WorldWideScience

Sample records for on-chip genetic detection

  1. SVM classifier on chip for melanoma detection.

    Science.gov (United States)

    Afifi, Shereen; GholamHosseini, Hamid; Sinha, Roopak

    2017-07-01

    Support Vector Machine (SVM) is a common classifier used for efficient classification with high accuracy. SVM shows high accuracy for classifying melanoma (skin cancer) clinical images within computer-aided diagnosis systems used by skin cancer specialists to detect melanoma early and save lives. We aim to develop a medical low-cost handheld device that runs a real-time embedded SVM-based diagnosis system for use in primary care for early detection of melanoma. In this paper, an optimized SVM classifier is implemented onto a recent FPGA platform using the latest design methodology to be embedded into the proposed device for realizing online efficient melanoma detection on a single system on chip/device. The hardware implementation results demonstrate a high classification accuracy of 97.9% and a significant acceleration factor of 26 from equivalent software implementation on an embedded processor, with 34% of resources utilization and 2 watts for power consumption. Consequently, the implemented system meets crucial embedded systems constraints of high performance and low cost, resources utilization and power consumption, while achieving high classification accuracy.

  2. A Miniaturized On-Chip Colorimeter for Detecting NPK Elements.

    Science.gov (United States)

    Liu, Rui-Tao; Tao, Lu-Qi; Liu, Bo; Tian, Xiang-Guang; Mohammad, Mohammad Ali; Yang, Yi; Ren, Tian-Ling

    2016-08-04

    Recently, precision agriculture has become a globally attractive topic. As one of the most important factors, the soil nutrients play an important role in estimating the development of precision agriculture. Detecting the content of nitrogen, phosphorus and potassium (NPK) elements more efficiently is one of the key issues. In this paper, a novel chip-level colorimeter was fabricated to detect the NPK elements for the first time. A light source-microchannel photodetector in a sandwich structure was designed to realize on-chip detection. Compared with a commercial colorimeter, all key parts are based on MEMS (Micro-Electro-Mechanical System) technology so that the volume of this on-chip colorimeter can be minimized. Besides, less error and high precision are achieved. The cost of this colorimeter is two orders of magnitude less than that of a commercial one. All these advantages enable a low-cost and high-precision sensing operation in a monitoring network. The colorimeter developed herein has bright prospects for environmental and biological applications.

  3. Lab-on-chip components for molecular detection

    Science.gov (United States)

    Adam, Tijjani; Dhahi, Th S.; Mohammed, Mohammed; Hashim, U.; Noriman, N. Z.; Dahham, Omar S.

    2017-09-01

    We successfully fabricated Lab on chip components and integrated for possible use in biomedical application. The sensor was fabricated by using conventional photolithography method integrated with PDMS micro channels for smooth delivery of sample to the sensing domain. The sensor was silanized and aminated with 3-Aminopropyl triethoxysilane (APTES) to functionalize the surface with biomolecules and create molecular binding chemistry. The resulting Si-O-Si- components were functionalized with oligonucleotides probe of HPV, which interacted with the single stranded HPV DNA target to create a field across on the device. The fabrication, immobilization and hybridization processes were characterized with current voltage (I-V) characterization (KEITHLEY, 6487). The sensor show selectivity for the HPV DNA target in a linear range from concentration 0.1 nM to 1 µM. This strategy presented a simple, rapid and sensitive platform for HPV detection and would become a powerful tool for pathogenic microorganisms screening in clinical diagnosis.

  4. A low-cost 2D fluorescence detection system for mm sized beads on-chip

    NARCIS (Netherlands)

    Segerink, Loes Irene; Koster, Maarten J.; Sprenkels, A.J.; van den Berg, Albert

    2012-01-01

    In this paper we describe a compact fluorescence detection system for on-chip analysis of beads, comprising a low-cost optical HD-DVD pickup. The complete system consists of a fluorescence detection unit, a control unit and a microfluidic chip containing microchannels and optical markers. With these

  5. A Miniaturized On-Chip Colorimeter for Detecting NPK Elements

    OpenAIRE

    Liu, Rui-Tao; Tao, Lu-Qi; Liu, Bo; Tian, Xiang-Guang; Mohammad, Mohammad Ali; Yang, Yi; Ren, Tian-Ling

    2016-01-01

    Recently, precision agriculture has become a globally attractive topic. As one of the most important factors, the soil nutrients play an important role in estimating the development of precision agriculture. Detecting the content of nitrogen, phosphorus and potassium (NPK) elements more efficiently is one of the key issues. In this paper, a novel chip-level colorimeter was fabricated to detect the NPK elements for the first time. A light source–microchannel photodetector in a sandwich structu...

  6. VLSI Design of SVM-Based Seizure Detection System With On-Chip Learning Capability.

    Science.gov (United States)

    Feng, Lichen; Li, Zunchao; Wang, Yuanfa

    2018-02-01

    Portable automatic seizure detection system is very convenient for epilepsy patients to carry. In order to make the system on-chip trainable with high efficiency and attain high detection accuracy, this paper presents a very large scale integration (VLSI) design based on the nonlinear support vector machine (SVM). The proposed design mainly consists of a feature extraction (FE) module and an SVM module. The FE module performs the three-level Daubechies discrete wavelet transform to fit the physiological bands of the electroencephalogram (EEG) signal and extracts the time-frequency domain features reflecting the nonstationary signal properties. The SVM module integrates the modified sequential minimal optimization algorithm with the table-driven-based Gaussian kernel to enable efficient on-chip learning. The presented design is verified on an Altera Cyclone II field-programmable gate array and tested using the two publicly available EEG datasets. Experiment results show that the designed VLSI system improves the detection accuracy and training efficiency.

  7. Determination of aminoglycoside antibiotics using an on-chip microfluidic device with chemiluminescence detection

    International Nuclear Information System (INIS)

    Sierra-Rodero, M.; Fernandez-Romero, J.M.; Gomez-Hens, A.

    2012-01-01

    We describe an on-chip microflow injection (μFI) approach for the determination of aminoglycoside antibiotics using chemiluminescence (CL) detection. The method is based on the inhibition of the Cu(II)-catalyzed CL reaction of luminol and hydrogen peroxide by the aminoglycosides due to the formation of a complex between the antibiotic and Cu(II). The main features of the method include small sample volumes and a fast response. Syringe pumps were used to insert the sample and the reagents into the microfluidic device. CL was collected using a fiber optic bundle connected to a luminescence detector. All instrumental, hydrodynamic and chemical variables involved in the system were optimized using neomycin as the aminoglycoside model. Inhibition is proportional to the concentration of the antibiotics. The dynamic ranges of the calibration graphs obtained for neomycin, streptomycin and amikacin are 0.3-3.3, 0.9-13.7, and 0.8-8.5 μmol L -1 , and the detection limits are 0.09, 0.28 and 0.24 μmol L -1 , respectively. The precision of the methods, expressed as relative standard deviation, is in the range from 0.8 to 5.0 %. The method was successfully applied to the determination of neomycin in water samples, with recoveries ranging from 80 to 120 %. (author)

  8. On-chip skin color detection using a triple-well CMOS process

    Science.gov (United States)

    Boussaid, Farid; Chai, Douglas; Bouzerdoum, Abdesselam

    2004-03-01

    In this paper, a current-mode VLSI architecture enabling on read-out skin detection without the need for any on-chip memory elements is proposed. An important feature of the proposed architecture is that it removes the need for demosaicing. Color separation is achieved using the strong wavelength dependence of the absorption coefficient in silicon. This wavelength dependence causes a very shallow absorption of blue light and enables red light to penetrate deeply in silicon. A triple-well process, allowing a P-well to be placed inside an N-well, is chosen to fabricate three vertically integrated photodiodes acting as the RGB color detector for each pixel. Pixels of an input RGB image are classified as skin or non-skin pixels using a statistical skin color model, chosen to offer an acceptable trade-off between skin detection performance and implementation complexity. A single processing unit is used to classify all pixels of the input RGB image. This results in reduced mismatch and also in an increased pixel fill-factor. Furthermore, the proposed current-mode architecture is programmable, allowing external control of all classifier parameters to compensate for mismatch and changing lighting conditions.

  9. Wide-field optical detection of nanoparticles using on-chip microscopy and self-assembled nanolenses

    Science.gov (United States)

    Mudanyali, Onur; McLeod, Euan; Luo, Wei; Greenbaum, Alon; Coskun, Ahmet F.; Hennequin, Yves; Allier, Cédric P.; Ozcan, Aydogan

    2013-03-01

    The direct observation of nanoscale objects is a challenging task for optical microscopy because the scattering from an individual nanoparticle is typically weak at optical wavelengths. Electron microscopy therefore remains one of the gold standard visualization methods for nanoparticles, despite its high cost, limited throughput and restricted field-of-view. Here, we describe a high-throughput, on-chip detection scheme that uses biocompatible wetting films to self-assemble aspheric liquid nanolenses around individual nanoparticles to enhance the contrast between the scattered and background light. We model the effect of the nanolens as a spatial phase mask centred on the particle and show that the holographic diffraction pattern of this effective phase mask allows detection of sub-100 nm particles across a large field-of-view of >20 mm2. As a proof-of-concept demonstration, we report on-chip detection of individual polystyrene nanoparticles, adenoviruses and influenza A (H1N1) viral particles.

  10. On-chip detection of gel transition temperature using a novel micro-thermomechanical method.

    Directory of Open Access Journals (Sweden)

    Tsenguun Byambadorj

    Full Text Available We present a new thermomechanical method and a platform to measure the phase transition temperature at microscale. A thin film metal sensor on a membrane simultaneously measures both temperature and mechanical strain of the sample during heating and cooling cycles. This thermomechanical principle of operation is described in detail. Physical hydrogel samples are prepared as a disc-shaped gels (200 μm thick and 1 mm diameter and placed between an on-chip heater and sensor devices. The sol-gel transition temperature of gelatin solution at various concentrations, used as a model physical hydrogel, shows less than 3% deviation from in-depth rheological results. The developed thermomechanical methodology is promising for precise characterization of phase transition temperature of thermogels at microscale.

  11. On-chip bio-analyte detection utilizing the velocity of magnetic microparticles in a fluid

    KAUST Repository

    Giouroudi, Ioanna

    2011-03-22

    A biosensing principle utilizing the motion of suspended magnetic microparticles in a microfluidic system is presented. The system utilizes the innovative concept of the velocity dependence of magnetic microparticles (MPs) due to their volumetric change when analyte is attached to their surface via antibody–antigen binding. When the magnetic microparticles are attracted by a magnetic field within a microfluidic channel their velocity depends on the presence of analyte. Specifically, their velocity decreases drastically when the magnetic microparticles are covered by (nonmagnetic) analyte (LMPs) due to the increased drag force in the opposite direction to that of the magnetic force. Experiments were carried out as a proof of concept. A promising 52% decrease in the velocity of the LMPs in comparison to that of the MPs was measured when both of them were accelerated inside a microfluidic channel using an external permanent magnet. The presented biosensing methodology offers a compact and integrated solution for a new kind of on-chip analysis with potentially high sensitivity and shorter acquisition time than conventional laboratory based systems.

  12. On-Chip Microfluidic Components for In Situ Analysis, Separation, and Detection of Amino Acids

    Science.gov (United States)

    Zheng, Yun; Getty, Stephanie; Dworkin, Jason; Balvin, Manuel; Kotecki, Carl

    2013-01-01

    The Astrobiology Analytical Laboratory at GSFC has identified amino acids in meteorites and returned cometary samples by using liquid chromatography-electrospray ionization time-of-flight mass spectrometry (LCMS). These organic species are key markers for life, having the property of chirality that can be used to distinguish biological from non-biological amino acids. One of the critical components in the benchtop instrument is liquid chromatography (LC) analytical column. The commercial LC analytical column is an over- 250-mm-long and 4.6-mm-diameter stainless steel tube filled with functionized microbeads as stationary phase to separate the molecular species based on their chemistry. Miniaturization of this technique for spaceflight is compelling for future payloads for landed missions targeting astrobiology objectives. A commercial liquid chromatography analytical column consists of an inert cylindrical tube filled with a stationary phase, i.e., microbeads, that has been functionalized with a targeted chemistry. When analyte is sent through the column by a pressurized carrier fluid (typically a methanol/ water mixture), compounds are separated in time due to differences in chemical interactions with the stationary phase. Different species of analyte molecules will interact more strongly with the column chemistry, and will therefore take longer to traverse the column. In this way, the column will separate molecular species based on their chemistry. A lab-on-chip liquid analysis tool was developed. The microfluidic analytical column is capable of chromatographically separating biologically relevant classes of molecules based on their chemistry. For this analytical column, fabrication, low leak rate, and stationary phase incorporation of a serpentine microchannel were demonstrated that mimic the dimensions of a commercial LC column within a 5 10 1 mm chip. The microchannel in the chip has a 75- micrometer-diameter oval-shaped cross section. The serpentine

  13. Lab-on-chip system combining a microfluidic-ELISA with an array of amorphous silicon photosensors for the detection of celiac disease epitopes

    Directory of Open Access Journals (Sweden)

    Francesca Costantini

    2015-12-01

    Full Text Available This work presents a lab-on-chip system, which combines a glass-polydimethilsiloxane microfluidic network and an array of amorphous silicon photosensors for the diagnosis and follow-up of Celiac disease. The microfluidic chip implements an on-chip enzyme-linked immunosorbent assay (ELISA, relying on a sandwich immunoassay between antibodies against gliadin peptides (GPs and a secondary antibody marked with horseradish peroxidase (Ig-HRP. This enzyme catalyzes a chemiluminescent reaction, whose light intensity is detected by the amorphous silicon photosensors and transduced into an electrical signal that can be processed to recognize the presence of antibodies against GPs in the serum of people affected by Celiac syndrome.The correct operation of the developed lab-on-chip has been demonstrated using rabbit serum in the microfluidic ELISA. In particular, optimizing the dilution factors of both sera and Ig-HRP samples in the flowing solutions, the specific and non-specific antibodies against GPs can be successfully distinguished, showing the suitability of the presented device to effectively screen celiac disease epitopes. Keywords: Lab-on-chip, Celiac disease, Microfluidics, On-chip detection, ELISA, Amorphous silicon photosensors

  14. A Novel On-Chip Impedance Sensor for the Detection of Particle Contamination in Hydraulic Oil

    Directory of Open Access Journals (Sweden)

    Hongpeng Zhang

    2017-08-01

    Full Text Available A novel impedance sensor based on a microfluidic chip is presented. The sensor consists of two single-layer coils and a straight micro-channel, and can detect, not only ferromagnetic and non-ferromagnetic particles in oil as an inductive sensor, but also, water droplets and air bubbles in oil as a capacitive sensor. The experiments are carried out at different excitation frequencies, number of coil turns and particle sizes. For the inductance detection, the inductance signals are found to increase with the excitation frequency and the noise is constant; both the inductance signals and the noise increase with the number of coil turns, but because the noise increases at a faster rate than the signal, the signal-to-noise ratio decreases with the number of coil turns. We demonstrate the successful detection of 40 μm iron particles and 110 μm copper particles using the coil with 20 turns at the excitation frequency of 2 MHz. For the capacitance detection, capacitance signals decrease with the excitation frequency and the noise is constant; the capacitance signals decrease with the number of coil turns, while the noise increases, thus, the signal-to-noise ratio decreases with the number of coil turns. We can detect 100 μm water droplets and 180 μm bubbles successfully using the coil with 20 turns at the excitation frequency of 0.3 MHz.

  15. On-chip microparticle detection and sizing using a dual-wavelength waveguide laser

    NARCIS (Netherlands)

    Bernhardi, Edward H.; van der Werf, Kees O; Hollink, Anton J F; Worhoff, Kerstin; De Ridder, Rene M.; Subramaniam, Vinod; Pollnau, Markus

    2013-01-01

    An integrated intra-laser-cavity microparticle sensor based on a dual-phase-shift, dual-wavelength distributed-feedback channel waveguide laser in Al2O3:Yb3+ is presented. Real-time detection and accurate size measurement of single microparticles with diameters ranging between 1 μm and 20 μm are

  16. NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs.

    Science.gov (United States)

    Morisset, Dany; Dobnik, David; Hamels, Sandrine; Zel, Jana; Gruden, Kristina

    2008-10-01

    We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all fields of biology requiring simultaneous detection of low copy number DNA targets. In a first step, the use of tailed primers allows the multiplex synthesis of template DNAs in a primer extension reaction. A second step of the procedure consists of transcription-based amplification using universal primers. The cRNA product is further on directly ligated to fluorescent dyes labelled 3DNA dendrimers allowing signal amplification and hybridized without further purification on an oligonucleotide probe-based microarray for multiplex detection. Two triplex systems have been applied to test maize samples containing several transgenic lines, and NAIMA has shown to be sensitive down to two target copies and to provide quantitative data on the transgenic contents in a range of 0.1-25%. Performances of NAIMA are comparable to singleplex quantitative real-time PCR. In addition, NAIMA amplification is faster since 20 min are sufficient to achieve full amplification.

  17. On-chip microparticle detection and sizing using a dual-wavelength waveguide laser

    NARCIS (Netherlands)

    Bernhardi, Edward; van der Werf, Kees; Hollink, Anton; Worhoff, Kerstin; de Ridder, R.M.; Subramaniam, Vinod; Pollnau, Markus

    An integrated intra-laser-cavity microparticle sensor based on a dual-phase-shift, dual-wavelength distributed-feedback channel waveguide laser in ytterbium-doped aluminium oxide is presented. Single micro-particles with diameters ranging between 1 μm and 20 μm are detected.

  18. On-Chip Spyhole Nanoelectrospray Ionization Mass Spectrometry for Sensitive Biomarker Detection in Small Volumes

    Science.gov (United States)

    Zhong, Xiaoqin; Qiao, Liang; Stauffer, Géraldine; Liu, Baohong; Girault, Hubert H.

    2018-03-01

    A polyimide microfluidic chip with a microhole emitter (Ø 10-12 μm) created on top of a microchannel by scanning laser ablation has been designed for nanoelectrospray ionization (spyhole-nanoESI) to couple microfluidics with mass spectrometry. The spyhole-nanoESI showed higher sensitivity compared to standard ESI and microESI from the end of the microchannel. The limits of detection (LOD) for peptide with the spyhole-nanoESI MS reached 50 pM, which was 600 times lower than that with standard ESI. The present microchip emitter allows the analysis of small volumes of samples. As an example, a small cell lung cancer biomarker, neuron-specific enolase (NSE), was detected by monitoring the transition of its unique peptide with the spyhole-nanoESI MS/MS. NSE at 0.2 nM could be well identified with a signal to noise ratio (S/N) of 50, and thereby its LOD was estimated to be 12 pM. The potential application of the spyhole-nanoESI MS/MS in cancer diagnosis was further demonstrated with the successful detection of 2 nM NSE from 1 μL of human serum. Before the detection, the serum sample spiked with NSE was first depleted with immune spin column, then desalted by centrifugal filter device, and finally digested by trypsin, without any other complicated preparation steps. The concentration matched the real condition of clinical samples. In addition, the microchips can be disposable to avoid any cross contamination. The present technique provides a highly efficient way to couple microfluidics with MS, which brings additional values to various microfluidics and MS-based analysis.

  19. On-chip integrated labelling, transport and detection of tumour cells.

    Science.gov (United States)

    Woods, Jane; Docker, Peter T; Dyer, Charlotte E; Haswell, Stephen J; Greenman, John

    2011-11-01

    Microflow cytometry represents a promising tool for the investigation of diagnostic and prognostic cellular cancer markers, particularly if integrated within a device that allows primary cells to be freshly isolated from the solid tumour biopsies that more accurately reflect patient-specific in vivo tissue microenvironments at the time of staining. However, current tissue processing techniques involve several sequential stages with concomitant cell losses, and as such are inappropriate for use with small biopsies. Accordingly, we present a simple method for combined antibody-labelling and dissociation of heterogeneous cells from a tumour mass, which reduces the number of processing steps. Perfusion of ex vivo tissue at 4°C with antibodies and enzymes slows cellular activity while allowing sufficient time for the diffusion of minimally active enzymes. In situ antibody-labelled cells are then dissociated at 37°C from the tumour mass, whereupon hydrogel-filled channels allow the release of relatively low cell numbers (<1000) into a biomimetic microenvironment. This novel approach to sample processing is then further integrated with hydrogel-based electrokinetic transport of the freshly liberated fluorescent cells for downstream detection. It is anticipated that this integrated microfluidic methodology will have wide-ranging biomedical and clinical applications. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. A Single-Chip CMOS Pulse Oximeter with On-Chip Lock-In Detection

    Directory of Open Access Journals (Sweden)

    Diwei He

    2015-07-01

    Full Text Available Pulse oximetry is a noninvasive and continuous method for monitoring the blood oxygen saturation level. This paper presents the design and testing of a single-chip pulse oximeter fabricated in a 0.35 µm CMOS process. The chip includes photodiode, transimpedance amplifier, analogue band-pass filters, analogue-to-digital converters, digital signal processor and LED timing control. The experimentally measured AC and DC characteristics of individual circuits including the DC output voltage of the transimpedance amplifier, transimpedance gain of the transimpedance amplifier, and the central frequency and bandwidth of the analogue band-pass filters, show a good match (within 1% with the circuit simulations. With modulated light source and integrated lock-in detection the sensor effectively suppresses the interference from ambient light and 1/f noise. In a breath hold and release experiment the single chip sensor demonstrates consistent and comparable performance to commercial pulse oximetry devices with a mean of 1.2% difference. The single-chip sensor enables a compact and robust design solution that offers a route towards wearable devices for health monitoring.

  1. A Single-Chip CMOS Pulse Oximeter with On-Chip Lock-In Detection.

    Science.gov (United States)

    He, Diwei; Morgan, Stephen P; Trachanis, Dimitrios; van Hese, Jan; Drogoudis, Dimitris; Fummi, Franco; Stefanni, Francesco; Guarnieri, Valerio; Hayes-Gill, Barrie R

    2015-07-14

    Pulse oximetry is a noninvasive and continuous method for monitoring the blood oxygen saturation level. This paper presents the design and testing of a single-chip pulse oximeter fabricated in a 0.35 µm CMOS process. The chip includes photodiode, transimpedance amplifier, analogue band-pass filters, analogue-to-digital converters, digital signal processor and LED timing control. The experimentally measured AC and DC characteristics of individual circuits including the DC output voltage of the transimpedance amplifier, transimpedance gain of the transimpedance amplifier, and the central frequency and bandwidth of the analogue band-pass filters, show a good match (within 1%) with the circuit simulations. With modulated light source and integrated lock-in detection the sensor effectively suppresses the interference from ambient light and 1/f noise. In a breath hold and release experiment the single chip sensor demonstrates consistent and comparable performance to commercial pulse oximetry devices with a mean of 1.2% difference. The single-chip sensor enables a compact and robust design solution that offers a route towards wearable devices for health monitoring.

  2. On-chip Detection of Rolling Circle Amplified DNA Molecules from Bacillus Globigii spores and Vibrio Cholerae

    DEFF Research Database (Denmark)

    Østerberg, Frederik Westergaard; Rizzi, Giovanni; Donolato, Marco

    2014-01-01

    For the first time DNA coils formed by rolling circle amplification are quantified on-chip by Brownian relaxation measurements on magnetic nanobeads using a magnetoresistive sensor. No external magnetic fields are required besides the magnetic field arising from the current through the sensor...

  3. Development of a lab-on-chip electrochemical immunosensor for detection of Polycyclic Aromatic Hydrocarbons (PAH) in environmental water

    Science.gov (United States)

    Felemban, Shifa; Vazquez, Patricia; Dehnert, Jan; Goridko, Vadim; Tijero, Maria; Moore, Eric

    2017-06-01

    The work described in this manuscript focuses on how the integration of immunoassay techniques in combination with electrochemical detection can provide a portable and very accurate solution for detection of water pollutants that are detrimental for human health. In particular, we focus our work on the quantification of polycyclic aromatic hydrocarbons (PAHs) in polluted water. Our integrative approach facilitates a real-time detection of this family of organic compounds, by reducing the time of analysis to less than one hour. Additionally, the use of a lab-on-a-chip platform delivers a portable solution that could be used in situ. Optimization of a displacement assay that investigates the presence and concentration of Benzo[a]pyrene in water, allows with the miniaturization of the standard ELISA format into a highly accurate system that provides fast results. The limits of detection obtained are comparable to those of available state-of-the art tools, and achieve the values set by European Drinking Water Directive, 0.10ng/l, as the limit for PAHs in drinking water.

  4. On-Chip Magnetic Bead Manipulation and Detection Using a Magnetoresistive Sensor-Based Micro-Chip: Design Considerations and Experimental Characterization

    KAUST Repository

    Gooneratne, Chinthaka Pasan; Kodzius, Rimantas; Li, Fuquan; Foulds, Ian G.; Kosel, Jü rgen

    2016-01-01

    The remarkable advantages micro-chip platforms offer over cumbersome, time-consuming equipment currently in use for bio-analysis are well documented. In this research, a micro-chip that includes a unique magnetic actuator (MA) for the manipulation of superparamagnetic beads (SPBs), and a magnetoresistive sensor for the detection of SPBs is presented. A design methodology, which takes into account the magnetic volume of SPBs, diffusion and heat transfer phenomena, is presented with the aid of numerical analysis to optimize the parameters of the MA. The MA was employed as a magnetic flux generator and experimental analysis with commercially available COMPEL™ and Dynabeads® demonstrated the ability of the MA to precisely transport a small number of SPBs over long distances and concentrate SPBs to a sensing site for detection. Moreover, the velocities of COMPEL™ and Dynabead® SPBs were correlated to their magnetic volumes and were in good agreement with numerical model predictions. We found that 2.8 μm Dynabeads® travel faster, and can be attracted to a magnetic source from a longer distance, than 6.2 μm COMPEL™ beads at magnetic flux magnitudes of less than 10 mT. The micro-chip system could easily be integrated with electronic circuitry and microfluidic functions, paving the way for an on-chip biomolecule quantification device

  5. On-Chip Magnetic Bead Manipulation and Detection Using a Magnetoresistive Sensor-Based Micro-Chip: Design Considerations and Experimental Characterization

    KAUST Repository

    Gooneratne, Chinthaka Pasan

    2016-08-26

    The remarkable advantages micro-chip platforms offer over cumbersome, time-consuming equipment currently in use for bio-analysis are well documented. In this research, a micro-chip that includes a unique magnetic actuator (MA) for the manipulation of superparamagnetic beads (SPBs), and a magnetoresistive sensor for the detection of SPBs is presented. A design methodology, which takes into account the magnetic volume of SPBs, diffusion and heat transfer phenomena, is presented with the aid of numerical analysis to optimize the parameters of the MA. The MA was employed as a magnetic flux generator and experimental analysis with commercially available COMPEL™ and Dynabeads® demonstrated the ability of the MA to precisely transport a small number of SPBs over long distances and concentrate SPBs to a sensing site for detection. Moreover, the velocities of COMPEL™ and Dynabead® SPBs were correlated to their magnetic volumes and were in good agreement with numerical model predictions. We found that 2.8 μm Dynabeads® travel faster, and can be attracted to a magnetic source from a longer distance, than 6.2 μm COMPEL™ beads at magnetic flux magnitudes of less than 10 mT. The micro-chip system could easily be integrated with electronic circuitry and microfluidic functions, paving the way for an on-chip biomolecule quantification device

  6. On-Chip Magnetic Bead Manipulation and Detection Using a Magnetoresistive Sensor-Based Micro-Chip: Design Considerations and Experimental Characterization

    Directory of Open Access Journals (Sweden)

    Chinthaka P. Gooneratne

    2016-08-01

    Full Text Available The remarkable advantages micro-chip platforms offer over cumbersome, time-consuming equipment currently in use for bio-analysis are well documented. In this research, a micro-chip that includes a unique magnetic actuator (MA for the manipulation of superparamagnetic beads (SPBs, and a magnetoresistive sensor for the detection of SPBs is presented. A design methodology, which takes into account the magnetic volume of SPBs, diffusion and heat transfer phenomena, is presented with the aid of numerical analysis to optimize the parameters of the MA. The MA was employed as a magnetic flux generator and experimental analysis with commercially available COMPEL™ and Dynabeads® demonstrated the ability of the MA to precisely transport a small number of SPBs over long distances and concentrate SPBs to a sensing site for detection. Moreover, the velocities of COMPEL™ and Dynabead® SPBs were correlated to their magnetic volumes and were in good agreement with numerical model predictions. We found that 2.8 μm Dynabeads® travel faster, and can be attracted to a magnetic source from a longer distance, than 6.2 μm COMPEL™ beads at magnetic flux magnitudes of less than 10 mT. The micro-chip system could easily be integrated with electronic circuitry and microfluidic functions, paving the way for an on-chip biomolecule quantification device.

  7. Dual-Functional On-Chip AlGaAs/GaAs Schottky Diode for RF Power Detection and Low-Power Rectenna Applications

    Directory of Open Access Journals (Sweden)

    Abdul Manaf Hashim

    2011-08-01

    Full Text Available A Schottky diode has been designed and fabricated on an n-AlGaAs/GaAs high-electron-mobility-transistor (HEMT structure. Current-voltage (I-V measurements show good device rectification, with a Schottky barrier height of 0.4349 eV for Ni/Au metallization. The differences between the Schottky barrier height and the theoretical value (1.443 eV are due to the fabrication process and smaller contact area. The RF signals up to 1 GHz are rectified well by the fabricated Schottky diode and a stable DC output voltage is obtained. The increment ratio of output voltage vs input power is 0.2 V/dBm for all tested frequencies, which is considered good enough for RF power detection. Power conversion efficiency up to 50% is obtained at frequency of 1 GHz and input power of 20 dBm with series connection between diode and load, which also shows the device’s good potential as a rectenna device with further improvement. The fabricated n-AlGaAs/GaAs Schottky diode thus provides a conduit for breakthrough designs for RF power detectors, as well as ultra-low power on-chip rectenna device technology to be integrated in nanosystems.

  8. Dual-functional on-chip AlGaAs/GaAs Schottky diode for RF power detection and low-power rectenna applications.

    Science.gov (United States)

    Hashim, Abdul Manaf; Mustafa, Farahiyah; Rahman, Shaharin Fadzli Abd; Rahman, Abdul Rahim Abdul

    2011-01-01

    A Schottky diode has been designed and fabricated on an n-AlGaAs/GaAs high-electron-mobility-transistor (HEMT) structure. Current-voltage (I-V) measurements show good device rectification, with a Schottky barrier height of 0.4349 eV for Ni/Au metallization. The differences between the Schottky barrier height and the theoretical value (1.443 eV) are due to the fabrication process and smaller contact area. The RF signals up to 1 GHz are rectified well by the fabricated Schottky diode and a stable DC output voltage is obtained. The increment ratio of output voltage vs input power is 0.2 V/dBm for all tested frequencies, which is considered good enough for RF power detection. Power conversion efficiency up to 50% is obtained at frequency of 1 GHz and input power of 20 dBm with series connection between diode and load, which also shows the device's good potential as a rectenna device with further improvement. The fabricated n-AlGaAs/GaAs Schottky diode thus provides a conduit for breakthrough designs for RF power detectors, as well as ultra-low power on-chip rectenna device technology to be integrated in nanosystems.

  9. Variation Tolerant On-Chip Interconnects

    CERN Document Server

    Nigussie, Ethiopia Enideg

    2012-01-01

    This book presents design techniques, analysis and implementation of high performance and power efficient, variation tolerant on-chip interconnects.  Given the design paradigm shift to multi-core, interconnect-centric designs and the increase in sources of variability and their impact in sub-100nm technologies, this book will be an invaluable reference for anyone concerned with the design of next generation, high-performance electronics systems. Provides comprehensive, circuit-level explanation of high-performance, energy-efficient, variation-tolerant on-chip interconnect; Describes design techniques to mitigate problems caused by variation; Includes techniques for design and implementation of self-timed on-chip interconnect, delay variation insensitive communication protocols, high speed signaling techniques and circuits, bit-width independent completion detection and process, voltage and temperature variation tolerance.                          

  10. Development and evaluation of a real-time fluorogenic loop-mediated isothermal amplification assay integrated on a microfluidic disc chip (on-chip LAMP) for rapid and simultaneous detection of ten pathogenic bacteria in aquatic animals.

    Science.gov (United States)

    Zhou, Qian-Jin; Wang, Lei; Chen, Jiong; Wang, Rui-Na; Shi, Yu-Hong; Li, Chang-Hong; Zhang, De-Min; Yan, Xiao-Jun; Zhang, Yan-Jun

    2014-09-01

    Rapid, low-cost, and user-friendly strategies are urgently needed for early disease diagnosis and timely treatment, particularly for on-site screening of pathogens in aquaculture. In this study, we successfully developed a real-time fluorogenic loop-mediated isothermal amplification assay integrated on a microfluidic disc chip (on-chip LAMP), which was capable of simultaneously detecting 10 pathogenic bacteria in aquatic animals, i.e., Nocardia seriolae, Pseudomonas putida, Streptococcus iniae, Vibrio alginolyticus, Vibrio anguillarum, Vibrio fluvialis, Vibrio harveyi, Vibrio parahaemolyticus, Vibrio rotiferianus, and Vibrio vulnificus. The assay provided a nearly-automated approach, with only a single pipetting step per chip for sample dispensing. This technique could achieve limits of detection (LOD) ranging from 0.40 to 6.42pg per 1.414μL reaction in less than 30 min. The robust reproducibility was demonstrated by a little variation among duplications for each bacterium with the coefficient of variation (CV) for time to positive (Tp) value less than 0.10. The clinical sensitivity and specificity of this on-chip LAMP assay in detecting field samples were 96.2% and 93.8% by comparison with conventional microbiological methods. Compared with other well-known techniques, on-chip LAMP assay provides low sample and reagent consumption, ease-of-use, accelerated analysis, multiple bacteria and on-site detection, and high reproducibility, indicating that such a technique would be applicable for on-site detection and routine monitoring of multiple pathogens in aquaculture. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Tunable on chip optofluidic laser

    DEFF Research Database (Denmark)

    Bakal, Avraham; Vannahme, Christoph; Kristensen, Anders

    2016-01-01

    On chip tunable laser is demonstrated by realizing a microfluidic droplet array. The periodicity is controlled by the pressure applied to two separate inlets, allowing to tune the lasing frequency over a broad spectral range.......On chip tunable laser is demonstrated by realizing a microfluidic droplet array. The periodicity is controlled by the pressure applied to two separate inlets, allowing to tune the lasing frequency over a broad spectral range....

  12. Nano lab-on-chip systems for biomedical and environmental ...

    African Journals Online (AJOL)

    In recent years, nano lab-on-chip (NLOC) has emerged as a powerful tool for biosensing and an active area of research particularly in DNA genetic and genetic related investigations. Compared with conventional sensing techniques, distinctive advantages of using NLOC for biomedicine and other related area include ...

  13. Advances in genetic detection of kidney disease

    International Nuclear Information System (INIS)

    Dosekun, Akinsan K.; Foringer, John R.; Kone, Bruce C.

    2003-01-01

    The Human Genome Project has provided a vast amount of molecular genetic information for the analysis of normal and diseased genes. This new information provides new opportunities for precise diagnosis, assessment of predisposition and risk factors and novel therapeutic strategies. At the same time, this constantly expanding knowledge base represents on e of the most difficult challenges in molecular medicine. For monogenic disease nearly 2000 human disease genes have thus for been identified. Most of these conditions are characterized by large mutational variation and even greater phenotypic variation. In nephrology, several genetic diseases have been elucidated that provide new insight into the structure, function and developmental biology of the glomerulus, tubules and urogenital tracts, as well as renal cell tumors. Great improvements in the diagnostic resolution of genetic diseases have been achieved, such that single base pair mutations can be readily detected. Because of accurate diagnosis and risk assessment, genetic testing may be valuable in improving disease management and preventive care when genotype-specific therapies are available. Moreover, such testing may identify de novo mutations and potentially aid in understanding the disease process. This review summarizes recent advances in the renal genetic database and methods for genetic testing of renal diseases. (author)

  14. On-chip photonic particle sensor

    Science.gov (United States)

    Singh, Robin; Ma, Danhao; Agarwal, Anu; Anthony, Brian

    2018-02-01

    We propose an on-chip photonic particle sensor design that can perform particle sizing and counting for various environmental applications. The sensor is based on micro photonic ring resonators that are able to detect the presence of the free space particles through the interaction with their evanescent electric field tail. The sensor can characterize a wide range of the particle size ranging from a few nano meters to micron ( 1 micron). The photonic platform offers high sensitivity, compactness, fast response of the device. Further, FDTD simulations are performed to analyze different particle-light interactions. Such a compact and portable platform, packaged with integrated photonic circuit provides a useful sensing modality in space shuttle and environmental applications.

  15. On-chip graphene electrode, methods of making, and methods of use

    KAUST Repository

    Nayak, Pranati

    2018-01-25

    Embodiments of the present disclosure provide a device including an on-chip electrode platform including one or more three dimensional laser scribed graphene electrodes, methods of making the on-chip electrode platform, methods of analyzing (e.g., detecting, quantifying, and the like) chemicals and biochemicals, and the like.

  16. Variable self-powered light detection CMOS chip with real-time adaptive tracking digital output based on a novel on-chip sensor.

    Science.gov (United States)

    Wang, HongYi; Fan, Youyou; Lu, Zhijian; Luo, Tao; Fu, Houqiang; Song, Hongjiang; Zhao, Yuji; Christen, Jennifer Blain

    2017-10-02

    This paper provides a solution for a self-powered light direction detection with digitized output. Light direction sensors, energy harvesting photodiodes, real-time adaptive tracking digital output unit and other necessary circuits are integrated on a single chip based on a standard 0.18 µm CMOS process. Light direction sensors proposed have an accuracy of 1.8 degree over a 120 degree range. In order to improve the accuracy, a compensation circuit is presented for photodiodes' forward currents. The actual measurement precision of output is approximately 7 ENOB. Besides that, an adaptive under voltage protection circuit is designed for variable supply power which may undulate with temperature and process.

  17. On-site detection of Phytophthora spp.—single-stranded target DNA as the limiting factor to improve on-chip hybridization

    International Nuclear Information System (INIS)

    Schwenkbier, Lydia; Pollok, Sibyll; Popp, Jürgen; Weber, Karina; König, Stephan; Wagner, Stefan; Werres, Sabine; Weber, Jörg; Hentschel, Martin

    2014-01-01

    We report on a lab-on-a-chip approach for on-site detection of Phytophthora species that allows visual signal readout. The results demonstrate the significance of single-stranded DNA (ssDNA) generation in terms of improving the intensity of the hybridization signal and to improve the reliability of the method. Conventional PCR with subsequent heat denaturation, sodium hydroxide-based denaturation, lambda exonuclease digestion and two asymmetric PCR methods were investigated for the species P. fragariae, P. kernoviae, and P. ramorum. The positioning of the capture probe within the amplified yeast GTP-binding protein (YPT1) target DNA was also of interest because it significantly influences the intensity of the signal. Statistical tests were used to validate the impact of the ssDNA generation methods and the capture-target probe position. The single-stranded target DNA generated by Linear-After-The-Exponential PCR (LATE-PCR) was found to produce signal intensities comparable to post-PCR exonuclease treatment. The LATE-PCR is the best method for the on-site detection of Phytophthora because the enzymatic digestion after PCR is more laborious and time-consuming. (author)

  18. Biosensors-on-chip: a topical review

    International Nuclear Information System (INIS)

    Chen, Sensen; Shamsi, Mohtashim H

    2017-01-01

    This review will examine the integration of two fields that are currently at the forefront of science, i.e. biosensors and microfluidics. As a lab-on-a-chip (LOC) technology, microfluidics has been enriched by the integration of various detection tools for analyte detection and quantitation. The application of such microfluidic platforms is greatly increased in the area of biosensors geared towards point-of-care diagnostics. Together, the merger of microfluidics and biosensors has generated miniaturized devices for sample processing and sensitive detection with quantitation. We believe that microfluidic biosensors (biosensors-on-chip) are essential for developing robust and cost effective point-of-care diagnostics. This review is relevant to a variety of disciplines, such as medical science, clinical diagnostics, LOC technologies including MEMs/NEMs, and analytical science. Specifically, this review will appeal to scientists working in the two overlapping fields of biosensors and microfluidics, and will also help new scientists to find their directions in developing point-of-care devices. (topical review)

  19. Photonic network-on-chip design

    CERN Document Server

    Bergman, Keren; Biberman, Aleksandr; Chan, Johnnie; Hendry, Gilbert

    2013-01-01

    This book provides a comprehensive synthesis of the theory and practice of photonic devices for networks-on-chip. It outlines the issues in designing photonic network-on-chip architectures for future many-core high performance chip multiprocessors. The discussion is built from the bottom up: starting with the design and implementation of key photonic devices and building blocks, reviewing networking and network-on-chip theory and existing research, and finishing with describing various architectures, their characteristics, and the impact they will have on a computing system. After acquainting

  20. On-chip power delivery and management

    CERN Document Server

    Vaisband, Inna P; Popovich, Mikhail; Mezhiba, Andrey V; Köse, Selçuk; Friedman, Eby G

    2016-01-01

    This book describes methods for distributing power in high speed, high complexity integrated circuits with power levels exceeding many tens of watts and power supplies below a volt. It provides a broad and cohesive treatment of power delivery and management systems and related design problems, including both circuit network models and design techniques for on-chip decoupling capacitors, providing insight and intuition into the behavior and design of on-chip power distribution systems. Organized into subareas to provide a more intuitive flow to the reader, this fourth edition adds more than a hundred pages of new content, including inductance models for interdigitated structures, design strategies for multi-layer power grids, advanced methods for efficient power grid design and analysis, and methodologies for simultaneously placing on-chip multiple power supplies and decoupling capacitors. The emphasis of this additional material is on managing the complexity of on-chip power distribution networks.

  1. On-chip Magnetic Separation and Cell Encapsulation in Droplets

    Science.gov (United States)

    Chen, A.; Byvank, T.; Bharde, A.; Miller, B. L.; Chalmers, J. J.; Sooryakumar, R.; Chang, W.-J.; Bashir, R.

    2012-02-01

    The demand for high-throughput single cell assays is gaining importance because of the heterogeneity of many cell suspensions, even after significant initial sorting. These suspensions may display cell-to-cell variability at the gene expression level that could impact single cell functional genomics, cancer, stem-cell research and drug screening. The on-chip monitoring of individual cells in an isolated environment could prevent cross-contamination, provide high recovery yield and ability to study biological traits at a single cell level These advantages of on-chip biological experiments contrast to conventional methods, which require bulk samples that provide only averaged information on cell metabolism. We report on a device that integrates microfluidic technology with a magnetic tweezers array to combine the functionality of separation and encapsulation of objects such as immunomagnetically labeled cells or magnetic beads into pico-liter droplets on the same chip. The ability to control the separation throughput that is independent of the hydrodynamic droplet generation rate allows the encapsulation efficiency to be optimized. The device can potentially be integrated with on-chip labeling and/or bio-detection to become a powerful single-cell analysis device.

  2. Detection of Genetically Modified Food: Has Your Food Been Genetically Modified?

    Science.gov (United States)

    Brandner, Diana L.

    2002-01-01

    Explains the benefits and risks of genetically-modified foods and describes methods for genetically modifying food. Presents a laboratory experiment using a polymerase chain reaction (PCR) test to detect foreign DNA in genetically-modified food. (Contains 18 references.) (YDS)

  3. Cytostretch, an Organ-on-Chip Platform

    NARCIS (Netherlands)

    Gaio, N.; van Meer, B.; Quiros Solano, W.F.; Bergers, L.; van de Stolpe, A; Mummery, CL; Sarro, P.M.; Dekker, R.

    2016-01-01

    Organ-on-Chips (OOCs) are micro-fabricated devices which are used to culture cells in order to mimic functional units of human organs. The devices are designed to simulate the physiological environment of tissues in vivo. Cells in some types of OOCs can be stimulated in situ by electrical and/or

  4. On-chip mode division multiplexing technologies

    DEFF Research Database (Denmark)

    Ding, Yunhong; Frellsen, Louise Floor; Guan, Xiaowei

    2016-01-01

    Space division multiplexing (SDM) is currently widely investigated in order to provide enhanced capacity thanks to the utilization of space as a new degree of multiplexing freedom in both optical fiber communication and on-chip interconnects. Basic components allowing the processing of spatial...... photonic integrated circuit mode (de) multiplexer for few-mode fibers (FMFs)....

  5. Detection of Genetic Modification 'ac2' in Potato Foodstuffs

    Directory of Open Access Journals (Sweden)

    Petr Kralik

    2009-01-01

    Full Text Available The genetic modification 'ac2' is based on the insertion and expression of ac2 gene, originally found in seeds of amaranth (Amaranthus caudatus, into the genome of potatoes (Solanum tuberosum. The purpose of the present study is to develop a PCR method for the detection of the mentioned genetically modified potatoes in various foodstuffs. The method was used to test twenty different potato-based products; none of them was positive for the genetic modification 'ac2'. The European Union legislation requires labelling of products made of or containing more than 0.9 % of genetically modified organisms. The genetic modification 'ac2' is not allowed on the European Union market. For that reason it is suitable to have detection methods, not only for the approved genetic modifications, but also for the 'unknown' ones, which could still occur in foodstuffs.

  6. Privacy preserving protocol for detecting genetic relatives using rare variants.

    Science.gov (United States)

    Hormozdiari, Farhad; Joo, Jong Wha J; Wadia, Akshay; Guan, Feng; Ostrosky, Rafail; Sahai, Amit; Eskin, Eleazar

    2014-06-15

    High-throughput sequencing technologies have impacted many areas of genetic research. One such area is the identification of relatives from genetic data. The standard approach for the identification of genetic relatives collects the genomic data of all individuals and stores it in a database. Then, each pair of individuals is compared to detect the set of genetic relatives, and the matched individuals are informed. The main drawback of this approach is the requirement of sharing your genetic data with a trusted third party to perform the relatedness test. In this work, we propose a secure protocol to detect the genetic relatives from sequencing data while not exposing any information about their genomes. We assume that individuals have access to their genome sequences but do not want to share their genomes with anyone else. Unlike previous approaches, our approach uses both common and rare variants which provide the ability to detect much more distant relationships securely. We use a simulated data generated from the 1000 genomes data and illustrate that we can easily detect up to fifth degree cousins which was not possible using the existing methods. We also show in the 1000 genomes data with cryptic relationships that our method can detect these individuals. The software is freely available for download at http://genetics.cs.ucla.edu/crypto/. © The Author 2014. Published by Oxford University Press.

  7. Microengineered physiological biomimicry: organs-on-chips.

    Science.gov (United States)

    Huh, Dongeun; Torisawa, Yu-suke; Hamilton, Geraldine A; Kim, Hyun Jung; Ingber, Donald E

    2012-06-21

    Microscale engineering technologies provide unprecedented opportunities to create cell culture microenvironments that go beyond current three-dimensional in vitro models by recapitulating the critical tissue-tissue interfaces, spatiotemporal chemical gradients, and dynamic mechanical microenvironments of living organs. Here we review recent advances in this field made over the past two years that are focused on the development of 'Organs-on-Chips' in which living cells are cultured within microfluidic devices that have been microengineered to reconstitute tissue arrangements observed in living organs in order to study physiology in an organ-specific context and to develop specialized in vitro disease models. We discuss the potential of organs-on-chips as alternatives to conventional cell culture models and animal testing for pharmaceutical and toxicology applications. We also explore challenges that lie ahead if this field is to fulfil its promise to transform the future of drug development and chemical safety testing.

  8. On-Chip Microwave Quantum Hall Circulator

    Directory of Open Access Journals (Sweden)

    A. C. Mahoney

    2017-01-01

    Full Text Available Circulators are nonreciprocal circuit elements that are integral to technologies including radar systems, microwave communication transceivers, and the readout of quantum information devices. Their nonreciprocity arises from the interference of microwaves over the centimeter scale of the signal wavelength, in the presence of bulky magnetic media that breaks time-reversal symmetry. Here, we realize a completely passive on-chip microwave circulator with size 1/1000th the wavelength by exploiting the chiral, “slow-light” response of a two-dimensional electron gas in the quantum Hall regime. For an integrated GaAs device with 330  μm diameter and about 1-GHz center frequency, a nonreciprocity of 25 dB is observed over a 50-MHz bandwidth. Furthermore, the nonreciprocity can be dynamically tuned by varying the voltage at the port, an aspect that may enable reconfigurable passive routing of microwave signals on chip.

  9. Irradiation influence on the detection of genetic-modified soybeans

    International Nuclear Information System (INIS)

    Villavicencio, A.L.C.H.; Araujo, M.M.; Baldasso, J.G.; Aquino, S.; Konietzny, U.; Greiner, R.

    2004-01-01

    Three soybean varieties were analyzed to evaluate the irradiation influence on the detection of genetic modification. Samples were treated in a 60 Co facility at dose levels of 0, 500, 800, and 1000 Gy. The seeds were at first analyzed by Comet Assay as a rapid screening irradiation detection method. Secondly, germination test was performed to detect the viability of irradiated soybeans. Finally, because of its high sensitivity, its specificity and rapidity the polimerase chain reaction was the method applied for genetic modified organism detection. The analysis of DNA by the single technique of microgel electrophoresis of single cells (DNA Comet Assay) showed that DNA damage increased with increasing radiation doses. No negative influence of irradiation on the genetic modification detection was found

  10. Routing algorithms in networks-on-chip

    CERN Document Server

    Daneshtalab, Masoud

    2014-01-01

    This book provides a single-source reference to routing algorithms for Networks-on-Chip (NoCs), as well as in-depth discussions of advanced solutions applied to current and next generation, many core NoC-based Systems-on-Chip (SoCs). After a basic introduction to the NoC design paradigm and architectures, routing algorithms for NoC architectures are presented and discussed at all abstraction levels, from the algorithmic level to actual implementation.  Coverage emphasizes the role played by the routing algorithm and is organized around key problems affecting current and next generation, many-core SoCs. A selection of routing algorithms is included, specifically designed to address key issues faced by designers in the ultra-deep sub-micron (UDSM) era, including performance improvement, power, energy, and thermal issues, fault tolerance and reliability.   ·         Provides a comprehensive overview of routing algorithms for Networks-on-Chip and NoC-based, manycore systems; ·         Describe...

  11. TMTI Task 1.6 Genetic Engineering Methods and Detection

    Energy Technology Data Exchange (ETDEWEB)

    Slezak, T; Lenhoff, R; Allen, J; Borucki, M; Vitalis, E; Gardner, S

    2009-12-04

    A large number of GE techniques can be adapted from other microorganisms to biothreat bacteria and viruses. Detection of GE in a microorganism increases in difficulty as the size of the genetic change decreases. In addition to the size of the engineered change, the consensus genomic sequence of the microorganism can impact the difficulty of detecting an engineered change in genomes that are highly variable from strain to strain. This problem will require comprehensive databases of whole genome sequences for more genetically variable biothreat bacteria and viruses. Preliminary work with microarrays for detecting synthetic elements or virulence genes and analytic bioinformatic approaches for whole genome sequence comparison to detect genetic engineering show promise for attacking this difficult problem but a large amount of future work remains.

  12. On-chip antenna: Practical design and characterization considerations

    KAUST Repository

    Shamim, Atif; Salama, Khaled N.; Sedky, S.; Soliman, E. A.

    2012-01-01

    This paper highlights the challenges of an emergent field, namely, on-chip antenna design. Consistent with the RF System-on-Chip (SoC) concept, co-design strategy for circuits and on-chip antennas is described. A number of design and layout issues, arising from the highly integrated nature of this kind of systems, are discussed. The characterization difficulties related to on-chip antennas radiation properties are also highlighted. Finally, a novel on-wafer test fixture is proposed to measure the gain and radiation pattern of the on-chip antennas in the anechoic chamber.

  13. On-chip antenna: Practical design and characterization considerations

    KAUST Repository

    Shamim, Atif

    2012-07-28

    This paper highlights the challenges of an emergent field, namely, on-chip antenna design. Consistent with the RF System-on-Chip (SoC) concept, co-design strategy for circuits and on-chip antennas is described. A number of design and layout issues, arising from the highly integrated nature of this kind of systems, are discussed. The characterization difficulties related to on-chip antennas radiation properties are also highlighted. Finally, a novel on-wafer test fixture is proposed to measure the gain and radiation pattern of the on-chip antennas in the anechoic chamber.

  14. Method of detecting genetic deletions identified with chromosomal abnormalities

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Joe W; Pinkel, Daniel; Tkachuk, Douglas

    2013-11-26

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acids probes are typically of a complexity greater tha 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particlularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar ut genetically different diseases, and for many prognostic and diagnostic applications.

  15. Chromosome-specific staining to detect genetic rearrangements

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Joe W.; Pinkel, Daniel; Tkachuk, Douglas; Westbrook, Carol

    2013-04-09

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

  16. Computer System Design System-on-Chip

    CERN Document Server

    Flynn, Michael J

    2011-01-01

    The next generation of computer system designers will be less concerned about details of processors and memories, and more concerned about the elements of a system tailored to particular applications. These designers will have a fundamental knowledge of processors and other elements in the system, but the success of their design will depend on the skills in making system-level tradeoffs that optimize the cost, performance and other attributes to meet application requirements. This book provides a new treatment of computer system design, particularly for System-on-Chip (SOC), which addresses th

  17. On-chip digital power supply control for system-on-chip applications

    NARCIS (Netherlands)

    Meijer, M.; Pineda de Gyvez, J.; Otten, R.H.J.M.

    2005-01-01

    The authors presented an on-chip, fully-digital, power-supply control system. The scheme consists of two independent control loops that regulate power supply variations due to semiconductor process spread, temperature, and chip's workload. Smart power-switches working as linear voltage regulators

  18. Electrochemiluminescence polymerase chain reaction detection of genetically modified organisms

    International Nuclear Information System (INIS)

    Liu Jinfeng; Xing Da; Shen Xingyan; Zhu Debin

    2005-01-01

    With the development of biotechnology, more and more genetically modified organisms (GMOs) have entered commercial market. Because of the safety concerns, detection and characterization of GMOs have attracted much attention recently. Electrochemiluminescence (ECL) method is a chemiluminescent (CL) reaction of species generated electrochemically on an electrode surface. It is a highly efficient and accurate detection method. In this paper, ECL polymerase chain reaction (PCR) combined with two types of nucleic acid probes hybridization was applied to detect GMOs for the first time. Whether the organisms contain GM components was discriminated by detecting the cauliflower mosaic virus 35S (CaMV35S) promoter and nopaline synthase (NOS) terminator. The experiment results show that the detection limit is 100 fmol of PCR products. The promoter and the terminator can be clearly detected in GMOs. The method may provide a new means for the detection of GMOs due to its simplicity and high efficiency

  19. Laser Light-field Fusion for Wide-field Lensfree On-chip Phase Contrast Microscopy of Nanoparticles

    Science.gov (United States)

    Kazemzadeh, Farnoud; Wong, Alexander

    2016-12-01

    Wide-field lensfree on-chip microscopy, which leverages holography principles to capture interferometric light-field encodings without lenses, is an emerging imaging modality with widespread interest given the large field-of-view compared to lens-based techniques. In this study, we introduce the idea of laser light-field fusion for lensfree on-chip phase contrast microscopy for detecting nanoparticles, where interferometric laser light-field encodings acquired using a lensfree, on-chip setup with laser pulsations at different wavelengths are fused to produce marker-free phase contrast images of particles at the nanometer scale. As a proof of concept, we demonstrate, for the first time, a wide-field lensfree on-chip instrument successfully detecting 300 nm particles across a large field-of-view of ~30 mm2 without any specialized or intricate sample preparation, or the use of synthetic aperture- or shift-based techniques.

  20. On-chip spin-controlled orbital angular momentum directional coupling

    Science.gov (United States)

    Xie, Zhenwei; Lei, Ting; Si, Guangyuan; Du, Luping; Lin, Jiao; Min, Changjun; Yuan, Xiaocong

    2018-01-01

    Optical vortex beams have many potential applications in the particle trapping, quantum encoding, optical orbital angular momentum (OAM) communications and interconnects. However, the on-chip compact OAM detection is still a big challenge. Based on a holographic configuration and a spin-dependent structure design, we propose and demonstrate an on-chip spin-controlled OAM-mode directional coupler, which can couple the OAM signal to different directions due to its topological charge. While the directional coupling function can be switched on/off by altering the spin of incident beam. Both simulation and experimental measurements verify the validity of the proposed approach. This work would benefit the on-chip OAM devices for optical communications and high dimensional quantum coding/decoding in the future.

  1. Computational On-Chip Imaging of Nanoparticles and Biomolecules using Ultraviolet Light

    KAUST Repository

    Daloglu, Mustafa Ugur; Ray, Aniruddha; Gorocs, Zoltan; Xiong, Matthew; Malik, Ravinder; Bitan, Gal; McLeod, Euan; Ozcan, Aydogan

    2017-01-01

    wavelength (UV) of 266 nm. The increased forward scattering from nanoscale objects at this short wavelength has enabled us to detect individual sub-30 nm nanoparticles over a large field-of-view of >16 mm2 using an on-chip imaging platform, where the sample

  2. On-chip measurement of the Brownian relaxation frequency of magnetic beads using magnetic tunneling junctions

    DEFF Research Database (Denmark)

    Donolato, M.; Sogne, E.; Dalslet, Bjarke Thomas

    2011-01-01

    We demonstrate the detection of the Brownian relaxation frequency of 250 nm diameter magnetic beads using a lab-on-chip platform based on current lines for exciting the beads with alternating magnetic fields and highly sensitive magnetic tunnel junction (MTJ) sensors with a superparamagnetic free...

  3. Detection of genetically modified maize ( Zea mays L.) in seed ...

    African Journals Online (AJOL)

    Maize is the second major cereal in Nepal; its food biosafety and ecological conservation is an important concern. To address this issue, it is necessary to detect genetically modified (GM) maize and establish a monitoring and regulatory system in Nepal. Currently, Nepal does not have legal regulations or labeling directives ...

  4. Comparing genetic variants detected in the 1000 genomes project ...

    Indian Academy of Sciences (India)

    Single-nucleotide polymorphisms (SNPs) determined based on SNP arrays from the international HapMap consortium (HapMap) and the genetic variants detected in the 1000 genomes project (1KGP) can serve as two references for genomewide association studies (GWAS). We conducted comparative analyses to provide ...

  5. Safety assessment and detection methods of genetically modified organisms.

    Science.gov (United States)

    Xu, Rong; Zheng, Zhe; Jiao, Guanglian

    2014-01-01

    Genetically modified organisms (GMOs), are gaining importance in agriculture as well as the production of food and feed. Along with the development of GMOs, health and food safety concerns have been raised. These concerns for these new GMOs make it necessary to set up strict system on food safety assessment of GMOs. The food safety assessment of GMOs, current development status of safety and precise transgenic technologies and GMOs detection have been discussed in this review. The recent patents about GMOs and their detection methods are also reviewed. This review can provide elementary introduction on how to assess and detect GMOs.

  6. Genetics and Early Detection in Idiopathic Pulmonary Fibrosis

    Science.gov (United States)

    Putman, Rachel K.; Rosas, Ivan O.

    2014-01-01

    Genetic studies hold promise in helping to identify patients with early idiopathic pulmonary fibrosis (IPF). Recent studies using chest computed tomograms (CTs) in smokers and in the general population have demonstrated that imaging abnormalities suggestive of an early stage of pulmonary fibrosis are not uncommon and are associated with respiratory symptoms, physical examination abnormalities, and physiologic decrements expected, but less severe than those noted in patients with IPF. Similarly, recent genetic studies have demonstrated strong and replicable associations between a common promoter polymorphism in the mucin 5B gene (MUC5B) and both IPF and the presence of abnormal imaging findings in the general population. Despite these findings, it is important to note that the definition of early-stage IPF remains unclear, limited data exist to definitively connect abnormal imaging findings to IPF, and genetic studies assessing early-stage pulmonary fibrosis remain in their infancy. In this perspective we provide updated information on interstitial lung abnormalities and their connection to IPF. We summarize information on the genetics of pulmonary fibrosis by focusing on the recent genetic findings of MUC5B. Finally, we discuss the implications of these findings and suggest a roadmap for the use of genetics in the detection of early IPF. PMID:24547893

  7. On-Chip Bondwire Magnetics with Ferrite-Epoxy Glob Coating for Power Systems on Chip

    Directory of Open Access Journals (Sweden)

    Jian Lu

    2008-01-01

    Full Text Available A novel concept of on-chip bondwire inductors and transformers with ferrite epoxy glob coating is proposed to offer a cost effective approach realizing power systems on chip (SOC. We have investigated the concept both experimentally and with finite element modeling. A Q factor of 30–40 is experimentally demonstrated for the bondwire inductors which represents an improvement by a factor of 3–30 over the state-of-the-art MEMS micromachined inductors. Transformer parameters including self- and mutual inductance and coupling factors are extracted from both modeled and measured S-parameters. More importantly, the bondwire magnetic components can be easily integrated into SOC manufacturing processes with minimal changes and open enormous possibilities for realizing cost-effective, high-current, high-efficiency power SOCs.

  8. Current perspectives on genetically modified crops and detection methods.

    Science.gov (United States)

    Kamle, Madhu; Kumar, Pradeep; Patra, Jayanta Kumar; Bajpai, Vivek K

    2017-07-01

    Genetically modified (GM) crops are the fastest adopted commodities in the agribiotech industry. This market penetration should provide a sustainable basis for ensuring food supply for growing global populations. The successful completion of two decades of commercial GM crop production (1996-2015) is underscored by the increasing rate of adoption of genetic engineering technology by farmers worldwide. With the advent of introduction of multiple traits stacked together in GM crops for combined herbicide tolerance, insect resistance, drought tolerance or disease resistance, the requirement of reliable and sensitive detection methods for tracing and labeling genetically modified organisms in the food/feed chain has become increasingly important. In addition, several countries have established threshold levels for GM content which trigger legally binding labeling schemes. The labeling of GM crops is mandatory in many countries (such as China, EU, Russia, Australia, New Zealand, Brazil, Israel, Saudi Arabia, Korea, Chile, Philippines, Indonesia, Thailand), whereas in Canada, Hong Kong, USA, South Africa, and Argentina voluntary labeling schemes operate. The rapid adoption of GM crops has increased controversies, and mitigating these issues pertaining to the implementation of effective regulatory measures for the detection of GM crops is essential. DNA-based detection methods have been successfully employed, while the whole genome sequencing using next-generation sequencing (NGS) technologies provides an advanced means for detecting genetically modified organisms and foods/feeds in GM crops. This review article describes the current status of GM crop commercialization and discusses the benefits and shortcomings of common and advanced detection systems for GMs in foods and animal feeds.

  9. Energy Model of Networks-on-Chip and a Bus

    NARCIS (Netherlands)

    Wolkotte, P.T.; Smit, Gerardus Johannes Maria; Kavaldjiev, N.K.; Becker, Jens E.; Becker, Jürgen; Nurmi, J.; Takala, J.; Hamalainen, T.D.

    2005-01-01

    A Network-on-Chip (NoC) is an energy-efficient onchip communication architecture for Multi-Processor Systemon-Chip (MPSoC) architectures. In earlier papers we proposed two Network-on-Chip architectures based on packet-switching and circuit-switching. In this paper we derive an energy model for both

  10. Detecting structural breaks in time series via genetic algorithms

    DEFF Research Database (Denmark)

    Doerr, Benjamin; Fischer, Paul; Hilbert, Astrid

    2016-01-01

    of the time series under consideration is available. Therefore, a black-box optimization approach is our method of choice for detecting structural breaks. We describe a genetic algorithm framework which easily adapts to a large number of statistical settings. To evaluate the usefulness of different crossover...... and mutation operations for this problem, we conduct extensive experiments to determine good choices for the parameters and operators of the genetic algorithm. One surprising observation is that use of uniform and one-point crossover together gave significantly better results than using either crossover...... operator alone. Moreover, we present a specific fitness function which exploits the sparse structure of the break points and which can be evaluated particularly efficiently. The experiments on artificial and real-world time series show that the resulting algorithm detects break points with high precision...

