WorldWideScience

Sample records for on-chip genetic detection

  1. On-Chip Detection of Cellular Activity

    Science.gov (United States)

    Almog, R.; Daniel, R.; Vernick, S.; Ron, A.; Ben-Yoav, H.; Shacham-Diamand, Y.

    The use of on-chip cellular activity monitoring for biological/chemical sensing is promising for environmental, medical and pharmaceutical applications. The miniaturization revolution in microelectronics is harnessed to provide on-chip detection of cellular activity, opening new horizons for miniature, fast, low cost and portable screening and monitoring devices. In this chapter we survey different on-chip cellular activity detection technologies based on electrochemical, bio-impedance and optical detection. Both prokaryotic and eukaryotic cell-on-chip technologies are mentioned and reviewed.

  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

    2016-01-01

    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 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. PMID:27527177

  3. On-Chip Hydrodynamic Chromatography Separation and Detection of Nanoparticles and Biomolecules

    NARCIS (Netherlands)

    Blom, M.T.; Chmela, Emil; Oosterbroek, R.E.; Tijssen, Robert; van den Berg, Albert

    2003-01-01

    For the first time, on-chip planar hydrodynamic chromatography is combined with UV absorption detection. This technique is suitable for size characterization of synthetic polymers, biopolymers, and particles. Possible advantages of an on-chip hydrodynamic chromatography system over conventional

  4. Light interference detection on-chip by integrated SNSPD counters

    Directory of Open Access Journals (Sweden)

    Paul Cavalier

    2011-12-01

    Full Text Available A SWIFTS device (Stationary Wave Integrated Fourier Transform Spectrometer has been realized with an array of 24 Superconducting Nanowire Single Photon Detectors (SNSPD, on-chip integrated under a Si3N4 monomode rib-waveguide interferometer. Colored light around 1.55μm wavelength is introduced through end-fire coupling, producing a counter-propagative stationary interferogram over the 40nm wide, 120nm spaced, 4nm thick epi-NbN nanowire array. Modulations in the source bandwidth have been detected using individual waveguide coupled SNSPDs operating in single photon counting mode, which is a step towards light spectrum reconstruction by inverse Fourier transform of the stationary wave intensity. We report the design, fabrication process and in-situ measurement at 4.2K of light power modulation in the interferometer, obtained with variable laser wavelength. Such micro-SWIFTS configuration with 160nm sampling period over 3.84μm distance allows a spectral bandwidth of 2μm and a wavelength resolution of 170nm. The light interferences direct sampling ability is unique and raises wide interest with several potential applications like fringe-tracking, metrology, cryptography or optical tomography.

  5. Migration selection of strategies for parallel genetic algorithms: implementation on networks on chips

    Science.gov (United States)

    Mourelle, L.; Ferreira, R. E.; Nedjah, N.

    2010-10-01

    The aim of the work described in this article is to investigate migration strategies for the execution of parallel genetic algorithms in a multi-processor system-on-chip (MPSoC). Some multimedia and internet applications for wireless communications are using genetic algorithms and can benefit from the advantages provided by parallel processing on MPSoCs. In order to run such algorithms, we use a network-on-chip platform, which provides the interconnection network required for the communication between processors. Two migration strategies are employed in order to analyse the speedup and efficiency each one can provide, considering the communication costs they require.

  6. Scattering detection using a photonic-microfluidic integrated device with on-chip collection capabilities.

    Science.gov (United States)

    Watts, Benjamin R; Zhang, Zhiyi; Xu, Chang Qing; Cao, Xudong; Lin, Min

    2014-02-01

    SU-8-based photonic-microfluidic integrated devices with on-chip beam shaping and collection capabilities were demonstrated in a scattering detection and counting application. Through the proper deployment of the tailored beam geometries via the on-chip excitation optics, excellent CV values were measured for 1, 2, and 5 μm blank beads, 16.4, 11.0, and 12.5%, respectively, coupled with a simple free-space optical detection scheme. The performance of these devices was found dependent on the combination of on-chip, lens-shaped beam geometry and bead size. While very low CVs were obtained when the combination was ideal, a nonideal combination could still result in acceptable CVs for flow cytometry; the reliability was confirmed via devices being able to resolve separate populations of 2.0 and 5.0 μm beads from their mixture with low CV values of 15.9 and 18.5%, respectively. On-chip collection using integrated on-chip optical waveguides was shown to be very reliable in comparison with a free-space collection scheme, yielding a coincident rate of 94.2%. A CV as low as 19.2% was obtained from the on-chip excitation and collection of 5 μm beads when the on-chip lens-shaped beam had a 6.0-μm beam waist.

  7. On-chip detection performed by amorphous silicon balanced photosensor for lab-on chip application

    Directory of Open Access Journals (Sweden)

    G. de Cesare

    2015-03-01

    The experiments have been carried out measuring the differential current in several conditions. All the experiments have been executed under a large background light intensity to reproduce realistic operating conditions in biomedical applications. We have found that the proposed device is able to detect the presence or absence of water flow in the channel and the presence of fluorescent marker. In particular, under identical channel conditions the differential current is at least a factor 60 lower that the current flowing in each diode.

  8. Integrated separation and optical detection for novel on-chip chemical analysis

    Energy Technology Data Exchange (ETDEWEB)

    Warren, M.E.; Anex, D.S.; Rakestraw, D.; Gourley, P.L.

    1998-03-01

    This report represents the completion of a two years Laboratory Directed Research and Development (LDRD) program to investigate miniaturized systems for chemical detection and analysis. The future of advanced chemical detection and analysis is in miniature devices that are able to characterize increasingly complex samples, a laboratory on a chip. In this concept, chemical operations used to analyze complicated samples in a chemical laboratory sample handling, species separation, chemical derivitization and detection are incorporated into a miniature device. By using electrokinetic flow, this approach does not require pumps or valves, as fluids in microfabricated channels can be driven by externally applied voltages. This is ideal for sample handling in miniature devices. This project was to develop truly miniature on-chip optical systems based on Vertical Cavity Surface Emitting Lasers (VCSELs) and diffractive optics. These can be built into a complete system that also has on-chip electrokinetic fluid handling and chemical separation in a microfabricated column. The primary goal was the design and fabrication of an on-chip separation column with fluorescence sources and detectors that, using electrokinetic flow, can be used as the basis of an automated chemical analysis system. Secondary goals involved investigation of a dispersed fluorescence module that can be used to extend the versatility of the basic system and on chip, intracavity laser absorption as a high sensitivity detection technique.

  9. On-chip detection of ferromagnetic resonance of a single submicron Permalloy strip

    NARCIS (Netherlands)

    Costache, M. V.; Sladkov, M.; van der Wal, C. H.; van Wees, B. J.

    2006-01-01

    The authors measured ferromagnetic resonance of a single submicron ferromagnetic strip, embedded in an on-chip microwave transmission line device. The method used is based on detection of the oscillating magnetic flux due to the magnetization dynamics, with an inductive pickup loop. The dependence o

  10. Point Mutation Identification Using On-Chip Ligase Detection Reaction

    Institute of Scientific and Technical Information of China (English)

    李艳; 曾令文; 程京

    2004-01-01

    An efficient method was developed to detect point mutations using oligonucleotide microarrays and the ligase detection reaction (LDR).Allele-specific LDR primers were immobilized on polylysine-coated glass slides to perform LDR on a chip.The spotting concentration and detection limit were analyzed using a synthesized oligonucleotide as a template.The optimal primer spotting concentration was 20 (mol/L and the lowest detectable template concentration was 0.33 nmol/L.The method was successfully employed to identify malignant mutations of hypertrophic cardiomyopathy.Asymmetric polymerase chain reaction was employed to prepare single stranded DNA as LDR templates from cloned plasmids.The discrimination ratios for AC,TC,GT,TT,GA,and AA mismatches are 32.82,44.24,17.75,18.34,11.66,and 8.91,respectively.This method may allow construction of multiple mutation detection systems.

  11. On-chip optical detection of laser cooled atoms.

    Science.gov (United States)

    Quinto-Su, P; Tscherneck, M; Holmes, M; Bigelow, N

    2004-10-18

    We have used an optical fiber based system to implement optical detection of atoms trapped on a reflective "atom-chip". A fiber pair forms an emitter-detector setup that is bonded to the atom-chip surface to optically detect and probe laser cooled atoms trapped in a surface magneto-optical trap. We demonstrate the utility of this scheme by measuring the linewidth of the Cs D2 line at different laser intensities.

  12. On-chip mid-infrared gas detection using chalcogenide glass waveguide

    Science.gov (United States)

    Han, Z.; Lin, P.; Singh, V.; Kimerling, L.; Hu, J.; Richardson, K.; Agarwal, A.; Tan, D. T. H.

    2016-04-01

    We demonstrate an on-chip sensor for room-temperature detection of methane gas using a broadband spiral chalcogenide glass waveguide coupled with off-chip laser and detector. The waveguide is fabricated using UV lithography patterning and lift-off after thermal evaporation. We measure the intensity change due to the presence and concentration of methane gas in the mid-infrared (MIR) range. This work provides an approach for broadband planar MIR gas sensing.

  13. Detection of silver nanoparticles on a lab-on-chip platform.

    Science.gov (United States)

    Chua, Chun Kiang; Pumera, Martin

    2013-07-01

    The prevalent use of silver nanoparticles (AgNPs) in commercial goods has brought forth an urgent need for environmental salvation. With the global river systems being contaminated by AgNPs, fast and efficient detection systems are needed to trace the presence of AgNPs in common water to prevent detrimental effects to the public health. In this work, the detection of AgNPs via electrochemical oxidation has been achieved on a "Lab-on-chip" platform. This platform provides a fast, convenient, and portable detection system for the detection of AgNPs in common water.

  14. Low-power system-on-chip implementation for respiratory rate detection and transmission.

    Science.gov (United States)

    Padasdao, Bryson; Yee, Roxanne; Boric-Lubecke, Olga

    2012-01-01

    Recent biosensors can measure respiratory rate non-invasively, but limits patient mobility or requires regular battery replacement. Respiratory effort, which can scavenge mW, may power the sensor, but requires minimal sensor power usage. This paper demonstrates feasibility of respiratory rate measurement by using a comparator instead of ADC. A low-power system-on-chip can implement respiratory rate detection and wireless data transmission with a total power consumption under 82 µW. This approach produces significant power savings, and transmission uses under 30% of total power consumption.

  15. On-chip, self-detected THz dual-comb spectrometer

    CERN Document Server

    Rösch, Markus; Villares, Gustavo; Bosco, Lorenzo; Beck, Mattias; Faist, Jérôme

    2016-01-01

    We present a directly generated on-chip dual-comb source at THz frequencies. The multi-heterodyne beating signal of two free-running THz quantum cascade laser frequency combs is measured electrically using one of the combs as a detector, fully exploiting the unique characteristics of quantum cascade active regions. Up to 30 modes can be detected corresponding to a spectral bandwidth of 630 GHz, being the available bandwidth of the dual comb configuration. The multi-heterodyne signal is used to investigate the equidistance of the comb modes showing an accuracy of $10^{-12}$ at the carrier frequency of 2.5 THz.

  16. On-chip detection of radiation guided by dielectric-loaded plasmonic waveguides

    CERN Document Server

    Han, Zhanghua; Mazurski, Noa; Desiatov, Boris; Beermann, Jonas; Albrektsen, Ole; Levy, Uriel; Bozhevolnyi, Sergey I

    2016-01-01

    We report a novel approach for on-chip electrical detection of the radiation guided by dielectric-loaded surface plasmon polariton waveguides (DLSPPW) and DLSPPW-based components. The detection is realized by fabricating DLSPPW components on the surface of a gold (Au) pad supported by a silicon (Si) substrate supplied with aluminum pads facilitating electrical connections, with the gold pad being perforated in a specific locations below the DLSPPWs in order to allow a portion of the DLSPPW-guided radiation to leak into the Si-substrate, where it is absorbed and electrically detected. We present two-dimensional photocurrent maps obtained when the laser beam is scanning across the gold pad containing the fabricated DLSPPW components that are excited via grating couplers located at the DLSPPW tapered terminations. By comparing photocurrent signals obtained when scanning over a DLSPPW straight waveguide with those related to a DLSPPW racetrack resonator, we first determine the background signal level and then the...

  17. Nondestructive on-chip detection of optical orbital angular momentum through a single plasmonic nanohole

    CERN Document Server

    Wei, Dunzhao; Liu, Dongmei; Zhu, Yunzhi; Zhong, Weihao; Fang, Xinyuan; Zhang, Yong; Xiao, Min

    2016-01-01

    Optical orbital angular momentum (OAM) provides an additional dimension for photons to carry information in high-capacity optical communication. Although the practical needs have intrigued the generations of miniaturized devices to manipulate the OAM modes in various integrated platforms, the on-chip OAM detection is still challenging to match the newly-developed compact OAM emitter and OAM transmission fiber. Here, we demonstrate an ultra-compact device, i.e., a single plasmonic nanohole, to efficiently measure an optical beam's OAM state in a nondestructive way. The device size is reduced down to a few hundreds of nanometers, which can be easily fabricated and installed in the current OAM devices. It is a flexible and robust way for in-situ OAM monitoring and detection in optical fiber networks and long-distance optical communication systems. With proper optimization of the nanohole parameters, this approach could be further extended to discriminate the OAM information multiplexed in multiple wavelengths an...

  18. Handheld analyzer with on-chip molecularly-imprinted biosensors for electrical detection of propofol in plasma samples.

    Science.gov (United States)

    Hong, Chien-Chong; Lin, Chih-Chung; Hong, Chian-Lang; Lin, Zi-Xiang; Chung, Meng-Hua; Hsieh, Pei-Wen

    2016-12-15

    This paper proposes a novel handheld analyzer with disposable lab-on-a-chip technology for the electrical detection of the anesthetic propofol in human plasma samples for clinical diagnoses. The developed on-chip biosensors are based on the conduction of molecularly imprinted polymers (MIPs) that employ label-free electrical detection techniques. Propofol in total intravenous anesthesia is widely used with a target-controlled infusion system. At present, the methods employed for detecting blood propofol concentrations in hospitals comprise high-performance liquid chromatography and ion mobility spectrometry. These conventional instruments are bulky, expensive, and difficult to access. In this study, we developed a novel plastic microfluidic biochip with an on-chip anesthetic biosensor that was characterized for the rapid detection of propofol concentrations. The experimental results revealed that the response time of the developed propofol biosensors was 25s. The specific binding of an MIP to a nonimprinted polymer (NIP) reached up to 560%. Moreover, the detection limit of the biosensors was 0.1μg/mL, with a linear detection range of 0.1-30μg/mL. The proposed disposable microfluidic biochip with an on-chip anesthetic biosensor using MIPs exhibited excellent performance in the separation and sensing of propofol molecules in the human plasma samples. Compared with large-scale conventional instruments, the developed microfluidic biochips with on-chip MIP biosensors present the advantages of a compact size, high selectivity, low cost, rapid response, and single-step detection.

  19. Integration of programmable microfluidics and on-chip fluorescence detection for biosensing applications

    Science.gov (United States)

    Parks, J. W.; Olson, M. A.; Kim, J.; Ozcelik, D.; Cai, H.; Carrion, R.; Patterson, J. L.; Mathies, R. A.; Hawkins, A. R.; Schmidt, H.

    2014-01-01

    We describe the integration of an actively controlled programmable microfluidic sample processor with on-chip optical fluorescence detection to create a single, hybrid sensor system. An array of lifting gate microvalves (automaton) is fabricated with soft lithography, which is reconfigurably joined to a liquid-core, anti-resonant reflecting optical waveguide (ARROW) silicon chip fabricated with conventional microfabrication. In the automaton, various sample handling steps such as mixing, transporting, splitting, isolating, and storing are achieved rapidly and precisely to detect viral nucleic acid targets, while the optofluidic chip provides single particle detection sensitivity using integrated optics. Specifically, an assay for detection of viral nucleic acid targets is implemented. Labeled target nucleic acids are first captured and isolated on magnetic microbeads in the automaton, followed by optical detection of single beads on the ARROW chip. The combination of automated microfluidic sample preparation and highly sensitive optical detection opens possibilities for portable instruments for point-of-use analysis of minute, low concentration biological samples. PMID:25584111

  20. Integration of programmable microfluidics and on-chip fluorescence detection for biosensing applications.

    Science.gov (United States)

    Parks, J W; Olson, M A; Kim, J; Ozcelik, D; Cai, H; Carrion, R; Patterson, J L; Mathies, R A; Hawkins, A R; Schmidt, H

    2014-09-01

    We describe the integration of an actively controlled programmable microfluidic sample processor with on-chip optical fluorescence detection to create a single, hybrid sensor system. An array of lifting gate microvalves (automaton) is fabricated with soft lithography, which is reconfigurably joined to a liquid-core, anti-resonant reflecting optical waveguide (ARROW) silicon chip fabricated with conventional microfabrication. In the automaton, various sample handling steps such as mixing, transporting, splitting, isolating, and storing are achieved rapidly and precisely to detect viral nucleic acid targets, while the optofluidic chip provides single particle detection sensitivity using integrated optics. Specifically, an assay for detection of viral nucleic acid targets is implemented. Labeled target nucleic acids are first captured and isolated on magnetic microbeads in the automaton, followed by optical detection of single beads on the ARROW chip. The combination of automated microfluidic sample preparation and highly sensitive optical detection opens possibilities for portable instruments for point-of-use analysis of minute, low concentration biological samples.

  1. Conditions for efficient on-chip magnetic bead detection via magnetoresistive sensors.

    Science.gov (United States)

    Albisetti, E; Petti, D; Cantoni, M; Damin, F; Torti, A; Chiari, M; Bertacco, R

    2013-09-15

    A commonly used figure of merit of magnetoresistive sensors employed to detect magnetic beads labeling biomolecules in lab-on-chip applications is the sensor sensitivity (S0) to external magnetic fields in the linear region of the sensor. In this paper we show that, in case of lock-in detection and bead excitation by a small AC magnetic field, S0 is not the good figure of merit to optimize. Indeed, the highest sensitivity to the magnetic beads is achieved biasing the sensor in the region of its characteristics where the product between the DC bias field and the second derivative of the resistance with respect to the magnetic field is maximum. The validity of this criterion, derived from a phenomenological model of bead detection, is proved in case of magnetic tunneling junction sensors detecting magnetic beads with 250nm diameter. This work paves the way to the development of a new generation of sensors properly designed to maximize the bead sensitivity.

  2. On-chip purification and detection of hepatitis C virus RNA from human plasma.

    Science.gov (United States)

    Vaghi, V; Potrich, C; Pasquardini, L; Lunelli, L; Vanzetti, L; Ebranati, E; Lai, A; Zehender, G; Mombello, D; Cocuzza, M; Pirri, C F; Pederzolli, C

    2016-01-01

    Hepatitis C virus (HCV) is one of the main causes of chronic liver disease worldwide. The diagnosis and monitoring of HCV infection is a crucial need in the clinical management. The conventional diagnostic technologies are challenged when trying to address molecular diagnostics, especially because they require a complex and time-consuming sample preparation phase. Here, a new concept based on surface functionalization was applied to viral RNA purification: first of all polydimethylsiloxane (PDMS) flat surfaces were modified to hold RNA adsorption. After a careful chemical and morphological analysis of the modified surfaces, the functionalization protocols giving the best RNA adsorbing surfaces were applied to PDMS microdevices. The functionalized microdevices were then used for RNA purification from HCV infected human plasma samples. RNA purification and RT were successfully performed in the same microdevice chamber, saving time of analysis, reagents, and labor. The PCR protocol for HCV cDNA amplification was also implemented in the microdevice, demonstrating that the entire process of HCV analysis, from plasma to molecular readout, could be performed on-chip. Not only HCV but also other microdevice-based viral RNA detection could therefore result in a successful Point-of-Care (POC) diagnostics for resource-limited settings. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Smart Integrated Sensor for Multiple Detections of Glucose and L-Lactate Using On-Chip Electrochemical System

    Directory of Open Access Journals (Sweden)

    Tomoyuki Yamazaki

    2011-01-01

    Full Text Available Multiple sensor electrodes, a supplementary electrode, a reference electrode, and signal-processing circuits were integrated on a single chip to develop a chip-shaped electrochemical sensing system. L-lactate and glucose were measured using on-chip working electrodes modified by polyion complex to immobilize lactate oxidase and glucose oxidase, respectively. Cyclic voltammetry measurements were conducted using an on-chip potentiostat. Selective and quantitative detection of glucose and L-lactate and the interference behavior were studied. Hydrogen peroxide generated by enzymatic reactions was detected by an increase in anodic oxidation current. Reaction currents at +0.7 V versus Ag/AgCl were used to obtain calibration plots. The measured dynamic ranges for L-lactate and glucose were 0.2–1.0 mM and 2.0–8.0 mM, respectively. The sensitivities were 65 nA/mM and 15 nA/mM, respectively, using a working electrode of 0.5 mm2. The 3σ detection limit was 0.19 mM and 1.1 mM, respectively. We have achieved multiple biomaterial detections on a circuit-equipped single chip. This integrated electrochemical sensor chip could be the best candidate for realizing point-of-care testing due to its portability and potential for mass production.

  4. Lab-on-chip microfluidic impedance measurement for laminar flow ratio sensing and differential conductivity difference detection

    Science.gov (United States)

    Kong, Tian Fook; Shen, Xinhui; Marcos, Yang, Chun

    2017-06-01

    We present a microfluidic impedance device for achieving both the flow ratio sensing and the conductivity difference detection between sample stream and reference buffer. By using a flow focusing configuration, with the core flow having a higher conductivity sample than the sheath flow streams, the conductance of the device varies linearly with the flow ratio, with R2 > 0.999. On the other hand, by using deionized (DI)-water sheath flow as a reference, we can detect the difference in conductivity between the buffer of core flow and sheath DI-water with a high detection sensitivity of up to 1 nM of sodium chloride solution. Our study provides a promising approach for on-chip flow mixing characterization and bacteria detection.

  5. On-Chip Microplasmas for the Detection of Radioactive Cesium Contamination in Seawater

    Directory of Open Access Journals (Sweden)

    Joshua B. Joffrion

    2017-08-01

    Full Text Available On-chip microplasmas have previously been used in designing a compact and portable device for identifying pollutants in a water sample. By exciting a liquid sample with a high energy microdischarge and recording the spectral wavelengths emitted, the individual elements in the liquid are distinguishable. In particular, this study focuses on cesium, a contaminant from nuclear incidents such as the collapse of the nuclear power plant in Fukushima, Japan. This article shows that not only can the presence of cesium be clearly determined at concentrations as low as 10 ppb, but the relative concentration contained in the sample can be determined through the discharges’ relative spectral intensity.

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

    Science.gov (United States)

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

    2015-12-15

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

  7. 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.

  8. 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

  9. A novel lab-on-chip platform with integrated solid phase PCR and Supercritical Angle Fluorescence (SAF) microlens array for highly sensitive and multiplexed pathogen detection

    DEFF Research Database (Denmark)

    Hung, Tran Quang; Chin, Wai Hoe; Sun, Yi

    2016-01-01

    Solid-phase PCR (SP-PCR) has become increasingly popular for molecular diagnosis and there have been a few attempts to incorporate SP-PCR into lab-on-a-chip (LOC) devices. However, their applicability for on-line diagnosis is hindered by the lack of sensitive and portable on-chip optical detectio......-PCR and SAF microlens array allows for on-chip highly sensitive and multiplexed pathogen detection with low-cost and compact optical components. The LOC platform would be widely used as a high-throughput biosensor to analyze food, clinical and environmental samples....

  10. Detection of urinary tract infections on lab-on-chip device by measuring photons emitted from ATP bioluminescence.

    Science.gov (United States)

    Feng, Shilun; Dong, Tao; Yang, Zhaochu

    2014-01-01

    A microfluidic Lab-on-chip (LOC) platform for in vitro detecting Urinary Tract Infections (UTI) for clinical diagnostic applications has been built. Based on one commercial adenosine 5'-triphosphate (ATP) assay kit, one chip designed before was applied to detect UTI with the help of photomultiplier tube (PMT) and quantitative determination was made by measuring the photons of light emitted in the bioluminescent reaction of ATP with the enzyme luciferase. The chip had been tested and materials had been well prepared before testing the PMT detecting system. The data from PMT were visualized by the Labview™, appearing good linearity between voltage values and the concentration of the ATP ranging from 2×10(-12) M to 2×10(-8) M. Fresh urine sample with different amounts of Escherichia coli had been measured by the system, appearing good linearity trend between the voltage values and number of the E.coli. This study successfully expressed the concept of measuring ATP directly in the urine to quickly and accurately detect UTI on a microfluidic chip.

  11. A polymer lab-on-a-chip for magnetic immunoassay with on-chip sampling and detection capabilities.

    Science.gov (United States)

    Do, Jaephil; Ahn, Chong H

    2008-04-01

    This paper presents a new polymer lab-on-a-chip for magnetic bead-based immunoassay with fully on-chip sampling and detection capabilities, which provides a smart platform of magnetic immunoassay-based lab-on-a-chip for point-of-care testing (POCT) toward biochemical hazardous agent detection, food inspection or clinical diagnostics. In this new approach, the polymer lab-on-a-chip for magnetic bead-based immunoassay consists of a magnetic bead-based separator, an interdigitated array (IDA) micro electrode, and a microfluidic system, which are fully incorporated into a lab-on-a-chip on cyclic olefin copolymer (COC). Since the polymer lab-on-a-chip was realized using low cost, high throughput polymer microfabrication techniques such as micro injection molding and hot embossing method, a disposable polymer lab-on-a-chip for the magnetic bead-based immunoassay can be successfully realized in a disposable platform. With this newly developed polymer lab-on-a-chip, an enzyme-labelled electrochemical immunoassay (ECIA) was performed using magnetic beads as the mobile solid support, and the final enzyme product produced from the ECIA was measured using chronoamperometry. A sampling and detection of as low as 16.4 ng mL(-1) of mouse IgG has been successfully performed in 35 min for the entire procedure.

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

    Energy Technology Data Exchange (ETDEWEB)

    Shao, Guocheng; Wang, Jun; Li, Zhaohui; Saraf, Laxmikant V.; Wang, Wanjun; Lin, Yuehe

    2011-09-20

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

  13. Lab-on-Chip Cytometry Based on Magnetoresistive Sensors for Bacteria Detection in Milk

    Directory of Open Access Journals (Sweden)

    Ana C. Fernandes

    2014-08-01

    Full Text Available Flow cytometers have been optimized for use in portable platforms, where cell separation, identification and counting can be achieved in a compact and modular format. This feature can be combined with magnetic detection, where magnetoresistive sensors can be integrated within microfluidic channels to detect magnetically labelled cells. This work describes a platform for in-flow detection of magnetically labelled cells with a magneto-resistive based cell cytometer. In particular, we present an example for the validation of the platform as a magnetic counter that identifies and quantifies Streptococcus agalactiae in milk.

  14. Off surface matrix based on-chip electrochemical biosensor platform for protein biomarker detection in undiluted serum.

    Science.gov (United States)

    Arya, Sunil K; Kongsuphol, Patthara; Park, Mi Kyoung

    2017-06-15

    The manuscript describes a concept of using off surface matrix modified with capturing biomolecule for on-chip electrochemical biosensing. 3D matrix made by laser engraving of polymethyl methacrylate (PMMA) sheet as off surface matrix was integrated in very close vicinity of the electrode surface. Laser engraving and holes in PMMA along with spacing from surface provide fluidic channel and incubation chamber. Covalent binding of capturing biomolecule (anti-TNF-α antibody) on off-surface matrix was achieved via azide group activity of 4-fluoro-3-nitro-azidobenzene (FNAB), which act as cross-linker and further covalently binds to anti-TNF-α antibody via thermal reaction. Anti-TNF-α/FNAB/PMMA matrix was then integrated over comb structured gold electrode array based sensor chip. Separate surface modification followed by integration of sensor helped to prevent the sensor chip surface from fouling during functionalization. Nonspecific binding was prevented using starting block T20 (PBS). Results for estimating protein biomarker (TNF-α) in undiluted serum using Anti-TNF-α/FNAB/PMMA/Au reveal that system can detect TNF-α in 100pg/ml to 100ng/ml range with high sensitivity of 119nA/(ng/ml), with negligible interference from serum proteins and other cytokines. Thus, use of off surface matrix may provide the opportunity to electrochemically sense biomarkers sensitively to ng/ml range with negligible nonspecific binding and false signal in undiluted serum.

