fabricated and tested for the implementation of DNA amplification through the Polymerase Chain Reaction (PCR) with thermal cycling among three different temperatures on a single site. The glass has been connected to an electronic system that drives the heaters and controls the temperature and light sensors. It has been optically and thermally coupled with another glass hosting a microfluidic network made in polydimethylsiloxane that includes thermally actuated microvalves and a PCR process chamber. The successful DNA amplification has been verified off-chip by using a standard fluorometer. Copyright © 2016 Elsevier B.V. All rights reserved.

Chemical, biochemical, and environmental fiber sensors III; Proceedings of the Meeting, Boston, MA, Sept. 4, 5, 1991

NASA Astrophysics Data System (ADS)

Lieberman, Robert A.

Various papers on chemical, biochemical, and environmental fiber sensors are presented. Individual topics addressed include: fiber optic pressure sensor for combustion monitoring and control, viologen-based fiber optic oxygen sensors, renewable-reagent fiber optic sensor for ocean pCO2, transition metal complexes as indicators for a fiber optic oxygen sensor, fiber optic pH measurements using azo indicators, simple reversible fiber optic chemical sensors using solvatochromic dyes, totally integrated optical measuring sensors, integrated optic biosensor for environmental monitoring, radiation dosimetry using planar waveguide sensors, optical and piezoelectric analysis of polymer films for chemical sensor characterization, source polarization effects in an optical fiber fluorosensor, lens-type refractometer for on-line chemical analysis, fiber optic hydrocarbon sensor system, chemical sensors for environmental monitoring, optical fibers for liquid-crystal sensing and logic devices, suitability of single-mode fluoride fibers for evanescent-wave sensing, integrated modules for fiber optic sensors, optoelectronic sensors based on narrowband A3B5 alloys, fiber Bragg grating chemical sensor.

Mathematical Modeling Approaches in Plant Metabolomics.

PubMed

Fürtauer, Lisa; Weiszmann, Jakob; Weckwerth, Wolfram; Nägele, Thomas

2018-01-01

The experimental analysis of a plant metabolome typically results in a comprehensive and multidimensional data set. To interpret metabolomics data in the context of biochemical regulation and environmental fluctuation, various approaches of mathematical modeling have been developed and have proven useful. In this chapter, a general introduction to mathematical modeling is presented and discussed in context of plant metabolism. A particular focus is laid on the suitability of mathematical approaches to functionally integrate plant metabolomics data in a metabolic network and combine it with other biochemical or physiological parameters.

Biochemical, endocrine, and hematological factors in human oxygen tolerance extension: Predictive studies 6

NASA Technical Reports Server (NTRS)

Lambertsen, C. J.; Clark, J. M.

1992-01-01

The Predictive Studies VI (Biochemical, endocrine, and hematological factors in human oxygen tolerance extension) Program consisted of two related areas of research activity, integrated in design and performance, that were each based on an ongoing analysis of human organ oxygen tolerance data obtained for the continuous oxygen exposures of the prior Predictive Studies V Program. The two research areas effectively blended broad investigation of systematically varied intermittent exposure patterns in animals with very selective evaluation of specific exposure patterns in man.

How Do Structure and Charge Affect Metal-Complex Binding to DNA? An Upper-Division Integrated Laboratory Project Using Cyclic Voltammetry

ERIC Educational Resources Information Center

Kulczynska, Agnieszka; Johnson, Reed; Frost, Tony; Margerum, Lawrence D.

2011-01-01

An advanced undergraduate laboratory project is described that integrates inorganic, analytical, physical, and biochemical techniques to reveal differences in binding between cationic metal complexes and anionic DNA (herring testes). Students were guided to formulate testable hypotheses based on the title question and a list of different metal…