  11. Modelling, Synthesis, and Configuration of Networks-on-Chips

    DEFF Research Database (Denmark)

    Stuart, Matthias Bo

    This thesis presents three contributions in two different areas of network-on-chip and system-on-chip research: Application modelling and identifying and solving different optimization problems related to two specific network-on-chip architectures. The contribution related to application modelling...... is an analytical method for deriving the worst-case traffic pattern caused by an application and the cache-coherence protocol in a cache-coherent shared-memory system. The contributions related to network-on-chip optimization problems consist of two parts: The development and evaluation of six heuristics...... for solving the network synthesis problem in the MANGO network-on-chip, and the identification and formalization of the ReNoC configuration problem together with three heuristics for solving it....

  12. On-chip particle trapping and manipulation

    Science.gov (United States)

    Leake, Kaelyn Danielle

    The ability to control and manipulate the world around us is human nature. Humans and our ancestors have used tools for millions of years. Only in recent years have we been able to control objects at such small levels. In order to understand the world around us it is frequently necessary to interact with the biological world. Optical trapping and manipulation offer a non-invasive way to move, sort and interact with particles and cells to see how they react to the world around them. Optical tweezers are ideal in their abilities but they require large, non-portable, and expensive setups limiting how and where we can use them. A cheap portable platform is required in order to have optical manipulation reach its full potential. On-chip technology offers a great solution to this challenge. We focused on the Liquid-Core Anti-Resonant Reflecting Optical Waveguide (liquid-core ARROW) for our work. The ARROW is an ideal platform, which has anti-resonant layers which allow light to be guided in liquids, allowing for particles to easily be manipulated. It is manufactured using standard silicon manufacturing techniques making it easy to produce. The planner design makes it easy to integrate with other technologies. Initially I worked to improve the ARROW chip by reducing the intersection losses and by reducing the fluorescence and background on the ARROW chip. The ARROW chip has already been used to trap and push particles along its channel but here I introduce several new methods of particle trapping and manipulation on the ARROW chip. Traditional two beam traps use two counter propagating beams. A trapping scheme that uses two orthogonal beams which counter to first instinct allow for trapping at their intersection is introduced. This scheme is thoroughly predicted and analyzed using realistic conditions. Simulations of this method were done using a program which looks at both the fluidics and optical sources to model complex situations. These simulations were also used to

  13. Population genetic diversity and hybrid detection in captive zebras.

    Science.gov (United States)

    Ito, Hideyuki; Langenhorst, Tanya; Ogden, Rob; Inoue-Murayama, Miho

    2015-08-21

    Zebras are members of the horse family. There are three species of zebras: the plains zebra Equus quagga, the Grevy's zebra E. grevyi and the mountain zebra E. zebra. The Grevy's zebra and the mountain zebra are endangered, and hybridization between the Grevy's zebra and the plains zebra has been documented, leading to a requirement for conservation genetic management within and between the species. We characterized 28 microsatellite markers in Grevy's zebra and assessed cross-amplification in plains zebra and two of its subspecies, as well as mountain zebra. A range of standard indices were employed to examine population genetic diversity and hybrid populations between Grevy's and plains zebra were simulated to investigate subspecies and hybrid detection. Microsatellite marker polymorphism was conserved across species with sufficient variation to enable individual identification in all populations. Comparative diversity estimates indicated greater genetic variation in plains zebra and its subspecies than Grevy's zebra, despite potential ascertainment bias. Species and subspecies differentiation were clearly demonstrated and F1 and F2 hybrids were correctly identified. These findings provide insights into captive population genetic diversity in zebras and support the use of these markers for identifying hybrids, including the known hybrid issue in the endangered Grevy's zebra.

  14. Detection genetic variability of secale cereale L. by scot markers

    Directory of Open Access Journals (Sweden)

    Lenka Petrovičová

    2017-01-01

    Full Text Available Rye (Secale cereale L. is our traditional cereal used for baking. The genetic variability of grown rye has been reduced by modern agronomic practices, which subsequently prompted the importance of search for species that could be useful as a gene pool for the improving of flour quality for human consumption or for other industrial uses. Therefore, the aim of this study was to detect genetic variability among the set of 45 rye genotypes using 8 SCoT markers. Amplification of genomic DNA of 45 genotypes, using SCoT analysis, yielded 114 fragments, with an average of 14.25 polymorphic fragments per primer. The most polymorphic primer was SCoT 36, where 21 polymorphic amplification products were detected. In contract the lowest polymorphic primer was SCoT 45 with 5 polymorphic products. Genetic polymorphism was characterized based on diversity index (DI, probability of identity (PI and polymorphic information content (PIC. The hierarchical cluster analysis showed that the rye genotypes were divided into 2 main clusters. One rye genotype Motto, origin from Poland formed a separate subcluster (1b. Subscluster 2a included only genotype Valtické (CSK. In this experiment, SCoT proved to be a rapid, reliable and practicable method for revealing of polymorphism in the rye cultivars. Normal 0 21 false false false EN-GB X-NONE X-NONE

  15. Perspectives on genetically modified crops and food detection

    Directory of Open Access Journals (Sweden)

    Chih-Hui Lin

    2016-01-01

    Full Text Available Genetically modified (GM crops are a major product of the global food industry. From 1996 to 2014, 357 GM crops were approved and the global value of the GM crop market reached 35% of the global commercial seed market in 2014. However, the rapid growth of the GM crop-based industry has also created controversies in many regions, including the European Union, Egypt, and Taiwan. The effective detection and regulation of GM crops/foods are necessary to reduce the impact of these controversies. In this review, the status of GM crops and the technology for their detection are discussed. As the primary gap in GM crop regulation exists in the application of detection technology to field regulation, efforts should be made to develop an integrated, standardized, and high-throughput GM crop detection system. We propose the development of an integrated GM crop detection system, to be used in combination with a standardized international database, a decision support system, high-throughput DNA analysis, and automated sample processing. By integrating these technologies, we hope that the proposed GM crop detection system will provide a method to facilitate comprehensive GM crop regulation.

  16. Perspectives on genetically modified crops and food detection.

    Science.gov (United States)

    Lin, Chih-Hui; Pan, Tzu-Ming

    2016-01-01

    Genetically modified (GM) crops are a major product of the global food industry. From 1996 to 2014, 357 GM crops were approved and the global value of the GM crop market reached 35% of the global commercial seed market in 2014. However, the rapid growth of the GM crop-based industry has also created controversies in many regions, including the European Union, Egypt, and Taiwan. The effective detection and regulation of GM crops/foods are necessary to reduce the impact of these controversies. In this review, the status of GM crops and the technology for their detection are discussed. As the primary gap in GM crop regulation exists in the application of detection technology to field regulation, efforts should be made to develop an integrated, standardized, and high-throughput GM crop detection system. We propose the development of an integrated GM crop detection system, to be used in combination with a standardized international database, a decision support system, high-throughput DNA analysis, and automated sample processing. By integrating these technologies, we hope that the proposed GM crop detection system will provide a method to facilitate comprehensive GM crop regulation. Copyright © 2015. Published by Elsevier B.V.

  17. Cytostretch, an Organ-on-Chip Platform

    Directory of Open Access Journals (Sweden)

    Nikolas Gaio

    2016-07-01

    Full Text Available Organ-on-Chips (OOCs are micro-fabricated devices which are used to culture cells in order to mimic functional units of human organs. The devices are designed to simulate the physiological environment of tissues in vivo. Cells in some types of OOCs can be stimulated in situ by electrical and/or mechanical actuators. These actuations can mimic physiological conditions in real tissue and may include fluid or air flow, or cyclic stretch and strain as they occur in the lung and heart. These conditions similarly affect cultured cells and may influence their ability to respond appropriately to physiological or pathological stimuli. To date, most focus has been on devices specifically designed to culture just one functional unit of a specific organ: lung alveoli, kidney nephrons or blood vessels, for example. In contrast, the modular Cytostretch membrane platform described here allows OOCs to be customized to different OOC applications. The platform utilizes silicon-based micro-fabrication techniques that allow low-cost, high-volume manufacturing. We describe the platform concept and its modules developed to date. Membrane variants include membranes with (i through-membrane pores that allow biological signaling molecules to pass between two different tissue compartments; (ii a stretchable micro-electrode array for electrical monitoring and stimulation; (iii micro-patterning to promote cell alignment; and (iv strain gauges to measure changes in substrate stress. This paper presents the fabrication and the proof of functionality for each module of the Cytostretch membrane. The assessment of each additional module demonstrate that a wide range of OOCs can be achieved.

  18. ROAD DETECTION BY NEURAL AND GENETIC ALGORITHM IN URBAN ENVIRONMENT

    Directory of Open Access Journals (Sweden)

    A. Barsi

    2012-07-01

    Full Text Available In the urban object detection challenge organized by the ISPRS WG III/4 high geometric and radiometric resolution aerial images about Vaihingen/Stuttgart, Germany are distributed. The acquired data set contains optical false color, near infrared images and airborne laserscanning data. The presented research focused exclusively on the optical image, so the elevation information was ignored. The road detection procedure has been built up of two main phases: a segmentation done by neural networks and a compilation made by genetic algorithms. The applied neural networks were support vector machines with radial basis kernel function and self-organizing maps with hexagonal network topology and Euclidean distance function for neighborhood management. The neural techniques have been compared by hyperbox classifier, known from the statistical image classification practice. The compilation of the segmentation is realized by a novel application of the common genetic algorithm and by differential evolution technique. The genes were implemented to detect the road elements by evaluating a special binary fitness function. The results have proven that the evolutional technique can automatically find major road segments.

  19. Crosstalk in modern on-chip interconnects a FDTD approach

    CERN Document Server

    Kaushik, B K; Patnaik, Amalendu

    2016-01-01

    The book provides accurate FDTD models for on-chip interconnects, covering most recent advancements in materials and design. Furthermore, depending on the geometry and physical configurations, different electrical equivalent models for CNT and GNR based interconnects are presented. Based on the electrical equivalent models the performance comparison among the Cu, CNT and GNR-based interconnects are also discussed in the book. The proposed models are validated with the HSPICE simulations. The book introduces the current research scenario in the modeling of on-chip interconnects. It presents the structure, properties, and characteristics of graphene based on-chip interconnects and the FDTD modeling of Cu based on-chip interconnects. The model considers the non-linear effects of CMOS driver as well as the transmission line effects of interconnect line that includes coupling capacitance and mutual inductance effects. In a more realistic manner, the proposed model includes the effect of width-dependent MFP of the ...

  20. Error Control for Network-on-Chip Links

    CERN Document Server

    Fu, Bo

    2012-01-01

    As technology scales into nanoscale regime, it is impossible to guarantee the perfect hardware design. Moreover, if the requirement of 100% correctness in hardware can be relaxed, the cost of manufacturing, verification, and testing will be significantly reduced. Many approaches have been proposed to address the reliability problem of on-chip communications. This book focuses on the use of error control codes (ECCs) to improve on-chip interconnect reliability. Coverage includes detailed description of key issues in NOC error control faced by circuit and system designers, as well as practical error control techniques to minimize the impact of these errors on system performance. Provides a detailed background on the state of error control methods for on-chip interconnects; Describes the use of more complex concatenated codes such as Hamming Product Codes with Type-II HARQ, while emphasizing integration techniques for on-chip interconnect links; Examines energy-efficient techniques for integrating multiple error...

  1. Pollen genetic markers for detection of mutagens in the environment

    International Nuclear Information System (INIS)

    Nilan, R.A.; Rosichan, J.L.; Arenaz, P.; Hodgdon, A.L.; Kleinhofs, A.

    1980-01-01

    To utilize and exploit pollen for in situ mutagen monitoring, screening and toxicology, the range of genetic traits in pollen must be identified and analyzed. To be useful for the development of mutagen detection systems proteins should be: (1) activity stainable or immunologically identifiable in the pollen, (2) the products of one to three loci; and (3) gametophytic and nuclear in origin. Several proteins, including alcohol dehydrogenase in maize, which meet these criteria are discussed. The waxy locus in barley and maize which controls starch deposition for pollen screening and mutant detection. Thirty waxy mutant lines, induced by sodium azide and gamma-rays are characterized for spontaneous and induced reversion frequencies, allelism, karyotype, amylose content, and UDPglucose glucosyltransferase (waxy gene product) activity. Twelve mutant alleles are being mapped by recombinant frequencies

  2. Reliability, Availability and Serviceability of Networks-on-Chip

    CERN Document Server

    Cota, Érika; Soares Lubaszewski, Marcelo

    2012-01-01

    This book presents an overview of the issues related to the test, diagnosis and fault-tolerance of Network on Chip-based systems. It is the first book dedicated to the quality aspects of NoC-based systems and will serve as an invaluable reference to the problems, challenges, solutions, and trade-offs related to designing and implementing state-of-the-art, on-chip communication architectures.

  3. An integrated lab-on-chip for rapid identification and simultaneous differentiation of tropical pathogens.

    Directory of Open Access Journals (Sweden)

    Jeslin J L Tan

    Full Text Available Tropical pathogens often cause febrile illnesses in humans and are responsible for considerable morbidity and mortality. The similarities in clinical symptoms provoked by these pathogens make diagnosis difficult. Thus, early, rapid and accurate diagnosis will be crucial in patient management and in the control of these diseases. In this study, a microfluidic lab-on-chip integrating multiplex molecular amplification and DNA microarray hybridization was developed for simultaneous detection and species differentiation of 26 globally important tropical pathogens. The analytical performance of the lab-on-chip for each pathogen ranged from 102 to 103 DNA or RNA copies. Assay performance was further verified with human whole blood spiked with Plasmodium falciparum and Chikungunya virus that yielded a range of detection from 200 to 4×105 parasites, and from 250 to 4×107 PFU respectively. This lab-on-chip was subsequently assessed and evaluated using 170 retrospective patient specimens in Singapore and Thailand. The lab-on-chip had a detection sensitivity of 83.1% and a specificity of 100% for P. falciparum; a sensitivity of 91.3% and a specificity of 99.3% for P. vivax; a positive 90.0% agreement and a specificity of 100% for Chikungunya virus; and a positive 85.0% agreement and a specificity of 100% for Dengue virus serotype 3 with reference methods conducted on the samples. Results suggested the practicality of an amplification microarray-based approach in a field setting for high-throughput detection and identification of tropical pathogens.

  4. Detecting Major Genetic Loci Controlling Phenotypic Variability in Experimental Crosses

    Science.gov (United States)

    Rönnegård, Lars; Valdar, William

    2011-01-01

    Traditional methods for detecting genes that affect complex diseases in humans or animal models, milk production in livestock, or other traits of interest, have asked whether variation in genotype produces a change in that trait’s average value. But focusing on differences in the mean ignores differences in variability about that mean. The robustness, or uniformity, of an individual’s character is not only of great practical importance in medical genetics and food production but is also of scientific and evolutionary interest (e.g., blood pressure in animal models of heart disease, litter size in pigs, flowering time in plants). We describe a method for detecting major genes controlling the phenotypic variance, referring to these as vQTL. Our method uses a double generalized linear model with linear predictors based on probabilities of line origin. We evaluate our method on simulated F2 and collaborative cross data, and on a real F2 intercross, demonstrating its accuracy and robustness to the presence of ordinary mean-controlling QTL. We also illustrate the connection between vQTL and QTL involved in epistasis, explaining how these concepts overlap. Our method can be applied to a wide range of commonly used experimental crosses and may be extended to genetic association more generally. PMID:21467569

  5. Integration of microcoils for on-chip immunosensors based on magnetic nanoparticles capture

    Directory of Open Access Journals (Sweden)

    Olivier Lefebvre

    2017-04-01

    Full Text Available Immunoassays using magnetic nanoparticles (MNP are generally performed under the control of permanent magnet close to the micro-tube of reaction. Using a magnet gives a powerful method for driving MNP but remains unreliable or insufficient for a fully integrated immunoassay on lab-on-chip. The aim of this study is to develop a novel lab-on-chip concept for high efficient immunoassays to detect ovalbumin (Biodefense model molecule with microcoils employed for trapping MNP during the biofunctionalization steps. The objectives are essentially to optimize their efficiency for biological recognition by assuring a better bioactivity (antibodies-ovalbumin, and detect small concentrations of the targeted protein (~10 pg/mL. In this work, we studied the response of immunoassays complex function of ovalbumin concentration. The impact of MNP diameter in the biografting protocol was studied and permitted to choose a convenient MNP size for efficient biorecognition. We realized different immunoassays by controlling MNP in test tube and in microfluidic device using a permanent magnet. The comparison between these two experiments allows us to highlight an improvement of the limit of detection in microfluidic conditions by controlling MNP trapping with a magnet. Keywords: Bacteria, Lab-on-chip, ELISA, Magnetic nanoparticles, Ovalbumin, Microcoils, Fluorescent microscopy

  6. Improved Genetic Algorithm Optimization for Forward Vehicle Detection Problems

    Directory of Open Access Journals (Sweden)

    Longhui Gang

    2015-07-01

    Full Text Available Automated forward vehicle detection is an integral component of many advanced driver-assistance systems. The method based on multi-visual information fusion, with its exclusive advantages, has become one of the important topics in this research field. During the whole detection process, there are two key points that should to be resolved. One is to find the robust features for identification and the other is to apply an efficient algorithm for training the model designed with multi-information. This paper presents an adaptive SVM (Support Vector Machine model to detect vehicle with range estimation using an on-board camera. Due to the extrinsic factors such as shadows and illumination, we pay more attention to enhancing the system with several robust features extracted from a real driving environment. Then, with the introduction of an improved genetic algorithm, the features are fused efficiently by the proposed SVM model. In order to apply the model in the forward collision warning system, longitudinal distance information is provided simultaneously. The proposed method is successfully implemented on a test car and evaluation experimental results show reliability in terms of both the detection rate and potential effectiveness in a real-driving environment.

  7. Genetically modified crops: detection strategies and biosafety issues.

    Science.gov (United States)

    Kamle, Suchitra; Ali, Sher

    2013-06-15

    Genetically modified (GM) crops are increasingly gaining acceptance but concurrently consumers' concerns are also increasing. The introduction of Bacillus thuringiensis (Bt) genes into the plants has raised issues related to its risk assessment and biosafety. The International Regulations and the Codex guidelines regulate the biosafety requirements of the GM crops. In addition, these bodies synergize and harmonize the ethical issues related to the release and use of GM products. The labeling of GM crops and their products are mandatory if the genetically modified organism (GMO) content exceeds the levels of a recommended threshold. The new and upcoming GM crops carrying multiple stacked traits likely to be commercialized soon warrant sensitive detection methods both at the DNA and protein levels. Therefore, traceability of the transgene and its protein expression in GM crops is an important issue that needs to be addressed on a priority basis. The advancement in the area of molecular biology has made available several bioanalytical options for the detection of GM crops based on DNA and protein markers. Since the insertion of a gene into the host genome may even cause copy number variation, this may be uncovered using real time PCR. Besides, assessing the exact number of mRNA transcripts of a gene, correlation between the template activity and expressed protein may be established. Here, we present an overview on the production of GM crops, their acceptabilities, detection strategies, biosafety issues and potential impact on society. Further, overall future prospects are also highlighted. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Speed Bump Detection Using Accelerometric Features: A Genetic Algorithm Approach.

    Science.gov (United States)

    Celaya-Padilla, Jose M; Galván-Tejada, Carlos E; López-Monteagudo, F E; Alonso-González, O; Moreno-Báez, Arturo; Martínez-Torteya, Antonio; Galván-Tejada, Jorge I; Arceo-Olague, Jose G; Luna-García, Huizilopoztli; Gamboa-Rosales, Hamurabi

    2018-02-03

    Among the current challenges of the Smart City, traffic management and maintenance are of utmost importance. Road surface monitoring is currently performed by humans, but the road surface condition is one of the main indicators of road quality, and it may drastically affect fuel consumption and the safety of both drivers and pedestrians. Abnormalities in the road, such as manholes and potholes, can cause accidents when not identified by the drivers. Furthermore, human-induced abnormalities, such as speed bumps, could also cause accidents. In addition, while said obstacles ought to be signalized according to specific road regulation, they are not always correctly labeled. Therefore, we developed a novel method for the detection of road abnormalities (i.e., speed bumps). This method makes use of a gyro, an accelerometer, and a GPS sensor mounted in a car. After having the vehicle cruise through several streets, data is retrieved from the sensors. Then, using a cross-validation strategy, a genetic algorithm is used to find a logistic model that accurately detects road abnormalities. The proposed model had an accuracy of 0.9714 in a blind evaluation, with a false positive rate smaller than 0.018, and an area under the receiver operating characteristic curve of 0.9784. This methodology has the potential to detect speed bumps in quasi real-time conditions, and can be used to construct a real-time surface monitoring system.

  9. Speed Bump Detection Using Accelerometric Features: A Genetic Algorithm Approach

    Directory of Open Access Journals (Sweden)

    Jose M. Celaya-Padilla

    2018-02-01

    Full Text Available Among the current challenges of the Smart City, traffic management and maintenance are of utmost importance. Road surface monitoring is currently performed by humans, but the road surface condition is one of the main indicators of road quality, and it may drastically affect fuel consumption and the safety of both drivers and pedestrians. Abnormalities in the road, such as manholes and potholes, can cause accidents when not identified by the drivers. Furthermore, human-induced abnormalities, such as speed bumps, could also cause accidents. In addition, while said obstacles ought to be signalized according to specific road regulation, they are not always correctly labeled. Therefore, we developed a novel method for the detection of road abnormalities (i.e., speed bumps. This method makes use of a gyro, an accelerometer, and a GPS sensor mounted in a car. After having the vehicle cruise through several streets, data is retrieved from the sensors. Then, using a cross-validation strategy, a genetic algorithm is used to find a logistic model that accurately detects road abnormalities. The proposed model had an accuracy of 0.9714 in a blind evaluation, with a false positive rate smaller than 0.018, and an area under the receiver operating characteristic curve of 0.9784. This methodology has the potential to detect speed bumps in quasi real-time conditions, and can be used to construct a real-time surface monitoring system.

  10. Detection and traceability of genetically modified organisms in the food production chain

    NARCIS (Netherlands)

    Miraglia, M.; Berdal, K.G.; Brera, C.; Corbisier, P.; Holst - Jensen, A.; Kok, E.J.; Marvin, H.J.P.; Schimmel, H.; Rentsch, J.; Rie, van J.P.P.F.; Zagon, J.

    2004-01-01

    Both labelling and traceability of genetically modified organisms are current issues that are considered in trade and regulation. Currently, labelling of genetically modified foods containing detectable transgenic material is required by EU legislation. A proposed package of legislation would extend

  11. On-chip signal amplification of magnetic bead-based immunoassay by aviating magnetic bead chains.

    Science.gov (United States)

    Jalal, Uddin M; Jin, Gyeong Jun; Eom, Kyu Shik; Kim, Min Ho; Shim, Joon S

    2017-11-06

    In this work, a Lab-on-a-Chip (LOC) platform is used to electromagnetically actuate magnetic bead chains for an enhanced immunoassay. Custom-made electromagnets generate a magnetic field to form, rotate, lift and lower the magnetic bead chains (MBCs). The cost-effective, disposable LOC platform was made with a polymer substrate and an on-chip electrochemical sensor patterned via the screen-printing process. The movement of the MBCs is controlled to improve the electrochemical signal up to 230% when detecting beta-type human chorionic gonadotropin (β-hCG). Thus, the proposed on-chip MBC-based immunoassay is applicable for rapid, qualitative electrochemical point-of-care (POC) analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Design of a CMOS integrated on-chip oscilloscope for spin wave characterization

    Directory of Open Access Journals (Sweden)

    Eugen Egel

    2017-05-01

    Full Text Available Spin waves can perform some optically-inspired computing algorithms, e.g. the Fourier transform, directly than it is done with the CMOS logic. This article describes a new approach for on-chip characterization of spin wave based devices. The readout circuitry for the spin waves is simulated with 65-nm CMOS technology models. Commonly used circuits for Radio Frequency (RF receivers are implemented to detect a sinusoidal ultra-wideband (5-50 GHz signal with an amplitude of at least 15 μV picked up by a loop antenna. First, the RF signal is amplified by a Low Noise Amplifier (LNA. Then, it is down-converted by a mixer to Intermediate Frequency (IF. Finally, an Operational Amplifier (OpAmp brings the IF signal to higher voltages (50-300 mV. The estimated power consumption and the required area of the readout circuit is approximately 55.5 mW and 0.168 mm2, respectively. The proposed On-Chip Oscilloscope (OCO is highly suitable for on-chip spin wave characterization regarding the frequency, amplitude change and phase information. It offers an integrated low power alternative to current spin wave detecting systems.

  13. DNA barcode detects high genetic structure within neotropical bird species.

    Directory of Open Access Journals (Sweden)

    Erika Sendra Tavares

    Full Text Available BACKGROUND: Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. METHODS AND FINDINGS: Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520 of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N = 21 or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N = 20. Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. CONCLUSIONS: The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent

  14. Improved optical solutions for on-chip light scattering detection

    DEFF Research Database (Denmark)

    Jensen, Thomas Glasdam

    nødvendigt at udvikle LabVIEW programmet "RayLab" for at kunne simulere den optiske opførsel af forskellige bølgeleder og mikrolinse konfigurationer. Det første vellykkede eksperiment blev lavet med en mikrofluid enhed bestående af et glas substrat med et SU-8 og et polydimethylsiloxan (PDMS) lag. Enheden...

  15. Network Partitioning Domain Knowledge Multiobjective Application Mapping for Large-Scale Network-on-Chip

    Directory of Open Access Journals (Sweden)

    Yin Zhen Tei

    2014-01-01

    Full Text Available This paper proposes a multiobjective application mapping technique targeted for large-scale network-on-chip (NoC. As the number of intellectual property (IP cores in multiprocessor system-on-chip (MPSoC increases, NoC application mapping to find optimum core-to-topology mapping becomes more challenging. Besides, the conflicting cost and performance trade-off makes multiobjective application mapping techniques even more complex. This paper proposes an application mapping technique that incorporates domain knowledge into genetic algorithm (GA. The initial population of GA is initialized with network partitioning (NP while the crossover operator is guided with knowledge on communication demands. NP reduces the large-scale application mapping complexity and provides GA with a potential mapping search space. The proposed genetic operator is compared with state-of-the-art genetic operators in terms of solution quality. In this work, multiobjective optimization of energy and thermal-balance is considered. Through simulation, knowledge-based initial mapping shows significant improvement in Pareto front compared to random initial mapping that is widely used. The proposed knowledge-based crossover also shows better Pareto front compared to state-of-the-art knowledge-based crossover.

  16. Swarm, genetic and evolutionary programming algorithms applied to multiuser detection

    Directory of Open Access Journals (Sweden)

    Paul Jean Etienne Jeszensky

    2005-02-01

    Full Text Available In this paper, the particles swarm optimization technique, recently published in the literature, and applied to Direct Sequence/Code Division Multiple Access systems (DS/CDMA with multiuser detection (MuD is analyzed, evaluated and compared. The Swarm algorithm efficiency when applied to the DS-CDMA multiuser detection (Swarm-MuD is compared through the tradeoff performance versus computational complexity, being the complexity expressed in terms of the number of necessary operations in order to reach the performance obtained through the optimum detector or the Maximum Likelihood detector (ML. The comparison is accomplished among the genetic algorithm, evolutionary programming with cloning and Swarm algorithm under the same simulation basis. Additionally, it is proposed an heuristics-MuD complexity analysis through the number of computational operations. Finally, an analysis is carried out for the input parameters of the Swarm algorithm in the attempt to find the optimum parameters (or almost-optimum for the algorithm applied to the MuD problem.

  17. Effect of on-chip filter on Coulomb blockade thermometer

    International Nuclear Information System (INIS)

    Roschier, L; Penttilä, J S; Gunnarsson, D; Prunnila, M; Meschke, M; Savin, A

    2012-01-01

    Coulomb Blockade Thermometer (CBT) is a primary thermometer based on electric conductance of normal tunnel junction arrays. One limitation for CBT use at the lowest temperatures has been due to environmental noise heating. To improve on this limitation, we have done measurements on CBT sensors fabricated with different on-chip filtering structures in a dilution refrigerator with a base temperature of 10 mK. The CBT sensors were produced with a wafer scale tunnel junction process. We present how the different on-chip filtering schemes affect the limiting saturation temperatures and show that CBT sensors with proper on-chip filtering work at temperatures below 20 mK and are tolerant to noisy environment.

  18. Microneedle Array Interface to CE on Chip

    NARCIS (Netherlands)

    Lüttge, Regina; Gardeniers, Johannes G.E.; Vrouwe, E.X.; van den Berg, Albert; Northrup, M.A.; Jensen, K.F; Harrison, D.J.

    2003-01-01

    This paper presents a microneedle array sampler interfaced to a capillary electrophoresis (CE) glass chip with integrated conductivity detection electrodes. A solution of alkali ions was electrokinetically loaded through the microneedles onto the chip and separation was demonstrated compared to a

  19. On-chip growth of semiconductor metal oxide nanowires for gas sensors: A review

    Directory of Open Access Journals (Sweden)

    Chu Manh Hung

    2017-09-01

    Full Text Available Semiconductor metal oxide nanowires (SMO-NWs show great potential for novel gas sensor applications because of their distinct properties, such as a high surface area to volume aspect ratio, high crystallinity and perfect pathway for electron transfer (length of NW. SMO-NW sensors can be configured as resistors or field-effect transistors for gas detection and different configurations, such as a single NW, multiple NWs, and networked NW films, have been established. Surface-functionalizing NWs with catalyst elements and self-heating NWs provide additional advantages for highly selective and low-power consumption gas sensors. However, an appropriate design of SMO-NWs is of practical importance in enhancing the gas-sensing performance of SMO-NW sensors. The on-chip growth of SMO-NWs possesses many advantages which can thus be effectively used for the large-scale fabrication of SMO-NW sensors with improved gas response and stability. This review aims to provide up-to-date information on the on-chip fabrication of SnO2, ZnO, WO3, CuO, and other SMO-NW sensors. It also discusses a variety of promising approaches that help advance the on-chip fabrication of SMO-NW-based gas sensors and other NW-based devices.

  20. On-chip magnetic bead-based DNA melting curve analysis using a magnetoresistive sensor

    DEFF Research Database (Denmark)

    Rizzi, Giovanni; Østerberg, Frederik Westergaard; Henriksen, Anders Dahl

    2014-01-01

    We present real-time measurements of DNA melting curves in a chip-based system that detects the amount of surface-bound magnetic beads using magnetoresistive magnetic field sensors. The sensors detect the difference between the amount of beads bound to the top and bottom sensor branches....... The beads are magnetized by the field arising from the bias current passed through the sensors. We demonstrate the first on-chip measurements of the melting of DNA hybrids upon a ramping of the temperature. This overcomes the limitation of using a single washing condition at constant temperature. Moreover...

  1. Amplification of biological targets via on-chip culture for biosensing

    Science.gov (United States)

    Harper, Jason C.; Edwards, Thayne L.; Carson, Bryan; Finley, Melissa; Arndt, William

    2018-01-02

    The present invention, in part, relates to methods and apparatuses for on-chip amplification and/or detection of various targets, including biological targets and any amplifiable targets. In some examples, the microculture apparatus includes a single-use, normally-closed fluidic valve that is initially maintained in the closed position by a valve element bonded to an adhesive coating. The valve is opened using a magnetic force. The valve element includes a magnetic material or metal. Such apparatuses and methods are useful for in-field or real-time detection of targets, especially in limited resource settings.

  2. Designing network on-chip architectures in the nanoscale era

    CERN Document Server

    Flich, Jose

    2010-01-01

    Going beyond isolated research ideas and design experiences, Designing Network On-Chip Architectures in the Nanoscale Era covers the foundations and design methods of network on-chip (NoC) technology. The contributors draw on their own lessons learned to provide strong practical guidance on various design issues.Exploring the design process of the network, the first part of the book focuses on basic aspects of switch architecture and design, topology selection, and routing implementation. In the second part, contributors discuss their experiences in the industry, offering a roadmap to recent p

  3. Reliability of genetic bottleneck tests for detecting recent population declines

    NARCIS (Netherlands)

    Peery, M. Zachariah; Kirby, Rebecca; Reid, Brendan N.; Stoelting, Ricka; Doucet-Beer, Elena; Robinson, Stacie; Vasquez-Carrillo, Catalina; Pauli, Jonathan N.; Palsboll, Per J.

    The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and

  4. Design of Networks-on-Chip for Real-Time Multi-Processor Systems-on-Chip

    DEFF Research Database (Denmark)

    Sparsø, Jens

    2012-01-01

    This paper addresses the design of networks-on-chips for use in multi-processor systems-on-chips - the hardware platforms used in embedded systems. These platforms typically have to guarantee real-time properties, and as the network is a shared resource, it has to provide service guarantees...... (bandwidth and/or latency) to different communication flows. The paper reviews some past work in this field and the lessons learned, and the paper discusses ongoing research conducted as part of the project "Time-predictable Multi-Core Architecture for Embedded Systems" (T-CREST), supported by the European...

  5. On-chip RF-to-optical transducer (Conference Presentation)

    Science.gov (United States)

    Simonsen, Anders; Tsaturyan, Yeghishe; Seis, Yannick; Schmid, Silvan; Schliesser, Albert; Polzik, Eugene S.

    2016-04-01

    Recent advances in the fabrication of nano- and micromechanical elements enable the realization of high-quality mechanical resonators with masses so small that the forces from optical photons can have a significant impact on their motion. This facilitates a strong interaction between mechanical motion and light, or phonons and photons. This interaction is the corner stone of the field of optomechanics and allows, for example, for ultrasensitive detection and manipulation of mechanical motion using laser light. Remarkably, today these techniques can be extended into the quantum regime, in which fundamental fluctuations of light and mechanics govern the system's behavior. Micromechanical elements can also interact strongly with other physical systems, which is the central aspect of many micro-electro-mechanical based sensors. Micromechanical elements can therefore act as a bridge between these diverse systems, plus technologies that utilize them, and the mature toolbox of optical techniques that routinely operates at the quantum limit. In a previous work [1], we demonstrated such a bridge by realizing simultaneous coupling between an electronic LC circuit and a quantum-noise limited optical interferometer. The coupling was mediated by a mechanical oscillator forming a mechanically compliant capacitor biased with a DC voltage. The latter enhances the electromechanical interaction all the way to the strong coupling regime. That scheme allowed optical detection of electronic signals with effective noise temperatures far below the actual temperature of the mechanical element. On-chip integration of the electrical, mechanical and optical elements is necessary for an implementation of the transduction scheme that is viable for commercial applications. Reliable assembly of a strongly coupled electromechanical device, and inclusion of an optical cavity for enhanced optical readout, are key features of the new platform. Both can be achieved with standard cleanroom fabrication

  6. Automation of diagnostic genetic testing: mutation detection by cyclic minisequencing.

    Science.gov (United States)

    Alagrund, Katariina; Orpana, Arto K

    2014-01-01

    The rising role of nucleic acid testing in clinical decision making is creating a need for efficient and automated diagnostic nucleic acid test platforms. Clinical use of nucleic acid testing sets demands for shorter turnaround times (TATs), lower production costs and robust, reliable methods that can easily adopt new test panels and is able to run rare tests in random access principle. Here we present a novel home-brew laboratory automation platform for diagnostic mutation testing. This platform is based on the cyclic minisequecing (cMS) and two color near-infrared (NIR) detection. Pipetting is automated using Tecan Freedom EVO pipetting robots and all assays are performed in 384-well micro plate format. The automation platform includes a data processing system, controlling all procedures, and automated patient result reporting to the hospital information system. We have found automated cMS a reliable, inexpensive and robust method for nucleic acid testing for a wide variety of diagnostic tests. The platform is currently in clinical use for over 80 mutations or polymorphisms. Additionally to tests performed from blood samples, the system performs also epigenetic test for the methylation of the MGMT gene promoter, and companion diagnostic tests for analysis of KRAS and BRAF gene mutations from formalin fixed and paraffin embedded tumor samples. Automation of genetic test reporting is found reliable and efficient decreasing the work load of academic personnel.

  7. Power and Thermal Management of System-on-Chip

    DEFF Research Database (Denmark)

    Liu, Wei

    , are necessary at the chip design level. In this work, we investigate the power and thermal management of System-on- Chips (SoCs). Thermal analysis is performed in a SPICE simulation approach based on the electrical-thermal analogy. We investigate the impact of inter- connects on heat distribution...

  8. Exploration within the Network-on-Chip Paradigm

    NARCIS (Netherlands)

    Wolkotte, P.T.

    2009-01-01

    A general purpose processor used to consist of a single processing core, which performed and controlled all tasks on the chip. Its functionality and maximum clock frequency grew steadily over the years. Due to the continuous increase of the number of transistors available on-chip and the operational

  9. Design of an on-chip reflectance map

    NARCIS (Netherlands)

    Terwisscha van Scheltinga, Jeroen; Smit, Jaap; Bosma, Marco

    1995-01-01

    A reflectance map design is described which uses a minimal amount of memory for the table, in order to be applicable as an on-chip shader. The shader is designed for use with the volumetric super resolution hardware, which performs shading at supersampled locations. However, the design may be used

  10. On-chip integrated lasers for biophotonic applications

    DEFF Research Database (Denmark)

    Mappes, Timo; Wienhold, Tobias; Bog, Uwe

    Meeting the need of biomedical users, we develop disposable Lab-on-a-Chip systems based on commercially available polymers. We are combining passive microfluidics with active optical elements on-chip by integrating multiple solid-state and liquid-core lasers. While covering a wide range of laser ...

  11. Comparison of a Ring On-Chip Network and a Code-Division Multiple-Access On-Chip Network

    Directory of Open Access Journals (Sweden)

    Xin Wang

    2007-01-01

    Full Text Available Two network-on-chip (NoC designs are examined and compared in this paper. One design applies a bidirectional ring connection scheme, while the other design applies a code-division multiple-access (CDMA connection scheme. Both of the designs apply globally asynchronous locally synchronous (GALS scheme in order to deal with the issue of transferring data in a multiple-clock-domain environment of an on-chip system. The two NoC designs are compared with each other by their network structures, data transfer principles, network node structures, and their asynchronous designs. Both the synchronous and the asynchronous designs of the two on-chip networks are realized using a hardware-description language (HDL in order to make the entire designs suit the commonly used synchronous design tools and flow. The performance estimation and comparison of the two NoC designs which are based on the HDL realizations are addressed. By comparing the two NoC designs, the advantages and disadvantages of applying direct connection and CDMA connection schemes in an on-chip communication network are discussed.

  12. Comparison of genetic detection efficiency of different markers ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-03

    Jun 3, 2009 ... Chinese native sheep populations, Hu sheep, Tong sheep, Small-tailed Han sheep and Tan sheep were used to study the efficiency of genetic markers. The genetic markers used in this study include morphological and ecological indices, blood protein enzyme, microsatellite DNA and the combination of.

  13. Prevalence and detection of psychosocial problems in cancer genetic counseling

    NARCIS (Netherlands)

    Eijzenga, W.; Bleiker, E.M.A.; Hahn, D.E.E.; van der Kolk, L.E.; Sidharta, G.N.; Aaronson, N.K.

    2015-01-01

    Only a minority of individuals who undergo cancer genetic counseling experience heightened levels of psychological distress, but many more experience a range of cancer genetic-specific psychosocial problems. The aim of this study was to estimate the prevalence of such psychosocial problems, and to

  14. On-chip spectroscopy with thermally tuned high-Q photonic crystal cavities

    Energy Technology Data Exchange (ETDEWEB)

    Liapis, Andreas C., E-mail: andreas.liapis@gmail.com; Gao, Boshen; Siddiqui, Mahmudur R. [The Institute of Optics, University of Rochester, Rochester, New York 14627 (United States); Shi, Zhimin [Department of Physics, University of South Florida, Tampa, Florida 33620 (United States); Boyd, Robert W. [The Institute of Optics, University of Rochester, Rochester, New York 14627 (United States); Department of Physics and School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa, Ontario K1N 6N5 (Canada)

    2016-01-11

    Spectroscopic methods are a sensitive way to determine the chemical composition of potentially hazardous materials. Here, we demonstrate that thermally tuned high-Q photonic crystal cavities can be used as a compact high-resolution on-chip spectrometer. We have used such a chip-scale spectrometer to measure the absorption spectra of both acetylene and hydrogen cyanide in the 1550 nm spectral band and show that we can discriminate between the two chemical species even though the two materials have spectral features in the same spectral region. Our results pave the way for the development of chip-size chemical sensors that can detect toxic substances.

  15. On-chip immunoelectrophoresis of extracellular vesicles released from human breast cancer cells.

    Directory of Open Access Journals (Sweden)

    Takanori Akagi

    Full Text Available Extracellular vesicles (EVs including exosomes and microvesicles have attracted considerable attention in the fields of cell biology and medicine. For a better understanding of EVs and further exploration of their applications, the development of analytical methods for biological nanovesicles has been required. In particular, considering the heterogeneity of EVs, methods capable of measuring individual vesicles are desired. Here, we report that on-chip immunoelectrophoresis can provide a useful method for the differential protein expression profiling of individual EVs. Electrophoresis experiments were performed on EVs collected from the culture supernatant of MDA-MB-231 human breast cancer cells using a measurement platform comprising a microcapillary electrophoresis chip and a laser dark-field microimaging system. The zeta potential distribution of EVs that reacted with an anti-human CD63 (exosome and microvesicle marker antibody showed a marked positive shift as compared with that for the normal immunoglobulin G (IgG isotype control. Thus, on-chip immunoelectrophoresis could sensitively detect the over-expression of CD63 glycoproteins on EVs. Moreover, to explore the applicability of on-chip immunoelectrophoresis to cancer diagnosis, EVs collected from the blood of a mouse tumor model were analyzed by this method. By comparing the zeta potential distributions of EVs after their immunochemical reaction with normal IgG, and the anti-human CD63 and anti-human CD44 (cancer stem cell marker antibodies, EVs of tumor origin circulating in blood were differentially detected in the real sample. The result indicates that the present method is potentially applicable to liquid biopsy, a promising approach to the low-invasive diagnosis of cancer.

  16. Priming nanoparticle-guided diagnostics and therapeutics towards human organs-on-chips microphysiological system

    Science.gov (United States)

    Choi, Jin-Ha; Lee, Jaewon; Shin, Woojung; Choi, Jeong-Woo; Kim, Hyun Jung

    2016-10-01

    Nanotechnology and bioengineering have converged over the past decades, by which the application of multi-functional nanoparticles (NPs) has been emerged in clinical and biomedical fields. The NPs primed to detect disease-specific biomarkers or to deliver biopharmaceutical compounds have beena validated in conventional in vitro culture models including two dimensional (2D) cell cultures or 3D organoid models. However, a lack of experimental models that have strong human physiological relevance has hampered accurate validation of the safety and functionality of NPs. Alternatively, biomimetic human "Organs-on-Chips" microphysiological systems have recapitulated the mechanically dynamic 3D tissue interface of human organ microenvironment, in which the transport, cytotoxicity, biocompatibility, and therapeutic efficacy of NPs and their conjugates may be more accurately validated. Finally, integration of NP-guided diagnostic detection and targeted nanotherapeutics in conjunction with human organs-on-chips can provide a novel avenue to accelerate the NP-based drug development process as well as the rapid detection of cellular secretomes associated with pathophysiological processes.

  17. Rapid detection of genetic modification for GMO monitoring in agriculture

    Directory of Open Access Journals (Sweden)

    Petrović Sofija

    2015-01-01

    Full Text Available Transgenic technology has expanded the ways of new genetic variability creation. Genetically modified organisms (GMOs are organisms which total genome is altered in a way that could not happen in nature. GM crops recorded a steady increase in its share in agricultural production. However, for the most part, GMO in agriculture has been limited to two cultivars - soy and corn, and the two genetic modifications, the total herbicide resistance and pest of the Lepidoptera genus. In order to monitor cultivation and trade of GMOs, tests of different precision are used, qualitatively and/or quantitatively determining the presence of genetic modification. Tests for the rapid determination of the presence of GM are suitable, since they can be implemented quickly and accurately, in terms of declared sensitivity, outside or in the laboratory. The example of the use of rapid tests demonstrates their value in use for rapid and efficient monitoring.

  18. On-chip Mach-Zehnder interferometer for OCT systems

    Science.gov (United States)

    van Leeuwen, Ton G.; Akca, Imran B.; Angelou, Nikolaos; Weiss, Nicolas; Hoekman, Marcel; Leinse, Arne; Heideman, Rene G.

    2018-04-01

    By using integrated optics, it is possible to reduce the size and cost of a bulky optical coherence tomography (OCT) system. One of the OCT components that can be implemented on-chip is the interferometer. In this work, we present the design and characterization of a Mach-Zehnder interferometer consisting of the wavelength-independent splitters and an on-chip reference arm. The Si3N4 was chosen as the material platform as it can provide low losses while keeping the device size small. The device was characterized by using a home-built swept source OCT system. A sensitivity value of 83 dB, an axial resolution of 15.2 μm (in air) and a depth range of 2.5 mm (in air) were all obtained.

  19. On-chip dual comb source for spectroscopy

    OpenAIRE

    Dutt, Avik; Joshi, Chaitanya; Ji, Xingchen; Cardenas, Jaime; Okawachi, Yoshitomo; Luke, Kevin; Gaeta, Alexander L.; Lipson, Michal

    2016-01-01

    Dual-comb spectroscopy is a powerful technique for real-time, broadband optical sampling of molecular spectra which requires no moving components. Recent developments with microresonator-based platforms have enabled frequency combs at the chip scale. However, the need to precisely match the resonance wavelengths of distinct high-quality-factor microcavities has hindered the development of an on-chip dual comb source. Here, we report the first simultaneous generation of two microresonator comb...

  20. On-chip microsystems in silicon: opportunities and limitations

    Science.gov (United States)

    Wolffenbuttel, R. F.

    1996-03-01

    Integrated on-chip micro-instrumentation systems in silicon are complete data acquisition systems on a single chip. This concept has appeared to be the ultimate solution in many applications, as it enables in principle the metamorphosis of a basic sensing element, affected with many shortcomings, into an on-chip data acquisition unit that provides an output digital data stream in a standard format not corrupted by sensor non-idealities. Market acceptance would be maximum, as no special knowledge about the internal operation is required, self-test and self-calibration can be included and the dimensions are not different from those of the integrated circuit. The various aspects that are relevant in estimating the constraints for successful implementation of the integrated silicon smart sensor will be outlined in comparison with the properties of more conventional sensor fabrication technologies. It will be shown that the acceptance of on-chip functional integration in an application depends primarily on the added value in terms of improved specification or functionality that the resulting device provides in that application. The economic viability is therefore decisive rather than the technological constraints. This is in contrast to the traditional technology push prevailing in sensor research over market pull mechanisms.

  1. An Energy-Efficient Reconfigurable Circuit Switched Network-on-Chip

    NARCIS (Netherlands)

    Wolkotte, P.T.; Smit, Gerardus Johannes Maria; Rauwerda, G.K.; Smit, L.T.

    Network-on-Chip (NoC) is an energy-efficient on-chip communication architecture for multi-tile System-on-Chip (SoC) architectures. The SoC architecture, including its run-time software, can replace inflexible ASICs for future ambient systems. These ambient systems have to be flexible as well as

  2. Microfluidic organ-on-chip technology for blood-brain barrier research

    NARCIS (Netherlands)

    van der Helm, Marieke Willemijn; van der Meer, Andries Dirk; Eijkel, Jan C.T.; van den Berg, Albert; Segerink, Loes Irene

    2016-01-01

    Organs-on-chips are a new class of microengineered laboratory models that combine several of the advantages of current in vivo and in vitro models. In this review, we summarize the advances that have been made in the development of organ-on-chip models of the blood-brain barrier (BBBs-on-chips) and

  3. An FPGA design flow for reconfigurable network-based multi-processor systems on chip

    NARCIS (Netherlands)

    Kumar, A.; Hansson, M.A; Huisken, J.; Corporaal, H.

    2007-01-01

    Multi-processor systems on chip (MPSoC) platforms are becoming increasingly more heterogeneous and are shifting towards a more communication-centric methodology. Networks on chip (NoC) have emerged as the design paradigm for scalable on-chip communication architectures. As the system complexity

  4. Prevalence and detection of psychosocial problems in cancer genetic counseling.

    Science.gov (United States)

    Eijzenga, W; Bleiker, E M A; Hahn, D E E; Van der Kolk, L E; Sidharta, G N; Aaronson, N K

    2015-12-01

    Only a minority of individuals who undergo cancer genetic counseling experience heightened levels of psychological distress, but many more experience a range of cancer genetic-specific psychosocial problems. The aim of this study was to estimate the prevalence of such psychosocial problems, and to identify possible demographic and clinical variables associated significantly with them. Consenting individuals scheduled to undergo cancer genetic counseling completed the Psychosocial Aspects of Hereditary Cancer (PAHC) questionnaire, the Hospital Anxiety and Depression Scale (HADS) and the Distress Thermometer (DT) prior to or immediately following their counseling session. More than half of the 137 participants reported problems on three or more domains of the PAHC, most often in the domains 'living with cancer' (84%), 'family issues' (46%), 'hereditary predisposition' (45%), and 'child-related issues' (42%). Correlations between the PAHC, the HADS and the DT were low. Previous contact with a psychosocial worker, and having a personal history of cancer were associated significantly with HADS scores, but explained little variance (9%). No background variables were associated significantly with the DT. Previous contact with a psychosocial worker, and having children were significantly associated with several PAHC domains, again explaining only a small percentage of the variance (2-14%). The majority of counselees experience specific cancer genetic counseling-related psychosocial problems. Only a few background variables are associated significantly with distress or psychosocial problems. Thus we recommend using the PAHC or a similar problem-oriented questionnaire routinely in cancer genetic counseling to identify individuals with such problems.

  5. Molecular profiling techniques as tools to detect potential unintended effects in genetically engineered maize

    CSIR Research Space (South Africa)

    Barros, E

    2010-05-01

    Full Text Available Molecular Profiling Techniques as Tools to Detect Potential Unintended Effects in Genetically Engineered Maize Eugenia Barros Introduction In the early stages of production and commercialization of foods derived from genetically engineered (GE) plants... systems. In a recent paper published in Plant Biotechnology Journal,4 we compared two transgenic white maize lines with the non-transgenic counterpart to investigate two possible sources of variation: genetic engineering and environmental variation...

  6. High-performance, scalable optical network-on-chip architectures

    Science.gov (United States)

    Tan, Xianfang

    The rapid advance of technology enables a large number of processing cores to be integrated into a single chip which is called a Chip Multiprocessor (CMP) or a Multiprocessor System-on-Chip (MPSoC) design. The on-chip interconnection network, which is the communication infrastructure for these processing cores, plays a central role in a many-core system. With the continuously increasing complexity of many-core systems, traditional metallic wired electronic networks-on-chip (NoC) became a bottleneck because of the unbearable latency in data transmission and extremely high energy consumption on chip. Optical networks-on-chip (ONoC) has been proposed as a promising alternative paradigm for electronic NoC with the benefits of optical signaling communication such as extremely high bandwidth, negligible latency, and low power consumption. This dissertation focus on the design of high-performance and scalable ONoC architectures and the contributions are highlighted as follow: 1. A micro-ring resonator (MRR)-based Generic Wavelength-routed Optical Router (GWOR) is proposed. A method for developing any sized GWOR is introduced. GWOR is a scalable non-blocking ONoC architecture with simple structure, low cost and high power efficiency compared to existing ONoC designs. 2. To expand the bandwidth and improve the fault tolerance of the GWOR, a redundant GWOR architecture is designed by cascading different type of GWORs into one network. 3. The redundant GWOR built with MRR-based comb switches is proposed. Comb switches can expand the bandwidth while keep the topology of GWOR unchanged by replacing the general MRRs with comb switches. 4. A butterfly fat tree (BFT)-based hybrid optoelectronic NoC (HONoC) architecture is developed in which GWORs are used for global communication and electronic routers are used for local communication. The proposed HONoC uses less numbers of electronic routers and links than its counterpart of electronic BFT-based NoC. It takes the advantages of

  7. Counselling considerations for chromosomal mosaicism detected by preimplantation genetic screening.

    Science.gov (United States)

    Besser, Andria G; Mounts, Emily L

    2017-04-01

    The evolution of preimplantation genetic screening (PGS) for aneuploidy to blastocyst biopsy and more sensitive 24-chromosome screening techniques has resulted in a new diagnostic category of PGS results: those classified as mosaic. This diagnosis presents significant challenges for clinicians in developing policies regarding transfer and storage of such embryos, as well as in providing genetic counselling for patients prior to and following PGS. Given the high frequency of mosaic PGS results and the wide range of possible associated outcomes, there is an urgent need to understand how to appropriately counsel patients regarding such embryos. This is the first commentary to thoroughly address pre- and post-test genetic counselling recommendations, as well as considerations regarding prenatal screening and diagnosis. Current data on mosaic PGS results are summarized along with embryo selection considerations and potential outcomes of embryos diagnosed as mosaic. Copyright © 2017 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  8. [Genetically modified organisms in food--production, detection and risks].

    Science.gov (United States)

    Zeljezić, Davor

    2004-11-01

    The first genetically modified plant (GMP) was a tobacco resistant to antibiotics in 1983. In 1996, the first genetically altered crop, a delayed-ripening tomato was commercially released. In the year 2003, the estimated global area of GM crops for was 67.7 million hectares. To produce such a plant a gene of interest has to be isolated from the donor. Together with a promoter, terminator sequence and marker gene it has to be introduced into the plant cell which is then stimulated to generate a whole GMP expressing new characteristics (herbicide/insect resistance, delayed ripening). The last few months have seen a strong public debate over genetically modified organisms which has raised scientific, economic, political, and ethical issues. Some questions concerning the safety of GMPs are still to be answered, and decisions about their future should be based on scientifically validated information.

  9. 60 GHz system-on-chip (SoC) with built-in memory and an on-chip antenna

    KAUST Repository

    Ghaffar, Farhan A.; Arsalan, Muhammad; Cheema, Hammad; Salama, Khaled N.; Shamim, Atif

    2014-01-01

    A novel 60 GHz transmitter SoC with an on-chip antenna and integrated memory in CMOS 65 nm technology is presented in this paper. This highly integrated transmitter design can support a data rate of 2 GBPS with a transmission range of 1 m. The transmitter consists of a fundamental frequency 60 GHz PLL which covers the complete ISM band. The modulator following the PLL can support both BPSK and OOK modulation schemes. Both stored data on the integrated memory or directly from an external source can be transmitted. A tapered slot on chip antenna is integrated with the power amplifier to complete the front end of the transmitter design. Size of the complete transmitter with on-chip antenna is only 1.96 mm × 1.96 mm. The core circuits consume less than 100 mW of power. The high data rate capability of the design makes it extremely suitable for bandwidth hungry applications such as unencrypted HD video streaming and transmission.

  10. 60 GHz system-on-chip (SoC) with built-in memory and an on-chip antenna

    KAUST Repository

    Ghaffar, Farhan A.

    2014-04-01

    A novel 60 GHz transmitter SoC with an on-chip antenna and integrated memory in CMOS 65 nm technology is presented in this paper. This highly integrated transmitter design can support a data rate of 2 GBPS with a transmission range of 1 m. The transmitter consists of a fundamental frequency 60 GHz PLL which covers the complete ISM band. The modulator following the PLL can support both BPSK and OOK modulation schemes. Both stored data on the integrated memory or directly from an external source can be transmitted. A tapered slot on chip antenna is integrated with the power amplifier to complete the front end of the transmitter design. Size of the complete transmitter with on-chip antenna is only 1.96 mm × 1.96 mm. The core circuits consume less than 100 mW of power. The high data rate capability of the design makes it extremely suitable for bandwidth hungry applications such as unencrypted HD video streaming and transmission.

  11. On-chip, photon-number-resolving, telecommunication-band detectors for scalable photonic information processing

    Energy Technology Data Exchange (ETDEWEB)

    Gerrits, Thomas; Lita, Adriana E.; Calkins, Brice; Tomlin, Nathan A.; Fox, Anna E.; Linares, Antia Lamas; Mirin, Richard P.; Nam, Sae Woo [National Institute of Standards and Technology, Boulder, Colorado, 80305 (United States); Thomas-Peter, Nicholas; Metcalf, Benjamin J.; Spring, Justin B.; Langford, Nathan K.; Walmsley, Ian A. [Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU (United Kingdom); Gates, James C.; Smith, Peter G. R. [Optoelectronics Research Centre, University of Southampton, Highfield SO17 1BJ (United Kingdom)

    2011-12-15

    Integration is currently the only feasible route toward scalable photonic quantum processing devices that are sufficiently complex to be genuinely useful in computing, metrology, and simulation. Embedded on-chip detection will be critical to such devices. We demonstrate an integrated photon-number-resolving detector, operating in the telecom band at 1550 nm, employing an evanescently coupled design that allows it to be placed at arbitrary locations within a planar circuit. Up to five photons are resolved in the guided optical mode via absorption from the evanescent field into a tungsten transition-edge sensor. The detection efficiency is 7.2{+-}0.5 %. The polarization sensitivity of the detector is also demonstrated. Detailed modeling of device designs shows a clear and feasible route to reaching high detection efficiencies.

  12. Techniques for detecting genetically modified crops and products ...

    African Journals Online (AJOL)

    The cultivation of genetically modified crops is becoming increasingly important; more traits are emerging and more acres than ever before are being planted with GM varieties. The release of GM crops and products in the markets worldwide has increased the regulatory need to monitor and verify the presence and the ...

  13. Comparing genetic variants detected in the 1000 genomes project ...

    Indian Academy of Sciences (India)

    2015-12-11

    Dec 11, 2015 ... three key benefits: better diagnoses and earlier interven- tions, more ... research field in human genetics and personalized medicine. Based on the ... to amino acid changes and were found associated with breast .... were common between two datasets or unique SNPs if they were found only in one dataset.

  14. A VLSI System-on-Chip for Particle Detectors

    CERN Document Server

    AUTHOR|(CDS)2078019

    In this thesis I present a System-on-Chip (SoC) I designed to oer a self- contained, compact data acquisition platform for micromegas detector mon- itoring. I carried on my work within the RD-51 collab oration of CERN. With a companion ADC, my architecture is capable to acquire the signal from a detector electro de, pro cess the data and p erform monitoring tests. The SoC is built around on a custom 8-bit micropro cessor with internal mem- ory resources and emb eds the p eripherals to b e interf...

  15. Custom Topology Generation for Network-on-Chip

    DEFF Research Database (Denmark)

    Stuart, Matthias Bo; Sparsø, Jens

    2007-01-01

    This paper compares simulated annealing and tabu search for generating custom topologies for applications with periodic behaviour executing on a network-on-chip. The approach differs from previous work by starting from a fixed mapping of IP-cores to routers and performing design space exploration...... around an initial topology. The tabu search has been modified from its normally encountered form to allow easier escaping from local minima. A number of synthetic benchmarks are used for tuning the parameters of both heuristics and for testing the quality of the solutions each heuristic produces...

  16. On-chip photonic interconnects a computer architect's perspective

    CERN Document Server

    Nitta, Christopher J; Akella, Venkatesh

    2013-01-01

    As the number of cores on a chip continues to climb, architects will need to address both bandwidth and power consumption issues related to the interconnection network. Electrical interconnects are not likely to scale well to a large number of processors for energy efficiency reasons, and the problem is compounded by the fact that there is a fixed total power budget for a die, dictated by the amount of heat that can be dissipated without special (and expensive) cooling and packaging techniques. Thus, there is a need to seek alternatives to electrical signaling for on-chip interconnection appli

  17. A Time-predictable Memory Network-on-Chip

    DEFF Research Database (Denmark)

    Schoeberl, Martin; Chong, David VH; Puffitsch, Wolfgang

    2014-01-01

    To derive safe bounds on worst-case execution times (WCETs), all components of a computer system need to be time-predictable: the processor pipeline, the caches, the memory controller, and memory arbitration on a multicore processor. This paper presents a solution for time-predictable memory...... arbitration and access for chip-multiprocessors. The memory network-on-chip is organized as a tree with time-division multiplexing (TDM) of accesses to the shared memory. The TDM based arbitration completely decouples processor cores and allows WCET analysis of the memory accesses on individual cores without...

  18. Multicore systems on-chip practical software/hardware design

    CERN Document Server

    Abdallah, Abderazek Ben

    2013-01-01

    System on chips designs have evolved from fairly simple unicore, single memory designs to complex heterogeneous multicore SoC architectures consisting of a large number of IP blocks on the same silicon. To meet high computational demands posed by latest consumer electronic devices, most current systems are based on such paradigm, which represents a real revolution in many aspects in computing.The attraction of multicore processing for power reduction is compelling. By splitting a set of tasks among multiple processor cores, the operating frequency necessary for each core can be reduced, allowi

  19. System on chip module configured for event-driven architecture

    Science.gov (United States)

    Robbins, Kevin; Brady, Charles E.; Ashlock, Tad A.

    2017-10-17

    A system on chip (SoC) module is described herein, wherein the SoC modules comprise a processor subsystem and a hardware logic subsystem. The processor subsystem and hardware logic subsystem are in communication with one another, and transmit event messages between one another. The processor subsystem executes software actors, while the hardware logic subsystem includes hardware actors, the software actors and hardware actors conform to an event-driven architecture, such that the software actors receive and generate event messages and the hardware actors receive and generate event messages.

  20. Advancing Software Development for a Multiprocessor System-on-Chip

    Directory of Open Access Journals (Sweden)

    Stephen Bique

    2007-06-01

    Full Text Available A low-level language is the right tool to develop applications for some embedded systems. Notwithstanding, a high-level language provides a proper environment to develop the programming tools. The target device is a system-on-chip consisting of an array of processors with only local communication. Applications include typical streaming applications for digital signal processing. We describe the hardware model and stress the advantages of a flexible device. We introduce IDEA, a graphical integrated development environment for an array. A proper foundation for software development is a UML and standard programming abstractions in object-oriented languages.

  1. Computational On-Chip Imaging of Nanoparticles and Biomolecules using Ultraviolet Light

    KAUST Repository

    Daloglu, Mustafa Ugur

    2017-03-09

    Significant progress in characterization of nanoparticles and biomolecules was enabled by the development of advanced imaging equipment with extreme spatial-resolution and sensitivity. To perform some of these analyses outside of well-resourced laboratories, it is necessary to create robust and cost-effective alternatives to existing high-end laboratory-bound imaging and sensing equipment. Towards this aim, we have designed a holographic on-chip microscope operating at an ultraviolet illumination wavelength (UV) of 266 nm. The increased forward scattering from nanoscale objects at this short wavelength has enabled us to detect individual sub-30 nm nanoparticles over a large field-of-view of >16 mm2 using an on-chip imaging platform, where the sample is placed at ≤0.5 mm away from the active area of an opto-electronic sensor-array, without any lenses in between. The strong absorption of this UV wavelength by biomolecules including nucleic acids and proteins has further enabled high-contrast imaging of nanoscopic aggregates of biomolecules, e.g., of enzyme Cu/Zn-superoxide dismutase, abnormal aggregation of which is linked to amyotrophic lateral sclerosis (ALS) - a fatal neurodegenerative disease. This UV-based wide-field computational imaging platform could be valuable for numerous applications in biomedical sciences and environmental monitoring, including disease diagnostics, viral load measurements as well as air- and water-quality assessment.