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

    Science.gov (United States)

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

    2008-01-01

    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. PMID:18710880

  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 detection of a single nucleotide polymorphism without polymerase amplification.

    Science.gov (United States)

    Han, Jinhee; Tan, Matthew; Sudheendra, Lakshmana; Weiss, Robert H; Kennedy, Ian M

    2014-09-01

    A nanoparticle-assembled photonic crystal (PC) array was used to detect single nucleotide polymorphism (SNP). The assay platform with PC nanostructure enhanced the fluorescent signal from nanoparticle-hybridized DNA complexes due to phase matching of excitation and emission. Nanoparticles coupled with probe DNA were trapped into nanowells in an array by using an electrophoretic particle entrapment system. The PC/DNA assay platform was able to identify a 1 base pair (bp) difference in synthesized nucleotide sequences that mimicked the mutation seen in a feline model of human autosomal dominant polycystic kidney disease (PKD) with a sensitivity of 0.9 fg/mL (50 aM)-sensitivity, which corresponds to 30 oligos/array. The reliability of the PC/DNA assay platform to detect SNP in a real sample was demonstrated by using genomic DNA (gDNA) extracted from the urine and blood of two PKD(-) wild type and three PKD positive cats. The standard curves for PKD positive (PKD(+)) and negative (PKD(-)) DNA were created using two feline-urine samples. An additional three urine samples were analyzed in a similar fashion and showed satisfactory agreement with the standard curve, confirming the presence of the mutation in affected urine. The limit of detection (LOD) was 0.005 ng/mL which corresponds to 6 fg per array for gDNA in urine and blood. The PC system demonstrated the ability to detect a number of genome equivalents for the PKD SNP that was very similar to the results reported with real time polymerase chain reaction (PCR). The favorable comparison with quantitative PCR suggests that the PC technology may find application well beyond the detection of the PKD SNP, into areas where a simple, cheap and portable nucleic acid analysis is desirable.

  18. Capillary flow of blood in a microchannel with differential wetting for blood plasma separation and on-chip glucose detection.

    Science.gov (United States)

    Maria, M Sneha; Rakesh, P E; Chandra, T S; Sen, A K

    2016-09-01

    We report capillary flow of blood in a microchannel with differential wetting for the separation of a plasma from sample blood and subsequent on-chip detection of glucose present in a plasma. A rectangular polydimethylsiloxane microchannel with hydrophilic walls (on three sides) achieved by using oxygen plasma exposure enables capillary flow of blood introduced at the device inlet through the microchannel. A hydrophobic region (on all four sides) in the microchannel impedes the flow of sample blood, and the accumulated blood cells at the region form a filter to facilitate the separation of a plasma. The modified wetting property of the walls and hence the device performance could be retained for a few weeks by covering the channels with deionised water. The effects of the channel cross-section, exposure time, waiting time, and location and length of the hydrophobic region on the volume of the collected plasma are studied. Using a channel cross-section of 1000 × 400 μm, an exposure time of 2 min, a waiting time of 10 min, and a hydrophobic region of width 1.0 cm located at 10 mm from the device inlet, 450 nl of plasma was obtained within 15 min. The performance of the device was found to be unaffected (provides 450 nl of plasma in 15 min) even after 15 days. The purification efficiency and plasma recovery of the device were measured and found to be comparable with that obtained using the conventional centrifugation process. Detection of glucose at different concentrations in whole blood of normal and diabetic patients was performed (using 5 μl of sample blood within 15 min) to demonstrate the compatibility of the device with integrated detection modules.

  19. 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.

  20. On-Chip Detection of Entangled Photons by Scalable Integration of Single-Photon Detectors

    CERN Document Server

    Najafi, Faraz; Harris, Nicholas; Bellei, Francesco; Dane, Andrew; Lee, Catherine; Kharel, Prashanta; Marsili, Francesco; Assefa, Solomon; Berggren, Karl K; Englund, Dirk

    2014-01-01

    Photonic integrated circuits (PICs) have emerged as a scalable platform for complex quantum technologies using photonic and atomic systems. A central goal has been to integrate photon-resolving detectors to reduce optical losses, latency, and wiring complexity associated with off-chip detectors. Superconducting nanowire single-photon detectors (SNSPDs) are particularly attractive because of high detection efficiency, sub-50-ps timing jitter, nanosecond-scale reset time, and sensitivity from the visible to the mid-infrared spectrum. However, while single SNSPDs have been incorporated into individual waveguides, the system efficiency of multiple SNSPDs in one photonic circuit has been limited below 0.2% due to low device yield. Here we introduce a micrometer-scale flip-chip process that enables scalable integration of SNSPDs on a range of PICs. Ten low-jitter detectors were integrated on one PIC with 100% device yield. With an average system efficiency beyond 10% for multiple SNSPDs on one PIC, we demonstrate h...

  1. On-chip free-flow magnetophoresis: Separation and detection of mixtures of magnetic particles in continuous flow

    NARCIS (Netherlands)

    Pamme, Nicole; Eijkel, Jan C.T.; Manz, Andreas

    2006-01-01

    The complete separation of mixtures of magnetic particles was achieved by on-chip free-flow magnetophoresis. In continuous flow, magnetic particles were deflected from the direction of larninar flow by a perpendicular magnetic field depending on their magnetic susceptibility and size and on the flow

  2. On-Chip Isothermal Nucleic Acid Amplification on Flow-Based Chemiluminescence Microarray Analysis Platform for the Detection of Viruses and Bacteria.

    Science.gov (United States)

    Kunze, A; Dilcher, M; Abd El Wahed, A; Hufert, F; Niessner, R; Seidel, M

    2016-01-01

    This work presents an on-chip isothermal nucleic acid amplification test (iNAAT) for the multiplex amplification and detection of viral and bacterial DNA by a flow-based chemiluminescence microarray. In a principle study, on-chip recombinase polymerase amplification (RPA) on defined spots of a DNA microarray was used to spatially separate the amplification reaction of DNA from two viruses (Human adenovirus 41, Phi X 174) and the bacterium Enterococcus faecalis, which are relevant for water hygiene. By establishing the developed assay on the microarray analysis platform MCR 3, the automation of isothermal multiplex-amplification (39 °C, 40 min) and subsequent detection by chemiluminescence imaging was realized. Within 48 min, the microbes could be identified by the spot position on the microarray while the generated chemiluminescence signal correlated with the amount of applied microbe DNA. The limit of detection (LOD) determined for HAdV 41, Phi X 174, and E. faecalis was 35 GU/μL, 1 GU/μL, and 5 × 10(3) GU/μL (genomic units), which is comparable to the sensitivity reported for qPCR analysis, respectively. Moreover the simultaneous amplification and detection of DNA from all three microbes was possible. The presented assay shows that complex enzymatic reactions like an isothermal amplification can be performed in an easy-to-use experimental setup. Furthermore, iNAATs can be potent candidates for multipathogen detection in clinical, food, or environmental samples in routine or field monitoring approaches.

  3. A novel lab-on-chip platform with integrated solid phase PCR and Supercritical Angle Fluorescence (SAF) microlens array for highly sensitive and multiplexed pathogen detection.

    Science.gov (United States)

    Hung, Tran Quang; Chin, Wai Hoe; Sun, Yi; Wolff, Anders; Bang, Dang Duong

    2017-04-15

    Solid-phase PCR (SP-PCR) has become increasingly popular for molecular diagnosis and there have been a few attempts to incorporate SP-PCR into lab-on-a-chip (LOC) devices. However, their applicability for on-line diagnosis is hindered by the lack of sensitive and portable on-chip optical detection technology. In this paper, we addressed this challenge by combining the SP-PCR with super critical angle fluorescence (SAF) microlens array embedded in a microchip. We fabricated miniaturized SAF microlens array as part of a microfluidic chamber in thermoplastic material and performed multiplexed SP-PCR directly on top of the SAF microlens array. Attribute to the high fluorescence collection efficiency of the SAF microlens array, the SP-PCR assay on the LOC platform demonstrated a high sensitivity of 1.6 copies/µL, comparable to off-chip detection using conventional laser scanner. The combination of SP-PCR and SAF microlens array allows for on-chip highly sensitive and multiplexed pathogen detection with low-cost and compact optical components. The LOC platform would be widely used as a high-throughput biosensor to analyze food, clinical and environmental samples.

  4. Uniform droplet splitting and detection using Lab-on-Chip flow cytometry on a microfluidic PDMS device

    DEFF Research Database (Denmark)

    Kunstmann-Olsen, Casper; Hanczyc, Martin; Hoyland, James

    2016-01-01

    A PDMS chip is fabricated using soft lithography and applied to investigate the formation and division of nitrobenzene (NB) droplets in a two-phase system stabilized by oleic acid. Using an integrated on-chip flow cytometer setup, effected with optical fibers, droplet size distributions...... are analyzed in situ based on optical signal intensities. By controlling the hydrodynamic flow focusing, uniform droplets of sizes between 100 μm and 300 μm are created with precise size control. Cross-flow shearing allows one to divide these droplets into anything from 2 to 9 individual droplets, depending...

  5. Ion chromatography on-chip.

    Science.gov (United States)

    Murrihy, J P; Breadmore, M C; Tan, A; McEnery, M; Alderman, J; O'Mathuna, C; O'Neill, A P; O'Brien, P; Avdalovic, N; Haddad, P R; Glennon, J D; Advoldvic, N

    2001-07-27

    On-chip separation of inorganic anions by ion-exchange chromatography was realized. Micro separation channels were fabricated on a silicon wafer and sealed with a Pyrex cover plate using standard photolithography, wet and dry chemical etching, and anodic bonding techniques. Quaternary ammonium latex particles were employed for the first time to coat the separation channels on-chip. Owing to the narrow depths of the channels on the chip, 0.5-10 microm, there were more interactions of the analytes with the stationary phase on the chip than in a 50-microm I.D. capillary. With off-chip injection (20 nl) and UV detection, NO2-, NO3-, I-, and thiourea were separated using 1 mM KCl as the eluent. The linear ranges for NO2- and NO3- are from 5 to 1000 microM with the detection limits of 0.5 microM.

  6. A low-cost, label-free DNA detection method in lab-on-chip format based on electrohydrodynamic instabilities, with application to long-range PCR.

    Science.gov (United States)

    Diakité, Mohamed Lemine Youba; Champ, Jerôme; Descroix, Stephanie; Malaquin, Laurent; Amblard, François; Viovy, Jean-Louis

    2012-11-21

    In order to evolve from a "chip in the lab" to a "lab on a chip" paradigm, there is still a strong demand for low-cost, portable detection technologies, notably for analytes at low concentrations. Here we report a new label-free DNA detection method with direct electronic read, and apply it to long-range PCR. This method uses a nonlinear electrohydrodynamic phenomenon: when subjected to high electric fields (typically above 100 V cm(-1)), suspensions of large polyelectrolytes, such as long DNA molecules, create "giant" dynamic concentration fluctuations. These fluctuations are associated with large conductivity inhomogeneities, and we use here a contact-mode local conductivity detector to detect these fluctuations. In order to decouple the detection electronics from the high voltage excitation one, an original "doubly symmetric" floating mode battery-operated detection scheme was developed. A wavelet analysis was then applied, to unravel from the chaotic character of the electohydrodynamic instabilities a scalar signal robustly reflecting the amplification of DNA. As a first proof of concept, we measured the products of the off-chip amplification of 10 kbp DNA from lambda phage DNA, achieving a sensitivity better than 100 fg DNA in the original 50 μl sample. This corresponds to the amplification products of less than 100 initial copies of target DNA. The companion enabling technologies developed to implement this new concept, i.e. the doubly symmetric contact conductivity detection and wavelet analysis, may also find various other applications in lab-on-chips.

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

    KAUST Repository

    Gooneratne, Chinthaka P.

    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

  8. 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.

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

    Science.gov (United States)

    Gooneratne, Chinthaka P; Kodzius, Rimantas; Li, Fuquan; Foulds, Ian G; Kosel, Jürgen

    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.

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

    National Research Council Canada - National Science Library

    Francesca Costantini; Cristiana Sberna; Giulia Petrucci; Cesare Manetti; Giampiero de Cesare; Augusto Nascetti; Domenico Caputo

    2015-01-01

    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...

  11. 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.

  12. 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.

  13. 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

    , which makes the setup very compact. Limits of detection down to 500 Bacillus globigii spores and 2 pM of Vibrio cholerae are demonstrated, which are on the same order of magnitude or lower than those achieved previously using a commercial macro-scale AC susceptometer. The chipbased readout...

  14. On-chip SERS analysis for single mimic pathogen detection using Raman-labeled nanoaggregate-embedded beads with a dielectrophoretic chip

    Science.gov (United States)

    Huang, Chen-Han; Lin, Hsing-Ying; Kuo, I.-Ting; Hsieh, Wen-Hsin; Huang, Ping-Ji; Yang, Tzyy-Schiuan; Chau, Lai-Kwan

    2012-02-01

    The integration of Raman-labeled nanoaggregate-embedded beads (NAEBs) for high performance SERS analysis of single mimic pathogen on a self-designed dielectrophoretic chip is demonstrated. The Raman tags called NAEBs are silica-coated, dye-induced aggregates of a small number of gold nanoparticles (AuNPs). In this work, NAEBs consisting of a Raman dye tetramethyl-rhodamine-5-isothiosyanate (TRITC) are chemically functionalized with streptavidin to detect biotin-functionalized polystyrene (PS) microspheres which mimic as pathogens. The sample solution of completely mixed streptavidin-functionalized NAEBs and biotin-functionalized PS microspheres is pumped into the microfluidic channel of a dielectrophoretic chip. By giving an AC voltage on the embedded electrodes, a single mimic pathogen can be caught via the non-contact dielectrophoretic force and suspended at the central cross of four aluminum electrodes for subsequent Raman spectroscopic detection. The SERS signal of TRITC is used as a spectral signature of specific mimic pathogen recognition, otherwise only the background Raman signal of a PS microsphere is observed. A pathogen-specific biosensor based on the dielectrophoresis-Raman spectroscopy system is developed, and the proof-ofconcept is confirmed by the specific molecular interaction model of streptavidin with biotin. Therefore, the on-chip multiplex SERS analysis of pathogens can be anticipated by employing different dye-tagged NAEBs simultaneously in a sample solution. We believe this bioassay has the ability to screen and detect multiple pathogens with minimal sample processing and handling even a small number of pathogens is present.

  15. On-chip immune cell activation and subsequent time-resolved magnetic bead-based cytokine detection.

    Science.gov (United States)

    Kongsuphol, Patthara; Liu, Yunxiao; Ramadan, Qasem

    2016-10-01

    Cytokine profiling and immunophenotyping offer great potential for understanding many disease mechanisms, personalized diagnosis, and immunotherapy. Here, we demonstrate a time-resolved detection of cytokine from a single cell cluster using an in situ magnetic immune assay. An array of triple-layered microfluidic chambers was fabricated to enable simultaneous cell culture under perfusion flow and detection of the induced cytokines at multiple time-points. Each culture chamber comprises three fluidic compartments which are dedicated to, cell culture, perfusion and immunoassay. The three compartments are separated by porous membranes, which allow the diffusion of fresh nutrient from the perfusion compartment into the cell culture compartment and cytokines secretion from the cell culture compartment into the immune assay compartment. This structure hence enables capturing the released cytokines without disturbing the cell culture and without minimizing benefit gain from perfusion. Functionalized magnetic beads were used as a solid phase carrier for cytokine capturing and quantification. The cytokines released from differential stimuli were quantified in situ in non-differentiated U937 monocytes and differentiated macrophages.

  16. Microfluidic on chip viscometers.

    Science.gov (United States)

    Chevalier, J; Ayela, F

    2008-07-01

    We present the design and the process of fabrication of micromachined capillary on chip rheometers which have performed wall shear stress and shear rate measurements on silicon oil and ethanol-based nanofluids. The originality of these devices comes from the fact that local pressure drop measurements are performed inside the microchannels. Thus, the advantage over existing microviscometers is that they can be used with the fluid under test alone; no reference fluid nor posttreatment of the data are needed. Each on chip viscometer consists of anodically bonded silicon-Pyrex derivative microchannels equipped with local probes. The anodic bonding allows to reach relatively high pressure levels (up to approximately 10 bars) in the channels, and a broad range of shear stress and shear rate values is attainable. Dielectrophoretic and electrorheological effects can be highlighted by employing alternate microstripe electrodes patterned onto the inner side of the Pyrex wall.

  17. Influence of Self-Assembled Alkanethiol Monolayers on Stochastic Amperometric On-Chip Detection of Silver Nanoparticles.

    Science.gov (United States)

    Krause, Kay J; Adly, Nouran; Yakushenko, Alexey; Schnitker, Jan; Mayer, Dirk; Offenhäusser, Andreas; Wolfrum, Bernhard

    2016-04-01

    We investigate the influence of self-assembled alkanethiol monolayers at the surface of platinum microelectrode arrays on the stochastic amperometric detection of citrate-stabilized silver nanoparticles in aqueous solutions. The measurements were performed using a microelectrode array featuring 64 individually addressable electrodes that are recorded in parallel with a sampling rate of 10 kHz for each channel. We show that both the functional end group and the total length of the alkanethiol influence the charge transfer. Three different terminal groups, an amino, a hydroxyl, and a carboxyl, were investigated using two different molecule lengths of 6 and 11 carbon atoms. Finally, we show that a monolayer of alkanethiols with a length of 11 carbon atoms and a carboxyl terminal group can efficiently block the charge transfer of free nanoparticles in an aqueous solution.

  18. 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.                          

  19. 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

    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.

  20. Transient and permanent error control for networks-on-chip

    CERN Document Server

    Yu, Qiaoyan

    2012-01-01

    This book addresses reliability and energy efficiency of on-chip networks using a configurable error control coding (ECC) scheme for datalink-layer transient error management. The method can adjust both error detection and correction strengths at runtime by varying the number of redundant wires for parity-check bits. Methods are also presented to tackle joint transient and permanent error correction, exploiting the redundant resources already available on-chip. A parallel and flexible network simulator is also introduced, which facilitates examining the impact of various error control methods on network-on-chip performance. Includes a complete survey of error control methods for reliable networks-on-chip, evaluated for reliability, energy and performance metrics; Provides analysis of error control in various network-on-chip layers, as well as presentation of an innovative multi-layer error control coding technique; Presents state-of-the-art solutions to address simultaneously reliability, energy and performan...

  1. Detecting lateral genetic material transfer

    CERN Document Server

    Calderón, C; Mireles, V; Miramontes, P

    2012-01-01

    The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several semilocal variables that depend on DNA primary sequence and that reflect thermodynamic as well as physico-chemical magnitudes that are able to tell apart the genome of different organisms. After combining these variables in a neural classificator, we obtain results whose power of resolution go as far as to detect the exchange of genomic material between bacteria that are phylogenetically close.

  2. 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.

  3. Adaptive Genetic Algorithm Model for Intrusion Detection

    Directory of Open Access Journals (Sweden)

    K. S. Anil Kumar

    2012-09-01

    Full Text Available Intrusion detection systems are intelligent systems designed to identify and prevent the misuse of computer networks and systems. Various approaches to Intrusion Detection are currently being used, but they are relatively ineffective. Thus the emerging network security systems need be part of the life system and this ispossible only by embedding knowledge into the network. The Adaptive Genetic Algorithm Model - IDS comprising of K-Means clustering Algorithm, Genetic Algorithm and Neural Network techniques. Thetechnique is tested using multitude of background knowledge sets in DARPA network traffic datasets.

  4. On-chip electrical detection of parallel loop-mediated isothermal amplification with DG-BioFETs for the detection of foodborne bacterial pathogens

    Science.gov (United States)

    The use of field effect transistors (FETs) as the transduction element for the detection of DNA amplification reactions will enable portable and inexpensive nucleic acid analysis. Transistors used as biological sensors,or BioFETs, minimize the cost and size of detection platforms by leveraging fabri...

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

    National Research Council Canada - National Science Library

    Tan, Jeslin J L; Capozzoli, Monica; Sato, Mitsuharu; Watthanaworawit, Wanitda; Ling, Clare L; Mauduit, Marjorie; Malleret, Benoît; Grüner, Anne-Charlotte; Tan, Rosemary; Nosten, François H; Snounou, Georges; Rénia, Laurent; Ng, Lisa F P

    2014-01-01

    .... 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...

  6. 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....

  7. Lab-on-chip for the detection of food borne pathogenic bacteria%微流体芯片技术检测食源性致病菌的应用研究

    Institute of Scientific and Technical Information of China (English)

    陈炯; 屠丽红; 陈艳新; 秦胜营

    2014-01-01

    Objective To set up an onsite protocol for abrupt emergencies of public health e-vents, with both the sensitivity and accuracy of the lab-on-chip(microfluidic chip), for the detection of food borne pathogenic bacterium including Vibrio cholera , Salmonella , Vibrio parahaemolyticus and Shigellaare exanimated . [ Methods] By comparison of the results from the chips and fluorescence quantitative PCR were analyzed the specificity , sensitivity, accuracy and repeatability of the Lab-on-chip. [ Results] Acceptable specificity , accuracy and repeatability of the chips had been well achieved , the detection limit of the chips for the Vibrio cholera , Salmonella, Vibrio parahaemolyticus and Shigella was 5 ×103 ~103 DNA Copies/mL. [ Conclusion] Lab-on-chip is believed to be a fast , convenient , efficient tool with accept-able accuracy for public health emergencies .%[目的]通过应用微流体芯片( lab-on-chip)技术检测食源性致病菌,包括霍乱弧菌、沙门菌、副溶血性弧菌、志贺菌等细菌的灵敏度和精确度,从而建立突发公共卫生事件现场实验室的解决方案。[方法]分别采用Lab-on-chip平台食源性病原体微流检测芯片和荧光PCR方法对食源性病原菌样本进行检测,对比分析食源性微流芯片检测方法的特异性、敏感度、准确性和重复性。根据Lab-on-chip说明书以及荧光定量PCP试剂盒操作说明进行操作。[结果] Lab-on-chip方法的霍乱弧菌、沙门菌、志贺菌、副溶血性弧菌检出限为5×103~103 DNA Copies/mL。特异性、准确性和重复性都获得了良好的结果。[结论] Lab-on-chip方法具有快速、便捷、高效、准确等优点,可以在突发公共卫生事件中作为良好的检测工具和方法。

  8. Reconfigurable Networks-on-Chip

    CERN Document Server

    Chen, Sao-Jie; Tsai, Wen-Chung; Hu, Yu-Hen

    2012-01-01

    This book provides a comprehensive survey of recent progress in the design and implementation of Networks-on-Chip. It addresses a wide spectrum of on-chip communication problems, ranging from physical, network, to application layers. Specific topics that are explored in detail include packet routing, resource arbitration, error control/correction, application mapping, and communication scheduling. Additionally, a novel bi-directional communication channel NoC (BiNoC) architecture is described, with detailed explanation.   Written for practicing engineers in need of practical knowledge about the design and implementation of networks-on-chip; Includes tutorial-like details to introduce readers to a diverse range of NoC designs, as well as in-depth analysis for designers with NoC experience to explore advanced issues; Describes a variety of on-chip communication architectures, including a novel bi-directional communication channel NoC.     From the Foreword: Overall this book shows important advances over the...

  9. On-chip data communication

    NARCIS (Netherlands)

    Schinkel, Daniel

    2011-01-01

    On-chip data communication is an active research area, as interconnects are rapidly becoming a speed, power and reliability bottleneck for digital CMOS systems. Especially for global interconnects that have to span large parts of a chip, there is an increasing gap between transistor speed and interc

  10. On-chip data communication

    NARCIS (Netherlands)

    Schinkel, Daniel

    2011-01-01

    On-chip data communication is an active research area, as interconnects are rapidly becoming a speed, power and reliability bottleneck for digital CMOS systems. Especially for global interconnects that have to span large parts of a chip, there is an increasing gap between transistor speed and

  11. Trapping molecules on chips

    CERN Document Server

    Santambrogio, Gabriele

    2015-01-01

    In the last years, it was demonstrated that neutral molecules can be loaded on a microchip directly from a supersonic beam. The molecules are confined in microscopic traps that can be moved smoothly over the surface of the chip. Once the molecules are trapped, they can be decelerated to a standstill, for instance, or pumped into selected quantum states by laser light or microwaves. Molecules are detected on the chip by time-resolved spatial imaging, which allows for the study of the distribution in the phase space of the molecular ensemble.

  12. On-chip plasmonic spectrometer.

    Science.gov (United States)

    Tsur, Yuval; Arie, Ady

    2016-08-01

    We report a numerical and experimental study of an on-chip optical spectrometer, utilizing propagating surface plasmon polaritons in the telecom spectral range. The device is based on two holographic gratings, one for coupling, and the other for decoupling free-space radiation with the surface plasmons. This 800 μm×100 μm on-chip spectrometer resolves 17 channels spectrally separated by 3.1 nm, spanning a freely tunable spectral window, and is based on standard lithography fabrication technology. We propose two potential applications for this new device; the first employs the holographic control over the amplitude and phase of the input spectrum, for intrinsically filtering unwanted frequencies, like pump radiation in Raman spectroscopy. The second prospect utilizes the unique plasmonic field enhancement at the metal-dielectric boundary for the spectral analysis of very small samples (e.g., Mie scatterers) placed between the two gratings.

  13. Combination of capillary micellar liquid chromatography with on-chip microfluidic chemiluminescence detection for direct analysis of buspirone in human plasma.

    Science.gov (United States)

    Al Lawati, Haider A J; Kadavilpparampu, Afsal Mohammed; Suliman, FakhrEldin O

    2014-09-01

    Microfluidic based chemiluminescence (CL) detector having novel channel design for enhanced mixing has been developed and investigated in terms of its applicability with micellar mode of liquid chromatography (MLC). The newly developed detector was found to be highly sensitive and an alternative detection technique to combine with capillary MLC. This combination was successfully employed for direct detection of a model analyte using Ru(III)-peroxydisulphate CL system. The selected analyte, buspirone hydrochloride (BUS), was detected selectively at therapeutic concentration levels in human plasma without any sample pretreatment. By incorporating eight flow split units within the spiral channel of microfluidic chip, an enhancement of 140% in CL emission was observed. We also evaluated the effect of non- ionic surfactant, Brij-35, which used as mobile phase modifier in MLC, on CL emission. The CL signal was improved by 52% compared to aqueous-organic mobile phase combinations. Various parameters influencing the micellar chromatographic performance and the CL emission were optimized. This allowed highly sensitive analysis of BUS with limit of detection (LOD) of 0.27 ng mL(-1) (3σ/s) and limit of quantification (LOQ) of 0.89 ng mL(-1) (10σ/s). The analyte recovery from human plasma at three different concentration level ranges from 88% to 96% (RSD 1.9-5.3%). The direct analysis of BUS in human plasma was achieved within 6 min. Therefore, combining microfluidic CL detection with micellar mode of separation is an efficient, cost-effective and highly sensitive technique that can utilize MLC in its full capacity for various bioanalytical procedures.