  2. High throughput on-chip analysis of high-energy charged particle tracks using lensfree imaging

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Wei; Shabbir, Faizan; Gong, Chao; Gulec, Cagatay; Pigeon, Jeremy; Shaw, Jessica; Greenbaum, Alon; Tochitsky, Sergei; Joshi, Chandrashekhar [Electrical Engineering Department, University of California, Los Angeles, California 90095 (United States); Ozcan, Aydogan, E-mail: ozcan@ucla.edu [Electrical Engineering Department, University of California, Los Angeles, California 90095 (United States); Bioengineering Department, University of California, Los Angeles, California 90095 (United States); California NanoSystems Institute (CNSI), University of California, Los Angeles, California 90095 (United States)

    2015-04-13

    We demonstrate a high-throughput charged particle analysis platform, which is based on lensfree on-chip microscopy for rapid ion track analysis using allyl diglycol carbonate, i.e., CR-39 plastic polymer as the sensing medium. By adopting a wide-area opto-electronic image sensor together with a source-shifting based pixel super-resolution technique, a large CR-39 sample volume (i.e., 4 cm × 4 cm × 0.1 cm) can be imaged in less than 1 min using a compact lensfree on-chip microscope, which detects partially coherent in-line holograms of the ion tracks recorded within the CR-39 detector. After the image capture, using highly parallelized reconstruction and ion track analysis algorithms running on graphics processing units, we reconstruct and analyze the entire volume of a CR-39 detector within ∼1.5 min. This significant reduction in the entire imaging and ion track analysis time not only increases our throughput but also allows us to perform time-resolved analysis of the etching process to monitor and optimize the growth of ion tracks during etching. This computational lensfree imaging platform can provide a much higher throughput and more cost-effective alternative to traditional lens-based scanning optical microscopes for ion track analysis using CR-39 and other passive high energy particle detectors.

  3. Laser Doppler Blood Flow Imaging Using a CMOS Imaging Sensor with On-Chip Signal Processing

    Directory of Open Access Journals (Sweden)

    Cally Gill

    2013-09-01

    Full Text Available The first fully integrated 2D CMOS imaging sensor with on-chip signal processing for applications in laser Doppler blood flow (LDBF imaging has been designed and tested. To obtain a space efficient design over 64 × 64 pixels means that standard processing electronics used off-chip cannot be implemented. Therefore the analog signal processing at each pixel is a tailored design for LDBF signals with balanced optimization for signal-to-noise ratio and silicon area. This custom made sensor offers key advantages over conventional sensors, viz. the analog signal processing at the pixel level carries out signal normalization; the AC amplification in combination with an anti-aliasing filter allows analog-to-digital conversion with a low number of bits; low resource implementation of the digital processor enables on-chip processing and the data bottleneck that exists between the detector and processing electronics has been overcome. The sensor demonstrates good agreement with simulation at each design stage. The measured optical performance of the sensor is demonstrated using modulated light signals and in vivo blood flow experiments. Images showing blood flow changes with arterial occlusion and an inflammatory response to a histamine skin-prick demonstrate that the sensor array is capable of detecting blood flow signals from tissue.

  4. Computational On-Chip Imaging of Nanoparticles and Biomolecules using Ultraviolet Light.

    Science.gov (United States)

    Daloglu, Mustafa Ugur; Ray, Aniruddha; Gorocs, Zoltan; Xiong, Matthew; Malik, Ravinder; Bitan, Gal; McLeod, Euan; Ozcan, Aydogan

    2017-03-09

    Significant progress in characterization of nanoparticles and biomolecules was enabled by the development of advanced imaging equipment with extreme spatial-resolution and sensitivity. To perform some of these analyses outside of well-resourced laboratories, it is necessary to create robust and cost-effective alternatives to existing high-end laboratory-bound imaging and sensing equipment. Towards this aim, we have designed a holographic on-chip microscope operating at an ultraviolet illumination wavelength (UV) of 266 nm. The increased forward scattering from nanoscale objects at this short wavelength has enabled us to detect individual sub-30 nm nanoparticles over a large field-of-view of >16 mm 2 using an on-chip imaging platform, where the sample is placed at ≤0.5 mm away from the active area of an opto-electronic sensor-array, without any lenses in between. The strong absorption of this UV wavelength by biomolecules including nucleic acids and proteins has further enabled high-contrast imaging of nanoscopic aggregates of biomolecules, e.g., of enzyme Cu/Zn-superoxide dismutase, abnormal aggregation of which is linked to amyotrophic lateral sclerosis (ALS) - a fatal neurodegenerative disease. This UV-based wide-field computational imaging platform could be valuable for numerous applications in biomedical sciences and environmental monitoring, including disease diagnostics, viral load measurements as well as air- and water-quality assessment.

  5. On-chip real-time single-copy polymerase chain reaction in picoliter droplets

    Energy Technology Data Exchange (ETDEWEB)

    Beer, N R; Hindson, B; Wheeler, E; Hall, S B; Rose, K A; Kennedy, I; Colston, B

    2007-04-20

    The first lab-on-chip system for picoliter droplet generation and PCR amplification with real-time fluorescence detection has performed PCR in isolated droplets at volumes 10{sup 6} smaller than commercial real-time PCR systems. The system utilized a shearing T-junction in a silicon device to generate a stream of monodisperse picoliter droplets that were isolated from the microfluidic channel walls and each other by the oil phase carrier. An off-chip valving system stopped the droplets on-chip, allowing them to be thermal cycled through the PCR protocol without droplet motion. With this system a 10-pL droplet, encapsulating less than one copy of viral genomic DNA through Poisson statistics, showed real-time PCR amplification curves with a cycle threshold of {approx}18, twenty cycles earlier than commercial instruments. This combination of the established real-time PCR assay with digital microfluidics is ideal for isolating single-copy nucleic acids in a complex environment.

  6. Laser doppler blood flow imaging using a CMOS imaging sensor with on-chip signal processing.

    Science.gov (United States)

    He, Diwei; Nguyen, Hoang C; Hayes-Gill, Barrie R; Zhu, Yiqun; Crowe, John A; Gill, Cally; Clough, Geraldine F; Morgan, Stephen P

    2013-09-18

    The first fully integrated 2D CMOS imaging sensor with on-chip signal processing for applications in laser Doppler blood flow (LDBF) imaging has been designed and tested. To obtain a space efficient design over 64 × 64 pixels means that standard processing electronics used off-chip cannot be implemented. Therefore the analog signal processing at each pixel is a tailored design for LDBF signals with balanced optimization for signal-to-noise ratio and silicon area. This custom made sensor offers key advantages over conventional sensors, viz. the analog signal processing at the pixel level carries out signal normalization; the AC amplification in combination with an anti-aliasing filter allows analog-to-digital conversion with a low number of bits; low resource implementation of the digital processor enables on-chip processing and the data bottleneck that exists between the detector and processing electronics has been overcome. The sensor demonstrates good agreement with simulation at each design stage. The measured optical performance of the sensor is demonstrated using modulated light signals and in vivo blood flow experiments. Images showing blood flow changes with arterial occlusion and an inflammatory response to a histamine skin-prick demonstrate that the sensor array is capable of detecting blood flow signals from tissue.

  7. Diatomite Photonic Crystals for Facile On-Chip Chromatography and Sensing of Harmful Ingredients from Food.

    Science.gov (United States)

    Kong, Xianming; Yu, Qian; Li, Erwen; Wang, Rui; Liu, Qing; Wang, Alan X

    2018-03-31

    Diatomaceous earth-otherwise called diatomite-is essentially composed of hydrated biosilica with periodic nanopores. Diatomite is derived from fossilized remains of diatom frustules and possesses photonic-crystal features. In this paper, diatomite simultaneously functions as the matrix of the chromatography plate and the substrate for surface-enhanced Raman scattering (SERS), by which the photonic crystal-features could enhance the optical field intensity. The on-chip separation performance of the device was confirmed by separating and detecting industrial dye (Sudan I) in an artificial aqueous mixture containing 4-mercaptobenzoic acid (MBA), where concentrated plasmonic Au colloid was casted onto the analyte spot for SERS measurement. The plasmonic-photonic hybrid mode between the Au nanoparticles (NP) and the diatomite layer could supply nearly 10 times the increment of SERS signal (MBA) intensity compared to the common silica gel chromatography plate. Furthermore, this lab-on-a-chip photonic crystal device was employed for food safety sensing in real samples and successfully monitored histamine in salmon and tuna. This on-chip food sensor can be used as a cheap, robust, and portable sensing platform for monitoring for histamine or other harmful ingredients at trace levels in food products.

  8. Diatomite Photonic Crystals for Facile On-Chip Chromatography and Sensing of Harmful Ingredients from Food

    Directory of Open Access Journals (Sweden)

    Xianming Kong

    2018-03-01

    Full Text Available Diatomaceous earth—otherwise called diatomite—is essentially composed of hydrated biosilica with periodic nanopores. Diatomite is derived from fossilized remains of diatom frustules and possesses photonic-crystal features. In this paper, diatomite simultaneously functions as the matrix of the chromatography plate and the substrate for surface-enhanced Raman scattering (SERS, by which the photonic crystal-features could enhance the optical field intensity. The on-chip separation performance of the device was confirmed by separating and detecting industrial dye (Sudan I in an artificial aqueous mixture containing 4-mercaptobenzoic acid (MBA, where concentrated plasmonic Au colloid was casted onto the analyte spot for SERS measurement. The plasmonic-photonic hybrid mode between the Au nanoparticles (NP and the diatomite layer could supply nearly 10 times the increment of SERS signal (MBA intensity compared to the common silica gel chromatography plate. Furthermore, this lab-on-a-chip photonic crystal device was employed for food safety sensing in real samples and successfully monitored histamine in salmon and tuna. This on-chip food sensor can be used as a cheap, robust, and portable sensing platform for monitoring for histamine or other harmful ingredients at trace levels in food products.

  9. Genetic basis and detection of unintended effects in genetically modified crop plants

    NARCIS (Netherlands)

    Ladics, G.S.; Bartholomaeus, A.; Bregitzer, P.; Doerrer, N.G.; Gray, A.; Holzhauzer, T.; Jordan, M.; Keese, P.; Kok, E.J.; Macdonald, P.; Parrott, W.; Privalle, L.; Raybould, A.; Rhee, S.Y.; Rice, E.; Romeis, J.; Vaughn, J.; Wal, J.M.; Glenn, K.

    2015-01-01

    In January 2014, an international meeting sponsored by the International Life Sciences Institute/Health and Environmental Sciences Institute and the Canadian Food Inspection Agency titled “Genetic Basis of Unintended Effects in Modified Plants” was held in Ottawa, Canada, bringing together over 75

  10. Detection and traceability of genetically modified organisms in the food production chain.

    Science.gov (United States)

    Miraglia, M; Berdal, K G; Brera, C; Corbisier, P; Holst-Jensen, A; Kok, E J; Marvin, H J P; Schimmel, H; Rentsch, J; van Rie, J P P F; Zagon, J

    2004-07-01

    Both labelling and traceability of genetically modified organisms are current issues that are considered in trade and regulation. Currently, labelling of genetically modified foods containing detectable transgenic material is required by EU legislation. A proposed package of legislation would extend this labelling to foods without any traces of transgenics. These new legislations would also impose labelling and a traceability system based on documentation throughout the food and feed manufacture system. The regulatory issues of risk analysis and labelling are currently harmonised by Codex Alimentarius. The implementation and maintenance of the regulations necessitates sampling protocols and analytical methodologies that allow for accurate determination of the content of genetically modified organisms within a food and feed sample. Current methodologies for the analysis of genetically modified organisms are focused on either one of two targets, the transgenic DNA inserted- or the novel protein(s) expressed- in a genetically modified product. For most DNA-based detection methods, the polymerase chain reaction is employed. Items that need consideration in the use of DNA-based detection methods include the specificity, sensitivity, matrix effects, internal reference DNA, availability of external reference materials, hemizygosity versus homozygosity, extrachromosomal DNA, and international harmonisation. For most protein-based methods, enzyme-linked immunosorbent assays with antibodies binding the novel protein are employed. Consideration should be given to the selection of the antigen bound by the antibody, accuracy, validation, and matrix effects. Currently, validation of detection methods for analysis of genetically modified organisms is taking place. In addition, new methodologies are developed, including the use of microarrays, mass spectrometry, and surface plasmon resonance. Challenges for GMO detection include the detection of transgenic material in materials

  11. Self-powered integrated systems-on-chip (energy chip)

    KAUST Repository

    Hussain, Muhammad Mustafa

    2010-04-23

    In today\\'s world, consumer driven technology wants more portable electronic gadgets to be developed, and the next big thing in line is self-powered handheld devices. Therefore to reduce the power consumption as well as to supply sufficient power to run those devices, several critical technical challenges need to be overcome: a. Nanofabrication of macro/micro systems which incorporates the direct benefit of light weight (thus portability), low power consumption, faster response, higher sensitivity and batch production (low cost). b. Integration of advanced nano-materials to meet the performance/cost benefit trend. Nano-materials may offer new functionalities that were previously underutilized in the macro/micro dimension. c. Energy efficiency to reduce power consumption and to supply enough power to meet that low power demand. We present a pragmatic perspective on a self-powered integrated System on Chip (SoC). We envision the integrated device will have two objectives: low power consumption/dissipation and on-chip power generation for implementation into handheld or remote technologies for defense, space, harsh environments and medical applications. This paper provides insight on materials choices, intelligent circuit design, and CMOS compatible integration.

  12. 3D Printing of Organs-On-Chips

    Science.gov (United States)

    Yi, Hee-Gyeong; Lee, Hyungseok; Cho, Dong-Woo

    2017-01-01

    Organ-on-a-chip engineering aims to create artificial living organs that mimic the complex and physiological responses of real organs, in order to test drugs by precisely manipulating the cells and their microenvironments. To achieve this, the artificial organs should to be microfabricated with an extracellular matrix (ECM) and various types of cells, and should recapitulate morphogenesis, cell differentiation, and functions according to the native organ. A promising strategy is 3D printing, which precisely controls the spatial distribution and layer-by-layer assembly of cells, ECMs, and other biomaterials. Owing to this unique advantage, integration of 3D printing into organ-on-a-chip engineering can facilitate the creation of micro-organs with heterogeneity, a desired 3D cellular arrangement, tissue-specific functions, or even cyclic movement within a microfluidic device. Moreover, fully 3D-printed organs-on-chips more easily incorporate other mechanical and electrical components with the chips, and can be commercialized via automated massive production. Herein, we discuss the recent advances and the potential of 3D cell-printing technology in engineering organs-on-chips, and provides the future perspectives of this technology to establish the highly reliable and useful drug-screening platforms. PMID:28952489

  13. 3D Printing of Organs-On-Chips.

    Science.gov (United States)

    Yi, Hee-Gyeong; Lee, Hyungseok; Cho, Dong-Woo

    2017-01-25

    Organ-on-a-chip engineering aims to create artificial living organs that mimic the complex and physiological responses of real organs, in order to test drugs by precisely manipulating the cells and their microenvironments. To achieve this, the artificial organs should to be microfabricated with an extracellular matrix (ECM) and various types of cells, and should recapitulate morphogenesis, cell differentiation, and functions according to the native organ. A promising strategy is 3D printing, which precisely controls the spatial distribution and layer-by-layer assembly of cells, ECMs, and other biomaterials. Owing to this unique advantage, integration of 3D printing into organ-on-a-chip engineering can facilitate the creation of micro-organs with heterogeneity, a desired 3D cellular arrangement, tissue-specific functions, or even cyclic movement within a microfluidic device. Moreover, fully 3D-printed organs-on-chips more easily incorporate other mechanical and electrical components with the chips, and can be commercialized via automated massive production. Herein, we discuss the recent advances and the potential of 3D cell-printing technology in engineering organs-on-chips, and provides the future perspectives of this technology to establish the highly reliable and useful drug-screening platforms.

  14. 3D Printing of Organs-On-Chips

    Directory of Open Access Journals (Sweden)

    Hee-Gyeong Yi

    2017-01-01

    Full Text Available Organ-on-a-chip engineering aims to create artificial living organs that mimic the complex and physiological responses of real organs, in order to test drugs by precisely manipulating the cells and their microenvironments. To achieve this, the artificial organs should to be microfabricated with an extracellular matrix (ECM and various types of cells, and should recapitulate morphogenesis, cell differentiation, and functions according to the native organ. A promising strategy is 3D printing, which precisely controls the spatial distribution and layer-by-layer assembly of cells, ECMs, and other biomaterials. Owing to this unique advantage, integration of 3D printing into organ-on-a-chip engineering can facilitate the creation of micro-organs with heterogeneity, a desired 3D cellular arrangement, tissue-specific functions, or even cyclic movement within a microfluidic device. Moreover, fully 3D-printed organs-on-chips more easily incorporate other mechanical and electrical components with the chips, and can be commercialized via automated massive production. Herein, we discuss the recent advances and the potential of 3D cell-printing technology in engineering organs-on-chips, and provides the future perspectives of this technology to establish the highly reliable and useful drug-screening platforms.

  15. Self-powered integrated systems-on-chip (energy chip)

    Science.gov (United States)

    Hussain, M. M.; Fahad, H.; Rojas, J.; Hasan, M.; Talukdar, A.; Oommen, J.; Mink, J.

    2010-04-01

    In today's world, consumer driven technology wants more portable electronic gadgets to be developed, and the next big thing in line is self-powered handheld devices. Therefore to reduce the power consumption as well as to supply sufficient power to run those devices, several critical technical challenges need to be overcome: a. Nanofabrication of macro/micro systems which incorporates the direct benefit of light weight (thus portability), low power consumption, faster response, higher sensitivity and batch production (low cost). b. Integration of advanced nano-materials to meet the performance/cost benefit trend. Nano-materials may offer new functionalities that were previously underutilized in the macro/micro dimension. c. Energy efficiency to reduce power consumption and to supply enough power to meet that low power demand. We present a pragmatic perspective on a self-powered integrated System on Chip (SoC). We envision the integrated device will have two objectives: low power consumption/dissipation and on-chip power generation for implementation into handheld or remote technologies for defense, space, harsh environments and medical applications. This paper provides insight on materials choices, intelligent circuit design, and CMOS compatible integration.

  16. On-Chip Correlator for Passive Wireless SAW Multisensor Systems

    Directory of Open Access Journals (Sweden)

    Liqiang Xie

    2016-01-01

    Full Text Available For decoding the asynchronous superposition of response signals from different sensors, it is a challenge to achieve correlation in a code division multiplexing (CDM based passive wireless surface acoustic wave (SAW multisensor system. Therefore, an on-chip correlator scheme is developed in this paper. In contrast to conventional CDM-based systems, this novel scheme enables the correlations to be operated at the SAW sensors, instead of the reader. Thus, the response signals arriving at the reader are the result of cross-correlation on the chips. It is then easy for the reader to distinguish the sensor that is matched with the interrogating signal. The operation principle, signal analysis, and simulation of the novel scheme are described in the paper. The simulation results show the response signals from the correlations of the sensors. A clear spike pulse is presented in the response signals, when a sensor code is matched with the interrogating code. Simulations verify the feasibility of the on-chip correlator concept.

  17. On-chip enucleation of an oocyte by untethered microrobots

    International Nuclear Information System (INIS)

    Ichikawa, Akihiko; Sakuma, Shinya; Sugita, Masakuni; Shoda, Tatsuro; Tamakoshi, Takahiro; Arai, Fumihito; Akagi, Satoshi

    2014-01-01

    We propose a novel on-chip enucleation of an oocyte with zona pellucida by using a combination of untethered microrobots. To achieve enucleation within the closed space of a microfluidic chip, two microrobots, a microknife and a microgripper were integrated into the microfluidic chip. These microrobots were actuated by an external magnetic force produced by permanent magnets placed on the robotic stage. The tip of the microknife was designed by considering the biological geometric feature of an oocyte, i.e. the oocyte has a polar body in maturation stage II. Moreover, the microknife was fabricated by using grayscale lithography, which allows fabrication of three-dimensional microstructures. The microgripper has a gripping function that is independent of the driving mechanism. On-chip enucleation was demonstrated, and the enucleated oocytes are spherical, indicating that the cell membrane of the oocytes remained intact. To confirm successful enucleation using this method, we investigated the viability of oocytes after enucleation. The results show that the production rate, i.e. the ratio between the number of oocytes that reach the blastocyst stage and the number of bovine oocytes after nucleus transfer, is 100%. The technique will contribute to complex cell manipulation such as cell surgery in lab-on-a-chip devices. (paper)

  18. Variability of individual genetic load: consequences for the detection of inbreeding depression.

    Science.gov (United States)

    Restoux, Gwendal; Huot de Longchamp, Priscille; Fady, Bruno; Klein, Etienne K

    2012-03-01

    Inbreeding depression is a key factor affecting the persistence of natural populations, particularly when they are fragmented. In species with mixed mating systems, inbreeding depression can be estimated at the population level by regressing the average progeny fitness by the selfing rate of their mothers. We applied this method using simulated populations to investigate how population genetic parameters can affect the detection power of inbreeding depression. We simulated individual selfing rates and genetic loads from which we computed fitness values. The regression method yielded high statistical power, inbreeding depression being detected as significant (5 % level) in 92 % of the simulations. High individual variation in selfing rate and high mean genetic load led to better detection of inbreeding depression while high among-individual variation in genetic load made it more difficult to detect inbreeding depression. For a constant sampling effort, increasing the number of progenies while decreasing the number of individuals per progeny enhanced the detection power of inbreeding depression. We discuss the implication of among-mother variability of genetic load and selfing rate on inbreeding depression studies.

  19. An economic evaluation of second-trimester genetic ultrasonography for prenatal detection of down syndrome.

    Science.gov (United States)

    Vintzileos, A M; Ananth, C V; Fisher, A J; Smulian, J C; Day-Salvatore, D; Beazoglou, T; Knuppel, R A

    1998-11-01

    The objective of this study was to perform an economic evaluation of second-trimester genetic ultrasonography for prenatal detection of Down syndrome. More specifically, we sought to determine the following: (1) the diagnostic accuracy requirements (from the cost-benefit point of view) of genetic ultrasonography versus genetic amniocentesis for women at increased risk for fetal Down syndrome and (2) the possible economic impact of second-trimester genetic ultrasonography for the US population on the basis of the ultrasonographic accuracies reported in previously published studies. A cost-benefit equation was developed from the hypothesis that the cost of universal genetic amniocentesis of patients at increased risk for carrying a fetus with Down syndrome should be at least equal to the cost of universal genetic ultrasonography with amniocentesis used only for those with abnormal ultrasonographic results. The main components of the equation included the diagnostic accuracy of genetic ultrasonography (sensitivity and specificity for detecting Down syndrome), the costs of the amniocentesis package and genetic ultrasonography, and the lifetime cost of Down syndrome cases not detected by the genetic ultrasonography. After appropriate manipulation of the equation a graph was constructed, representing the balance between sensitivity and false-positive rate of genetic ultrasonography; this was used to examine the accuracy of previously published studies from the cost-benefit point of view. Sensitivity analyses included individual risks for Down syndrome ranging from 1:261 (risk of a 35-year-old at 18 weeks' gestation) to 1:44 (risk of a 44-year-old at 18 weeks' gestation). This economic evaluation was conducted from the societal perspective. Genetic ultrasonography was found to be economically beneficial only if the overall sensitivity for detecting Down syndrome was >74%. Even then, the cost-benefit ratio depended on the corresponding false-positive rate. Of the 7

  20. Pulse Detecting Genetic Circuit – A New Design Approach

    Science.gov (United States)

    Inniss, Mara; Iba, Hitoshi; Way, Jeffrey C.

    2016-01-01

    A robust cellular counter could enable synthetic biologists to design complex circuits with diverse behaviors. The existing synthetic-biological counters, responsive to the beginning of the pulse, are sensitive to the pulse duration. Here we present a pulse detecting circuit that responds only at the falling edge of a pulse–analogous to negative edge triggered electric circuits. As biological events do not follow precise timing, use of such a pulse detector would enable the design of robust asynchronous counters which can count the completion of events. This transcription-based pulse detecting circuit depends on the interaction of two co-expressed lambdoid phage-derived proteins: the first is unstable and inhibits the regulatory activity of the second, stable protein. At the end of the pulse the unstable inhibitor protein disappears from the cell and the second protein triggers the recording of the event completion. Using stochastic simulation we showed that the proposed design can detect the completion of the pulse irrespective to the pulse duration. In our simulation we also showed that fusing the pulse detector with a phage lambda memory element we can construct a counter which can be extended to count larger numbers. The proposed design principle is a new control mechanism for synthetic biology which can be integrated in different circuits for identifying the completion of an event. PMID:27907045

  1. Genetic diversity of Pinus halepensis Mill. populations detected by RAPD loci

    OpenAIRE

    Gómez , Aránzazu; Alía , Ricardo; Bueno , María

    2001-01-01

    International audience; Genetic diversity of Pinus halepensis Mill. was analysed in nine populations (six Spanish populations and one each from Tunisia, France and Greece). Twenty four RAPD loci were amplified with 60 megagametophyte DNA samples from each population. Populations' contribution to Nei gene diversity and to allelic richness were calculated. Results showed higher within population genetic variation but also a $G_{{\\rm ST}} = 13.6\\%$ higher than those detected in previous studies ...

  2. An economic evaluation of first-trimester genetic sonography for prenatal detection of Down syndrome.

    Science.gov (United States)

    Vintzileos, A M; Ananth, C V; Fisher, A J; Smulian, J C; Day-Salvatore, D; Beazoglou, T

    1998-04-01

    To determine 1) the diagnostic accuracy requirements of first-trimester genetic sonography from the cost-benefit point of view and 2) the economic impact of first-trimester genetic sonography for the United States on the basis of the accuracy of previously published studies. A cost-benefit equation was developed on the basis of the hypothesis that the cost of chorionic villus sampling (CVS) in pregnant women with advanced maternal age (at least 35 years old) should be at least equal to the cost of genetic sonography with CVS used only for those with abnormal ultrasound results. The components of the equation included the diagnostic accuracy of genetic ultrasound (sensitivity and specificity for detecting Down syndrome), the costs of the CVS package and genetic ultrasound, and the lifetime cost of Down syndrome cases. First-trimester genetic sonography was found to be beneficial if the overall sensitivity for detecting Down syndrome was greater than 70%, and even then, the cost-benefit ratio depended on the corresponding false-positive rate. The required minimum ultrasound sensitivity varied according to the maternal age-specific prevalence of Down syndrome and ranged between 40% (for women 35 years old) to 96% (for women 44 years old). Of eight published cohorts using nuchal translucency thickness for genetic sonography, five had accuracies of genetic ultrasound compatible with net benefits. The benefits of first-trimester genetic sonography depend on its diagnostic accuracy. First-trimester genetic sonography has the potential for annual savings of 22 million dollars in the United States.

  3. Detection of DNA of genetically modified maize by a silicon nanowire field-effect transistor

    International Nuclear Information System (INIS)

    Pham, Van Binh; Tung Pham, Xuan Thanh; Duong Dang, Ngoc Thuy; Tuyen Le, Thi Thanh; Tran, Phu Duy; Nguyen, Thanh Chien; Nguyen, Van Quoc; Dang, Mau Chien; Tong, Duy Hien; Van Rijn, Cees J M

    2011-01-01

    A silicon nanowire field-effect transistor based sensor (SiNW-FET) has been proved to be the most sensitive and powerful device for bio-detection applications. In this paper, SiNWs were first fabricated by using our recently developed deposition and etching under angle technique (DEA), then used to build up the complete SiNW device based biosensor. The fabricated SiNW biosensor was used to detect DNA of genetically modified maize. As the DNA of the genetically modified maize has particular DNA sequences of 35S promoter, we therefore designed 21 mer DNA oligonucleotides, which are used as a receptor to capture the transferred DNA of maize. In our work, the SiNW biosensor could detect DNA of genetically modified maize with concentrations down to about 200 pM

  4. Variable-Width Datapath for On-Chip Network Static Power Reduction

    Energy Technology Data Exchange (ETDEWEB)

    Michelogiannakis, George; Shalf, John

    2013-11-13

    With the tight power budgets in modern large-scale chips and the unpredictability of application traffic, on-chip network designers are faced with the dilemma of designing for worst- case bandwidth demands and incurring high static power overheads, or designing for an average traffic pattern and risk degrading performance. This paper proposes adaptive bandwidth networks (ABNs) which divide channels and switches into lanes such that the network provides just the bandwidth necessary in each hop. ABNs also activate input virtual channels (VCs) individually and take advantage of drowsy SRAM cells to eliminate false VC activations. In addition, ABNs readily apply to silicon defect tolerance with just the extra cost for detecting faults. For application traffic, ABNs reduce total power consumption by an average of 45percent with comparable performance compared to single-lane power-gated networks, and 33percent compared to multi-network designs.

  5. A piezo-ring-on-chip microfluidic device for simple and low-cost mass spectrometry interfacing.

    Science.gov (United States)

    Tsao, Chia-Wen; Lei, I-Chao; Chen, Pi-Yu; Yang, Yu-Liang

    2018-02-12

    Mass spectrometry (MS) interfacing technology provides the means for incorporating microfluidic processing with post MS analysis. In this study, we propose a simple piezo-ring-on-chip microfluidic device for the controlled spraying of MALDI-MS targets. This device uses a low-cost, commercially-available ring-shaped piezoelectric acoustic atomizer (piezo-ring) directly integrated into a polydimethylsiloxane microfluidic device to spray the sample onto the MS target substrate. The piezo-ring-on-chip microfluidic device's design, fabrication, and actuation, and its pulsatile pumping effects were evaluated. The spraying performance was examined by depositing organic matrix samples onto the MS target substrate by using both an automatic linear motion motor, and manual deposition. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was performed to analyze the peptide samples on the MALDI target substrates. Using our technique, model peptides with 10 -6 M concentration can be successfully detected. The results also indicate that the piezo-ring-on-chip approach forms finer matrix crystals and presents better MS signal uniformity with little sample consumption compared to the conventional pipetting method.

  6. Synthesis of on-chip control circuits for mVLSI biochips

    DEFF Research Database (Denmark)

    Potluri, Seetal; Schneider, Alexander Rüdiger; Hørslev-Petersen, Martin

    2017-01-01

    them to laboratory environments. To address this issue, researchers have proposed methods to reduce the number of offchip pressure sources, through integration of on-chip pneumatic control logic circuits fabricated using three-layer monolithic membrane valve technology. Traditionally, mVLSI biochip......-chip control circuit design and (iii) the integration of on-chip control in the placement and routing design tasks. In this paper we present a design methodology for logic synthesis and physical synthesis of mVLSI biochips that use on-chip control. We show how the proposed methodology can be successfully...... applied to generate biochip layouts with integrated on-chip pneumatic control....

  7. [Genetic diversity of wild Cynodon dactylon germplasm detected by SRAP markers].

    Science.gov (United States)

    Yi, Yang-Jie; Zhang, Xin-Quan; Huang, Lin-Kai; Ling, Yao; Ma, Xiao; Liu, Wei

    2008-01-01

    Sequence-related amplified polymorphism (SRAP) molecular markers were used to detect the genetic diversity of 32 wild accessions of Cynodon dactylon collected from Sichuan, Chongqing, Guizhou and Tibet, China. The following results were obtained. (1) Fourteen primer pairs produced 132 polymorphic bands, averaged 9.4 bands per primer pair. The percentage of polymorphic bands in average was 79.8%. The Nei's genetic similarity coefficient of the tested accessions ranged from 0.591 to 0.957, and the average Nei's coefficient was 0.759. These results suggested that there was rich genetic diversity among the wild resources of Cynodon dactylon tested. (2) Thirty two wild accessions were clustered into four groups. Moreover, the accessions from the same origin frequently clustered into one group. The findings implied that a correlation among the wild resources, geographical and ecological environment. (3) Genetic differentiation between and within six eco-geographical groups of C. dactylon was estimated by Shannon's diversity index, which showed that 65.56% genetic variance existed within group, and 34.44% genetic variance was among groups. (4) Based on Nei's unbiased measures of genetic identity, UPGMA cluster analysis measures of six eco-geographical groups of Cynodon dactylon, indicated that there was a correlation between genetic differentiation and eco-geographical habits among the groups.

  8. Various on-chip sensors with microfluidics for biological applications.

    Science.gov (United States)

    Lee, Hun; Xu, Linfeng; Koh, Domin; Nyayapathi, Nikhila; Oh, Kwang W

    2014-09-12

    In this paper, we review recent advances in on-chip sensors integrated with microfluidics for biological applications. Since the 1990s, much research has concentrated on developing a sensing system using optical phenomena such as surface plasmon resonance (SPR) and surface-enhanced Raman scattering (SERS) to improve the sensitivity of the device. The sensing performance can be significantly enhanced with the use of microfluidic chips to provide effective liquid manipulation and greater flexibility. We describe an optical image sensor with a simpler platform for better performance over a larger field of view (FOV) and greater depth of field (DOF). As a new trend, we review consumer electronics such as smart phones, tablets, Google glasses, etc. which are being incorporated in point-of-care (POC) testing systems. In addition, we discuss in detail the current optical sensing system integrated with a microfluidic chip.

  9. Various On-Chip Sensors with Microfluidics for Biological Applications

    Directory of Open Access Journals (Sweden)

    Hun Lee

    2014-09-01

    Full Text Available In this paper, we review recent advances in on-chip sensors integrated with microfluidics for biological applications. Since the 1990s, much research has concentrated on developing a sensing system using optical phenomena such as surface plasmon resonance (SPR and surface-enhanced Raman scattering (SERS to improve the sensitivity of the device. The sensing performance can be significantly enhanced with the use of microfluidic chips to provide effective liquid manipulation and greater flexibility. We describe an optical image sensor with a simpler platform for better performance over a larger field of view (FOV and greater depth of field (DOF. As a new trend, we review consumer electronics such as smart phones, tablets, Google glasses, etc. which are being incorporated in point-of-care (POC testing systems. In addition, we discuss in detail the current optical sensing system integrated with a microfluidic chip.

  10. Network on chip master control board for neutron acquisition

    International Nuclear Information System (INIS)

    Ruiz-Martinez, E.; Mary, T.; Mutti, P.; Ratel, J.; Rey, F.

    2012-01-01

    The acquisition master control board is designed to assemble the various acquisition modes in use at the Institut Laue-Langevin (ILL). The main goal is to make the card common for all the ILL's instruments in a simple, modular and open way, giving the possibility to add new functionalities in order to follow the evolving demand. It has been necessary to define a central element to provide synchronization to the rest of the units. The backbone of the proposed acquisition control system is the denominated master acquisition board. The master board consists on a VME64X configurable high density I/O connection carrier board based on the latest Xilinx Virtex-6T FPGA. The internal architecture of the FPGA is designed as a Network on Chip (NoC) approach. The complete system also includes a display board and n histogram modules for live display of the data from the detectors. (authors)

  11. On-chip RF-to-optical transducer

    DEFF Research Database (Denmark)

    Simonsen, Anders; Tsaturyan, Yeghishe; Seis, Yannick

    2016-01-01

    these diverse systems, plus technologies that utilize them, and the mature toolbox of optical techniques that routinely operates at the quantum limit. In a previous work [1], we demonstrated such a bridge by realizing simultaneous coupling between an electronic LC circuit and a quantum-noise limited optical...... noise temperatures far below the actual temperature of the mechanical element. On-chip integration of the electrical, mechanical and optical elements is necessary for an implementation of the transduction scheme that is viable for commercial applications. Reliable assembly of a strongly coupled...... electromechanical device, and inclusion of an optical cavity for enhanced optical readout, are key features of the new platform. Both can be achieved with standard cleanroom fabrication techniques. We will furthermore present ongoing work to couple our transducer to an RF or microwave antenna, for low...

  12. Near-Field, On-Chip Optical Brownian Ratchets.

    Science.gov (United States)

    Wu, Shao-Hua; Huang, Ningfeng; Jaquay, Eric; Povinelli, Michelle L

    2016-08-10

    Nanoparticles in aqueous solution are subject to collisions with solvent molecules, resulting in random, Brownian motion. By breaking the spatiotemporal symmetry of the system, the motion can be rectified. In nature, Brownian ratchets leverage thermal fluctuations to provide directional motion of proteins and enzymes. In man-made systems, Brownian ratchets have been used for nanoparticle sorting and manipulation. Implementations based on optical traps provide a high degree of tunability along with precise spatiotemporal control. Here, we demonstrate an optical Brownian ratchet based on the near-field traps of an asymmetrically patterned photonic crystal. The system yields over 25 times greater trap stiffness than conventional optical tweezers. Our technique opens up new possibilities for particle manipulation in a microfluidic, lab-on-chip environment.

  13. Cache-aware network-on-chip for chip multiprocessors

    Science.gov (United States)

    Tatas, Konstantinos; Kyriacou, Costas; Dekoulis, George; Demetriou, Demetris; Avraam, Costas; Christou, Anastasia

    2009-05-01

    This paper presents the hardware prototype of a Network-on-Chip (NoC) for a chip multiprocessor that provides support for cache coherence, cache prefetching and cache-aware thread scheduling. A NoC with support to these cache related mechanisms can assist in improving systems performance by reducing the cache miss ratio. The presented multi-core system employs the Data-Driven Multithreading (DDM) model of execution. In DDM thread scheduling is done according to data availability, thus the system is aware of the threads to be executed in the near future. This characteristic of the DDM model allows for cache aware thread scheduling and cache prefetching. The NoC prototype is a crossbar switch with output buffering that can support a cache-aware 4-node chip multiprocessor. The prototype is built on the Xilinx ML506 board equipped with a Xilinx Virtex-5 FPGA.

  14. A Hardware Framework for on-Chip FPGA Acceleration

    DEFF Research Database (Denmark)

    Lomuscio, Andrea; Cardarilli, Gian Carlo; Nannarelli, Alberto

    2016-01-01

    In this work, we present a new framework to dynamically load hardware accelerators on reconfigurable platforms (FPGAs). Provided a library of application-specific processors, we load on-the-fly the specific processor in the FPGA, and we transfer the execution from the CPU to the FPGA-based accele......In this work, we present a new framework to dynamically load hardware accelerators on reconfigurable platforms (FPGAs). Provided a library of application-specific processors, we load on-the-fly the specific processor in the FPGA, and we transfer the execution from the CPU to the FPGA......-based accelerator. Results show that significant speed-up can be obtained by the proposed acceleration framework on system-on-chips where reconfigurable fabric is placed next to the CPUs. The speed-up is due to both the intrinsic acceleration in the application-specific processors, and to the increased parallelism....

  15. On-chip generation of heralded photon-number states

    Science.gov (United States)

    Vergyris, Panagiotis; Meany, Thomas; Lunghi, Tommaso; Sauder, Gregory; Downes, James; Steel, M. J.; Withford, Michael J.; Alibart, Olivier; Tanzilli, Sébastien

    2016-10-01

    Beyond the use of genuine monolithic integrated optical platforms, we report here a hybrid strategy enabling on-chip generation of configurable heralded two-photon states. More specifically, we combine two different fabrication techniques, i.e., non-linear waveguides on lithium niobate for efficient photon-pair generation and femtosecond-laser-direct-written waveguides on glass for photon manipulation. Through real-time device manipulation capabilities, a variety of path-coded heralded two-photon states can be produced, ranging from product to entangled states. Those states are engineered with high levels of purity, assessed by fidelities of 99.5 ± 8% and 95.0 ± 8%, respectively, obtained via quantum interferometric measurements. Our strategy therefore stands as a milestone for further exploiting entanglement-based protocols, relying on engineered quantum states, and enabled by scalable and compatible photonic circuits.

  16. On-Chip generation of polymer microcapsules through droplet coalescence

    Science.gov (United States)

    Eqbal, Md Danish; Gundabala, Venkat; Gundabala lab Team

    Alginate microbeads and microcapsules have numerous applications in drug delivery, tissue engineering and other biomedical areas due to their unique properties. Microcapsules with liquid core are of particular interest in the area of cell encapsulation. Various methods such as coacervation, emulsification, micro-nozzle, etc. exist for the generation of microbeads and microcapsules. However, these methods have several drawbacks like coagulation, non-uniformity, and polydispersity. In this work we present a method for complete on chip generation of alginate microcapsules (single core as well as double core) through the use of droplet merging technique. For this purpose, a combined Coflow and T-junction configuration is implemented in a hybrid glass-PDMS (Polydimethylsiloxane) microfluidic device. Efficient generation is achieved through precise matching of the generation rates of the coalescing drops. Through this approach, microcapsules with intact single and double (liquid) cores surrounded by alginate shell have been successfully generated and characterized.

  17. Detection of genetically modified soybean in crude soybean oil.

    Science.gov (United States)

    Nikolić, Zorica; Vasiljević, Ivana; Zdjelar, Gordana; Ðorđević, Vuk; Ignjatov, Maja; Jovičić, Dušica; Milošević, Dragana

    2014-02-15

    In order to detect presence and quantity of Roundup Ready (RR) soybean in crude oil extracted from soybean seed with a different percentage of GMO seed two extraction methods were used, CTAB and DNeasy Plant Mini Kit. The amplifications of lectin gene, used to check the presence of soybean DNA, were not achieved in all CTAB extracts of DNA, while commercial kit gave satisfactory results. Comparing actual and estimated GMO content between two extraction methods, root mean square deviation for kit is 0.208 and for CTAB is 2.127, clearly demonstrated superiority of kit over CTAB extraction. The results of quantification evidently showed that if the oil samples originate from soybean seed with varying percentage of RR, it is possible to monitor the GMO content at the first stage of processing crude oil. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Endocrine system on chip for a diabetes treatment model.

    Science.gov (United States)

    Nguyen, Dao Thi Thuy; van Noort, Danny; Jeong, In-Kyung; Park, Sungsu

    2017-02-21

    The endocrine system is a collection of glands producing hormones which, among others, regulates metabolism, growth and development. One important group of endocrine diseases is diabetes, which is caused by a deficiency or diminished effectiveness of endogenous insulin. By using a microfluidic perfused 3D cell-culture chip, we developed an 'endocrine system on chip' to potentially be able to screen drugs for the treatment of diabetes by measuring insulin release over time. Insulin-secreting β-cells are located in the pancreas, while L-cells, located in the small intestines, stimulate insulin secretion. Thus, we constructed a co-culture of intestinal-pancreatic cells to measure the effect of glucose on the production of glucagon-like peptide-1 (GLP-1) from the L-cell line (GLUTag) and insulin from the pancreatic β-cell line (INS-1). After three days of culture, both cell lines formed aggregates, exhibited 3D cell morphology, and showed good viability (>95%). We separately measured the dynamic profile of GLP-1 and insulin release at glucose concentrations of 0.5 and 20 mM, as well as the combined effect of GLP-1 on insulin production at these glucose concentrations. In response to glucose stimuli, GLUTag and INS-1 cells produced higher amounts of GLP-1 and insulin, respectively, compared to a static 2D cell culture. INS-1 combined with GLUTag cells exhibited an even higher insulin production in response to glucose stimulation. At higher glucose concentrations, the diabetes model on chip showed faster saturation of the insulin level. Our results suggest that the endocrine system developed in this study is a useful tool for observing dynamical changes in endocrine hormones (GLP-1 and insulin) in a glucose-dependent environment. Moreover, it can potentially be used to screen GLP-1 analogues and natural insulin and GLP-1 stimulants for diabetes treatment.

  19. Silicon Nanophotonics for Many-Core On-Chip Networks

    Science.gov (United States)

    Mohamed, Moustafa

    Number of cores in many-core architectures are scaling to unprecedented levels requiring ever increasing communication capacity. Traditionally, architects follow the path of higher throughput at the expense of latency. This trend has evolved into being problematic for performance in many-core architectures. Moreover, the trends of power consumption is increasing with system scaling mandating nontraditional solutions. Nanophotonics can address these problems, offering benefits in the three frontiers of many-core processor design: Latency, bandwidth, and power. Nanophotonics leverage circuit-switching flow control allowing low latency; in addition, the power consumption of optical links is significantly lower compared to their electrical counterparts at intermediate and long links. Finally, through wave division multiplexing, we can keep the high bandwidth trends without sacrificing the throughput. This thesis focuses on realizing nanophotonics for communication in many-core architectures at different design levels considering reliability challenges that our fabrication and measurements reveal. First, we study how to design on-chip networks for low latency, low power, and high bandwidth by exploiting the full potential of nanophotonics. The design process considers device level limitations and capabilities on one hand, and system level demands in terms of power and performance on the other hand. The design involves the choice of devices, designing the optical link, the topology, the arbitration technique, and the routing mechanism. Next, we address the problem of reliability in on-chip networks. Reliability not only degrades performance but can block communication. Hence, we propose a reliability-aware design flow and present a reliability management technique based on this flow to address reliability in the system. In the proposed flow reliability is modeled and analyzed for at the device, architecture, and system level. Our reliability management technique is

  20. Development of a lab-on-chip electrochemical biosensor for water quality analysis based on microalgal photosynthesis.

    Science.gov (United States)

    Tsopela, A; Laborde, A; Salvagnac, L; Ventalon, V; Bedel-Pereira, E; Séguy, I; Temple-Boyer, P; Juneau, P; Izquierdo, R; Launay, J

    2016-05-15

    The present work was dedicated to the development of a lab-on-chip device for water toxicity analysis and more particularly herbicide detection in water. It consists in a portable system for on-site detection composed of three-electrode electrochemical microcells, integrated on a fluidic platform constructed on a glass substrate. The final goal is to yield a system that gives the possibility of conducting double, complementary detection: electrochemical and optical and therefore all materials used for the fabrication of the lab-on-chip platform were selected in order to obtain a device compatible with optical technology. The basic detection principle consisted in electrochemically monitoring disturbances in metabolic photosynthetic activities of algae induced by the presence of Diuron herbicide. Algal response, evaluated through oxygen (O2) monitoring through photosynthesis was different for each herbicide concentration in the examined sample. A concentration-dependent inhibition effect of the herbicide on photosynthesis was demonstrated. Herbicide detection was achieved through a range (blank - 1 µM Diuron herbicide solution) covering the limit of maximum acceptable concentration imposed by Canadian government (0.64 µM), using a halogen white light source for the stimulation of algal photosynthetic apparatus. Superior sensitivity results (limit of detection of around 0.1 µM) were obtained with an organic light emitting diode (OLED), having an emission spectrum adapted to algal absorption spectrum and assembled on the final system. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Loop-mediated isothermal amplification (LAMP) method for detection of genetically modified maize T25.

    Science.gov (United States)

    Xu, Junyi; Zheng, Qiuyue; Yu, Ling; Liu, Ran; Zhao, Xin; Wang, Gang; Wang, Qinghua; Cao, Jijuan

    2013-11-01

    The loop-mediated isothermal amplification (LAMP) assay indicates a potential and valuable means for genetically modified organism (GMO) detection especially for its rapidity, simplicity, and low cost. We developed and evaluated the specificity and sensitivity of the LAMP method for rapid detection of the genetically modified (GM) maize T25. A set of six specific primers was successfully designed to recognize six distinct sequences on the target gene, including a pair of inner primers, a pair of outer primers, and a pair of loop primers. The optimum reaction temperature and time were verified to be 65°C and 45 min, respectively. The detection limit of this LAMP assay was 5 g kg(-1) GMO component. Comparative experiments showed that the LAMP assay was a simple, rapid, accurate, and specific method for detecting the GM maize T25.

  2. Design of a DNA chip for detection of unknown genetically modified organisms (GMOs).

    Science.gov (United States)

    Nesvold, Håvard; Kristoffersen, Anja Bråthen; Holst-Jensen, Arne; Berdal, Knut G

    2005-05-01

    Unknown genetically modified organisms (GMOs) have not undergone a risk evaluation, and hence might pose a danger to health and environment. There are, today, no methods for detecting unknown GMOs. In this paper we propose a novel method intended as a first step in an approach for detecting unknown genetically modified (GM) material in a single plant. A model is designed where biological and combinatorial reduction rules are applied to a set of DNA chip probes containing all possible sequences of uniform length n, creating probes capable of detecting unknown GMOs. The model is theoretically tested for Arabidopsis thaliana Columbia, and the probabilities for detecting inserts and receiving false positives are assessed for various parameters for this organism. From a theoretical standpoint, the model looks very promising but should be tested further in the laboratory. The model and algorithms will be available upon request to the corresponding author.

  3. Diffusion-weighted MRI for detecting prostate tumour in men at increased genetic risk

    International Nuclear Information System (INIS)

    Souza, Nandita M. de; Morgan, Veronica A.; Bancroft, Elizabeth; Sohaib, S. Aslam; Giles, Sharon L.; Kote-Jarai, Zsofia; Castro, Elena; Hazell, Steven; Jafar, Maysam; Eeles, Rosalind

    2014-01-01

    •Endorectal T2W + DW-MRI is potentially useful for prostate cancer screening.•MRI is specific for detecting prostate cancer in men with increased genetic risk.•Detection of prostate cancer in men at genetically low risk with MRI is limited. Endorectal T2W + DW-MRI is potentially useful for prostate cancer screening. MRI is specific for detecting prostate cancer in men with increased genetic risk. Detection of prostate cancer in men at genetically low risk with MRI is limited. Diffusion-weighted (DW)-MRI is invaluable in detecting prostate cancer. We determined its sensitivity and specificity and established interobserver agreement for detecting tumour in men with a family history of prostate cancer stratified by genetic risk. 51 men with a family history of prostate cancer underwent T2-W + DW-endorectal MRI at 3.0 T. Presence of tumour was noted at right and left apex, mid and basal prostate sextants by 2 independent observers, 1 experienced and the other inexperienced in endorectal MRI. Sensitivity and specificity against a 10-core sampling technique (lateral and medial cores at each level considered together) in men with >2× population risk based on 71 SNP analysis versus those with lower genetic risk scores was established. Interobserver agreement was determined at a subject level. Biopsies indicated cancer in 28 sextants in 13/51 men; 32 of 51 men had twice the population risk (>0.25) based on 71 SNP profiling. Sensitivity/specificity per-subject for patients was 90.0%/86.4% (high-risk) vs. 66.7%/100% (low-risk, observer 1) and 60.0%/86.3% (high-risk) vs. 33.3%/93.8% (low-risk, observer 2) with moderate overall inter-observer agreement (kappa = 0.42). Regional sensitivities/specificities for high-risk vs. low-risk for observer 1 apex 72.2%/100% [33.3%/100%], mid 100%/93.1% [100%/97.3%], base 16.7%/98.3% [0%/100%] and for observer 2 apex 36.4%/98.1% [0%/100%], mid 28.6%/96.5% [100%/100%], base 20%/100% [0%/97.3%] were poorer as they failed to detect

  4. Optimizing the on-chip communication architecture of low power Systems-on-Chip in Deep Sub-Micron technology

    OpenAIRE

    Leroy, Anthony

    2006-01-01

    Ce mémoire traite des systèmes intégrés sur puce (System-on-Chip) à faible consommation d'énergie tels que ceux qui seront utilisés dans les équipements portables de future génération (ordinateurs de poche (PDA), téléphones mobiles). S'agissant d'équipements alimentés par des batteries, la consommation énergétique est un problème critique. Ces plateformes contiendront probablement une douzaine de coeurs de processeur et une quantité importante de mémoire embarquée. Une architecture de communi...

  5. Genetics similarity among four breeds of sheep in Egypt detected by ...

    African Journals Online (AJOL)

    A genetic analysis using RAPD markers was performed for studying variation in four breeds of sheep (Baladi, Barki, Rahmani and Saffolk). Nineteen random primers were used to amplify DNA fragments in these breeds. RAPD patterns with a level of polymorphism were detected between breeds. Results showed closer ...

  6. Graphene nanoribbon field effect transistor for nanometer-size on-chip temperature sensor

    Science.gov (United States)

    Banadaki, Yaser M.; Srivastava, Ashok; Sharifi, Safura

    2016-04-01

    Graphene has been extensively investigated as a promising material for various types of high performance sensors due to its large surface-to-volume ratio, remarkably high carrier mobility, high carrier density, high thermal conductivity, extremely high mechanical strength and high signal-to-noise ratio. The power density and the corresponding die temperature can be tremendously high in scaled emerging technology designs, urging the on-chip sensing and controlling of the generated heat in nanometer dimensions. In this paper, we have explored the feasibility of a thin oxide graphene nanoribbon (GNR) as nanometer-size temperature sensor for detecting local on-chip temperature at scaled bias voltages of emerging technology. We have introduced an analytical model for GNR FET for 22nm technology node, which incorporates both thermionic emission of high-energy carriers and band-to-band-tunneling (BTBT) of carriers from drain to channel regions together with different scattering mechanisms due to intrinsic acoustic phonons and optical phonons and line-edge roughness in narrow GNRs. The temperature coefficient of resistivity (TCR) of GNR FET-based temperature sensor shows approximately an order of magnitude higher TCR than large-area graphene FET temperature sensor by accurately choosing of GNR width and bias condition for a temperature set point. At gate bias VGS = 0.55 V, TCR maximizes at room temperature to 2.1×10-2 /K, which is also independent of GNR width, allowing the design of width-free GNR FET for room temperature sensing applications.

  7. A scalable single-chip multi-processor architecture with on-chip RTOS kernel

    NARCIS (Netherlands)

    Theelen, B.D.; Verschueren, A.C.; Reyes Suarez, V.V.; Stevens, M.P.J.; Nunez, A.

    2003-01-01

    Now that system-on-chip technology is emerging, single-chip multi-processors are becoming feasible. A key problem of designing such systems is the complexity of their on-chip interconnects and memory architecture. It is furthermore unclear at what level software should be integrated. An example of a

  8. On-chip network interfaces supporting automatic burst write creation, posted writes and read prefetch

    NARCIS (Netherlands)

    Stefan, R.; Windt, de J.; Goossens, K.G.W.

    2010-01-01

    Networks-on-Chip are seen as a scalable solution for facilitating the development of Systems-on-Chip with an increasing number of IP cores. Many studies already address the implementation details of such networks and a large effort has been invested in optimizing the routing strategy and the

  9. Avoiding Message-Dependent Deadlock in Network-Based Systems on Chip

    NARCIS (Netherlands)

    Hansson, A.; Goossens, K.; Rãdulescu, A.

    2007-01-01

    Networks on chip (NoCs) are an essential component of systems on chip (SoCs) and much research is devoted to deadlock avoidance in NoCs. Prior work focuses on the router network while protocol interactions between NoC and intellectual property (IP) modules are not considered. These interactions

  10. Co-design of on-chip antennas and circuits for a UNII band monolithic transceiver

    KAUST Repository

    Shamim, Atif; Arsalan, Muhammad; Roy, L; Salama, Khaled N.

    2012-01-01

    with two on-chip antennas. Both antennas are characterized for their radiation properties through an on-wafer custom measurement setup. The strategy to co-design on-chip antennas with circuits, resultant trade-offs and measurement challenges have also been

  11. A survey of research and practices of network-on-chip

    DEFF Research Database (Denmark)

    Bjerregaard, Tobias; Mahadevan, Shankar

    2006-01-01

    The scaling of microchip technologies has enabled large scale systems-on-chip (SoC). Network-on-chip (NoC) research addresses global communication in SoC, involving (i) a move from computation-centric to communication-centric design and (ii) the implementation of scalable communication structures...

  12. On-chip photonic integrated circuit structures for millimeter and terahertz wave signal generation

    NARCIS (Netherlands)

    Gordón, C.; Guzmán, R. C.; Corral, V.; Carpintero, G.; Leijtens, X.

    2015-01-01

    We present two different on-chip photonic integrated circuit (PIC) structures for continuous-wave generation of millimeter and terahertz waves, each one using a different approach. One approach is the optical heterodyne method, using an on-chip arrayed waveguide grating laser (OC-AWGL) which is

  13. An FPGA bridge preserving traffing quality of service for on-chip network-based systems

    NARCIS (Netherlands)

    Nejad, A.B.; Escudero Martinez, M.; Goossens, K.G.W.

    2011-01-01

    FPGA prototyping of recent large Systems on Chip (SoCs) is very challenging due to the resource limitation of a single FPGA. Moreover, having external access to SoCs for verification and debug purposes is essential. In this paper, we suggest to partition a network-on-chip (NoC) based system into

  14. Microfluidic organ-on-chip technology for blood-brain barrier research.

    Science.gov (United States)

    van der Helm, Marinke W; van der Meer, Andries D; Eijkel, Jan C T; van den Berg, Albert; Segerink, Loes I

    2016-01-01

    Organs-on-chips are a new class of microengineered laboratory models that combine several of the advantages of current in vivo and in vitro models. In this review, we summarize the advances that have been made in the development of organ-on-chip models of the blood-brain barrier (BBBs-on-chips) and the challenges that are still ahead. The BBB is formed by specialized endothelial cells and separates blood from brain tissue. It protects the brain from harmful compounds from the blood and provides homeostasis for optimal neuronal function [corrected]. Studying BBB function and dysfunction is important for drug development and biomedical research. Microfluidic BBBs-on-chips enable real-time study of (human) cells in an engineered physiological microenvironment, for example incorporating small geometries and fluid flow as well as sensors. Examples of BBBs-on-chips in literature already show the potential of more realistic microenvironments and the study of organ-level functions. A key challenge in the field of BBB-on-chip development is the current lack of standardized quantification of parameters such as barrier permeability and shear stress. This limits the potential for direct comparison of the performance of different BBB-on-chip models to each other and existing models. We give recommendations for further standardization in model characterization and conclude that the rapidly emerging field of BBB-on-chip models holds great promise for further studies in BBB biology and drug development.

  15. Detection of genetically modified maize in processed foods sold commercially in iran by qualitative PCR.

    Science.gov (United States)

    Rabiei, Maryam; Mehdizadeh, Mehrangiz; Rastegar, Hossein; Vahidi, Hossein; Alebouyeh, Mahmoud

    2013-01-01

    Detection of genetically modified organisms (GMOs) in food is an important issue for all the subjects involved in food control and customer's right. Due to the increasing number of GMOs imported to Iran during the past few years, it has become necessary to screen the products in order to determine the identity of the consumed daily foodstuffs. In this study, following the extraction of genomic DNA from processed foods sold commercially in Iran, qualitative PCR was performed to detect genetically modified maize. The recombinant DNA target sequences were detected with primers highly specific for each investigated transgene such as CaMV35s gene, Bt-11, MON810 and Bt-176 separately. Based on the gel electrophoresis results, Bt- 11 and MON810 events were detected in some maize samples, while, in none of them Bt- 176 modified gene was detected. For the first time, the results demonstrate the presence of genetically modified maize in Iranian food products, reinforcing the need for the development of labeling system and valid quantitative methods in routine analyses.

  16. Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics

    Science.gov (United States)

    Safner, T.; Miller, M.P.; McRae, B.H.; Fortin, M.-J.; Manel, S.

    2011-01-01

    Recently, techniques available for identifying clusters of individuals or boundaries between clusters using genetic data from natural populations have expanded rapidly. Consequently, there is a need to evaluate these different techniques. We used spatially-explicit simulation models to compare three spatial Bayesian clustering programs and two edge detection methods. Spatially-structured populations were simulated where a continuous population was subdivided by barriers. We evaluated the ability of each method to correctly identify boundary locations while varying: (i) time after divergence, (ii) strength of isolation by distance, (iii) level of genetic diversity, and (iv) amount of gene flow across barriers. To further evaluate the methods' effectiveness to detect genetic clusters in natural populations, we used previously published data on North American pumas and a European shrub. Our results show that with simulated and empirical data, the Bayesian spatial clustering algorithms outperformed direct edge detection methods. All methods incorrectly detected boundaries in the presence of strong patterns of isolation by distance. Based on this finding, we support the application of Bayesian spatial clustering algorithms for boundary detection in empirical datasets, with necessary tests for the influence of isolation by distance. ?? 2011 by the authors; licensee MDPI, Basel, Switzerland.

  17. Simultaneous Detection of Genetically Modified Organisms in a Mixture by Multiplex PCR-Chip Capillary Electrophoresis.

    Science.gov (United States)

    Patwardhan, Supriya; Dasari, Srikanth; Bhagavatula, Krishna; Mueller, Steffen; Deepak, Saligrama Adavigowda; Ghosh, Sudip; Basak, Sanjay

    2015-01-01

    An efficient PCR-based method to trace genetically modified food and feed products is in demand due to regulatory requirements and contaminant issues in India. However, post-PCR detection with conventional methods has limited sensitivity in amplicon separation that is crucial in multiplexing. The study aimed to develop a sensitive post-PCR detection method by using PCR-chip capillary electrophoresis (PCR-CCE) to detect and identify specific genetically modified organisms in their genomic DNA mixture by targeting event-specific nucleotide sequences. Using the PCR-CCE approach, novel multiplex methods were developed to detect MON531 cotton, EH 92-527-1 potato, Bt176 maize, GT73 canola, or GA21 maize simultaneously when their genomic DNAs in mixtures were amplified using their primer mixture. The repeatability RSD (RSDr) of the peak migration time was 0.06 and 3.88% for the MON531 and Bt176, respectively. The RSD (RSDR) of the Cry1Ac peak ranged from 0.12 to 0.40% in multiplex methods. The method was sensitive in resolving amplicon of size difference up to 4 bp. The PCR-CCE method is suitable to detect multiple genetically modified events in a composite DNA sample by tagging their event specific sequences.

  18. Analysis of single-cell differences by use of an on-chip microculture system and optical trapping.

    Science.gov (United States)

    Wakamoto, Y; Inoue, I; Moriguchi, H; Yasuda, K

    2001-09-01

    A method is described for continuous observation of isolated single cells that enables genetically identical cells to be compared; it uses an on-chip microculture system and optical tweezers. Photolithography is used to construct microchambers with 5-microm-high walls made of thick photoresist (SU-8) on the surface of a glass slide. These microchambers are connected by a channel through which cells are transported, by means of optical tweezers, from a cultivation microchamber to an analysis microchamber, or from the analysis microchamber to a waste microchamber. The microchambers are covered with a semi-permeable membrane to separate them from nutrient medium circulating through a "cover chamber" above. Differential analysis of isolated direct descendants of single cells showed that this system could be used to compare genetically identical cells under contamination-free conditions. It should thus help in the clarification of heterogeneous phenomena, for example unequal cell division and cell differentiation.

  19. Statistical methods to detect novel genetic variants using publicly available GWAS summary data.

    Science.gov (United States)

    Guo, Bin; Wu, Baolin

    2018-03-01

    We propose statistical methods to detect novel genetic variants using only genome-wide association studies (GWAS) summary data without access to raw genotype and phenotype data. With more and more summary data being posted for public access in the post GWAS era, the proposed methods are practically very useful to identify additional interesting genetic variants and shed lights on the underlying disease mechanism. We illustrate the utility of our proposed methods with application to GWAS meta-analysis results of fasting glucose from the international MAGIC consortium. We found several novel genome-wide significant loci that are worth further study. Copyright © 2018 Elsevier Ltd. All rights reserved.

  20. On-chip dual-comb source for spectroscopy.

    Science.gov (United States)

    Dutt, Avik; Joshi, Chaitanya; Ji, Xingchen; Cardenas, Jaime; Okawachi, Yoshitomo; Luke, Kevin; Gaeta, Alexander L; Lipson, Michal

    2018-03-01

    Dual-comb spectroscopy is a powerful technique for real-time, broadband optical sampling of molecular spectra, which requires no moving components. Recent developments with microresonator-based platforms have enabled frequency combs at the chip scale. However, the need to precisely match the resonance wavelengths of distinct high quality-factor microcavities has hindered the development of on-chip dual combs. We report the simultaneous generation of two microresonator combs on the same chip from a single laser, drastically reducing experimental complexity. We demonstrate broadband optical spectra spanning 51 THz and low-noise operation of both combs by deterministically tuning into soliton mode-locked states using integrated microheaters, resulting in narrow (lasers or microwave oscillators. We demonstrate high signal-to-noise ratio absorption spectroscopy spanning 170 nm using the dual-comb source over a 20-μs acquisition time. Our device paves the way for compact and robust spectrometers at nanosecond time scales enabled by large beat-note spacings (>1 GHz).

  1. Multimedia Terminal System-on-Chip Design and Simulation

    Directory of Open Access Journals (Sweden)

    Barbieri Ivano

    2005-01-01

    Full Text Available This paper proposes a design approach based on integrated architectural and system-on-chip (SoC simulations. The main idea is to have an efficient framework for the design and the evaluation of multimedia terminals, allowing a fast system simulation with a definable degree of accuracy. The design approach includes the simulation of very long instruction word (VLIW digital signal processors (DSPs, the utilization of a device multiplexing the media streams, and the emulation of the real-time media acquisition. This methodology allows the evaluation of both the multimedia algorithm implementations and the hardware platform, giving feedback on the complete SoC including the interaction between modules and conflicts in accessing either the bus or shared resources. An instruction set architecture (ISA simulator and an SoC simulation environment compose the integrated framework. In order to validate this approach, the evaluation of an audio-video multiprocessor terminal is presented, and the complete simulation test results are reported.

  2. A multilevel Lab on chip platform for DNA analysis.

    Science.gov (United States)

    Marasso, Simone Luigi; Giuri, Eros; Canavese, Giancarlo; Castagna, Riccardo; Quaglio, Marzia; Ferrante, Ivan; Perrone, Denis; Cocuzza, Matteo

    2011-02-01

    Lab-on-chips (LOCs) are critical systems that have been introduced to speed up and reduce the cost of traditional, laborious and extensive analyses in biological and biomedical fields. These ambitious and challenging issues ask for multi-disciplinary competences that range from engineering to biology. Starting from the aim to integrate microarray technology and microfluidic devices, a complex multilevel analysis platform has been designed, fabricated and tested (All rights reserved-IT Patent number TO2009A000915). This LOC successfully manages to interface microfluidic channels with standard DNA microarray glass slides, in order to implement a complete biological protocol. Typical Micro Electro Mechanical Systems (MEMS) materials and process technologies were employed. A silicon/glass microfluidic chip and a Polydimethylsiloxane (PDMS) reaction chamber were fabricated and interfaced with a standard microarray glass slide. In order to have a high disposable system all micro-elements were passive and an external apparatus provided fluidic driving and thermal control. The major microfluidic and handling problems were investigated and innovative solutions were found. Finally, an entirely automated DNA hybridization protocol was successfully tested with a significant reduction in analysis time and reagent consumption with respect to a conventional protocol.

  3. On-chip microwave circulators using quantum Hall plasmonics

    Science.gov (United States)

    Mahoney, Alice; Colless, James; Pauka, Sebastian; Hornibrook, John; Doherty, Andrew; Reilly, David; Peeters, Lucas; Fox, Eli; Goldhaber-Gordon, David; Kou, Xuefeng; Pan, Lei; Wang, Kang; Watson, John; Gardner, Geoffrey; Manfra, Michael

    Circulators are directional circuit elements integral to technologies including radar systems, microwave communication transceivers and the readout of quantum information devices. Their non-reciprocity commonly arises from the interference of microwaves over the centimetre-scale of the signal wavelength in the presence of bulky magnetic media that breaks time-reversal symmetry. We present a completely passive on-chip microwave circulator with size 1/1000th the wavelength by exploiting the chiral, `slow-light' response of a GaAs/AlGaAs 2-dimensional electron gas in the quantum Hall regime. Further, by implementing this circulator design on a thin film of a magnetic topological insulator (Cr0.12(Bi0.26Sb0.62)2Te3), we show that similar non-reciprocity can be achieved at zero magnetic field. This additional mode of operation serves as a non-invasive probe of edge states in the quantum anomalous Hall effect, while also extending the possibility for integration with superconducting devices.

  4. An electrochemical pumping system for on-chip gradient generation.

    Science.gov (United States)

    Xie, Jun; Miao, Yunan; Shih, Jason; He, Qing; Liu, Jun; Tai, Yu-Chong; Lee, Terry D

    2004-07-01

    Within the context of microfluidic systems, it has been difficult to devise pumping systems that can deliver adequate flow rates at high pressure for applications such as HPLC. An on-chip electrochemical pumping system based on electrolysis that offers certain advantages over designs that utilize electroosmotic driven flow has been fabricated and tested. The pump was fabricated on both silicon and glass substrates using photolithography. The electrolysis electrodes were formed from either platinum or gold, and SU8, an epoxy-based photoresist, was used to form the pump chambers. A glass cover plate and a poly(dimethylsiloxane) (PDMS) gasket were used to seal the chambers. Filling of the chambers was accomplished by using a syringe to inject liquid via filling ports, which were later sealed using a glass cover plate. The current supplied to the electrodes controlled the rate of gas formation and, thus, the resulting fluid flow rate. At low backpressures, flow rates >1 microL/min have been demonstrated using polymer electrospray nozzle, we have confirmed the successful generation of a solvent gradient via a mass spectrometer.

  5. Hardware implementation of on -chip learning using re configurable FPGAS

    International Nuclear Information System (INIS)

    Kelash, H.M.; Sorour, H.S; Mahmoud, I.I.; Zaki, M; Haggag, S.S.

    2009-01-01

    The multilayer perceptron (MLP) is a neural network model that is being widely applied in the solving of diverse problems. A supervised training is necessary before the use of the neural network.A highly popular learning algorithm called back-propagation is used to train this neural network model. Once trained, the MLP can be used to solve classification problems. An interesting method to increase the performance of the model is by using hardware implementations. The hardware can do the arithmetical operations much faster than software. In this paper, a design and implementation of the sequential mode (stochastic mode) of backpropagation algorithm with on-chip learning using field programmable gate arrays (FPGA) is presented, a pipelined adaptation of the on-line back propagation algorithm (BP) is shown.The hardware implementation of forward stage, backward stage and update weight of backpropagation algorithm is also presented. This implementation is based on a SIMD parallel architecture of the forward propagation the diagnosis of the multi-purpose research reactor of Egypt accidents is used to test the proposed system

  6. Statistical power to detect genetic (covariance of complex traits using SNP data in unrelated samples.

    Directory of Open Access Journals (Sweden)

    Peter M Visscher

    2014-04-01

    Full Text Available We have recently developed analysis methods (GREML to estimate the genetic variance of a complex trait/disease and the genetic correlation between two complex traits/diseases using genome-wide single nucleotide polymorphism (SNP data in unrelated individuals. Here we use analytical derivations and simulations to quantify the sampling variance of the estimate of the proportion of phenotypic variance captured by all SNPs for quantitative traits and case-control studies. We also derive the approximate sampling variance of the estimate of a genetic correlation in a bivariate analysis, when two complex traits are either measured on the same or different individuals. We show that the sampling variance is inversely proportional to the number of pairwise contrasts in the analysis and to the variance in SNP-derived genetic relationships. For bivariate analysis, the sampling variance of the genetic correlation additionally depends on the harmonic mean of the proportion of variance explained by the SNPs for the two traits and the genetic correlation between the traits, and depends on the phenotypic correlation when the traits are measured on the same individuals. We provide an online tool for calculating the power of detecting genetic (covariation using genome-wide SNP data. The new theory and online tool will be helpful to plan experimental designs to estimate the missing heritability that has not yet been fully revealed through genome-wide association studies, and to estimate the genetic overlap between complex traits (diseases in particular when the traits (diseases are not measured on the same samples.

  7. On-chip ultra-thin layer chromatography and surface enhanced Raman spectroscopy.

    Science.gov (United States)

    Chen, Jing; Abell, Justin; Huang, Yao-wen; Zhao, Yiping

    2012-09-07

    We demonstrate that silver nanorod (AgNR) array substrates can be used for on-chip separation and detection of chemical mixtures by combining ultra-thin layer chromatography (UTLC) and surface enhanced Raman spectroscopy (SERS). The UTLC-SERS plate consists of an AgNR array fabricated by oblique angle deposition. The capability of the AgNR substrates to separate the different compounds in a mixture was explored using a mixture of four dyes and a mixture of melamine and Rhodamine 6G at varied concentrations with different mobile phase solvents. After UTLC separation, spatially-resolved SERS spectra were collected along the mobile phase development direction and the intensities of specific SERS peaks from each component were used to generate chromatograms. The AgNR substrates demonstrate the potential for separating the test dyes with plate heights as low as 9.6 μm. The limits of detection are between 10(-5)-10(-6) M. Furthermore, we show that the coupling of UTLC with SERS improves the SERS detection specificity, as small amounts of target analytes can be separated from the interfering background components.

  8. Molecular detection and genetic diversity of Babesia gibsoni in dogs in Bangladesh.

    Science.gov (United States)

    Terao, Masashi; Akter, Shirin; Yasin, Md Golam; Nakao, Ryo; Kato, Hirotomo; Alam, Mohammad Zahangir; Katakura, Ken

    2015-04-01

    Babesia gibsoni is a tick-borne hemoprotozoan parasite of dogs that often causes fever and hemolytic illness. Detection of B. gibsoni has been predominantly reported in Asian countries, including Japan, Korea, Taiwan, Malaysia, Bangladesh and India. The present study shows the first molecular characterization of B. gibsoni detected from dogs in Bangladesh. Blood samples were collected on FTA® Elute cards from 50 stray dogs in Mymensingh District in Bangladesh. DNA eluted from the cards was subjected to nested PCR for the 18S rRNA gene of Babesia species. Approximately 800bp PCR products were detected in 15 of 50 dogs (30%). Based on restriction fragment length polymorphism (RFLP) and direct sequencing of the PCR products, all parasite isolates were identified as B. gibsoni. Furthermore, the BgTRAP (B. gibsoni thrombospondin-related adhesive protein) gene fragments were detected in 13 of 15 18S rRNA gene PCR positive blood samples. Phylogenetic analysis of the BgTRAP gene revealed that B. gibsoni parasites in Bangladesh formed a cluster, which was genetically different from other Asian B. gibsoni isolates. In addition, tandem repeat analysis of the BgTRAP gene clearly showed considerable genetic variation among Bangladeshi isolates. These results suggested that B. gibsoni parasites in a different genetic clade are endemic in dogs in Bangladesh. Further studies are required to elucidate the origin, distribution, vector and pathogenesis of B. gibsoni parasites circulating in dogs in Bangladesh. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. A practicable detection system for genetically modified rice by SERS-barcoded nanosensors.

    Science.gov (United States)

    Chen, Kun; Han, Heyou; Luo, Zhihui; Wang, Yanjun; Wang, Xiuping

    2012-04-15

    Since the global cultivation of genetically modified crops constantly expands, it remains a high demand to establish different ways to sort food and feed that consist or contain genetically modified organisms. Surface-enhanced Raman scattering (SERS) spectroscopy is a flexible tool for biological analysis due to its excellent properties for detecting wide varieties of target biomolecules including nucleic acids. In the present study, a SERS-barcoded nanosensor was developed to detect Bacillus thuringiensis (Bt) gene-transformed rice expressing insecticidal proteins. The barcoded sensor was designed by encapsulation of gold nanoparticles with silica and conjugation of oligonucleotide strands for targeting DNA strands. The transition between the cry1A(b) and cry1A(c) fusion gene sequence was used to construct a specific SERS-based detection method with a detection limit of 0.1 pg/mL. In order to build the determination models to screen transgene, a series mixture of Bt rice and normal rice were prepared for SERS assay, and the limit of detection was 0.1% (w/w) transgenic Bt rice relative to normal rice. The sensitivity and accuracy of the SERS-based assay was comparable with real-time PCR. The SERS-barcoded analytical method would provide precise detection of transgenic rice varieties but also informative supplement to avoid false positive outcomes. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

  10. Plasmonic nanoparticles-decorated diatomite biosilica: extending the horizon of on-chip chromatography and label-free biosensing.

    Science.gov (United States)

    Kong, Xianming; Li, Erwen; Squire, Kenny; Liu, Ye; Wu, Bo; Cheng, Li-Jing; Wang, Alan X

    2017-11-01

    Diatomite consists of fossilized remains of ancient diatoms and is a type of naturally abundant photonic crystal biosilica with multiple unique physical and chemical functionalities. In this paper, we explored the fluidic properties of diatomite as the matrix for on-chip chromatography and, simultaneously, the photonic crystal effects to enhance the plasmonic resonances of metallic nanoparticles for surface-enhanced Raman scattering (SERS) biosensing. The plasmonic nanoparticle-decorated diatomite biosilica provides a lab-on-a-chip capability to separate and detect small molecules from mixture samples with ultra-high detection sensitivity down to 1 ppm. We demonstrate the significant potential for biomedical applications by screening toxins in real biofluid, achieving simultaneous label-free biosensing of phenethylamine and miR21cDNA in human plasma with unprecedented sensitivity and specificity. To the best of our knowledge, this is the first time demonstration to detect target molecules from real biofluids by on-chip chromatography-SERS techniques. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Detection of genetically modified organisms in foreign-made processed foods containing corn and potato.

    Science.gov (United States)

    Monma, Kimio; Araki, Rie; Sagi, Naoki; Satoh, Masaki; Ichikawa, Hisatsugu; Satoh, Kazue; Tobe, Takashi; Kamata, Kunihiro; Hino, Akihiro; Saito, Kazuo

    2005-06-01

    Investigations of the validity of labeling regarding genetically modified (GM) products were conducted using polymerase chain reaction (PCR) methods for foreign-made processed foods made from corn and potato purchased in the Tokyo area and in the USA. Several kinds of GM crops were detected in 12 of 32 samples of processed corn samples. More than two GM events for which safety reviews have been completed in Japan were simultaneously detected in 10 samples. GM events MON810 and Bt11 were most frequently detected in the samples by qualitative PCR methods. MON810 was detected in 11 of the 12 samples, and Bt11 was detected in 6 of the 12 samples. In addition, Roundup Ready soy was detected in one of the 12 samples. On the other hand, CBH351, for which the safety assessment was withdrawn in Japan, was not detected in any of the 12 samples. A trial quantitative analysis was performed on six of the GM maize qualitatively positive samples. The estimated amounts of GM maize in these samples ranged from 0.2 to 2.8%, except for one sample, which contained 24.1%. For this sample, the total amount found by event-specific quantitative analysis was 23.8%. Additionally, Roundup Ready soy was detected in one sample of 21 potato-processed foods, although GM potatoes were not detected in any sample.

  12. Electrical lysis: dynamics revisited and advances in On-chip operation.

    Science.gov (United States)

    Morshed, Bashir; Shams, Maitham; Mussivand, Tofy

    2013-01-01

    Electrical lysis (EL) is the process of breaking the cell membrane to expose the internal contents under an applied high electric field. Lysis is an important phenomenon for cellular analysis, medical treatment, and biofouling control. This paper aims to review, summarize, and analyze recent advancements on EL. Major databases including PubMed, Ei Engineering Village, IEEE Xplore, and Scholars Portal were searched using relevant keywords. More than 50 articles published in English since 1997 are cited in this article. EL has several key advantages compared to other lysis techniques such as chemical, mechanical, sonication, or laser, including rapid speed of operation, ability to control, miniaturization, low cost, and low power requirement. A variety of cell types have been investigated for including protoplasts, E. coli, yeasts, blood cells, and cancer cells. EL has been developed and applied for decontamination, cytology, genetics, single-cell analysis, cancer treatment, and other applications. On-chip EL is a promising technology for multiplexed automated implementation of cell-sample preparation and processing with micro- or nanoliter reagents.

  13. Integration of systems biology with organs-on-chips to humanize therapeutic development

    Science.gov (United States)

    Edington, Collin D.; Cirit, Murat; Chen, Wen Li Kelly; Clark, Amanda M.; Wells, Alan; Trumper, David L.; Griffith, Linda G.

    2017-02-01

    "Mice are not little people" - a refrain becoming louder as the gaps between animal models and human disease become more apparent. At the same time, three emerging approaches are headed toward integration: powerful systems biology analysis of cell-cell and intracellular signaling networks in patient-derived samples; 3D tissue engineered models of human organ systems, often made from stem cells; and micro-fluidic and meso-fluidic devices that enable living systems to be sustained, perturbed and analyzed for weeks in culture. Integration of these rapidly moving fields has the potential to revolutionize development of therapeutics for complex, chronic diseases, including those that have weak genetic bases and substantial contributions from gene-environment interactions. Technical challenges in modeling complex diseases with "organs on chips" approaches include the need for relatively large tissue masses and organ-organ cross talk to capture systemic effects, such that current microfluidic formats often fail to capture the required scale and complexity for interconnected systems. These constraints drive development of new strategies for designing in vitro models, including perfusing organ models, as well as "mesofluidic" pumping and circulation in platforms connecting several organ systems, to achieve the appropriate physiological relevance.

  14. Fishing on chips: up-and-coming technological advances in analysis of zebrafish and Xenopus embryos.

    Science.gov (United States)

    Zhu, Feng; Skommer, Joanna; Huang, Yushi; Akagi, Jin; Adams, Dany; Levin, Michael; Hall, Chris J; Crosier, Philip S; Wlodkowic, Donald

    2014-11-01

    Biotests performed on small vertebrate model organisms provide significant investigative advantages as compared with bioassays that employ cell lines, isolated primary cells, or tissue samples. The main advantage offered by whole-organism approaches is that the effects under study occur in the context of intact physiological milieu, with all its intercellular and multisystem interactions. The gap between the high-throughput cell-based in vitro assays and low-throughput, disproportionally expensive and ethically controversial mammal in vivo tests can be closed by small model organisms such as zebrafish or Xenopus. The optical transparency of their tissues, the ease of genetic manipulation and straightforward husbandry, explain the growing popularity of these model organisms. Nevertheless, despite the potential for miniaturization, automation and subsequent increase in throughput of experimental setups, the manipulation, dispensing and analysis of living fish and frog embryos remain labor-intensive. Recently, a new generation of miniaturized chip-based devices have been developed for zebrafish and Xenopus embryo on-chip culture and experimentation. In this work, we review the critical developments in the field of Lab-on-a-Chip devices designed to alleviate the limits of traditional platforms for studies on zebrafish and clawed frog embryo and larvae. © 2014 International Society for Advancement of Cytometry. © 2014 International Society for Advancement of Cytometry.

  15. Evaluation of terrestrial microcosms for detection, fate, and survival analysis of genetically engineered microorganisms and their recombinant genetic material

    Energy Technology Data Exchange (ETDEWEB)

    Fredrickson, J.K.; Seidler, R.J.

    1989-02-01

    The research included in this document represents the current scientific information available regarding the applicability of terrestrial microcosms and related methodologies for evaluating detection methods and the fate and survival of microorganisms in the environment. The three terrestrial microcosms described in this document were used to evaluate the survival and fate of recombinant bacteria in soils and in association with plant surfaces and insects and their transport through soil with percolating water and root systems, and to test new methods and procedures to improve detection and enumeration of bacteria in soil. Simple (potting soil composed of peat mix and perlite, lacking environmental control and monitoring) and complex microcosms (agricultural soil with partial control and monitoring of environmental conditions) were demonstrated to be useful tools for preliminary assessments of microbial viability in terrestrial ecosystems. These studies evaluated the survival patterns of Enterobacter cloacae (pBR322) in soil and on plant surfaces and the ingestion of this same microorganism by cutworms and survival in the foregut and frass. The Versacore microcosm design was used to monitor the fate and competitiveness of genetically engineered bacteria in soil. Both selective media and gene probes were used successfully to follow the fate of two recombinant Pseudomonas sp. introduced into Versacore microcosms. Intact soil-core microcosms were employed to evaluate the fate and transport of genetically altered Azospirillum sp. and Pseudomonas sp. in soil and the plant rhizosphere. The usefulness of these various microcosms as a tool for risk assessment is underscored by the ease in obtaining soil from a proposed field release site to evaluate subsequent GEM fate and survival.

  16. Co-design of on-chip antennas and circuits for a UNII band monolithic transceiver

    KAUST Repository

    Shamim, Atif

    2012-07-28

    The surge of highly integrated and multifunction wireless devices has necessitated the designers to think outside the box for solutions that are unconventional. The new trends have provided the impetus for low cost and compact RF System-on-Chip (SoC) approaches [1]. The major advantages of SoC are miniaturization and cost reduction. A major bottleneck to the true realization of monolithic RF SoC transceivers is the implementation of on-chip antennas with circuitry. Though complete integrated transceivers with on-chip antennas have been demonstrated, these designs are generally for high frequencies. Moreover, they either use non-standard CMOS processes or additional fabrication steps to enhance the antenna efficiency, which in turn adds to the cost of the system [2-3]. Another challenge related to the on-chip antennas is the characterization of their radiation properties. Most of the recently reported work (summarized in Table I) shows that very few on-chip antennas are characterized. Our previous work [4], demonstrated a Phase Lock Loop (PLL) based transmitter (TX) with an on-chip antenna. However, the radiation from the on-chip antenna experienced strong interference due to 1) some active circuitry on one side of the chip and 2) the PCB used to mount the chip in the anechoic chamber. This paper presents, for the first time, a complete 5.2 GHz (UNII band) transceiver with separate TX and receiver (RX) antennas. To the author\\'s best knowledge, its size of 3 mm2 is the smallest reported for a UNII band transceiver with two on-chip antennas. Both antennas are characterized for their radiation properties through an on-wafer custom measurement setup. The strategy to co-design on-chip antennas with circuits, resultant trade-offs and measurement challenges have also been discussed. © 2010 IEEE.

  17. Epileptic MEG Spike Detection Using Statistical Features and Genetic Programming with KNN

    Directory of Open Access Journals (Sweden)

    Turky N. Alotaiby

    2017-01-01

    Full Text Available Epilepsy is a neurological disorder that affects millions of people worldwide. Monitoring the brain activities and identifying the seizure source which starts with spike detection are important steps for epilepsy treatment. Magnetoencephalography (MEG is an emerging epileptic diagnostic tool with high-density sensors; this makes manual analysis a challenging task due to the vast amount of MEG data. This paper explores the use of eight statistical features and genetic programing (GP with the K-nearest neighbor (KNN for interictal spike detection. The proposed method is comprised of three stages: preprocessing, genetic programming-based feature generation, and classification. The effectiveness of the proposed approach has been evaluated using real MEG data obtained from 28 epileptic patients. It has achieved a 91.75% average sensitivity and 92.99% average specificity.

  18. Applications of holographic on-chip microscopy (Conference Presentation)

    Science.gov (United States)

    Ozcan, Aydogan

    2017-02-01

    My research focuses on the use of computation/algorithms to create new optical microscopy, sensing, and diagnostic techniques, significantly improving existing tools for probing micro- and nano-objects while also simplifying the designs of these analysis tools. In this presentation, I will introduce a set of computational microscopes which use lens-free on-chip imaging to replace traditional lenses with holographic reconstruction algorithms. Basically, 3D images of specimens are reconstructed from their "shadows" providing considerably improved field-of-view (FOV) and depth-of-field, thus enabling large sample volumes to be rapidly imaged, even at nanoscale. These new computational microscopes routinely generate benefit of this technology is that it lends itself to field-portable and cost-effective designs which easily integrate with smartphones to conduct giga-pixel tele-pathology and microscopy even in resource-poor and remote settings where traditional techniques are difficult to implement and sustain, thus opening the door to various telemedicine applications in global health. Through the development of similar computational imagers, I will also report the discovery of new 3D swimming patterns observed in human and animal sperm. One of this newly discovered and extremely rare motion is in the form of "chiral ribbons" where the planar swings of the sperm head occur on an osculating plane creating in some cases a helical ribbon and in some others a twisted ribbon. Shedding light onto the statistics and biophysics of various micro-swimmers' 3D motion, these results provide an important example of how biomedical imaging significantly benefits from emerging computational algorithms/theories, revolutionizing existing tools for observing various micro- and nano-scale phenomena in innovative, high-throughput, and yet cost-effective ways.

  19. 3D on-chip microscopy of optically cleared tissue

    Science.gov (United States)

    Zhang, Yibo; Shin, Yoonjung; Sung, Kevin; Yang, Sam; Chen, Harrison; Wang, Hongda; Teng, Da; Rivenson, Yair; Kulkarni, Rajan P.; Ozcan, Aydogan

    2018-02-01

    Traditional pathology relies on tissue biopsy, micro-sectioning, immunohistochemistry and microscopic imaging, which are relatively expensive and labor-intensive, and therefore are less accessible in resource-limited areas. Low-cost tissue clearing techniques, such as the simplified CLARITY method (SCM), are promising to potentially reduce the cost of disease diagnosis by providing 3D imaging and phenotyping of thicker tissue samples with simpler preparation steps. However, the mainstream imaging approach for cleared tissue, fluorescence microscopy, suffers from high-cost, photobleaching and signal fading. As an alternative approach to fluorescence, here we demonstrate 3D imaging of SCMcleared tissue using on-chip holography, which is based on pixel-super-resolution and multi-height phase recovery algorithms to digitally compute the sample's amplitude and phase images at various z-slices/depths through the sample. The tissue clearing procedures and the lens-free imaging system were jointly optimized to find the best illumination wavelength, tissue thickness, staining solution pH, and the number of hologram heights to maximize the imaged tissue volume, minimize the amount of acquired data, while maintaining a high contrast-to-noise ratio for the imaged cells. After this optimization, we achieved 3D imaging of a 200-μm thick cleared mouse brain tissue over a field-of-view of based microscope (20× 0.75NA). Moreover, the lens-free microscope achieves an order-of-magnitude better data efficiency compared to its lens-based counterparts for volumetric imaging of samples. The presented low-cost and high-throughput lens-free tissue imaging technique enabled by CLARITY can be used in various biomedical applications in low-resource-settings.

  20. Improved On-Chip Measurement of Delay in an FPGA or ASIC

    Science.gov (United States)

    Chen, Yuan; Burke, Gary; Sheldon, Douglas

    2007-01-01

    An improved design has been devised for on-chip-circuitry for measuring the delay through a chain of combinational logic elements in a field-programmable gate array (FPGA) or application-specific integrated circuit (ASIC). In the improved design, the delay chain does not include input and output buffers and is not configured as an oscillator. Instead, the delay chain is made part of the signal chain of an on-chip pulse generator. The duration of the pulse is measured on-chip and taken to equal the delay.

  1. A system-level multiprocessor system-on-chip modeling framework

    DEFF Research Database (Denmark)

    Virk, Kashif Munir; Madsen, Jan

    2004-01-01

    We present a system-level modeling framework to model system-on-chips (SoC) consisting of heterogeneous multiprocessors and network-on-chip communication structures in order to enable the developers of today's SoC designs to take advantage of the flexibility and scalability of network-on-chip and...... SoC design. We show how a hand-held multimedia terminal, consisting of JPEG, MP3 and GSM applications, can be modeled as a multiprocessor SoC in our framework....

  2. Detection and genetic characterization of a novel parvovirus distantly related to human bufavirus in domestic pigs.

    Science.gov (United States)

    Hargitai, Renáta; Pankovics, Péter; Kertész, Attila Mihály; Bíró, Hunor; Boros, Ákos; Phan, Tung Gia; Delwart, Eric; Reuter, Gábor

    2016-04-01

    In this study, a novel parvovirus (strain swine/Zsana3/2013/HUN, KT965075) was detected in domestic pigs and genetically characterized by viral metagenomics and PCR methods. The novel parvovirus was distantly related to the human bufaviruses and was detected in 19 (90.5 %) of the 21 and five (33.3 %) of the 15 faecal samples collected from animals with and without cases of posterior paraplegia of unknown etiology from five affected farms and one control farm in Hungary, respectively. Swine/Zsana3/2013/HUN is highly prevalent in domestic pigs and potentially represents a novel parvovirus species in the subfamily Parvovirinae.

  3. Dew inspired breathing-based detection of genetic point mutation visualized by naked eye

    Science.gov (United States)

    Xie, Liping; Wang, Tongzhou; Huang, Tianqi; Hou, Wei; Huang, Guoliang; Du, Yanan

    2014-09-01

    A novel label-free method based on breathing-induced vapor condensation was developed for detection of genetic point mutation. The dew-inspired detection was realized by integration of target-induced DNA ligation with rolling circle amplification (RCA). The vapor condensation induced by breathing transduced the RCA-amplified variances in DNA contents into visible contrast. The image could be recorded by a cell phone for further or even remote analysis. This green assay offers a naked-eye-reading method potentially applied for point-of-care liver cancer diagnosis in resource-limited regions.

  4. [Detection of recombinant-DNA in foods from stacked genetically modified plants].

    Science.gov (United States)

    Sorokina, E Iu; Chernyshova, O N

    2012-01-01

    A quantitative real-time multiplex polymerase chain reaction method was applied to the detection and quantification of MON863 and MON810 in stacked genetically modified maize MON 810xMON 863. The limit of detection was approximately 0,1%. The accuracy of the quantification, measured as bias from the accepted value and the relative repeatability standard deviation, which measures the intra-laboratory variability, were within 25% at each GM-level. A method verification has demonstrated that the MON 863 and the MON810 methods can be equally applied in quantification of the respective events in stacked MON810xMON 863.

  5. Apparatus, System and Method for Fast Detection of Genetic Information by PCR in an Interchangeable Chip

    KAUST Repository

    Wen, Weijia

    2011-03-03

    A polymerase chain reaction (PCR) device for fast amplification and detection of DNA includes an interchangeable PCR chamber, a temperature control component, and an optical detection system. The DNA amplification is performed on an interchangeable chip with volumes as small as 1.25 µl, while the heating and cooling rate may be as fast as 12.7 °C/second ensuring that the total time needed of only 25 minutes to complete the 35 cycle PCR amplification. The PCR may be performed according to a two-temperature approach for denaturing and annealing (Td and Ta) of DNA with the PCR chip, with which the amplification of male-specific SRY gene marker by utilizing raw saliva may be achieved. The genetic identification may be in-situ detected after PCR by the optical detection system.

  6. Fast detection of genetic information by an optimized PCR in an interchangeable chip.

    KAUST Repository

    Wu, Jinbo

    2012-02-01

    In this paper, we report the construction of a polymerase chain reaction (PCR) device for fast amplification and detection of DNA. This device consists of an interchangeable PCR chamber, a temperature control component as well as an optical detection system. The DNA amplification happens on an interchangeable chip with the volumes as low as 1.25 μl, while the heating and cooling rate was as fast as 12.7°C/second ensuring that the total time needed of only 25 min to complete the 35 cycle PCR amplification. An optimized PCR with two-temperature approach for denaturing and annealing (Td and Ta) of DNA was also formulated with the PCR chip, with which the amplification of male-specific sex determining region Y (SRY) gene marker by utilizing raw saliva was successfully achieved and the genetic identification was in-situ detected right after PCR by the optical detection system.

  7. Vibration-Based Damage Detection in Beams by Cooperative Coevolutionary Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Kittipong Boonlong

    2014-03-01

    Full Text Available Vibration-based damage detection, a nondestructive method, is based on the fact that vibration characteristics such as natural frequencies and mode shapes of structures are changed when the damage happens. This paper presents cooperative coevolutionary genetic algorithm (CCGA, which is capable for an optimization problem with a large number of decision variables, as the optimizer for the vibration-based damage detection in beams. In the CCGA, a minimized objective function is a numerical indicator of differences between vibration characteristics of the actual damage and those of the anticipated damage. The damage detection in a uniform cross-section cantilever beam, a uniform strength cantilever beam, and a uniform cross-section simply supported beam is used as the test problems. Random noise in the vibration characteristics is also considered in the damage detection. In the simulation analysis, the CCGA provides the superior solutions to those that use standard genetic algorithms presented in previous works, although it uses less numbers of the generated solutions in solution search. The simulation results reveal that the CCGA can efficiently identify the occurred damage in beams for all test problems including the damage detection in a beam with a large number of divided elements such as 300 elements.

  8. Automatic Mexico Gulf Oil Spill Detection from Radarsat-2 SAR Satellite Data Using Genetic Algorithm

    Science.gov (United States)

    Marghany, Maged

    2016-10-01

    In this work, a genetic algorithm is exploited for automatic detection of oil spills of small and large size. The route is achieved using arrays of RADARSAT-2 SAR ScanSAR Narrow single beam data obtained in the Gulf of Mexico. The study shows that genetic algorithm has automatically segmented the dark spot patches related to small and large oil spill pixels. This conclusion is confirmed by the receiveroperating characteristic (ROC) curve and ground data which have been documented. The ROC curve indicates that the existence of oil slick footprints can be identified with the area under the curve between the ROC curve and the no-discrimination line of 90%, which is greater than that of other surrounding environmental features. The small oil spill sizes represented 30% of the discriminated oil spill pixels in ROC curve. In conclusion, the genetic algorithm can be used as a tool for the automatic detection of oil spills of either small or large size and the ScanSAR Narrow single beam mode serves as an excellent sensor for oil spill patterns detection and surveying in the Gulf of Mexico.

  9. Molecular Detection of Bladder Cancer by Fluorescence Microsatellite Analysis and an Automated Genetic Analyzing System

    Directory of Open Access Journals (Sweden)

    Sarel Halachmi

    2007-01-01

    Full Text Available To investigate the ability of an automated fluorescent analyzing system to detect microsatellite alterations, in patients with bladder cancer. We investigated 11 with pathology proven bladder Transitional Cell Carcinoma (TCC for microsatellite alterations in blood, urine, and tumor biopsies. DNA was prepared by standard methods from blood, urine and resected tumor specimens, and was used for microsatellite analysis. After the primers were fluorescent labeled, amplification of the DNA was performed with PCR. The PCR products were placed into the automated genetic analyser (ABI Prism 310, Perkin Elmer, USA and were subjected to fluorescent scanning with argon ion laser beams. The fluorescent signal intensity measured by the genetic analyzer measured the product size in terms of base pairs. We found loss of heterozygocity (LOH or microsatellite alterations (a loss or gain of nucleotides, which alter the original normal locus size in all the patients by using fluorescent microsatellite analysis and an automated analyzing system. In each case the genetic changes found in urine samples were identical to those found in the resected tumor sample. The studies demonstrated the ability to detect bladder tumor non-invasively by fluorescent microsatellite analysis of urine samples. Our study supports the worldwide trend for the search of non-invasive methods to detect bladder cancer. We have overcome major obstacles that prevented the clinical use of an experimental system. With our new tested system microsatellite analysis can be done cheaper, faster, easier and with higher scientific accuracy.

  10. Optical biosensor based on a silicon nanowire ridge waveguide for lab on chip applications

    International Nuclear Information System (INIS)

    Gamal, Rania; Ismail, Yehea; Swillam, Mohamed A

    2015-01-01

    We propose a novel sensor using a silicon nanowire ridge waveguide (SNRW). This waveguide is comprised of an array of silicon nanowires on an insulator substrate that has the envelope of a ridge waveguide. The SNRW inherently maximizes the overlap between the material-under-test and the incident light wave by introducing voids to the otherwise bulk structure. When a sensing sample is injected, the voids within the SNRW adopt the refractive index of the material-under-test. Hence, the strong contribution of the material-under-test to the overall modal effective index will greatly augment the sensitivity. Additionally, the ridge structure provides a fabrication convenience as it covers the entire substrate, ensuring that the etching process would not damage the substrate. Finite-difference time-domain simulations are conducted and showed that the percentage change in the effective index due to a 1% change in the surrounding environment is more than 170 times the change perceived in an evanescent-detection based bulk silicon ridge waveguide. Moreover, the SNRW proves to be more sensitive than recent other, non-evanescent sensors. In addition, the detection limit for this structure was revealed to be as small as 10 −8 . A compact bimodal waveguide based on SNRW is designed and tested. It delivers high sensitivity values that offer comparable performance to similar low-index light-guiding sensing configurations; however, our proposed structure has much smaller footprints and allows high dense integration for lab-on-chip applications. (paper)

  11. On-chip magnetic bead-based DNA melting curve analysis using a magnetoresistive sensor

    International Nuclear Information System (INIS)

    Rizzi, Giovanni; Østerberg, Frederik W.; Henriksen, Anders D.; Dufva, Martin; Hansen, Mikkel F.

    2015-01-01

    We present real-time measurements of DNA melting curves in a chip-based system that detects the amount of surface-bound magnetic beads using magnetoresistive magnetic field sensors. The sensors detect the difference between the amount of beads bound to the top and bottom sensor branches of the differential sensor geometry. The sensor surfaces are functionalized with wild type (WT) and mutant type (MT) capture probes, differing by a single base insertion (a single nucleotide polymorphism, SNP). Complementary biotinylated targets in suspension couple streptavidin magnetic beads to the sensor surface. The beads are magnetized by the field arising from the bias current passed through the sensors. We demonstrate the first on-chip measurements of the melting of DNA hybrids upon a ramping of the temperature. This overcomes the limitation of using a single washing condition at constant temperature. Moreover, we demonstrate that a single sensor bridge can be used to genotype a SNP. - Highlights: • We apply magnetoresistive sensors to study solid-surface hybridization kinetics of DNA. • We measure DNA melting profiles for perfectly matching DNA duplexes and for a single base mismatch. • We present a procedure to correct for temperature dependencies of the sensor output. • We reliably extract melting temperatures for the DNA hybrids. • We demonstrate direct measurement of differential binding signal for two probes on a single sensor

  12. Computational sensing of herpes simplex virus using a cost-effective on-chip microscope

    KAUST Repository

    Ray, Aniruddha

    2017-07-03

    Caused by the herpes simplex virus (HSV), herpes is a viral infection that is one of the most widespread diseases worldwide. Here we present a computational sensing technique for specific detection of HSV using both viral immuno-specificity and the physical size range of the viruses. This label-free approach involves a compact and cost-effective holographic on-chip microscope and a surface-functionalized glass substrate prepared to specifically capture the target viruses. To enhance the optical signatures of individual viruses and increase their signal-to-noise ratio, self-assembled polyethylene glycol based nanolenses are rapidly formed around each virus particle captured on the substrate using a portable interface. Holographic shadows of specifically captured viruses that are surrounded by these self-assembled nanolenses are then reconstructed, and the phase image is used for automated quantification of the size of each particle within our large field-of-view, ~30 mm2. The combination of viral immuno-specificity due to surface functionalization and the physical size measurements enabled by holographic imaging is used to sensitively detect and enumerate HSV particles using our compact and cost-effective platform. This computational sensing technique can find numerous uses in global health related applications in resource-limited environments.

  13. Magnetic actuator for the control and mixing of magnetic bead-based reactions on-chip.

    Science.gov (United States)

    Berenguel-Alonso, Miguel; Granados, Xavier; Faraudo, Jordi; Alonso-Chamarro, Julián; Puyol, Mar

    2014-10-01

    While magnetic bead (MB)-based bioassays have been implemented in integrated devices, their handling on-chip is normally either not optimal--i.e. only trapping is achieved, with aggregation of the beads--or requires complex actuator systems. Herein, we describe a simple and low-cost magnetic actuator to trap and move MBs within a microfluidic chamber in order to enhance the mixing of a MB-based reaction. The magnetic actuator consists of a CD-shaped plastic unit with an arrangement of embedded magnets which, when rotating, generate the mixing. The magnetic actuator has been used to enhance the amplification reaction of an enzyme-linked fluorescence immunoassay to detect Escherichia coli O157:H7 whole cells, an enterohemorrhagic strain, which have caused several outbreaks in food and water samples. A 2.7-fold sensitivity enhancement was attained with a detection limit of 603 colony-forming units (CFU) /mL, when employing the magnetic actuator.

  14. An Impedance-Based Mold Sensor with on-Chip Optical Reference

    Directory of Open Access Journals (Sweden)

    Poornachandra Papireddy Vinayaka

    2016-09-01

    Full Text Available A new miniaturized sensor system with an internal optical reference for the detection of mold growth is presented. The sensor chip comprises a reaction chamber provided with a culture medium that promotes the growth of mold species from mold spores. The mold detection is performed by measuring impedance changes with integrated electrodes fabricated inside the reaction chamber. The impedance change in the culture medium is caused by shifts in the pH (i.e., from 5.5 to 8 as the mold grows. In order to determine the absolute pH value without the need for calibration, a methyl red indicator dye has been added to the culture medium. It changes the color of the medium as the pH passes specific values. This colorimetric principle now acts as a reference measurement. It also allows the sensitivity of the impedance sensor to be established in terms of impedance change per pH unit. Major mold species that are involved in the contamination of food, paper and indoor environments, like Fusarium oxysporum, Fusarium incarnatum, Eurotium amstelodami, Aspergillus penicillioides and Aspergillus restrictus, have been successfully analyzed on-chip.

  15. The power to detect recent fragmentation events using genetic differentiation methods.

    Directory of Open Access Journals (Sweden)

    Michael W Lloyd

    Full Text Available Habitat loss and fragmentation are imminent threats to biological diversity worldwide and thus are fundamental issues in conservation biology. Increased isolation alone has been implicated as a driver of negative impacts in populations associated with fragmented landscapes. Genetic monitoring and the use of measures of genetic divergence have been proposed as means to detect changes in landscape connectivity. Our goal was to evaluate the sensitivity of Wright's F st, Hedrick' G'st , Sherwin's MI, and Jost's D to recent fragmentation events across a range of population sizes and sampling regimes. We constructed an individual-based model, which used a factorial design to compare effects of varying population size, presence or absence of overlapping generations, and presence or absence of population sub-structuring. Increases in population size, overlapping generations, and population sub-structuring each reduced F st, G'st , MI, and D. The signal of fragmentation was detected within two generations for all metrics. However, the magnitude of the change in each was small in all cases, and when N e was >100 individuals it was extremely small. Multi-generational sampling and population estimates are required to differentiate the signal of background divergence from changes in Fst , G'st , MI, and D associated with fragmentation. Finally, the window during which rapid change in Fst , G'st , MI, and D between generations occurs can be small, and if missed would lead to inconclusive results. For these reasons, use of F st, G'st , MI, or D for detecting and monitoring changes in connectivity is likely to prove difficult in real-world scenarios. We advocate use of genetic monitoring only in conjunction with estimates of actual movement among patches such that one could compare current movement with the genetic signature of past movement to determine there has been a change.

  16. JRC GMO-Matrix: a web application to support Genetically Modified Organisms detection strategies.

    Science.gov (United States)

    Angers-Loustau, Alexandre; Petrillo, Mauro; Bonfini, Laura; Gatto, Francesco; Rosa, Sabrina; Patak, Alexandre; Kreysa, Joachim

    2014-12-30

    The polymerase chain reaction (PCR) is the current state of the art technique for DNA-based detection of Genetically Modified Organisms (GMOs). A typical control strategy starts by analyzing a sample for the presence of target sequences (GM-elements) known to be present in many GMOs. Positive findings from this "screening" are then confirmed with GM (event) specific test methods. A reliable knowledge of which GMOs are detected by combinations of GM-detection methods is thus crucial to minimize the verification efforts. In this article, we describe a novel platform that links the information of two unique databases built and maintained by the European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) at the Joint Research Centre (JRC) of the European Commission, one containing the sequence information of known GM-events and the other validated PCR-based detection and identification methods. The new platform compiles in silico determinations of the detection of a wide range of GMOs by the available detection methods using existing scripts that simulate PCR amplification and, when present, probe binding. The correctness of the information has been verified by comparing the in silico conclusions to experimental results for a subset of forty-nine GM events and six methods. The JRC GMO-Matrix is unique for its reliance on DNA sequence data and its flexibility in integrating novel GMOs and new detection methods. Users can mine the database using a set of web interfaces that thus provide a valuable support to GMO control laboratories in planning and evaluating their GMO screening strategies. The platform is accessible at http://gmo-crl.jrc.ec.europa.eu/jrcgmomatrix/ .

  17. Essential issues in SOC design designing complex systems-on-chip

    CERN Document Server

    Lin, Youn-long Steve

    2007-01-01

    Covers issues related to system-on-chip (SoC) design. This book covers IP development, verification, integration, chip implementation, testing and software. It contains valuable academic and industrial examples for those involved with the design of complex SOCs.

  18. Implementation of Guaranteed Services in the MANGO Clockless Network-on-Chip

    DEFF Research Database (Denmark)

    Bjerregaard, Tobias; Sparsø, Jens

    2006-01-01

    (clockless implementation, standard socket access points, and guaranteed communication services) make MANGO suitable for a modular SoC design flow is explained. Among the advantages of using clockless circuit techniques are inherent global timing closure, low forward latency in pipelines, and zero dynamic......Shared, segmented, on-chip interconnection networks, known as networks-on-chip (NoC), may become the preferred way of interconnecting intellectual property (IP) cores in future giga-scale system-on-chip (SoC) designs. A NoC can provide the required communication bandwidth while accommodating...... the effects of scaling microchip technologies. Equally important, a NoC facilitates a truly modular and scalable design flow. The MANGO (message-passing asynchronous network-on-chip providing guaranteed services over open core protocol (OCP) interfaces) NoC is presented, and how its key characteristics...

  19. Direct quantification of transendothelial electrical resistance in organs-on-chips

    NARCIS (Netherlands)

    van der Helm, Marieke Willemijn; Odijk, Mathieu; Frimat, Jean-Philippe; van der Meer, Andries Dirk; Eijkel, Jan C.T.; van den Berg, Albert; Segerink, Loes Irene

    2016-01-01

    Measuring transendothelial or transepithelial electrical resistance (TEER) is a widely used method to monitor cellular barrier tightness in organs-on-chips. Unfortunately, integrated electrodes close to the cellular barrier hamper visual inspection of the cells or require specialized cleanroom

  20. Optical chromatography using a photonic crystal fiber with on-chip fluorescence excitation

    CSIR Research Space (South Africa)

    Ashok, AC

    2010-03-01

    Full Text Available The authors describe the realization of integrated optical chromatography, in conjunction with on-chip fluorescence excitation, in a monolithically fabricated poly-dimethylsiloxane (PDMS) microfluidic chip. The unique endlessly-single-mode guiding...

  1. Endpoint visual detection of three genetically modified rice events by loop-mediated isothermal amplification.

    Science.gov (United States)

    Chen, Xiaoyun; Wang, Xiaofu; Jin, Nuo; Zhou, Yu; Huang, Sainan; Miao, Qingmei; Zhu, Qing; Xu, Junfeng

    2012-11-07

    Genetically modified (GM) rice KMD1, TT51-1, and KF6 are three of the most well known transgenic Bt rice lines in China. A rapid and sensitive molecular assay for risk assessment of GM rice is needed. Polymerase chain reaction (PCR), currently the most common method for detecting genetically modified organisms, requires temperature cycling and relatively complex procedures. Here we developed a visual and rapid loop-mediated isothermal amplification (LAMP) method to amplify three GM rice event-specific junction sequences. Target DNA was amplified and visualized by two indicators (SYBR green or hydroxy naphthol blue [HNB]) within 60 min at an isothermal temperature of 63 °C. Different kinds of plants were selected to ensure the specificity of detection and the results of the non-target samples were negative, indicating that the primer sets for the three GM rice varieties had good levels of specificity. The sensitivity of LAMP, with detection limits at low concentration levels (0.01%−0.005% GM), was 10- to 100-fold greater than that of conventional PCR. Additionally, the LAMP assay coupled with an indicator (SYBR green or HNB) facilitated analysis. These findings revealed that the rapid detection method was suitable as a simple field-based test to determine the status of GM crops.

  2. Endpoint Visual Detection of Three Genetically Modified Rice Events by Loop-Mediated Isothermal Amplification

    Directory of Open Access Journals (Sweden)

    Qing Zhu

    2012-11-01

    Full Text Available Genetically modified (GM rice KMD1, TT51-1, and KF6 are three of the most well known transgenic Bt rice lines in China. A rapid and sensitive molecular assay for risk assessment of GM rice is needed. Polymerase chain reaction (PCR, currently the most common method for detecting genetically modified organisms, requires temperature cycling and relatively complex procedures. Here we developed a visual and rapid loop-mediated isothermal amplification (LAMP method to amplify three GM rice event-specific junction sequences. Target DNA was amplified and visualized by two indicators (SYBR green or hydroxy naphthol blue [HNB] within 60 min at an isothermal temperature of 63 °C. Different kinds of plants were selected to ensure the specificity of detection and the results of the non-target samples were negative, indicating that the primer sets for the three GM rice varieties had good levels of specificity. The sensitivity of LAMP, with detection limits at low concentration levels (0.01%–0.005% GM, was 10- to 100-fold greater than that of conventional PCR. Additionally, the LAMP assay coupled with an indicator (SYBR green or HNB facilitated analysis. These findings revealed that the rapid detection method was suitable as a simple field-based test to determine the status of GM crops.

  3. Runtime adaptive multi-processor system-on-chip: RAMPSoC

    OpenAIRE

    Göhringer, D.; Hübner, M.; Schatz, V.; Becker, J.

    2008-01-01

    Current trends in high performance computing show, that the usage of multiprocessor systems on chip are one approach for the requirements of computing intensive applications. The multiprocessor system on chip (MPSoC) approaches often provide a static and homogeneous infrastructure of networked microprocessor on the chip die. A novel idea in this research area is to introduce the dynamic adaptivity of reconfigurable hardware in order to provide a flexible heterogeneous set of processing elemen...

  4. Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches

    Directory of Open Access Journals (Sweden)

    Li Hai-Long

    2011-06-01

    Full Text Available Abstract Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp..

  5. Genetic characterization, species differentiation and detection of Fasciola spp. by molecular approaches.

    Science.gov (United States)

    Ai, Lin; Chen, Mu-Xin; Alasaad, Samer; Elsheikha, Hany M; Li, Juan; Li, Hai-Long; Lin, Rui-Qing; Zou, Feng-Cai; Zhu, Xing-Quan; Chen, Jia-Xu

    2011-06-10

    Liver flukes belonging to the genus Fasciola are among the causes of foodborne diseases of parasitic etiology. These parasites cause significant public health problems and substantial economic losses to the livestock industry. Therefore, it is important to definitively characterize the Fasciola species. Current phenotypic techniques fail to reflect the full extent of the diversity of Fasciola spp. In this respect, the use of molecular techniques to identify and differentiate Fasciola spp. offer considerable advantages. The advent of a variety of molecular genetic techniques also provides a powerful method to elucidate many aspects of Fasciola biology, epidemiology, and genetics. However, the discriminatory power of these molecular methods varies, as does the speed and ease of performance and cost. There is a need for the development of new methods to identify the mechanisms underpinning the origin and maintenance of genetic variation within and among Fasciola populations. The increasing application of the current and new methods will yield a much improved understanding of Fasciola epidemiology and evolution as well as more effective means of parasite control. Herein, we provide an overview of the molecular techniques that are being used for the genetic characterization, detection and genotyping of Fasciola spp..

  6. Detecting novel genetic mutations in Chinese Usher syndrome families using next-generation sequencing technology.

    Science.gov (United States)

    Qu, Ling-Hui; Jin, Xin; Xu, Hai-Wei; Li, Shi-Ying; Yin, Zheng-Qin

    2015-02-01

    Usher syndrome (USH) is the most common cause of combined blindness and deafness inherited in an autosomal recessive mode. Molecular diagnosis is of great significance in revealing the molecular pathogenesis and aiding the clinical diagnosis of this disease. However, molecular diagnosis remains a challenge due to high phenotypic and genetic heterogeneity in USH. This study explored an approach for detecting disease-causing genetic mutations in candidate genes in five index cases from unrelated USH families based on targeted next-generation sequencing (NGS) technology. Through systematic data analysis using an established bioinformatics pipeline and segregation analysis, 10 pathogenic mutations in the USH disease genes were identified in the five USH families. Six of these mutations were novel: c.4398G > A and EX38-49del in MYO7A, c.988_989delAT in USH1C, c.15104_15105delCA and c.6875_6876insG in USH2A. All novel variations segregated with the disease phenotypes in their respective families and were absent from ethnically matched control individuals. This study expanded the mutation spectrum of USH and revealed the genotype-phenotype relationships of the novel USH mutations in Chinese patients. Moreover, this study proved that targeted NGS is an accurate and effective method for detecting genetic mutations related to USH. The identification of pathogenic mutations is of great significance for elucidating the underlying pathophysiology of USH.

  7. Comparison between genetic algorithm and self organizing map to detect botnet network traffic

    Science.gov (United States)

    Yugandhara Prabhakar, Shinde; Parganiha, Pratishtha; Madhu Viswanatham, V.; Nirmala, M.

    2017-11-01

    In Cyber Security world the botnet attacks are increasing. To detect botnet is a challenging task. Botnet is a group of computers connected in a coordinated fashion to do malicious activities. Many techniques have been developed and used to detect and prevent botnet traffic and the attacks. In this paper, a comparative study is done on Genetic Algorithm (GA) and Self Organizing Map (SOM) to detect the botnet network traffic. Both are soft computing techniques and used in this paper as data analytics system. GA is based on natural evolution process and SOM is an Artificial Neural Network type, uses unsupervised learning techniques. SOM uses neurons and classifies the data according to the neurons. Sample of KDD99 dataset is used as input to GA and SOM.

  8. PCR Based Detection of Genetically Modified Soy in Processed Foods Commercially Available in Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Ibrahim Abdullah Alaraidh

    2009-06-01

    Full Text Available In this research, PCR (polymerase chain reaction technique was applied to detect the presence of GMO sold in the Saudi Arabian market. This method was applied to detect genetically modified soy (GM-soy in particular the roundup ready soy (RRS. To confirm the presence of soy, samples were first tested for the existence of the soy specific lectin gene.  A total of eighty samples were tested out of which two samples tested positive as GM-soy. Not surprisingly, the findings showed the existence of GM-soy in food products in Saudi. This supports the necessity of developing precise quantitative and qualitative ways for routine analyses and detection of GMO products in the Saudi Arabian market. With the discovery of GM products in the Saudi Arabian market it would be of no surprise that other Middle Eastern nations also knowingly or unknowingly import GM crops.

  9. New trends in bioanalytical tools for the detection of genetically modified organisms: an update.

    Science.gov (United States)

    Michelini, Elisa; Simoni, Patrizia; Cevenini, Luca; Mezzanotte, Laura; Roda, Aldo

    2008-10-01

    Despite the controversies surrounding genetically modified organisms (GMOs), the production of GM crops is increasing, especially in developing countries. Thanks to new technologies involving genetic engineering and unprecedented access to genomic resources, the next decade will certainly see exponential growth in GMO production. Indeed, EU regulations based on the precautionary principle require any food containing more than 0.9% GM content to be labeled as such. The implementation of these regulations necessitates sampling protocols, the availability of certified reference materials and analytical methodologies that allow the accurate determination of the content of GMOs. In order to qualify for the validation process, a method should fulfil some criteria, defined as "acceptance criteria" by the European Network of GMO Laboratories (ENGL). Several methods have recently been developed for GMO detection and quantitation, mostly based on polymerase chain reaction (PCR) technology. PCR (including its different formats, e.g., double competitive PCR and real-time PCR) remains the technique of choice, thanks to its ability to detect even small amounts of transgenes in raw materials and processed foods. Other approaches relying on DNA detection are based on quartz crystal microbalance piezoelectric biosensors, dry reagent dipstick-type sensors and surface plasmon resonance sensors. The application of visible/near-infrared (vis/NIR) spectroscopy or mass spectrometry combined with chemometrics techniques has also been envisaged as a powerful GMO detection tool. Furthermore, in order to cope with the multiplicity of GMOs released onto the market, the new challenge is the development of routine detection systems for the simultaneous detection of numerous GMOs, including unknown GMOs.

  10. Using Genetic Algorithm for Eye Detection and Tracking in Video Sequence

    Directory of Open Access Journals (Sweden)

    Takuya Akashi

    2007-04-01

    Full Text Available We propose a high-speed size and orientation invariant eye tracking method, which can acquire numerical parameters to represent the size and orientation of the eye. In this paper, we discuss that high tolerance in human head movement and real-time processing that are needed for many applications, such as eye gaze tracking. The generality of the method is also important. We use template matching with genetic algorithm, in order to overcome these problems. A high speed and accuracy tracking scheme using Evolutionary Video Processing for eye detection and tracking is proposed. Usually, a genetic algorithm is unsuitable for a real-time processing, however, we achieved real-time processing. The generality of this proposed method is provided by the artificial iris template used. In our simulations, an eye tracking accuracy is 97.9% and, an average processing time of 28 milliseconds per frame.

  11. An information-gain approach to detecting three-way epistatic interactions in genetic association studies

    DEFF Research Database (Denmark)

    Hu, Ting; Chen, Yuanzhu; Kiralis, Jeff W

    2013-01-01

    Background Epistasis has been historically used to describe the phenomenon that the effect of a given gene on a phenotype can be dependent on one or more other genes, and is an essential element for understanding the association between genetic and phenotypic variations. Quantifying epistasis......-way epistasis. Methods Such a measure is based on information gain, and is able to separate all lower order effects from pure three-way epistasis. Results Our method was verified on synthetic data and applied to real data from a candidate-gene study of tuberculosis in a West African population....... In the tuberculosis data, we found a statistically significant pure three-way epistatic interaction effect that was stronger than any lower-order associations. Conclusion Our study provides a methodological basis for detecting and characterizing high-order gene-gene interactions in genetic association studies....

  12. Capillary electrophoresis with electrochemiluminescent detection for highly sensitive assay of genetically modified organisms.

    Science.gov (United States)

    Guo, Longhua; Yang, Huanghao; Qiu, Bin; Xiao, Xueyang; Xue, Linlin; Kim, Donghwan; Chen, Guonan

    2009-12-01

    A capillary electrophoresis coupled with electrochemiluminescent detection system (CE-ECL) was developed for the detection of polymerase chain reaction (PCR) amplicons. The ECL luminophore, tris(1,10-phenanthroline) ruthenium(II) (Ru(phen)(3)(2+)), was labeled to the PCR primers before amplification. Ru(phen)(3)(2+) was then introduced to PCR amplicons by PCR amplification. Eventually, the PCR amplicons were separated and detected by the homemade CE-ECL system. The detection of a typical genetically modified organism (GMO), Roundup Ready Soy (RRS), was shown as an example to demonstrate the reliability of the proposed approach. Four pairs of primers were amplified by multiple PCR (MPCR) simultaneously, three of which were targeted on the specific sequence of exogenous genes of RRS, and another was targeted on the endogenous reference gene of soybean. Both the conditions for PCR amplification and CE-ECL separation and detection were investigated in detail. Results showed that, under the optimal conditions, the proposed method can accurately identifying RRS. The corresponding limit of detection (LOD) was below 0.01% with 35 PCR cycles.

  13. System on chip thermal vacuum sensor based on standard CMOS process

    International Nuclear Information System (INIS)

    Li Jinfeng; Tang Zhenan; Wang Jiaqi

    2009-01-01

    An on-chip microelectromechanical system was fabricated in a 0.5 μm standard CMOS process for gas pressure detection. The sensor was based on a micro-hotplate (MHP) and had been integrated with a rail to rail operational amplifier and an 8-bit successive approximation register (SAR) A/D converter. A tungsten resistor was manufactured on the MHP as the sensing element, and the sacrificial layer of the sensor was made from polysilicon and etched by surface-micromachining technology. The operational amplifier was configured to make the sensor operate in constant current mode. A digital bit stream was provided as the system output. The measurement results demonstrate that the gas pressure sensitive range of the vacuum sensor extends from 1 to 10 5 Pa. In the gas pressure range from 1 to 100 Pa, the sensitivity of the sensor is 0.23 mV/ Pa, the linearity is 4.95%, and the hysteresis is 8.69%. The operational amplifier can drive 200 ω resistors distortionlessly, and the SAR A/D converter achieves a resolution of 7.4 bit with 100 kHz sample rate. The performance of the operational amplifier and the SAR A/D converter meets the requirements of the sensor system.

  14. On-Chip Production of Size-Controllable Liquid Metal Microdroplets Using Acoustic Waves.

    Science.gov (United States)

    Tang, Shi-Yang; Ayan, Bugra; Nama, Nitesh; Bian, Yusheng; Lata, James P; Guo, Xiasheng; Huang, Tony Jun

    2016-07-01

    Micro- to nanosized droplets of liquid metals, such as eutectic gallium indium (EGaIn) and Galinstan, have been used for developing a variety of applications in flexible electronics, sensors, catalysts, and drug delivery systems. Currently used methods for producing micro- to nanosized droplets of such liquid metals possess one or several drawbacks, including the lack in ability to control the size of the produced droplets, mass produce droplets, produce smaller droplet sizes, and miniaturize the system. Here, a novel method is introduced using acoustic wave-induced forces for on-chip production of EGaIn liquid-metal microdroplets with controllable size. The size distribution of liquid metal microdroplets is tuned by controlling the interfacial tension of the metal using either electrochemistry or electrocapillarity in the acoustic field. The developed platform is then used for heavy metal ion detection utilizing the produced liquid metal microdroplets as the working electrode. It is also demonstrated that a significant enhancement of the sensing performance is achieved by introducing acoustic streaming during the electrochemical experiments. The demonstrated technique can be used for developing liquid-metal-based systems for a wide range of applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Towards on-chip integration of brain imaging photodetectors using standard CMOS process.

    Science.gov (United States)

    Kamrani, Ehsan; Lesage, Frederic; Sawan, Mohamad

    2013-01-01

    The main effects of on-chip integration on the performance and efficiency of silicon avalanche photodiode (SiAPD) and photodetector front-end is addressed in this paper based on the simulation and fabrication experiments. Two different silicon APDs are fabricated separately and also integrated with a transimpedance amplifier (TIA) front-end using standard CMOS technology. SiAPDs are designed in p+/n-well structure with guard rings realized in different shapes. The TIA front-end has been designed using distributed-gain concept combined with resistive-feedback and common-gate topology to reach low-noise and high gain-bandwidth product (GBW) characteristics. The integrated SiAPDs show higher signal-to-noise ratio (SNR), sensitivity and detection efficiency comparing to the separate SiAPDs. The integration does not show a significant effect on the gain and preserves the low power consumption. Using APDs with p-well guard-ring is preferred due to the higher observed efficiency after integration.

  16. Ultrahigh-speed Si-integrated on-chip laser with tailored dynamic characteristics

    DEFF Research Database (Denmark)

    Park, Gyeong Cheol; Xue, Weiqi; Piels, Molly

    2016-01-01

    -pumped compact optical feedback structure can be realised, which together tailor the frequency response function for achieving a very high speed at low injection currents. Furthermore, light can be emitted laterally into a Si waveguide. From an 1.54-μm optically-pumped laser, a 3-dB frequency of 27 GHz...... was obtained at a pumping level corresponding to sub-mA. Using measured 3-dB frequen-cies and calculated equivalent currents, the modulation current efficiency factor (MCEF) is estimated to be 42.1 GHz/mA(1/2), which is superior among microcavity lasers. This shows a high potential for a very high speed at low......For on-chip interconnects, an ideal light source should have an ultralow energy consumption per bandwidth (operating en-ergy) as well as sufficient output power for error-free detection. Nanocavity lasers have been considered the most ideal for smaller operating energy. However, they have...

  17. An automated microfluidic DNA microarray platform for genetic variant detection in inherited arrhythmic diseases.

    Science.gov (United States)

    Huang, Shu-Hong; Chang, Yu-Shin; Juang, Jyh-Ming Jimmy; Chang, Kai-Wei; Tsai, Mong-Hsun; Lu, Tzu-Pin; Lai, Liang-Chuan; Chuang, Eric Y; Huang, Nien-Tsu

    2018-03-12

    In this study, we developed an automated microfluidic DNA microarray (AMDM) platform for point mutation detection of genetic variants in inherited arrhythmic diseases. The platform allows for automated and programmable reagent sequencing under precise conditions of hybridization flow and temperature control. It is composed of a commercial microfluidic control system, a microfluidic microarray device, and a temperature control unit. The automated and rapid hybridization process can be performed in the AMDM platform using Cy3 labeled oligonucleotide exons of SCN5A genetic DNA, which produces proteins associated with sodium channels abundant in the heart (cardiac) muscle cells. We then introduce a graphene oxide (GO)-assisted DNA microarray hybridization protocol to enable point mutation detection. In this protocol, a GO solution is added after the staining step to quench dyes bound to single-stranded DNA or non-perfectly matched DNA, which can improve point mutation specificity. As proof-of-concept we extracted the wild-type and mutant of exon 12 and exon 17 of SCN5A genetic DNA from patients with long QT syndrome or Brugada syndrome by touchdown PCR and performed a successful point mutation discrimination in the AMDM platform. Overall, the AMDM platform can greatly reduce laborious and time-consuming hybridization steps and prevent potential contamination. Furthermore, by introducing the reciprocating flow into the microchannel during the hybridization process, the total assay time can be reduced to 3 hours, which is 6 times faster than the conventional DNA microarray. Given the automatic assay operation, shorter assay time, and high point mutation discrimination, we believe that the AMDM platform has potential for low-cost, rapid and sensitive genetic testing in a simple and user-friendly manner, which may benefit gene screening in medical practice.

  18. One Novel Multiple-Target Plasmid Reference Molecule Targeting Eight Genetically Modified Canola Events for Genetically Modified Canola Detection.