  14. 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)

  15. 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)

  16. Physiologically relevant organs on chips.

    Science.gov (United States)

    Yum, Kyungsuk; Hong, Soon Gweon; Healy, Kevin E; Lee, Luke P

    2014-01-01

    Recent advances in integrating microengineering and tissue engineering have generated promising microengineered physiological models for experimental medicine and pharmaceutical research. Here we review the recent development of microengineered physiological systems, or also known as "ogans-on-chips", that reconstitute the physiologically critical features of specific human tissues and organs and their interactions. This technology uses microengineering approaches to construct organ-specific microenvironments, reconstituting tissue structures, tissue-tissue interactions and interfaces, and dynamic mechanical and biochemical stimuli found in specific organs, to direct cells to assemble into functional tissues. We first discuss microengineering approaches to reproduce the key elements of physiologically important, dynamic mechanical microenvironments, biochemical microenvironments, and microarchitectures of specific tissues and organs in microfluidic cell culture systems. This is followed by examples of microengineered individual organ models that incorporate the key elements of physiological microenvironments into single microfluidic cell culture systems to reproduce organ-level functions. Finally, microengineered multiple organ systems that simulate multiple organ interactions to better represent human physiology, including human responses to drugs, is covered in this review. This emerging organs-on-chips technology has the potential to become an alternative to 2D and 3D cell culture and animal models for experimental medicine, human disease modeling, drug development, and toxicology.

  17. 微芯片上金属离子检测研究进展%Research development of on-chip detection system of metal ions

    Institute of Scientific and Technical Information of China (English)

    张靖; 廖俊生

    2012-01-01

    The detection systems of metal ions on the microfluidic chips in recent 10 years are summarized in this study, including optical detectors, electrochemical detectors, mass spectrometry detectors and some other detectors. The problems existing in the detection of metal ion on microfluidic chips are proposed. The development and application trends are prospected as well.%总结了最近10年微流控芯片上金属离子常用的检测方法,主要有光学检测、电化学检测、质谱检测和其他检测方法.提出了微流控芯片在金属离子检测中存在的问题,并对微流控芯片检测的发展和应用进行了展望.

  18. GARD: a genetic algorithm for recombination detection

    National Research Council Canada - National Science Library

    Kosakovsky Pond, Sergei L; Posada, David; Gravenor, Michael B; Woelk, Christopher H; Frost, Simon D W

    2006-01-01

    .... We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences...

  19. Survey of Hardware Trojan Horse Detection on Chip%芯片级木马检测技术研究综述

    Institute of Scientific and Technical Information of China (English)

    王晨旭; 姜佩贺; 喻明艳

    2012-01-01

    集成电路在各个领域都具有极其重要的作用,但是在当今集成电路设计、制造、测试、封装各种环节相分离的产业模式下,用户所使用的芯片可能会被别有用心者植入硬件特洛伊木马电路,这给信息安全领域带来了严重威胁,芯片级硬件木马的检测技术已经成为了芯片安全研究领域的新热点.首先介绍了硬件木马的概念、危害以及分类方式;然后对硬件木马检测技术国内外有影响的研究成果进行了详细的总结和评述,着重阐述了目前比较有效的旁路分析方法,指出基于功耗指纹分析的硬件木马检测技术是当前最有前途的一种检测方法;最后简要总结了硬件木马的主动防御机制.%The integrated circuit (IC) plays an important role in many fields, but the Hardware Trojan Horse (HTH) can be maliciously implanted into Ics by attackers because of separated IC design and fabrication mode. The existence of HTH threatens the information security. HTH detection begins to attract widely attention and comes into a new research field. Firstly, the concept of HTH, its hazards and its classification were described. Then some important researches on HTH detection approach were summarized. The researchers focus on side channel analysis detection, in which the power finger analysis techniques are the promising method to detect HTH. Finally, the proactive defense mechanisms of HTH were also summed up briefly.

  20. Femtosecond laser fabrication for the integration of optical sensors in microfluidic lab-on-chip devices

    NARCIS (Netherlands)

    Osellame, R.; Martinez-Vazquez, R.; Dongre, C.; Dekker, R.; Hoekstra, H.J.W.M.; Ramponi, R.; Pollnau, M.; Cerullo, G.; Corkum, P.; Silvestri, de S.; Nelson, K.A.; Riedle, E.; Schoenlein, R.W.

    2009-01-01

    Femtosecond lasers enable the fabrication of both optical waveguides and buried microfluidic channels on a glass substrate. The waveguides are used to integrate optical detection in a commercial microfluidic lab-on-chip for capillary electrophoresis.

  1. Femtosecond laser fabrication for the integration of optical sensors in microfluidic lab-on-chip devices

    NARCIS (Netherlands)

    Osellame, R.; Martinez Vazquez, R.; Dongre, C.; Dekker, R.; Hoekstra, H.J.W.M.; Pollnau, M.; Ramponi, R.; Cerullo, G.

    2008-01-01

    Femtosecond lasers enable the fabrication of both optical waveguides and buried microfluidic channels on a glass substrate. The waveguides are used to integrate optical detection in a commercial microfluidic lab-on-chip for capillary electrophoresis

  2. Asynchronous design of Networks-on-Chip

    DEFF Research Database (Denmark)

    Sparsø, Jens

    2007-01-01

    The Network-on-chip concept has evolved as a solution to a broad range of problems related to the design of complex systems-on-chip (SoC) with tenths or hundreds of (heterogeneous) IP-cores. The paper introduces the NoC concept, identifies a range of possible timing organizations (globally...

  3. Towards Dependable Network-on-Chip Architectures

    NARCIS (Netherlands)

    Chen, C.

    2015-01-01

    The aggressive semiconductor technology scaling provides the means for doubling the amount of transistors on a single chip each and every 18 months. To efficiently utilize these vast chip resources, Multi-Processor Systems on Chip (MPSoCs) integrated with a Network-on-Chip (NoC) communication infras

  4. On-Chip Random Spectrometer

    CERN Document Server

    Redding, Brandon; Sarma, Raktim

    2013-01-01

    Light scattering in disordered media has been studied extensively due to its prevalence in natural and artificial systems [1]. In the field of photonics most of the research has focused on understanding and mitigating the effects of scattering, which are often detrimental. For certain applications, however, intentionally introducing disorder can actually improve the device performance, e.g., in photovoltaics optical scattering improves the efficiency of light harvesting [2-5]. Here, we utilize multiple scattering in a random photonic structure to build a compact on-chip spectrometer. The probe signal diffuses through a scattering medium generating wavelength-dependent speckle patterns which can be used to recover the input spectrum after calibration. Multiple scattering increases the optical pathlength by folding the paths in a confined geometry, enhancing the spectral decorrelation of speckle patterns and thus increasing the spectral resolution. By designing and fabricating the spectrometer on a silicon wafe...

  5. On-chip spiral spectrometer

    CERN Document Server

    Redding, Brandon; Bromberg, Yaron; Sarma, Raktim; Cao, Hui

    2016-01-01

    We designed an on-chip spectrometer based on an evanescently-coupled multimode spiral waveguide. Interference between the modes in the waveguide forms a wavelength-dependent speckle pattern which can be used as a fingerprint to identify the input wavelength after calibration. Evanescent coupling between neighboring arms of the spiral enhances the temporal spread of light propagating through the spiral, leading to a dramatic increase in the spectral resolution. Experimentally, we demonstrated that a 250 {\\mu}m radius spiral spectrometer provides a resolution of 0.01 nm at a wavelength of 1520 nm. Spectra containing 40 independent spectral channels can be recovered simultaneously and the operation bandwidth can be increased further when measuring sparse spectra.

  6. Quantifying the lag time to detect barriers in landscape genetics

    Science.gov (United States)

    E. L. Landguth; S. A Cushman; M. K. Schwartz; K. S. McKelvey; M. Murphy; G. Luikart

    2010-01-01

    Understanding how spatial genetic patterns respond to landscape change is crucial for advancing the emerging field of landscape genetics. We quantified the number of generations for new landscape barrier signatures to become detectable and for old signatures to disappear after barrier removal. We used spatially explicit, individualbased simulations to examine the...

  7. Improved Genetic Algorithm Application in Textile Defect Detection

    Institute of Scientific and Technical Information of China (English)

    GENG Zhao-feng; Li Bei-bei; ZHAO Zhi-hong

    2007-01-01

    Based on an efficient improved genetic algorithm,a pattern recognition approach is represented for textile defects inspection. An image process is developed to automatically detect the drawbacks on textile caused by three circumstances: break, dual, and jump of yams. By statistic method, some texture feature values of the image with defects points can be achieved. Therefore, the textile defects are classified properly. The advanced process of the defect image is done. Image segmentation is realized by an improved genetic algorithm to detect the defects. This method can be used to automatically classify and detect textile defects. According to different users' requirements, ifferent types of textile material can be detected.

  8. Biosensors-on-chip: a topical review

    Science.gov (United States)

    Chen, Sensen; Shamsi, Mohtashim H.

    2017-08-01

    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.

  9. Edge detection of range images using genetic neural networks

    Institute of Scientific and Technical Information of China (English)

    FAN Jian-ying; DU Ying; ZHOU Yang; WANG Yang

    2009-01-01

    Due to the complexity and asymmetrical illumination, the images of object are difficult to be effectively segmented by some routine method. In this paper, a kind of edge detection method based on image features and genetic algorithms neural network for range images was proposed. Fully considering the essential difference between an edge point and a noise point, some characteristic parameters were extracted from range maps as the input nodes of the network in the algorithm. Firstly, a genetic neural network was designed and implemented. The neural network is trained by genetic algorithm, and then genetic neural network algorithm is combined with the virtue of global optimization of genetic algorithm and the virtue of parallel computation of neural network, so that this algorithm is of good global property. The experimental results show that this method can get much faster and more accurate detection results than the classical differential algorithm, and has better anti-noise performance.

  10. 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

  11. Small target detection using quantum genetic morphological filter

    Science.gov (United States)

    Deng, Lizhen; Zhu, Hu; Wei, Yantao; Lu, Guanmin; Wei, Yu

    2015-12-01

    Small target detection plays a crucial role in infrared warning and tracking systems. A background suppression method using morphological filter based on quantum genetic algorithm (QGMF) is presented to detect small targets in infrared image. Structure element of morphological filter is encoded and the best structure element is selected using quantum genetic algorithm. The optimized structure element is used for background suppression to detect small target. Experimental results demonstrate that QGMF has good performance in clutter suppression, and obtains higher signal-to-clutter ratio gain (SCRG) and background suppression factor (BSF) than the one using the fixed structure element with the same size.

  12. 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.

  13. 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.

  14. Open Tiled Manycore System-on-Chip

    OpenAIRE

    Wallentowitz, Stefan; Wagner, Philipp; Tempelmeier, Michael; Wild, Thomas; Herkersdorf, Andreas

    2013-01-01

    Manycore System-on-Chip include an increasing amount of processing elements and have become an important research topic for improvements of both hardware and software. While research can be conducted using system simulators, prototyping requires a variety of components and is very time consuming. With the Open Tiled Manycore System-on-Chip (OpTiMSoC) we aim at building such an environment for use in our and other research projects as prototyping platform. This paper describes the project goal...

  15. Detection of genetically modified organisms by electrochemiluminescence PCR method.

    Science.gov (United States)

    Liu, Jinfeng; Xing, Da; Shen, Xingyan; Zhu, Debin

    2004-10-15

    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. In this study, electrochemiluminescence polymerase chain reaction (ECL-PCR) combined with hybridization technique was applied to detect the GMOs in genetically modified (GM) soybeans and papayas for the first time. Whether the soybeans and the papayas contain GM components was discriminated by detecting the Cauliflower mosaic virus 35S (CaMV35S) promoter. The experiment results show that the detection limit for CaMV35S promoter is 100 fmol, and the GM components can be clearly identified in GM soybeans and papayas. The technique may provide a new means in GMOs detection due to its simplicity and high efficiency.

  16. Method of detecting genetic translocations identified with chromosomal abnormalities

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Joe W. (Livermore, CA); Pinkel, Daniel (Walnut Creek, CA); Tkachuk, Douglas (Livermore, CA)

    2001-01-01

    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 analyses. 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.

  17. Incorporating privileged genetic information for fundus image based glaucoma detection.

    Science.gov (United States)

    Duan, Lixin; Xu, Yanwu; Li, Wen; Chen, Lin; Wing, Damon Wing Kee; Wong, Tien Yin; Liu, Jiang

    2014-01-01

    Visual features extracted from retinal fundus images have been increasingly used for glaucoma detection, as those images are generally easy to acquire. In recent years, genetic researchers have found that some single nucleic polymorphisms (SNPs) play important roles in the manifestation of glaucoma and also show superiority over fundus images for glaucoma detection. In this work, we propose to use the SNPs to form the so-called privileged information and deal with a practical problem where both fundus images and privileged genetic information exist for the training subjects, while the test objects only have fundus images. To solve this problem, we present an effective approach based on the learning using privileged information (LUPI) paradigm to train a predictive model for the image visual features. Extensive experiments demonstrate the usefulness of our approach in incorporating genetic information for fundus image based glaucoma detection.

  18. 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.

  19. 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.

  20. Method of detecting genetic deletions identified with chromosomal abnormalities

    Science.gov (United States)

    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.

  1. Chromosome-specific staining to detect genetic rearrangements

    Science.gov (United States)

    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.

  2. 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.

  3. Multivariate Outlier Detection in Genetic Evaluation in Nordic Jersey Cattle

    DEFF Research Database (Denmark)

    Gao, Hongding; Madsen, Per; Pösö, Jukka

    A procedure was developed for detection of multivariate outliers based on an approximation for Mahanalobis Distance (MD) and was implemented in the Nordic Jersey population. Evaluations are carried out by Nordic Cattle Genetic Evaluation (NAV), who uses a 9 trait model for milk, protein and fat...

  4. 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.

  5. Genetics and early detection in idiopathic pulmonary fibrosis.

    Science.gov (United States)

    Putman, Rachel K; Rosas, Ivan O; Hunninghake, Gary M

    2014-04-01

    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.

  6. Communication architectures for systems-on-chip

    CERN Document Server

    Ayala, Jose L

    2011-01-01

    A presentation of state-of-the-art approaches from an industrial applications perspective, Communication Architectures for Systems-on-Chip shows professionals, researchers, and students how to attack the problem of data communication in the manufacture of SoC architectures. With its lucid illustration of current trends and research improving the performance, quality, and reliability of transactions, this is an essential reference for anyone dealing with communication mechanisms for embedded systems, systems-on-chip, and multiprocessor architectures--or trying to overcome existing limitations.

  7. 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.

  8. An Adaptive Immune Genetic Algorithm for Edge Detection

    Science.gov (United States)

    Li, Ying; Bai, Bendu; Zhang, Yanning

    An adaptive immune genetic algorithm (AIGA) based on cost minimization technique method for edge detection is proposed. The proposed AIGA recommends the use of adaptive probabilities of crossover, mutation and immune operation, and a geometric annealing schedule in immune operator to realize the twin goals of maintaining diversity in the population and sustaining the fast convergence rate in solving the complex problems such as edge detection. Furthermore, AIGA can effectively exploit some prior knowledge and information of the local edge structure in the edge image to make vaccines, which results in much better local search ability of AIGA than that of the canonical genetic algorithm. Experimental results on gray-scale images show the proposed algorithm perform well in terms of quality of the final edge image, rate of convergence and robustness to noise.

  9. On-chip mode division multiplexing technologies

    DEFF Research Database (Denmark)

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

    2016-01-01

    using one-dimensional (1D) photonic crystal silicon waveguides. We furthermore use the fabricated devices to demonstrate on-chip point-to-point mode division multiplexing transmission, and all-optical signal processing by mode-selective wavelength conversion. Finally, we report an efficient silicon...

  10. On-chip entangled photon source

    Energy Technology Data Exchange (ETDEWEB)

    Soh, Daniel B. S.; Bisson, Scott E.

    2016-11-22

    Various technologies pertaining to an on-chip entangled photon source are described herein. A light source is used to pump two resonator cavities that are resonant at two different respective wavelengths and two different respective polarizations. The resonator cavities are coupled to a four-wave mixing cavity that receives the light at the two wavelengths and outputs polarization-entangled photons.

  11. An Innovative Gas Sensor with On-Chip Reference Using Monolithic Twin Laser

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yong-Gang; TIAN Zhao-Bing; ZHANG Xiao-Jun; GU Yi; LI Ai-Zhen; ZHU Xiang-Rong; ZHENG Yan-Lan; LIU Sheng

    2007-01-01

    An innovative gas sensor with on-chip reference using a monolithic twin laser is proposed. In this sensor a monolithic twin laser generates two closer laser beams with slight different wavelengths alternatively, one photodiode is used to catch both absorption and reference signals by time division multiplexing. The detection of nitrous oxide adopting this scheme using a 2.1 μm antimonide laser and an InGaAs photodiode has been demonstrated experimentally with detection limit below 1 ppm. Using this on chip reference scheme the fluctuations from the optical path and devices can be compensated effectively; the sensor system is simplified distinctly.

  12. 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 modellin...... 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....

  13. Detection methods and performance criteria for genetically modified organisms.

    Science.gov (United States)

    Bertheau, Yves; Diolez, Annick; Kobilinsky, André; Magin, Kimberly

    2002-01-01

    Detection methods for genetically modified organisms (GMOs) are necessary for many applications, from seed purity assessment to compliance of food labeling in several countries. Numerous analytical methods are currently used or under development to support these needs. The currently used methods are bioassays and protein- and DNA-based detection protocols. To avoid discrepancy of results between such largely different methods and, for instance, the potential resulting legal actions, compatibility of the methods is urgently needed. Performance criteria of methods allow evaluation against a common standard. The more-common performance criteria for detection methods are precision, accuracy, sensitivity, and specificity, which together specifically address other terms used to describe the performance of a method, such as applicability, selectivity, calibration, trueness, precision, recovery, operating range, limit of quantitation, limit of detection, and ruggedness. Performance criteria should provide objective tools to accept or reject specific methods, to validate them, to ensure compatibility between validated methods, and be used on a routine basis to reject data outside an acceptable range of variability. When selecting a method of detection, it is also important to consider its applicability, its field of applications, and its limitations, by including factors such as its ability to detect the target analyte in a given matrix, the duration of the analyses, its cost effectiveness, and the necessary sample sizes for testing. Thus, the current GMO detection methods should be evaluated against a common set of performance criteria.

  14. Packetizing OCP Transactions in the MANGO Network-on-Chip

    DEFF Research Database (Denmark)

    Bjerregaard, Tobias; Sparsø, Jens

    2006-01-01

    The scaling of CMOS technology causes a widening gap between the performance of on-chip communication and computation. This calls for a communication-centric design flow. The MANGO network-on-chip architecture enables globally asynchronous locally synchronous (GALS) system-on-chip design, while...

  15. Lab-on-chip systems for integrated bioanalyses.

    Science.gov (United States)

    Conde, João Pedro; Madaboosi, Narayanan; Soares, Ruben R G; Fernandes, João Tiago S; Novo, Pedro; Moulas, Geraud; Chu, Virginia

    2016-06-30

    Biomolecular detection systems based on microfluidics are often called lab-on-chip systems. To fully benefit from the miniaturization resulting from microfluidics, one aims to develop 'from sample-to-answer' analytical systems, in which the input is a raw or minimally processed biological, food/feed or environmental sample and the output is a quantitative or qualitative assessment of one or more analytes of interest. In general, such systems will require the integration of several steps or operations to perform their function. This review will discuss these stages of operation, including fluidic handling, which assures that the desired fluid arrives at a specific location at the right time and under the appropriate flow conditions; molecular recognition, which allows the capture of specific analytes at precise locations on the chip; transduction of the molecular recognition event into a measurable signal; sample preparation upstream from analyte capture; and signal amplification procedures to increase sensitivity. Seamless integration of the different stages is required to achieve a point-of-care/point-of-use lab-on-chip device that allows analyte detection at the relevant sensitivity ranges, with a competitive analysis time and cost.

  16. Lab-on-chip systems for integrated bioanalyses

    Science.gov (United States)

    Madaboosi, Narayanan; Soares, Ruben R.G.; Fernandes, João Tiago S.; Novo, Pedro; Moulas, Geraud; Chu, Virginia

    2016-01-01

    Biomolecular detection systems based on microfluidics are often called lab-on-chip systems. To fully benefit from the miniaturization resulting from microfluidics, one aims to develop ‘from sample-to-answer’ analytical systems, in which the input is a raw or minimally processed biological, food/feed or environmental sample and the output is a quantitative or qualitative assessment of one or more analytes of interest. In general, such systems will require the integration of several steps or operations to perform their function. This review will discuss these stages of operation, including fluidic handling, which assures that the desired fluid arrives at a specific location at the right time and under the appropriate flow conditions; molecular recognition, which allows the capture of specific analytes at precise locations on the chip; transduction of the molecular recognition event into a measurable signal; sample preparation upstream from analyte capture; and signal amplification procedures to increase sensitivity. Seamless integration of the different stages is required to achieve a point-of-care/point-of-use lab-on-chip device that allows analyte detection at the relevant sensitivity ranges, with a competitive analysis time and cost. PMID:27365042

  17. 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.

  18. Electrochemiluminescence-PCR detection of genetically modified organisms

    Science.gov (United States)

    Liu, Jinfeng; Xing, Da; Shen, Xingyan; Zhu, Debin

    2005-01-01

    The detection methods for genetically modified (GM) components in foods have been developed recently. But many of them are complicated and time-consuming; some of them need to use the carcinogenic substance, and can"t avoid false-positive results. In this study, an electrochemiluminescence polymerase chain reaction (ECL-PCR) method for detection GM tobaccos is proposed. The Cauliflower mosaic virus 35S (CaMV35S) promoter was amplified by PCR, Then hybridized with a Ru(bpy)32+ (TBR)-labeled and a biotinylated probe. The hybridization products were captured onto streptavidin-coated paramagnetic beads, and detected by measuring the electrochemiluminescence (ECL) signal of the TBR label. Whether the tobaccos contain GM components was discriminated by detecting the ECL signal of CaMV35S promoter. The experiment results show that the detection limit for CaMV35S promoter is 100 fmol, and the GM components can be clearly identified in GM tobaccos. The ECL-PCR method provide a new means in GMOs detection due to its safety, 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 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.

  1. Multivariate Outlier Detection in Genetic Evaluation in Nordic Jersey Cattle

    DEFF Research Database (Denmark)

    Gao, Hongding; Madsen, Per; Pösö, Jukka

    A procedure was developed for detection of multivariate outliers based on an approximation for Mahanalobis Distance (MD) and was implemented in the Nordic Jersey population. Evaluations are carried out by Nordic Cattle Genetic Evaluation (NAV), who uses a 9 trait model for milk, protein and fat...... means and co-variance matrix for the actual PY, lactation and DIM. Accuracy of EBV’s is improved for animals having extreme outlier record(s) deleted compared to EBV’s based on data not filtered for MD....

  2. Detecting structural breaks in time series via genetic algorithms

    DEFF Research Database (Denmark)

    Doerr, Benjamin; Fischer, Paul; Hilbert, Astrid

    2016-01-01

    Detecting structural breaks is an essential task for the statistical analysis of time series, for example, for fitting parametric models to it. In short, structural breaks are points in time at which the behaviour of the time series substantially changes. Typically, no solid background knowledge...... 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...

  3. On-Chip Single-Photon Sifter

    CERN Document Server

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

    2016-01-01

    Quantum states of light play a pivotal role in modern science[1] and future photonic applications[2]. While impressive progress has been made in their generation and manipulation with high fidelities, the common table-top approach is reaching its limits for practical quantum applications. Since the advent of integrated quantum nanophotonics[3] different material platforms based on III-V nanostructures-, color centers-, and nonlinear waveguides[4-8] as on-chip light sources have been investigated. Each platform has unique advantages and limitations in terms of source properties, optical circuit complexity, and scaling potentials. However, all implementations face major challenges with efficient and tunable filtering of individual quantum states[4], scalable integration and deterministic multiplexing of on-demand selected quantum emitters[9], and on-chip excitation-suppression[10]. Here we overcome all of these challenges with a novel hybrid and scalable nanofabrication approach to generate quantum light on-chi...

  4. On-Chip Microwave Quantum Hall Circulator

    Science.gov (United States)

    Mahoney, A. C.; Colless, J. I.; Pauka, S. J.; Hornibrook, J. M.; Watson, J. D.; Gardner, G. C.; Manfra, M. J.; Doherty, A. C.; Reilly, D. J.

    2017-01-01

    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 /1000 th 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 μ m 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.

  5. On-chip plasmonic waveguide optical waveplate

    Science.gov (United States)

    Gao, Linfei; Huo, Yijie; Zang, Kai; Paik, Seonghyun; Chen, Yusi; Harris, James S.; Zhou, Zhiping

    2015-10-01

    Polarization manipulation is essential in almost every photonic system ranging from telecommunications to bio-sensing to quantum information. This is traditionally achieved using bulk waveplates. With the developing trend of photonic systems towards integration and miniaturization, the need for an on-chip waveguide type waveplate becomes extremely urgent. However, this is very challenging using conventional dielectric waveguides, which usually require complex 3D geometries to alter the waveguide symmetry and are also difficult to create an arbitrary optical axis. Recently, a waveguide waveplate was realized using femtosecond laser writing, but the device length is in millimeter range. Here, for the first time we propose and experimentally demonstrate an ultracompact, on-chip waveplate using an asymmetric hybrid plasmonic waveguide to create an arbitrary optical axis. The device is only in several microns length and produced in a flexible integratable IC compatible format, thus opening up the potential for integration into a broad range of systems.

  6. 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.

  7. Microfabrication of human organs-on-chips.

    Science.gov (United States)

    Huh, Dongeun; Kim, Hyun Jung; Fraser, Jacob P; Shea, Daniel E; Khan, Mohammed; Bahinski, Anthony; Hamilton, Geraldine A; Ingber, Donald E

    2013-11-01

    'Organs-on-chips' are microengineered biomimetic systems containing microfluidic channels lined by living human cells, which replicate key functional units of living organs to reconstitute integrated human organ-level pathophysiology in vitro. These microdevices can be used to test efficacy and toxicity of drugs and chemicals, and to create in vitro models of human disease. Thus, they potentially represent low-cost alternatives to conventional animal models for pharmaceutical, chemical and environmental applications. Here we describe a protocol for the fabrication, microengineering and operation of these microfluidic organ-on-chip systems. First, microengineering is used to fabricate a multilayered microfluidic device that contains two parallel elastomeric microchannels separated by a thin porous flexible membrane, along with two full-height, hollow vacuum chambers on either side; this requires ∼3.5 d to complete. To create a 'breathing' lung-on-a-chip that mimics the mechanically active alveolar-capillary interface of the living human lung, human alveolar epithelial cells and microvascular endothelial cells are cultured in the microdevice with physiological flow and cyclic suction applied to the side chambers to reproduce rhythmic breathing movements. We describe how this protocol can be easily adapted to develop other human organ chips, such as a gut-on-a-chip lined by human intestinal epithelial cells that experiences peristalsis-like motions and trickling fluid flow. Also, we discuss experimental techniques that can be used to analyze the cells in these organ-on-chip devices.

  8. 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...

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. On-chip cell analysis platform: Implementation of contact fluorescence microscopy in microfluidic chips

    Science.gov (United States)

    Takehara, Hiroaki; Kazutaka, Osawa; Haruta, Makito; Noda, Toshihiko; Sasagawa, Kiyotaka; Tokuda, Takashi; Ohta, Jun

    2017-09-01

    Although fluorescence microscopy is the gold standard tool for biomedical research and clinical applications, their use beyond well-established laboratory infrastructures remains limited. The present study investigated a novel on-chip cell analysis platform based on contact fluorescence microscopy and microfluidics. Combined use of a contact fluorescence imager based on complementary metal-oxide semiconductor technology and an ultra-thin glass bottom microfluidic chip enabled both to observe living cells with minimal image distortion and to ease controlling and handling of biological samples (e.g. cells and biological molecules) in the imaged area. A proof-of-concept experiment of on-chip detection of cellular response to endothelial growth factor demonstrated promising use for the recently developed on-chip cell analysis platform. Contact fluorescence microscopy has numerous desirable features including compatibility with plastic microfluidic chips and compatibility with the electrical control system, and thus will fulfill the requirements of a fully automated cell analysis system.