    Science.gov (United States)

    Li, Zhuqing; Li, Xiang; Wang, Canhua; Song, Guiwen; Pi, Liqun; Zheng, Lan; Zhang, Dabing; Yang, Litao

    2017-09-27

    Multiple-target plasmid DNA reference materials have been generated and utilized as good substitutes of matrix-based reference materials in the analysis of genetically modified organisms (GMOs). Herein, we report the construction of one multiple-target plasmid reference molecule, pCAN, which harbors eight GM canola event-specific sequences (RF1, RF2, MS1, MS8, Topas 19/2, Oxy235, RT73, and T45) and a partial sequence of the canola endogenous reference gene PEP. The applicability of this plasmid reference material in qualitative and quantitative PCR assays of the eight GM canola events was evaluated, including the analysis of specificity, limit of detection (LOD), limit of quantification (LOQ), and performance of pCAN in the analysis of various canola samples, etc. The LODs are 15 copies for RF2, MS1, and RT73 assays using pCAN as the calibrator and 10 genome copies for the other events. The LOQ in each event-specific real-time PCR assay is 20 copies. In quantitative real-time PCR analysis, the PCR efficiencies of all event-specific and PEP assays are between 91% and 97%, and the squared regression coefficients (R 2 ) are all higher than 0.99. The quantification bias values varied from 0.47% to 20.68% with relative standard deviation (RSD) from 1.06% to 24.61% in the quantification of simulated samples. Furthermore, 10 practical canola samples sampled from imported shipments in the port of Shanghai, China, were analyzed employing pCAN as the calibrator, and the results were comparable with those assays using commercial certified materials as the calibrator. Concluding from these results, we believe that this newly developed pCAN plasmid is one good candidate for being a plasmid DNA reference material in the detection and quantification of the eight GM canola events in routine analysis.

  19. Application of a New Genetic Deafness Microarray for Detecting Mutations in the Deaf in China.

    Directory of Open Access Journals (Sweden)

    Hong Wu

    Full Text Available The aim of this study was to evaluate the GoldenGate microarray as a diagnostic tool and to elucidate the contribution of the genes on this array to the development of both nonsyndromic and syndromic sensorineural hearing loss in China.We developed a microarray to detect 240 mutations underlying syndromic and nonsyndromic sensorineural hearing loss. The microarray was then used for analysis of 382 patients with nonsyndromic sensorineural hearing loss (including 15 patients with enlarged vestibular aqueduct syndrome, 21 patients with Waardenburg syndrome, and 60 unrelated controls. Subsequently, we analyzed the sensitivity, specificity, and reproducibility of this new approach after Sanger sequencing-based verification, and also determined the contribution of the genes on this array to the development of distinct hearing disorders.The sensitivity and specificity of the microarray chip were 98.73% and 98.34%, respectively. Genetic defects were identified in 61.26% of the patients with nonsyndromic sensorineural hearing loss, and 9 causative genes were identified. The molecular etiology was confirmed in 19.05% and 46.67% of the patients with Waardenburg syndrome and enlarged vestibular aqueduct syndrome, respectively.Our new mutation-based microarray comprises an accurate and comprehensive genetic tool for the detection of sensorineural hearing loss. This microarray-based detection method could serve as a first-pass screening (before next-generation-sequencing screening for deafness-causing mutations in China.

  20. Detection of alien genetic introgressions in bread wheat using dot-blot genomic hybridisation.

    Science.gov (United States)

    Rey, María-Dolores; Prieto, Pilar

    2017-01-01

    Simple, reliable methods for the identification of alien genetic introgressions are required in plant breeding programmes. The use of genomic dot-blot hybridisation allows the detection of small Hordeum chilense genomic introgressions in the descendants of genetic crosses between wheat and H. chilense addition or substitution lines in wheat when molecular markers are difficult to use. Based on genomic in situ hybridisation, DNA samples from wheat lines carrying putatively H. chilense introgressions were immobilised on a membrane, blocked with wheat genomic DNA and hybridised with biotin-labelled H. chilense genomic DNA as a probe. This dot-blot screening reduced the number of plants necessary to be analysed by molecular markers or in situ hybridisation, saving time and money. The technique was sensitive enough to detect a minimum of 5 ng of total genomic DNA immobilised on the membrane or about 1/420 dilution of H. chilense genomic DNA in the wheat background. The robustness of the technique was verified by in situ hybridisation. In addition, the detection of other wheat relative species such as Hordeum vulgare , Secale cereale and Agropyron cristatum in the wheat background was also reported .

  1. Establishing a diagnostic system for detecting Ralstonia solanacearum and genetic differentiation using RAPD molecular markers

    Directory of Open Access Journals (Sweden)

    Edisson Chavarro Mesa

    2006-01-01

    Full Text Available A polymerase chain reaction-based diagnostic test (PCR has been developed for amplifying a región and obtaining a 292 bp product by using specific 16S rDNA primers for the rapid and precise identification of the causative agent (Ralstonia solanacearum of bacterial withering of potato in asymptomatic tubers. The bacteria was isolated from potato tubers and banana fruit using culturing techniques and immunological and molecular ELISA-NCM and PCR tests, respectively. PCR detected the presence of R. solanacearum on asymptomatic tubers by contrast with ELISA-NCM which did not detect this pathogen. Analysing random amplified polymorphic DNA (RAPD led to differentiating and grouping R. solanacearum by geographical región and bacterial strain, suggesting that differences exist amongst existing collections according to their place of origin, presenting high genetic variability. The results showed that PCR is a sensitive and specific test for detecting R. solanacearum and can therefore be implemented as a method for controlling this pathogen in seed production and certification programmes in áreas free of the disease. The pathogen has been shown to be genetically heterogeneous according to the samples' geographical área thereby hampering control in áreas of Colombia experiencing phytosanitary problems with R. solanacearum in potato crops Key words: bacterial withered, moko, PCR-16S rADN, ELISA-NCM, PCR-RAPD.

  2. Design of a 40-nm CMOS integrated on-chip oscilloscope for 5-50 GHz spin wave characterization

    Science.gov (United States)

    Egel, Eugen; Csaba, György; Dietz, Andreas; Breitkreutz-von Gamm, Stephan; Russer, Johannes; Russer, Peter; Kreupl, Franz; Becherer, Markus

    2018-05-01

    Spin wave (SW) devices are receiving growing attention in research as a strong candidate for low power applications in the beyond-CMOS era. All SW applications would require an efficient, low power, on-chip read-out circuitry. Thus, we provide a concept for an on-chip oscilloscope (OCO) allowing parallel detection of the SWs at different frequencies. The readout system is designed in 40-nm CMOS technology and is capable of SW device characterization. First, the SWs are picked up by near field loop antennas, placed below yttrium iron garnet (YIG) film, and amplified by a low noise amplifier (LNA). Second, a mixer down-converts the radio frequency (RF) signal of 5 - 50 GHz to lower intermediate frequencies (IF) around 10 - 50 MHz. Finally, the IF signal can be digitized and analyzed regarding the frequency, amplitude and phase variation of the SWs. The power consumption and chip area of the whole OCO are estimated to 166.4 mW and 1.31 mm2, respectively.

  3. On-Chip Method to Measure Mechanical Characteristics of a Single Cell by Using Moiré Fringe

    Directory of Open Access Journals (Sweden)

    Hirotaka Sugiura

    2015-06-01

    Full Text Available We propose a method to characterize the mechanical properties of cells using a robot-integrated microfluidic chip (robochip and microscopy. The microfluidic chip is designed to apply the specified deformations to a single detached cell using an on-chip actuator probe. The reaction force is simultaneously measured using an on-chip force sensor composed of a hollow folded beam and probe structure. In order to measure the cellular characteristics in further detail, a sub-pixel level of resolution of probe position is required. Therefore, we utilize the phase detection of moiré fringe. Using this method, the experimental resolution of the probe position reaches 42 nm. This is approximately ten times smaller than the optical wavelength, which is the limit of sharp imaging with a microscope. Calibration of the force sensor is also important in accurately measuring cellular reaction forces. We calibrated the spring constant from the frequency response, by the proposed sensing method of the probe position. As a representative of mechanical characteristics, we measured the elastic modulus of Madin-Darby Cannie Kidney (MDCK cells. In spite of the rigid spring constant, the resolution and sensitivity were twice that achieved in our previous study. Unique cellular characteristics can be elucidated by the improvements in sensing resolution and accuracy.

  4. Detecting un-authorized genetically modified organisms (GMOs) and derived materials.

    Science.gov (United States)

    Holst-Jensen, Arne; Bertheau, Yves; de Loose, Marc; Grohmann, Lutz; Hamels, Sandrine; Hougs, Lotte; Morisset, Dany; Pecoraro, Sven; Pla, Maria; Van den Bulcke, Marc; Wulff, Doerte

    2012-01-01

    Genetically modified plants, in the following referred to as genetically modified organisms or GMOs, have been commercially grown for almost two decades. In 2010 approximately 10% of the total global crop acreage was planted with GMOs (James, 2011). More than 30 countries have been growing commercial GMOs, and many more have performed field trials. Although the majority of commercial GMOs both in terms of acreage and specific events belong to the four species: soybean, maize, cotton and rapeseed, there are another 20+ species where GMOs are commercialized or in the pipeline for commercialization. The number of GMOs cultivated in field trials or for commercial production has constantly increased during this time period. So have the number of species, the number of countries involved, the diversity of novel (added) genetic elements and the global trade. All of these factors contribute to the increasing complexity of detecting and correctly identifying GMO derived material. Many jurisdictions, including the European Union (EU), legally distinguish between authorized (and therefore legal) and un-authorized (and therefore illegal) GMOs. Information about the developments, field trials, authorizations, cultivation, trade and observations made in the official GMO control laboratories in different countries around the world is often limited, despite several attempts such as the OECD BioTrack for voluntary dissemination of data. This lack of information inevitably makes it challenging to detect and identify GMOs, especially the un-authorized GMOs. The present paper reviews the state of the art technologies and approaches in light of coverage, practicability, sensitivity and limitations. Emphasis is put on exemplifying practical detection of un-authorized GMOs. Although this paper has a European (EU) bias when examples are given, the contents have global relevance. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. Interlaboratory validation data on real-time polymerase chain reaction detection for unauthorized genetically modified papaya line PRSV-YK

    Directory of Open Access Journals (Sweden)

    Kosuke Nakamura

    2016-06-01

    Real-time polymerase chain reaction (PCR detection method for unauthorized genetically modified (GM papaya (Carica papaya L. line PRSV-YK (PRSV-YK detection method was developed using whole genome sequence data (DDBJ Sequenced Read Archive under accession No. PRJDB3976. Interlaboratory validation datasets for PRSV-YK detection method were provided. Data indicating homogeneity of samples prepared for interlaboratory validation were included. Specificity and sensitivity test data for PRSV-YK detection method were also provided.

  6. Capacitance variation induced by microfluidic two-phase flow across insulated interdigital electrodes in lab-on-chip devices.

    Science.gov (United States)

    Dong, Tao; Barbosa, Cátia

    2015-01-26

    Microfluidic two-phase flow detection has attracted plenty of interest in various areas of biology, medicine and chemistry. This work presents a capacitive sensor using insulated interdigital electrodes (IDEs) to detect the presence of droplets in a microchannel. This droplet sensor is composed of a glass substrate, patterned gold electrodes and an insulation layer. A polydimethylsiloxane (PDMS) cover bonded to the multilayered structure forms a microchannel. Capacitance variation induced by the droplet passage was thoroughly investigated with both simulation and experimental work. Olive oil and deionized water were employed as the working fluids in the experiments to demonstrate the droplet sensor. The results show a good sensitivity of the droplet with the appropriate measurement connection. This capacitive droplet sensor is promising to be integrated into a lab-on-chip device for in situ monitoring/counting of droplets or bubbles.

  7. Estimation of genetic parameters and detection of quantitative trait loci for metabolites in Danish Holstein milk

    DEFF Research Database (Denmark)

    Buitenhuis, Albert Johannes; Sundekilde, Ulrik; Poulsen, Nina Aagaard

    2013-01-01

    Small components and metabolites in milk are significant for the utilization of milk, not only in dairy food production but also as disease predictors in dairy cattle. This study focused on estimation of genetic parameters and detection of quantitative trait loci for metabolites in bovine milk. F...... for lactic acid to >0.8 for orotic acid and β-hydroxybutyrate. A single SNP association analysis revealed 7 genome-wide significant quantitative trait loci [malonate: Bos taurus autosome (BTA)2 and BTA7; galactose-1-phosphate: BTA2; cis-aconitate: BTA11; urea: BTA12; carnitine: BTA25...

  8. Genetic Local Search for Optimum Multiuser Detection Problem in DS-CDMA Systems

    Science.gov (United States)

    Wang, Shaowei; Ji, Xiaoyong

    Optimum multiuser detection (OMD) in direct-sequence code-division multiple access (DS-CDMA) systems is an NP-complete problem. In this paper, we present a genetic local search algorithm, which consists of an evolution strategy framework and a local improvement procedure. The evolution strategy searches the space of feasible, locally optimal solutions only. A fast iterated local search algorithm, which employs the proprietary characteristics of the OMD problem, produces local optima with great efficiency. Computer simulations show the bit error rate (BER) performance of the GLS outperforms other multiuser detectors in all cases discussed. The computation time is polynomial complexity in the number of users.

  9. Microgels produced using microfluidic on-chip polymer blending for controlled released of VEGF encoding lentivectors.

    Science.gov (United States)

    Madrigal, Justin L; Sharma, Shonit N; Campbell, Kevin T; Stilhano, Roberta S; Gijsbers, Rik; Silva, Eduardo A

    2018-03-15

    Alginate hydrogels are widely used as delivery vehicles due to their ability to encapsulate and release a wide range of cargos in a gentle and biocompatible manner. The release of encapsulated therapeutic cargos can be promoted or stunted by adjusting the hydrogel physiochemical properties. However, the release from such systems is often skewed towards burst-release or lengthy retention. To address this, we hypothesized that the overall magnitude of burst release could be adjusted by combining microgels with distinct properties and release behavior. Microgel suspensions were generated using a process we have termed on-chip polymer blending to yield composite suspensions of a range of microgel formulations. In this manner, we studied how alginate percentage and degradation relate to the release of lentivectors. Whereas changes in alginate percentage had a minimal impact on lentivector release, microgel degradation led to a 3-fold increase, and near complete release, over 10 days. Furthermore, by controlling the amount of degradable alginate present within microgels the relative rate of release can be adjusted. A degradable formulation of microgels was used to deliver vascular endothelial growth factor (VEGF)-encoding lentivectors in the chick chorioallantoic membrane (CAM) assay and yielded a proangiogenic response in comparison to the same lentivectors delivered in suspension. The utility of blended microgel suspensions may provide an especially appealing platform for the delivery of lentivectors or similarly sized therapeutics. Genetic therapeutics hold considerable potential for the treatment of diseases and disorders including ischemic cardiovascular diseases. To realize this potential, genetic vectors must be precisely and efficiently delivered to targeted regions of the body. However, conventional methods of delivery do not provide sufficient spatial and temporal control. Here, we demonstrate how alginate microgels provide a basis for developing systems for

  10. Highly specific detection of genetic modification events using an enzyme-linked probe hybridization chip.

    Science.gov (United States)

    Zhang, M Z; Zhang, X F; Chen, X M; Chen, X; Wu, S; Xu, L L

    2015-08-10

    The enzyme-linked probe hybridization chip utilizes a method based on ligase-hybridizing probe chip technology, with the principle of using thio-primers for protection against enzyme digestion, and using lambda DNA exonuclease to cut multiple PCR products obtained from the sample being tested into single-strand chains for hybridization. The 5'-end amino-labeled probe was fixed onto the aldehyde chip, and hybridized with the single-stranded PCR product, followed by addition of a fluorescent-modified probe that was then enzymatically linked with the adjacent, substrate-bound probe in order to achieve highly specific, parallel, and high-throughput detection. Specificity and sensitivity testing demonstrated that enzyme-linked probe hybridization technology could be applied to the specific detection of eight genetic modification events at the same time, with a sensitivity reaching 0.1% and the achievement of accurate, efficient, and stable results.

  11. Developing a Genetically Encoded, Cross-Species Biosensor for Detecting Ammonium and Regulating Biosynthesis of Cyanophycin.

    Science.gov (United States)

    Xiao, Yi; Jiang, Wen; Zhang, Fuzhong

    2017-10-20

    Responding to nitrogen status is essential for all living organisms. Bacteria have evolved various complex and exquisite regulatory systems to control nitrogen metabolism. However, natural nitrogen regulatory systems, owing to their complexity, often function only in their original hosts and do not respond properly when transferred to another species. By harnessing the Lactococcus GlnRA system, we developed a genetically encoded, cross-species ammonium biosensor that displays a dynamic range up to 9-fold upon detection of ammonium ion. We demonstrated applications of this ammonium biosensor in three different species (Escherichia coli, Pseudomonas putida, and Synechocystis sp.) to detect different nitrogen sources. This ammonium sensor was further used to regulate the biosynthesis of a nitrogen-rich polymer, cyanophycin, based on ammonium concentration. Given the importance of nitrogen responses, the developed biosensor should be broadly applicable to synthetic biology and bioengineering.

  12. A review for detecting gene-gene interactions using machine learning methods in genetic epidemiology.

    Science.gov (United States)

    Koo, Ching Lee; Liew, Mei Jing; Mohamad, Mohd Saberi; Salleh, Abdul Hakim Mohamed

    2013-01-01

    Recently, the greatest statistical computational challenge in genetic epidemiology is to identify and characterize the genes that interact with other genes and environment factors that bring the effect on complex multifactorial disease. These gene-gene interactions are also denoted as epitasis in which this phenomenon cannot be solved by traditional statistical method due to the high dimensionality of the data and the occurrence of multiple polymorphism. Hence, there are several machine learning methods to solve such problems by identifying such susceptibility gene which are neural networks (NNs), support vector machine (SVM), and random forests (RFs) in such common and multifactorial disease. This paper gives an overview on machine learning methods, describing the methodology of each machine learning methods and its application in detecting gene-gene and gene-environment interactions. Lastly, this paper discussed each machine learning method and presents the strengths and weaknesses of each machine learning method in detecting gene-gene interactions in complex human disease.

  13. The Molecular Epidemiology and Genetic Environment of Carbapenemases Detected in Africa.

    Science.gov (United States)

    Sekyere, John Osei; Govinden, Usha; Essack, Sabiha

    2016-01-01

    Research articles describing carbapenemases and their genetic environments in Gram-negative bacteria were reviewed to determine the molecular epidemiology of carbapenemases in Africa. The emergence of resistance to the carbapenems, the last resort antibiotic for difficult to treat bacterial infections, affords clinicians few therapeutic options, with a resulting increase in morbidities, mortalities, and healthcare costs. However, the molecular epidemiology of carbapenemases throughout Africa is less described. Research articles and conference proceedings describing the genetic environment and molecular epidemiology of carbapenemases in Africa were retrieved from Google Scholar, Scifinder, Pubmed, Web of Science, and Science Direct databases. Predominant carbapenemase genes so far described in Africa include the blaOXA-48 type, blaIMP, blaVIM, and blaNDM in Acinetobacter baumannii, Klebsiella pneumoniae, Enterobacter cloacae, Citrobacter spp., and Escherichia coli carried on various plasmid types and sizes, transposons, and integrons. Class D and class B carbapenemases, mainly prevalent in A. baumannii, K. pneumoniae, E. cloacae, Citrobacter spp., and E. coli were the commonest carbapenemases. Carbapenemases are mainly reported in North and South Africa as under-resourced laboratories, lack of awareness and funding preclude the detection and reporting of carbapenemase-mediated resistance. Consequently, the true molecular epidemiology of carbapenemases and their genetic environment in Africa is still unknown.

  14. Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal.

    Directory of Open Access Journals (Sweden)

    Rachel Daniels

    Full Text Available Using parasite genotyping tools, we screened patients with mild uncomplicated malaria seeking treatment at a clinic in Thiès, Senegal, from 2006 to 2011. We identified a growing frequency of infections caused by genetically identical parasite strains, coincident with increased deployment of malaria control interventions and decreased malaria deaths. Parasite genotypes in some cases persisted clonally across dry seasons. The increase in frequency of genetically identical parasite strains corresponded with decrease in the probability of multiple infections. Further, these observations support evidence of both clonal and epidemic population structures. These data provide the first evidence of a temporal correlation between the appearance of identical parasite types and increased malaria control efforts in Africa, which here included distribution of insecticide treated nets (ITNs, use of rapid diagnostic tests (RDTs for malaria detection, and deployment of artemisinin combination therapy (ACT. Our results imply that genetic surveillance can be used to evaluate the effectiveness of disease control strategies and assist a rational global malaria eradication campaign.

  15. APPLICATION OF RYE SSR MARKERS FOR DETECTION OF GENETIC DIVERSITY IN TRITICALE

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    Želmíra Balážová

    2016-06-01

    Full Text Available Present study aims to testify usefulness of particular rye SSR markers for the detection of genetic diversity degree in the set of 20 triticale cultivars coming from different European countries. For this purpose, a set of six rye SSR markers were used. The set of six polymorphic markers provided 22 alleles with an average frequency of 3.67 alleles per locus. The number of alleles ranged between 2 (SCM43 and 5 (SCM28, SCM86. Resulting from the number and frequency of alleles diversity index (DI, polymorphic information content (PIC and probability of identity (PI were calculated. An average value of PIC for 6 SSR markers was 0.505, the highest value was calculated for rye SSR marker SCM86 (0.706. Based on UPGMA algorithm, a dendrogram was constructed. In dendrogram cultivars were divided into two main clusters. The first cluster contained two cultivars, Russian cultivar Greneder and Slovak cultivar Largus, and second included 18 cultivars. Genetically the closest were two Greek cultivars (Niobi and Thisbi and were close to other Greek cultivar Vrodi. It was possible to separate triticale cultivars of spring and winter form in dendrogram. Results showed the utility of rye microsatellite markers for estimation of genetic diversity of European triticale genotypes leading to genotype identification.

  16. Detecting Genetic Interactions for Quantitative Traits Using m-Spacing Entropy Measure

    Directory of Open Access Journals (Sweden)

    Jaeyong Yee

    2015-01-01

    Full Text Available A number of statistical methods for detecting gene-gene interactions have been developed in genetic association studies with binary traits. However, many phenotype measures are intrinsically quantitative and categorizing continuous traits may not always be straightforward and meaningful. Association of gene-gene interactions with an observed distribution of such phenotypes needs to be investigated directly without categorization. Information gain based on entropy measure has previously been successful in identifying genetic associations with binary traits. We extend the usefulness of this information gain by proposing a nonparametric evaluation method of conditional entropy of a quantitative phenotype associated with a given genotype. Hence, the information gain can be obtained for any phenotype distribution. Because any functional form, such as Gaussian, is not assumed for the entire distribution of a trait or a given genotype, this method is expected to be robust enough to be applied to any phenotypic association data. Here, we show its use to successfully identify the main effect, as well as the genetic interactions, associated with a quantitative trait.

  17. Detection of genetically modified DNA in fresh and processed foods sold in Kuwait.

    Science.gov (United States)

    Al-Salameen, Fadila; Kumar, Vinod; Al-Aqeel, Hamed; Al-Hashash, Hanadi; Hejji, Ahmed Bin

    2012-01-01

    Developments in genetic engineering technology have led to an increase in number of food products that contain genetically engineered crops in the global market. However, due to lack of scientific studies, the presence of genetically modified organisms (GMOs) in the Kuwaiti food market is currently ambiguous. Foods both for human and animal consumption are being imported from countries that are known to produce GM food. Therefore, an attempt has been made to screen foods sold in the Kuwaiti market to detect GMOs in the food. For this purpose, samples collected from various markets in Kuwait have been screened by SYBR green-based real time polymerase chain reaction (RT-PCR) method. Further confirmation and GMO quantification was performed by TaqMan-based RT-PCR. Results indicated that a significant number of food commodities sold in Kuwait were tested positive for the presence of GMO. Interestingly, certain processed foods were tested positive for more than one transgenic events showing complex nature of GMOs in food samples. Results of this study clearly indicate the need for well-defined legislations and regulations on the marketing of approved GM food and its labeling to protect consumer's rights.

  18. Detection vs. selection: integration of genetic, epigenetic and environmental cues in fluctuating environments.

    Science.gov (United States)

    McNamara, John M; Dall, Sasha R X; Hammerstein, Peter; Leimar, Olof

    2016-10-01

    There are many inputs during development that influence an organism's fit to current or upcoming environments. These include genetic effects, transgenerational epigenetic influences, environmental cues and developmental noise, which are rarely investigated in the same formal framework. We study an analytically tractable evolutionary model, in which cues are integrated to determine mature phenotypes in fluctuating environments. Environmental cues received during development and by the mother as an adult act as detection-based (individually observed) cues. The mother's phenotype and a quantitative genetic effect act as selection-based cues (they correlate with environmental states after selection). We specify when such cues are complementary and tend to be used together, and when using the most informative cue will predominate. Thus, we extend recent analyses of the evolutionary implications of subsets of these effects by providing a general diagnosis of the conditions under which detection and selection-based influences on development are likely to evolve and coexist. © 2016 John Wiley & Sons Ltd/CNRS.

  19. [Application of DNA extraction kit, 'GM quicker' for detection of genetically modified soybeans].

    Science.gov (United States)

    Sato, Noriko; Sugiura, Yoshitsugu; Tanaka, Toshitsugu

    2012-01-01

    Several DNA extraction methods have been officially introduced to detect genetically modified soybeans, but the choice of DNA extraction kits depend on the nature of the samples, such as grains or processed foods. To overcome this disadvantage, we examined whether the GM quicker kit is available for both grains and processed foods. We compared GM quicker with four approved DNA extraction kits in respect of DNA purity, copy numbers of lectin gene, and working time. We found that the DNA quality of GM quicker was superior to that of the other kits for grains, and the procedure was faster. However, in the case of processed foods, GM quicker was not superior to the other kits. We therefore investigated an unapproved GM quicker 3 kit, which is available for DNA extraction from processed foods, such as tofu and boiled soybeans. The GM quicker 3 kit provided good DNA quality from both grains and processed foods, so we made a minor modification of the GM quicker-based protocol that was suitable for processed foods, using GM quicker and its reagents. The modified method enhanced the performance of GM quicker with processed foods. We believe that GM quicker with the modified protocol is an excellent tool to obtain high-quality DNA from grains and processed foods for detection of genetically modified soybeans.

  20. DNA extraction methods for detecting genetically modified foods: A comparative study.

    Science.gov (United States)

    Elsanhoty, Rafaat M; Ramadan, Mohamed Fawzy; Jany, Klaus Dieter

    2011-06-15

    The work presented in this manuscript was achieved to compare six different methods for extracting DNA from raw maize and its derived products. The methods that gave higher yield and quality of DNA were chosen to detect the genetic modification in the samples collected from the Egyptian market. The different methods used were evaluated for extracting DNA from maize kernels (without treatment), maize flour (mechanical treatment), canned maize (sweet corn), frozen maize (sweet corn), maize starch, extruded maize, popcorn, corn flacks, maize snacks, and bread made from corn flour (mechanical and thermal treatments). The quality and quantity of the DNA extracted from the standards, containing known percentages of GMO material and from the different food products were evaluated. For qualitative detection of the GMO varieties in foods, the GMOScreen 35S/NOS test kit was used, to screen the genetic modification in the samples. The positive samples for the 35S promoter and/or the NOS terminator were identified by the standard methods adopted by EU. All of the used methods extracted yielded good DNA quality. However, we noted that the purest DNA extract were obtained using the DNA extraction kit (Roche) and this generally was the best method for extracting DNA from most of the maize-derived foods. We have noted that the yield of DNA extracted from maize-derived foods was generally lower in the processed products. The results indicated that 17 samples were positive for the presence of 35S promoter, while 34% from the samples were positive for the genetically modified maize line Bt-176. Copyright © 2010 Elsevier Ltd. All rights reserved.

  1. A Low-Power Integrated Humidity CMOS Sensor by Printing-on-Chip Technology

    Directory of Open Access Journals (Sweden)

    Chang-Hung Lee

    2014-05-01

    Full Text Available A low-power, wide-dynamic-range integrated humidity sensing chip is implemented using a printable polymer sensing material with an on-chip pulse-width-modulation interface circuit. By using the inkjet printing technique, poly(3,4-ethylene-dioxythiophene/polystyrene sulfonate that has humidity sensing features can be printed onto the top metal layer of a 0.35 μm CMOS IC. The developed printing-on-chip humidity sensor achieves a heterogeneous three dimensional sensor system-on-chip architecture. The humidity sensing of the implemented printing-on-chip sensor system is experimentally tested. The sensor shows a sensitivity of 0.98% to humidity in the atmosphere. The maximum dynamic range of the readout circuit is 9.8 MΩ, which can be further tuned by the frequency of input signal to fit the requirement of the resistance of printed sensor. The power consumption keeps only 154 μW. This printing-on-chip sensor provides a practical solution to fulfill an ultra-small integrated sensor for the applications in miniaturized sensing systems.

  2. A low-power integrated humidity CMOS sensor by printing-on-chip technology.

    Science.gov (United States)

    Lee, Chang-Hung; Chuang, Wen-Yu; Cowan, Melissa A; Wu, Wen-Jung; Lin, Chih-Ting

    2014-05-23

    A low-power, wide-dynamic-range integrated humidity sensing chip is implemented using a printable polymer sensing material with an on-chip pulse-width-modulation interface circuit. By using the inkjet printing technique, poly(3,4-ethylene-dioxythiophene)/polystyrene sulfonate that has humidity sensing features can be printed onto the top metal layer of a 0.35 μm CMOS IC. The developed printing-on-chip humidity sensor achieves a heterogeneous three dimensional sensor system-on-chip architecture. The humidity sensing of the implemented printing-on-chip sensor system is experimentally tested. The sensor shows a sensitivity of 0.98% to humidity in the atmosphere. The maximum dynamic range of the readout circuit is 9.8 MΩ, which can be further tuned by the frequency of input signal to fit the requirement of the resistance of printed sensor. The power consumption keeps only 154 μW. This printing-on-chip sensor provides a practical solution to fulfill an ultra-small integrated sensor for the applications in miniaturized sensing systems.

  3. A simplified and accurate detection of the genetically modified wheat MON71800 with one calibrator plasmid.

    Science.gov (United States)

    Kim, Jae-Hwan; Park, Saet-Byul; Roh, Hyo-Jeong; Park, Sunghoon; Shin, Min-Ki; Moon, Gui Im; Hong, Jin-Hwan; Kim, Hae-Yeong

    2015-06-01

    With the increasing number of genetically modified (GM) events, unauthorized GMO releases into the food market have increased dramatically, and many countries have developed detection tools for them. This study described the qualitative and quantitative detection methods of unauthorized the GM wheat MON71800 with a reference plasmid (pGEM-M71800). The wheat acetyl-CoA carboxylase (acc) gene was used as the endogenous gene. The plasmid pGEM-M71800, which contains both the acc gene and the event-specific target MON71800, was constructed as a positive control for the qualitative and quantitative analyses. The limit of detection in the qualitative PCR assay was approximately 10 copies. In the quantitative PCR assay, the standard deviation and relative standard deviation repeatability values ranged from 0.06 to 0.25 and from 0.23% to 1.12%, respectively. This study supplies a powerful and very simple but accurate detection strategy for unauthorized GM wheat MON71800 that utilizes a single calibrator plasmid. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Molecular Approaches for High Throughput Detection and Quantification of Genetically Modified Crops: A Review

    Directory of Open Access Journals (Sweden)

    Ibrahim B. Salisu

    2017-10-01

    Full Text Available As long as the genetically modified crops are gaining attention globally, their proper approval and commercialization need accurate and reliable diagnostic methods for the transgenic content. These diagnostic techniques are mainly divided into two major groups, i.e., identification of transgenic (1 DNA and (2 proteins from GMOs and their products. Conventional methods such as PCR (polymerase chain reaction and enzyme-linked immunosorbent assay (ELISA were routinely employed for DNA and protein based quantification respectively. Although, these Techniques (PCR and ELISA are considered as significantly convenient and productive, but there is need for more advance technologies that allow for high throughput detection and the quantification of GM event as the production of more complex GMO is increasing day by day. Therefore, recent approaches like microarray, capillary gel electrophoresis, digital PCR and next generation sequencing are more promising due to their accuracy and precise detection of transgenic contents. The present article is a brief comparative study of all such detection techniques on the basis of their advent, feasibility, accuracy, and cost effectiveness. However, these emerging technologies have a lot to do with detection of a specific event, contamination of different events and determination of fusion as well as stacked gene protein are the critical issues to be addressed in future.

  5. Visual detection of multiple genetically modified organisms in a capillary array.

    Science.gov (United States)

    Shao, Ning; Chen, Jianwei; Hu, Jiaying; Li, Rong; Zhang, Dabing; Guo, Shujuan; Hui, Junhou; Liu, Peng; Yang, Litao; Tao, Sheng-Ce

    2017-01-31

    There is an urgent need for rapid, low-cost multiplex methodologies for the monitoring of genetically modified organisms (GMOs). Here, we report a C[combining low line]apillary A[combining low line]rray-based L[combining low line]oop-mediated isothermal amplification for M[combining low line]ultiplex visual detection of nucleic acids (CALM) platform for the simple and rapid monitoring of GMOs. In CALM, loop-mediated isothermal amplification (LAMP) primer sets are pre-fixed to the inner surface of capillaries. The surface of the capillary array is hydrophobic while the capillaries are hydrophilic, enabling the simultaneous loading and separation of the LAMP reaction mixtures into each capillary by capillary forces. LAMP reactions in the capillaries are then performed in parallel, and the results are visually detected by illumination with a hand-held UV device. Using CALM, we successfully detected seven frequently used transgenic genes/elements and five plant endogenous reference genes with high specificity and sensitivity. Moreover, we found that measurements of real-world blind samples by CALM are consistent with results obtained by independent real-time PCRs. Thus, with an ability to detect multiple nucleic acids in a single easy-to-operate test, we believe that CALM will become a widely applied technology in GMO monitoring.

  6. Grizzly Bear Noninvasive Genetic Tagging Surveys: Estimating the Magnitude of Missed Detections.

    Directory of Open Access Journals (Sweden)

    Jason T Fisher

    Full Text Available Sound wildlife conservation decisions require sound information, and scientists increasingly rely on remotely collected data over large spatial scales, such as noninvasive genetic tagging (NGT. Grizzly bears (Ursus arctos, for example, are difficult to study at population scales except with noninvasive data, and NGT via hair trapping informs management over much of grizzly bears' range. Considerable statistical effort has gone into estimating sources of heterogeneity, but detection error-arising when a visiting bear fails to leave a hair sample-has not been independently estimated. We used camera traps to survey grizzly bear occurrence at fixed hair traps and multi-method hierarchical occupancy models to estimate the probability that a visiting bear actually leaves a hair sample with viable DNA. We surveyed grizzly bears via hair trapping and camera trapping for 8 monthly surveys at 50 (2012 and 76 (2013 sites in the Rocky Mountains of Alberta, Canada. We used multi-method occupancy models to estimate site occupancy, probability of detection, and conditional occupancy at a hair trap. We tested the prediction that detection error in NGT studies could be induced by temporal variability within season, leading to underestimation of occupancy. NGT via hair trapping consistently underestimated grizzly bear occupancy at a site when compared to camera trapping. At best occupancy was underestimated by 50%; at worst, by 95%. Probability of false absence was reduced through successive surveys, but this mainly accounts for error imparted by movement among repeated surveys, not necessarily missed detections by extant bears. The implications of missed detections and biased occupancy estimates for density estimation-which form the crux of management plans-require consideration. We suggest hair-trap NGT studies should estimate and correct detection error using independent survey methods such as cameras, to ensure the reliability of the data upon which species

  7. Grizzly Bear Noninvasive Genetic Tagging Surveys: Estimating the Magnitude of Missed Detections.

    Science.gov (United States)

    Fisher, Jason T; Heim, Nicole; Code, Sandra; Paczkowski, John

    2016-01-01

    Sound wildlife conservation decisions require sound information, and scientists increasingly rely on remotely collected data over large spatial scales, such as noninvasive genetic tagging (NGT). Grizzly bears (Ursus arctos), for example, are difficult to study at population scales except with noninvasive data, and NGT via hair trapping informs management over much of grizzly bears' range. Considerable statistical effort has gone into estimating sources of heterogeneity, but detection error-arising when a visiting bear fails to leave a hair sample-has not been independently estimated. We used camera traps to survey grizzly bear occurrence at fixed hair traps and multi-method hierarchical occupancy models to estimate the probability that a visiting bear actually leaves a hair sample with viable DNA. We surveyed grizzly bears via hair trapping and camera trapping for 8 monthly surveys at 50 (2012) and 76 (2013) sites in the Rocky Mountains of Alberta, Canada. We used multi-method occupancy models to estimate site occupancy, probability of detection, and conditional occupancy at a hair trap. We tested the prediction that detection error in NGT studies could be induced by temporal variability within season, leading to underestimation of occupancy. NGT via hair trapping consistently underestimated grizzly bear occupancy at a site when compared to camera trapping. At best occupancy was underestimated by 50%; at worst, by 95%. Probability of false absence was reduced through successive surveys, but this mainly accounts for error imparted by movement among repeated surveys, not necessarily missed detections by extant bears. The implications of missed detections and biased occupancy estimates for density estimation-which form the crux of management plans-require consideration. We suggest hair-trap NGT studies should estimate and correct detection error using independent survey methods such as cameras, to ensure the reliability of the data upon which species management and

  8. Detection of HbsAg and hATIII genetically modified goats (Caprahircus) by loop-mediated isothermal amplification.

    Science.gov (United States)

    Tao, Chenyu; Zhang, Qingde; Zhai, Shanli; Liu, Bang

    2013-11-01

    In this study, sensitive and rapid detection systems were designed using a loop-mediated isothermal amplification (LAMP) method to detect the genetically modified goats. A set of 4 primers were designed for each exogenous nucleic acids HBsAg and hATIII. The DNA samples were first amplified with the outer and inner primers and released a single-stranded DNA,of which both ends were stem-loop structure. Then one inner primer hybridized with the loop, and initiated displacement synthesis in less than 1 h. The result could be visualized by both agarose gel electrophoresis and unaided eyes directly after adding SYBR GREEN 1. The detection limit of LAMP was ten copies of target molecules, indicating that LAMP was tenfold more sensitive than the classical PCR. Furthermore, all the samples of genetically modified goats were tested positively by LAMP, and the results demonstrated that the LAMP was a rapid and sensitive method for detecting the genetically modified organism.

  9. Direct detection of common and rare inversion mutations in the genetic diagnosis of severe hemophilia A

    Energy Technology Data Exchange (ETDEWEB)

    Windsor, A.S.; Lillicrap, D.P.; Taylor, S.A.M. [Queen`s Univ., Ontario (Canada)

    1994-09-01

    Approximately 50% of the cases of severe hemophilia A (factor VIII:C < 0.01 units/ml) may be due to gross rearrangements of the factor VIII gene. The mutation involves homologous sequences upstream of the factor VIII locus and within intron 22 in an intrachromosomal recombination, inversion, event. The rearrangements can readily be detected on a Southern blot using a probe that is complementary to sequences from within intron 22. We describe here the analysis of this mutation in 71 severe hemophilia A patients. Thirty two of the patients (45%) showed evidence of a rearrangement. Five different patterns of rearrangements were seen, two of which have previously been described and account for the majority of cases (pattern 1, 70% and pattern 2, 16%). Three other abnormal patterns were observed. The inversion mechanism does not usually result in the loss or gain of any genetic material, but in one patient, in whom a unique rearrangement pattern was observed (pattern 3), we have previously documented a gross deletion which removes exons 1-22 of the factor VII gene as well as sequences 5{prime} to the gene. In another individual a fourth pattern in which an extra 19.0 kb band is present was detected. In this case it is unclear as to whether the rearrangement is responsible for the disease or is simply coincident normal variation. A fifth pattern, in which an extra 16.0 kb band was detected, was observed in a family with a new mutation causing hemophilia A. The affected individual and his mother inherited a de novo rearrangement of the factor VIII gene from his unaffected grandfather, implicating it as the cause of the disease. In conclusion, testing for the factor VIII inversion mutation was positive in approximately 45% of severe hemophiliacs, 72% of whom were isolated cases, and as such should constitute the initial stage in the genetic testing protocol for these patients` families.

  10. Detection and genetic analysis of human sapoviruses in river water in Japan.

    Science.gov (United States)

    Kitajima, Masaaki; Oka, Tomoichiro; Haramoto, Eiji; Katayama, Hiroyuki; Takeda, Naokazu; Katayama, Kazuhiko; Ohgaki, Shinichiro

    2010-04-01

    We investigated the prevalence of sapoviruses (SaVs) in the Tamagawa River in Japan from April 2003 to March 2004 and performed genetic analysis of the SaV genes identified in river water. A total of 60 river water samples were collected from five sites along the river, and 500 ml was concentrated using the cation-coated filter method. By use of a real-time reverse transcription (RT)-PCR assay, 12 (20%) of the 60 samples were positive for SaV. SaV sequences were obtained from 15 (25%) samples, and a total of 30 SaV strains were identified using six RT-PCR assays followed by cloning and sequence analysis. A newly developed nested RT-PCR assay utilizing a broadly reactive forward primer showed the highest detection efficiency and amplified more diverse SaV genomes in the samples. SaV sequences were frequently detected from November to March, whereas none were obtained in April, July, September, or October. No SaV sequences were detected in the upstream portion of the river, whereas the midstream portion showed high positive rates. Based on phylogenetic analysis, SaV strains identified in the river water samples were classified into nine genotypes, namely, GI/1, GI/2, GI/3, GI/5, GI/untyped, GII/1, GII/2, GII/3, and GV/1. To our knowledge, this is the first study describing seasonal and spatial distributions and genetic diversity of SaVs in river water. A combination of real-time RT-PCR assay and newly developed nested RT-PCR assay is useful for identifying and characterizing SaV strains in a water environment.

  11. Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar.

    Science.gov (United States)

    Razanajatovo, Norosoa H; Nomenjanahary, Lalaina A; Wilkinson, David A; Razafimanahaka, Julie H; Goodman, Steven M; Jenkins, Richard K; Jones, Julia P G; Heraud, Jean-Michel

    2015-03-12

    Bats are amongst the natural reservoirs of many coronaviruses (CoVs) of which some can lead to severe infection in human. African bats are known to harbor a range of pathogens (e.g., Ebola and Marburg viruses) that can infect humans and cause disease outbreaks. A recent study in South Africa isolated a genetic variant closely related to MERS-CoV from an insectivorous bat. Though Madagascar is home to 44 bat species (41 insectivorous and 3 frugivorous) of which 34 are endemic, no data exists concerning the circulation of CoVs in the island's chiropteran fauna. Certain Malagasy bats can be frequently found in close contact with humans and frugivorous bats feed in the same trees where people collect and consume fruits and are hunted and consumed as bush meat. The purpose of our study is to detect and identify CoVs from frugivorous bats in Madagascar to evaluate the risk of human infection from infected bats. Frugivorous bats belonging to three species were captured in four different regions of Madagascar. We analyzed fecal and throat swabs to detect the presence of virus through amplification of the RNA-dependent RNA polymerase (RdRp) gene, which is highly conserved in all known coronaviruses. Phylogenetic analyses were performed from positive specimens. From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Phylogenetic analysis revealed that the Malagasy strains belong to the genus Betacoronavirus but form three distinct clusters, which seem to represent previously undescribed genetic lineages. Our findings suggest that CoVs circulate in frugivorous bats of Madagascar, demonstrating the needs to evaluate spillover risk to human populations especially for individuals that hunt and consume infected bats. Possible dispersal mechanisms as to how coronaviruses arrived on Madagascar are discussed.

  12. A novel approach for the detection and genetic analysis of live melanoma circulating tumor cells.

    Directory of Open Access Journals (Sweden)

    Melody J Xu

    Full Text Available Circulating tumor cell (CTC detection and genetic analysis may complement currently available disease assessments in patients with melanoma to improve risk stratification and monitoring. We therefore sought to establish the feasibility of a telomerase-based assay for detecting and isolating live melanoma CTCs.The telomerase-based CTC assay utilizes an adenoviral vector that, in the presence of elevated human telomerase activity, drives the amplification of green fluorescent protein. Tumor cells are then identified via an image processing system. The protocol was tested on melanoma cells in culture or spiked into control blood, and on samples from patients with metastatic melanoma. Genetic analysis of the isolated melanoma CTCs was then performed for BRAF mutation status.The adenoviral vector was effective for all melanoma cell lines tested with sensitivity of 88.7% (95%CI 85.6-90.4% and specificity of 99.9% (95%CI 99.8-99.9%. In a pilot trial of patients with metastatic disease, CTCs were identified in 9 of 10 patients, with a mean of 6.0 CTCs/mL. At a cutoff of 1.1 CTCs/mL, the telomerase-based assay exhibits test performance of 90.0% sensitivity and 91.7% specificity. BRAF mutation analysis of melanoma cells isolated from culture or spiked control blood, or from pilot patient samples was found to match the known BRAF mutation status of the cell lines and primary tumors.To our knowledge, this is the first report of a telomerase-based assay effective for detecting and isolating live melanoma CTCs. These promising findings support further studies, including towards integrating into the management of patients with melanoma receiving multimodality therapy.

  13. Low-cost low-power UHF RFID tag with on-chip antenna

    Energy Technology Data Exchange (ETDEWEB)

    Xi Jingtian; Yan Na; Che Wenyi; Xu Conghui; Wang Xiao; Yang Yuqing; Jian Hongyan; Min Hao, E-mail: jtxi@fudan.edu.c [State Key Laboratory of ASIC and System, Auto-ID Laboratory, Fudan University, Shanghai 201203 (China)

    2009-07-15

    This paper presents an EPC Class 1 Generation 2 compatible tag with on-chip antenna implemented in the SMIC 0.18 {mu}m standard CMOS process. The UHF tag chip includes an RF/analog front-end, a digital baseband, and a 640-bit EEPROM memory. The on-chip antenna is optimized based on a novel parasitic-aware model. The rectifier is optimized to achieve a power conversion efficiency up to 40% by applying a self-bias feedback and threshold compensation techniques. A good match between the tag circuits and the on-chip antenna is realized by adjusting the rectifier input impedance. Measurements show that the presented tag can achieve a communication range of 1 cm with 1 W reader output power using a 1 x 1 cm{sup 2} single-turn loop reader antenna.

  14. A Performance Analytical Strategy for Network-on-Chip Router with Input Buffer Architecture

    Directory of Open Access Journals (Sweden)

    WANG, J.

    2012-11-01

    Full Text Available In this paper, a performance analytical strategy is proposed for Network-on-Chip router with input buffer architecture. First, an analytical model is developed based on semi-Markov process. For the non-work-conserving router with small buffer size, the model can be used to analyze the schedule delay and the average service time for each buffer when given the related parameters. Then, the packet average delay in router is calculated by using the model. Finally, we validate the effectiveness of our strategy by simulation. By comparing our analytical results to simulation results, we show that our strategy successfully captures the Network-on-Chip router performance and it performs better than the state-of-art technology. Therefore, our strategy can be used as an efficiency performance analytical tool for Network-on-Chip design.

  15. CMOS On-Chip Optoelectronic Neural Interface Device with Integrated Light Source for Optogenetics

    International Nuclear Information System (INIS)

    Sawadsaringkarn, Y; Kimura, H; Maezawa, Y; Nakajima, A; Kobayashi, T; Sasagawa, K; Noda, T; Tokuda, T; Ohta, J

    2012-01-01

    A novel optoelectronic neural interface device is proposed for target applications in optogenetics for neural science. The device consists of a light emitting diode (LED) array implemented on a CMOS image sensor for on-chip local light stimulation. In this study, we designed a suitable CMOS image sensor equipped with on-chip electrodes to drive the LEDs, and developed a device structure and packaging process for LED integration. The prototype device produced an illumination intensity of approximately 1 mW with a driving current of 2.0 mA, which is expected to be sufficient to activate channelrhodopsin (ChR2). We also demonstrated the functions of light stimulation and on-chip imaging using a brain slice from a mouse as a target sample.

  16. Scalable Motion Estimation Processor Core for Multimedia System-on-Chip Applications

    Science.gov (United States)

    Lai, Yeong-Kang; Hsieh, Tian-En; Chen, Lien-Fei

    2007-04-01

    In this paper, we describe a high-throughput and scalable motion estimation processor architecture for multimedia system-on-chip applications. The number of processing elements (PEs) is scalable according to the variable algorithm parameters and the performance required for different applications. Using the PE rings efficiently and an intelligent memory-interleaving organization, the efficiency of the architecture can be increased. Moreover, using efficient on-chip memories and a data management technique can effectively decrease the power consumption and memory bandwidth. Techniques for reducing the number of interconnections and external memory accesses are also presented. Our results demonstrate that the proposed scalable PE-ringed architecture is a flexible and high-performance processor core in multimedia system-on-chip applications.

  17. Genetic diversity of five local Swedish chicken breeds detected by microsatellite markers.

    Directory of Open Access Journals (Sweden)

    Abiye Shenkut Abebe

    Full Text Available This study aimed at investigating the genetic diversity, relationship and population structure of 110 local Swedish chickens derived from five breeds (Gotlandshöna, Hedemorahöna, Öländsk dvärghöna, Skånsk blommehöna, and Bohuslän- Dals svarthöna, in the rest of the paper the shorter name Svarthöna is used using 24 microsatellite markers. In total, one hundred thirteen alleles were detected in all populations, with a mean of 4.7 alleles per locus. For the five chicken breeds, the observed and expected heterozygosity ranged from 0.225 to 0.408 and from 0.231 to 0.515, with the lowest scores for the Svarthöna and the highest scores for the Skånsk blommehöna breeds, respectively. Similarly, the average within breed molecular kinship varied from 0.496 to 0.745, showing high coancestry, with Skånsk blommehöna having the lowest and Svarthöna the highest coancestry. Furthermore, all breeds showed significant deviations from Hardy-Weinberg expectations. Across the five breeds, the global heterozygosity deficit (FIT was 0.545, population differentiation index (FST was 0.440, and the global inbreeding of individuals within breed (FIS was 0.187. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed two main clusters, with Hedemorahöna and Öländsk dvärghöna breeds in one cluster, and Gotlandshöna and Svarthöna breeds in the second cluster leaving the Skånsk blommehöna in the middle. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the five breeds was at K = 4, with Hedemorahöna, Gotlandshöna and Svarthöna breeds forming their own distinct clusters, while Öländsk dvärghöna and Skånsk blommehöna breeds clustered together. Losses in the overall genetic diversity of local Swedish chickens due to breeds extinction varied from -1.46% to -6

  18. Genetics

    International Nuclear Information System (INIS)

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  19. GA-DoSLD: Genetic Algorithm Based Denial-of-Sleep Attack Detection in WSN

    Directory of Open Access Journals (Sweden)

    Mahalakshmi Gunasekaran

    2017-01-01

    Full Text Available Denial-of-sleep (DoSL attack is a special category of denial-of-service attack that prevents the battery powered sensor nodes from going into the sleep mode, thus affecting the network performance. The existing schemes used for the DoSL attack detection do not provide an optimal energy conservation and key pairing operation. Hence, in this paper, an efficient Genetic Algorithm (GA based denial-of-sleep attack detection (GA-DoSLD algorithm is suggested for analyzing the misbehaviors of the nodes. The suggested algorithm implements a Modified-RSA (MRSA algorithm in the base station (BS for generating and distributing the key pair among the sensor nodes. Before sending/receiving the packets, the sensor nodes determine the optimal route using Ad Hoc On-Demand Distance Vector Routing (AODV protocol and then ensure the trustworthiness of the relay node using the fitness calculation. The crossover and mutation operations detect and analyze the methods that the attackers use for implementing the attack. On determining an attacker node, the BS broadcasts the blocked information to all the other sensor nodes in the network. Simulation results prove that the suggested algorithm is optimal compared to the existing algorithms such as X-MAC, ZKP, and TE2P schemes.

  20. LAND COVER CHANGE DETECTION BASED ON GENETICALLY FEATURE AELECTION AND IMAGE ALGEBRA USING HYPERION HYPERSPECTRAL IMAGERY

    Directory of Open Access Journals (Sweden)

    S. T. Seydi

    2015-12-01

    Full Text Available The Earth has always been under the influence of population growth and human activities. This process causes the changes in land use. Thus, for optimal management of the use of resources, it is necessary to be aware of these changes. Satellite remote sensing has several advantages for monitoring land use/cover resources, especially for large geographic areas. Change detection and attribution of cultivation area over time present additional challenges for correctly analyzing remote sensing imagery. In this regards, for better identifying change in multi temporal images we use hyperspectral images. Hyperspectral images due to high spectral resolution created special placed in many of field. Nevertheless, selecting suitable and adequate features/bands from this data is crucial for any analysis and especially for the change detection algorithms. This research aims to automatically feature selection for detect land use changes are introduced. In this study, the optimal band images using hyperspectral sensor using Hyperion hyperspectral images by using genetic algorithms and Ratio bands, we select the optimal band. In addition, the results reveal the superiority of the implemented method to extract change map with overall accuracy by a margin of nearly 79% using multi temporal hyperspectral imagery.

  1. Genetically Engineered Virulent Phage Banks in the Detection and Control of Emergent Pathogenic Bacteria

    Science.gov (United States)

    Blois, Hélène; Iris, François

    2010-01-01

    Natural outbreaks of multidrug-resistant microorganisms can cause widespread devastation, and several can be used or engineered as agents of bioterrorism. From a biosecurity standpoint, the capacity to detect and then efficiently control, within hours, the spread and the potential pathological effects of an emergent outbreak, for which there may be no effective antibiotics or vaccines, become key challenges that must be met. We turned to phage engineering as a potentially highly flexible and effective means to both detect and eradicate threats originating from emergent (uncharacterized) bacterial strains. To this end, we developed technologies allowing us to (1) concurrently modify multiple regions within the coding sequence of a gene while conserving intact the remainder of the gene, (2) reversibly interrupt the lytic cycle of an obligate virulent phage (T4) within its host, (3) carry out efficient insertion, by homologous recombination, of any number of engineered genes into the deactivated genomes of a T4 wild-type phage population, and (4) reactivate the lytic cycle, leading to the production of engineered infective virulent recombinant progeny. This allows the production of very large, genetically engineered lytic phage banks containing, in an E. coli host, a very wide spectrum of variants for any chosen phage-associated function, including phage host-range. Screening of such a bank should allow the rapid isolation of recombinant T4 particles capable of detecting (ie, diagnosing), infecting, and destroying hosts belonging to gram-negative bacterial species far removed from the original E. coli host. PMID:20569057

  2. Data in support of the detection of genetically modified organisms (GMOs) in food and feed samples.

    Science.gov (United States)

    Alasaad, Noor; Alzubi, Hussein; Kader, Ahmad Abdul

    2016-06-01

    Food and feed samples were randomly collected from different sources, including local and imported materials from the Syrian local market. These included maize, barley, soybean, fresh food samples and raw material. GMO detection was conducted by PCR and nested PCR-based techniques using specific primers for the most used foreign DNA commonly used in genetic transformation procedures, i.e., 35S promoter, T-nos, epsps, cryIA(b) gene and nptII gene. The results revealed for the first time in Syria the presence of GM foods and feeds with glyphosate-resistant trait of P35S promoter and NOS terminator in the imported soybean samples with high frequency (5 out of the 6 imported soybean samples). While, tests showed negative results for the local samples. Also, tests revealed existence of GMOs in two imported maize samples detecting the presence of 35S promoter and nos terminator. Nested PCR results using two sets of primers confirmed our data. The methods applied in the brief data are based on DNA analysis by Polymerase Chain Reaction (PCR). This technique is specific, practical, reproducible and sensitive enough to detect up to 0.1% GMO in food and/or feedstuffs. Furthermore, all of the techniques mentioned are economic and can be applied in Syria and other developing countries. For all these reasons, the DNA-based analysis methods were chosen and preferred over protein-based analysis.

  3. Detection of genetically modified maize events in Brazilian maize-derived food products

    Directory of Open Access Journals (Sweden)

    Maria Regina Branquinho

    2013-09-01

    Full Text Available The Brazilian government has approved many transgenic maize lines for commercialization and has established a threshold of 1% for food labeling, which underscores need for monitoring programs. Thirty four samples including flours and different types of nacho chips were analyzed by conventional and real-time PCR in 2011 and 2012. The events MON810, Bt11, and TC1507 were detected in most of the samples, and NK603 was present only in the samples analyzed in 2012. The authorized lines GA21, T25, and the unauthorized Bt176 were not detected. All positive samples in the qualitative tests collected in 2011 showed a transgenic content higher than 1%, and none of them was correctly labeled. Regarding the samples collected in 2012, all positive samples were quantified higher than the threshold, and 47.0% were not correctly labeled. The overall results indicated that the major genetically modified organisms detected were MON810, TC1507, Bt11, and NK603 events. Some industries that had failed to label their products in 2011 started labeling them in 2012, demonstrating compliance with the current legislation observing the consumer rights. Although these results are encouraging, it has been clearly demonstrated the need for continuous monitoring programs to ensure consumers that food products are labeled properly.

  4. Advanced Technology for Ultra-Low Power System-on-Chip (SoC)

    Science.gov (United States)

    2017-06-01

    was proposed for lower power applications with Ioff=10pA/μm and VDD=0.5V. In this project, the optimized structure shows great potential in both Lg...AFRL-RY-WP-TR-2017-0115 ADVANCED TECHNOLOGY FOR ULTRA-LOW POWER SYSTEM-ON-CHIP (SoC) Jason Woo, Weicong Li, and Peng Lu University of California...September 2015 – 31 March 2017 4. TITLE AND SUBTITLE ADVANCED TECHNOLOGY FOR ULTRA-LOW POWER SYSTEM-ON- CHIP (SoC) 5a. CONTRACT NUMBER FA8650-15-1-7574 5b

  5. CMOS capacitive sensors for lab-on-chip applications a multidisciplinary approach

    CERN Document Server

    Ghafar-Zadeh, Ebrahim

    2010-01-01

    The main components of CMOS capacitive biosensors including sensing electrodes, bio-functionalized sensing layer, interface circuitries and microfluidic packaging are verbosely explained in chapters 2-6 after a brief introduction on CMOS based LoCs in Chapter 1. CMOS Capacitive Sensors for Lab-on-Chip Applications is written in a simple pedagogical way. It emphasises practical aspects of fully integrated CMOS biosensors rather than mathematical calculations and theoretical details. By using CMOS Capacitive Sensors for Lab-on-Chip Applications, the reader will have circuit design methodologies,

  6. Optical and Electric Multifunctional CMOS Image Sensors for On-Chip Biosensing Applications

    Directory of Open Access Journals (Sweden)

    Kiyotaka Sasagawa

    2010-12-01

    Full Text Available In this review, the concept, design, performance, and a functional demonstration of multifunctional complementary metal-oxide-semiconductor (CMOS image sensors dedicated to on-chip biosensing applications are described. We developed a sensor architecture that allows flexible configuration of a sensing pixel array consisting of optical and electric sensing pixels, and designed multifunctional CMOS image sensors that can sense light intensity and electric potential or apply a voltage to an on-chip measurement target. We describe the sensors’ architecture on the basis of the type of electric measurement or imaging functionalities.

  7. Autonomic networking-on-chip bio-inspired specification, development, and verification

    CERN Document Server

    Cong-Vinh, Phan

    2011-01-01

    Despite the growing mainstream importance and unique advantages of autonomic networking-on-chip (ANoC) technology, Autonomic Networking-On-Chip: Bio-Inspired Specification, Development, and Verification is among the first books to evaluate research results on formalizing this emerging NoC paradigm, which was inspired by the human nervous system. The FIRST Book to Assess Research Results, Opportunities, & Trends in ""BioChipNets"" The third book in the Embedded Multi-Core Systems series from CRC Press, this is an advanced technical guide and reference composed of contributions from prominent re

  8. Fabrication and characterization of on-chip optical nonlinear chalcogenide nanofiber devices.

    Science.gov (United States)

    Zhang, Qiming; Li, Ming; Hao, Qiang; Deng, Dinghuan; Zhou, Hui; Zeng, Heping; Zhan, Li; Wu, Xiang; Liu, Liying; Xu, Lei

    2010-11-15

    Chalcogenide (As(2)S(3)) nanofibers as narrow as 200 nm in diameter are drawn by the fiber pulling method, are successfully embedded in SU8 polymer, and form on-chip waveguides and high-Q microknot resonators (Q = 3.9 × 10(4)) with smooth cleaved end faces. Resonance tuning of resonators is realized by localized laser irradiation. Strong supercontinuum generation with a bandwidth of 500 nm is achieved in a 7-cm-long on-chip chalcogenide waveguide. Our result provides a method for the development of compact, high-optical-quality, and robust photonic devices.

  9. Applications of geological labs on chip for CO_2 storage issues

    International Nuclear Information System (INIS)

    Morais, Sandy

    2016-01-01

    CO_2 geological storage in deep saline aquifers represents a mediation solution for reducing the anthropogenic CO_2 emissions. Consequently, this kind of storage requires adequate scientific knowledge to evaluate injection scenarios, estimate reservoir capacity and assess leakage risks. In this context, we have developed and used high pressure/high temperature micro-fluidic tools to investigate the different mechanisms associated with CO_2 geological storage in deep saline aquifers. The silicon-Pyrex 2D porous networks (Geological Labs On Chips) can replicate the reservoir p,T conditions (25 ≤ T ≤ 50 C, 50 ≤ p ≤ 10 MPa), geological and topological properties. This thesis manuscript first highlights the strategies developed during this work to fabricate the GLoCs and to access to global characteristics of our porous media such as porosity and permeability, which are later compared to numerical modelling results. The carbon dioxide detection in GLoCs mimicking p,T conditions of geological reservoirs by using the direct integration of optical fiber for IR spectroscopy is presented. I then detail the strategies for following the dissolution of carbonates in GLoCs with X-rays laminography experiments.Then, the manuscript focuses on the use of GLoCs to investigate each CO_2 trapping mechanism at the pore scale. The direct optical visualization and image processing allow us to follow the evolution of the injected CO_2/aqueous phase within the reservoir, including displacement mechanisms and pore saturation levels. Eventually, I present the ongoing works such as experiments with reactive brines and hydrates formations in porous media [fr

  10. On-Chip Immunoassay for Determination of Urinary Albumin

    Directory of Open Access Journals (Sweden)

    Adisorn Tuantranont

    2009-12-01

    Full Text Available An immunoassay performed on a portable microfluidic device was evaluated for the determination of urinary albumin. An increase in absorbance at 500 nm resulting from immunoagglutination was monitored directly on the poly(dimethylsiloxane (PDMS microchip using a portable miniature fibre-optic spectrometer. A calibration curve was linear up to 10 mg L–1 (r2 = 0.993, with a detection limit of 0.81 mg L–1 (S/N = 3. The proposed system showed good precision, with relative standard deviations (RSDs of 5.1%, when evaluated with 10 mg L–1 albumin (n = 10. Determination of urinary albumin with the proposed system gave results highly similar to those determined by the conventional spectrophotometric method using immunoturbidimetric detection (r2 = 0.995; n = 15.

  11. Yellow fever virus: genetic and phenotypic diversity and implications for detection, prevention and therapy.

    Science.gov (United States)

    Beasley, David W C; McAuley, Alexander J; Bente, Dennis A

    2015-03-01

    Yellow fever virus (YFV) is the prototypical hemorrhagic fever virus, yet our understanding of its phenotypic diversity and any molecular basis for observed differences in disease severity and epidemiology is lacking, when compared to other arthropod-borne and haemorrhagic fever viruses. This is, in part, due to the availability of safe and effective vaccines resulting in basic YFV research taking a back seat to those viruses for which no effective vaccine occurs. However, regular outbreaks occur in endemic areas, and the spread of the virus to new, previously unaffected, areas is possible. Analysis of isolates from endemic areas reveals a strong geographic association for major genotypes, and recent epidemics have demonstrated the emergence of novel sequence variants. This review aims to outline the current understanding of YFV genetic and phenotypic diversity and its sources, as well as the available animal models for characterizing these differences in vivo. The consequences of genetic diversity for detection and diagnosis of yellow fever and development of new vaccines and therapeutics are discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Optimal Feature Space Selection in Detecting Epileptic Seizure based on Recurrent Quantification Analysis and Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Saleh LAshkari

    2016-06-01

    Full Text Available Selecting optimal features based on nature of the phenomenon and high discriminant ability is very important in the data classification problems. Since it doesn't require any assumption about stationary condition and size of the signal and the noise in Recurrent Quantification Analysis (RQA, it may be useful for epileptic seizure Detection. In this study, RQA was used to discriminate ictal EEG from the normal EEG where optimal features selected by combination of algorithm genetic and Bayesian Classifier. Recurrence plots of hundred samples in each two categories were obtained with five distance norms in this study: Euclidean, Maximum, Minimum, Normalized and Fixed Norm. In order to choose optimal threshold for each norm, ten threshold of ε was generated and then the best feature space was selected by genetic algorithm in combination with a bayesian classifier. The results shown that proposed method is capable of discriminating the ictal EEG from the normal EEG where for Minimum norm and 0.1˂ε˂1, accuracy was 100%. In addition, the sensitivity of proposed framework to the ε and the distance norm parameters was low. The optimal feature presented in this study is Trans which it was selected in most feature spaces with high accuracy.

  13. Finding the joker among the maize endogenous reference genes for genetically modified organism (GMO) detection.

    Science.gov (United States)

    Paternò, Annalisa; Marchesi, Ugo; Gatto, Francesco; Verginelli, Daniela; Quarchioni, Cinzia; Fusco, Cristiana; Zepparoni, Alessia; Amaddeo, Demetrio; Ciabatti, Ilaria

    2009-12-09

    The comparison of five real-time polymerase chain reaction (PCR) methods targeted at maize ( Zea mays ) endogenous sequences is reported. PCR targets were the alcohol dehydrogenase (adh) gene for three methods and high-mobility group (hmg) gene for the other two. The five real-time PCR methods have been checked under repeatability conditions at several dilution levels on both pooled DNA template from several genetically modified (GM) maize certified reference materials (CRMs) and single CRM DNA extracts. Slopes and R(2) coefficients of all of the curves obtained from the adopted regression model were compared within the same method and among all of the five methods, and the limit of detection and limit of quantitation were analyzed for each PCR system. Furthermore, method equivalency was evaluated on the basis of the ability to estimate the target haploid genome copy number at each concentration level. Results indicated that, among the five methods tested, one of the hmg-targeted PCR systems can be considered equivalent to the others but shows the best regression parameters and a higher repeteability along the dilution range. Thereby, it is proposed as a valid module to be coupled to different event-specific real-time PCR for maize genetically modified organism (GMO) quantitation. The resulting practicability improvement on the analytical control of GMOs is discussed.

  14. Critical assessment of digital PCR for the detection and quantification of genetically modified organisms.

    Science.gov (United States)

    Demeke, Tigst; Dobnik, David

    2018-07-01

    The number of genetically modified organisms (GMOs) on the market is steadily increasing. Because of regulation of cultivation and trade of GMOs in several countries, there is pressure for their accurate detection and quantification. Today, DNA-based approaches are more popular for this purpose than protein-based methods, and real-time quantitative PCR (qPCR) is still the gold standard in GMO analytics. However, digital PCR (dPCR) offers several advantages over qPCR, making this new technique appealing also for GMO analysis. This critical review focuses on the use of dPCR for the purpose of GMO quantification and addresses parameters which are important for achieving accurate and reliable results, such as the quality and purity of DNA and reaction optimization. Three critical factors are explored and discussed in more depth: correct classification of partitions as positive, correctly determined partition volume, and dilution factor. This review could serve as a guide for all laboratories implementing dPCR. Most of the parameters discussed are applicable to fields other than purely GMO testing. Graphical abstract There are generally three different options for absolute quantification of genetically modified organisms (GMOs) using digital PCR: droplet- or chamber-based and droplets in chambers. All have in common the distribution of reaction mixture into several partitions, which are all subjected to PCR and scored at the end-point as positive or negative. Based on these results GMO content can be calculated.

  15. The Use of TILLING Technique to Detect Mutations and genetic diversity in Potato

    International Nuclear Information System (INIS)

    Elias, R; Al-Safadi, B; Till, B

    2008-01-01

    TILLING technique has been used, for the first time, to detect genetic variation, at the molecular level, among potato mutants (induced by gamma irradiation) and genetic diversity among 3 potato cultivars. Three potato mutant lines (every mutant represents a cultivar) tolerant to salinity have been used along with their controls. Three primer pairs were designed with the help of Potato Genome Sequencing Consortium on the web and were evaluated using agarose gel then sequencing. Primer pairs passing these tests were fluorescently labeled. Li-Cor based TILLING was applied using 2 forward primers one of them is labeled and 2 reverse primers one of them is labeled. The results have shown the success of using this technique on potato (tetraploid species) where the average density of nucleotide polymorphisms per sample was 16 polymorphisms per 1 kb. The optimal concentration was also determined between 0.1 and 1 ng/ul for potato genomic DNAs to be used in Li-Cor based TILLING assays. (author)

  16. TESTING BAYESIAN ALGORITHMS TO DETECT GENETIC STRUCTURE IN TWO CLOSELY RELATED OAK TAXA

    Directory of Open Access Journals (Sweden)

    Cristian Mihai Enescu

    2013-12-01

    Full Text Available The aim of this study was to test the Bayesian algorithm implemented in the software STRUCTURE in order to detect the number of clusters, by using microsatellite data from four oak species. Several assignment models, with or without a priori grouping of individuals to species, were proposed. Better results were obtained by using the sampling location information and when only two taxa were analyzed. Particularly, pedunculate oak and sessile oak formed distinct clusters whatever the assignment model we use. By contrast, no separation between the two oaks from series Lanuginosae was observed. This can be explained, on one hand, by the small sampling size for Italian oak, or by the genetic similarities of the two pubescent oaks, namely Quercus pubescens and Q. virgiliana, on the other hand. Our findings support the hypothesis according which Italian oak is an intraspecific taxonomic unit of pubescent oak.

  17. Optimal filter design with progressive genetic algorithm for local damage detection in rolling bearings

    Science.gov (United States)

    Wodecki, Jacek; Michalak, Anna; Zimroz, Radoslaw

    2018-03-01

    Harsh industrial conditions present in underground mining cause a lot of difficulties for local damage detection in heavy-duty machinery. For vibration signals one of the most intuitive approaches of obtaining signal with expected properties, such as clearly visible informative features, is prefiltration with appropriately prepared filter. Design of such filter is very broad field of research on its own. In this paper authors propose a novel approach to dedicated optimal filter design using progressive genetic algorithm. Presented method is fully data-driven and requires no prior knowledge of the signal. It has been tested against a set of real and simulated data. Effectiveness of operation has been proven for both healthy and damaged case. Termination criterion for evolution process was developed, and diagnostic decision making feature has been proposed for final result determinance.

  18. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  19. Development of a qualitative real-time PCR method to detect 19 targets for identification of genetically modified organisms.

    Science.gov (United States)

    Peng, Cheng; Wang, Pengfei; Xu, Xiaoli; Wang, Xiaofu; Wei, Wei; Chen, Xiaoyun; Xu, Junfeng

    2016-01-01

    As the amount of commercially available genetically modified organisms (GMOs) grows recent years, the diversity of target sequences for molecular detection techniques are eagerly needed. Considered as the gold standard for GMO analysis, the real-time PCR technology was optimized to produce a high-throughput GMO screening method. With this method we can detect 19 transgenic targets. The specificity of the assays was demonstrated to be 100 % by the specific amplification of DNA derived from reference material from 20 genetically modified crops and 4 non modified crops. Furthermore, most assays showed a very sensitive detection, reaching the limit of ten copies. The 19 assays are the most frequently used genetic elements present in GM crops and theoretically enable the screening of the known GMO described in Chinese markets. Easy to use, fast and cost efficient, this method approach fits the purpose of GMO testing laboratories.

  20. On-Chip Immunoassay for Determination of Urinary Albumin

    OpenAIRE

    Laiwattanapaisal, Wanida; Songjaroen, Temsiri; Maturos, Thitima; Lomas, Tanom; Sappat, Assawapong; Tuantranont, Adisorn

    2009-01-01

    An immunoassay performed on a portable microfluidic device was evaluated for the determination of urinary albumin. An increase in absorbance at 500 nm resulting from immunoagglutination was monitored directly on the poly(dimethylsiloxane) (PDMS) microchip using a portable miniature fibre-optic spectrometer. A calibration curve was linear up to 10 mg L–1 (r2 = 0.993), with a detection limit of 0.81 mg L–1 (S/N = 3). The proposed system showed good precision, with relative standard deviations (...

  1. Self-Powered Functional Device Using On-Chip Power Generation

    KAUST Repository

    Hussain, Muhammad Mustafa

    2012-01-26

    An apparatus, system, and method for a self-powered device using on-chip power generation. In some embodiments, the apparatus includes a substrate, a power generation module on the substrate, and a power storage module on the substrate. The power generation module may include a thermoelectric generator made of bismuth telluride.

  2. MEMS-based wavelength and orbital angular momentum demultiplexer for on-chip applications

    DEFF Research Database (Denmark)

    Lyubopytov, Vladimir; Porfirev, Alexey P.; Gurbatov, Stanislav O.

    2017-01-01

    Summary form only given. We demonstrate a new tunable MEMS-based WDM&OAM Fabry-Pérot filter for simultaneous wavelength (WDM) and Orbital Angular Momentum (OAM) (de)multiplexing. The WDM&OAM filter is suitable for dense on-chip integration and dedicated for the next generation of optical...

  3. A Network Traffic Generator Model for Fast Network-on-Chip Simulation

    DEFF Research Database (Denmark)

    Mahadevan, Shankar; Angiolini, Frederico; Storgaard, Michael

    2005-01-01

    For Systems-on-Chip (SoCs) development, a predominant part of the design time is the simulation time. Performance evaluation and design space exploration of such systems in bit- and cycle-true fashion is becoming prohibitive. We propose a traffic generation (TG) model that provides a fast...

  4. Standardized and modular microfluidic platform for fast lab on chip system development

    NARCIS (Netherlands)

    Dekker, Stefan; van den Berg, Albert; Odijk, Mathieu; Lee, Abraham; DeVoe, Don

    2017-01-01

    This paper reports a modular microfluidic system with standardized parts, enabling rapid prototyping of lab on chip systems. Herewith contributing to the technology transfer from academy to industry. The use of standardized parts also makes it possible to design a microfluidic systems in a top down

  5. Two-Dimensional Programmable Manipulation of Magnetic Nanoparticles on-Chip

    DEFF Research Database (Denmark)

    Sarella, Anandakumar; Torti, Andrea; Donolato, Marco

    2014-01-01

    A novel device is designed for on-chip selective trap and two-dimensional remote manipulation of single and multiple fluid-borne magnetic particles using field controlled magnetic domain walls in circular nanostructures. The combination of different ring-shaped nanostructures and field sequences ...

  6. On-chip COMA cache-coherence protocol for microgrids of microthreaded cores

    NARCIS (Netherlands)

    Zhang, L.; Jesshope, C.

    2008-01-01

    This paper describes an on-chip COMA cache coherency protocol to support the microthread model of concurrent program composition. The model gives a sound basis for building multi-core computers as it captures concurrency, abstracts communication and identifies resources, such as processor groups

  7. Advanced Nanofabrication Process Development for Self-Powered System-on-Chip

    KAUST Repository

    Rojas, Jhonathan Prieto

    2010-01-01

    In summary, by using a novel sustainable energy component and scalable nano-patterning for logic and computing module, this work has successfully collected the essential base knowledge and joined two different elements that synergistically will contribute for the future implementation of a Self-Powered System-on-Chip.

  8. DAEDALUS: System-Level Design Methodology for Streaming Multiprocessor Embedded Systems on Chips

    NARCIS (Netherlands)

    Stefanov, T.; Pimentel, A.; Nikolov, H.; Ha, S.; Teich, J.

    2017-01-01

    The complexity of modern embedded systems, which are increasingly based on heterogeneous multiprocessor system-on-chip (MPSoC) architectures, has led to the emergence of system-level design. To cope with this design complexity, system-level design aims at raising the abstraction level of the design

  9. Global On-Chip Differential Interconnects with Optimally-Placed Twists

    NARCIS (Netherlands)

    Mensink, E.; Schinkel, Daniel; Klumperink, Eric A.M.; van Tuijl, Adrianus Johannes Maria; Nauta, Bram

    2005-01-01

    Global on-chip communication is receiving quite some attention as global interconnects are rapidly becoming a speed, power and reliability bottleneck for digital CMOS systems. Recently, we proposed a bus-transceiver test chip in 0.13 μm CMOS using 10 mm long uninterrupted differential interconnects

  10. Self-Powered Functional Device Using On-Chip Power Generation

    KAUST Repository

    Hussain, Muhammad Mustafa

    2012-01-01

    An apparatus, system, and method for a self-powered device using on-chip power generation. In some embodiments, the apparatus includes a substrate, a power generation module on the substrate, and a power storage module on the substrate. The power generation module may include a thermoelectric generator made of bismuth telluride.

  11. On-Chip Manipulation of Protein-Coated Magnetic Beads via Domain-Wall Conduits

    DEFF Research Database (Denmark)

    Donolato, Marco; Vavassori, Paolo; Gobbi, Marco

    2010-01-01

    Geometrically constrained magnetic domain walls (DWs) in magnetic nanowires can be manipulated at the nanometer scale. The inhomogeneous magnetic stray field generated by a DW can capture a magnetic nanoparticle in solution. On-chip nanomanipulation of individual magnetic beads coated with proteins...

  12. On-chip single photon filtering and multiplexing in hybrid quantum photonic circuits.

    Science.gov (United States)

    Elshaari, Ali W; Zadeh, Iman Esmaeil; Fognini, Andreas; Reimer, Michael E; Dalacu, Dan; Poole, Philip J; Zwiller, Val; Jöns, Klaus D

    2017-08-30

    Quantum light plays a pivotal role in modern science and future photonic applications. Since the advent of integrated quantum nanophotonics different material platforms based on III-V nanostructures-, colour centers-, and nonlinear waveguides as on-chip light sources have been investigated. Each platform has unique advantages and limitations; however, all implementations face major challenges with filtering of individual quantum states, scalable integration, deterministic multiplexing of selected quantum emitters, and on-chip excitation suppression. Here we overcome all of these challenges with a hybrid and scalable approach, where single III-V quantum emitters are positioned and deterministically integrated in a complementary metal-oxide-semiconductor-compatible photonic circuit. We demonstrate reconfigurable on-chip single-photon filtering and wavelength division multiplexing with a foot print one million times smaller than similar table-top approaches, while offering excitation suppression of more than 95 dB and efficient routing of single photons over a bandwidth of 40 nm. Our work marks an important step to harvest quantum optical technologies' full potential.Combining different integration platforms on the same chip is currently one of the main challenges for quantum technologies. Here, Elshaari et al. show III-V Quantum Dots embedded in nanowires operating in a CMOS compatible circuit, with controlled on-chip filtering and tunable routing.

  13. Power Efficient Gigabit Communication Over Capacitively Driven RC-Limited On-Chip Interconnects

    NARCIS (Netherlands)

    Mensink, E.; Schinkel, Daniel; Klumperink, Eric A.M.; van Tuijl, Adrianus Johannes Maria; Nauta, Bram

    2010-01-01

    Abstract—This paper presents a set of circuit techniques to achieve high data rate point-to-point communication over long on-chip RC-limited wire-pairs. The ideal line termination impedances for a flat transfer function with linear phase (pure delay) are derived, using an s-parameter wire-pair

  14. Synthesis and Layout of an Asynchronous Network-on-Chip using Standard EDA Tools

    DEFF Research Database (Denmark)

    Müller, Christoph; Kasapaki, Evangelia; Sørensen, Rasmus Bo

    2014-01-01

    is the key role that clock signals play in specifying time-constraints for the synthesis. In this paper explain how we handled the synthesis and layout of an asynchronous network-on-chip for a multi-core platform. Focus is on the design process while the actual NOC-design and its performance are presented...

  15. A Statically Scheduled Time-Division-Multiplexed Network-on-Chip for Real-Time Systems

    DEFF Research Database (Denmark)

    Schoeberl, Martin; Brandner, Florian; Sparsø, Jens

    2012-01-01

    This paper explores the design of a circuit-switched network-on-chip (NoC) based on time-division-multiplexing (TDM) for use in hard real-time systems. Previous work has primarily considered application-specific systems. The work presented here targets general-purpose hardware platforms. We...

  16. Heat management in integrated circuits on-chip and system-level monitoring and cooling

    CERN Document Server

    Ogrenci-Memik, Seda

    2016-01-01

    This essential overview covers the subject of thermal monitoring and management in integrated circuits. Specifically, it focuses on devices and materials that are intimately integrated on-chip (as opposed to in-package or on-board) for the purposes of thermal monitoring and thermal management.

  17. An On-Chip interconnect and protocol stack for multiple communication paradigms and programming models

    NARCIS (Netherlands)

    Hansson, A.; Goossens, Kees

    2009-01-01

    A growing number of applications, with diverse requirements, are integrated on the same System on Chip (SoC) in the form of hardware and software Intellectual Property (IP). The diverse requirements, coupled with the IPs being developed by unrelated design teams, lead to multiple communication

  18. An on-chip interconnect and protocol stack for multiple communication paradigms and programming models

    NARCIS (Netherlands)

    Hansson, M.A.; Goossens, K.G.W.

    2009-01-01

    A growing number of applications, with diverse requirements, are integrated on the same System on Chip (SoC) in the form of hardware and software Intellectual Property (IP). The diverse requirements, coupled with the IPs being developed by unrelated design teams, lead to multiple communication

  19. Integrated lab-on-chip biosensing systems based on magnetic particle actuation : a comprehensive review

    NARCIS (Netherlands)

    Reenen, van A.; Jong, de A.M.; Toonder, den J.M.J.; Prins, M.W.J.

    2014-01-01

    The demand for easy to use and cost effective medical technologies inspires scientists to develop inno-vative lab-on-chip technologies for in-vitro diagnostic testing. To fulfill the medical needs, the tests should be rapid, sensitive, quantitative, miniaturizable, and need to integrate all steps

  20. Dynamic magnetic particle actuation for integrated lab-on-chip biosensing

    NARCIS (Netherlands)

    Jong, de A.M.; Reenen, van A.; Prins, M.W.J.

    2014-01-01

    The demand for easy to use and cost effective medical technologies inspires scientists to develop innovative lab-on-chip technologies for in-vitro diagnostic testing. We study the use of magnetic particles actuated by magnetic fields to perform different microfluidic handling steps of an integrated

  1. Vertical Integration of System-on-Chip Concepts in the Digital Design Curriculum

    Science.gov (United States)

    Tang, Ying; Head, L. M.; Ramachandran, R. P.; Chatman, L. M.

    2011-01-01

    The rapid evolution of System-on-Chip (SoC) challenges academic curricula to keep pace with multidisciplinary/interdisciplinary system thinking. This paper presents a curricular prototype that cuts across artificial course boundaries and provides a meaningful exploration of diverse facets of SoC design. Specifically, experimental contents of a…

  2. Cache aware mapping of streaming apllications on a multiprocessor system-on-chip

    NARCIS (Netherlands)

    Moonen, A.J.M.; Bekooij, M.J.G.; Berg, van den R.M.J.; Meerbergen, van J.; Sciuto, D.; Peng, Z.

    2008-01-01

    Efficient use of the memory hierarchy is critical for achieving high performance in a multiprocessor system- on-chip. An external memory that is shared between processors is a bottleneck in current and future systems. Cache misses and a large cache miss penalty contribute to a low processor

  3. Nanotechnology and the Developing World: Lab-on-Chip Technology for Health and Environmental Applications

    Science.gov (United States)

    Mehta, Michael D.

    2008-01-01

    This article argues that advances in nanotechnology in general, and lab-on-chip technology in particular, have the potential to benefit the developing world in its quest to control risks to human health and the environment. Based on the "risk society" thesis of Ulrich Beck, it is argued that the developed world must realign its science and…

  4. Technology for On-Chip Qubit Control with Microfabricated Surface Ion Traps

    Energy Technology Data Exchange (ETDEWEB)

    Highstrete, Clark [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Quantum Information Sciences Dept.; Scott, Sean Michael [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). RF/Optoelectronics Dept.; Nordquist, Christopher D. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). RF/Optoelectronics Dept.; Sterk, Jonathan David [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Photonic Microsystem Technologies Dept.; Maunz, Peter Lukas Wilhelm [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Photonic Microsystem Technologies Dept.; Tigges, Christopher P. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Photonic Microsystem Technologies Dept.; Blain, Matthew Glenn [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Photonic Microsystem Technologies Dept.; Heller, Edwin J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Microsystems Integration Dept.; Stevens, James E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). MESAFab Operations 2 Dept.

    2013-11-01

    Trapped atomic ions are a leading physical system for quantum information processing. However, scalability and operational fidelity remain limiting technical issues often associated with optical qubit control. One promising approach is to develop on-chip microwave electronic control of ion qubits based on the atomic hyperfine interaction. This project developed expertise and capabilities at Sandia toward on-chip electronic qubit control in a scalable architecture. The project developed a foundation of laboratory capabilities, including trapping the 171Yb+ hyperfine ion qubit and developing an experimental microwave coherent control capability. Additionally, the project investigated the integration of microwave device elements with surface ion traps utilizing Sandia’s state-of-the-art MEMS microfabrication processing. This effort culminated in a device design for a multi-purpose ion trap experimental platform for investigating on-chip microwave qubit control, laying the groundwork for further funded R&D to develop on-chip microwave qubit control in an architecture that is suitable to engineering development.

  5. A Review for Detecting Gene-Gene Interactions Using Machine Learning Methods in Genetic Epidemiology

    Directory of Open Access Journals (Sweden)

    Ching Lee Koo

    2013-01-01

    Full Text Available Recently, the greatest statistical computational challenge in genetic epidemiology is to identify and characterize the genes that interact with other genes and environment factors that bring the effect on complex multifactorial disease. These gene-gene interactions are also denoted as epitasis in which this phenomenon cannot be solved by traditional statistical method due to the high dimensionality of the data and the occurrence of multiple polymorphism. Hence, there are several machine learning methods to solve such problems by identifying such susceptibility gene which are neural networks (NNs, support vector machine (SVM, and random forests (RFs in such common and multifactorial disease. This paper gives an overview on machine learning methods, describing the methodology of each machine learning methods and its application in detecting gene-gene and gene-environment interactions. Lastly, this paper discussed each machine learning method and presents the strengths and weaknesses of each machine learning method in detecting gene-gene interactions in complex human disease.

  6. Quartz crystal microbalance (QCM) affinity biosensor for genetically modified organisms (GMOs) detection.

    Science.gov (United States)

    Mannelli, Ilaria; Minunni, Maria; Tombelli, Sara; Mascini, Marco

    2003-03-01

    A DNA piezoelectric sensor has been developed for the detection of genetically modified organisms (GMOs). Single stranded DNA (ssDNA) probes were immobilised on the sensor surface of a quartz crystal microbalance (QCM) device and the hybridisation between the immobilised probe and the target complementary sequence in solution was monitored. The probe sequences were internal to the sequence of the 35S promoter (P) and Nos terminator (T), which are inserted sequences in the genome of GMOs regulating the transgene expression. Two different probe immobilisation procedures were applied: (a) a thiol-dextran procedure and (b) a thiol-derivatised probe and blocking thiol procedure. The system has been optimised using synthetic oligonucleotides, which were then applied to samples of plasmidic and genomic DNA isolated from the pBI121 plasmid, certified reference materials (CRM), and real samples amplified by the polymerase chain reaction (PCR). The analytical parameters of the sensor have been investigated (sensitivity, reproducibility, lifetime etc.). The results obtained showed that both immobilisation procedures enabled sensitive and specific detection of GMOs, providing a useful tool for screening analysis in food samples.

  7. Designing multilayered nanoplatforms for SERS-based detection of genetically modified organisms

    Science.gov (United States)

    Uluok, Saadet; Guven, Burcu; Eksi, Haslet; Ustundag, Zafer; Tamer, Ugur; Boyaci, Ismail Hakki

    2015-01-01

    In this study, the multilayered surface-enhanced Raman spectroscopy (SERS) platforms were developed for the analysis of genetically modified organisms (GMOs). For this purpose, two molecules [11-mercaptoundecanoic acid (11-MUA) and 2-mercaptoethylamine (2-MEA)] were attached with Aurod and Auspherical nanoparticles to form multilayered constructions on the gold (Au)slide surface. The best multilayered platform structure was chosen depending on SERS enhancement, and this surface was characterised with atomic force microscopy (AFM) and attenuated total reflectance Fourier transform infrared spectroscopy. After the optimum multilayered SERS platform and nanoparticle interaction was identified, the oligonucleotides on the Aurod nanoparticles and Auslide were combined to determine target concentrations from the 5,5'-dithiobis (2-nitrobenzoic acid) (DTNB) signals using SERS. The correlation between the SERS intensities for DTNB and target concentrations was found to be linear within a range of 10 pM to 1 µM, and with a detection limit of 34 fM. The selectivity and specificity of the developed sandwich assay were tested using negative and positive controls, and nonsense and real sample studies. The obtained results showed that the multilayered SERS sandwich method allows for sensitive, selective, and specific detection of oligonucleotide sequences.

  8. Development of a recombinant DNA assay system for the detection of genetic change in astronauts' cells

    International Nuclear Information System (INIS)

    Atchley, S.V.; Chen, D.J.C.; Strniste, G.F.; Walters, R.A.; Moyzis, R.K.

    1984-01-01

    We are developing a new recombinant DNA system for the detection and measurement of genetic change in humans caused by exposure to low level ionizing radiation. A unique feature of the method is the use of cloned repetitive DNA probes to assay human DNA for structural changes during or after irradiation. Repetitive sequences exist in different families. Collectively they constitute over 25% of the DNA in a human cell. Repeat families have between 10 and 500,000 members. We have constructed repetitive DNA sequence libraries using recombinant DNA techniques. From these libraries we have isolated and characterized individual repeats comprising 75 to 90% of the mass of human repetitive DNA. Repeats used in our assay system exist in tandem arrays in the genome. Perturbation of these sequences in a cell, followed by detection with a repeat probe, produces a new, multimeric ''ladder'' pattern on an autoradiogram. The repeat probe used in our initial study is complementary to 1% of human DNA. Therefore, the sensitivity of this method is several orders of magnitude better than existing assays. Preliminary evidence from human skin cells exposed to acute, low-dose x-ray treatments indicates that DNA is affected at a dose as low as 5R. The radiation doses used in this system are well within the range of doses received by astronauts during spaceflight missions. Due to its small material requirements, this technique could easily be adapted for use in space. 16 refs., 1 fig

  9. Detecting Cyber-Attacks on Wireless Mobile Networks Using Multicriterion Fuzzy Classifier with Genetic Attribute Selection

    Directory of Open Access Journals (Sweden)

    El-Sayed M. El-Alfy

    2015-01-01

    Full Text Available With the proliferation of wireless and mobile network infrastructures and capabilities, a wide range of exploitable vulnerabilities emerges due to the use of multivendor and multidomain cross-network services for signaling and transport of Internet- and wireless-based data. Consequently, the rates and types of cyber-attacks have grown considerably and current security countermeasures for protecting information and communication may be no longer sufficient. In this paper, we investigate a novel methodology based on multicriterion decision making and fuzzy classification that can provide a viable second-line of defense for mitigating cyber-attacks. The proposed approach has the advantage of dealing with various types and sizes of attributes related to network traffic such as basic packet headers, content, and time. To increase the effectiveness and construct optimal models, we augmented the proposed approach with a genetic attribute selection strategy. This allows efficient and simpler models which can be replicated at various network components to cooperatively detect and report malicious behaviors. Using three datasets covering a variety of network attacks, the performance enhancements due to the proposed approach are manifested in terms of detection errors and model construction times.

  10. Electron Spin Resonance Measurement with Microinductor on Chip

    Directory of Open Access Journals (Sweden)

    Akio Kitagawa

    2011-01-01

    Full Text Available The detection of radicals on a chip is demonstrated. The proposed method is based on electron spin resonance (ESR spectroscopy and the measurement of high-frequency impedance of the microinductor fabricated on the chip. The measurement was by using a frequency sweep of approximately 100 MHz. The ESR spectra of di(phenyl-(2,4,6-trinitrophenyliminoazanium (DPPH dropped on the microinductor which is fabricated with CMOS 350-nm technology were observed at room temperature. The volume of the DPPH ethanol solution was 2 μL, and the number of spins on the micro-inductor was estimated at about 1014. The sensitivity is not higher than that of the standard ESR spectrometers. However, the result indicates the feasibility of a near field radical sensor in which the microinductor as a probe head and ESR signal processing circuit are integrated.

  11. Fiber Bragg grating sensor interrogators on chip: challenges and opportunities

    Science.gov (United States)

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

    2017-04-01

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

  12. A dual-unit pressure sensor for on-chip self-compensation of zero-point temperature drift

    International Nuclear Information System (INIS)

    Wang, Jiachou; Li, Xinxin

    2014-01-01

    A novel dual-unit piezoresistive pressure sensor, consisting of a sensing unit and a dummy unit, is proposed and developed for on-chip self-compensation for zero-point temperature drift. With an MIS (microholes inter-etch and sealing) process implemented only from the front side of single (1 1 1) silicon wafers, a pressure sensitive unit and another identically structured pressure insensitive dummy unit are compactly integrated on-chip to eliminate unbalance factors induced zero-point temperature-drift by mutual compensation between the two units. Besides, both units are physically suspended from silicon substrate to further suppress packaging-stress induced temperature drift. A simultaneously processes ventilation hole-channel structure is connected with the pressure reference cavity of the dummy unit to make it insensitive to detected pressure. In spite of the additional dummy unit, the sensor chip dimensions are still as small as 1.2 mm × 1.2 mm × 0.4 mm. The proposed dual-unit sensor is fabricated and tested, with the tested sensitivity being 0.104 mV kPa −1 3.3 V −1 , nonlinearity of less than 0.08% · FSO and overall accuracy error of ± 0.18% · FSO. Without using any extra compensation method, the sensor features an ultra-low temperature coefficient of offset (TCO) of 0.002% °C −1 · FSO that is much better than the performance of conventional pressure sensors. The highly stable and small-sized sensors are promising for low cost production and applications. (paper)

  13. Organs-on-Chips in Drug Development: The Importance of Involving Stakeholders in Early Health Technology Assessment

    NARCIS (Netherlands)

    Middelkamp, Heleen H.T.; van der Meer, Andries Dirk; Hummel, J. Marjan; Stamatialis, Dimitrios; Mummery, Christine Lindsay; Passier, Petrus Christianus Johannes Josephus; IJzerman, Maarten Joost

    2016-01-01

    Organs-on-chips are three-dimensional, microfluidic cell culture systems that simulate the function of tissues and organ subunits. Organ-on-chip systems are expected to contribute to drug candidate screening and the reduction of animal tests in preclinical drug development and may increase

  14. Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

    Directory of Open Access Journals (Sweden)

    Kiwako S Araki

    Full Text Available In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals. We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers. We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms

  15. Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

    Science.gov (United States)

    Araki, Kiwako S; Kubo, Takuya; Kudoh, Hiroshi

    2017-01-01

    In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for

  16. Low-Noise CMOS Circuits for On-Chip Signal Processing in Focal-Plane Arrays

    Science.gov (United States)

    Pain, Bedabrata

    The performance of focal-plane arrays can be significantly enhanced through the use of on-chip signal processing. Novel, in-pixel, on-focal-plane, analog signal-processing circuits for high-performance imaging are presented in this thesis. The presence of a high background-radiation is a major impediment for infrared focal-plane array design. An in-pixel, background-suppression scheme, using dynamic analog current memory circuit, is described. The scheme also suppresses spatial noise that results from response non-uniformities of photo-detectors, leading to background limited infrared detector readout performance. Two new, low-power, compact, current memory circuits, optimized for operation at ultra-low current levels required in infrared-detection, are presented. The first one is a self-cascading current memory that increases the output impedance, and the second one is a novel, switch feed-through reducing current memory, implemented using error-current feedback. This circuit can operate with a residual absolute -error of less than 0.1%. The storage-time of the memory is long enough to also find applications in neural network circuits. In addition, a voltage-mode, accurate, low-offset, low-power, high-uniformity, random-access sample-and-hold cell, implemented using a CCD with feedback, is also presented for use in background-suppression and neural network applications. A new, low noise, ultra-low level signal readout technique, implemented by individually counting photo-electrons within the detection pixel, is presented. The output of each unit-cell is a digital word corresponding to the intensity of the photon flux, and the readout is noise free. This technique requires the use of unit-cell amplifiers that feature ultra-high-gain, low-power, self-biasing capability and noise in sub-electron levels. Both single-input and differential-input implementations of such amplifiers are investigated. A noise analysis technique is presented for analyzing sampled

  17. APOL1 Nephropathy: A Population Genetics and Evolutionary Medicine Detective Story.

    Science.gov (United States)

    Kruzel-Davila, Etty; Wasser, Walter G; Skorecki, Karl

    2017-11-01

    Common DNA sequence variants rarely have a high-risk association with a common disease. When such associations do occur, evolutionary forces must be sought, such as in the association of apolipoprotein L1 (APOL1) gene risk variants with nondiabetic kidney diseases in populations of African ancestry. The variants originated in West Africa and provided pathogenic resistance in the heterozygous state that led to high allele frequencies owing to an adaptive evolutionary selective sweep. However, the homozygous state is disadvantageous and is associated with a markedly increased risk of a spectrum of kidney diseases encompassing hypertension-attributed kidney disease, focal segmental glomerulosclerosis, human immunodeficiency virus nephropathy, sickle cell nephropathy, and progressive lupus nephritis. This scientific success story emerged with the help of the tools developed over the past 2 decades in human genome sequencing and population genomic databases. In this introductory article to a timely issue dedicated to illuminating progress in this area, we describe this unique population genetics and evolutionary medicine detective story. We emphasize the paradox of the inheritance mode, the missing heritability, and unresolved associations, including cardiovascular risk and diabetic nephropathy. We also highlight how genetic epidemiology elucidates mechanisms and how the principles of evolution can be used to unravel conserved pathways affected by APOL1 that may lead to novel therapies. The APOL1 gene provides a compelling example of a common variant association with common forms of nondiabetic kidney disease occurring in a continental population isolate with subsequent global admixture. Scientific collaboration using multiple experimental model systems and approaches should further clarify pathomechanisms further, leading to novel therapies. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Micromotor-based lab-on-chip immunoassays

    Science.gov (United States)

    García, Miguel; Orozco, Jahir; Guix, Maria; Gao, Wei; Sattayasamitsathit, Sirilak; Escarpa, Alberto; Merkoçi, Arben; Wang, Joseph

    2013-01-01

    Here we describe the first example of using self-propelled antibody-functionalized synthetic catalytic microengines for capturing and transporting target proteins between the different reservoirs of a lab-on-a-chip (LOC) device. A new catalytic polymer/Ni/Pt microtube engine, containing carboxy moieties on its mixed poly(3,4-ethylenedioxythiophene) (PEDOT)/COOH-PEDOT polymeric outermost layer, is further functionalized with the antibody receptor to selectively recognize and capture the target protein. The new motor-based microchip immunoassay operations are carried out without any bulk fluid flow, replacing the common washing steps in antibody-based protein bioassays with the active transport of the captured protein throughout the different reservoirs, where each step of the immunoassay takes place. A first microchip format involving an `on-the-fly' double-antibody sandwich assay (DASA) is used for demonstrating the selective capture of the target protein, in the presence of excess of non-target proteins. A secondary antibody tagged with a polymeric-sphere tracer allows the direct visualization of the binding events. In a second approach the immuno-nanomotor captures and transports the microsphere-tagged antigen through a microchannel network. An anti-protein-A modified microengine is finally used to demonstrate the selective capture, transport and convenient label-free optical detection of a Staphylococcus aureus target bacteria (containing proteinA in its cell wall) in the presence of a large excess of non-target (Saccharomyces cerevisiae) cells. The resulting nanomotor-based microchip immunoassay offers considerable potential for diverse applications in clinical diagnostics, environmental and security monitoring fields.Here we describe the first example of using self-propelled antibody-functionalized synthetic catalytic microengines for capturing and transporting target proteins between the different reservoirs of a lab-on-a-chip (LOC) device. A new catalytic

  19. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.

    Science.gov (United States)

    Holst-Jensen, Arne; Spilsberg, Bjørn; Arulandhu, Alfred J; Kok, Esther; Shi, Jianxin; Zel, Jana

    2016-07-01

    The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.

  20. Comparison of different real-time PCR chemistries and their suitability for detection and quantification of genetically modified organisms

    NARCIS (Netherlands)

    Gasparic, M.B.; Cankar, K.; Zel, J.; Gruden, K.

    2008-01-01

    Background: The real-time polymerase chain reaction is currently the method of choice for quantifying nucleic acids in different DNA based quantification applications. It is widely used also for detecting and quantifying genetically modified components in food and feed, predominantly employing

  1. Evaluation of real-time PCR detection methods for detecting rice products contaminated by rice genetically modified with a CpTI-KDEL-T-nos transgenic construct.

    Science.gov (United States)

    Nakamura, Kosuke; Akiyama, Hiroshi; Kawano, Noriaki; Kobayashi, Tomoko; Yoshimatsu, Kayo; Mano, Junichi; Kitta, Kazumi; Ohmori, Kiyomi; Noguchi, Akio; Kondo, Kazunari; Teshima, Reiko

    2013-12-01

    Genetically modified (GM) rice (Oryza sativa) lines, such as insecticidal Kefeng and Kemingdao, have been developed and found unauthorised in processed rice products in many countries. Therefore, qualitative detection methods for the GM rice are required for the GM food regulation. A transgenic construct for expressing cowpea (Vigna unguiculata) trypsin inhibitor (CpTI) was detected in some imported processed rice products contaminated with Kemingdao. The 3' terminal sequence of the identified transgenic construct for expression of CpTI included an endoplasmic reticulum retention signal coding sequence (KDEL) and nopaline synthase terminator (T-nos). The sequence was identical to that in a report on Kefeng. A novel construct-specific real-time polymerase chain reaction (PCR) detection method for detecting the junction region sequence between the CpTI-KDEL and T-nos was developed. The imported processed rice products were evaluated for the contamination of the GM rice using the developed construct-specific real-time PCR methods, and detection frequency was compared with five event-specific detection methods. The construct-specific detection methods detected the GM rice at higher frequency than the event-specific detection methods. Therefore, we propose that the construct-specific detection method is a beneficial tool for screening the contamination of GM rice lines, such as Kefeng, in processed rice products for the GM food regulation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Detecting genetic introgression: high levels of intersubspecific recombination found in Xylella fastidiosa in Brazil.

    Science.gov (United States)

    Nunney, Leonard; Yuan, Xiaoli; Bromley, Robin E; Stouthamer, Richard

    2012-07-01

    Documenting the role of novel mutation versus homologous recombination in bacterial evolution, and especially in the invasion of new hosts, is central to understanding the long-term dynamics of pathogenic bacteria. We used multilocus sequence typing (MLST) to study this issue in Xylella fastidiosa subsp. pauca from Brazil, a bacterium causing citrus variegated chlorosis (CVC) and coffee leaf scorch (CLS). All 55 citrus isolates typed (plus one coffee isolate) defined three similar sequence types (STs) dominated by ST11 (85%), while the remaining 22 coffee isolates defined two STs, mainly ST16 (74%). This low level of variation masked unusually large allelic differences (>1% divergence with no intermediates) at five loci (leuA, petC, malF, cysG, and holC). We developed an introgression test to detect whether these large differences were due to introgression via homologous recombination from another X. fastidiosa subspecies. Using additional sequencing around these loci, we established that the seven randomly chosen MLST targets contained seven regions of introgression totaling 2,172 bp of 4,161 bp (52%), only 409 bp (10%) of which were detected by other recombination tests. This high level of introgression suggests the hypothesis that X. fastidiosa subsp. pauca became pathogenic on citrus and coffee (crops cultivated in Brazil for several hundred years) only recently after it gained genetic variation via intersubspecific recombination, facilitating a switch from native hosts. A candidate donor is the subspecies infecting plum in the region since 1935 (possibly X. fastidiosa subsp. multiplex). This hypothesis predicts that nonrecombinant native X. fastidiosa subsp. pauca (not yet isolated) does not cause disease in citrus or coffee.

  3. Rearrangeable and exchangeable optical module with system-on-chip for wearable functional near-infrared spectroscopy system.

    Science.gov (United States)

    Funane, Tsukasa; Numata, Takashi; Sato, Hiroki; Hiraizumi, Shinsuke; Hasegawa, Yuichi; Kuwabara, Hidenobu; Hasegawa, Kiyoshi; Kiguchi, Masashi

    2018-01-01

    We developed a system-on-chip (SoC)-incorporated light-emitting diode (LED) and avalanche photodiode (APD) modules to improve the usability and flexibility of a fiberless wearable functional near-infrared spectroscopy (fNIRS) system. The SoC has a microprocessing unit and programmable circuits. The time division method and the lock-in method were used for separately detecting signals from different positions and signals of different wavelengths, respectively. Each module autonomously works for this time-divided-lock-in measurement with a high sensitivity for haired regions. By supplying [Formula: see text] of power and base and data clocks, the LED module emits both 730- and 855-nm wavelengths of light, amplitudes of which are modulated in each lock-in frequency generated from the base clock, and the APD module provides the lock-in detected signals synchronizing with the data clock. The SoC provided many functions, including automatic-power-control of the LED, automatic judgment of detected power level, and automatic-gain-control of the programmable gain amplifier. The number and the arrangement of modules can be adaptively changed by connecting this exchangeable modules in a daisy chain and setting the parameters dependent on the probing position. Therefore, users can configure a variety of arrangements (single- or multidistance combinations) of them with this module-based system.

  4. Obstacle Recognition Based on Machine Learning for On-Chip LiDAR Sensors in a Cyber-Physical System

    Directory of Open Access Journals (Sweden)

    Fernando Castaño

    2017-09-01

    Full Text Available Collision avoidance is an important feature in advanced driver-assistance systems, aimed at providing correct, timely and reliable warnings before an imminent collision (with objects, vehicles, pedestrians, etc.. The obstacle recognition library is designed and implemented to address the design and evaluation of obstacle detection in a transportation cyber-physical system. The library is integrated into a co-simulation framework that is supported on the interaction between SCANeR software and Matlab/Simulink. From the best of the authors’ knowledge, two main contributions are reported in this paper. Firstly, the modelling and simulation of virtual on-chip light detection and ranging sensors in a cyber-physical system, for traffic scenarios, is presented. The cyber-physical system is designed and implemented in SCANeR. Secondly, three specific artificial intelligence-based methods for obstacle recognition libraries are also designed and applied using a sensory information database provided by SCANeR. The computational library has three methods for obstacle detection: a multi-layer perceptron neural network, a self-organization map and a support vector machine. Finally, a comparison among these methods under different weather conditions is presented, with very promising results in terms of accuracy. The best results are achieved using the multi-layer perceptron in sunny and foggy conditions, the support vector machine in rainy conditions and the self-organized map in snowy conditions.

  5. Obstacle Recognition Based on Machine Learning for On-Chip LiDAR Sensors in a Cyber-Physical System.

    Science.gov (United States)

    Castaño, Fernando; Beruvides, Gerardo; Haber, Rodolfo E; Artuñedo, Antonio

    2017-09-14

    Collision avoidance is an important feature in advanced driver-assistance systems, aimed at providing correct, timely and reliable warnings before an imminent collision (with objects, vehicles, pedestrians, etc.). The obstacle recognition library is designed and implemented to address the design and evaluation of obstacle detection in a transportation cyber-physical system. The library is integrated into a co-simulation framework that is supported on the interaction between SCANeR software and Matlab/Simulink. From the best of the authors' knowledge, two main contributions are reported in this paper. Firstly, the modelling and simulation of virtual on-chip light detection and ranging sensors in a cyber-physical system, for traffic scenarios, is presented. The cyber-physical system is designed and implemented in SCANeR. Secondly, three specific artificial intelligence-based methods for obstacle recognition libraries are also designed and applied using a sensory information database provided by SCANeR. The computational library has three methods for obstacle detection: a multi-layer perceptron neural network, a self-organization map and a support vector machine. Finally, a comparison among these methods under different weather conditions is presented, with very promising results in terms of accuracy. The best results are achieved using the multi-layer perceptron in sunny and foggy conditions, the support vector machine in rainy conditions and the self-organized map in snowy conditions.

  6. PCR detection and genetic diversity of bovine hemoprotozoan parasites in Vietnam.

    Science.gov (United States)

    Sivakumar, Thillaiampalam; Lan, Dinh Thi Bich; Long, Phung Thang; Yoshinari, Takeshi; Tattiyapong, Muncharee; Guswanto, Azirwan; Okubo, Kazuhiro; Igarashi, Ikuo; Inoue, Noboru; Xuan, Xuenan; Yokoyama, Naoaki

    2013-11-01

    Hemoprotozoan infections often cause serious production losses in livestock. In the present study, we conducted a PCR-based survey of Babesia bovis, Babesia bigemina, Theileria annulata, Theileria orientalis, Trypanosoma evansi and Trypanosoma theileri, using 423 DNA samples extracted from blood samples of cattle (n=202), water buffaloes (n=43), sheep (n=51) and goats (n=127) bred in the Hue and Hanoi provinces of Vietnam. With the exception of T. annulata and T. evansi, all other parasite species (B. bovis, B. bigemina, T. orientalis and T. theileri) were detected in the cattle populations with B. bovis being the most common among them. Additionally, four water buffaloes and a single goat were infected with B. bovis and B. bigemina, respectively. The Hue province had more hemoprotozoan-positive animals than those from the Hanoi region. In the phylogenetic analyses, B. bovis-MSA-2b, B. bigemina-AMA-1 and T. theileri-CATL gene sequences were dispersed across four, one and three different clades in the respective phylograms. This is the first study in which the presence of Babesia, Theileria and Trypanosoma parasites was simultaneously investigated by PCR in Vietnam. The findings suggest that hemoprotozoan parasites, some of which are genetically diverse, continue to be a threat to the livestock industry in this country.

  7. Spectroscopic detection of fluorescent protein marker gene activity in genetically modified plants

    Science.gov (United States)

    Liew, O. W.; Chong, Jenny P. C.; Asundi, Anand K.

    2005-04-01

    This work focuses on developing a portable fibre optic fluorescence analyser for rapid identification of genetically modified plants tagged with a fluorescent marker gene. Independent transgenic tobacco plant lines expressing the enhanced green fluorescence protein (EGFP) gene were regenerated following Agrobacterium-mediated gene transfer. Molecular characterisation of these plant lines was carried out at the DNA level by PCR screening to confirm their transgenic status. Conventional transgene expression analysis was then carried out at the RNA level by RT-PCR and at the protein level by Western blotting using anti-GFP rabbit antiserum. The amount of plant-expressed EGFP on a Western blot was quantified against known amounts of purified EGFP by scanning densitometry. The expression level of EGFP in transformed plants was found to range from 0.1 - 0.6% of total extractable protein. A comparison between conventional western analysis of transformants and direct spectroscopic quantification using the fibre optic fluorescence analyser was made. The results showed that spectroscopic measurements of fluorescence emission from strong EGFP expressors correlated positively with Western blot data. However, the fluorescence analyser was also able to identify weakly expressing plant transformants below the detection limit of colorimetric Western blotting.

  8. Statistical framework for detection of genetically modified organisms based on Next Generation Sequencing.

    Science.gov (United States)

    Willems, Sander; Fraiture, Marie-Alice; Deforce, Dieter; De Keersmaecker, Sigrid C J; De Loose, Marc; Ruttink, Tom; Herman, Philippe; Van Nieuwerburgh, Filip; Roosens, Nancy

    2016-02-01

    Because the number and diversity of genetically modified (GM) crops has significantly increased, their analysis based on real-time PCR (qPCR) methods is becoming increasingly complex and laborious. While several pioneers already investigated Next Generation Sequencing (NGS) as an alternative to qPCR, its practical use has not been assessed for routine analysis. In this study a statistical framework was developed to predict the number of NGS reads needed to detect transgene sequences, to prove their integration into the host genome and to identify the specific transgene event in a sample with known composition. This framework was validated by applying it to experimental data from food matrices composed of pure GM rice, processed GM rice (noodles) or a 10% GM/non-GM rice mixture, revealing some influential factors. Finally, feasibility of NGS for routine analysis of GM crops was investigated by applying the framework to samples commonly encountered in routine analysis of GM crops. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. A novel reference plasmid for the qualitative detection of genetically modified rice in food and feed.

    Science.gov (United States)

    Li, Liang; Dong, Mei; An, Na; Liang, Lixia; Wan, Yusong; Jin, Wujun

    2015-01-01

    Rice is one of the most important food crops in the world. Genetically modified (GM) technology has been used in rice to confer herbicide tolerance and pathogen or insect resistance. China invests heavily in research on GM rice. By the end of 2014, at least 250 transgenic rice lines had been developed in China. To monitor the presence of GM rice in food and feed, we collected information on foreign elements from 250 transgenic rice lines and found 5 elements, including the Agrobacterium tumefaciens nopaline synthase terminator (T-NOS), the cauliflower mosaic virus 35S promoter (CaMV35S), the ubiquitin gene (Ubi), the bar gene, and the hygromycin phosphotransferase gene (Hpt), that are commonly present in GM rice. Therefore, we constructed a novel plasmid (pBJGMM001) that contains fragments of these elements and two endogenous reference genes (the sucrose phosphate synthase gene, SPS, and the phosphoenolpyruvate carboxylase gene, PEPC). pBJGMM001 can serve as a standard for detecting 96% of GM rice lines in China. The primers, amplicons, reaction mixture, and PCR program were developed based on Chinese National Standards. The protocol was validated and determined to be suitable for practical use in monitoring and identifying GM rice.

  10. A Novel Reference Plasmid for the Qualitative Detection of Genetically Modified Rice in Food and Feed

    Directory of Open Access Journals (Sweden)

    Liang Li

    2015-01-01

    Full Text Available Rice is one of the most important food crops in the world. Genetically modified (GM technology has been used in rice to confer herbicide tolerance and pathogen or insect resistance. China invests heavily in research on GM rice. By the end of 2014, at least 250 transgenic rice lines had been developed in China. To monitor the presence of GM rice in food and feed, we collected information on foreign elements from 250 transgenic rice lines and found 5 elements, including the Agrobacterium tumefaciens nopaline synthase terminator (T-NOS, the cauliflower mosaic virus 35S promoter (CaMV35S, the ubiquitin gene (Ubi, the bar gene, and the hygromycin phosphotransferase gene (Hpt, that are commonly present in GM rice. Therefore, we constructed a novel plasmid (pBJGMM001 that contains fragments of these elements and two endogenous reference genes (the sucrose phosphate synthase gene, SPS, and the phosphoenolpyruvate carboxylase gene, PEPC. pBJGMM001 can serve as a standard for detecting 96% of GM rice lines in China. The primers, amplicons, reaction mixture, and PCR program were developed based on Chinese National Standards. The protocol was validated and determined to be suitable for practical use in monitoring and identifying GM rice.

  11. Utilization of a genetic algorithm for the automatic detection of oil spill from RADARSAT-2 SAR satellite data

    International Nuclear Information System (INIS)

    Marghany, Maged

    2014-01-01

    Highlights: • An oil platform located 70 km from the coast of Louisiana sank on Thursday. • Oil spill has backscatter values of −25 dB in RADARSAT-2 SAR. • Oil spill is portrayed in SCNB mode by shallower incidence angle. • Ideal detection of oil spills in SAR images requires moderate wind speeds. • Genetic algorithm is excellent tool for automatic detection of oil spill in RADARSAT-2 SAR data. - Abstract: In this work, a genetic algorithm is applied for the automatic detection of oil spills. The procedure is implemented using sequences from RADARSAT-2 SAR ScanSAR Narrow single-beam data acquired in the Gulf of Mexico. The study demonstrates that the implementation of crossover allows for the generation of an accurate oil spill pattern. This conclusion is confirmed by the receiver-operating characteristic (ROC) curve. The ROC curve indicates that the existence of oil slick footprints can be identified using the area between the ROC curve and the no-discrimination line of 90%, which is greater than that of other surrounding environmental features. In conclusion, the genetic algorithm can be used as a tool for the automatic detection of oil spills, and the ScanSAR Narrow single-beam mode serves as an excellent sensor for oil spill detection and survey

  12. Genetic diversity detection of the domestic horse (Equus caballus by genes associated with coat color

    Directory of Open Access Journals (Sweden)

    Luz Correa A

    2015-09-01

    Full Text Available Objective. To assess the population structure and genetic diversity in populations of domestic horse (Equus caballus in the municipality Cienaga de Oro-Córdoba (Colombia. Materials and methods. Random sampling were conducted between August and October 2013, in adult animals on farms seven districts, which was carried out phenotypic characterization of each animal, based on autosomal markers encoding morphological Extension (E , Agouti (A, Cream (C, White (W, Gray (G, Tobiano (TO, Overo (O and Roan (RN. Population genetic parameters: allele frequency, genetic diversity, gene flow, Hardy-Weinberg equilibrium and genetic distance were calculated through the program POPGENE 1.31; the genetic structure was assessed using the program FSTAT v. 2.9.3.2. Results. 341 individuals were analyzed in the seven populations studied, where the Extension gene Was the MOST faq frequently as the Overo and Tobiano genes showed the lowest values. Insignificant values of genetic variability and population recorded a global level, likewise, low genetic differentiation among populations, accompanied by a high gene flow was obtained; an excess of heterozygotes at population and global level was observed; to this is added the presence of Hardy-Weinberg equilibrium in all populations relative to the markers studied and low genetic distance values were reported. Conclusions. The populations are highly genetically related, a situation that may result from the existing geographical proximity between them, favoring genetic exchange and the establishment of a metapopulation.

  13. First application of a microsphere-based immunoassay to the detection of genetically modified organisms (GMOs): quantification of Cry1Ab protein in genetically modified maize.

    Science.gov (United States)

    Fantozzi, Anna; Ermolli, Monica; Marini, Massimiliano; Scotti, Domenico; Balla, Branko; Querci, Maddalena; Langrell, Stephen R H; Van den Eede, Guy

    2007-02-21

    An innovative covalent microsphere immunoassay, based on the usage of fluorescent beads coupled to a specific antibody, was developed for the quantification of the endotoxin Cry1Ab present in MON810 and Bt11 genetically modified (GM) maize lines. In particular, a specific protocol was developed to assess the presence of Cry1Ab in a very broad range of GM maize concentrations, from 0.1 to 100% [weight of genetically modified organism (GMO)/weight]. Test linearity was achieved in the range of values from 0.1 to 3%, whereas fluorescence signal increased following a nonlinear model, reaching a plateau at 25%. The limits of detection and quantification were equal to 0.018 and 0.054%, respectively. The present study describes the first application of quantitative high-throughput immunoassays in GMO analysis.

  14. ASIC design of a digital fuzzy system on chip for medical diagnostic applications.

    Science.gov (United States)

    Roy Chowdhury, Shubhajit; Roy, Aniruddha; Saha, Hiranmay

    2011-04-01

    The paper presents the ASIC design of a digital fuzzy logic circuit for medical diagnostic applications. The system on chip under consideration uses fuzzifier, memory and defuzzifier for fuzzifying the patient data, storing the membership function values and defuzzifying the membership function values to get the output decision. The proposed circuit uses triangular trapezoidal membership functions for fuzzification patients' data. For minimizing the transistor count, the proposed circuit uses 3T XOR gates and 8T adders for its design. The entire work has been carried out using TSMC 0.35 µm CMOS process. Post layout TSPICE simulation of the whole circuit indicates a delay of 31.27 ns and the average power dissipation of the system on chip is 123.49 mW which indicates a less delay and less power dissipation than the comparable embedded systems reported earlier.

  15. Debugging systems-on-chip communication-centric and abstraction-based techniques

    CERN Document Server

    Vermeulen, Bart

    2014-01-01

    This book describes an approach and supporting infrastructure to facilitate debugging the silicon implementation of a System-on-Chip (SOC), allowing its associated product to be introduced into the market more quickly.  Readers learn step-by-step the key requirements for debugging a modern, silicon SOC implementation, nine factors that complicate this debugging task, and a new debug approach that addresses these requirements and complicating factors.  The authors’ novel communication-centric, scan-based, abstraction-based, run/stop-based (CSAR) debug approach is discussed in detail, showing how it helps to meet debug requirements and address the nine, previously identified factors that complicate debugging silicon implementations of SOCs. The authors also derive the debug infrastructure requirements to support debugging of a silicon implementation of an SOC with their CSAR debug approach. This debug infrastructure consists of a generic on-chip debug architecture, a configurable automated design-for-debug ...

  16. On-Chip SDM Switching for Unicast, Multicast and Traffic Grooming in Data Center Networks

    DEFF Research Database (Denmark)

    Kamchevska, Valerija; Ding, Yunhong; Dalgaard, Kjeld

    2017-01-01

    This paper reports on the use of a novel photonic integrated circuit that facilitates multicast and grooming in an optical data center architecture. The circuit allows for on-chip spatial multiplexing and demultiplexing as well as fiber core switching. Using this device, we experimentally verify...... that multicast and/or grooming can be successfully performed along the full range of output ports, for different group size and different power ratio. Moreover, we experimentally demonstrate SDM transmission and 5 Tbit/s switching using the on-chip fiber switch with integrated fan-in/fan-out devices and achieve...... errorfree performance (BER≤10-9) for a network scenario including simultaneous unicast/multicast switching and traffic grooming....

  17. Core-shell magnetic nanoparticles for on-chip RF inductors

    KAUST Repository

    Koh, Kisik

    2013-01-01

    FeNi3 based core-shell magnetic nanoparticles are demonstrated as the magnetic core material for on-chip, radio frequency (RF) inductors. FeNi3 nanoparticles with 50-150 nm in diameter with 15-20 nm-thick SiO2 coating are chemically synthesized and deposited on a planar inductor as the magnetic core to enhance both inductance (L) and quality factor (Q) of the inductor. Experimentally, the ferromagnetic resonant frequency of the on-chip inductors based on FeNi3 core-shell nanoparticles has been shown to be over several GHz. A post-CMOS process has been developed to integrate the magnetic nanoparticles to a planar inductor and inductance enhancements up to 50% of the original magnitude with slightly enhanced Q-factor up to 1 GHz have been achieved. © 2013 IEEE.

  18. Pattern manipulation via on-chip phase modulation between orbital angular momentum beams

    International Nuclear Information System (INIS)

    Li, Huanlu; Strain, Michael J.; Meriggi, Laura; Sorel, Marc; Chen, Lifeng; Zhu, Jiangbo; Cicek, Kenan; Wang, Jianwei; Thompson, Mark G.; Cai, Xinlun; Yu, Siyuan

    2015-01-01

    An integrated approach to thermal modulation of relative phase between two optical vortices with opposite chirality has been demonstrated on a silicon-on-insulator substrate. The device consists of a silicon-integrated optical vortex emitter and a phase controlled 3 dB coupler. The relative phase between two optical vortices can be actively modulated on chip by applying a voltage on the integrated heater. The phase shift is shown to be linearly proportional to applied electrical power, and the rotation angle of the interference pattern is observed to be inversely proportional to topological charge. This scheme can be used in lab-on-chip, communications and sensing applications. It can be intentionally implemented with other modulation elements to achieve more complicated applications

  19. System-Level Design Methodologies for Networked Multiprocessor Systems-on-Chip

    DEFF Research Database (Denmark)

    Virk, Kashif Munir

    2008-01-01

    is the first such attempt in the published literature. The second part of the thesis deals with the issues related to the development of system-level design methodologies for networked multiprocessor systems-on-chip at various levels of design abstraction with special focus on the modeling and design...... at the system-level. The multiprocessor modeling framework is then extended to include models of networked multiprocessor systems-on-chip which is then employed to model wireless sensor networks both at the sensor node level as well as the wireless network level. In the third and the final part, the thesis...... to the transaction-level model. The thesis, as a whole makes contributions by describing a design methodology for networked multiprocessor embedded systems at three layers of abstraction from system-level through transaction-level to the cycle accurate level as well as demonstrating it practically by implementing...

  20. Modeling, analysis and optimization of network-on-chip communication architectures

    CERN Document Server

    Ogras, Umit Y

    2013-01-01

    Traditionally, design space exploration for Systems-on-Chip (SoCs) has focused on the computational aspects of the problem at hand. However, as the number of components on a single chip and their performance continue to increase, the communication architecture plays a major role in the area, performance and energy consumption of the overall system. As a result, a shift from computation-based to communication-based design becomes mandatory. Towards this end, network-on-chip (NoC) communication architectures have emerged recently as a promising alternative to classical bus and point-to-point communication architectures. This book explores outstanding research problems related to modeling, analysis and optimization of NoC communication architectures. More precisely, we present novel design methodologies, software tools and FPGA prototypes to aid the design of application-specific NoCs.

  1. Bioprinting and Organ-on-Chip Applications Towards Personalized Medicine for Bone Diseases.

    Science.gov (United States)

    Arrigoni, Chiara; Gilardi, Mara; Bersini, Simone; Candrian, Christian; Moretti, Matteo

    2017-06-01

    The skeleton supports and confers structure to the whole body but several pathological and traumatic conditions affect the bone tissue. Most of those pathological conditions are specific and different among different patients, such as bone defects due to traumatic injuries or bone remodeling alterations due to congenital diseases. In this context, the development of personalized therapies would be highly desirable. In recent years the advent of innovative techniques like bioprinting and microfluidic organ-on-chip raised hopes of achieving key tools helping the application of personalized therapies for bone diseases. In this review we will illustrate the latest progresses in the bioprinting of personalized bone grafts and generation of patient-specific bone-on-chip devices, describing current approaches and limitations and possible future improvements for more effective personalized bone grafts and disease models.

  2. On-chip high-voltage generator design design methodology for charge pumps

    CERN Document Server

    Tanzawa, Toru

    2016-01-01

    This book provides various design techniques for switched-capacitor on-chip high-voltage generators, including charge pump circuits, regulators, level shifters, references, and oscillators.  Readers will see these techniques applied to system design in order to address the challenge of how the on-chip high-voltage generator is designed for Flash memories, LCD drivers, and other semiconductor devices to optimize the entire circuit area and power efficiency with a low voltage supply, while minimizing the cost.  This new edition includes a variety of useful updates, including coverage of power efficiency and comprehensive optimization methodologies for DC-DC voltage multipliers, modeling of extremely low voltage Dickson charge pumps, and modeling and optimum design of AC-DC switched-capacitor multipliers for energy harvesting and power transfer for RFID.

  3. A Fully Integrated Humidity Sensor System-on-Chip Fabricated by Micro-Stamping Technology

    Science.gov (United States)

    Huang, Che-Wei; Huang, Yu-Jie; Lu, Shey-Shi; Lin, Chih-Ting

    2012-01-01

    A fully integrated humidity sensor chip was designed, implemented, and tested. Utilizing the micro-stamping technology, the pseudo-3D sensor system-on-chip (SSoC) architecture can be implemented by stacking sensing materials directly on the top of a CMOS-fabricated chip. The fabricated sensor system-on-chip (2.28 mm × 2.48 mm) integrated a humidity sensor, an interface circuit, a digital controller, and an On-Off Keying (OOK) wireless transceiver. With low power consumption, i.e., 750 μW without RF operation, the sensitivity of developed sensor chip was experimentally verified in the relative humidity (RH) range from 32% to 60%. The response time of the chip was also experimentally verified to be within 5 seconds from RH 36% to RH 64%. As a consequence, the implemented humidity SSoC paves the way toward the an ultra-small sensor system for various applications.

  4. Widely Tunable On-Chip Microwave Circulator for Superconducting Quantum Circuits

    Science.gov (United States)

    Chapman, Benjamin J.; Rosenthal, Eric I.; Kerckhoff, Joseph; Moores, Bradley A.; Vale, Leila R.; Mates, J. A. B.; Hilton, Gene C.; Lalumière, Kevin; Blais, Alexandre; Lehnert, K. W.