  11. A novel genetic programming approach for epileptic seizure detection.

    Science.gov (United States)

    Bhardwaj, Arpit; Tiwari, Aruna; Krishna, Ramesh; Varma, Vishaal

    2016-02-01

    The human brain is a delicate mix of neurons (brain cells), electrical impulses and chemicals, known as neurotransmitters. Any damage has the potential to disrupt the workings of the brain and cause seizures. These epileptic seizures are the manifestations of epilepsy. The electroencephalograph (EEG) signals register average neuronal activity from the cerebral cortex and label changes in activity over large areas. A detailed analysis of these electroencephalograph (EEG) signals provides valuable insights into the mechanisms instigating epileptic disorders. Moreover, the detection of interictal spikes and epileptic seizures in an EEG signal plays an important role in the diagnosis of epilepsy. Automatic seizure detection methods are required, as these epileptic seizures are volatile and unpredictable. This paper deals with an automated detection of epileptic seizures in EEG signals using empirical mode decomposition (EMD) for feature extraction and proposes a novel genetic programming (GP) approach for classifying the EEG signals. Improvements in the standard GP approach are made using a Constructive Genetic Programming (CGP) in which constructive crossover and constructive subtree mutation operators are introduced. A hill climbing search is integrated in crossover and mutation operators to remove the destructive nature of these operators. A new concept of selecting the Globally Prime offspring is also presented to select the best fitness offspring generated during crossover. To decrease the time complexity of GP, a new dynamic fitness value computation (DFVC) is employed to increase the computational speed. We conducted five different sets of experiments to evaluate the performance of the proposed model in the classification of different mixtures of normal, interictal and ictal signals, and the accuracies achieved are outstandingly high. The experimental results are compared with the existing methods on same datasets, and these results affirm the potential use of

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

    Science.gov (United States)

    Tan, Jeslin J L; Capozzoli, Monica; Sato, Mitsuharu; Watthanaworawit, Wanitda; Ling, Clare L; Mauduit, Marjorie; Malleret, Benoît; Grüner, Anne-Charlotte; Tan, Rosemary; Nosten, François H; Snounou, Georges; Rénia, Laurent; Ng, Lisa F P

    2014-01-01

    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.

  13. 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

    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 a chall...

  14. 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...

  15. Genetically engineered microorganisms for the detection of explosives' residues

    Directory of Open Access Journals (Sweden)

    Benjamin eShemer

    2015-10-01

    Full Text Available The manufacture and use of explosives throughout the past century has resulted in the extensive pollution of soils and groundwater, and the widespread interment of landmines imposes a major humanitarian risk and prevents civil development of large areas. As most current landmine detection technologies require actual presence at the surveyed areas, thus posing a significant risk to personnel, diverse research efforts are aimed at the development of remote detection solutions. One possible means proposed to fulfill this objective is the use of microbial bioreporters: genetically engineered microorganisms tailored to generate an optical signal in the presence of explosives’ vapors. The use of such sensor bacteria will allow to pinpoint the locations of explosive devices in a minefield. While no study has yet resulted in a commercially operational system, significant progress has been made in the design and construction of explosives-sensing bacterial strains. In this article we review the attempts to construct microbial bioreporters for the detection of explosives, and analyze the steps that need to be undertaken for this strategy to be applicable for landmine detection.

  16. Genetically engineered microorganisms for the detection of explosives’ residues

    Science.gov (United States)

    Shemer, Benjamin; Palevsky, Noa; Yagur-Kroll, Sharon; Belkin, Shimshon

    2015-01-01

    The manufacture and use of explosives throughout the past century has resulted in the extensive pollution of soils and groundwater, and the widespread interment of landmines imposes a major humanitarian risk and prevents civil development of large areas. As most current landmine detection technologies require actual presence at the surveyed areas, thus posing a significant risk to personnel, diverse research efforts are aimed at the development of remote detection solutions. One possible means proposed to fulfill this objective is the use of microbial bioreporters: genetically engineered microorganisms “tailored” to generate an optical signal in the presence of explosives’ vapors. The use of such sensor bacteria will allow to pinpoint the locations of explosive devices in a minefield. While no study has yet resulted in a commercially operational system, significant progress has been made in the design and construction of explosives-sensing bacterial strains. In this article we review the attempts to construct microbial bioreporters for the detection of explosives, and analyze the steps that need to be undertaken for this strategy to be applicable for landmine detection. PMID:26579085

  17. 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.

  18. Photonic crystal biosensors towards on-chip integration.

    Science.gov (United States)

    Threm, Daniela; Nazirizadeh, Yousef; Gerken, Martina

    2012-08-01

    Photonic crystal technology has attracted large interest in the last years. The possibility to generate highly sensitive sensor elements with photonic crystal structures is very promising for medical or environmental applications. The low-cost fabrication on the mass scale is as advantageous as the compactness and reliability of photonic crystal biosensors. The possibility to integrate microfluidic channels together with photonic crystal structures allows for highly compact devices. This article reviews different types of photonic crystal sensors including 1D photonic crystal biosensors, biosensors with photonic crystal slabs, photonic crystal waveguide biosensors and biosensors with photonic crystal microcavities. Their applications in biomolecular and pathogen detection are highlighted. The sensitivities and the detection limits of the different biosensors are compared. The focus is on the possibilities to integrate photonic crystal biosensors on-chip.

  19. Microfluidic cytometers with integrated on-chip optical components for blood cell analysis

    Science.gov (United States)

    Zhao, Yingying; Li, Qin; Hu, Xiao-Ming

    2016-10-01

    In the last two decades, microfluidic technologies have shown the great potential in developing portable and point-of care testing blood cell analysis devices. It is challenging to integrate all free-space detecting components in a single microfluidic platform. In this paper, a microfluidic cytometer with integrated on-chip optical components was demonstrated. To facilitate on-chip detection, the device integrated optical fibers and on-chip microlens with microfluidic channels on one polydimethylsiloxane layer by standard soft photolithography. This compact design increased the sensitivity of the device and also eliminated time-consuming free-space optical alignments. Polystyrene particles, together with red blood cells and platelets, were measured in the microfluidic cytometer by small angle forward scatter. Experimental results indicated that the performance of the microfluidic device was comparable to a conventional cytometer. And it was also demonstrated its ability to detect on-chip optical signals in a highly compact, simple, truly portable and low cost format which was perfect suitable for point-of-care testing clinical hematology diagnostics.

  20. 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

  1. 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

  2. Application of Ferrite Nanomaterial in RF On-Chip Inductors

    Directory of Open Access Journals (Sweden)

    Hua-Lin Cai

    2013-01-01

    Full Text Available Several kinds of ferrite-integrated on-chip inductors are presented. Ferrite nanomaterial applied in RF on-chip inductors is prepared and analyzed to show the properties of high permeability, high ferromagnetic resonance frequency, high resistivity, and low loss, which has the potential that will improve the performance of RF on-chip inductors. Simulations of different coil and ferrite nanomaterial parameters, inductor structures, and surrounding structures are also conducted to achieve the trend of gains of inductance and quality factor of on-chip inductors. By integrating the prepared ferrite magnetic nanomaterial to the on-chip inductors with different structures, the measurement performances show an obvious improvement even in GHz frequency range. In addition, the studies of CMOS compatible process to integrate the nanomaterial promote the widespread application of magnetic nanomaterial in RF on-chip inductors.

  3. 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

  4. Spin Seebeck devices using local on-chip heating

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Stephen M., E-mail: swu@anl.gov; Fradin, Frank Y.; Hoffman, Jason; Hoffmann, Axel; Bhattacharya, Anand [Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

    2015-05-07

    A micro-patterned spin Seebeck device is fabricated using an on-chip heater. Current is driven through a Au heater layer electrically isolated from a bilayer consisting of Fe{sub 3}O{sub 4} (insulating ferrimagnet) and a spin detector layer. It is shown that through this method it is possible to measure the longitudinal spin Seebeck effect (SSE) for small area magnetic devices, equivalent to traditional macroscopic SSE experiments. Using a lock-in detection technique, it is possible to more sensitively characterize both the SSE and the anomalous Nernst effect (ANE), as well as the inverse spin Hall effect in various spin detector materials. By using the spin detector layer as a thermometer, we can obtain a value for the temperature gradient across the device. These results are well matched to values obtained through electromagnetic/thermal modeling of the device structure and with large area spin Seebeck measurements.

  5. Cardio Vascular Detection with Neuro Computing and Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    T. John Peter

    2014-09-01

    Full Text Available For human the most fundamental requirement is having a healthy life, which is being difficult to maintain day to day as we are getting more progress in technological era. Among the possible reasons of unnatural death, heart disease based causes are showing very significant part. The diagnosis of heart diseases is a vital and intricate job. The recognition of heart disease from diverse features or signs is a multi-layered problem that is highly sensitive with respect diagnostic tests and establishing the relationship with multiple parameters is very difficult. In result decision is not free from false assumptions and is frequently accompanied by impulsive effects. This encourages developing a more reliable and cost effective knowledge based algorithmic approach to detect the heart disease. From engineering point of view, solution for detecting the presence of heart diseases is developed with the concept of artificial intelligence in data mining in this study. Feed forward architecture of neural network technology is taken as platform of computation to generate the intelligence in association with well established field of genetic algorithm (GA. A comparative performance has presented between both learning concepts with various different size of architecture.

  6. Bearing Fault Detection Using Artificial Neural Networks and Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Samanta B

    2004-01-01

    Full Text Available A study is presented to compare the performance of bearing fault detection using three types of artificial neural networks (ANNs, namely, multilayer perceptron (MLP, radial basis function (RBF network, and probabilistic neural network (PNN. The time domain vibration signals of a rotating machine with normal and defective bearings are processed for feature extraction. The extracted features from original and preprocessed signals are used as inputs to all three ANN classifiers: MLP, RBF, and PNN for two-class (normal or fault recognition. The characteristic parameters like number of nodes in the hidden layer of MLP and the width of RBF, in case of RBF and PNN along with the selection of input features, are optimized using genetic algorithms (GA. For each trial, the ANNs are trained with a subset of the experimental data for known machine conditions. The ANNs are tested using the remaining set of data. The procedure is illustrated using the experimental vibration data of a rotating machine with and without bearing faults. The results show the relative effectiveness of three classifiers in detection of the bearing condition.

  7. 基于遗传算法的特定应用片上网络映射研究%Research on Application-Specific Network-on-Chip Mapping Based on Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    赖国明

    2011-01-01

    片上网络是片上系统SoC通信问题的一种最有效解决方法,如何把知识产权核映射到网格之格件映射问题是NoC设计的关键问题之一。映射问题本质上是一种二次分配的NP难问题,遗传算法能够有效地求解问题的近似最优解。提出一种基于遗传的IP映射算法,实验结果表明,遗传算法能够在几分钟内求得最小能耗的映射。%Network-on-Chip(NoC) is the most promising solution for System-on-Chip(SoC) communication problems.The problem,how to map IP cores to the mesh tiles,is one of the key issues of NoC design.Mapping problem is naturally a quadratic assignment problem,which is known to be NP hard problem.Genetic Algorithm(GA) is suitable to solve the approximate solution to this kind of NP problems.Proposes a mapping method based on GA.The experimental result shows that GA can get the minimum energy consumption mapping within few minutes.

  8. 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.

    2012-01-01

    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 popula

  9. Laser light-field fusion for wide-field lensfree on-chip phase contrast nanoscopy

    CERN Document Server

    Kazemzadeh, Farnoud

    2016-01-01

    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. Nanoscopy is often synonymous with high equipment costs and limited FOV. In this study, we introduce the idea of laser light-field fusion for lensfree on-chip phase contrast nanoscopy, where interferometric laser light-field encodings acquired using an on-chip setup with laser pulsations at different wavelengths are fused to produce marker-free phase contrast images with resolving power below the pixel pitch of the sensor array as well as the wavelength of the probing light source, beyond the diffraction limit. Experimental results demonstrate, for the first time, a lensfree on-chip instrument successfully detecting 500 nm nanoparticles without any specialized or intricate sample preparation or the use of synthetic aperture- or lateral shift-based t...

  10. Overview of status and challenges of system testing on chip with embedded DRAMS

    Science.gov (United States)

    Falter, T.; Richter, D.

    2000-05-01

    The combination of logic together with DRAM as a system on chip (SOC) has many advantages for a large variety of computing and network applications. The goal of testing a system is to detect the fabrication caused faults in order to guarantee the defined quality. The increasing size of memories, shrinking dimensions, higher demands on application (frequency and temperature range) and quality cause new problems and higher costs of testing. On the other hand the pressure to serve the market with low cost products forces the test engineer to reduce test costs by reducing test times and using low cost test equipment. Different solutions are discussed in this paper in order to meet these challenges. The variety of test approaches for testing SOC with embedded DRAMs reaches from testing with completely chip external test logic, a simple on-chip test logic up to a full blown built-in self test (BIST) on chip. Which choice is the right one depends on different criteria e.g. memory size, quality demands and application of the product. As an example the modular embedded DRAM core concept from Infineon Technologies is discussed, which includes a dedicated modular test concept based on on-chip integration of a test controller.

  11. High Speed Global On-Chip Interconnects and Transceivers

    NARCIS (Netherlands)

    Mensink, E.

    2007-01-01

    The data rate of global on-chip interconnects (up to 10 mm) is limited by a large distributed resistance and capacitance. This thesis describes methods to increase the achievable data rate of global on-chip interconnects with minimal chip area and power consumption, while maintaining data integrity.

  12. Interconnects and On-Chip Data Communication Techniques

    NARCIS (Netherlands)

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

    Global on-chip communication is rapidly becoming a speed and power bottleneck in CMOS circuits. In this paper, a ‘mixed-signal’ approach is taken to analyze on-chip interconnects and it is investigated how data-rates can be improved. It is shown that complex signaling schemes such as OFDM and CDMA

  13. Thermal Management for Dependable On-Chip Systems

    OpenAIRE

    Ebi, Thomas

    2014-01-01

    This thesis addresses the dependability issues in on-chip systems from a thermal perspective. This includes an explanation and analysis of models to show the relationship between dependability and tempature. Additionally, multiple novel methods for on-chip thermal management are introduced aiming to optimize thermal properties. Analysis of the methods is done through simulation and through infrared thermal camera measurements.

  14. The ReNoC Reconfigurable Network-on-Chip

    DEFF Research Database (Denmark)

    Stuart, Matthias Bo; Stensgaard, Mikkel Bystrup; Sparsø, Jens

    2011-01-01

    This article presents a reconfigurable network-on-chip architecture called ReNoC, which is intended for use in general-purpose multiprocessor system-on-chip platforms, and which enables application-specific logical NoC topologies to be configured, thus providing both efficiency and flexibility...

  15. 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

  16. Unintended effects and their detection in genetically modified crops.

    Science.gov (United States)

    Cellini, F; Chesson, A; Colquhoun, I; Constable, A; Davies, H V; Engel, K H; Gatehouse, A M R; Kärenlampi, S; Kok, E J; Leguay, J-J; Lehesranta, S; Noteborn, H P J M; Pedersen, J; Smith, M

    2004-07-01

    The commercialisation of GM crops in Europe is practically non-existent at the present time. The European Commission has instigated changes to the regulatory process to address the concerns of consumers and member states and to pave the way for removing the current moratorium. With regard to the safety of GM crops and products, the current risk assessment process pays particular attention to potential adverse effects on human and animal health and the environment. This document deals with the concept of unintended effects in GM crops and products, i.e. effects that go beyond that of the original modification and that might impact primarily on health. The document first deals with the potential for unintended effects caused by the processes of transgene insertion (DNA rearrangements) and makes comparisons with genetic recombination events and DNA rearrangements in traditional breeding. The document then focuses on the potential value of evolving "profiling" or "omics" technologies as non-targeted, unbiased approaches, to detect unintended effects. These technologies include metabolomics (parallel analysis of a range of primary and secondary metabolites), proteomics (analysis of polypeptide complement) and transcriptomics (parallel analysis of gene expression). The technologies are described, together with their current limitations. Importantly, the significance of unintended effects on consumer health are discussed and conclusions and recommendations presented on the various approaches outlined.

  17. Genetically modified cotton in India and detection strategies.

    Science.gov (United States)

    Randhawa, Gurinder Jit; Chhabra, Rashmi

    2013-01-01

    India is one of the largest cotton-growing countries. Cotton is a fiber crop with varied applications from making tiny threads to fashionable clothing in the textile sector. In the near future, cotton crop will gain popularity as a multipurpose crop in India. The commercialization of Bt cotton in 2002 and consequently the fast adoption of Bt cotton hybrids by cotton farmers have enhanced the cotton production in India. Presently, genetically modified (GM) cotton has occupied 21.0 million hectares (mha) that comprise 14% of the global area under GM cultivation. In the coming years, improved cotton hybrids, with stacked and multiple gene events for improved fiber quality, insect resistance, drought tolerance, and herbicide tolerance, would further significantly improve the cotton production in India. With the dramatic increase in commercialization of GM crops, there is an urgent need to develop cost-effective and robust GM detection methods for effective risk assessment and management, post release monitoring, and to solve the legal disputes. DNA-based GM diagnostics are most robust assays due to their high sensitivity, specificity, and stability of DNA molecule.

  18. 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.

  19. An energy-efficient Network-on-Chip for a heterogeneous tiled reconfigurable System-on-Chip

    NARCIS (Netherlands)

    Kavaldjiev, N.K.; Smit, Gerardus Johannes Maria

    This paper proposes a Network-on-Chip architecture that offers high flexibility and performance. It is used in a System-on-Chip platform for future multimedia mobile devices. The network is packet switching wormhole network with virtual-channel flow control and source routing. The initial

  20. An energy-efficient Network-on-Chip for a heterogeneous tiled reconfigurable Systems-on-Chip

    NARCIS (Netherlands)

    Kavaldjiev, N.K.; Smit, Gerardus Johannes Maria

    This paper proposes a Network-on-Chip architecture that offers high flexibility and performance. It is used in a System-on-Chip platform for future multimedia mobile devices. The network is packet switching wormhole network with virtual-channel flow control and source routing. The initial

  1. 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...

  2. A lab-on-chip for malaria diagnosis and surveillance.

    Science.gov (United States)

    Taylor, Brian J; Howell, Anita; Martin, Kimberly A; Manage, Dammika P; Gordy, Walter; Campbell, Stephanie D; Lam, Samantha; Jin, Albert; Polley, Spencer D; Samuel, Roshini A; Atrazhev, Alexey; Stickel, Alex J; Birungi, Josephine; Mbonye, Anthony K; Pilarski, Linda M; Acker, Jason P; Yanow, Stephanie K

    2014-05-09

    Access to timely and accurate diagnostic tests has a significant impact in the management of diseases of global concern such as malaria. While molecular diagnostics satisfy this need effectively in developed countries, barriers in technology, reagent storage, cost and expertise have hampered the introduction of these methods in developing countries. In this study a simple, lab-on-chip PCR diagnostic was created for malaria that overcomes these challenges. The platform consists of a disposable plastic chip and a low-cost, portable, real-time PCR machine. The chip contains a desiccated hydrogel with reagents needed for Plasmodium specific PCR. Chips can be stored at room temperature and used on demand by rehydrating the gel with unprocessed blood, avoiding the need for sample preparation. These chips were run on a custom-built instrument containing a Peltier element for thermal cycling and a laser/camera setup for amplicon detection. This diagnostic was capable of detecting all Plasmodium species with a limit of detection for Plasmodium falciparum of 2 parasites/μL of blood. This exceeds the sensitivity of microscopy, the current standard for diagnosis in the field, by ten to fifty-fold. In a blind panel of 188 patient samples from a hyper-endemic region of malaria transmission in Uganda, the diagnostic had high sensitivity (97.4%) and specificity (93.8%) versus conventional real-time PCR. The test also distinguished the two most prevalent malaria species in mixed infections, P. falciparum and Plasmodium vivax. A second blind panel of 38 patient samples was tested on a streamlined instrument with LED-based excitation, achieving a sensitivity of 96.7% and a specificity of 100%. These results describe the development of a lab-on-chip PCR diagnostic from initial concept to ready-for-manufacture design. This platform will be useful in front-line malaria diagnosis, elimination programmes, and clinical trials. Furthermore, test chips can be adapted to detect other

  3. Technologies for autonomous integrated lab-on-chip systems for space missions

    Science.gov (United States)

    Nascetti, A.; Caputo, D.; Scipinotti, R.; de Cesare, G.

    2016-11-01

    Lab-on-chip devices are ideal candidates for use in space missions where experiment automation, system compactness, limited weight and low sample and reagent consumption are required. Currently, however, most microfluidic systems require external desktop instrumentation to operate and interrogate the chip, thus strongly limiting their use as stand-alone systems. In order to overcome the above-mentioned limitations our research group is currently working on the design and fabrication of "true" lab-on-chip systems that integrate in a single device all the analytical steps from the sample preparation to the detection without the need for bulky external components such as pumps, syringes, radiation sources or optical detection systems. Three critical points can be identified to achieve 'true' lab-on-chip devices: sample handling, analytical detection and signal transduction. For each critical point, feasible solutions are presented and evaluated. Proposed microfluidic actuation and control is based on electrowetting on dielectrics, autonomous capillary networks and active valves. Analytical detection based on highly specific chemiluminescent reactions is used to avoid external radiation sources. Finally, the integration on the same chip of thin film sensors based on hydrogenated amorphous silicon is discussed showing practical results achieved in different sensing tasks.

  4. Ultrasensitive interferometric on-chip microscopy of transparent objects

    Science.gov (United States)

    Terborg, Roland A.; Pello, Josselin; Mannelli, Ilaria; Torres, Juan P.; Pruneri, Valerio

    2016-01-01

    Light microscopes can detect objects through several physical processes, such as scattering, absorption, and reflection. In transparent objects, these mechanisms are often too weak, and interference effects are more suitable to observe the tiny refractive index variations that produce phase shifts. We propose an on-chip microscope design that exploits birefringence in an unconventional geometry. It makes use of two sheared and quasi-overlapped illuminating beams experiencing relative phase shifts when going through the object, and a complementary metal-oxide-semiconductor image sensor array to record the resulting interference pattern. Unlike conventional microscopes, the beams are unfocused, leading to a very large field of view (20 mm2) and detection volume (more than 0.5 cm3), at the expense of lateral resolution. The high axial sensitivity (<1 nm) achieved using a novel phase-shifting interferometric operation makes the proposed device ideal for examining transparent substrates and reading microarrays of biomarkers. This is demonstrated by detecting nanometer-thick surface modulations on glass and single and double protein layers. PMID:27386571

  5. 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 i

  6. 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.

  7. An Integrated Lab-on-Chip for Rapid Identification and Simultaneous Differentiation of Tropical Pathogens

    Science.gov (United States)

    Sato, Mitsuharu; Watthanaworawit, Wanitda; Ling, Clare L.; Mauduit, Marjorie; Malleret, Benoît; Grüner, Anne-Charlotte; Tan, Rosemary; Nosten, François H.; Snounou, Georges; Rénia, Laurent; Ng, Lisa F. P.

    2014-01-01

    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. PMID:25078474

  8. Microfluidics-Based Lab-on-Chip Systems in DNA-Based Biosensing: An Overview

    OpenAIRE

    Sabo Wada Dutse; Nor Azah Yusof

    2011-01-01

    Microfluidics-based lab-on-chip (LOC) systems are an active research area that is revolutionising high-throughput sequencing for the fast, sensitive and accurate detection of a variety of pathogens. LOCs also serve as portable diagnostic tools. The devices provide optimum control of nanolitre volumes of fluids and integrate various bioassay operations that allow the devices to rapidly sense pathogenic threat agents for environmental monitoring. LOC systems, such as microfluidic biochips, offe...

  9. Workshop meeting report Organs-on-Chips: human disease models.

    Science.gov (United States)

    van de Stolpe, Anja; den Toonder, Jaap

    2013-09-21

    The concept of "Organs-on-Chips" has recently evolved and has been described as 3D (mini-) organs or tissues consisting of multiple and different cell types interacting with each other under closely controlled conditions, grown in a microfluidic chip, and mimicking the complex structures and cellular interactions in and between different cell types and organs in vivo, enabling the real time monitoring of cellular processes. In combination with the emerging iPSC (induced pluripotent stem cell) field this development offers unprecedented opportunities to develop human in vitro models for healthy and diseased organ tissues, enabling the investigation of fundamental mechanisms in disease development, drug toxicity screening, drug target discovery and drug development, and the replacement of animal testing. Capturing the genetic background of the iPSC donor in the organ or disease model carries the promise to move towards "in vitro clinical trials", reducing costs for drug development and furthering the concept of personalized medicine and companion diagnostics. During the Lorentz workshop (Leiden, September 2012) an international multidisciplinary group of experts discussed the current state of the art, available and emerging technologies, applications and how to proceed in the field. Organ-on-a-chip platform technologies are expected to revolutionize cell biology in general and drug development in particular.

  10. 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.

  11. On-Chip Diamond Raman Laser

    CERN Document Server

    Latawiec, Pawel; Burek, Michael J; Hausmann, Birgit J M; Bulu, Irfan; Loncar, Marko

    2015-01-01

    Synthetic single-crystal diamond has recently emerged as a promising platform for Raman lasers at exotic wavelengths due to its giant Raman shift, large transparency window and excellent thermal properties yielding a greatly enhanced figure-of-merit compared to conventional materials. To date, diamond Raman lasers have been realized using bulk plates placed inside macroscopic cavities, requiring careful alignment and resulting in high threshold powers (~W-kW). Here we demonstrate an on-chip Raman laser based on fully-integrated, high quality-factor, diamond racetrack micro-resonators embedded in silica. Pumping at telecom wavelengths, we show Stokes output discretely tunable over a ~100nm bandwidth around 2-{\\mu}m with output powers >250 {\\mu}W, extending the functionality of diamond Raman lasers to an interesting wavelength range at the edge of the mid-infrared spectrum. Continuous-wave operation with only ~85 mW pump threshold power in the feeding waveguide is demonstrated along with continuous, mode-hop-fr...

  12. Congestion Prediction Algorithm for Network on Chip

    Directory of Open Access Journals (Sweden)

    Hua Cai

    2013-07-01

    Full Text Available Network on chip (NoC traffic congestion was one of the important reasons for the data transmission performance degradation. In this paper, we presented a congestion judgment algorithm, which was based on neural network. The congestion control algorithm firstly used the hamming network to compute the NoC’s link buffer congestion state, secondly used the competitive network to find the worst congestion node, and then adopted avoiding congested node  routing policy to improve the NoC’s transmission performance. In this paper, the congestion control algorithm can make the data stream as far as possible evenly distributed in the NoC’s nodes and links and reduce the transmission resource competition. The simulation results showed that the congestion control algorithm could achieve better network throughput and average transmission delay.

  13. Network-on-chip the next generation of system-on-chip integration

    CERN Document Server

    Kundu, Santanu

    2014-01-01

    ""What makes this book special as compared to the current literature in the field is that it provides a complete picture of NoC architectures. In fact, current books in the context of NoCs are usually specific and presuppose a basic knowledge of NoC architectures. Conversely, this book provides a complete guide for both unskilled readers and researchers working in the area, to acquire not only the basic concepts but also the advanced techniques for improving power, cost and performance metrics of the on-chip communication system.""-Maurizio Palesi, Kore University, Italy.

  14. On-Chip Network Design Automation with Source Routing Switches

    Institute of Scientific and Technical Information of China (English)

    MA Liwei; SUN Yihe

    2007-01-01

    Network-on-chip (NoC) is a new design paradigm for system-on-chip intraconnections in the billion-transistor era. Application specific on-chip network design is essential for NoC success in this new era.This paper presents a class of source routing switch that can be used to efficiently form arbitrary network topologies and that can be optimized for various applications. Hardware description language versions of the networks can be generated automatically for simulations and for syntheses. A series of switches and networks has been configured with their performances including latency, delay, area, and power, and analyzed theoretically and experimentally. The results show that this NoC architecture provides a large design space for application specific on-chip network designs.

  15. 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...

  16. 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 ...

  17. 一种用于人脸检测SoC中的加速协处理器设计%Co-processor implementation for fast face detection in a system-on-chip

    Institute of Scientific and Technical Information of China (English)

    焦继业; 穆荣; 郝跃

    2011-01-01

    提出了一种改进的、适合硬件并行实现的Adaboost算法多层分类器协处理器架构.该协处理器由积分图数据快速读取模块、多层分类器Haar型特征值运算模块、DMA数据存取模块和协处理器接口模块组成,模块间采用流水线以及FIFO缓存实现数据并行处理,用于人脸检测SoC中加速人脸检测迭代过程.将该协处理器嵌入一个实际的人脸检测SoC中,只增加了SoC的少量面积,却明显提高了人脸检测的处理速度.人脸检测SoC在CYCLONE-ⅡEP2C70 FPGA上通过验证.实验结果显示,在系统工作频率为70MHz时,能以10帧每秒的处理速度检测彩色QVGA图像中的人脸.%An improved co-processor architecture suitable for hardware parallel implementation is proposed to perform the feature classification based on the Adaboost algorithm. The co-processor consists of image quick access module, module for calculating the Haar features, DMA data transfer module, and interface to the coprocessor module. Modules use the pipeline and FIFO buffer to process data to accelerate the iterative process of face detection. The co-processor only increases a small area in face detection SoC, but significantly improves the speed of face detection. In addition, we implement the proposed SoC on a CYCLONE-Ⅱ EP2C70 FPGA to show that object detection can be achieved at 10 frames per second at the system operating frequency of 70 MHz on color QVGA camera video.

  18. 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.

  19. Nanofluidic Lab-On-Chip Technology for DNA Identification

    Science.gov (United States)

    2013-09-30

    technical 3. DATES COVERED (From - To) May 2012 - Jun 2013 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Nanofluidic LaB-ON-Chip Technology for DNA...AVAILABILITY STATEMENT Publicly available. 3-0/ 3/Oo3o%J - 14. ABSTRACT In this project we have investigated the potential of nanofluidic lab-on...chip nanofluidic platforms may enable rapid and inexpensive, characterization and analysis of DNA biomarkers. Advantages include overall ease of

  20. Signal processing for on-chip space division multiplexing

    DEFF Research Database (Denmark)

    Peucheret, Christophe; Ding, Yunhong; Xu, Jing;

    2015-01-01

    Our recent results on the demonstration of on-chip mode-division multiplexing are reviewed, with special emphasis on nonlinear all-optical signal processing. Mode-selective parametric processes are demonstrated in a silicon-on-insulator waveguide.......Our recent results on the demonstration of on-chip mode-division multiplexing are reviewed, with special emphasis on nonlinear all-optical signal processing. Mode-selective parametric processes are demonstrated in a silicon-on-insulator waveguide....

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

    Science.gov (United States)

    Egel, Eugen; Meier, Christian; Csaba, György; Breitkreutz-von Gamm, Stephan

    2017-05-01

    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.

  2. 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.

  3. The Detection of Genetically Modified Organisms: An Overview

    Science.gov (United States)

    Ovesná, Jaroslava; Demnerová, Kateřina; Pouchová, Vladimíra

    Genetically modified organisms (GMOs) are those whose genetic material has been altered by the insertion of a new gene or by the deletion of an existing one(s). Modern biotechnology, in particular, the rise of genetic engineering, has supported the development of GMOs suitable for research purposes and practical applications (Gepts, 2002; Novoselova,Meuwissen, & Huirne, 2007; Sakakibara & Saito, 2006). For over 20 years GM bacteria and other GM organisms have been used in laboratories for the study of gene functions (Maliga & Small, 2007; Ratledge & Kristiansen, 2006). Agricultural plants were the first GMOs to be released into the environment and placed on the market. Farmers around the world use GMsoybeans, GMcorn and GM cotton that are herbicide tolerant, or insect resistant, or combine several traits that reduce the costs associated with crop production (Corinne, Fernandez-Cornejo, & Goodhue, 2004).

  4. Integrated Millimeter-Wave Antennas for On-Chip Communication

    Directory of Open Access Journals (Sweden)

    S. Zainud-Deen

    2016-03-01

    Full Text Available This paper introduces the design and analysis of circularly polarized (CP and dual-polarized on-chip microstrip antennas for wireless communication at 60 GHz. The CP on-chip antenna consists of a circular aluminum patch with two overlapped circular slots fed by the transmission line. The radiation characteristics of the CP have been analyzed using the finite integration technique and finite element method based electromagnetic solvers. The CP antenna introduces left-hand circular polarization and employs as on-chip transmitter. A design of dual-polarized on-chip microstrip antenna at 60 GHz is investigated and is employed as on-chip receiver. The dual ports of the dual polarized antenna are designed with high isolation between them in order to be used as a two on-chip receivers. The radiation characteristics of the dual-port antenna have been calculated. The effect of the separation distance between the CP-antenna and the dual-polarized antenna on the same chip has been investigated. The performance parameters like the reflection coefficient, transmission coefficient, and the transmission gain of the two antennas at different separation distances have been introduced.

  5. Multifunctional System-on-Glass for Lab-on-Chip applications.

    Science.gov (United States)

    Petrucci, G; Caputo, D; Lovecchio, N; Costantini, F; Legnini, I; Bozzoni, I; Nascetti, A; de Cesare, G

    2017-07-15

    Lab-on-Chip are miniaturized systems able to perform biomolecular analysis in shorter time and with lower reagent consumption than a standard laboratory. Their miniaturization interferes with the multiple functions that the biochemical procedures require. In order to address this issue, our paper presents, for the first time, the integration on a single glass substrate of different thin film technologies in order to develop a multifunctional platform suitable for on-chip thermal treatments and on-chip detection of biomolecules. The proposed System on-Glass hosts thin metal films acting as heating sources; hydrogenated amorphous silicon diodes acting both as temperature sensors to monitor the temperature distribution and photosensors for the on-chip detection and a ground plane ensuring that the heater operation does not affect the photodiode currents. The sequence of the technological steps, the deposition temperatures of the thin films and the parameters of the photolithographic processes have been optimized in order to overcome all the issues of the technological integration. The device has been designed, fabricated and tested for the implementation of DNA amplification through the Polymerase Chain Reaction (PCR) with thermal cycling among three different temperatures on a single site. The glass has been connected to an electronic system that drives the heaters and controls the temperature and light sensors. It has been optically and thermally coupled with another glass hosting a microfluidic network made in polydimethylsiloxane that includes thermally actuated microvalves and a PCR process chamber. The successful DNA amplification has been verified off-chip by using a standard fluorometer.

  6. Plasmonic SERS biosensing nanochips for DNA detection.

    Science.gov (United States)

    Ngo, Hoan T; Wang, Hsin-Neng; Fales, Andrew M; Vo-Dinh, Tuan

    2016-03-01

    The development of rapid, cost-effective DNA detection methods for molecular diagnostics at the point-of-care (POC) has been receiving increasing interest. This article reviews several DNA detection techniques based on plasmonic-active nanochip platforms developed in our laboratory over the last 5 years, including the molecular sentinel-on-chip (MSC), the multiplex MSC, and the inverse molecular sentinel-on-chip (iMS-on-Chip). DNA probes were used as the recognition elements, and surface-enhanced Raman scattering (SERS) was used as the signal detection method. Sensing mechanisms were based on hybridization of target sequences and DNA probes, resulting in a distance change between SERS reporters and the nanochip's plasmonic-active surface. As the field intensity of the surface plasmon decays exponentially as a function of distance, the distance change in turn affects SERS signal intensity, thus indicating the presence and capture of the target sequences. Our techniques were single-step DNA detection techniques. Target sequences were detected by simple delivery of sample solutions onto DNA probe-functionalized nanochips and measuring the SERS signal after appropriate incubation times. Target sequence labeling or washing to remove unreacted components was not required, making the techniques simple, easy-to-use, and cost-effective. The usefulness of the nanochip platform-based techniques for medical diagnostics was illustrated by the detection of host genetic biomarkers for respiratory viral infection and of the dengue virus gene.

  7. A Domain-Independent Window Approach to Multiclass Object Detection Using Genetic Programming

    Directory of Open Access Journals (Sweden)

    Mengjie Zhang

    2003-07-01

    Full Text Available This paper describes a domain-independent approach to the use of genetic programming for object detection problems in which the locations of small objects of multiple classes in large images must be found. The evolved program is scanned over the large images to locate the objects of interest. The paper develops three terminal sets based on domain-independent pixel statistics and considers two different function sets. The fitness function is based on the detection rate and the false alarm rate. We have tested the method on three object detection problems of increasing difficulty. This work not only extends genetic programming to multiclass-object detection problems, but also shows how to use a single evolved genetic program for both object classification and localisation. The object classification map developed in this approach can be used as a general classification strategy in genetic programming for multiple-class classification problems.

  8. 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.

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

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-03

    Jun 3, 2009 ... in phenotypic differences (Parra et al., 2003; Brutsaert et al., 2005) ... tion of neutral genetic variation among popula-tions, and ... relationship among breeds and exploring the evolution .... was not only related with their origin, but also related with ... National High Technology Research and Development.

  10. Structural chromosomal anomalies detected by prenatal genetic diagnosis: our experience.

    Science.gov (United States)

    Farcaş, Simona; Crişan, C D; Andreescu, Nicoleta; Stoian, Monica; Motoc, A G M

    2013-01-01

    The prenatal diagnosis is currently widely spread and facilitates the acquiring of important genetic information about the fetus by a rate extremely accelerate and considered without precedent. In this paper, we like to present our experience concerning the genetic diagnosis and counseling offered for pregnancies in which a structural chromosomal aberration was found. The study group is formed by 528 prenatal samples of amniotic fluid and chorionic villi, received by our laboratory from 2006 through October 2012 for cytogenetic diagnosis. The appropriate genetic investigation was selected based on the indications for prenatal diagnosis. The cases with structural chromosomal anomalies and polymorphic variants were analyzed as regard to the maternal age, gestational age, referral indications and type of chromosomal anomaly found. A total number of 21 structural chromosomal anomalies and polymorphic variants were identified in the study group. Out of 21 structural chromosomal anomalies and polymorphic variants, six deletions and microdeletions, four situations with abnormal long "p" arm of acrocentric chromosomes, two duplications, two reciprocal translocations, two inversions, two additions, one Robertsonian translocation associating trisomy 13, one 9q heteromorphism and one complex chromosome rearrangement were noticed. To the best of our knowledge, this is the first Romanian study in which the diagnostic strategies and the management of the prenatal cases with structural rearrangements are presented. The data provided about the diagnosis strategy and the management of the prenatal cases with structural chromosomal anomalies represents a useful tool in genetic counseling of pregnancies diagnosed with rare structural chromosomal anomalies.

  11. Detected microsatellite polymorphisms in genetically altered inbred mouse strains.

    Science.gov (United States)

    Du, Xiaoyan; Cui, Jing; Wang, Chao; Huo, Xueyun; Lu, Jing; Li, Yichen; Chen, Zhenwen

    2013-08-01

    Microsatellites are 50-200 repetitive DNA sequences composed of 1- to 6-base-pair-long reiterative motifs within the genome. They are vulnerable to DNA modifications, such as recombination and/or integration, and are recognized as "sentinel" DNA. Our previous report indicated that the genotypes of the microsatellite loci could change from mono- to poly-morphisms (CMP) in gene knockout (KO) mice, implying that genetic modification induces microsatellite mutation. However, it is still unclear whether the random insertion of DNA fragments into mice genomes produced via transgene (Tg) or N-ethyl-N-nitrosourea (ENU) would also result in microsatellite mutations or microsatellite loci genotypes changes. This study was designed to find possible clues to answer this question. In brief, 198 microsatellite loci that were distributed among almost all of the chromosomes (except for the Y) were examined through polymerase chain reaction to screen possible CMPs in six Tg strains. First, for each strain, the microsatellite sequences of all loci were compared between Tg and the corresponding background strain to exclude genetic interference. Simultaneously, to exclude spontaneous mutation-related CMPs that might exist in the examined six strains, mice from five spontaneously mutated inbred strains were used as the negative controls. Additionally, the sequences of all loci in these spontaneous mutated mice were compared to corresponding genetic background controls. The results showed that 40 of the 198 (20.2%) loci were identified as having CMPs in the examined Tg mice strains. The CMP genotypes were either homozygous or heterozygous compared to the background controls. Next, we applied the 40 CMP positive loci in ENU-mutated mice and their corresponding background controls. After that, a general comparison of CMPs that exist among Tg, ENU-treated and KO mouse strains was performed. The results indicated that four (D11mit258, D13mit3, D14mit102 and DXmit172) of the 40 (10%) CMP

  12. 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.

  13. A Joint-Coding Scheme With Crosstalk Avoidance in Network On Chip

    Directory of Open Access Journals (Sweden)

    Fen Ge

    2013-01-01

    Full Text Available The reliable transfer in Network on Chip can be guaranteed by crosstalk avoidance and error detection code. In this paper,we propose a joint coding scheme combined with crosstalk avoidance coding with error control coding. The Fibonacci numeral system is applied to satisfy the requirement of crosstalk avoidance coding, and the error detection is achieved by adding parity bits. We also implement the codec in register transfer level. Furthermore, the schemes of codec applying to fault-tolerant router are analyzed. The experimental result shows that "once encode, multiple decode" scheme outperforms other schemes in trade-o_ of delay, area and power.

  14. Genetic algorithm for flood detection and evacuation route planning

    Science.gov (United States)

    Gomes, Rahul; Straub, Jeremy

    2017-05-01

    A genetic-type algorithm is presented that uses satellite geospatial data to determine the most probable path to safety for individuals in a disaster area, where a traditional routing system cannot be used. The algorithm uses geological features and disaster information to determine the shortest safe path. It predicts how a flood can change a landform over time and uses this data to predict alternate routes. It also predicts safe routes in rural locations where GPS/map-based routing data is unavailable or inaccurate. Reflectance and a supervised classification algorithm are used and the output is compared with RFPI and PCR-GLOBWB data.

  15. PERFORMANCE ENHANCED ROUTER DESIGN FOR NETWORK ON CHIP

    Directory of Open Access Journals (Sweden)

    Anbu chozhan.P

    2013-04-01

    Full Text Available Network on chip is a new paradigm for on chip design that is able to sustain the communication provisions for the SoC with the desired performance. NOC applies networking methodology concepts to system on chip data transfer and it gives noticeable elevation over conventionalbus based communication. NOC router is the backbone of on chip communication which directs the flow of data. In NOC router the arbiter is used during number of inputs request for the similar out port. Arbiter generates the grant based on the priority and previous granted input. For NOC router we have design the efficient round robin arbiter and analyse the power and area. In this paper on chip router is designed with a buffering technique of FWFT based asynchronous FIFO which improves timing and reduce power consumption. The proposed design of router is simulated and synthesized in Xilinx ISE 13.2 and the source code is written in Verilog. Cadence soc encounter of technology ami035 is used to generate layout of router and RTL compiler is used to compute area, power and timing.

  16. 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 s

  17. 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

  18. An Enhancement of the Replacement Steady State Genetic Algorithm for Intrusion Detection

    Directory of Open Access Journals (Sweden)

    Reyadh Naoum

    2014-06-01

    Full Text Available In these days, Internet and computer systems face many intrusions, thus for this purpose we need to build a detection or prevention security system. Intrusion Detection System (IDS is a system used to detect attacks, Steady State Genetic Algorithm (SSGA is applied to support IDS by supplying the rule pool with additional data, these data can be used in testing phase to detect the attacks. The main goal of this research is to enhance Replacement steady state genetic algorithm to detect intrusions. This enhancement has been achieved by comparing replacement methods. This research proved that the Triple Tournament Replacement is better than Binary Tournament Replacement to increase Detection Rate and there are no effects on False Positive Rate. In this research represent the results of DR equal 100% for three types of attack (DoS, Probe and R2T, and 53% for U2R.

  19. Prenetal Detection of Oral Clefts : Diagnostic, Genetic and Ethical Aspects

    NARCIS (Netherlands)

    Maarse, W.

    2015-01-01

    Since the introduction of routine prenatal screening with ultrasound in the Netherlands in 2007, parents are confronted with the diagnosis of oral cleft (OC) already during pregnancy. This imposed a new dimension in cleft care in the Netherlands. As a consequence to increasing prenatal detection rat

  20. 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...

  1. Waveguide coupled resonance fluorescence from on-chip quantum emitter.

    Science.gov (United States)

    Makhonin, Maxim N; Dixon, James E; Coles, Rikki J; Royall, Ben; Luxmoore, Isaac J; Clarke, Edmund; Hugues, Maxime; Skolnick, Maurice S; Fox, A Mark

    2014-12-10

    Resonantly driven quantum emitters offer a very promising route to obtain highly coherent sources of single photons required for applications in quantum information processing (QIP). Realizing this for on-chip scalable devices would be important for scientific advances and practical applications in the field of integrated quantum optics. Here we report on-chip quantum dot (QD) resonance fluorescence (RF) efficiently coupled into a single-mode waveguide, a key component of a photonic integrated circuit, with a negligible resonant laser background and show that the QD coherence is enhanced by more than a factor of 4 compared to off-resonant excitation. Single-photon behavior is confirmed under resonant excitation, and fast fluctuating charge dynamics are revealed in autocorrelation g((2)) measurements. The potential for triggered operation is verified in pulsed RF. These results pave the way to a novel class of integrated quantum-optical devices for on-chip quantum information processing with embedded resonantly driven quantum emitters.

  2. Exploring Alternative Topologies for Network-on-Chip Architectures

    Directory of Open Access Journals (Sweden)

    Shafi Patel

    2011-01-01

    Full Text Available With increase in integration density and complexity of the system-on-Chip (SOC, the conventional interconnects are not suitable to fulfill the demands. The application of traditional network technologies in the form of Network-on-Chip is a potential solution. NoC design space has many variables. Selection of a better topology results in lesser complexities and better power-efficiency. In the proposed work, key research area in Network-on-chip design targeting communication infrastructure specially focusing on optimized topology design is worked upon. The simulation is modeled using a conventional network simulator tool packet tracer 5.3, in which by selecting proposed Topology 35.7 % reduction in traversing the longest path is observed.

  3. Genetic characterization of feline bocavirus detected in cats in Japan.

    Science.gov (United States)

    Takano, Tomomi; Takadate, Yoshihiro; Doki, Tomoyoshi; Hohdatsu, Tsutomu

    2016-10-01

    Feline bocavirus (FBoV) has been classified into three genotypes (FBoV1-FBoV3). FBoVs are mainly detected in feces. In the present study, we collected rectal swabs from cats in Japan and examined the samples for the presence of FBoV. The FBoV infection rate was 9.9 % in 101 cats. No significant association was observed between FBoV infection and clinical symptoms. Based on the full-length NS1 protein, the three strains of FBoVs detected in the present study shared high homologies with the genotype 2 FBoV POR1 strain. This is the first study to report FBoV in Japan.

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

    Science.gov (United States)

    Ladics, Gregory S; Bartholomaeus, Andrew; Bregitzer, Phil; Doerrer, Nancy G; Gray, Alan; Holzhauser, Thomas; Jordan, Mark; Keese, Paul; Kok, Esther; Macdonald, Phil; Parrott, Wayne; Privalle, Laura; Raybould, Alan; Rhee, Seung Yon; Rice, Elena; Romeis, Jörg; Vaughn, Justin; Wal, Jean-Michel; Glenn, Kevin

    2015-08-01

    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 scientists from academia, government, and the agro-biotech industry. The objectives of the meeting were to explore current knowledge and identify areas requiring further study on unintended effects in plants and to discuss how this information can inform and improve genetically modified (GM) crop risk assessments. The meeting featured presentations on the molecular basis of plant genome variability in general, unintended changes at the molecular and phenotypic levels, and the development and use of hypothesis-driven evaluations of unintended effects in assessing conventional and GM crops. The development and role of emerging "omics" technologies in the assessment of unintended effects was also discussed. Several themes recurred in a number of talks; for example, a common observation was that no system for genetic modification, including conventional methods of plant breeding, is without unintended effects. Another common observation was that "unintended" does not necessarily mean "harmful". This paper summarizes key points from the information presented at the meeting to provide readers with current viewpoints on these topics.

  5. On-Chip Integration of Cell-Free Gene Expression

    Science.gov (United States)

    Buxboim, Amnon; Morpurgo, Margherita; Bar-Dagan, Maya; Frydman, Veronica; Zbaida, David; Bar-Ziv, Roy

    2006-03-01

    We present a synthetic approach for the study of gene networks in vitro which is complementary to traditional in vivo methodologies. We have developed a technology for submicron integration of functional genes and on-chip protein synthesis using a cell-free transcription/translation system. The interaction between genes is facilitated by diffusion of on-chip gene expression products from `source' genes towards `acceptor' genes. Our technology is simple and inexpensive and can serve as an improved platform for a wide variety of protein and DNA biochip applications.

  6. Entangled photons from on-chip slow light

    CERN Document Server

    Takesue, Hiroki; Kuramochi, Eiichi; Notomi, Masaya

    2014-01-01

    We report the first entanglement generation experiment using an on-chip slow light device. With highly efficient spontaneous four-wave mixing enhanced by the slow light effect in a coupled resonator optical waveguide based on a silicon photonic crystal, we generated 1.5-$\\mu$m-band high-dimensional time-bin entangled photon pairs. We undertook two-photon interference experiments and observed the coincidence fringes with visibilities $>74\\%$. The present result enables us to realize an on-chip entanglement source with a very small footprint, which is an essential function for quantum information processing based on integrated quantum photonics.

  7. Ultrasound assisted particle and cell manipulation on-chip.

    Science.gov (United States)

    Mulvana, Helen; Cochran, Sandy; Hill, Martyn

    2013-11-01

    Ultrasonic fields are able to exert forces on cells and other micron-scale particles, including microbubbles. The technology is compatible with existing lab-on-chip techniques and is complementary to many alternative manipulation approaches due to its ability to handle many cells simultaneously over extended length scales. This paper provides an overview of the physical principles underlying ultrasonic manipulation, discusses the biological effects relevant to its use with cells, and describes emerging applications that are of interest in the field of drug development and delivery on-chip. © 2013.

  8. 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

  9. On-chip photonic tweezers for photonics, microfluidics, and biology

    Science.gov (United States)

    Pin, Christophe; Renaut, Claude; Tardif, Manon; Jager, Jean-Baptiste; Delamadeleine, Eric; Picard, Emmanuel; Peyrade, David; Hadji, Emmanuel; de Fornel, Frédérique; Cluzel, Benoît

    2017-04-01

    Near-field optical forces arise from evanescent electromagnetic fields and can be advantageously used for on-chip optical trapping. In this work, we investigate how evanescent fields at the surface of photonic cavities can efficiently trap micro-objects such as polystyrene particles and bacteria. We study first the influence of trapped particle's size on the trapping potential and introduce an original optofluidic near-field optical microscopy technique. Then we analyze the rotational motion of trapped clusters of microparticles and investigate their possible use as microfluidic micro-tools such as integrated micro-flow vane. Eventually, we demonstrate efficient on-chip optical trapping of various kinds of bacteria.

  10. Advances on Microsized On-Chip Lithium-Ion Batteries.

    Science.gov (United States)

    Liu, Lixiang; Weng, Qunhong; Lu, Xueyi; Sun, Xiaolei; Zhang, Lin; Schmidt, Oliver G

    2017-09-27

    Development of microsized on-chip batteries plays an important role in the design of modern micro-electromechanical systems, miniaturized biomedical sensors, and many other small-scale electronic devices. This emerging field intimately correlates with the topics of rechargeable batteries, nanomaterials, on-chip microfabrication, etc. In recent years, a number of novel designs are proposed to increase the energy and power densities per footprint area, as well as other electrochemical performances of microsized lithium-ion batteries. These advances may guide the pathway for the future development of microbatteries. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Highly-integrated lab-on-chip system for point-of-care multiparameter analysis.

    Science.gov (United States)

    Schumacher, Soeren; Nestler, Jörg; Otto, Thomas; Wegener, Michael; Ehrentreich-Förster, Eva; Michel, Dirk; Wunderlich, Kai; Palzer, Silke; Sohn, Kai; Weber, Achim; Burgard, Matthias; Grzesiak, Andrzej; Teichert, Andreas; Brandenburg, Albrecht; Koger, Birgit; Albers, Jörg; Nebling, Eric; Bier, Frank F

    2012-02-07

    A novel innovative approach towards a marketable lab-on-chip system for point-of-care in vitro diagnostics is reported. In a consortium of seven Fraunhofer Institutes a lab-on-chip system called "Fraunhofer ivD-platform" has been established which opens up the possibility for an on-site analysis at low costs. The system features a high degree of modularity and integration. Modularity allows the adaption of common and established assay types of various formats. Integration lets the system move from the laboratory to the point-of-need. By making use of the microarray format the lab-on-chip system also addresses new trends in biomedicine. Research topics such as personalized medicine or companion diagnostics show that multiparameter analyses are an added value for diagnostics, therapy as well as therapy control. These goals are addressed with a low-cost and self-contained cartridge, since reagents, microfluidic actuators and various sensors are integrated within the cartridge. In combination with a fully automated instrumentation (read-out and processing unit) a diagnostic assay can be performed in about 15 min. Via a user-friendly interface the read-out unit itself performs the assay protocol, data acquisition and data analysis. So far, example assays for nucleic acids (detection of different pathogens) and protein markers (such as CRP and PSA) have been established using an electrochemical read-out based on redoxcycling or an optical read-out based on total internal reflectance fluorescence (TIRF). It could be shown that the assay performance within the cartridge is similar to that found for the same assay in a microtiter plate. Furthermore, recent developments are the integration of sample preparation and polymerase chain reaction (PCR) on-chip. Hence, the instrument is capable of providing heating-and-cooling cycles necessary for DNA-amplification. In addition to scientific aspects also the production of such a lab-on-chip system was part of the development since

  12. Detection of Babesia bigemina in cattle of different genetic groups and in Rhipicephalus (Boophilus) microplus tick.

    Science.gov (United States)

    Oliveira, M C S; Oliveira-Sequeira, T C G; Regitano, L C A; Alencar, M M; Néo, T A; Silva, A M; Oliveira, H N

    2008-08-17

    Babesia bigemina infections were investigated in four genetic groups of beef cattle and in Rhipicephalus (Boophilus) microplus engorged female ticks. Blood samples and engorged female ticks were collected from 15 cows and 15 calves from each of the following genetic groups: Nelore, Angus x Nelore, Canchim x Nelore, and Simmental x Nelore. Microscopic examination of blood smears and tick hemolymph revealed that merozoites of B. bigemina (6/60) as well as kinetes of Babesia spp. (9/549) were only detected in samples (blood and ticks, respectively) originated from calves. PCR-based methods using primers for specific detection of B. bigemina revealed 100% infection in both calves and cows, regardless the genetic group. Tick infection was detected by nested-PCR amplifications showing that the frequency of B. bigemina was higher (P0.05).