    2017-10-01

    We report on the design and performance of an on-chip microwave circulator with a widely (GHz) tunable operation frequency. Nonreciprocity is created with a combination of frequency conversion and delay, and requires neither permanent magnets nor microwave bias tones, allowing on-chip integration with other superconducting circuits without the need for high-bandwidth control lines. Isolation in the device exceeds 20 dB over a bandwidth of tens of MHz, and its insertion loss is small, reaching as low as 0.9 dB at select operation frequencies. Furthermore, the device is linear with respect to input power for signal powers up to hundreds of fW (≈103 circulating photons), and the direction of circulation can be dynamically reconfigured. We demonstrate its operation at a selection of frequencies between 4 and 6 GHz.

  5. On-chip integration of a superconducting microwave circulator and a Josephson parametric amplifier

    Science.gov (United States)

    Rosenthal, Eric I.; Chapman, Benjamin J.; Moores, Bradley A.; Kerckhoff, Joseph; Malnou, Maxime; Palken, D. A.; Mates, J. A. B.; Hilton, G. C.; Vale, L. R.; Ullom, J. N.; Lehnert, K. W.

    Recent progress in microwave amplification based on parametric processes in superconducting circuits has revolutionized the measurement of feeble microwave signals. These devices, which operate near the quantum limit, are routinely used in ultralow temperature cryostats to: readout superconducting qubits, search for axionic dark matter, and characterize astrophysical sensors. However, these amplifiers often require ferrite circulators to separate incoming and outgoing traveling waves. For this reason, measurement efficiency and scalability are limited. In order to facilitate the routing of quantum signals we have created a superconducting, on-chip microwave circulator without permanent magnets. We integrate our circulator on-chip with a Josephson parametric amplifier for the purpose of near quantum-limited directional amplification. In this talk I will present a design overview and preliminary measurements.

  6. Recent advances in graphene-based planar micro-supercapacitors for on-chip energy storage

    Institute of Scientific and Technical Information of China (English)

    Zhong-Shuai Wu; Xinliang Feng; Hui-Ming Cheng

    2014-01-01

    The current development trend towards miniaturized portable electronic devices has signiicantly increased the demand for ultrathin, lexible and sustainable on-chip micro-supercapacitors that have enormous potential to complement, or even to replace, micro-bateries and electrolytic capacitors. In this regard,graphene-based micro-supercapacitors with a planar geometry are promising micro-electrochemical energy-storage devices that can take full advantage of planar coniguration and unique features of graphene.his review summarizes the latest advances in on-chip graphene-based planar interdigital micro-supercapacitors, from the history of their development, representative graphene-based materials(graphene sheets, graphene quantum dots and graphene hybrids) for their manufacture, typical microfabrication strategies(photolithography techniques, electrochemical methods, laser writing, etc.),electrolyte(aqueous, organic, ionic and gel), to device coniguration(symmetric and asymmetric). Finally,the perspectives and possible development directions of future graphene-based micro-supercapacitors are briely discussed.

  7. On-chip nanofluidic integration of acoustic sensors towards high Q in liquid

    Science.gov (United States)

    Liang, Ji; Liu, Zifeng; Zhang, Hongxiang; Liu, Bohua; Zhang, Menglun; Zhang, Hao; Pang, Wei

    2017-11-01

    This paper reports an on-chip acoustic sensor comprising a piston-mode film bulk acoustic resonator and a monolithically integrated nanochannel. The resonator with the channel exhibits a resonance frequency (f) of 2.5 GHz and a quality (Q) factor of 436 in deionized water. The f × Q product is as high as 1.1 × 1012, which is the highest among all the acoustic wave sensors in the liquid phase. The sensor consumes 2 pl liquid volume and thus greatly saves the precious assays in biomedical testing. The Q factor is investigated, and real-time viscosity tests of glucose solution are demonstrated. The highly miniaturized and integrated sensor is capable to be arrayed with readout-circuitry, which opens an avenue for portable applications and lab-on-chip systems.

  8. Sequential and selective localized optical heating in water via on-chip dielectric nanopatterning.

    Science.gov (United States)

    Morsy, Ahmed M; Biswas, Roshni; Povinelli, Michelle L

    2017-07-24

    We study the use of nanopatterned silicon membranes to obtain optically-induced heating in water. We show that by varying the detuning between an absorptive optical resonance of the patterned membrane and an illumination laser, both the magnitude and response time of the temperature rise can be controlled. This allows for either sequential or selective heating of different patterned areas on chip. We obtain a steady-state temperature of approximately 100 °C for a 805.5nm CW laser power density of 66 µW/μm 2 and observe microbubble formation. The ability to spatially and temporally control temperature on the microscale should enable the study of heat-induced effects in a variety of chemical and biological lab-on-chip applications.

  9. On-chip electrochromic micro display for a disposable bio-sensor chip

    Science.gov (United States)

    Zhu, Yanjun; Tsukamoto, Takashiro; Tanaka, Shuji

    2017-12-01

    This paper reports an on-chip electrochromic micro display made of polyaniline (PANi) which can be easily made on a CMOS chip. Micro-patterned PANi thin films were selectively deposited on pre-patterned microelectrodes by using electrodeposition. The optimum conditions for deposition and electrochromism were investigated. An 8-pixel on-chip micro display was made on a Si chip. The color of each PANi film could be independently but simultaneously controlled, which means any 1-byte digital data could be displayed on the display. The PANi display had a response time as fast as about 100 ms, which means the transfer data rate was as fast as 80 bits per second.

  10. Soft error evaluation and vulnerability analysis in Xilinx Zynq-7010 system-on chip

    Energy Technology Data Exchange (ETDEWEB)

    Du, Xuecheng; He, Chaohui; Liu, Shuhuan, E-mail: liushuhuan@mail.xjtu.edu.cn; Zhang, Yao; Li, Yonghong; Xiong, Ceng; Tan, Pengkang

    2016-09-21

    Radiation-induced soft errors are an increasingly important threat to the reliability of modern electronic systems. In order to evaluate system-on chip's reliability and soft error, the fault tree analysis method was used in this work. The system fault tree was constructed based on Xilinx Zynq-7010 All Programmable SoC. Moreover, the soft error rates of different components in Zynq-7010 SoC were tested by americium-241 alpha radiation source. Furthermore, some parameters that used to evaluate the system's reliability and safety were calculated using Isograph Reliability Workbench 11.0, such as failure rate, unavailability and mean time to failure (MTTF). According to fault tree analysis for system-on chip, the critical blocks and system reliability were evaluated through the qualitative and quantitative analysis.

  11. Pattern manipulation via on-chip phase modulation between orbital angular momentum beams

    Energy Technology Data Exchange (ETDEWEB)

    Li, Huanlu [Department of Electrical and Electronic Engineering, University of Bristol, University Walk, Bristol BS8 1TR (United Kingdom); School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow G12 8LP (United Kingdom); Strain, Michael J. [School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow G12 8LP (United Kingdom); Wolfson Centre, Institute of Photonics, University of Strathclyde, 106 Rottenrow East, Glasgow G4 0NW (United Kingdom); Meriggi, Laura; Sorel, Marc [School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow G12 8LP (United Kingdom); Chen, Lifeng; Zhu, Jiangbo; Cicek, Kenan [Department of Electrical and Electronic Engineering, University of Bristol, University Walk, Bristol BS8 1TR (United Kingdom); Wang, Jianwei; Thompson, Mark G. [Centre for Quantum Photonics, H. H. Wills Physics Laboratory and Department of Electrical and Electronic Engineering, University of Bristol, Bristol BS8 1UB (United Kingdom); Cai, Xinlun, E-mail: caixlun5@mail.sysu.edu.cn [Centre for Quantum Photonics, H. H. Wills Physics Laboratory and Department of Electrical and Electronic Engineering, University of Bristol, Bristol BS8 1UB (United Kingdom); State Key Laboratory of Optoelectronic Materials and Technologies and School of Physics and Engineering, Sun Yat-sen University, Guangzhou 510275 (China); Yu, Siyuan, E-mail: s.yu@bristol.ac.uk [Department of Electrical and Electronic Engineering, University of Bristol, University Walk, Bristol BS8 1TR (United Kingdom); State Key Laboratory of Optoelectronic Materials and Technologies and School of Physics and Engineering, Sun Yat-sen University, Guangzhou 510275 (China)

    2015-08-03

    An integrated approach to thermal modulation of relative phase between two optical vortices with opposite chirality has been demonstrated on a silicon-on-insulator substrate. The device consists of a silicon-integrated optical vortex emitter and a phase controlled 3 dB coupler. The relative phase between two optical vortices can be actively modulated on chip by applying a voltage on the integrated heater. The phase shift is shown to be linearly proportional to applied electrical power, and the rotation angle of the interference pattern is observed to be inversely proportional to topological charge. This scheme can be used in lab-on-chip, communications and sensing applications. It can be intentionally implemented with other modulation elements to achieve more complicated applications.

  12. Laser subtractive-additive-welding microfabrication for Lab-On-Chip (LOC) applications

    Science.gov (United States)

    Jonušauskas, Linas; RekštytÄ--, Sima; Buivydas, Ričardas; Butkus, Simas; Paipulas, Domas; Gadonas, Roaldas; Juodkazis, Saulius; Malinauskas, Mangirdas

    2017-02-01

    An approach employing ultrafast laser hybrid microfabrication combining ablation, 3D nanolithography and welding is proposed for the realization of Lab-On-Chip (LOC) device. The same laser setup is shown to be suitable for fabricating microgrooves in glass slabs, polymerization of fine meshes inside them, and, lastly, sealing the whole chip with cover glass into one monolithic piece. The created micro fluidic device proved its particle sorting function by separating 1 μm and 10 μm polystyrene spheres from a mixture. Next, a lens adapter for a cell phone's camera was manufactured via thermal extrusion 3D printing technique which allowed to achieve sufficient magnification to clearly resolve <10 μm features. All together shows fs-laser microfabrication technology as a flexible and versatile tool for study and manufacturing of Lab-On-Chip devices.

  13. On-chip electro membrane extraction with online ultraviolet and mass spectrometric detection

    DEFF Research Database (Denmark)

    Petersen, Nickolaj Jacob; Foss, Sunniva Taule; Jensen, Henrik

    2011-01-01

    (SLM) consisted of 2-nitrophenyl octyl ether (NPOE) immobilized in the pores of the membrane. The driving force for the extraction was a 15 V direct current (DC) electrical potential applied across the SLM. Samples containing the basic drugs pethidine, nortriptyline, methadone, haloperidol, loperamide...

  14. Detection of On-Chip Generated Weak Microwave Radiation Using Superconducting Normal-Metal SET

    Directory of Open Access Journals (Sweden)

    Behdad Jalali-Jafari

    2016-01-01

    Full Text Available The present work addresses quantum interaction phenomena of microwave radiation with a single-electron tunneling system. For this study, an integrated circuit is implemented, combining on the same chip a Josephson junction (Al/AlO x /Al oscillator and a single-electron transistor (SET with the superconducting island (Al and normal-conducting leads (AuPd. The transistor is demonstrated to operate as a very sensitive photon detector, sensing down to a few tens of photons per second in the microwave frequency range around f ∼ 100 GHz. On the other hand, the Josephson oscillator, realized as a two-junction SQUID and coupled to the detector via a coplanar transmission line (Al, is shown to provide a tunable source of microwave radiation: controllable variations in power or in frequency were accompanied by significant changes in the detector output, when applying magnetic flux or adjusting the voltage across the SQUID, respectively. It was also shown that the effect of substrate-mediated phonons, generated by our microwave source, on the detector output was negligibly small.

  15. On-chip bio-analyte detection utilizing the velocity of magnetic microparticles in a fluid

    KAUST Repository

    Giouroudi, Ioanna; van den Driesche, Sander; Kosel, Jü rgen; Grössinger, Roland; Vellekoop, Michael J.

    2011-01-01

    change when analyte is attached to their surface via antibody–antigen binding. When the magnetic microparticles are attracted by a magnetic field within a microfluidic channel their velocity depends on the presence of analyte. Specifically, their velocity

  16. A Single-Chip CMOS Pulse Oximeter with On-Chip Lock-In Detection

    OpenAIRE

    Diwei He; Stephen P. Morgan; Dimitrios Trachanis; Jan van Hese; Dimitris Drogoudis; Franco Fummi; Francesco Stefanni; Valerio Guarnieri; Barrie R. Hayes-Gill

    2015-01-01

    Pulse oximetry is a noninvasive and continuous method for monitoring the blood oxygen saturation level. This paper presents the design and testing of a single-chip pulse oximeter fabricated in a 0.35 ?m CMOS process. The chip includes photodiode, transimpedance amplifier, analogue band-pass filters, analogue-to-digital converters, digital signal processor and LED timing control. The experimentally measured AC and DC characteristics of individual circuits including the DC output voltage of the...

  17. Non-Magnetic On-Chip Resonant Acousto-Optic Isolator at 780 nm

    Science.gov (United States)

    2017-08-04

    actuator on a piezoelectric substrate. We fabricated the device using only CMOS-compatible dielectric materials with the assistance of e- beam...on-chip, without the use of magnetic fields or magneto-optical materials. Our technical approach was to employ momentum-conservation in photon-phonon...interactions to break the propagation symmetry of light using a unidirectional acoustic pump. This acoustic wave was transduced using an RF-driven SAW

  18. On-chip photonic memory elements employing phase-change materials.

    Science.gov (United States)

    Rios, Carlos; Hosseini, Peiman; Wright, C David; Bhaskaran, Harish; Pernice, Wolfram H P

    2014-03-05

    Phase-change materials integrated into nanophotonic circuits provide a flexible way to realize tunable optical components. Relying on the enormous refractive-index contrast between the amorphous and crystalline states, such materials are promising candidates for on-chip photonic memories. Nonvolatile memory operation employing arrays of microring resonators is demonstrated as a route toward all-photonic chipscale information processing. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. A passive on-chip, superconducting circulator using rings of tunnel junctions

    OpenAIRE

    Müller, Clemens; Guan, Shengwei; Vogt, Nicolas; Cole, Jared H.; Stace, Thomas M.

    2017-01-01

    We present the design of a passive, on-chip microwave circulator based on a ring of superconducting tunnel junctions. We investigate two distinct physical realisations, based on either Josephson junctions (JJ) or quantum phase slip elements (QPS), with microwave ports coupled either capacitively (JJ) or inductively (QPS) to the ring structure. A constant bias applied to the center of the ring provides the symmetry breaking (effective) magnetic field, and no microwave or rf bias is required. W...

  20. Experimental realization of an on-chip all-optical analogue to electromagnetically induced transparency.

    Science.gov (United States)

    Xu, Qianfan; Sandhu, Sunil; Povinelli, Michelle L; Shakya, Jagat; Fan, Shanhui; Lipson, Michal

    2006-03-31

    We provide the first experimental observation of structure tuning of the electromagnetically induced transparency-like spectrum in integrated on-chip optical resonator systems. The system consists of coupled silicon ring resonators with 10 microm diameter on silicon, where the coherent interference between the two coupled resonators is tuned. We measured a transparency-resonance mode with a quality factor of 11,800.

  1. Advances in piezoelectric thin films for acoustic biosensors, acoustofluidics and lab-on-chip applications

    OpenAIRE

    Fu, Yong Qing; Luo, Jack; Nguyen, Nam-Trung; Walton, Anthony; Flewitt, Andrew; Zu, Xiao-Tao; Li, Yifan; McHale, Glen; Matthews, Allan; Iborra, Enrique; Du, Hejun; Milne, William

    2017-01-01

    Recently, piezoelectric thin films including zinc oxide (ZnO) and aluminium nitride (AlN) have found a broad range of lab-on-chip applications such as biosensing, particle/cell concentrating, sorting/patterning, pumping, mixing, nebulisation and jetting. Integrated acoustic wave sensing/microfluidic devices have been fabricated by depositing these piezoelectric films onto a number of substrates such as silicon, ceramics, diamond, quartz, glass, and more recently also polymer, metallic foils a...

  2. Legal Protection on IP Cores for System-on-Chip Designs

    Science.gov (United States)

    Kinoshita, Takahiko

    The current semiconductor industry has shifted from vertical integrated model to horizontal specialization model in term of integrated circuit manufacturing. In this circumstance, IP cores as solutions for System-on-Chip (SoC) have become increasingly important for semiconductor business. This paper examines to what extent IP cores of SoC effectively can be protected by current intellectual property system including integrated circuit layout design law, patent law, design law, copyright law and unfair competition prevention act.

  3. Evaluation of on-chip micro antennas for in vivo dosimetry application

    International Nuclear Information System (INIS)

    Villani, Giulio; Bose, Rajiv; Gabrielli, Alessandro

    2011-01-01

    The design, fabrication and evaluation of a set of micro antennas (ANTs) on chip is described. The size of the ANTs is 2 and has been chosen with a view to the development of a monolithic implantable sensor for in vivo dosimetry which is the ultimate focus of this project. Three different designs are currently being investigated, with a view to evaluate their RF performances in the communication-standard Medical Implant Communication Service (MICS) frequency band.

  4. Active 2D materials for on-chip nanophotonics and quantum optics

    Directory of Open Access Journals (Sweden)

    Shiue Ren-Jye

    2017-03-01

    Full Text Available Two-dimensional materials have emerged as promising candidates to augment existing optical networks for metrology, sensing, and telecommunication, both in the classical and quantum mechanical regimes. Here, we review the development of several on-chip photonic components ranging from electro-optic modulators, photodetectors, bolometers, and light sources that are essential building blocks for a fully integrated nanophotonic and quantum photonic circuit.

  5. Detection of Genetically Modified Sugarcane by Using Terahertz Spectroscopy and Chemometrics

    Science.gov (United States)

    Liu, J.; Xie, H.; Zha, B.; Ding, W.; Luo, J.; Hu, C.

    2018-03-01

    A methodology is proposed to identify genetically modified sugarcane from non-genetically modified sugarcane by using terahertz spectroscopy and chemometrics techniques, including linear discriminant analysis (LDA), support vector machine-discriminant analysis (SVM-DA), and partial least squares-discriminant analysis (PLS-DA). The classification rate of the above mentioned methods is compared, and different types of preprocessing are considered. According to the experimental results, the best option is PLS-DA, with an identification rate of 98%. The results indicated that THz spectroscopy and chemometrics techniques are a powerful tool to identify genetically modified and non-genetically modified sugarcane.

  6. On-chip sample preparation for complete blood count from raw blood.

    Science.gov (United States)

    Nguyen, John; Wei, Yuan; Zheng, Yi; Wang, Chen; Sun, Yu

    2015-03-21

    This paper describes a monolithic microfluidic device capable of on-chip sample preparation for both RBC and WBC measurements from whole blood. For the first time, on-chip sample processing (e.g. dilution, lysis, and filtration) and downstream single cell measurement were fully integrated to enable sample preparation and single cell analysis from whole blood on a single device. The device consists of two parallel sub-systems that perform sample processing and electrical measurements for measuring RBC and WBC parameters. The system provides a modular environment capable of handling solutions of various viscosities by adjusting the length of channels and precisely controlling mixing ratios, and features a new 'offset' filter configuration for increased duration of device operation. RBC concentration, mean corpuscular volume (MCV), cell distribution width, WBC concentration and differential are determined by electrical impedance measurement. Experimental characterization of over 100,000 cells from 10 patient blood samples validated the system's capability for performing on-chip raw blood processing and measurement.

  7. On-chip photonic microsystem for optical signal processing based on silicon and silicon nitride platforms

    Science.gov (United States)

    Li, Yu; Li, Jiachen; Yu, Hongchen; Yu, Hai; Chen, Hongwei; Yang, Sigang; Chen, Minghua

    2018-04-01

    The explosive growth of data centers, cloud computing and various smart devices is limited by the current state of microelectronics, both in terms of speed and heat generation. Benefiting from the large bandwidth, promising low power consumption and passive calculation capability, experts believe that the integrated photonics-based signal processing and transmission technologies can break the bottleneck of microelectronics technology. In recent years, integrated photonics has become increasingly reliable and access to the advanced fabrication process has been offered by various foundries. In this paper, we review our recent works on the integrated optical signal processing system. We study three different kinds of on-chip signal processors and use these devices to build microsystems for the fields of microwave photonics, optical communications and spectrum sensing. The microwave photonics front receiver was demonstrated with a signal processing range of a full-band (L-band to W-band). A fully integrated microwave photonics transceiver without the on-chip laser was realized on silicon photonics covering the signal frequency of up 10 GHz. An all-optical orthogonal frequency division multiplexing (OFDM) de-multiplier was also demonstrated and used for an OFDM communication system with the rate of 64 Gbps. Finally, we show our work on the monolithic integrated spectrometer with a high resolution of about 20 pm at the central wavelength of 1550 nm. These proposed on-chip signal processing systems potential applications in the fields of radar, 5G wireless communication, wearable devices and optical access networks.

  8. On-chip plasmon-induced transparency based on plasmonic coupled nanocavities.

    Science.gov (United States)

    Zhu, Yu; Hu, Xiaoyong; Yang, Hong; Gong, Qihuang

    2014-01-17

    On-chip plasmon-induced transparency offers the possibility of realization of ultrahigh-speed information processing chips. Unfortunately, little experimental progress has been made to date because it is difficult to obtain on-chip plasmon-induced transparency using only a single meta-molecule in plasmonic circuits. Here, we report a simple and efficient strategy to realize on-chip plasmon-induced transparency in a nanoscale U-shaped plasmonic waveguide side-coupled nanocavity pair. High tunability in the transparency window is achieved by covering the pair with different organic polymer layers. It is possible to realize ultrafast all-optical tunability based on pump light-induced refractive index change of a graphene cover layer. Compared with previous reports, the overall feature size of the plasmonic nanostructure is reduced by more than three orders of magnitude, while ultrahigh tunability of the transparency window is maintained. This work also provides a superior platform for the study of the various physical effects and phenomena of nonlinear optics and quantum optics.

  9. Blood cleaner on-chip design for artificial human kidney manipulation

    Directory of Open Access Journals (Sweden)

    Suwanpayak N

    2011-05-01

    Full Text Available N Suwanpayak1, MA Jalil2, MS Aziz3, FD Ismail3, J Ali3, PP Yupapin11Nanoscale Science and Engineering Research Alliance (N'SERA, Advanced Research Center for Photonics, Faculty of Science, King Mongkut's Institute of Technology, Ladkrabang, Bangkok, Thailand; 2Ibnu Sina Institute of Fundamental Science Studies (IIS, 3Institute of Advanced Photonics Science, Nanotechnology Research Alliance, Universiti Teknologi Malaysia, Johor Bahru, MalaysiaAbstract: A novel design of a blood cleaner on-chip using an optical waveguide known as a PANDA ring resonator is proposed. By controlling some suitable parameters, the optical vortices (gradient optical fields/wells can be generated and used to form the trapping tools in the same way as optical tweezers. In operation, the trapping force is formed by the combination between the gradient field and scattering photons by using the intense optical vortices generated within the PANDA ring resonator. This can be used for blood waste trapping and moves dynamically within the blood cleaner on-chip system (artificial kidney, and is performed within the wavelength routers. Finally, the blood quality test is exploited by the external probe before sending to the destination. The advantage of the proposed kidney on-chip system is that the unwanted substances can be trapped and filtered from the artificial kidney, which can be available for blood cleaning applications.Keywords: optical trapping, blood dialysis, blood cleaner, human kidney manipulation

  10. Electromagnetic design methods in systems-on-chip: integrated filters for wireless CMOS RFICs

    International Nuclear Information System (INIS)

    Contopanagos, Harry

    2005-01-01

    We present general methods for designing on-chip CMOS passives and utilizing these integrated elements to design on-chip CMOS filters for wireless communications. These methods rely on full-wave electromagnetic numerical calculations that capture all the physics of the underlying foundry technologies. This is especially crucial for deep sub-micron CMOS technologies as it is important to capture the physical effects of finite (and mediocre) Q-factors limited by material losses and constraints on expensive die area, low self-resonance frequencies and dual parasitics that are particularly prevalent in deep sub-micron CMOS processes (65 nm-0.18 μm. We use these integrated elements in an ideal synthesis of a Bluetooth/WLAN pass-band filter in single-ended or differential architectures, and show the significant deviations of the on-chip filter response from the ideal one. We identify which elements in the filter circuit need to maximize their Q-factors and which Q-factors do not affect the filter performance. This saves die area, and predicts the FET parameters (especially transconductances) and negative-resistance FET topologies that have to be integrated in the filter to restore its performance. (invited paper)

  11. On-chip steering of entangled photons in nonlinear photonic crystals.

    Science.gov (United States)

    Leng, H Y; Yu, X Q; Gong, Y X; Xu, P; Xie, Z D; Jin, H; Zhang, C; Zhu, S N

    2011-08-16

    One promising technique for working toward practical photonic quantum technologies is to implement multiple operations on a monolithic chip, thereby improving stability, scalability and miniaturization. The on-chip spatial control of entangled photons will certainly benefit numerous applications, including quantum imaging, quantum lithography, quantum metrology and quantum computation. However, external optical elements are usually required to spatially control the entangled photons. Here we present the first experimental demonstration of on-chip spatial control of entangled photons, based on a domain-engineered nonlinear photonic crystal. We manipulate the entangled photons using the inherent properties of the crystal during the parametric downconversion, demonstrating two-photon focusing and beam-splitting from a periodically poled lithium tantalate crystal with a parabolic phase profile. These experimental results indicate that versatile and precise spatial control of entangled photons is achievable. Because they may be operated independent of any bulk optical elements, domain-engineered nonlinear photonic crystals may prove to be a valuable ingredient in on-chip integrated quantum optics.

  12. Gain-Enhanced On-Chip Antenna Utilizing Artificial Magnetic Conductor Reflecting Surface at 94 GHz

    KAUST Repository

    Nafe, Mahmoud

    2015-01-01

    In this work, the use of specially patterned reflecting surfaces for improving on- chip antenna performance is investigated. By using a periodic metallic surface on top of a grounded substrate, the structure can mimic the behavior of a perfect mag- netic conductor, hence called Artificial Magnetic Conductor (AMC) surface. Unlike conventional ground plane reflecting surfaces, AMC surfaces generally enhance the radiation and impedance characteristics of close-by antennas. Based on this property, a ring-based AMC reflecting surface has been designed in the oxide layer for on-chip antennas operating at 94 GHz. Furthermore, a folded dipole antenna with its associ- ated planar feeding structures has been optimized and integrated with the developed ring-based AMC surface. The proposed design is then fabricated at KAUST clean- room facilities. Prototype characterization showed very promising results with good correlation to simulations, with the antenna exhibiting an impedance bandwidth of 10% (90-100 GHz) and peak gain of -1.4 dBi, which is the highest gain reported for on-chip antennas at this frequency band without the use of any external o↵-chip components or post-fabrication steps.

  13. Towards a Generic and Adaptive System-On-Chip Controller for Space Exploration Instrumentation

    Science.gov (United States)

    Iturbe, Xabier; Keymeulen, Didier; Yiu, Patrick; Berisford, Dan; Hand, Kevin; Carlson, Robert; Ozer, Emre

    2015-01-01

    This paper introduces one of the first efforts conducted at NASA’s Jet Propulsion Laboratory (JPL) to develop a generic System-on-Chip (SoC) platform to control science instruments that are proposed for future NASA missions. The SoC platform is named APEX-SoC, where APEX stands for Advanced Processor for space Exploration, and is based on a hybrid Xilinx Zynq that combines an FPGA and an ARM Cortex-A9 dual-core processor on a single chip. The Zynq implements a generic and customizable on-chip infrastructure that can be reused with a variety of instruments, and it has been coupled with a set of off-chip components that are necessary to deal with the different instruments. We have taken JPL’s Compositional InfraRed Imaging Spectrometer (CIRIS), which is proposed for NASA icy moons missions, as a use-case scenario to demonstrate that the entire data processing, control and interface of an instrument can be implemented on a single device using the on-chip infrastructure described in this paper. We show that the performance results achieved in this preliminary version of the instrumentation controller are sufficient to fulfill the science requirements demanded to the CIRIS instrument in future NASA missions, such as Europa.

  14. Electromagnetic design methods in systems-on-chip: integrated filters for wireless CMOS RFICs

    Energy Technology Data Exchange (ETDEWEB)

    Contopanagos, Harry [Institute for Microelectronics, NCSR ' Demokritos' , PO Box 60228, GR-153 10 Aghia Paraskevi, Athens (Greece)

    2005-01-01

    We present general methods for designing on-chip CMOS passives and utilizing these integrated elements to design on-chip CMOS filters for wireless communications. These methods rely on full-wave electromagnetic numerical calculations that capture all the physics of the underlying foundry technologies. This is especially crucial for deep sub-micron CMOS technologies as it is important to capture the physical effects of finite (and mediocre) Q-factors limited by material losses and constraints on expensive die area, low self-resonance frequencies and dual parasitics that are particularly prevalent in deep sub-micron CMOS processes (65 nm-0.18 {mu}m. We use these integrated elements in an ideal synthesis of a Bluetooth/WLAN pass-band filter in single-ended or differential architectures, and show the significant deviations of the on-chip filter response from the ideal one. We identify which elements in the filter circuit need to maximize their Q-factors and which Q-factors do not affect the filter performance. This saves die area, and predicts the FET parameters (especially transconductances) and negative-resistance FET topologies that have to be integrated in the filter to restore its performance. (invited paper)

  15. Manually operatable on-chip bistable pneumatic microstructures for microfluidic manipulations.

    Science.gov (United States)

    Chen, Arnold; Pan, Tingrui

    2014-09-07

    Bistable microvalves are of particular interest because of their distinct nature of requiring energy consumption only during the transition between the open and closed states. This characteristic can be highly advantageous in reducing the number of external inputs and the complexity of control circuitries since microfluidic devices as contemporary lab-on-a-chip platforms are transferring from research settings to low-resource environments with high integrability and a small form factor. In this paper, we first present manually operatable, on-chip bistable pneumatic microstructures (BPMs) for microfluidic manipulation. The structural design and operation of the BPM devices can be readily integrated into any pneumatically powered microfluidic network consisting of pneumatic and fluidic channels. It is mainly composed of a vacuum activation chamber (VAC) and a pressure release chamber (PRC), of which users have direct control through finger pressing to switch either to the bistable vacuum state (VS) or the atmospheric state (AS). We have integrated multiple BPM devices into a 4-to-1 microfluidic multiplexor to demonstrate on-chip digital flow switching from different sources. Furthermore, we have shown its clinical relevance in a point-of-care diagnostic chip that processes blood samples to identify the distinct blood types (A/B/O) on-chip.

  16. A Router Architecture for Connection-Oriented Service Guarantees in the MANGO Clockless Network-on-Chip

    DEFF Research Database (Denmark)

    Bjerregaard, Tobias; Sparsø, Jens

    2005-01-01

    On-chip networks for future system-on-chip designs need simple, high performance implementations. In order to promote system-level integrity, guaranteed services (GS) need to be provided. We propose a network-on-chip (NoC) router architecture to support this, and demonstrate with a CMOS standard...... cell design. Our implementation is based on clockless circuit techniques, and thus inherently supports a modular, GALS-oriented design flow. Our router exploits virtual channels to provide connection-oriented GS, as well as connection-less best-effort (BE) routing. The architecture is highly flexible...

  17. Current PCR Methods for the Detection, Identification and Quantification of Genetically Modified Organisms(GMOs: a Brief Review

    Directory of Open Access Journals (Sweden)

    Gadani F

    2014-12-01

    Full Text Available Analytical methods based on the polymerase chain reaction (PCR technology are increasingly used for the detection of deoxyribonucleic acid (DNA sequences associated with genetically modified organisms (GMOs. In the European Union and Switzerland, mandatory labeling of novel foods and food ingredients consisting of, or containing GMOs is required according to food regulations and is triggered by the presence of newly introduced foreign DNA sequences, or newly expressed proteins. In order to meet regulatory and consumer demand, numerous PCR-based methods have been developed which can detect, identify and quantify GMOs in agricultural crops, food and feed. Moreover, the determination of genetic identity allows for segregation and traceability (identity preservation throughout the supply chain of GM crops that have been enhanced with value-added quality traits. Prerequisites for GMO detection include a minimum amount of the target gene and prior knowledge of the type of genetic modification, such as virus or insect resistance traits, including controlling elements (promoters and terminators. Moreover, DNA extraction and purification is a critical step for the preparation of PCR-quality samples, particularly for processed agricultural crops such as tobacco. This paper reviews the state-of-the-art of PCR-based method development for the qualitative and quantitative determination and identification of GMOs, and includes a short summary of official and validated GMO detection methods.

  18. Establishment and application of a multiplex genetic mutation-detection method of lung cancer based on MassARRAY platform

    International Nuclear Information System (INIS)

    Tian, Hong-Xia; Zhang, Xu-Chao; Wang, Zhen; Chen, Jian-Guang; Chen, Shi-Liang; Guo, Wei-Bang; Wu, Yi-Long

    2016-01-01

    Objective: This study aims to establish a method for highly parallel multiplexed detection of genetic mutations in Chinese lung cancer samples through Agena iPLEX chemistry and matrix-assisted laser desorption ionization time-of-flight analysis on MassARRAY mass spectrometry platform. Methods: We reviewed the related literature and data on lung cancer treatments. We also identified 99 mutation hot spots in 13 target genes closely related to the pathogenesis, drug resistance, and metastasis of lung cancer. A total of 297 primers, composed of 99 paired forward and reverse amplification primers and 99 matched extension primers, were designed using Assay Design software. The detection method was established by analyzing eight cell lines and six lung cancer specimens. The proposed method was then validated through comparisons by using a LungCarta TM kit. The sensitivity and specificity of the proposed method were evaluated by directly sequencing EGFR and KRAS genes in 100 lung cancer cases. Results: The proposed method was able to detect multiplex genetic mutations in lung cancer cell lines. This finding was consistent with the observations on previously reported mutations. The proposed method can also detect such mutations in clinical lung cancer specimens. This result was consistent with the observations with LungCarta TM kit. However, an FGFR2 mutation was detected only through the proposed method. The measured sensitivity and specificity were 100% and 96.3%, respectively. Conclusions: The proposed MassARRAY technology-based multiplex method can detect genetic mutations in Chinese lung cancer patients. Therefore, the proposed method can be applied to detect mutations in other cancer tissues

  19. SURFACE FLUID REGISTRATION OF CONFORMAL REPRESENTATION: APPLICATION TO DETECT DISEASE BURDEN AND GENETIC INFLUENCE ON HIPPOCAMPUS

    Science.gov (United States)

    Shi, Jie; Thompson, Paul M.; Gutman, Boris; Wang, Yalin

    2013-01-01

    In this paper, we develop a new automated surface registration system based on surface conformal parameterization by holomorphic 1-forms, inverse consistentsurface fluid registration, and multivariate tensor-based morphometry (mTBM). First, we conformally map a surface onto a planar rectangle space with holomorphic 1-forms. Second, we compute surface conformal representation by combining its local conformal factor and mean curvature and linearly scale the dynamic range of the conformal representation to form the feature image of the surface. Third, we align the feature image with a chosen template image via the fluid image registration algorithm, which has been extended into the curvilinear coordinates to adjust for the distortion introduced by surface parameterization. The inverse consistent image registration algorithm is also incorporated in the system to jointly estimate the forward and inverse transformations between the study and template images. This alignment induces a corresponding deformation on the surface. We tested the system on Alzheimer's Disease Neuroimaging Initiative (ADNI) baseline dataset to study AD symptoms on hippocampus. In our system, by modeling a hippocampus as a 3D parametric surface, we nonlinearly registered each surface with a selected template surface. Then we used mTBM to analyze the morphometrydifference between diagnostic groups. Experimental results show that the new system has better performance than two publically available subcortical surface registration tools: FIRST and SPHARM. We also analyzed the genetic influence of the Apolipoprotein E ε4 allele (ApoE4),which is considered as the most prevalent risk factor for AD.Our work successfully detected statistically significant difference between ApoE4 carriers and non-carriers in both patients of mild cognitive impairment (MCI) and healthy control subjects. The results show evidence that the ApoE genotype may be associated with accelerated brain atrophy so that our workprovides

  20. Reliable allele detection using SNP-based PCR primers containing Locked Nucleic Acid: application in genetic mapping

    Directory of Open Access Journals (Sweden)

    Trognitz Friederike

    2007-02-01

    Full Text Available Abstract Background The diploid, Solanum caripense, a wild relative of potato and tomato, possesses valuable resistance to potato late blight and we are interested in the genetic base of this resistance. Due to extremely low levels of genetic variation within the S. caripense genome it proved impossible to generate a dense genetic map and to assign individual Solanum chromosomes through the use of conventional chromosome-specific SSR, RFLP, AFLP, as well as gene- or locus-specific markers. The ease of detection of DNA polymorphisms depends on both frequency and form of sequence variation. The narrow genetic background of close relatives and inbreds complicates the detection of persisting, reduced polymorphism and is a challenge to the development of reliable molecular markers. Nonetheless, monomorphic DNA fragments representing not directly usable conventional markers can contain considerable variation at the level of single nucleotide polymorphisms (SNPs. This can be used for the design of allele-specific molecular markers. The reproducible detection of allele-specific markers based on SNPs has been a technical challenge. Results We present a fast and cost-effective protocol for the detection of allele-specific SNPs by applying Sequence Polymorphism-Derived (SPD markers. These markers proved highly efficient for fingerprinting of individuals possessing a homogeneous genetic background. SPD markers are obtained from within non-informative, conventional molecular marker fragments that are screened for SNPs to design allele-specific PCR primers. The method makes use of primers containing a single, 3'-terminal Locked Nucleic Acid (LNA base. We demonstrate the applicability of the technique by successful genetic mapping of allele-specific SNP markers derived from monomorphic Conserved Ortholog Set II (COSII markers mapped to Solanum chromosomes, in S. caripense. By using SPD markers it was possible for the first time to map the S. caripense alleles

  1. Adaptive Code Division Multiple Access Protocol for Wireless Network-on-Chip Architectures

    Science.gov (United States)

    Vijayakumaran, Vineeth

    Massive levels of integration following Moore's Law ushered in a paradigm shift in the way on-chip interconnections were designed. With higher and higher number of cores on the same die traditional bus based interconnections are no longer a scalable communication infrastructure. On-chip networks were proposed enabled a scalable plug-and-play mechanism for interconnecting hundreds of cores on the same chip. Wired interconnects between the cores in a traditional Network-on-Chip (NoC) system, becomes a bottleneck with increase in the number of cores thereby increasing the latency and energy to transmit signals over them. Hence, there has been many alternative emerging interconnect technologies proposed, namely, 3D, photonic and multi-band RF interconnects. Although they provide better connectivity, higher speed and higher bandwidth compared to wired interconnects; they also face challenges with heat dissipation and manufacturing difficulties. On-chip wireless interconnects is one other alternative proposed which doesn't need physical interconnection layout as data travels over the wireless medium. They are integrated into a hybrid NOC architecture consisting of both wired and wireless links, which provides higher bandwidth, lower latency, lesser area overhead and reduced energy dissipation in communication. However, as the bandwidth of the wireless channels is limited, an efficient media access control (MAC) scheme is required to enhance the utilization of the available bandwidth. This thesis proposes using a multiple access mechanism such as Code Division Multiple Access (CDMA) to enable multiple transmitter-receiver pairs to send data over the wireless channel simultaneously. It will be shown that such a hybrid wireless NoC with an efficient CDMA based MAC protocol can significantly increase the performance of the system while lowering the energy dissipation in data transfer. In this work it is shown that the wireless NoC with the proposed CDMA based MAC protocol

  2. Laser annealed in-situ P-doped Ge for on-chip laser source applications (Conference Presentation)

    Science.gov (United States)

    Srinivasan, Ashwyn; Pantouvaki, Marianna; Shimura, Yosuke; Porret, Clement; Van Deun, Rik; Loo, Roger; Van Thourhout, Dries; Van Campenhout, Joris

    2016-05-01

    Realization of a monolithically integrated on-chip laser source remains the holy-grail of Silicon Photonics. Germanium (Ge) is a promising semiconductor for lasing applications when highly doped with Phosphorous (P) and or alloyed with Sn [1, 2]. P doping makes Ge a pseudo-direct band gap material and the emitted wavelengths are compatible with fiber-optic communication applications. However, in-situ P doping with Ge2H6 precursor allows a maximum active P concentration of 6×1019 cm-3 [3]. Even with such active P levels, n++ Ge is still an indirect band gap material and could result in very high threshold current densities. In this work, we demonstrate P-doped Ge layers with active n-type doping beyond 1020 cm-3, grown using Ge2H6 and PH3 and subsequently laser annealed, targeting power-efficient on-chip laser sources. The use of Ge2H6 precursors during the growth of P-doped Ge increases the active P concentration level to a record fully activated concentration of 1.3×1020 cm-3 when laser annealed with a fluence of 1.2 J/cm2. The material stack consisted of 200 nm thick P-doped Ge grown on an annealed 1 µm Ge buffer on Si. Ge:P epitaxy was performed with PH3 and Ge2H6 at 320oC. Low temperature growth enable Ge:P epitaxy far from thermodynamic equilibrium, resulting in an enhanced incorporation of P atoms [3]. At such high active P concentration, the n++ Ge layer is expected to be a pseudo-direct band gap material. The photoluminescence (PL) intensities for layers with highest active P concentration show an enhancement of 18× when compared to undoped Ge grown on Si as shown in Fig. 1 and Fig. 2. The layers were optically pumped with a 640 nm laser and an incident intensity of 410 mW/cm2. The PL was measured with a NIR spectrometer with a Hamamatsu R5509-72 NIR photomultiplier tube detector whose detectivity drops at 1620 nm. Due to high active P concentration, we expect band gap narrowing phenomena to push the PL peak to wavelengths beyond the detection limit

  3. Dynamic On-Chip micro Temperature and Flow Sensor for miniaturized lab-on-a-chip instruments

    Data.gov (United States)

    National Aeronautics and Space Administration — The purpose of this project is to design, fabricate, and characterize a Dynamic On-Chip Flow and Temperature Sensor (DOCFlaTS) to mature and enable miniaturized...

  4. Detection of nonauthorized genetically modified organisms using differential quantitative polymerase chain reaction: application to 35S in maize.

    Science.gov (United States)

    Cankar, Katarina; Chauvensy-Ancel, Valérie; Fortabat, Marie-Noelle; Gruden, Kristina; Kobilinsky, André; Zel, Jana; Bertheau, Yves

    2008-05-15

    Detection of nonauthorized genetically modified organisms (GMOs) has always presented an analytical challenge because the complete sequence data needed to detect them are generally unavailable although sequence similarity to known GMOs can be expected. A new approach, differential quantitative polymerase chain reaction (PCR), for detection of nonauthorized GMOs is presented here. This method is based on the presence of several common elements (e.g., promoter, genes of interest) in different GMOs. A statistical model was developed to study the difference between the number of molecules of such a common sequence and the number of molecules identifying the approved GMO (as determined by border-fragment-based PCR) and the donor organism of the common sequence. When this difference differs statistically from zero, the presence of a nonauthorized GMO can be inferred. The interest and scope of such an approach were tested on a case study of different proportions of genetically modified maize events, with the P35S promoter as the Cauliflower Mosaic Virus common sequence. The presence of a nonauthorized GMO was successfully detected in the mixtures analyzed and in the presence of (donor organism of P35S promoter). This method could be easily transposed to other common GMO sequences and other species and is applicable to other detection areas such as microbiology.

  5. Detection of the genetically modified organisms from food products/ Detecţia organismelor modificate genetic din produse alimentare

    Directory of Open Access Journals (Sweden)

    Curticăpean Manuela

    2014-09-01

    Full Text Available Încă de la apariţia primelor culturi modificate genetic, oamenii de ştiinţă au avut păreri pro şi contra asupra cultivării si utilizării lor, datorită potenţialelor riscuri pe care le pot avea asupra sănătăţii şi mediului înconjurător. Legislaţia europeană actuală (Directiva 2003/18/CE prevede obligativitatea informării publicului, a monitorizării efectelor pe termen lung, a etichetării şi trasabilităţii în toate stadiile introducerii pe piaţă a OMG. Scopul acestui studiu a fost evaluarea calitativă a produselor alimentare existente pe piaţă, în ceea ce priveşte detecţia prezenţei/ absenţei OMG. În acest sens au fost analizate două tipuri de făină de porumb şi patru tipuri de produse din soia, în perioada 2013. Kit-ul utilizat pentru detecţia prezenţei/absenţei OMG în probele testate, cuprinde etape de izolare ADN, amplificare ADN prin PCR şi electroforeza în gel de agaroză a produşilor amplificaţi şi foloseşte două secvenţe asociate OMG - promotorul 35S şi terminatorul NOS de la Agrobacterium tumefaciens. În urma studiului, au fost pozitive în ceea ce priveşte prezenţa OMG, o probă de mălai extra şi o probă de soia. Rezultatele obţinute ilustrează necesitatea efectuării de analize suplimentare pentru identificarea tipului exact de OMG şi pentru stabilirea cantităţii de OMG (pragul limită impus de legislaţia europeană fiind de 0,9% la nivel de ingredient.

  6. Detecting Instability in Animal Social Networks: Genetic Fragmentation Is Associated with Social Instability in Rhesus Macaques

    OpenAIRE

    Beisner, Brianne A.; Jackson, Megan E.; Cameron, Ashley N.; McCowan, Brenda

    2011-01-01

    The persistence of biological systems requires evolved mechanisms which promote stability. Cohesive primate social groups are one example of stable biological systems, which persist in spite of regular conflict. We suggest that genetic relatedness and its associated kinship structure are a potential source of stability in primate social groups as kinship structure is an important organizing principle in many animal societies. We investigated the effect of average genetic relatedness per matri...

  7. Detection of genetically modified rice: Collaborative validation study of a PCR based detection of genetically modified rice Oryza sativa commercially available in Saudi Arabia

    OpenAIRE

    Ibrahim, Mohamed; Alaraidh, Ibrahim; Amid, Azura; Farouk, Abd-El Aziem; Bazaid, Salih; Greiner, Ralf; Alghunaim, Abdullah

    2011-01-01

    A collaborative trial study has been conducted for validation of an extraction method and a subsequent PCR for  the detection of transgenic rice sold in Saudi Arabia. The tests were carried out in Saudi Arabia using Real-Time PCR and the positive samples were validated in another lab in Malaysia using PCR and agarose gel visualization.  The samples were tested for the existence of the NOS Terminator. A total of 150 samples were tested out of which three samples tested positi...

  8. PCR-free detection of genetically modified organisms using magnetic capture technology and fluorescence cross-correlation spectroscopy.

    Directory of Open Access Journals (Sweden)

    Xiaoming Zhou

    2009-11-01

    Full Text Available The safety of genetically modified organisms (GMOs has attracted much attention recently. Polymerase chain reaction (PCR amplification is a common method used in the identification of GMOs. However, a major disadvantage of PCR is the potential amplification of non-target DNA, causing false-positive identification. Thus, there remains a need for a simple, reliable and ultrasensitive method to identify and quantify GMO in crops. This report is to introduce a magnetic bead-based PCR-free method for rapid detection of GMOs using dual-color fluorescence cross-correlation spectroscopy (FCCS. The cauliflower mosaic virus 35S (CaMV35S promoter commonly used in transgenic products was targeted. CaMV35S target was captured by a biotin-labeled nucleic acid probe and then purified using streptavidin-coated magnetic beads through biotin-streptavidin linkage. The purified target DNA fragment was hybridized with two nucleic acid probes labeled respectively by Rhodamine Green and Cy5 dyes. Finally, FCCS was used to detect and quantify the target DNA fragment through simultaneously detecting the fluorescence emissions from the two dyes. In our study, GMOs in genetically engineered soybeans and tomatoes were detected, using the magnetic bead-based PCR-free FCCS method. A detection limit of 50 pM GMOs target was achieved and PCR-free detection of GMOs from 5 microg genomic DNA with magnetic capture technology was accomplished. Also, the accuracy of GMO determination by the FCCS method is verified by spectrophotometry at 260 nm using PCR amplified target DNA fragment from GM tomato. The new method is rapid and effective as demonstrated in our experiments and can be easily extended to high-throughput and automatic screening format. We believe that the new magnetic bead-assisted FCCS detection technique will be a useful tool for PCR-free GMOs identification and other specific nucleic acids.

  9. System-on-Chip Integration of a New Electromechanical Impedance Calculation Method for Aircraft Structure Health Monitoring

    Directory of Open Access Journals (Sweden)

    Daniel Medale

    2012-10-01

    Full Text Available The work reported on this paper describes a new methodology implementation for active structural health monitoring of recent aircraft parts made from carbon-fiber-reinforced polymer. This diagnosis is based on a new embedded method that is capable of measuring the local high frequency impedance spectrum of the structure through the calculation of the electro-mechanical impedance of a piezoelectric patch pasted non-permanently onto its surface. This paper involves both the laboratory based E/M impedance method development, its implementation into a CPU with limited resources as well as a comparison with experimental testing data needed to demonstrate the feasibility of flaw detection on composite materials and answer the question of the method reliability. The different development steps are presented and the integration issues are discussed. Furthermore, we present the unique advantages that the reconfigurable electronics through System-on-Chip (SoC technology brings to the system scaling and flexibility. At the end of this article, we demonstrate the capability of a basic network of sensors mounted onto a real composite aircraft part specimen to capture its local impedance spectrum signature and to diagnosis different delamination sizes using a comparison with a baseline.

  10. System-on-chip integration of a new electromechanical impedance calculation method for aircraft structure health monitoring.

    Science.gov (United States)

    Boukabache, Hamza; Escriba, Christophe; Zedek, Sabeha; Medale, Daniel; Rolet, Sebastien; Fourniols, Jean Yves

    2012-10-11

    The work reported on this paper describes a new methodology implementation for active structural health monitoring of recent aircraft parts made from carbon-fiber-reinforced polymer. This diagnosis is based on a new embedded method that is capable of measuring the local high frequency impedance spectrum of the structure through the calculation of the electro-mechanical impedance of a piezoelectric patch pasted non-permanently onto its surface. This paper involves both the laboratory based E/M impedance method development, its implementation into a CPU with limited resources as well as a comparison with experimental testing data needed to demonstrate the feasibility of flaw detection on composite materials and answer the question of the method reliability. The different development steps are presented and the integration issues are discussed. Furthermore, we present the unique advantages that the reconfigurable electronics through System-on-Chip (SoC) technology brings to the system scaling and flexibility. At the end of this article, we demonstrate the capability of a basic network of sensors mounted onto a real composite aircraft part specimen to capture its local impedance spectrum signature and to diagnosis different delamination sizes using a comparison with a baseline.

  11. A Lab-on-Chip Design for Miniature Autonomous Bio-Chemoprospecting Planetary Rovers

    Science.gov (United States)

    Santoli, S.

    The performance of the so-called ` Lab-on-Chip ' devices, featuring micrometre size components and employed at present for carrying out in a very fast and economic way the extremely high number of sequence determinations required in genomic analyses, can be largely improved as to further size reduction, decrease of power consumption and reaction efficiency through development of nanofluidics and of nano-to-micro inte- grated systems. As is shown, such new technologies would lead to robotic, fully autonomous, microwatt consumption and complete ` laboratory on a chip ' units for accurate, fast and cost-effective astrobiological and planetary exploration missions. The theory and the manufacturing technologies for the ` active chip ' of a miniature bio/chemoprospecting planetary rover working on micro- and nanofluidics are investigated. The chip would include micro- and nanoreactors, integrated MEMS (MicroElectroMechanical System) components, nanoelectronics and an intracavity nanolaser for highly accurate and fast chemical analysis as an application of such recently introduced solid state devices. Nano-reactors would be able to strongly speed up reaction kinetics as a result of increased frequency of reactive collisions. The reaction dynamics may also be altered with respect to standard macroscopic reactors. A built-in miniature telemetering unit would connect a network of other similar rovers and a central, ground-based or orbiting control unit for data collection and transmission to an Earth-based unit through a powerful antenna. The development of the ` Lab-on-Chip ' concept for space applications would affect the economy of space exploration missions, as the rover's ` Lab-on-Chip ' development would link space missions with the ever growing terrestrial market and business concerning such devices, largely employed in modern genomics and bioinformatics, so that it would allow the recoupment of space mission costs.

  12. All-Digital Time-Domain CMOS Smart Temperature Sensor with On-Chip Linearity Enhancement.

    Science.gov (United States)

    Chen, Chun-Chi; Chen, Chao-Lieh; Lin, Yi

    2016-01-30

    This paper proposes the first all-digital on-chip linearity enhancement technique for improving the accuracy of the time-domain complementary metal-oxide semiconductor (CMOS) smart temperature sensor. To facilitate on-chip application and intellectual property reuse, an all-digital time-domain smart temperature sensor was implemented using 90 nm Field Programmable Gate Arrays (FPGAs). Although the inverter-based temperature sensor has a smaller circuit area and lower complexity, two-point calibration must be used to achieve an acceptable inaccuracy. With the help of a calibration circuit, the influence of process variations was reduced greatly for one-point calibration support, reducing the test costs and time. However, the sensor response still exhibited a large curvature, which substantially affected the accuracy of the sensor. Thus, an on-chip linearity-enhanced circuit is proposed to linearize the curve and achieve a new linearity-enhanced output. The sensor was implemented on eight different Xilinx FPGA using 118 slices per sensor in each FPGA to demonstrate the benefits of the linearization. Compared with the unlinearized version, the maximal inaccuracy of the linearized version decreased from 5 °C to 2.5 °C after one-point calibration in a range of -20 °C to 100 °C. The sensor consumed 95 μW using 1 kSa/s. The proposed linearity enhancement technique significantly improves temperature sensing accuracy, avoiding costly curvature compensation while it is fully synthesizable for future Very Large Scale Integration (VLSI) system.

  13. An Efficient Radio Access Control Mechanism for Wireless Network-On-Chip Architectures

    Directory of Open Access Journals (Sweden)

    Maurizio Palesi

    2015-03-01

    Full Text Available Modern systems-on-chip (SoCs today contain hundreds of cores, and this number is predicted to reach the thousands by the year 2020. As the number of communicating elements increases, there is a need for an efficient, scalable and reliable communication infrastructure. As technology geometries shrink to the deep submicron regime, however, the communication delay and power consumption of global interconnections become the major bottleneck. The network-on-chip (NoC design paradigm, based on a modular packet-switched mechanism, can address many of the on-chip communication issues, such as the performance limitations of long interconnects and integration of large number of cores on a chip. Recently, new communication technologies based on the NoC concept have emerged with the aim of improving the scalability limitations of conventional NoC-based architectures. Among them, wireless NoCs (WiNoCs use the radio medium for reducing the performance and energy penalties of long-range and multi-hop communications. As the radio medium can be accessed by a single transmitter at a time, a radio access control mechanism (RACM is needed. In this paper, we present a novel RACM, which allows one to improve both the performance and energy figures of the WiNoC. Experiments, carried out on both synthetic and real traffic scenarios, have shown the effectiveness of the proposed RACM. On average, a 30% reduction in communication delay and a 25% energy savings have been observed when the proposed RACM is applied to a known WiNoC architecture.

  14. Apparatus, System and Method for Fast Detection of Genetic Information by PCR in an Interchangeable Chip

    KAUST Repository

    Wen, Weijia; Wu, Jinbo; Kodzius, Rimantas

    2011-01-01

    A polymerase chain reaction (PCR) device for fast amplification and detection of DNA includes an interchangeable PCR chamber, a temperature control component, and an optical detection system. The DNA amplification is performed on an interchangeable

  15. Wake on LAN over Internet as web service system on chip

    OpenAIRE

    Maciá Pérez, Francisco; Gil Martínez-Abarca, Juan Antonio; Ramos Morillo, Héctor; Mora Gimeno, Francisco José; Marcos Jorquera, Diego; Gilart Iglesias, Virgilio

    2009-01-01

    In this paper we introduce a System on Chip (SoC) designed to run a particular Web Service (WS) in an Application-Specific Integrated Circuit (ASIC). The system has been designed devoid of processor and software and conceived as a hardware pattern for a trouble-free design of network services offered as WS in Service-Oriented Architecture (SOA). Therefore, the chip is not only able to act as SOAP Service Provider but, it is also capable of registering the service on its own in an external Bro...

  16. Support for Programming Models in Network-on-Chip-based Many-core Systems

    DEFF Research Database (Denmark)

    Rasmussen, Morten Sleth

    This thesis addresses aspects of support for programming models in Network-on- Chip-based many-core architectures. The main focus is to consider architectural support for a plethora of programming models in a single system. The thesis has three main parts. The first part considers parallelization...... models to be supported by a single architecture. The architecture features a specialized network interface processor which allows extensive configurability of the memory system. Based on this architecture, a detailed implementation of the cache coherent shared memory programming model is presented...

  17. A simple clockless Network-on-Chip for a commercial audio DSP chip

    DEFF Research Database (Denmark)

    Stensgaard, Mikkel Bystrup; Bjerregaard, Tobias; Sparsø, Jens

    2006-01-01

    We design a very small, packet-switched, clockless Network-on-Chip (NoC) as a replacement for the existing crossbar-based communication infrastructure in a commercial audio DSP chip. Both solutions are laid out in a 0.18 um process, and compared in terms of area, power consumption and routing...... to the existing crossbar, it allows all blocks to communicate. The total wire length is decreased by 22% which eases the layout process and makes the design less prone to routing congestion. Not least, the communicating blocks are decoupled by means of the NoC, providing a Globally-Asynchronous, Locally...

  18. An acoustic on-chip goniometer for room temperature macromolecular crystallography.

    Science.gov (United States)

    Burton, C G; Axford, D; Edwards, A M J; Gildea, R J; Morris, R H; Newton, M I; Orville, A M; Prince, M; Topham, P D; Docker, P T

    2017-12-05

    This paper describes the design, development and successful use of an on-chip goniometer for room-temperature macromolecular crystallography via acoustically induced rotations. We present for the first time a low cost, rate-tunable, acoustic actuator for gradual in-fluid sample reorientation about varying axes and its utilisation for protein structure determination on a synchrotron beamline. The device enables the efficient collection of diffraction data via a rotation method from a sample within a surface confined droplet. This method facilitates efficient macromolecular structural data acquisition in fluid environments for dynamical studies.

  19. Magnetically engineered smart thin films: toward lab-on-chip ultra-sensitive molecular imaging.

    Science.gov (United States)

    Hassan, Muhammad A; Saqib, Mudassara; Shaikh, Haseeb; Ahmad, Nasir M; Elaissari, Abdelhamid

    2013-03-01

    Magnetically responsive engineered smart thin films of nanoferrites as contrast agent are employed to develop surface based magnetic resonance imaging to acquire simple yet fast molecular imaging. The work presented here can be of significant potential for future lab-on-chip point-of-care diagnostics from the whole blood pool on almost any substrates to reduce or even prevent clinical studies involve a living organism to enhance the non-invasive imaging to advance the '3Rs' of work in animals-replacement, refinement and reduction.

  20. Identification of microfluidic two-phase flow patterns in lab-on-chip devices.

    Science.gov (United States)

    Yang, Zhaochu; Dong, Tao; Halvorsen, Einar

    2014-01-01

    This work describes a capacitive sensor for identification of microfluidic two-phase flow in lab-on-chip devices. With interdigital electrodes and thin insulation layer utilized, this sensor is capable of being integrated with the microsystems easily. Transducing principle and design considerations are presented with respect to the microfluidic gas/liquid flow patterns. Numerical simulation results verify the operational principle. And the factors affecting the performance of the sensor are discussed. Besides, a feasible process flow for the fabrication is also proposed.

  1. On-chip optical filter comprising Fabri-Perot resonator structure and spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Han, Seunghoon; Horie, Yu; Faraon, Andrei; Arbabi, Amir

    2018-04-10

    An on-chip optical filter having Fabri-Perot resonators and a spectrometer may include a first sub-wavelength grating (SWG) reflecting layer and a second SWG reflecting layer facing each other. A plurality of Fabri-Perot resonators are formed by the first SWG reflecting layer and the second SWG reflecting layer facing each other. Each of the Fabri-Perot resonators may transmit light corresponding to a resonance wavelength of the Fabri-Perot resonator. The resonance wavelengths of the Fabri-Perot resonators may be determined according to duty cycles of grating patterns.

  2. Interfacing Hardware Accelerators to a Time-Division Multiplexing Network-on-Chip

    DEFF Research Database (Denmark)

    Pezzarossa, Luca; Sørensen, Rasmus Bo; Schoeberl, Martin

    2015-01-01

    This paper addresses the integration of stateless hardware accelerators into time-predictable multi-core platforms based on time-division multiplexing networks-on-chip. Stateless hardware accelerators, like floating-point units, are typically attached as co-processors to individual processors in ...... implementation. The design evaluation is carried out using the open source T-CREST multi-core platform implemented on an Altera Cyclone IV FPGA. The size of the proposed design, including a floating-point accelerator, is about two-thirds of a processor....

  3. A novel compact model for on-chip stacked transformers in RF-CMOS technology

    Science.gov (United States)

    Jun, Liu; Jincai, Wen; Qian, Zhao; Lingling, Sun

    2013-08-01

    A novel compact model for on-chip stacked transformers is presented. The proposed model topology gives a clear distinction to the eddy current, resistive and capacitive losses of the primary and secondary coils in the substrate. A method to analytically determine the non-ideal parasitics between the primary coil and substrate is provided. The model is further verified by the excellent match between the measured and simulated S -parameters on the extracted parameters for a 1 : 1 stacked transformer manufactured in a commercial RF-CMOS technology.

  4. Embedded 3D Graphics Core for FPGA-based System-on-Chip Applications

    DEFF Research Database (Denmark)

    Holten-Lund, Hans Erik

    2005-01-01

    This paper presents a 3D graphics accelerator core for an FPGA based system, and illustrates how to build a System-on-Chip containing a Xilinx MicroBlaze soft-core CPU and our 3D graphics accelerator core. The system is capable of running uClinux and hardware accelerated 3D graphics applications......, and the video display which periodically reads from memory to display the final rendered graphics. The graphics core uses internal scratch-pad memory to reduce its external bandwidth requirement, this is achieved by implementing a tile-based rendering algorithm. Reduced external bandwidth means that the power...

  5. The use of PCR techniques to detect genetic variations in Cassava (Manihot esculenta L. Crantz): minisatellite and RAPD analysis

    International Nuclear Information System (INIS)

    Pawlicki, N.; Sangwan, R.S.; Sangwan-Norreel, B.; Koffi Konan, N.

    1998-01-01

    Cassava is an important tuber crop grown in the tropical and subtropical regions. Recently, we developed protocols for efficient somatic embryogenesis using zygotic embryos and nodal axillary meristems in order to reduce the genotype effect. Thereafter flow cytophotometry and randomly amplified polymorphic DNA (RAPD) markers were used to assess the ploidy level and the genetic fidelity of cassava plants regenerated by somatic embryogenesis. No change in the ploidy level of the regenerated plants was observed in comparison with the control plants. In the same way, monomorphic profiles of RAPD were obtained for the different cassava plants regenerated by somatic embryogenesis. The genetic analysis of calli showed only a few differences. Using two pairs of heterologous micro satellite primers developed in a wild African grass, a monomorphic pattern was also detected. Moreover, cultivars of different origins were also analysed using these PCR techniques. Our data from RAPD and materialistic analyses suggested that these techniques can be efficiently used to detect genetic variations in cassava. (author)

  6. Application of DNA Hybridization Biosensor as a Screening Method for the Detection of Genetically Modified Food Components

    Directory of Open Access Journals (Sweden)

    Marian Filipiak

    2008-03-01

    Full Text Available An electrochemical biosensor for the detection of genetically modified food components is presented. The biosensor was based on 21-mer single-stranded oligonucleotide (ssDNA probe specific to either 35S promoter or nos terminator, which are frequently present in transgenic DNA cassettes. ssDNA probe was covalently attached by 5’-phosphate end to amino group of cysteamine self-assembled monolayer (SAM on gold electrode surface with the use of activating reagents – water soluble 1-ethyl-3(3’- dimethylaminopropyl-carbodiimide (EDC and N-hydroxy-sulfosuccinimide (NHS. The hybridization reaction on the electrode surface was detected via methylene blue (MB presenting higher affinity to ssDNA probe than to DNA duplex. The electrode modification procedure was optimized using 19-mer oligoG and oligoC nucleotides. The biosensor enabled distinction between DNA samples isolated from soybean RoundupReady® (RR soybean and non-genetically modified soybean. The frequent introduction of investigated DNA sequences in other genetically modified organisms (GMOs give a broad perspectives for analytical application of the biosensor.

  7. High-speed detection of emergent market clustering via an unsupervised parallel genetic algorithm

    Directory of Open Access Journals (Sweden)

    Dieter Hendricks

    2016-02-01

    Full Text Available We implement a master-slave parallel genetic algorithm with a bespoke log-likelihood fitness function to identify emergent clusters within price evolutions. We use graphics processing units (GPUs to implement a parallel genetic algorithm and visualise the results using disjoint minimal spanning trees. We demonstrate that our GPU parallel genetic algorithm, implemented on a commercially available general purpose GPU, is able to recover stock clusters in sub-second speed, based on a subset of stocks in the South African market. This approach represents a pragmatic choice for low-cost, scalable parallel computing and is significantly faster than a prototype serial implementation in an optimised C-based fourth-generation programming language, although the results are not directly comparable because of compiler differences. Combined with fast online intraday correlation matrix estimation from high frequency data for cluster identification, the proposed implementation offers cost-effective, near-real-time risk assessment for financial practitioners.

  8. Detection and genetic distance of resistant populations of Pseudosuccinea columella (Mollusca: Lymnaeidae) to Fasciola hepatica (Trematoda: Digenea) using RAPD markers.

    Science.gov (United States)

    Calienes, Aymé Fernandez; Fraga, Jorge; Pointier, Jean-Pierre; Yong, Mary; Sanchez, Jorge; Coustau, Christine; Gutiérrez, Alfredo; Théron, André

    2004-09-01

    Twelve natural populations of Pseudosuccinea columella snails, sampled in the western and central regions of Cuba, were analyzed using the RAPD-PCR technique to screen for resistance to Fasciola hepatica. Ten OPA primers previously shown to produce marker bands for resistance and susceptibility were tested. A new population of P. columella (El Azufre, Pinar del Río) exhibited the amplification patterns of resistant snails, and its resistant status was confirmed after experimental exposure to miracidia. No genetic variability was detected across or within the susceptible isolates. Similarly, the novel resistant isolate displayed an RAPD profile identical to the profile of two other isolates previously identified as resistant to F. hepatica. However, clear differences in RAPD banding patterns and genetic distance were observed between resistant and susceptible isolates.

  9. Using multiple PCR and CE with chemiluminescence detection for simultaneous qualitative and quantitative analysis of genetically modified organism.

    Science.gov (United States)

    Guo, Longhua; Qiu, Bin; Chi, Yuwu; Chen, Guonan

    2008-09-01

    In this paper, an ultrasensitive CE-CL detection system coupled with a novel double-on-column coaxial flow detection interface was developed for the detection of PCR products. A reliable procedure based on this system had been demonstrated for qualitative and quantitative analysis of genetically modified organism-the detection of Roundup Ready Soy (RRS) samples was presented as an example. The promoter, terminator, function and two reference genes of RRS were amplified with multiplex PCR simultaneously. After that, the multiplex PCR products were labeled with acridinium ester at the 5'-terminal through an amino modification and then analyzed by the proposed CE-CL system. Reproducibility of analysis times and peak heights for the CE-CL analysis were determined to be better than 0.91 and 3.07% (RSD, n=15), respectively, for three consecutive days. It was shown that this method could accurately and qualitatively detect RRS standards and the simulative samples. The evaluation in terms of quantitative analysis of RRS provided by this new method was confirmed by comparing our assay results with those of the standard real-time quantitative PCR (RT-QPCR) using SYBR Green I dyes. The results showed a good coherence between the two methods. This approach demonstrated the possibility for accurate qualitative and quantitative detection of GM plants in a single run.

  10. A highly sensitive and specific method for the screening detection of genetically modified organisms based on digital PCR without pretreatment.

    Science.gov (United States)

    Fu, Wei; Zhu, Pengyu; Wang, Chenguang; Huang, Kunlun; Du, Zhixin; Tian, Wenying; Wang, Qin; Wang, Huiyu; Xu, Wentao; Zhu, Shuifang

    2015-08-04

    Digital PCR has developed rapidly since it was first reported in the 1990 s. It was recently reported that an improved method facilitated the detection of genetically modified organisms (GMOs). However, to use this improved method, the samples must be pretreated, which could introduce inaccuracy into the results. In our study, we explored a pretreatment-free digital PCR detection method for the screening for GMOs. We chose the CaMV35s promoter and the NOS terminator as the templates in our assay. To determine the specificity of our method, 9 events of GMOs were collected, including MON810, MON863, TC1507, MIR604, MIR162, GA21, T25, NK603 and Bt176. Moreover, the sensitivity, intra-laboratory and inter-laboratory reproducibility of our detection method were assessed. The results showed that the limit of detection of our method was 0.1%, which was lower than the labeling threshold level of the EU. The specificity and stability among the 9 events were consistent, respectively. The intra-laboratory and inter-laboratory reproducibility were both good. Finally, the perfect fitness for the detection of eight double-blind samples indicated the good practicability of our method. In conclusion, the method in our study would allow more sensitive, specific and stable screening detection of the GMO content of international trading products.

  11. Microsatellite-aided detection of genetic redundancy improves management of the International Cocoa Genebank, Trinidad

    Science.gov (United States)

    Cacao (Theobroma cacao L.), the tree from which cocoa butter and chocolate is derived, is conserved in field genebanks. The largest of these ex situ collections in the public domain is the International Cocoa Genebank, Trinidad (ICG,T). Reduction of genetic redundancy is essential to improve the acc...

  12. Detection of Genetic Relationship in the Tree of Life of Some Quail Through Molecular Markers Analyses

    Directory of Open Access Journals (Sweden)

    Lamiaa Elsayed Mokhtar Deef

    2017-08-01

    Full Text Available ABSTRACT Quail is an important and interesting group of galliform birds. The Common quail (Coturnix coturnix; the Japanese quail (Coturnix japonica; the Panda quail (Coturnix japonica; the Dotted white quail (Coturnix japonica and the Bobwhite quail (Colinus virginianus were used in this study. PCR-RFLP and SDS-proteins were performed to reveal the genetic characterization and genetic relationship of the studied quails. Analysis of fragments generated by digestion of PCR product with restriction enzyme NlaIII recorded highly polymorphic restriction profiles. There is a wide intraspecific COI, SEMA3E and TLX genes variability among the studied quails. Protein bands varied from10 to 18 between quails with minimum number of bands were in the Dotted white quail (10 bands and the maximum were in the Japanese quail (18 bands as measured by SDS-polyacrylamide gel electrophoresis. The Dotted white quail revealed the lowest similarity to the Bobwhite with a coefficient of 0.18 while The similarity coefficients between the Common quail and each one of the other quails were 0.67, 0.62, 0.45 and 0.42 for the Japanese, Panda, Dotted white and the Bobwhite quails, respectively. The results indicate that, PCR-RFLP and protein analyses are good techniques to evaluate genetic characterization and genetic relationship of these quails.

  13. Detecting instability in animal social networks: genetic fragmentation is associated with social instability in rhesus macaques.

    Directory of Open Access Journals (Sweden)

    Brianne A Beisner

    2011-01-01

    Full Text Available The persistence of biological systems requires evolved mechanisms which promote stability. Cohesive primate social groups are one example of stable biological systems, which persist in spite of regular conflict. We suggest that genetic relatedness and its associated kinship structure are a potential source of stability in primate social groups as kinship structure is an important organizing principle in many animal societies. We investigated the effect of average genetic relatedness per matrilineal family on the stability of matrilineal grooming and agonistic interactions in 48 matrilines from seven captive groups of rhesus macaques. Matrilines with low average genetic relatedness show increased family-level instability such as: more sub-grouping in their matrilineal groom network, more frequent fighting with kin, and higher rates of wounding. Family-level instability in multiple matrilines within a group is further associated with group-level instability such as increased wounding. Stability appears to arise from the presence of clear matrilineal structure in the rhesus macaque group hierarchy, which is derived from cohesion among kin in their affiliative and agonistic interactions with each other. We conclude that genetic relatedness and kinship structure are an important source of group stability in animal societies, particularly when dominance and/or affilative interactions are typically governed by kinship.

  14. Detection of genetic diversity of Anaplasma marginale isolates in Minas Gerais, Brazil

    Czech Academy of Sciences Publication Activity Database

    Pohl, A.E.; Cabezas Cruz, Alejandro; Ribeiro, M.F.B.; Goncalves da Silvera, J.; Silaghi, C.; Pfister, K.; Friche Passos, L.M.

    2013-01-01

    Roč. 22, č. 1 (2013), s. 129-135 ISSN 1984-2961 Institutional support: RVO:60077344 Keywords : Anaplasma marginale * MSP1a * DNA sequencing * microsatellites * tandem repeats * Brazil Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.961, year: 2013

  15. Depauperate genetic variability detected in the American and European bison using genomic techniques

    DEFF Research Database (Denmark)

    Pertoldi, Cino; Tokarska, Magorzata; Wójcik, Jan M

    2009-01-01

    , likely reflecting drift overwhelming selection. We suggest that utilization of genome-wide screening technologies, followed by utilization of less expensive techniques (e.g. VeraCode and Fluidigm EP1), holds large potential for genetic monitoring of populations. Additionally, these techniques will allow...

  16. Data compression can discriminate broilers by selection line, detect haplotypes, and estimate genetic potential for complex phenotypes.

    Science.gov (United States)

    Hudson, N J; Hawken, R J; Okimoto, R; Sapp, R L; Reverter, A

    2017-09-01

    Accurately establishing the relationships among individuals lays the foundation for genetic analyses such as genome-wide association studies and identification of selection signatures. Of particular interest to the poultry industry are estimates of genetic merit based on molecular data. These estimates can be commercially exploited in marker-assisted breeding programs to accelerate genetic improvement. Here, we test the utility of a new method we have recently developed to estimate animal relatedness and applied it to genetic parameter estimation in commercial broilers. Our approach is based on the concept of data compression from information theory. Using the real-world compressor gzip to estimate normalized compression distance (NCD) we have built compression-based relationship matrices (CRM) for 988 chickens from 4 commercial broiler lines-2 male and 2 female lines. For all pairs of individuals, we found a strong negative relationship between the commonly used genomic relationship matrix (GRM) and NCD. This reflects the fact that "similarity" is the inverse of "distance." The CRM explained more genetic variation than the corresponding GRM in 2 of 3 phenotypes, with corresponding improvements in accuracy of genomic-enabled predictions of breeding value. A sliding-window version of the analysis highlighted haplotype regions of the genome apparently under selection in a line-specific manner. In the male lines, we retrieved high population-specific scores for IGF-1 and a cognate receptor, INSR. For the female lines, we detected an extreme score for a region containing a reproductive hormone receptor (GNRHR). We conclude that our compression-based method is a valid approach to established relationships and identify regions under selective pressure in commercial lines of broiler chickens. © 2017 Poultry Science Association Inc.

  17. Marker Pen Lithography for Flexible and Curvilinear On-Chip Energy Storage

    KAUST Repository

    Jiang, Qiu

    2015-07-14

    On-chip energy storage using microsupercapacitors can serve the dual role of supplementing batteries for pulse power delivery, and replacement of bulky electrolytic capacitors in ac-line filtering applications. Despite complexity and processing costs, microfabrication techniques are being employed in fabricating a great variety of microsupercapacitor devices. Here, a simple, cost-effective, and versatile strategy is proposed to fabricate flexible and curvilinear microsupercapacitors (MSCs). The protocol involves writing sacrificial ink patterns using commercial marker pens on rigid, flexible, and curvilinear substrates. It is shown that this process can be used in both lift-off and etching modes, and the possibility of multistack design of active materials using simple pen lithography is demonstrated. As a prototype, this method is used to produce conducting polymer MSCs involving both poly(3,4-ethylenedioxythiophene), polyaniline, and metal oxide (MnO2) electrode materials. Typical values of energy density in the range of 5-11 mWh cm-3 at power densities of 1-6 W cm-3 are achieved, which is comparable to thin film batteries and superior to the carbon and metal oxide based microsupercapacitors reported in the literature. The simplicity and broad scope of this innovative strategy can open up new avenues for easy and scalable fabrication of a wide variety of on-chip energy storage devices. © 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim.

  18. Looking to the future of organs-on-chips: interview with Professor John Wikswo.

    Science.gov (United States)

    Wikswo, John P

    2017-06-01

    John Wikswo talks to Francesca Lake, Managing Editor: John is the founding Director of the Vanderbilt Institute for Integrative Biosystems Research and Education (VIIBRE). He is also the Gordon A Cain University Professor; a B learned Professor of Living State Physics; and a Professor of Biomedical Engineering, Molecular Physiology and Biophysics, and Physics. John earned his PhD in physics at Stanford University (CA, USA). After serving as a Research Fellow in Cardiology at Stanford, he joined the Department of Physics and Astronomy at Vanderbilt University (TN, USA), where he went on to make the first measurement of the magnetic field of an isolated nerve. He founded VIIBRE at Vanderbilt in 2001 in order to foster and enhance interdisciplinary research in the biophysical sciences, bioengineering and medicine. VIIBRE efforts have led to the development of devices integral to organ-on-chip research. He is focusing on the neurovascular unit-on-a-chip, heart-on-a-chip, a missing organ microformulator, and microfluidic pumps and valves to control and analyze organs-on-chips.

  19. HARDWARE IMPLEMENTATION OF PIPELINE BASED ROUTER DESIGN FOR ON-CHIP NETWORK

    Directory of Open Access Journals (Sweden)

    U. Saravanakumar

    2012-12-01

    Full Text Available As the feature size is continuously decreasing and integration density is increasing, interconnections have become a dominating factor in determining the overall quality of a chip. Due to the limited scalability of system bus, it cannot meet the requirement of current System-on-Chip (SoC implementations where only a limited number of functional units can be supported. Long global wires also cause many design problems, such as routing congestion, noise coupling, and difficult timing closure. Network-on-Chip (NoC architectures have been proposed to be an alternative to solve the above problems by using a packet-based communication network. In this paper, the Circuit-Switched (CS Router was designed and analysed the various parameters such as power, timing and area. The CS router has taken more number of cycles to transfer the data from source to destination. So the pipelining concept was implemented by adding registers in the CS router architecture. The proposed architecture increases the speed of operation and reduces the critical path of the circuit. The router has been implemented using Verilog HDL. The parameters area, power and timing were calculated in 130 nm CMOS technology using Synopsys tool with nominal operating voltage of 1V and packet size is 39 bits. Finally power, area and time of these two routers have been analysed and compared.

  20. On-Chip Laser-Power Delivery System for Dielectric Laser Accelerators

    Science.gov (United States)

    Hughes, Tyler W.; Tan, Si; Zhao, Zhexin; Sapra, Neil V.; Leedle, Kenneth J.; Deng, Huiyang; Miao, Yu; Black, Dylan S.; Solgaard, Olav; Harris, James S.; Vuckovic, Jelena; Byer, Robert L.; Fan, Shanhui; England, R. Joel; Lee, Yun Jo; Qi, Minghao

    2018-05-01

    We propose an on-chip optical-power delivery system for dielectric laser accelerators based on a fractal "tree-network" dielectric waveguide geometry. This system replaces experimentally demanding free-space manipulations of the driving laser beam with chip-integrated techniques based on precise nanofabrication, enabling access to orders-of-magnitude increases in the interaction length and total energy gain for these miniature accelerators. Based on computational modeling, in the relativistic regime, our laser delivery system is estimated to provide 21 keV of energy gain over an acceleration length of 192 μ m with a single laser input, corresponding to a 108-MV/m acceleration gradient. The system may achieve 1 MeV of energy gain over a distance of less than 1 cm by sequentially illuminating 49 identical structures. These findings are verified by detailed numerical simulation and modeling of the subcomponents, and we provide a discussion of the main constraints, challenges, and relevant parameters with regard to on-chip laser coupling for dielectric laser accelerators.

  1. Implantable Biomedical Signal Monitoring Using RF Energy Harvestingand On-Chip Antenna

    Directory of Open Access Journals (Sweden)

    Jiann-Shiun Yuan

    2015-08-01

    Full Text Available This paper presents the design of an energy harvesting wireless and battery-less silicon-on-chip (SoC device that can be implanted in the human body to monitor certain health conditions. The proposed architecture has been designed on TSMC 0.18μm CMOS ICs and is an integrated system with a rectenna (antenna and rectifier and transmitting circuit, all on a single chip powered by an external transmitter and that is small enough to be inserted in the human eye, heart or brain. The transmitting and receiving antennas operate in the 5.8- GHz ISM band and have a -10dB gain. The distinguishing feature of this design is the rectenna that comprises of a singlestage diode connected NMOS rectifier and a 3-D on-chip antenna that occupies only 2.5 × 1 × 2.8 mm3 of chip area and has the ability to communicate within proximity of 5 cm while giving 10% efficiency. The external source is a reader that powers up the RF rectifier in the implantable chip triggering it to start sending data back to the reader enabling an efficient method of health evaluation for the patient.

  2. DANoC: An Efficient Algorithm and Hardware Codesign of Deep Neural Networks on Chip.

    Science.gov (United States)

    Zhou, Xichuan; Li, Shengli; Tang, Fang; Hu, Shengdong; Lin, Zhi; Zhang, Lei

    2017-07-18

    Deep neural networks (NNs) are the state-of-the-art models for understanding the content of images and videos. However, implementing deep NNs in embedded systems is a challenging task, e.g., a typical deep belief network could exhaust gigabytes of memory and result in bandwidth and computational bottlenecks. To address this challenge, this paper presents an algorithm and hardware codesign for efficient deep neural computation. A hardware-oriented deep learning algorithm, named the deep adaptive network, is proposed to explore the sparsity of neural connections. By adaptively removing the majority of neural connections and robustly representing the reserved connections using binary integers, the proposed algorithm could save up to 99.9% memory utility and computational resources without undermining classification accuracy. An efficient sparse-mapping-memory-based hardware architecture is proposed to fully take advantage of the algorithmic optimization. Different from traditional Von Neumann architecture, the deep-adaptive network on chip (DANoC) brings communication and computation in close proximity to avoid power-hungry parameter transfers between on-board memory and on-chip computational units. Experiments over different image classification benchmarks show that the DANoC system achieves competitively high accuracy and efficiency comparing with the state-of-the-art approaches.

  3. Marker Pen Lithography for Flexible and Curvilinear On-Chip Energy Storage

    KAUST Repository

    Jiang, Qiu; Kurra, Narendra; Alshareef, Husam N.

    2015-01-01

    On-chip energy storage using microsupercapacitors can serve the dual role of supplementing batteries for pulse power delivery, and replacement of bulky electrolytic capacitors in ac-line filtering applications. Despite complexity and processing costs, microfabrication techniques are being employed in fabricating a great variety of microsupercapacitor devices. Here, a simple, cost-effective, and versatile strategy is proposed to fabricate flexible and curvilinear microsupercapacitors (MSCs). The protocol involves writing sacrificial ink patterns using commercial marker pens on rigid, flexible, and curvilinear substrates. It is shown that this process can be used in both lift-off and etching modes, and the possibility of multistack design of active materials using simple pen lithography is demonstrated. As a prototype, this method is used to produce conducting polymer MSCs involving both poly(3,4-ethylenedioxythiophene), polyaniline, and metal oxide (MnO2) electrode materials. Typical values of energy density in the range of 5-11 mWh cm-3 at power densities of 1-6 W cm-3 are achieved, which is comparable to thin film batteries and superior to the carbon and metal oxide based microsupercapacitors reported in the literature. The simplicity and broad scope of this innovative strategy can open up new avenues for easy and scalable fabrication of a wide variety of on-chip energy storage devices. © 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim.

  4. Improved color metrics in solid-state lighting via utilization of on-chip quantum dots

    Science.gov (United States)

    Mangum, Benjamin D.; Landes, Tiemo S.; Theobald, Brian R.; Kurtin, Juanita N.

    2017-02-01

    While Quantum Dots (QDs) have found commercial success in display applications, there are currently no widely available solid state lighting products making use of QD nanotechnology. In order to have real-world success in today's lighting market, QDs must be capable of being placed in on-chip configurations, as remote phosphor configurations are typically much more expensive. Here we demonstrate solid-state lighting devices made with on-chip QDs. These devices show robust reliability under both dry and wet high stress conditions. High color quality lighting metrics can easily be achieved using these narrow, tunable QD downconverters: CRI values of Ra > 90 as well as R9 values > 80 are readily available when combining QDs with green phosphors. Furthermore, we show that QDs afford a 15% increase in overall efficiency compared to traditional phosphor downconverted SSL devices. The fundamental limit of QD linewidth is examined through single particle QD emission studies. Using standard Cd-based QD synthesis, it is found that single particle linewidths of 20 nm FWHM represent a lower limit to the narrowness of QD emission in the near term.

  5. A Fully Integrated Humidity Sensor System-on-Chip Fabricated by Micro-Stamping Technology

    Directory of Open Access Journals (Sweden)

    Chih-Ting Lin

    2012-08-01

    Full Text Available A fully integrated humidity sensor chip was designed, implemented, and tested. Utilizing the micro-stamping technology, the pseudo-3D sensor system-on-chip (SSoC architecture can be implemented by stacking sensing materials directly on the top of a CMOS-fabricated chip. The fabricated sensor system-on-chip (2.28 mm × 2.48 mm integrated a humidity sensor, an interface circuit, a digital controller, and an On-Off Keying (OOK wireless transceiver. With low power consumption, i.e., 750 μW without RF operation, the sensitivity of developed sensor chip was experimentally verified in the relative humidity (RH range from 32% to 60%. The response time of the chip was also experimentally verified to be within 5 seconds from RH 36% to RH 64%. As a consequence, the implemented humidity SSoC paves the way toward the an ultra-small sensor system for various applications.

  6. An Implantable Cardiovascular Pressure Monitoring System with On-Chip Antenna and RF Energy Harvesting

    Directory of Open Access Journals (Sweden)

    Yu-Chun Liu

    2015-08-01

    Full Text Available An implantable wireless system with on-chip antenna for cardiovascular pressure monitor is studied. The implantable device is operated in a batteryless manner, powered by an external radio frequency (RF power source. The received RF power level can be sensed and wirelessly transmitted along with blood pressure signal for feedback control of the external RF power. The integrated electronic system, consisting of a capacitance-to-voltage converter, an adaptive RF powering system, an RF transmitter and digital control circuitry, is simulated using a TSMC 0.18 μm CMOS technology. The implanted RF transmitter circuit is combined with a low power voltage-controlled oscillator resonating at 5.8 GHz and a power amplifier. For the design, the simulation model is setup using ADS and HFSS software. The dimension of the antenna is 1 × 0.6 × 4.8 mm3 with a 1 × 0.6 mm2 on-chip circuit which is small enough to place in human carotid artery.

  7. Six-port optical switch for cluster-mesh photonic network-on-chip

    Science.gov (United States)

    Jia, Hao; Zhou, Ting; Zhao, Yunchou; Xia, Yuhao; Dai, Jincheng; Zhang, Lei; Ding, Jianfeng; Fu, Xin; Yang, Lin

    2018-05-01

    Photonic network-on-chip for high-performance multi-core processors has attracted substantial interest in recent years as it offers a systematic method to meet the demand of large bandwidth, low latency and low power dissipation. In this paper we demonstrate a non-blocking six-port optical switch for cluster-mesh photonic network-on-chip. The architecture is constructed by substituting three optical switching units of typical Spanke-Benes network to optical waveguide crossings. Compared with Spanke-Benes network, the number of optical switching units is reduced by 20%, while the connectivity of routing path is maintained. By this way the footprint and power consumption can be reduced at the expense of sacrificing the network latency performance in some cases. The device is realized by 12 thermally tuned silicon Mach-Zehnder optical switching units. Its theoretical spectral responses are evaluated by establishing a numerical model. The experimental spectral responses are also characterized, which indicates that the optical signal-to-noise ratios of the optical switch are larger than 13.5 dB in the wavelength range from 1525 nm to 1565 nm. Data transmission experiment with the data rate of 32 Gbps is implemented for each optical link.

  8. Embedded memory design for multi-core and systems on chip

    CERN Document Server

    Mohammad, Baker

    2014-01-01

    This book describes the various tradeoffs systems designers face when designing embedded memory.  Readers designing multi-core systems and systems on chip will benefit from the discussion of different topics from memory architecture, array organization, circuit design techniques and design for test.  The presentation enables a multi-disciplinary approach to chip design, which bridges the gap between the architecture level and circuit level, in order to address yield, reliability and power-related issues for embedded memory.  ·         Provides a comprehensive overview of embedded memory design and associated challenges and choices; ·         Explains tradeoffs and dependencies across different disciplines involved with multi-core and system on chip memory design; ·         Includes detailed discussion of memory hierarchy and its impact on energy and performance; ·         Uses real product examples to demonstrate embedded memory design flow from architecture, to circuit ...

  9. Source-synchronous networks-on-chip circuit and architectural interconnect modeling

    CERN Document Server

    Mandal, Ayan; Mahapatra, Rabi

    2014-01-01

    This book describes novel methods for network-on-chip (NoC) design, using source-synchronous high-speed resonant clocks.  The authors discuss NoCs from the bottom up, providing circuit level details, before providing architectural simulations. As a result, readers will get a complete picture of how a NoC can be designed and optimized.  Using the methods described in this book, readers are enabled to design NoCs that are 5X better than existing approaches in terms of latency and throughput and can also sustain a significantly greater amount of traffic.   • Describes novel methods for high-speed network-on-chip (NoC) design; • Enables readers to understand NoC design from both circuit and architectural levels; • Provides circuit-level details of the NoC (including clocking, router design), along with a high-speed, resonant clocking style which is used in the NoC; • Includes architectural simulations of the NoC, demonstrating significantly superior performance over the state-of-the-art.

  10. A full on-chip CMOS low-dropout voltage regulator with VCCS compensation

    Energy Technology Data Exchange (ETDEWEB)

    Gao Leisheng; Zhou Yumei; Wu Bin; Jiang Jianhua, E-mail: gaoleisheng@ime.ac.c [Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029 (China)

    2010-08-15

    A full on-chip CMOS low-dropout (LDO) voltage regulator with high PSR is presented. Instead of relying on the zero generated by the load capacitor and its equivalent series resistance, the proposed LDO generates a zero by voltage-controlled current sources for stability. The compensating capacitor for the proposed scheme is only 0.18 pF, which is much smaller than the capacitor of the conventional compensation scheme. The full on-chip LDO was fabricated in commercial 0.35 {mu}m CMOS technology. The active chip area of the LDO (including the bandgap voltage reference) is 400 x 270 {mu}m{sup 2}. Experimental results show that the PSR of the LDO is -58.7 dB at a frequency of 10 Hz and -20 dB at a frequency of 1 MHz. The proposed LDO is capable of sourcing an output current up to 50 mA. (semiconductor integrated circuits)

  11. A full on-chip CMOS low-dropout voltage regulator with VCCS compensation

    International Nuclear Information System (INIS)

    Gao Leisheng; Zhou Yumei; Wu Bin; Jiang Jianhua

    2010-01-01

    A full on-chip CMOS low-dropout (LDO) voltage regulator with high PSR is presented. Instead of relying on the zero generated by the load capacitor and its equivalent series resistance, the proposed LDO generates a zero by voltage-controlled current sources for stability. The compensating capacitor for the proposed scheme is only 0.18 pF, which is much smaller than the capacitor of the conventional compensation scheme. The full on-chip LDO was fabricated in commercial 0.35 μm CMOS technology. The active chip area of the LDO (including the bandgap voltage reference) is 400 x 270 μm 2 . Experimental results show that the PSR of the LDO is -58.7 dB at a frequency of 10 Hz and -20 dB at a frequency of 1 MHz. The proposed LDO is capable of sourcing an output current up to 50 mA. (semiconductor integrated circuits)

  12. Small-scale, self-propagating combustion realized with on-chip porous silicon.

    Science.gov (United States)

    Piekiel, Nicholas W; Morris, Christopher J

    2015-05-13

    For small-scale energy applications, energetic materials represent a high energy density source that, in certain cases, can be accessed with a very small amount of energy input. Recent advances in microprocessing techniques allow for the implementation of a porous silicon energetic material onto a crystalline silicon wafer at the microscale; however, combustion at a small length scale remains to be fully investigated, particularly with regards to the limitations of increased relative heat loss during combustion. The present study explores the critical dimensions of an on-chip porous silicon energetic material (porous silicon + sodium perchlorate (NaClO4)) required to propagate combustion. We etched ∼97 μm wide and ∼45 μm deep porous silicon channels that burned at a steady rate of 4.6 m/s, remaining steady across 90° changes in direction. In an effort to minimize the potential on-chip footprint for energetic porous silicon, we also explored the minimum spacing between porous silicon channels. We demonstrated independent burning of porous silicon channels at a spacing of 0.5 m on a chip surface area of 1.65 cm(2). Smaller porous silicon channels of ∼28 μm wide and ∼14 μm deep were also utilized. These samples propagated combustion, but at times, did so unsteadily. This result may suggest that we are approaching a critical length scale for self-propagating combustion in a porous silicon energetic material.

  13. Detection of genetically modified organisms (GMOs) using isothermal amplification of target DNA sequences.

    Science.gov (United States)

    Lee, David; La Mura, Maurizio; Allnutt, Theo R; Powell, Wayne

    2009-02-02

    The most common method of GMO detection is based upon the amplification of GMO-specific DNA amplicons using the polymerase chain reaction (PCR). Here we have applied the loop-mediated isothermal amplification (LAMP) method to amplify GMO-related DNA sequences, 'internal' commonly-used motifs for controlling transgene expression and event-specific (plant-transgene) junctions. We have tested the specificity and sensitivity of the technique for use in GMO studies. Results show that detection of 0.01% GMO in equivalent background DNA was possible and dilutions of template suggest that detection from single copies of the template may be possible using LAMP. This work shows that GMO detection can be carried out using LAMP for routine screening as well as for specific events detection. Moreover, the sensitivity and ability to amplify targets, even with a high background of DNA, here demonstrated, highlights the advantages of this isothermal amplification when applied for GMO detection.

  14. Gain-Enhanced On-Chip Antenna Utilizing Artificial Magnetic Conductor Reflecting Surface at 94 GHz

    KAUST Repository

    Nafe, Mahmoud

    2015-08-04

    Nowadays, there is a growing demand for high frequency-bandwidth mm-wave (30-300 GHz) electronic wireless transceiver systems to support applications such as high data-rate wireless communication and high resolution imaging. Such mm-wave systems are becoming more feasible due to the extreme transistor downscaling in silicon-based integrated circuits, which enabled densely-integrated high-speed elec- tronics operating up to more than 100 GHz with low fabrication cost. To further enhance system integrability, it is required to implement all wireless system compo- nents on the chip. Presently, the last major barrier to true System-on-Chip (SoC) realization is the antenna implementation on the silicon chip. Although at mm-wave frequencies the antenna size becomes small enough to fit on chip, the antenna performance is greatly deteriorated due the high conductivity and high relative permittivity of the silicon substrate. The negative e↵ects of the silicon substrate could be avoided by using a metallic reflecting surface on top of silicon, which e↵ectively isolates the antenna from the silicon. However, this approach has the shortcoming of having to implement the antenna on the usually very thin silicon oxide layer of a typical CMOS fabrication process (10’s of μm). This forces the antenna to be in a very close proximity (less than one hundredth of a wavelength) to the reflecting surface. In this regime, the use of conventional metallic reflecting surface for silicon shielding has severe e↵ects on the antenna performance as it tends to reduce the antenna radiation resistance resulting in most of the energy being absorbed rather than radiated. In this work, the use of specially patterned reflecting surfaces for improving on- chip antenna performance is investigated. By using a periodic metallic surface on top of a grounded substrate, the structure can mimic the behavior of a perfect mag- netic conductor, hence called Artificial Magnetic Conductor (AMC) surface

  15. On-chip acoustophoretic isolation of microflora including S. typhimurium from raw chicken, beef and blood samples.

    Science.gov (United States)

    Ngamsom, Bongkot; Lopez-Martinez, Maria J; Raymond, Jean-Claude; Broyer, Patrick; Patel, Pradip; Pamme, Nicole

    2016-04-01

    Pathogen analysis in food samples routinely involves lengthy growth-based pre-enrichment and selective enrichment of food matrices to increase the ratio of pathogen to background flora. Similarly, for blood culture analysis, pathogens must be isolated and enriched from a large excess of blood cells to allow further analysis. Conventional techniques of centrifugation and filtration are cumbersome, suffer from low sample throughput, are not readily amenable to automation and carry a risk of damaging biological samples. We report on-chip acoustophoresis as a pre-analytical technique for the resolution of total microbial flora from food and blood samples. The resulting 'clarified' sample is expected to increase the performance of downstream systems for the specific detection of the pathogens. A microfluidic chip with three inlets, a central separation channel and three outlets was utilized. Samples were introduced through the side inlets, and buffer solution through the central inlet. Upon ultrasound actuation, large debris particles (10-100 μm) from meat samples were continuously partitioned into the central buffer channel, leaving the 'clarified' outer sample streams containing both, the pathogenic cells and the background flora (ca. 1 μm) to be collected over a 30 min operation cycle before further analysis. The system was successfully tested with Salmonella typhimurium-spiked (ca. 10(3)CFU mL(-1)) samples of chicken and minced beef, demonstrating a high level of the pathogen recovery (60-90%). When applied to S. typhimurium contaminated blood samples (10(7)CFU mL(-1)), acoustophoresis resulted in a high depletion (99.8%) of the red blood cells (RBC) which partitioned in the buffer stream, whilst sufficient numbers of the viable S. typhimurium remained in the outer channels for further analysis. These results indicate that the technology may provide a generic approach for pre-analytical sample preparation prior to integrated and automated downstream detection of

  16. Early detection of abnormal prion protein in genetic human prion diseases now possible using real-time QUIC assay.

    Directory of Open Access Journals (Sweden)

    Kazunori Sano

    Full Text Available INTRODUCTION: The definitive diagnosis of genetic prion diseases (gPrD requires pathological confirmation. To date, diagnosis has relied upon the finding of the biomarkers 14-3-3 protein and total tau (t-tau protein in the cerebrospinal fluid (CSF, but many researchers have reported that these markers are not sufficiently elevated in gPrD, especially in Gerstmann-Sträussler-Scheinker syndrome (GSS. We recently developed a new in vitro amplification technology, designated "real-time quaking-induced conversion (RT-QUIC", to detect the abnormal form of prion protein in CSF from sporadic Creutzfeldt-Jakob disease (sCJD patients. In the present study, we aimed to investigate the presence of biomarkers and evaluate RT-QUIC assay in patients with gPrD, as the utility of RT-QUIC as a diagnostic tool in gPrD has yet to be determined. METHOD/PRINCIPAL FINDINGS: 56 CSF samples were obtained from gPrD patients, including 20 cases of GSS with P102L mutation, 12 cases of fatal familial insomnia (FFI; D178N, and 24 cases of genetic CJD (gCJD, comprising 22 cases with E200K mutation and 2 with V203I mutation. We subjected all CSF samples to RT-QUIC assay, analyzed 14-3-3 protein by Western blotting, and measured t-tau protein using an ELISA kit. The detection sensitivities of RT-QUIC were as follows: GSS (78%, FFI (100%, gCJD E200K (87%, and gCJD V203I (100%. On the other hand the detection sensitivities of biomarkers were considerably lower: GSS (11%, FFI (0%, gCJD E200K (73%, and gCJD V203I (67%. Thus, RT-QUIC had a much higher detection sensitivity compared with testing for biomarkers, especially in patients with GSS and FFI. CONCLUSION/SIGNIFICANCE: RT-QUIC assay is more sensitive than testing for biomarkers in gPrD patients. RT-QUIC method would thus be useful as a diagnostic tool when the patient or the patient's family does not agree to genetic testing, or to confirm the diagnosis in the presence of a positive result for genetic testing.

  17. Real-time PCR array as a universal platform for the detection of genetically modified crops and its application in identifying unapproved genetically modified crops in Japan.

    Science.gov (United States)

    Mano, Junichi; Shigemitsu, Natsuki; Futo, Satoshi; Akiyama, Hiroshi; Teshima, Reiko; Hino, Akihiro; Furui, Satoshi; Kitta, Kazumi

    2009-01-14

    We developed a novel type of real-time polymerase chain reaction (PCR) array with TaqMan chemistry as a platform for the comprehensive and semiquantitative detection of genetically modified (GM) crops. Thirty primer-probe sets for the specific detection of GM lines, recombinant DNA (r-DNA) segments, endogenous reference genes, and donor organisms were synthesized, and a 96-well PCR plate was prepared with a different primer-probe in each well as the real-time PCR array. The specificity and sensitivity of the array were evaluated. A comparative analysis with the data and publicly available information on GM crops approved in Japan allowed us to assume the possibility of unapproved GM crop contamination. Furthermore, we designed a Microsoft Excel spreadsheet application, Unapproved GMO Checker version 2.01, which helps process all the data of real-time PCR arrays for the easy assumption of unapproved GM crop contamination. The spreadsheet is available free of charge at http://cse.naro.affrc.go.jp/jmano/index.html .

  18. On-chip cellomics assay enabling algebraic and geometric understanding of epigenetic information in cellular networks of living systems. 1. Temporal aspects of epigenetic information in bacteria.

    Science.gov (United States)

    Yasuda, Kenji

    2012-01-01

    A series of studies aimed at developing methods and systems of analyzing epigenetic information in cells and in cell networks, as well as that of genetic information, was examined to expand our understanding of how living systems are determined. Because cells are minimum units reflecting epigenetic information, which is considered to map the history of a parallel-processing recurrent network of biochemical reactions, their behaviors cannot be explained by considering only conventional DNA information-processing events. The role of epigenetic information on cells, which complements their genetic information, was inferred by comparing predictions from genetic information with cell behaviour observed under conditions chosen to reveal adaptation processes, population effects and community effects. A system of analyzing epigenetic information was developed starting from the twin complementary viewpoints of cell regulation as an "algebraic" system (emphasis on temporal aspects) and as a "geometric" system (emphasis on spatial aspects). Exploiting the combination of latest microfabrication technology and measurement technologies, which we call on-chip cellomics assay, we can control and re-construct the environments and interaction of cells from "algebraic" and "geometric" viewpoints. In this review, temporal viewpoint of epigenetic information, a part of the series of single-cell-based "algebraic" and "geometric" studies of celluler systems in our research groups, are summerized and reported. The knowlege acquired from this study may lead to the use of cells that fully control practical applications like cell-based drug screening and the regeneration of organs.

  19. PCR-free quantitative detection of genetically modified organism from raw materials. An electrochemiluminescence-based bio bar code method.

    Science.gov (United States)

    Zhu, Debin; Tang, Yabing; Xing, Da; Chen, Wei R

    2008-05-15

    A bio bar code assay based on oligonucleotide-modified gold nanoparticles (Au-NPs) provides a PCR-free method for quantitative detection of nucleic acid targets. However, the current bio bar code assay requires lengthy experimental procedures including the preparation and release of bar code DNA probes from the target-nanoparticle complex and immobilization and hybridization of the probes for quantification. Herein, we report a novel PCR-free electrochemiluminescence (ECL)-based bio bar code assay for the quantitative detection of genetically modified organism (GMO) from raw materials. It consists of tris-(2,2'-bipyridyl) ruthenium (TBR)-labeled bar code DNA, nucleic acid hybridization using Au-NPs and biotin-labeled probes, and selective capture of the hybridization complex by streptavidin-coated paramagnetic beads. The detection of target DNA is realized by direct measurement of ECL emission of TBR. It can quantitatively detect target nucleic acids with high speed and sensitivity. This method can be used to quantitatively detect GMO fragments from real GMO products.

  20. Candidate genes detected in transcriptome studies are strongly dependent on genetic background.

    Directory of Open Access Journals (Sweden)

    Pernille Sarup

    2011-01-01

    Full Text Available Whole genome transcriptomic studies can point to potential candidate genes for organismal traits. However, the importance of potential candidates is rarely followed up through functional studies and/or by comparing results across independent studies. We have analysed the overlap of candidate genes identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same genetic backgrounds. Putative candidates found using transcriptomics therefore appear very sensitive to genetic background and this can mask or override effects of treatments. The functional importance of putative candidate genes emerging from transcriptome studies needs to be validated through additional experiments and in future studies we suggest a focus on the genes, networks and pathways affecting traits in a consistent manner across backgrounds.

  1. SERS-based detection methods for screening of genetically modified bacterial strains

    DEFF Research Database (Denmark)

    Morelli, Lidia

    factories vary largely, including industrial production of valuable compounds for biofuels, polymer synthesis and food, cosmetic and pharmaceutical industry. The improvement of computational and biochemical tools has revolutionized the synthesis of novel modified microbial strains, opening up new......The importance of metabolic engineering has been growing over the last decades, establishing the use of genetically modified microbial strains for overproduction of metabolites at industrial scale as an innovative, convenient and biosustainable method. Nowadays, application areas of microbial...

  2. Detection of Genetic Variations in Marine Algae Ulva lactuca (Chlorophyta Induced by Heavy Metal Pollutants

    Directory of Open Access Journals (Sweden)

    Basel Saleh

    2015-09-01

    Full Text Available Ulva lactuca (Chlorophyta green macroalgae has been successfully used as bioindicator for heavy metals pollution in ecosystems. Random amplified microsatellite polymorphism (RAMP marker was employed to investigate genetic DNA pattern variability in green U. lactuca 5 days after exposure to Cu, Pb, Cd and Zn heavy metals stress. Genomic template stability (GTS% value was employed as a qualitative DNA changes measurement based on RAMP technique. In this respect, estimated GTS% value was recorded to be 65.215, 64.630, 59.835 and 59.250% for Pb, Cu, Cd and Zn treatment, respectively. Moreover, genetic similarity (GS induced by the above heavy metals was also evaluated to measure genetic distance between algae treated plants and their respective control. In this respect, estimated GS values generated by RAMP marker ranged between 0.576 (between control and Zn treatment - 0.969 (for both case; between Pb and Cu and between Cd and Zn treatment with an average of 0.842. Based upon data presented herein based on variant bands number (VB, GTS% and GS values; the present study could be suggested that Pb and Cu followed similar tendency at genomic DNA changes. Similar finding was also observed with Cd and Zn ions. Thereby, RAMP marker successfully highlighted DNA change patterns induced by heavy metals stress.

  3. An endogenous reference gene of common and durum wheat for detection of genetically modified wheat.

    Science.gov (United States)

    Imai, Shinjiro; Tanaka, Keiko; Nishitsuji, Yasuyuki; Kikuchi, Yosuke; Matsuoka, Yasuyuki; Arami, Shin-Ichiro; Sato, Megumi; Haraguchi, Hiroyuki; Kurimoto, Youichi; Mano, Junichi; Furui, Satoshi; Kitta, Kazumi

    2012-01-01

    To develop a method for detecting GM wheat that may be marketed in the near future, we evaluated the proline-rich protein (PRP) gene as an endogenous reference gene of common wheat (Triticum aestivum L.) and durum wheat (Triticum durum L.). Real-time PCR analysis showed that only DNA of wheat was amplified and no amplification product was observed for phylogenetically related cereals, indicating that the PRP detection system is specific to wheat. The intensities of the amplification products and Ct values among all wheat samples used in this study were very similar, with no nonspecific or additional amplification, indicating that the PRP detection system has high sequence stability. The limit of detection was estimated at 5 haploid genome copies. The PRP region was demonstrated to be present as a single or double copy in the common wheat haploid genome. Furthermore, the PRP detection system showed a highly linear relationship between Ct values and the amount of plasmid DNA, indicating that an appropriate calibration curve could be constructed for quantitative detection of GM wheat. All these results indicate that the PRP gene is a suitable endogenous reference gene for PCR-based detection of GM wheat.

  4. A CMOS Gm-C complex filter with on-chip automatic tuning for wireless sensor network application

    International Nuclear Information System (INIS)

    Wan Chuanchuan; Li Zhiqun; Hou Ningbing

    2011-01-01

    A G m -C complex filter with on-chip automatic tuning for wireless sensor networks is designed and implemented using 0.18 μm CMOS process. This filter is synthesized from a low-pass 5th-order Chebyshev RLC ladder filter prototype by means of capacitors and fully balanced transconductors. A conventional phase-locked loop is used to realize the on-chip automatic tuning for both center frequency and bandwidth control. The filter is centered at 2 MHz with a bandwidth of 2.4 MHz. The measured results show that the filter provides more than 45 dB image rejection while the ripple in the pass-band is less than 1.2 dB. The complete filter including on-chip tuning circuit consumes 4.9 mA with 1.8 V single supply voltage. (semiconductor integrated circuits)

  5. FISH as A method for detection of radiation Induced genetic damage

    International Nuclear Information System (INIS)

    Lakatosova, M.; Holeckova, B.

    2006-01-01

    Fluorescence in situ hybridization (FISH) has been considered as a suitable method for rapid and easy detection of chromosome aberrations. In contrast to the standard conventional staining procedure, this technique enables the detection and specification of stable chromosomal re-arrangements, which are compatible with cellular division and thus, they could be transmitted from common ancestral to next cell generations. FISH chromosome - specific painting probes have been effectively applied for the detection of chromosomal damage after exposure to radiation. During last years, several specific fluorescent labeled probes were performed that allowed precise detection of centromeres, sub-telomeres or other regions (sequences) in genome. Our paper deals with describing of different types of FISH probes and their possibilities for application in radiobiology. (authors)

  6. Detection and linkage to mobile genetic elements of tetracycline resistance gene tet(M) in Escherichia coli isolates from pigs

    DEFF Research Database (Denmark)

    Jurado-Rabadan, Sonia; de la Fuente, Ricardo; Ruiz-Santa-Quiteria, Jose A.

    2014-01-01

    Background: In Escherichia coli the genes involved in the acquisition of tetracycline resistance are mainly tet(A) and tet(B). In addition, tet(M) is the most common tetracycline resistance determinant in enterococci and it is associated with conjugative transposons and plasmids. Although tet......(M) has been identified in E. coli, to our knowledge, there are no previous reports studying the linkage of the tet(M) gene in E. coli to different mobile genetic elements. The aim of this study was to determine the occurrence of tet(A), tet(B), and tet(M) genes in doxycycline-resistant E. coli isolates...... from pigs, as well as the detection of mobile genetic elements linked to tet(M) in E. coli and its possible transfer from enterococci. Results: tet(A) was the most frequently detected gene (87.9%) in doxycycline-resistant isolates. tet(M) was found in 13.1% E. coli isolates. The tet(M) gene...

  7. Development of melting temperature-based SYBR Green I polymerase chain reaction methods for multiplex genetically modified organism detection.

    Science.gov (United States)

    Hernández, Marta; Rodríguez-Lázaro, David; Esteve, Teresa; Prat, Salomé; Pla, Maria

    2003-12-15

    Commercialization of several genetically modified crops has been approved worldwide to date. Uniplex polymerase chain reaction (PCR)-based methods to identify these different insertion events have been developed, but their use in the analysis of all commercially available genetically modified organisms (GMOs) is becoming progressively insufficient. These methods require a large number of assays to detect all possible GMOs present in the sample and thereby the development of multiplex PCR systems using combined probes and primers targeted to sequences specific to various GMOs is needed for detection of this increasing number of GMOs. Here we report on the development of a multiplex real-time PCR suitable for multiple GMO identification, based on the intercalating dye SYBR Green I and the analysis of the melting curves of the amplified products. Using this method, different amplification products specific for Maximizer 176, Bt11, MON810, and GA21 maize and for GTS 40-3-2 soybean were obtained and identified by their specific Tm. We have combined amplification of these products in a number of multiplex reactions and show the suitability of the methods for identification of GMOs with a sensitivity of 0.1% in duplex reactions. The described methods offer an economic and simple alternative to real-time PCR systems based on sequence-specific probes (i.e., TaqMan chemistry). These methods can be used as selection tests and further optimized for uniplex GMO quantification.

  8. Single nucleotide primer extension to detect genetic diseases: Experimental application to hemophilia B (factor IX) and cystic fibrosis genes

    International Nuclear Information System (INIS)

    Kuppuswamy, M.N.; Hoffmann, J.W.; Spitzer, S.G.; Groce, S.L.; Bajaj, S.P.; Kasper, C.K.

    1991-01-01

    In this report, the authors describe an approach to detect the presence of abnormal alleles in those genetic diseases in which frequency of occurrence of the same mutation is high (e.g., hemophilia B). Initially, from each subject, the DNA fragment containing the putative mutation site is amplified by the polymerase chain reaction. For each fragment two reaction mixtures are then prepared. Each contains the amplified fragment, a primer (18-mer or longer) whose sequence is identical to the coding sequence of the normal gene immediately flanking the 5' end of the mutation site, and either an α- 32 P-labeled nucleotide corresponding to the normal coding sequence at the mutation site or an α- 32 P-labeled nucleotide corresponding to the mutant sequence. An essential feature of the present methodology is that the base immediately 3' to the template-bound primer is one of those altered in the mutant, since in this way an extension of the primer by a single base will give an extended molecule characteristic of either the mutant or the wild type. The method is rapid and should be useful in carrier detection and prenatal diagnosis of every genetic disease with a known sequence variation

  9. New genetic variants of influenza A(H1N1)pdm09 detected in Cuba during 2011-2013.

    Science.gov (United States)

    Arencibia, Amely; Acosta, Belsy; Muné, Mayra; Valdés, Odalys; Fernandez, Leandro; Medina, Isel; Savón, Clara; Oropesa, Suset; Gonzalez, Grehete; Roque, Rosmery; Gonzalez, Guelsys; Hernández, Bárbara; Goyenechea, Angel; Piñón, Alexander

    2015-06-01

    Influenza A(H1N1)pdm09 virus has evolved continually since its emergence in 2009. For influenza virus strains, genetic changes occurring in HA1 domain of the hemagglutinin cause the emergence of new variants. The aim of our study is to establish genetic associations between 35 A(H1N1)pdm09 viruses circulating in Cuba in 2011-2012 and 2012-2013 seasons, and A/California/07/2009 strain recommended by WHO as the H1N1 component of the influenza vaccine. The phylogenetic analysis revealed the circulation of clades 3, 6A, 6B, 6C and 7. Mutations were detected in the antigenic site or in the receptor-binding domains of HA1 segment, including S174P, S179N, K180Q, S202T, S220T and R222K. Substitutions S174P, S179N, K180Q and R222K were detected in Cuban strains for the first time. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Development of Rapid Detection and Genetic Characterization of Salmonella in Poultry Breeder Feeds

    Science.gov (United States)

    Jarquin, Robin; Hanning, Irene; Ahn, Soohyoun; Ricke, Steven C.

    2009-01-01

    Salmonella is a leading cause of foodborne illness in the United States, with poultry and poultry products being a primary source of infection to humans. Poultry may carry some Salmonella serovars without any signs or symptoms of disease and without causing any adverse effects to the health of the bird. Salmonella may be introduced to a flock by multiple environmental sources, but poultry feed is suspected to be a leading source. Detecting Salmonella in feed can be challenging because low levels of the bacteria may not be recovered using traditional culturing techniques. Numerous detection methodologies have been examined over the years for quantifying Salmonella in feeds and many have proven to be effective for Salmonella isolation and detection in a variety of feeds. However, given the potential need for increased detection sensitivity, molecular detection technologies may the best candidate for developing rapid sensitive methods for identifying small numbers of Salmonella in the background of large volumes of feed. Several studies have been done using polymerase chain reaction (PCR) assays and commercial kits to detect Salmonella spp. in a wide variety of feed sources. In addition, DNA array technology has recently been utilized to track the dissemination of a specific Salmonella serotype in feed mills. This review will discuss the processing of feeds and potential points in the process that may introduce Salmonella contamination to the feed. Detection methods currently used and the need for advances in these methods also will be discussed. Finally, implementation of rapid detection for optimizing control methods to prevent and remove any Salmonella contamination of feeds will be considered. PMID:22346699

  11. Development of Rapid Detection and Genetic Characterization of Salmonella in Poultry Breeder Feeds

    Directory of Open Access Journals (Sweden)

    Steven C. Ricke

    2009-07-01

    Full Text Available Salmonella is a leading cause of foodborne illness in the United States, with poultry and poultry products being a primary source of infection to humans. Poultry may carry some Salmonella serovars without any signs or symptoms of disease and without causing any adverse effects to the health of the bird. Salmonella may be introduced to a flock by multiple environmental sources, but poultry feed is suspected to be a leading source. Detecting Salmonella in feed can be challenging because low levels of the bacteria may not be recovered using traditional culturing techniques. Numerous detection methodologies have been examined over the years for quantifying Salmonella in feeds and many have proven to be effective for Salmonella isolation and detection in a variety of feeds. However, given the potential need for increased detection sensitivity, molecular detection technologies may the best candidate for developing rapid sensitive methods for identifying small numbers of Salmonella in the background of large volumes of feed. Several studies have been done using polymerase chain reaction (PCR assays and commercial kits to detect Salmonella spp. in a wide variety of feed sources. In addition, DNA array technology has recently been utilized to track the dissemination of a specific Salmonella serotype in feed mills. This review will discuss the processing of feeds and potential points in the process that may introduce Salmonella contamination to the feed. Detection methods currently used and the need for advances in these methods also will be discussed. Finally, implementation of rapid detection for optimizing control methods to prevent and remove any Salmonella contamination of feeds will be considered.

  12. Detection of genetically modified organisms (GMOs using isothermal amplification of target DNA sequences

    Directory of Open Access Journals (Sweden)

    La Mura Maurizio

    2009-02-01

    Full Text Available Abstract Background The most common method of GMO detection is based upon the amplification of GMO-specific DNA amplicons using the polymerase chain reaction (PCR. Here we have applied the loop-mediated isothermal amplification (LAMP method to amplify GMO-related DNA sequences, 'internal' commonly-used motifs for controlling transgene expression and event-specific (plant-transgene junctions. Results We have tested the specificity and sensitivity of the technique for use in GMO studies. Results show that detection of 0.01% GMO in equivalent background DNA was possible and dilutions of template suggest that detection from single copies of the template may be possible using LAMP. Conclusion This work shows that GMO detection can be carried out using LAMP for routine screening as well as for specific events detection. Moreover, the sensitivity and ability to amplify targets, even with a high background of DNA, here demonstrated, highlights the advantages of this isothermal amplification when applied for GMO detection.

  13. Detection of thermogenesis in rodents in response to anti-obesity drugs and genetic modification

    Directory of Open Access Journals (Sweden)

    Jonathan R S Arch

    2013-04-01

    Full Text Available Many compounds and genetic manipulations are claimed to confer resistance to obesity in rodents by raising energy expenditure. Examples taken from recent and older literature, demonstrate that such claims are often based on measurements of energy expenditure after body composition has changed and depend on comparisons of energy expenditure divided by body weight. This is misleading because white adipose tissue has less influence than lean tissue on energy expenditure. Application of this approach to human data would suggest that human obesity is usually due to a low metabolic rate, which is not an accepted view. Increased energy expenditure per animal is a surer way of demonstrating thermogenesis, but even then it is important to know whether this is due to altered body composition (repartitioning, or increased locomotor activity rather than thermogenesis per se. Regression analysis offers other approaches. The thermogenic response to some compounds has a rapid onset and so cannot be due to altered body composition. These compounds usually mimic or activate the sympathetic nervous system. Thermogenesis occurs in, but may not be confined to, brown adipose tissue. It should not be assumed that weight loss in response to these treatments is due to thermogenesis unless there is a sustained increase in 24-h energy expenditure. Thyroid hormones and fibroblast growth factor 21 also raise energy expenditure before they affect body composition. Some treatments and genetic modifications alter the diurnal rhythm of energy expenditure. It is important to establish whether this is due to altered locomotor activity or efficiency of locomotion. There are no good examples of compounds that do not affect short-term energy expenditure but have a delayed effect. How and under what conditions a genetic modification or compound increases energy expenditure influences the decision on whether to seek drugs for the target or take a candidate drug into clinical studies.

  14. Genetic variation and relationships of old maize genotypes (Zea mays l. detected using SDS-page

    Directory of Open Access Journals (Sweden)

    Martin Vivodík

    2016-11-01

    Full Text Available The assessment of genetic diversity among the members of a species is of vital importance for successful breeding and adaptability. In the present study 40 old genotypes of maize from Hungary, Union of Soviet Socialist Republics, Poland, Czechoslovakia, Yugoslavia and Slovak Republic  were evaluated for the total seed storage proteins using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE through vertical slab unit. The number of total scorable protein bands was twentythree as a result of SDS-PAGE technique but those that were not cosistent in reproducibility and showed occasional variation in sharpness and density were not considered. Out of twentythree polypeptide bands, 6 (31% were commonly present in all accessions and considered as monomorphic, while 17 (65% showed variations and considered as polymorphic. On the basis of banding profiles of proteins of different kDa, gel was divided into zones A, B and C. The major protein bands were lied in zones A and B, while minor bands were present in zones C. In zone A out of 10 protein bands, 1 were monomorphic and 9 were polymorphic. In zone B out of 8 protein bands, 3 was monomorphic and 5 was polymorphic and in zone C out of 5 protein bands, 2 were monomorphic whereas 3 polymorphic. The dendrogram tree demonstrated the relationship among the forty registered old maize genotypes according to the similarity index, using UPGMA cluster analysis. The dendrogram was divided into two main clusters. The first one contained eleven genotypes from maize, while the second cluster contained the twentynine genotypes of maize. Similarly the present study of genetic variability in the seed storage polypeptide determined by SDS-PAGE technique proved that it is fruitful to identify genetic diversity among accessions of maize. 

  15. Genetic variation of european maize genotypes (zea mays l. Detected using ssr markers

    Directory of Open Access Journals (Sweden)

    Martin Vivodík

    2017-01-01

    Full Text Available The SSR molecular markers were used to assess genetic diversity in 40 old European maize genotypes. Ten SSR primers revealed a total of 65 alleles ranging from 4 (UMC1060 to 8 (UMC2002 and UMC1155 alleles per locus with a mean value of 6.50 alleles per locus. The PIC values ranged from 0.713 (UMC1060 to 0.842 (UMC2002 with an average value of 0.810 and the DI value ranged from 0.734 (UMC1060 to 0.848 (UMC2002 with an average value of 0.819. 100% of used SSR markers had PIC and DI values higher than 0.7 that means high polymorphism of chosen markers used for analysis. Probability of identity (PI was low ranged from 0.004 (UMC1072 to 0.022 (UMC1060 with an average of 0.008. A dendrogram was constructed from a genetic distance matrix based on profiles of the 10 maize SSR loci using the unweighted pair-group method with the arithmetic average (UPGMA. According to analysis, the collection of 40 diverse accessions of maize was clustered into four clusters. The first cluster contained nine genotypes of maize, while the second cluster contained the four genotypes of maize. The third cluster contained 5 maize genotypes. Cluster 4 contained five genotypes from Hungary (22.73%, two genotypes from Poland (9.10%, seven genotypes of maize from Union of Soviet Socialist Republics (31.81%, six genotypes from Czechoslovakia (27.27%, one genotype from Slovak Republic (4.55% and one genotype of maize is from Yugoslavia (4.55%. We could not distinguish 4 maize genotypes grouped in cluster 4, (Voroneskaja and Kocovska Skora and 2 Hungarian maize genotypes - Feheres Sarga Filleres and Mindszentpusztai Feher, which are genetically the closest.

  16. A Novel Reference Plasmid for the Qualitative Detection of Genetically Modified Rice in Food and Feed

    OpenAIRE

    Li, Liang; Dong, Mei; An, Na; Liang, Lixia; Wan, Yusong; Jin, Wujun

    2015-01-01

    Rice is one of the most important food crops in the world. Genetically modified (GM) technology has been used in rice to confer herbicide tolerance and pathogen or insect resistance. China invests heavily in research on GM rice. By the end of 2014, at least 250 transgenic rice lines had been developed in China. To monitor the presence of GM rice in food and feed, we collected information on foreign elements from 250 transgenic rice lines and found 5 elements, including the Agrobacterium tumef...

  17. Detection and Genetic Analysis of Human Sapoviruses in River Water in Japan▿

    OpenAIRE

    Kitajima, Masaaki; Oka, Tomoichiro; Haramoto, Eiji; Katayama, Hiroyuki; Takeda, Naokazu; Katayama, Kazuhiko; Ohgaki, Shinichiro

    2010-01-01

    We investigated the prevalence of sapoviruses (SaVs) in the Tamagawa River in Japan from April 2003 to March 2004 and performed genetic analysis of the SaV genes identified in river water. A total of 60 river water samples were collected from five sites along the river, and 500 ml was concentrated using the cation-coated filter method. By use of a real-time reverse transcription (RT)-PCR assay, 12 (20%) of the 60 samples were positive for SaV. SaV sequences were obtained from 15 (25%) samples...

  18. On-chip integrated functional near infra-red spectroscopy (fNIRS) photoreceiver for portable brain imaging

    Science.gov (United States)

    Kamrani, Ehsan

    Optical brain imaging using functional near infra-red spectroscopy (fNIRS) offers a direct and noninvasive tool for monitoring of blood oxygenation. fNIRS is a noninvasive, safe, minimally intrusive, and high temporal-resolution technique for real-time and long-term brain imaging. It allows detecting both fast-neuronal and slow-hemodynamic signals. Besides the significant advantages of fNIRS systems, they still suffer from few drawbacks including low spatial-resolution, moderately high-level noise and high-sensitivity to movement. In order to overcome the limitations of currently available non-portable fNIRS systems, we have introduced a new low-power, miniaturized on-chip photodetector front-end intended for portable fNIRS systems. It includes silicon avalanche photodiode (SiAPD), Transimpedance amplifier (TIA), and Quench- Reset circuitry implemented using standard CMOS technologies to operate in both linear and Geiger modes. So it can be applied for both continuous-wave fNIRS (CW-fNIRS) and also single-photon counting applications. Several SiAPDs have been implemented in novel structures and shapes (Rectangular, Octagonal, Dual, Nested, Netted, Quadratic and Hexadecagonal) using different premature edge breakdown prevention techniques. The main characteristics of the SiAPDs are validated and the impact of each parameter and the device simulators (TCAD, COMSOL, etc.) have been studied based on the simulation and measurement results. Proposed techniques exhibit SiAPDs with high avalanche-gain (up to 119), low breakdown-voltage (around 12V) and high photon-detection efficiency (up to 72% in NIR region) in additional to a low dark-count rate (down to 30Hz at 1V excess bias voltage). Three new high gain-bandwidth product (GBW) and low-noise TIAs are introduced and implemented based on distributed-gain concept, logarithmic-amplification and automatic noise-rejection and have been applied in linear-mode of operation. The implemented TIAs offer a power

  19. A high-speed on-chip pseudo-random binary sequence generator for multi-tone phase calibration

    Science.gov (United States)

    Gommé, Liesbeth; Vandersteen, Gerd; Rolain, Yves

    2011-07-01

    An on-chip reference generator is conceived by adopting the technique of decimating a pseudo-random binary sequence (PRBS) signal in parallel sequences. This is of great benefit when high-speed generation of PRBS and PRBS-derived signals is the objective. The design implemented standard CMOS logic is available in commercial libraries to provide the logic functions for the generator. The design allows the user to select the periodicity of the PRBS and the PRBS-derived signals. The characterization of the on-chip generator marks its performance and reveals promising specifications.

  20. A high-speed on-chip pseudo-random binary sequence generator for multi-tone phase calibration

    International Nuclear Information System (INIS)

    Gommé, Liesbeth; Vandersteen, Gerd; Rolain, Yves

    2011-01-01

    An on-chip reference generator is conceived by adopting the technique of decimating a pseudo-random binary sequence (PRBS) signal in parallel sequences. This is of great benefit when high-speed generation of PRBS and PRBS-derived signals is the objective. The design implemented standard CMOS logic is available in commercial libraries to provide the logic functions for the generator. The design allows the user to select the periodicity of the PRBS and the PRBS-derived signals. The characterization of the on-chip generator marks its performance and reveals promising specifications