  13. Applied physics: Gravity measurements on chips

    Science.gov (United States)

    Rymer, Hazel

    2016-03-01

    Gravimeters have applications ranging from oil exploration to the detection of underground tunnels, but size and lack of portability have limited their field use. A device the size of a postage stamp promises fresh opportunities. See Letter p.614

  14. A Genetic Algorithm and Fuzzy Logic Approach for Video Shot Boundary Detection

    Directory of Open Access Journals (Sweden)

    Dalton Meitei Thounaojam

    2016-01-01

    Full Text Available This paper proposed a shot boundary detection approach using Genetic Algorithm and Fuzzy Logic. In this, the membership functions of the fuzzy system are calculated using Genetic Algorithm by taking preobserved actual values for shot boundaries. The classification of the types of shot transitions is done by the fuzzy system. Experimental results show that the accuracy of the shot boundary detection increases with the increase in iterations or generations of the GA optimization process. The proposed system is compared to latest techniques and yields better result in terms of F1score parameter.

  15. A Genetic Algorithm and Fuzzy Logic Approach for Video Shot Boundary Detection.

    Science.gov (United States)

    Thounaojam, Dalton Meitei; Khelchandra, Thongam; Manglem Singh, Kh; Roy, Sudipta

    2016-01-01

    This paper proposed a shot boundary detection approach using Genetic Algorithm and Fuzzy Logic. In this, the membership functions of the fuzzy system are calculated using Genetic Algorithm by taking preobserved actual values for shot boundaries. The classification of the types of shot transitions is done by the fuzzy system. Experimental results show that the accuracy of the shot boundary detection increases with the increase in iterations or generations of the GA optimization process. The proposed system is compared to latest techniques and yields better result in terms of F1score parameter.

  16. 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.

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

    CERN Document Server

    Liapis, Andreas C; Siddiqui, Mahmudur R; Shi, Zhimin; Boyd, Robert W

    2015-01-01

    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.

  18. 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.

  19. In situ detection of horizontal transfer of mobile genetic elements

    DEFF Research Database (Denmark)

    Haagensen, Janus Anders Juul; Hansen, Susse Kirkelund; Johansen, Tove;

    2002-01-01

    Plasmid transfer was investigated in microbial populations associated with different types of surfaces. The general strategy behind these investigations was to label the transferable plasmid with a gene encoding a fluorescent protein in order to make it a transfer reporter. This was achieved...... promoters (transfer reporters) it was thus possible to detect transfer events in situ and correlate these with either the location of donor and recipient cells or with the growth activity of the cells. In some cases, expression of unstable Gfp from a growth-controlled promoter, rrnB from Escherichia coli...... by fusing the reporter gene with a lac promoter expression cassette and combining this with a donor cell-associated lacI repressor cassette. After construction of a range of strains and plasmids with combinations of genes expressing fluorescent proteins from constitutive (cell tagging) or regulated...

  20. 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

  1. Comb Capacitor Structures for On-Chip Physical Uncloneable Function

    NARCIS (Netherlands)

    Roy, D.; Klootwijk, J.H.; Verhaegh, N.A.M.; Roosen, H.H.A.J.; Wolters, Robertus A.M.

    2009-01-01

    Planar inter-digitated comb capacitor structures are an excellent tool for on-chip capacitance measurement and evaluation of properties of coating layers with varying composition. These comb structures are easily fabricated in a single step in the last metallization layer of a standard IC process.

  2. 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...

  3. Exploration within the Network-on-Chip Paradigm

    NARCIS (Netherlands)

    Wolkotte, Pascal Theodoor

    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

  4. A virtual channel router for on-chip networks

    NARCIS (Netherlands)

    Kavaldjiev, Nikolay; Smit, Gerard J.M.; Jansen, Pierre G.

    2004-01-01

    This paper proposes an architecture of a virtual channel router for an on-chip network1. The router has simple dynamic arbitration which is deterministic and fair. We show that the size of the proposed router is reduced by 49% and the speed increases 1.4 times compared to a conventional virtual chan

  5. A virtual channel router for on-chip networks

    OpenAIRE

    Kavaldjiev, Nikolay; Smit, Gerard J.M.; Jansen, Pierre G.

    2004-01-01

    This paper proposes an architecture of a virtual channel router for an on-chip network1. The router has simple dynamic arbitration which is deterministic and fair. We show that the size of the proposed router is reduced by 49% and the speed increases 1.4 times compared to a conventional virtual channel router.

  6. Two Architectures for On-chip Virtual Channel Router

    NARCIS (Netherlands)

    Kavaldjiev, Nikolay; Smit, Gerard J.M.; Jansen, Pierre G.

    2004-01-01

    This paper compares the implementation results of two architectures for virtual channel router. Since the router is used for building an on-chip network, its small size is critical. Together with the total design area we provide information about the distribution of this area between the main router

  7. A Virtual Channel Router for On-chip Networks

    NARCIS (Netherlands)

    Kavaldjiev, Nikolay; Smit, Gerard J.M.; Jansen, Pierre G.

    2004-01-01

    This paper proposes an architecture of a virtual channel router for an on-chip network1. The router has simple dynamic arbitration which is deterministic and fair. We show that the size of the proposed router is reduced by 49% and the speed increases 1.4 times compared to a conventional virtual chan

  8. A Virtual Channel Router for On-chip Networks

    NARCIS (Netherlands)

    Kavaldjiev, N.K.; Smit, Gerardus Johannes Maria; Jansen, P.G.

    This paper proposes an architecture of a virtual channel router for an on-chip network1. The router has simple dynamic arbitration which is deterministic and fair. We show that the size of the proposed router is reduced by 49% and the speed increases 1.4 times compared to a conventional virtual

  9. Two Architectures for On-chip Virtual Channel Router

    NARCIS (Netherlands)

    Kavaldjiev, N.K.; Smit, Gerardus Johannes Maria; Jansen, P.G.

    2004-01-01

    This paper compares the implementation results of two architectures for virtual channel router. Since the router is used for building an on-chip network, its small size is critical. Together with the total design area we provide information about the distribution of this area between the main router

  10. On-chip separation and sensing systems for hydrodynamic chromatography

    NARCIS (Netherlands)

    Blom, M.T.

    2002-01-01

    The feasibility of on-chip analytical separations using planar hydrodynamic chromatography (HDC) in Pyrex-silicon and fused silica chips has been demonstrated. In order to sketch the analytical separations area in which the HDC chip has to operate, an introduction was given of important macro-scale

  11. Customizing and hardwiring on-chip interconnects in FPGAs

    NARCIS (Netherlands)

    Hur, J.Y.

    2011-01-01

    This thesis presents our investigations on how to efficiently utilize on-chip wires to improve network performance in reconfigurable hardware. A fieldprogrammable gate array (FPGA), as a key component in a modern reconfigurable platform, accommodates many-millions of wires and the on-demand

  12. Field Programmable Gate Arrays with Hardwired Networks on Chip

    NARCIS (Netherlands)

    Wahlah, M.A.

    2012-01-01

    Technology down-scaling and platform-based designs have enforced a number of application and architecture trends for system-on-chip (SOC) designs. A modern SOC is now a multi-functional machine that can execute a large number of complex applications by using tens or even hundreds of intellectual

  13. Reverse Engineering Human Pathophysiology with Organs-on-Chips.

    Science.gov (United States)

    Ingber, Donald E

    2016-03-10

    While studies of cultured cells have led to new insights into biological control, greater understanding of human pathophysiology requires the development of experimental systems that permit analysis of intercellular communications and tissue-tissue interactions in a more relevant organ context. Human organs-on-chips offer a potentially powerful new approach to confront this long-standing problem.

  14. Inkjet printed structures for smart lab-on-chip systems

    Science.gov (United States)

    Beckert, E.; Eberhardt, R.; Pabst, Oliver; Kemper, Falk; Shu, Zhe; Tünnermann, Andreas; Perelaer, Jolke; Schubert, Ulrich; Becker, Holger

    2013-03-01

    Inkjet printing is a digital printing technique that is capable of depositing not only inks, but functional materials onto different substrates in an additive way. In this paper, applications of inkjet printed structures for microfluidic lab-on-chip systems are discussed. Such systems are promising for different chemical or biochemical analysis tasks carried out at the Point-of-Care level and therefore due to cost reasons are often fabricated from polymers. The paper discusses inkjetprinted wiring structures and electroactive polymer (EAP) actuators for use in microfluidic lab-on-chip systems. Silver and gold wirings are shown that are fabricated by printing metal nanoparticle inks onto polymer substrates. After printing the structures are sintered using argon plasma sintering, a low-temperature sintering process that is compatible with polymer substrates. The wirings consist of several electrode like structures and contact pads and feature minimum structure sizes of approximately 70 μm. They can be used for electrodes, fluid presence detectors and localized ohmic heaters in lab-on-chip systems. Based on that an all inkjet-printed EAP actuator then is discussed. Membrane-type bending actuators generate deflections of approximately 5 μm when being driven at a resonance frequency of 1.8 kHz with 110 V. Derived from that and assuming passive valves on-chip pumping rates in the range of 0.5 ml/min can be estimated.

  15. Performance Analysis on Router Arbitration for On-chip Networking

    Directory of Open Access Journals (Sweden)

    G. Selvaraj

    2014-08-01

    Full Text Available This study is a comprehensive report on performance analyses of Round Robin and matrix arbitrations to enhance the reliability of on-chip networks. Arbiter is used in Network-on-Chip (NoC router when number of input ports requested is the same as output ports. If many inputs are requested for same output port, the matrix arbiter deals it by forming a 5×5 matrix based on input and output ports. Next, it allots the priority to the requested input ports and simultaneously generates a control signal for selecting the input port to send the packet to output port. The Robin arbiter generates the grant signal on the basis of priority allotted to the input ports. The simulation results of arbitration analysis shows that the router design of front end model consumes less power by 8% and occupies smaller area by 3% on chip. The area on chip is around 64% of available area using Round Robin arbitration compare to that of matrix arbitration. This study also implements hamming distance in order to check the error free data transmission of the NoC router.

  16. Novel on-chip spiral inductors with back hollow structure

    Science.gov (United States)

    Wang, Gang; Liu, Houfang; Li, Xiaoning; Qiu, Haochuan; Yang, Yi; Ren, Tian-Ling

    2017-01-01

    In this work, on-chip spiral inductors with back hollow structure have been prepared on the 500 μm thick silicon substrate with high resistivity (ρ > 5000Ωcm). The silicon underneath the inductor region has been completely etched by deep etching process in order to reduce the substrate eddy current losses. Several types of square spiral on-chip inductors with different metal width (w) and line spacing (s) in the case of w + s = 40μm were fabricated. The experimental results are verified by FEM simulation using HFSS software. The results show that the Q-factor and self-resonance frequency of back hollow structure inductors are both enhanced compared with the conventional inductors. Furthermore, narrower width of coils for the on-chip spiral inductors with back hollow structure can result in higher Q-factor, inductance L and self-resonance frequency, which provide some important design guides for the fabrication of the high performance on-chip inductors.

  17. Comb Capacitor Structures for On-Chip Physical Uncloneable Function

    NARCIS (Netherlands)

    Roy, D.; Klootwijk, J.H.; Verhaegh, N.A.M.; Roosen, H.H.A.J.; Wolters, R.A.M.

    2009-01-01

    Planar inter-digitated comb capacitor structures are an excellent tool for on-chip capacitance measurement and evaluation of properties of coating layers with varying composition. These comb structures are easily fabricated in a single step in the last metallization layer of a standard IC process. C

  18. 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

  19. A Light-Weight Statically Scheduled Network-on-Chip

    DEFF Research Database (Denmark)

    Sørensen, Rasmus Bo; Schoeberl, Martin; Sparsø, Jens

    2012-01-01

    This paper investigates how a light-weight, statically scheduled network-on-chip (NoC) for real-time systems can be designed and implemented. The NoC provides communication channels between all cores with equal bandwidth and latency. The design is FPGA-friendly and consumes a minimum of resources...

  20. Customizing and hardwiring on-chip interconnects in FPGAs

    NARCIS (Netherlands)

    Hur, J.Y.

    2011-01-01

    This thesis presents our investigations on how to efficiently utilize on-chip wires to improve network performance in reconfigurable hardware. A fieldprogrammable gate array (FPGA), as a key component in a modern reconfigurable platform, accommodates many-millions of wires and the on-demand reconfig

  1. Detection and Genetic Characterization of Rabies Virus from Human Patients

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Saliva and blood were collected from two patients who had not received post exposure prophylaxis in the cities of Wenzhou and Xinning respectively. Both patients were confirmed as positive for rabies by detection of rabies virus specific nucleoprotein antibodies in the sera by Western Blot. However, rabies virus specific RNA was only identified in the saliva collected from the patient in Wenzhou. Furthermore, the isolate Zhejiang Wz0 (H) was obtained by inoculating one-day-old suckling mice. Both nucleoprotein (N) and glycoprotein (G) genes from the isolate were amplified by RT-PCR and sequenced. Phylogenetic analysis indicated that the isolate belonged to classic rabies virus, and shared a higher homology with the street viruses from dogs in the main endemic areas in China and the street virus from dogs in Indonesia than with other known strains. Further comparison of the deduced amino acid sequences between the isolate and the vaccine strains used in China showed that the virus had a higher level of homology with the vaccine strain CTN than with the other vaccine strains (3aG, PV, PM and ERA). In particular, amino acid residues substitutions located in antigenic site Ⅲ in the G protein, which could react with the neutralizing antibodies, were observed. These results suggested that the virus belonged to the classic rabies virus, and both N and G genes diverged from the current vaccine strains used in China at either the nucleotide or the amino acid level.

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

    Science.gov (United States)

    Akagi, Takanori; Kato, Kei; Kobayashi, Masashi; Kosaka, Nobuyoshi; Ochiya, Takahiro; Ichiki, Takanori

    2015-01-01

    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.

  4. 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.

  5. Detection of Genetic Diversity in Synthetic Hexaploid Wheats Using Microsatellite Markers

    Institute of Scientific and Technical Information of China (English)

    CHEN Guo-yue; LI Li-hui

    2007-01-01

    Ninety-five synthetic hexaploid wheats(2n=6x=42,AABBDD)were analyzed using 45 microsatellite markers to investigate the potential genetic diversity in wheat breeding programs.A total of 326 alleles were detected by these microsatellite primer pairs,with an average of 6.65 alleles per locus.The polymorphic information content(PIC),Simpson index(SI),and genetic similarity(GS)coefficient showed that the D genome is of the highest genetic diversity among the A,B,and D genomes in the synthetic hexaploid wheats.The results also indicated that the synthetic hexaploid wheat is an efficient way to enrich wheat genetic backgrounds,especially to use the genetic variations of the D genome from Aegilops squarrosa for wheat improvement.The UPGMA dendogram,based on a similarity matrix by a simple matching coefficient algorithm,delineated the above accessions into 5 major clusters and was in accordance with the available pedigree information.The results demonstrated the utility of microsatellite markers in detecting DNA polymorphism and estimating genetic diversity.

  6. 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.

  7. 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.

  8. Detecting Genetic Isolation in Human Populations: A Study of European Language Minorities

    Science.gov (United States)

    Capocasa, Marco; Battaggia, Cinzia; Anagnostou, Paolo; Montinaro, Francesco; Boschi, Ilaria; Ferri, Gianmarco; Alù, Milena; Coia, Valentina; Crivellaro, Federica; Bisol, Giovanni Destro

    2013-01-01

    The identification of isolation signatures is fundamental to better understand the genetic structure of human populations and to test the relations between cultural factors and genetic variation. However, with current approaches, it is not possible to distinguish between the consequences of long-term isolation and the effects of reduced sample size, selection and differential gene flow. To overcome these limitations, we have integrated the analysis of classical genetic diversity measures with a Bayesian method to estimate gene flow and have carried out simulations based on the coalescent. Combining these approaches, we first tested whether the relatively short history of cultural and geographical isolation of four “linguistic islands” of the Eastern Alps (Lessinia, Sauris, Sappada and Timau) had left detectable signatures in their genetic structure. We then compared our findings to previous studies of European population isolates. Finally, we explored the importance of demographic and cultural factors in shaping genetic diversity among the groups under study. A combination of small initial effective size and continued genetic isolation from surrounding populations seems to provide a coherent explanation for the diversity observed among Sauris, Sappada and Timau, which was found to be substantially greater than in other groups of European isolated populations. Simulations of micro-evolutionary scenarios indicate that ethnicity might have been important in increasing genetic diversity among these culturally related and spatially close populations. PMID:23418562

  9. Genetic variation in the vulnerable and endemic Monkey Puzzle tree, detected using RAPDs.

    Science.gov (United States)

    Bekessy, Sarah A; Allnutt, T R; Premoli, A C; Lara, A; Ennos, R A; Burgman, M A; Cortes, M; Newton, A C

    2002-04-01

    Araucaria araucana (Monkey Puzzle), a southern South American tree species of exceptional cultural and economic importance, is of conservation concern owing to extensive historical clearance and current human pressures. Random amplified polymorphic DNA (RAPD) markers were used to characterise genetic heterogeneity within and among 13 populations of this species from throughout its natural range. Extensive genetic variability was detected and partitioned by analysis of molecular variance, with the majority of variation existing within populations (87.2%), but significant differentiation was recorded among populations (12.8%). Estimates of Shannon's genetic diversity and percent polymorphism were relatively high for all populations and provide no evidence for a major reduction in genetic diversity from historical events, such as glaciation. All pairwise genetic distance values derived from analysis of molecular variance (Phi(ST)) were significant when individual pairs of populations were compared. Although populations are geographically divided into Chilean Coastal, Chilean Andes and Argentinean regions, this grouping explained only 1.77% of the total variation. Within Andean groups there was evidence of a trend of genetic distance with increasing latitude, and clustering of populations across the Andes, suggesting postglacial migration routes from multiple refugia. Implications of these results for the conservation and use of the genetic resource of this species are discussed.

  10. 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.

  11. Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution

    Science.gov (United States)

    Accurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described cow feces-spec...

  12. 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

  13. 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...

  14. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  15. Epigenetic-genetic chromosome dosage approach for fetal trisomy 21 detection using an autosomal genetic reference marker.

    Directory of Open Access Journals (Sweden)

    Yu K Tong

    Full Text Available BACKGROUND: The putative promoter of the holocarboxylase synthetase (HLCS gene on chromosome 21 is hypermethylated in placental tissues and could be detected as a fetal-specific DNA marker in maternal plasma. Detection of fetal trisomy 21 (T21 has been demonstrated by an epigenetic-genetic chromosome dosage approach where the amount of hypermethylated HLCS in maternal plasma is normalized using a fetal genetic marker on the Y chromosome as a chromosome dosage reference marker. We explore if this method can be applied on both male and female fetuses with the use of a paternally-inherited fetal single nucleotide polymorphism (SNP allele on a reference chromosome for chromosome dosage normalization. METHODOLOGY: We quantified hypermethylated HLCS molecules using methylation-sensitive restriction endonuclease digestion followed by real-time or digital PCR analyses. For chromosome dosage analysis, we compared the amount of digestion-resistant HLCS to that of a SNP allele (rs6636, a C/G SNP that the fetus has inherited from the father but absent in the pregnant mother. PRINCIPAL FINDINGS: Using a fetal-specific SNP allele on a reference chromosome, we analyzed 20 euploid and nine T21 placental tissue samples. All samples with the fetal-specific C allele were correctly classified. One sample from each of the euploid and T21 groups were misclassified when the fetal-specific G allele was used as the reference marker. We then analyzed 33 euploid and 14 T21 maternal plasma samples. All but one sample from each of the euploid and T21 groups were correctly classified using the fetal-specific C allele, while correct classification was achieved for all samples using the fetal-specific G allele as the reference marker. CONCLUSIONS: As a proof-of-concept study, we have demonstrated that the epigenetic-genetic chromosome dosage approach can be applied to the prenatal diagnosis of trisomy 21 for both male and female fetuses.

  16. 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. PMID:24250568

  17. 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.

  18. 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.

  19. Preprogrammed, parallel on-chip immunoassay using system-level capillarity control.

    Science.gov (United States)

    Kim, Sung-Jin; Paczesny, Sophie; Takayama, Shuichi; Kurabayashi, Katsuo

    2013-07-16

    Fully manual use of conventional multiwell plates makes enzyme-linked immunosorbent assay (ELISA)-based immunoassays highly time-consuming and labor-intensive. Here, we present a capillarity-driven on-chip immunoassay that greatly saves time and labor with an inexpensive setup. Our immunoassay process starts with pipetting multiple solutions into multiwells constructed on a microfluidic device chip. Subsequently, capillarity spontaneously transports multiple sample solutions and common reagent solutions into assigned detection channels on the chip in a purely passive and preprogrammed manner. Our device implements capillarity-driven immunoassays involving four sample and six reagent solutions within 30 min by orchestrating the functions of on-chip passive components. Notably, our immunoassay technique reduces the total number of pipetting processes by ~5 times, as compared to assays on multiwell plates (48 vs 10). This assay technique allows us to quantify the concentrations of C-reactive protein and suppressor of tumorigenicity 2 with a detection limit of 8 and 90 pM, respectively. This device should be useful for sophisticated, parallel biochemical microfluidic processing in point-of-care settings under limited resources.

  20. On-chip Fabrication of High Performance Nanostructured ZnO UV Detectors

    Science.gov (United States)

    Alenezi, Mohammad R.; Henley, Simon J.; Silva, S. R. P.

    2015-02-01

    Developing rationally controlled bottom-up device fabrication processes is essential for the achievement of high performance optimal devices. We report a controlled, seedless and site-selective hydrothermal technique to fabricate high-performance nanostructured ZnO UV-detectors directly on-chip. We demonstrate that by controlling the nanowire growth process, via tuning the experimental parameters such as the concentration of reactants and the growth time, and by introducing a refresh of the growth solution, the device structure efficiency can be enhanced to significantly improve its performance. The on-chip fabricated bridging nanosyringe ultraviolet detector demonstrates improved sensitivity (~105), nanowatts detectability, and ultrafast response-time (90 ms) and recovery-time (210 ms). The improvement in response-time and recovery-time is attributed to the unique nanowire-nanowire junction barrier dominated resistance and the direct contact between ZnO and Au electrodes. Furthermore, the enhanced sensitivity and nanowatts detectability of the bridging nanosyringe device are due to the reduction in dimensionality and ultrahigh surface-to-volume ratio. This work paves the way toward low cost, large scale, low temperature, seedless and site-selective fabrication of high performance ZnO nanowire sensors on flexible and transparent substrates.

  1. Differential detection of genetic Loci underlying stem and root lignin content in Populus.

    Directory of Open Access Journals (Sweden)

    Tongming Yin

    Full Text Available In this study, we established a comprehensive genetic map with a large number of progeny from a three-generation hybrid Populus intercross, and phenotyped the lignin content, S/G ratio and 28 cell wall subcomponents both in stems and roots for the mapping individuals. Phenotypic analysis revealed that lignin content and syringyl-to-guaiacyl (S/G ratio using pyrolysis molecular beam mass spectroscopy (pyMBMS varied among mapping individuals. Phenotypic analysis revealed that stem lignin content is significantly higher than that in root and the quantified traits can be classified into four distinct groups, with strong correlations observed among components within organs. Altogether, 179 coordinating QTLs were detected, and they were co-localized into 49 genetic loci, 27 of which appear to be pleiotropic. Many of the detected genetic loci were detected differentially in stem and root. This is the first report of separate genetic loci controlling cell wall phenotypes above and below ground. These results suggest that it may be possible to modify lignin content and composition via breed and/or engineer as a means of simultaneously improving Populus for cellulosic ethanol production and carbon sequestration.

  2. On-chip, photon-number-resolving, telecom-band detectors for scalable photonic information processing

    CERN Document Server

    Gerrits, Thomas; Gates, James C; Lita, Adriana E; Metcalf, Benjamin J; Calkins, Brice; Tomlin, Nathan A; Fox, Anna E; Linares, Antía Lamas; Spring, Justin B; Langford, Nathan K; Mirin, Richard P; Smith, Peter G R; Walmsley, Ian A; Nam, Sae Woo

    2011-01-01

    Integration is currently the only feasible route towards 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 5 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 \\pm 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.

  3. 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.

  4. [Detection of genetic variability in Cercospora kikuchii isolates from a single soybean field].

    Science.gov (United States)

    Lurá, M C; Di Conza, J A; González, A M; Latorre Rapela, M G; Turino, L; Ibáñez, M M; Iacona, V

    2007-01-01

    Detection of genetic variability in Cercospora kikuchii isolates from a single soybean field. Current knowledge about epidemiology and population structure of Cercospora kikuchii is little developed and no studies regarding this subject have been reported in Argentina. The aim of this work was to select primers to study genetic variability in C. kikuchii isolated from the same soybean field using RAPD (Random Amplified Polymorphism DNA). RAPD was applied to the DNA of 5 C. kikuchii, isolated from diseased tissue of the soybean in the same field, another isolate, from a strain collection. Out of seven primers, five of them proved to be useful to study the population of C. kikuchii isolates.

  5. 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....... 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....

  6. An electrochemiluminescence non-PCR method for the detection of genetically modified organisms

    Science.gov (United States)

    Liu, Jinfeng; Xing, Da; Zhu, Debin

    2006-09-01

    An electrochemiluminescence non-PCR method has been developed for the detection of genetically modified organisms (GMOs) in crops. Genomic DNA of GMOs was digested with two restriction endonucleases (FOK I and BsrD I), and hybridized with three Ru(bpy) 3 2+ (TBR)-labeled and one biotinylated probes. The hybridization products were captured onto streptavidin-coated paramagnetic beads, and detected by measuring the electrochemiluminescence (ECL) signal of the TBR label. Whether the tobaccos contain GM components was discriminated by detecting the ECL signal of CaMV35S promoter. The experiment results show that the detection limit for CaMV35S promoter is 100 fmol, and the GM components can be clearly identified in GM tobaccos. The ECL non-PCR method will provide a new means in GMOs detection due to its safety, simplicity and high efficiency.

  7. On-chip noninterference angular momentum multiplexing of broadband light.

    Science.gov (United States)

    Ren, Haoran; Li, Xiangping; Zhang, Qiming; Gu, Min

    2016-05-13

    Angular momentum division has emerged as a physically orthogonal multiplexing method in high-capacity optical information technologies. However, the typical bulky elements used for information retrieval from the overall diffracted field, based on the interference method, impose a fundamental limit toward realizing on-chip multiplexing. We demonstrate noninterference angular momentum multiplexing by using a mode-sorting nanoring aperture with a chip-scale footprint as small as 4.2 micrometers by 4.2 micrometers, where nanoring slits exhibit a distinctive outcoupling efficiency on tightly confined plasmonic modes. The nonresonant mode-sorting sensitivity and scalability of our approach enable on-chip parallel multiplexing over a bandwidth of 150 nanometers in the visible wavelength range. The results offer the possibility of ultrahigh-capacity and miniaturized nanophotonic devices harnessing angular momentum division.

  8. Power management design for lab-on-chip biosensors.

    Science.gov (United States)

    Xiaojian Yu; Moez, Kambiz; I-Chyn Wey; Jie Chen

    2016-08-01

    Over the past decades, we have witnessed the growth demands of portable lab-on-chip biosensors. These lab-on-chip devices are mostly powered by battery, and intelligent power management systems are required to provide supply voltage for different functional units on biosensors (e.g. a microfluidic control system might require higher voltage than the rest working units of biosensors). In this paper, a fully integrated multiple-stage voltage multiplier is proposed to provide high-voltage power needs. The proposed design was implemented with the IBM's 0.13um CMOS process with a maximum power efficiency of 81.02% and maximum voltage conversion efficiency of 99.8% under a supply voltage of 1.2 V.

  9. An on-chip diamond optical parametric oscillator

    CERN Document Server

    Hausmann, B J M; Venkataraman, V; Deotare, P; Loncar, M

    2013-01-01

    Efficient, on-chip optical nonlinear processes are of great interest for the development of compact, robust, low-power consuming systems for applications in spectroscopy, metrology, sensing and classical and quantum optical information processing. Diamond holds promise for these applications, owing to its exceptional properties. However, although significant progress has been made in the development of an integrated diamond photonics platform, optical nonlinearities in diamond have not been explored much apart from Raman processes in bulk samples. Here, we demonstrate optical parametric oscillations (OPO) via four wave mixing (FWM) in single crystal diamond (SCD) optical networks on-chip consisting of waveguide-coupled microring resonators. Threshold powers as low as 20mW are enabled by ultra-high quality factor (1*10^6) diamond ring resonators operating at telecom wavelengths, and up to 20 new wavelengths are generated from a single-frequency pump laser. We also report the inferred nonlinear refractive index...

  10. Phase-modulating lasers toward on-chip integration.

    Science.gov (United States)

    Kurosaka, Yoshitaka; Hirose, Kazuyoshi; Sugiyama, Takahiro; Takiguchi, Yu; Nomoto, Yoshiro

    2016-07-26

    Controlling laser-beam patterns is indispensable in modern technology, where lasers are typically combined with phase-modulating elements such as diffractive optical elements or spatial light modulators. However, the combination of separate elements is not only a challenge for on-chip miniaturisation but also hinders their integration permitting the switchable control of individual modules. Here, we demonstrate the operation of phase-modulating lasers that emit arbitrarily configurable beam patterns without requiring any optical elements or scanning devices. We introduce a phase-modulating resonator in a semiconductor laser, which allows the concurrent realisation of lasing and phase modulation. The fabricated devices are on-chip-sized, making them suitable for integration. We believe this work will provide a breakthrough in various laser applications such as switchable illumination patterns for bio-medical applications, structured illuminations, and even real three-dimensional or highly realistic displays, which cannot be realised with simple combinations of conventional devices or elements.

  11. Energy Consumption Oriented Network-on-Chip Mapping Method

    Directory of Open Access Journals (Sweden)

    Feichao Wang

    2013-12-01

    Full Text Available In this paper, mapping algorithm has been mainly studied. The main work and contribution have been generalized as follows: Through the research of existing on-chip network mapping algorithm and global optimization algorithm, a multi-step mapping algorithm for low-power consumption have been designed, which is combined with the task allocation and the task scheduling. Compared with the traditional mapping algorithm, the algorithm in this paper takes the factors of task scheduling and allocation into account, mapping algorithm has three steps: task scheduling, IP core mapping and data block mapping. The simulation results show that the mapping method in this paper can effectively reduce Network-on-Chip (NoC power consumption. 

  12. 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.

  13. APPLICATION OF GENETIC DEAFNESS GENE CHIP FOR DETECTION OF GENE MUTATION OF DEAFNESS IN PREGNANT WOMEN

    Institute of Scientific and Technical Information of China (English)

    CHANG Liang; ZHONG Su; ZHAO Nan; LIU Ping; ZHAO Yangyu; QIAO Jie

    2014-01-01

    Objective The study is to identify the carrier rate of common deafness mutation in Chinese pregnant women via detecting deafness gene mutations with gene chip. Methods The pregnant women in obstetric clinic without hearing impairment and hearing disorders family history were selected. The informed consent was signed. Peripheral blood was taken to extract genom-ic DNA. Application of genetic deafness gene chip for detecting 9 mutational hot spot of the most common 4 Chinese deafness genes, namely GJB2 (35delG,176del16bp, 235delC, 299delAT), GJB3 (C538T) ,SLC26A4 ( IVS72A>G, A2168G) and mito-chondrial DNA 12S rRNA (A1555G, C1494T) . Further genetic testing were provided to the spouses and newborns of the screened carriers. Results Peripheral blood of 430 pregnant women were detected,detection of deafness gene mutation carri-ers in 24 cases(4.2%), including 13 cases of the GJB2 heterozygous mutation, 3 cases of SLC26A4 heterozygous mutation, 1 cases of GJB3 heterozygous mutation, and 1 case of mitochondrial 12S rRNA mutation. 18 spouses and 17 newborns took fur-ther genetic tests, and 6 newborns inherited the mutation from their mother. Conclusion The common deafness genes muta-tion has a high carrier rate in pregnant women group,235delC and IVS7-2A>G heterozygous mutations are common.

  14. 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.

  15. Object-Oriented System-on-Network-on-Chip Template and Implementation: H.263 Case Study

    Institute of Scientific and Technical Information of China (English)

    MA Liwei; SUN Yihe

    2008-01-01

    Network-on-chip (NoC) technology enables a new system-on-chip paradigm, the system-on-network-on-chip (SoNoC) paradigm. One of the challenges in designing application-specific networks is modeling the on-chip system behavior and determining on-chip traffic characteristics. A universal object message level model for SoNoC was defined and an object-oriented methodology was developed to imple-ment this model in hardware and software. The model supports "object to core" synthesis and "function in-voking to network" mapping. A case study of an H.263 system verifies the model and methodology. System prototypes are easily built and on-chip traffic can be observed using the SoNoC model to provide real benchmarks for on-chip network design.

  16. Performance Evaluation of CDMA Router for Network-On-Chip

    Directory of Open Access Journals (Sweden)

    Anant W. Hinganikar

    2012-06-01

    Full Text Available This paper presents the performance evaluation of router based on code division multiple access technique (CDMA for Network-on-Chip (NoC. The design is synthesized using Xilinx Virtex4 XC4VLX200 device. The functional behavior is verified using Modelsim XE III 6.2 C. The delay and throughput values are obtained for variable payload sizes. Throughput-Power and Delay-Power characteristics are also verified for NoC.

  17. Analysis and Management of Communication in On-Chip Networks

    OpenAIRE

    Jafari, Fahimeh

    2015-01-01

    Regarding the needs of low-power, high-performance embedded systems and the growing computation-intensive applications, the number of computing resources in a single chip has enormously increased. The current VLSI technology is able to support such an integration of transistors and add many computing resources such as CPU, DSP, specific IPs, etc to build a Systemon- Chip (SoC). However, interconnection between resources becomes another challenging issue which can be raised by using an on-chip...

  18. Low-cost on-chip clock jitter measurement scheme

    OpenAIRE

    Omana, Martin; Rossi, Daniele; Giaffreda, Daniele; Metra, Cecilia; Mak, T.M.; Raman, Asifur; Tam, Simon

    2014-01-01

    In this paper, we present a low-cost, on-chip clock jitter digital measurement scheme for high performance microprocessors. It enables in situ jitter measurement during the test or debug phase. It provides very high measurement resolution and accuracy, despite the possible presence of power supply noise (representing a major source of clock jitter), at low area and power costs. The achieved resolution is scalable with technology node and can in principle be increased as much as desired, at lo...

  19. Energy Consumption Oriented Network-on-Chip Mapping Method

    OpenAIRE

    Feichao Wang

    2013-01-01

    In this paper, mapping algorithm has been mainly studied. The main work and contribution have been generalized as follows: Through the research of existing on-chip network mapping algorithm and global optimization algorithm, a multi-step mapping algorithm for low-power consumption have been designed, which is combined with the task allocation and the task scheduling. Compared with the traditional mapping algorithm, the algorithm in this paper takes the factors of task scheduling and allocatio...

  20. On-chip High-Voltage Generator Design

    CERN Document Server

    Tanzawa, Toru

    2013-01-01

    This book describes high-voltage generator design with switched-capacitor multiplier techniques.  The author 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.   ·         Shows readers how to design charge pump circuits with lower voltage operation, higher power efficiency, and smaller circuit area; ·         Describes comprehensive circuits and systems design of on-chip high-voltage generators; ·         Covers all the component circuit blocks, including charge pumps, pump regulators, level shifters, oscillators, and references.

  1. Delay Optimized Architecture for On-Chip Communication

    Institute of Scientific and Technical Information of China (English)

    Sheraz Anjum; Jie Chen; Pei-Pei Yue; Jian Liu

    2009-01-01

    Networks-on-chip (NoC), a new system on chip (SoC) paradigm, has become a great focus of research by many groups during the last few years. Among all the NoC architectures that have been proposed until now, 2D-Mesh has proved to be the best architecture for implementation due to its regular and simple intercon- nection structure. In this paper, we propose a new interconnect architecture called 2D-diagonal mesh (2DDgl-Mesh) for on-chip communication. The 2DDgl- Mesh is almost similar to traditional 2D-Mesh in aspects of cost, area, and implementation, but it can outperform the later in delay. The both architectures are compared by using NS-2 (a network simulator) and CINSIM (a component based interconnection simulator) under the same traffic models and parametric conditions. The results of comparison show that under the proposed architecture, the packets can almost always be routed to their destinations in less time. In addition, our archi- tecture can sometimes perform better than 2D-Mesh in drop ratio for special fixed traffic models.

  2. Application Aware Topology Generation for Surface Wave Networks-on-Chip

    Institute of Scientific and Technical Information of China (English)

    Zhao Fu; Zheng-Bing Hu; Cheng Gong; Wen-Ming Pan; Guo-Bin Lv

    2014-01-01

    The networks-on-chip (NoC) communica-tion has an increasingly larger impact on the system power consumption and performance. Emerging technologies, like surface wave, are believed to have lower transmission latency and power consumption over the conventional wireless NoC. Therefore, this paper studies how to optimize the network performance and power consumption by giving the packet-switching fabric and traffic pattern of each application. Compared with the conventional method of wire-linked, which adds wireless transceivers by using the genetic algorithm (GA), the proposed maximal declining sorting algorithm (MDSA) can effectively reduce time consumption by as much as 20.4% to 35.6%. We also evaluate the power consumption and configuration time to prove the effective of the proposed algorithm.

  3. On-chip single-copy real-time reverse-transcription PCR in isolated picoliter droplets

    Energy Technology Data Exchange (ETDEWEB)

    Beer, N R; Wheeler, E; Lee-Houghton, L; Watkins, N; Nasarabadi, S; Hebert, N; Leung, P; Arnold, D; Bailey, C; Colston, B

    2007-12-19

    The first lab-on-chip system for picoliter droplet generation and RNA isolation, followed by reverse transcription, and PCR amplification with real-time fluorescence detection in the trapped droplets has been developed. The system utilized a shearing T-junction in a fused silica device to generate a stream of monodisperse picoliter-scale 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 thermal cycling for reverse transcription and subsequent PCR amplification without droplet motion. This combination of the established real-time reverse transcription-PCR assay with digital microfluidics is ideal for isolating single-copy RNA and virions from a complex environment, and will be useful in viral discovery and gene-profiling applications.

  4. 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.

  5. 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.

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

    Science.gov (United States)

    Park, Gyeong Cheol; Xue, Weiqi; Piels, Molly; Zibar, Darko; Mørk, Jesper; Semenova, Elizaveta; Chung, Il-Sug

    2016-12-01

    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 a challenge in obtaining a sufficient output power. Here, as an alternative, we propose an ultrahigh-speed microcavity laser structure, based on a vertical cavity with a high-contrast grating (HCG) mirror for transverse magnetic (TM) polarisation. By using the TM HCG, a very small mode volume and an un-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/mA1/2, which is superior among microcavity lasers. This shows a high potential for a very high speed at low injection currents or avery small heat generation at high bitrates, which are highly desirable for both on-chip and off-chip applications.

  7. 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.

  8. High performance magnesium anode in paper-based microfluidic battery, powering on-chip fluorescence assay.

    Science.gov (United States)

    Koo, Youngmi; Sankar, Jagannathan; Yun, Yeoheung

    2014-09-01

    A high power density and long-lasting stable/disposable magnesium battery anode was explored for a paper-based fluidic battery to power on-chip functions of various Point of Care (POC) devices. The single galvanic cell with magnesium foil anode and silver foil cathode in Origami cellulose chip provided open circuit potential, 2.2 V, and power density, 3.0 mW/cm(2). A paper-based fluidic galvanic cell was operated with one drop of water (80 μl) and continued to run until it was dry. To prove the concept about powering on-chip POC devices, two-serial galvanic cells are developed and incorporated with a UV-light emitting diode (λ = 365 nm) and fluorescence assay for alkaline phosphatase reaction. Further, detection using smart phones was performed for quantitative measurement of fluorescent density. To conclude, a magnesium-based fluidic battery paper chip was extremely low-cost, required minute sample volumes, was easy to dispose of, light weight, easy to stack, store and transport, easy to fabricate, scalable, and has faster analysis times.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

    2013-01-01

    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. PMID:24051525

  13. Real-time bacterial microcolony counting using on-chip microscopy

    Science.gov (United States)

    Jung, Jae Hee; Lee, Jung Eun

    2016-01-01

    Observing microbial colonies is the standard method for determining the microbe titer and investigating the behaviors of microbes. Here, we report an automated, real-time bacterial microcolony-counting system implemented on a wide field-of-view (FOV), on-chip microscopy platform, termed ePetri. Using sub-pixel sweeping microscopy (SPSM) with a super-resolution algorithm, this system offers the ability to dynamically track individual bacterial microcolonies over a wide FOV of 5.7 mm × 4.3 mm without requiring a moving stage or lens. As a demonstration, we obtained high-resolution time-series images of S. epidermidis at 20-min intervals. We implemented an image-processing algorithm to analyze the spatiotemporal distribution of microcolonies, the development of which could be observed from a single bacterial cell. Test bacterial colonies with a minimum diameter of 20 μm could be enumerated within 6 h. We showed that our approach not only provides results that are comparable to conventional colony-counting assays but also can be used to monitor the dynamics of colony formation and growth. This microcolony-counting system using on-chip microscopy represents a new platform that substantially reduces the detection time for bacterial colony counting. It uses chip-scale image acquisition and is a simple and compact solution for the automation of colony-counting assays and microbe behavior analysis with applications in antibacterial drug discovery. PMID:26902822

  14. 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

    2017-03-01

    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.

  15. 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.

  16. In vitro and in vivo on-chip biofluorescence imaging using a CMOS image sensor

    Science.gov (United States)

    Ng, David C.; Matsuo, Masamichi; Tokuda, Takashi; Kagawa, Keiichiro; Nunoshita, Masahiro; Ohta, Jun

    2006-02-01

    We have designed and fabricated a 176×144-pixels (QCIF) CMOS image sensor for on-chip bio-fluorescence imaging of the mouse brain. In our approach, a single CMOS image sensor chip without additional optics is used. This enables imaging at arbitrary depths into the brain; a clear advantage compared to existing optical microscopy methods. Packaging of the chip represents a challenge for in vivo imaging. We developed a novel packaging process whereby an excitation filter is applied onto the sensor. This eliminates the use of a filter cube found in conventional fluorescence microscopes. The fully packaged chip is about 350 μm thick. Using the device, we demonstrated in vitro on-chip fluorescence imaging of a 400 μm thick mouse brain slice detailing the hippocampus. The image obtained compares favorably to the image captured by conventional microscopes in terms of image resolution. In order to study imaging in vivo, we also developed a phantom media. In situ fluorophore measurement shows that detection through the turbid medium of up to 1 mm thickness is possible. We have successfully demonstrated imaging deep into the hippocampal region of the mouse brain where quantitative fluorometric measurements was made. This work is expected to lead to a promising new tool for imaging the brain in vivo.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Automated detection of lung nodules in CT images using shape-based genetic algorithm.

    Science.gov (United States)

    Dehmeshki, Jamshid; Ye, Xujiong; Lin, Xinyu; Valdivieso, Manlio; Amin, Hamdan

    2007-09-01

    A shape-based genetic algorithm template-matching (GATM) method is proposed for the detection of nodules with spherical elements. A spherical-oriented convolution-based filtering scheme is used as a pre-processing step for enhancement. To define the fitness function for GATM, a 3D geometric shape feature is calculated at each voxel and then combined into a global nodule intensity distribution. Lung nodule phantom images are used as reference images for template matching. The proposed method has been validated on a clinical dataset of 70 thoracic CT scans (involving 16,800 CT slices) that contains 178 nodules as a gold standard. A total of 160 nodules were correctly detected by the proposed method and resulted in a detection rate of about 90%, with the number of false positives at approximately 14.6/scan (0.06/slice). The high-detection performance of the method suggested promising potential for clinical applications.

  3. 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.

  4. Role of genetic detection in peritoneal washes with gastric carcinoma: The past, present and future

    Institute of Scientific and Technical Information of China (English)

    Hyun-Dong Chae

    2016-01-01

    The most frequent cause of treatment failure following surgery for gastric cancer is peritoneal dissemination, mainly caused by the seeding of free cancer cells from the primary gastric cancer, which is the most common type of spread. Unfortunately, there is no standard modality of intraperitoneal free cancer cells detection to predict peritoneal metastasis until now. We reviewed English literature in Pub Med was done using the Me SH terms for gastric cancer, peritoneal wash, and reverse transcriptase polymerase chain reaction. All the articles were reviewed and core information was tabulated for reference. After a comprehensive review of all articles, the data was evaluated by clinical implication and predictive value of each marker for peritoneal recurrence. There are still many limitations to overcome before the genetic diagnosis for free cancer cells detection can be considered as routine assay. To make it a reliable diagnostic tool for detecting free cancer cells, the process and method of genetic detection with peritoneal washes should be standardized, and the development of simple diagnostic devices and easily available kits are necessary. Herein, we reviewed the past, present and future perspectives of the peritoneal lavage for the detection of intraperitoneal free cancer cells in patients with gastric cancer.

  5. Model studies on the detectability of genetically modified feeds in milk.

    Science.gov (United States)

    Poms, R E; Hochsteiner, W; Luger, K; Glössl, J; Foissy, H

    2003-02-01

    Detecting the use of genetically modified feeds in milk has become important, because the voluntary labeling of milk and dairy products as "GMO free" or as "organically grown" prohibits the employment of genetically modified organisms (GMOs). The aim of this work was to investigate whether a DNA transfer from foodstuffs like soya and maize was analytically detectable in cow's milk after digestion and transportation via the bloodstream of dairy cows and, thus, whether milk could report for the employment of transgene feeds. Blood, milk, urine, and feces of dairy cows were examined, and foreign DNA was detected by polymerase chain reaction by specifically amplifying a 226-bp fragment of the maize invertase gene and a 118-bp fragment of the soya lectin gene. An intravenous application of purified plant DNA showed a fast elimination of marker DNA in blood or its reduction below the detection limit. With feeding experiments, it could be demonstrated that a specific DNA transfer from feeds into milk was not detectable. Therefore, foreign DNA in milk cannot serve as an indicator for the employment of transgene feeds unless milk is directly contaminated with feed components or airborne feed particles.

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

    Science.gov (United States)

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

    2015-04-01

    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.

  7. 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

    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......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...

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

    Directory of Open Access Journals (Sweden)

    Marghany Maged

    2016-10-01

    Full Text Available 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 receiver-operating 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.

  11. Detection of anthrax toxin genetic sequences by the solid phase oligo-probes

    Directory of Open Access Journals (Sweden)

    K C Addanki

    2011-01-01

    Full Text Available Purpose: There is an urgent need to detect a rapid field-based test to detect anthrax. We have developed a rapid, highly sensitive DNA-based method to detect the anthrax toxin lethal factor gene located in pXO1, which is necessary for the pathogenicity of Bacillus anthracis. Materials and Methods: We have adopted the enzyme-linked immunosorbent assay (ELISA so that instead of capturing antibodies we capture the DNA of the target sequence by a rapid oligo-based hybridization and then detect the captured DNA with another oligoprobe that binds to a different motif of the captured DNA sequences at a dissimilar location. We chose anthrax lethal factor endopeptidase sequences located in pXO1 and used complementary oligoprobe, conjugated with biotin, to detect the captured anthrax specific sequence by the streptavidin-peroxidase-based colorimetric assay. Result: Our system can detect picomoles (pMoles of anthrax (approximately 33 spores of anthrax and is >1000 times more sensitive than the current ELISA, which has a detection range of 0.1 to 1.0 ng/mL. False positive results can be minimized when various parameters and the colour development steps are optimized. Conclusion: Our results suggest that this assay can be adapted for the rapid detection of minuscule amounts of the anthrax spores that are aerosolized in the case of a bioterrorism attack. This detection system does not require polymerase chain reaction (PCR step and can be more specific than the antibody method. This method can also detect genetically engineered anthrax. Since, the antibody method is so specific to the protein epitope that bioengineered versions of anthrax may not be detected.

  12. 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.

  13. 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/ .

  14. Frequency modulated weak signal detection based on stochastic resonance and genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    XING; Hongyan; LU; Chunxia; ZHANG; Qiang

    2016-01-01

    Stochastic resonance system is subject to the restriction of small frequency parameter in weak signal detection,in order to solve this problem,a frequency modulated weak signal detection method based on stochastic resonance and genetic algorithm is presented in this paper. The frequency limit of stochastic resonance is eliminated by introducing carrier signal,which is multiplied with the measured signal to be injected in the stochastic resonance system,meanwhile,using genetic algorithm to optimize the carrier signal frequency,which determine the generated difference-frequency signal in the lowfrequency range,so as to achieve the stochastic resonance weak signal detection. Results showthat the proposed method is feasible and effective,which can significantly improve the output SNR of stochastic resonance,in addition,the system has the better self-adaptability,according to the operation result and output phenomenon,the unknown frequency of the signal to be measured can be obtained,so as to realize the weak signal detection of arbitrary frequency.

  15. 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.

  16. 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..

  17. Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome

    Science.gov (United States)

    Fan, Guang Yao; Ye, Yi; Hou, Yi Ping

    2016-01-01

    Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification. PMID:27535707

  18. 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.

  19. Whole genome sequence analysis of unidentified genetically modified papaya for development of a specific detection method.

    Science.gov (United States)

    Nakamura, Kosuke; Kondo, Kazunari; Akiyama, Hiroshi; Ishigaki, Takumi; Noguchi, Akio; Katsumata, Hiroshi; Takasaki, Kazuto; Futo, Satoshi; Sakata, Kozue; Fukuda, Nozomi; Mano, Junichi; Kitta, Kazumi; Tanaka, Hidenori; Akashi, Ryo; Nishimaki-Mogami, Tomoko

    2016-08-15

    Identification of transgenic sequences in an unknown genetically modified (GM) papaya (Carica papaya L.) by whole genome sequence analysis was demonstrated. Whole genome sequence data were generated for a GM-positive fresh papaya fruit commodity detected in monitoring using real-time polymerase chain reaction (PCR). The sequences obtained were mapped against an open database for papaya genome sequence. Transgenic construct- and event-specific sequences were identified as a GM papaya developed to resist infection from a Papaya ringspot virus. Based on the transgenic sequences, a specific real-time PCR detection method for GM papaya applicable to various food commodities was developed. Whole genome sequence analysis enabled identifying unknown transgenic construct- and event-specific sequences in GM papaya and development of a reliable method for detecting them in papaya food commodities.

  20. 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.

  1. 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...... emission wavelengths, the chips have the size of microscope cover slips and use optical and fluidic interconnects only. Here, we present our latest realizations of integrated optofluidic lasers using whispering gallery mode or distributed feedback laser cavities....

  2. 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

  3. 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...

  4. 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

  5. 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...

  6. 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.

  7. Two-photon tomography using on-chip quantum walks

    CERN Document Server

    Titchener, James; Sukhorukov, Andrey

    2016-01-01

    We present a conceptual approach to quantum tomography based on first expanding a quantum state across extra degrees of freedom and then exploiting the introduced sparsity to perform reconstruction. We formulate its application to photonic circuits, and show that measured spatial photon correlations at the output of a specially tailored discrete-continuous quantum-walk can enable full reconstruction of any two-photon spatially entangled and mixed state at the input. This approach does not require any tunable elements, so is well suited for integration with on-chip superconducting photon detectors.

  8. Microarchitecture of network-on-chip routers a designer's perspective

    CERN Document Server

    Dimitrakopoulos, Giorgos; Seitanidis, Ioannis

    2014-01-01

    This book provides a unified overview of network-on-chip router micro-architecture, the corresponding design opportunities and challenges, and existing solutions to overcome these challenges. The discussion focuses on the heart of a NoC, the NoC router, and how it interacts with the rest of the system. Coverage includes both basic and advanced design techniques that cover the entire router design space including router organization, flow control, pipelined operation, buffering architectures, as well as allocators' structure and algorithms. Router micro-architectural options are presented in a

  9. Compact models for nanophotonic structures and on-chip interconnects

    Science.gov (United States)

    Alam, Mehboob

    Over the last few years, scaling in deep submicron technologies has shifted the paradigm from device-dominated to interconnect-dominated design methodology. Consequently, there is an increasing interest towards the miniaturization of the guiding medium in nanoscale integrated circuits by exploring plasmon-based waveguides to alleviate the scaling issues associated with today's copper interconnect. In this thesis, we seek short and long-term solutions of on-chip interconnect by developing accurate compact models of on-chip interconnects and impedance characterization of nanophotonic structures. The developed system models are compact and accurate over the operating frequency range and the adopted approach have provided many critical insights and produced many important results. This thesis first presents a new modeling strategy that represents the nanostructure by its equivalent impedance. By applying either quasistatic approximation or separately solving for voltage and current for dominant mode, we reduce the field problem to a circuit problem. The impedance expressed in terms of circuit components is dependent on the material constant as well as the operating frequency. The modeling methodology is successfully applied to nanoparticles and oscillating nanosphere. The proposed model characterizes plasmon resonance in these nanostructures, thereby providing basic building block to develop spice models of complex plasmon-based waveguide for sub-wavelength propagation. We also presented several techniques to develop compact models of on-chip interconnects and passive components for accurate estimation of power, noise and delay of high speed integrated circuits. The automated method generates reduced order models that are accurate across either a narrow or a wide-range of frequencies. The proposed methods are based on Krylov subspace method with interpolation points dynamically selected using either spline based algorithm or discrete wavelet transform. Narrow and

  10. 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...

  11. On-chip fluorescence excitation and collection by focusing grating couplers

    Science.gov (United States)

    Kerman, Sarp; Vercruysse, Dries; Claes, Tom; Ul Hasan, Mahmud; Neutens, Pieter; Mukund, Vignesh; Rottenberg, Xavier; Lagae, Liesbet; Van Dorpe, Pol

    2016-05-01

    Fluorescence detection is a commonly used technique to detect particles. Microscopes are used for the fluorescence detection of the micro-particles. However, the conventional microscopes are bulky. It is cumbersome to integrate all the equipment used for detection in one setup. They can be replaced by photonic chips for the detection of micro-particles such as cells. Most of the biological detection techniques require the utilization of the visible range of the spectrum. SiN as a waveguide material stands out for biological applications due to its transparency in the visible spectrum. Specifically designed grating couplers can be exploited to focus from inside SiN waveguides at a designated location above the chip. Those SiN focusing grating couplers can mimic microscope objectives for on-chip biological detection applications such as fluorescence and Raman spectroscopy. In this report, we present a 2D SiN focusing grating coupler. We study the effect of the grating design on the focus properties of visible light using finite-difference time-domain simulations.

  12. Detecting populations in the 'ambiguous' zone : kinship-based estimation of population structure at low genetic divergence

    NARCIS (Netherlands)

    Palsboll, Per J.; Peery, M. Zachariah; Berube, Martine

    2010-01-01

    Identifying population structure is one of the most common and important objectives of spatial analyses using population genetic data. Population structure is detected either by rejecting the null hypothesis of a homogenous distribution of genetic variation, or by estimating low migration rates. Iss

  13. Detecting populations in the 'ambiguous' zone : kinship-based estimation of population structure at low genetic divergence

    NARCIS (Netherlands)

    Palsboll, Per J.; Peery, M. Zachariah; Berube, Martine

    2010-01-01

    Identifying population structure is one of the most common and important objectives of spatial analyses using population genetic data. Population structure is detected either by rejecting the null hypothesis of a homogenous distribution of genetic variation, or by estimating low migration rates. Iss

  14. Behavioral and Molecular Genetics of Reading-Related AM and FM Detection Thresholds.

    Science.gov (United States)

    Bruni, Matthew; Flax, Judy F; Buyske, Steven; Shindhelm, Amber D; Witton, Caroline; Brzustowicz, Linda M; Bartlett, Christopher W

    2017-03-01

    Auditory detection thresholds for certain frequencies of both amplitude modulated (AM) and frequency modulated (FM) dynamic auditory stimuli are associated with reading in typically developing and dyslexic readers. We present the first behavioral and molecular genetic characterization of these two auditory traits. Two extant extended family datasets were given reading tasks and psychoacoustic tasks to determine FM 2 Hz and AM 20 Hz sensitivity thresholds. Univariate heritabilities were significant for both AM (h (2)  = 0.20) and FM (h (2)  = 0.29). Bayesian posterior probability of linkage (PPL) analysis found loci for AM (12q, PPL = 81 %) and FM (10p, PPL = 32 %; 20q, PPL = 65 %). Bivariate heritability analyses revealed that FM is genetically correlated with reading, while AM was not. Bivariate PPL analysis indicates that FM loci (10p, 20q) are not also associated with reading.

  15. Trade-offs and noise tolerance in signal detection by genetic circuits.

    Directory of Open Access Journals (Sweden)

    Raúl Guantes

    Full Text Available Genetic circuits can implement elaborated tasks of amplitude or frequency signal detection. What type of constraints could circuits experience in the performance of these tasks, and how are they affected by molecular noise? Here, we consider a simple detection process-a signal acting on a two-component module-to analyze these issues. We show that the presence of a feedback interaction in the detection module imposes a trade-off on amplitude and frequency detection, whose intensity depends on feedback strength. A direct interaction between the signal and the output species, in a type of feed-forward loop architecture, greatly modifies these trade-offs. Indeed, we observe that coherent feed-forward loops can act simultaneously as good frequency and amplitude noise-tolerant detectors. Alternatively, incoherent feed-forward loop structures can work as high-pass filters improving high frequency detection, and reaching noise tolerance by means of noise filtering. Analysis of experimental data from several specific coherent and incoherent feed-forward loops shows that these properties can be realized in a natural context. Overall, our results emphasize the limits imposed by circuit structure on its characteristic stimulus response, the functional plasticity of coherent feed-forward loops, and the seemingly paradoxical advantage of improving signal detection with noisy circuit components.

  16. Detection limits of the strip test and PCR for genetically modified corn in Brazil.

    Science.gov (United States)

    Nascimento, V E; Von Pinho, É V R; Von Pinho, R G; do Nascimento, A D

    2012-08-16

    Brazilian legislation establishes a labeling limit for products that contain more than 1% material from genetically modified organisms (GMOs). We assessed the sensitivity of the lateral flow strip test in detection of the GMO corn varieties Bt11 and MON810 and the specificity and sensitivity of PCR techniques for their detection. For the strip test, the GMO seeds were mixed with conventional seeds at levels of 0.2, 0.4 and 0.8% for Bt11, and 0.4, 0.8 and 1.6% for MON810. Three different methodologies were assessed and whole seeds, their endosperm and embryonic axis were used. For the PCR technique, the GMO seeds of each of the two varieties were mixed with conventional seeds at levels of 20, 10, 5, 2, 1, and 0.5%. The seeds were ground and the DNA extracted. For detection of the GMO material, specific primers were used for MON810 and Bt11 and maize zein as an endogenous control. The sensitivity of the strip test varied for both maize varieties and methodologies. The test was positive for Bt11 only at 0.8%, in contrast with the detection limit of 0.4% indicated by the manufacturer. In the multiplex PCR, the primers proved to be specific for the different varieties. These varieties were detected in samples with one GMO seed in 100. Thus, this technique proved to be efficient in detecting contaminations equal to or greater than 1%.

  17. 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.

  18. 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.

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    Edisson Chavarro Mesa

    2007-02-01

    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.

  1. Rapid detection of genetically modified organisms on a continuous-flow polymerase chain reaction microfluidics.

    Science.gov (United States)

    Li, Yuyuan; Xing, Da; Zhang, Chunsun

    2009-02-01

    The ability to perform DNA amplification on a microfluidic device is very appealing. In this study, a compact continuous-flow polymerase chain reaction (PCR) microfluidics was developed for rapid analysis of genetically modified organisms (GMOs) in genetically modified soybeans. The device consists of three pieces of copper and a transparent polytetrafluoroethylene capillary tube embedded in the spiral channel fabricated on the copper. On this device, the P35S and Tnos sequences were successfully amplified within 9min, and the limit of detection of the DNA sample was estimated to be 0.005 ng microl(-1). Furthermore, a duplex continuous-flow PCR was also reported for the detection of the P35S and Tnos sequences in GMOs simultaneously. This method was coupled with the intercalating dye SYBR Green I and the melting curve analysis of the amplified products. Using this method, temperature differences were identified by the specific melting temperature values of two sequences, and the limit of detection of the DNA sample was assessed to be 0.01 ng microl(-1). Therefore, our results demonstrated that the continuous-flow PCR assay could discriminate the GMOs in a cost-saving and less time-consuming way.

  2. Nested PCR for detection and genotyping of Ehrlichia ruminantium: use in genetic diversity analysis.

    Science.gov (United States)

    Martinez, Dominique; Vachiéry, Nathalie; Stachurski, Frederic; Kandassamy, Yane; Raliniaina, Modestine; Aprelon, Rosalie; Gueye, Arona

    2004-10-01

    Ehrlichia ruminantium, the agent of cowdriosis transmitted by Amblyomma ticks, presents an extensive genetic and antigenic diversity of key importance for vaccine formulation. Two means of nested polymerase chain reaction (PCR) targeting were developed to conduct molecular epidemiology studies in the Caribbean and Africa. The first used a conserved DNA fragment for detection of the pathogen in animals and vectors, and the second relied on the polymorphic map1 gene for genotyping. As compared to a PCR, the nested PCR showed a 2-Log10 improvement of sensitivity and allowed amplification from ticks, blood, brain, and lungs from infected animals, providing a more accurate picture of the tick infection rate. In Guadeloupe, this rate reached 36% (N = 212) instead of 1.7% (N = 224), as previously estimated. Genetic typing was done by restriction fragment length polymorphism or sequencing of map1 amplification products. Molecular epidemiology studies conducted in field sites selected for vaccination trials with inactivated vaccine, revealed the circulation of genetically divergent strains in limited geographical areas. It is known, then, that genetic clustering based on map1 has no predictive value regarding the protective value of a given strain against a new strain. However, tracing the strains by this technique revealed the extent of E. ruminantium diversity that one can expect in a given region, and the method allows differentiation between an inadequate immune response and the challenge by a breakthrough strain on animals dying despite vaccination. Up to now, genetic typing does not avoid cross-protection studies, which were conducted in parallel, although on a more limited scale. The importance of pathogen diversity studies for optimization of vaccine design is discussed as well as the research for new polymorphic genes. These genes may allow better predictions on cross-protection, given the recent completion of the sequence of the full genome of two E. ruminantium

  3. 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.

  4. High quantum-efficiency photon-number-resolving detector for photonic on-chip information processing

    CERN Document Server

    Calkins, Brice; Lita, Adriana E; Metcalf, Benjamin J; Kolthammer, W Steven; Linares, Antia Lamas; Spring, Justin B; Humphreys, Peter C; Mirin, Richard P; Gates, James C; Smith, Peter G R; Walmsley, Ian A; Gerrits, Thomas; Nam, Sae Woo

    2013-01-01

    The integrated optical circuit is a promising architecture for the realization of complex quantum optical states and information networks. One element that is required for many of these applications is a high-efficiency photon detector capable of photon-number discrimination. We present an integrated photonic system in the telecom band at 1550 nm based on UV-written silica-on-silicon waveguides and modified transition-edge sensors capable of number resolution and over 40% efficiency. Exploiting the mode transmission failure of these devices, we multiplex three detectors in series to demonstrate a combined 79% +/- 2% detection efficiency with a single pass, and 88% +/- 3% at the operating wavelength of an on-chip terminal reflection grating. Furthermore, our optical measurements clearly demonstrate no significant unexplained loss in this system due to scattering or reflections. This waveguide and detector design therefore allows the placement of number-resolving single-photon detectors of predictable efficienc...

  5. Microfluidics-Based Lab-on-Chip Systems in DNA-Based Biosensing: An Overview

    Directory of Open Access Journals (Sweden)

    Sabo Wada Dutse

    2011-05-01

    Full Text Available Microfluidics-based lab-on-chip (LOC systems are an active research area that is revolutionising high-throughput sequencing for the fast, sensitive and accurate detection of a variety of pathogens. LOCs also serve as portable diagnostic tools. The devices provide optimum control of nanolitre volumes of fluids and integrate various bioassay operations that allow the devices to rapidly sense pathogenic threat agents for environmental monitoring. LOC systems, such as microfluidic biochips, offer advantages compared to conventional identification procedures that are tedious, expensive and time consuming. This paper aims to provide a broad overview of the need for devices that are easy to operate, sensitive, fast, portable and sufficiently reliable to be used as complementary tools for the control of pathogenic agents that damage the environment.

  6. Microfluidics-based lab-on-chip systems in DNA-based biosensing: an overview.

    Science.gov (United States)

    Dutse, Sabo Wada; Yusof, Nor Azah

    2011-01-01

    Microfluidics-based lab-on-chip (LOC) systems are an active research area that is revolutionising high-throughput sequencing for the fast, sensitive and accurate detection of a variety of pathogens. LOCs also serve as portable diagnostic tools. The devices provide optimum control of nanolitre volumes of fluids and integrate various bioassay operations that allow the devices to rapidly sense pathogenic threat agents for environmental monitoring. LOC systems, such as microfluidic biochips, offer advantages compared to conventional identification procedures that are tedious, expensive and time consuming. This paper aims to provide a broad overview of the need for devices that are easy to operate, sensitive, fast, portable and sufficiently reliable to be used as complementary tools for the control of pathogenic agents that damage the environment.

  7. Response of an on-chip coil-integrated superconducting tunnel junction to x-rays

    CERN Document Server

    Maehata, K; Taino, T

    2003-01-01

    An on-chip coil-integrated superconducting tunnel junction (OC sup 2 -STJ) was irradiated by X-rays emitted from an sup 5 sup 5 Fe source to the examine the performance of X-ray detection by applying a magnetic field produced by a superconducting microstrip coil integrated into the junction chip. Response characteristics were obtained for a diamond-shaped Nd-based tunnel junction with a sensitive area of 100 x 100 mu m sup 2 in the OC sup 2 -STJ chip. Two kinds of stable operation modes with different pulse heights were observed by changing the magnetic flux density in the barrier region of the junction. In the low-pulse-height mode, the pulse height distribution exhibits two full-energy peaks corresponding to signals created in the top and base electrodes. Stable operation of the OC sup 2 -STJ was demonstrated without using conventional external electromagnets. (author)

  8. On-chip Brownian relaxation measurements of magnetic nanobeads in the time domain

    DEFF Research Database (Denmark)

    Østerberg, Frederik Westergaard; Rizzi, Giovanni; Hansen, Mikkel Fougt

    2013-01-01

    magnetic fields are needed. First, the method is demonstrated on Brownian relaxation measurements of beads with nominal sizes of 40, 80, 130, and 250 nm. The results are found to compare well to those obtained by an already established measurement technique in the frequency domain. Next, we demonstrate......We present and demonstrate a new method for on-chip Brownian relaxation measurements on magnetic nanobeads in the time domain using magnetoresistive sensors. The beads are being magnetized by the sensor self-field arising from the bias current passed through the sensors and thus no external...... the time and frequency domain methods on Brownian relaxation detection of clustering of streptavidin coated magnetic beads in the presence of different concentrations of biotin-conjugated bovine serum albumin and obtain comparable results. In the time domain, a measurement is carried out in less than 30 s...

  9. 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.

  10. On-Chip Reconfigurable Hardware Accelerators for Popcount Computations

    Directory of Open Access Journals (Sweden)

    Valery Sklyarov

    2016-01-01

    Full Text Available Popcount computations are widely used in such areas as combinatorial search, data processing, statistical analysis, and bio- and chemical informatics. In many practical problems the size of initial data is very large and increase in throughput is important. The paper suggests two types of hardware accelerators that are (1 designed in FPGAs and (2 implemented in Zynq-7000 all programmable systems-on-chip with partitioning of algorithms that use popcounts between software of ARM Cortex-A9 processing system and advanced programmable logic. A three-level system architecture that includes a general-purpose computer, the problem-specific ARM, and reconfigurable hardware is then proposed. The results of experiments and comparisons with existing benchmarks demonstrate that although throughput of popcount computations is increased in FPGA-based designs interacting with general-purpose computers, communication overheads (in experiments with PCI express are significant and actual advantages can be gained if not only popcount but also other types of relevant computations are implemented in hardware. The comparison of software/hardware designs for Zynq-7000 all programmable systems-on-chip with pure software implementations in the same Zynq-7000 devices demonstrates increase in performance by a factor ranging from 5 to 19 (taking into account all the involved communication overheads between the programmable logic and the processing systems.

  11. On-chip inductor above dummy metal patterns

    Science.gov (United States)

    Hsu, Heng-Ming; Hsieh, Ming-Ming

    2008-07-01

    This work characterizes the on-chip inductor above dummy metals in CMOS technology. Since the dummy pattern influences the sheet resistance in chemical-mechanical planarization (CMP) process strongly [Schindler G, Steinlesberger G, Engelhardt M, Steinhögl W. Electrical characterization of copper interconnects with end-of-roadmap feature sizes. Solid-State Electron 2003;47:1233-36; Smith S, Walton AJ, Ross AWS, Bodammer GKH, Stevenson JTM. Evaluation of sheet resistance and electrical line width measurement techniques for copper damascene interconnect. IEEE Trans Semicond Manuf 2002;15:214-22.], three test structures are fabricated to compare the inductor performances in this paper. The measurements show that the Q value degrades 15.3% and self-resonance frequency decreases 9.5% in device with dummy metal pattern. Accordingly, an equivalent circuit is proposed to analyze this behavior, the results show that the insulator capacitor plays a key role in performance degradation. Result of this study quantifies the effect of on-chip inductor above dummy pattern.

  12. 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.

  13. A Survey of Network-On-Chip Tools

    Directory of Open Access Journals (Sweden)

    Ahmed Ben Achballah

    2013-10-01

    Full Text Available Nowadays System-On-Chips (SoCs have evolved considerably in term of performances, reliability and integration capacity. The last advantage has induced the growth of the number of cores or Intellectual Properties (IPs in a same chip. Unfortunately, this important number of IPs has caused a new issue which is the intra-communication between the elements of a same chip. To resolve this problem, a new paradigm has been introduced which is the Network-On-Chip (NoC. Since the introduction of the NoC paradigm in the last decade, new methodologies and approaches have been presented by research community and many of them have been adopted by industrials. The literature contains many relevant studies and surveys discussing NoC proposals and contributions. However, few of them have discussed or proposed a comparative study of NoC tools. The objective of this work is to establish a reliable survey about available design, simulation or implementation NoC tools. We collected an important amount of information and characteristics about NoC dedicated tools that we will present throughout this survey. This study is built around a respectable amount of references and we hope it will help scientists.

  14. 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.

  15. On-chip magnetic cooling of a nanoelectronic device

    Science.gov (United States)

    Bradley, D. I.; Guénault, A. M.; Gunnarsson, D.; Haley, R. P.; Holt, S.; Jones, A. T.; Pashkin, Yu. A.; Penttilä, J.; Prance, J. R.; Prunnila, M.; Roschier, L.

    2017-04-01

    We demonstrate significant cooling of electrons in a nanostructure below 10 mK by demagnetisation of thin-film copper on a silicon chip. Our approach overcomes the typical bottleneck of weak electron-phonon scattering by coupling the electrons directly to a bath of refrigerated nuclei, rather than cooling via phonons in the host lattice. Consequently, weak electron-phonon scattering becomes an advant- age. It allows the electrons to be cooled for an experimentally useful period of time to temperatures colder than the dilution refrigerator platform, the incoming electrical connections, and the host lattice. There are efforts worldwide to reach sub-millikelvin electron temperatures in nanostructures to study coherent electronic phenomena and improve the operation of nanoelectronic devices. On-chip magnetic cooling is a promising approach to meet this challenge. The method can be used to reach low, local electron temperatures in other nanostructures, obviating the need to adapt traditional, large demagnetisation stages. We demonstrate the technique by applying it to a nanoelectronic primary thermometer that measures its internal electron temperature. Using an optimised demagnetisation process, we demonstrate cooling of the on-chip electrons from 9 mK to below 5 mK for over 1000 seconds.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. Genetic and protein biomarkers in blood for the improved detection of GH abuse.

    Science.gov (United States)

    Ferro, P; Ventura, R; Pérez-Mañá, C; Farré, M; Segura, J

    2016-09-05

    Human Growth Hormone (hGH, somatotropin) is one of the relevant forbidden substances to be detected in sport drug testing. Since the appearance of recombinant hGH (rhGH) in the 80's, its expansion and availability through the black market have increased, so the detection of its abuse continues to be a challenge at present. New techniques or biomarkers that are robust, reliable, sensitive and allowing a large detection time window are welcome. rhGH produces an increase of insulin-like growth factor 1 (IGF-1). FN1 (fibronectin 1) and RAB31 (member of RAS oncogene family) genes have been suggested as two potential biomarkers for IGF-1 abuse. Following this line, in the present study some genetic and proteomic approaches have been performed with fourteen healthy male subjects treated with rhGH (which produces increase of IGF-1 concentrations) to study FN1 gene, FN1 protein, RAB31 gene and RAB31 protein as potential biomarkers for rhGH abuse. The results showed that both, RAB31 and FN1 genes and FN1 protein could be potential biomarkers for rhGH administration. Preliminary assessments of gender, age, acute sport activities and GHRP-2 (pralmorelin, a rhGH releasing peptide) influence suggest they are not relevant confounding factors. Thus, the selected markers present high sensitivity and a larger detection window for rhGH detection than IGF-1 itself.

  1. Detection of glycoalkaloids using disposable biosensors based on genetically modified enzymes.

    Science.gov (United States)

    Espinoza, Michelle Arredondo; Istamboulie, Georges; Chira, Ana; Noguer, Thierry; Stoytcheva, Margarita; Marty, Jean-Louis

    2014-07-15

    In this work we present a rapid, selective, and highly sensitive detection of α-solanine and α-chaconine using cholinesterase-based sensors. The high sensitivity of the devices is brought by the use of a genetically modified acetylcholinesterase (AChE), combined with a one-step detection method based on the measurement of inhibition slope. The selectivity was obtained by using butyrylcholinesterase (BChE), an enzyme able to detect these two toxins with differential inhibition kinetics. The enzymes were immobilized via entrapment in PVA-AWP polymer directly on the working electrode surface. The analysis of the resulting inhibition slope was performed employing linear regression function included in Matlab. The high toxicity of α-chaconine compared to α-solanine due to a better affinity to the active site was proved. The inhibition of glycoalkaloids (GAs) mixture was performed over AChE enzyme wild-type AChE and BChE biosensors resulting in the detection of synergism effect. The developed method allows the detection of (GAs) at 50 ppb in potato matrix.

  2. 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....... For this purpose, milk samples were collected in mid lactation from 371 Danish Holstein cows in first to third parity. A total of 31 metabolites were detected and identified in bovine milk by using 1H nuclear magnetic resonance (NMR) spectroscopy. Cows were genotyped using a bovine high-density single nucleotide...... polymorphism (SNP) chip. Based on the SNP data, a genomic relationship matrix was calculated and used as a random factor in a model together with 2 fixed factors (herd and lactation stage) to estimate the heritability and breeding value for individual metabolites in the milk. Heritability was in the range of 0...

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

    Directory of Open Access Journals (Sweden)

    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.

  4. 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.

  5. 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.

  6. 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.

  7. Genetic Variation of Inbred Lines of Maize Detected by SSR Markers

    Institute of Scientific and Technical Information of China (English)

    LI Xin-hai; FU Jun-hua; ZHANG Shi-huang; YUAN Li-xing; LI Ming-shun

    2001-01-01

    Simple sequence repeats (SSRs) were used to detect genetic variation among 21 maize(Zea mays L. ) inbred lines. Forty-three SSR primers selected from 69 primers gave stable amplification profiles, which could be clearly resolved on 3% Metaphor agarose gel, and produced 127 polymorphic amplified fragments.The average number of alleles per SSR locus was 2.95 with a range from 2 to 7. The polymorphism information content (PIC) for the SSR loci varied from 0.172 to 0.753 with an average of 0.511. Genetic similarities among the 21 lines ranged from 0.480 between the combination of Zhongzi451 vs. K12 up to 0.768 between CA156 vs. Ye478. The cluster analysis showed that 21 inbred lines could be classified into two distinct clusters with several subclusters, which corresponded to the heterotic groups determined by their pedigree information.Eight SSR primers, which had high level of polymorphism, could allow a rapid and efficient identification of 21 inbreds. Consequently, SSR markers could be used for measuring genetic variation of maize inbred lines and assigning them to heterotic groups.

  8. 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.

  9. Combined Dielectrophoresis and Impedance Systems for Bacteria Analysis in Microfluidic On-Chip Platforms.

    Science.gov (United States)

    Páez-Avilés, Cristina; Juanola-Feliu, Esteve; Punter-Villagrasa, Jaime; Del Moral Zamora, Beatriz; Homs-Corbera, Antoni; Colomer-Farrarons, Jordi; Miribel-Català, Pere Lluís; Samitier, Josep

    2016-09-16

    Bacteria concentration and detection is time-consuming in regular microbiology procedures aimed to facilitate the detection and analysis of these cells at very low concentrations. Traditional methods are effective but often require several days to complete. This scenario results in low bioanalytical and diagnostic methodologies with associated increased costs and complexity. In recent years, the exploitation of the intrinsic electrical properties of cells has emerged as an appealing alternative approach for concentrating and detecting bacteria. The combination of dielectrophoresis (DEP) and impedance analysis (IA) in microfluidic on-chip platforms could be key to develop rapid, accurate, portable, simple-to-use and cost-effective microfluidic devices with a promising impact in medicine, public health, agricultural, food control and environmental areas. The present document reviews recent DEP and IA combined approaches and the latest relevant improvements focusing on bacteria concentration and detection, including selectivity, sensitivity, detection time, and conductivity variation enhancements. Furthermore, this review analyses future trends and challenges which need to be addressed in order to successfully commercialize these platforms resulting in an adequate social return of public-funded investments.

  10. Combined Dielectrophoresis and Impedance Systems for Bacteria Analysis in Microfluidic On-Chip Platforms

    Directory of Open Access Journals (Sweden)

    Cristina Páez-Avilés

    2016-09-01

    Full Text Available Bacteria concentration and detection is time-consuming in regular microbiology procedures aimed to facilitate the detection and analysis of these cells at very low concentrations. Traditional methods are effective but often require several days to complete. This scenario results in low bioanalytical and diagnostic methodologies with associated increased costs and complexity. In recent years, the exploitation of the intrinsic electrical properties of cells has emerged as an appealing alternative approach for concentrating and detecting bacteria. The combination of dielectrophoresis (DEP and impedance analysis (IA in microfluidic on-chip platforms could be key to develop rapid, accurate, portable, simple-to-use and cost-effective microfluidic devices with a promising impact in medicine, public health, agricultural, food control and environmental areas. The present document reviews recent DEP and IA combined approaches and the latest relevant improvements focusing on bacteria concentration and detection, including selectivity, sensitivity, detection time, and conductivity variation enhancements. Furthermore, this review analyses future trends and challenges which need to be addressed in order to successfully commercialize these platforms resulting in an adequate social return of public-funded investments.

  11. Unambiguous molecular detections with multiple genetic approach for the complicated chromosome 22q11 deletion syndrome

    Directory of Open Access Journals (Sweden)

    Lin Lung-Huang

    2009-02-01

    Full Text Available Abstract Background Chromosome 22q11 deletion syndrome (22q11DS causes a developmental disorder during the embryonic stage, usually because of hemizygous deletions. The clinical pictures of patients with 22q11DS vary because of polymorphisms: on average, approximately 93% of affected individuals have a de novo deletion of 22q11, and the rest have inherited the same deletion from a parent. Methods using multiple genetic markers are thus important for the accurate detection of these microdeletions. Methods We studied 12 babies suspected to carry 22q11DS and 18 age-matched healthy controls from unrelated Taiwanese families. We determined genomic variance using microarray-based comparative genomic hybridization (array-CGH, quantitative real-time polymerase chain reaction (qPCR and multiplex ligation-dependent probe amplification (MLPA. Results Changes in genomic copy number were significantly associated with clinical manifestations for the classical criteria of 22q11DS using MPLA and qPCR (p Conclusion Both MLPA and qPCR could produce a clearly defined range of deleted genomic DNA, whereas there must be a deleted genome that is not distinguishable using MLPA. These data demonstrate that such multiple genetic approaches are necessary for the unambiguous molecular detection of these types of complicated genomic syndromes.

  12. Comparative analyses of different genetic markers for the detection of Acanthamoeba spp. isolates.

    Science.gov (United States)

    Derda, Monika; Wojtkowiak-Giera, Agnieszka; Hadaś, Edward

    2014-09-01

    Acanthamoeba are widespread free-living amoebae which may cause granulomatous amoebic encephalitis (GAE), keratitis, skin ulcerations and disseminated tissue infection. An important diagnostic and prognostic factor for the treatment of infection is a quick and correct diagnosis of amoebae strains. The aim of our study was to develop a rapid method for detection and identification of pathogenic Acanthamoeba spp. strains from diagnostic material collected from water. In this study we analysed five amplification-based genetic markers (Aca 16S, Ac6/210, GP, JDP, Nelson) used for identification of pathogenic Acanthamoeba spp. strains isolated in water sources in Poland, Iceland and Sweden. Our results demonstrated the presence of pathogenic Acanthamoeba strains in tap water. PCR assay appeared to be a more rapid and sensitive method to detect the presence of amoebae than the limited conventional techniques. Based on our observations, we can confirm that the use of four out of five genetic markers (Aca 16S, Ac 6/210, JDP, GP, Nelson) may be helpful in identification of Acanthamoeba spp. strains, but only one Aca 16S primer pair is a highly specific marker that distinguishes between pathogenic strains of Acanthamoeba and other free-living amoeba families.

  13. Balanced reciprocal translocation at amniocentesis: cytogenetic detection and implications for genetic counseling.

    Science.gov (United States)

    Zhang, H G; Zhang, X Y; Zhang, H Y; Tian, T; Xu, S B; Liu, R Z

    2016-08-19

    Balanced translocation is a common structural chromosomal rearrangement in humans. Carriers can be phenotypically normal but have an increased risk of pregnancy loss, fetal death, and the transmission of chromosomal abnormalities to their offspring. Existing prenatal screening technologies and diagnostic procedures fail to detect balanced translocation, so genetic counseling for carriers remains a challenge. Here, we report the characteristics of chromosomal reciprocal translocation in 3807 amniocentesis cases. Of the 16 detected cases of fetal reciprocal translocation, 8 cases (50%) showed positive biochemical marker screening; 3 cases (18.75%) were the parental carriers of a chromosomal abnormality; 2 (12.5%) were of advanced maternal age, 2 (12.5%) had a previous history of children with genetic disorders, and 1 case (6.25%) was associated with positive soft markers in obstetric ultrasound. Chromosomes 5 and 19 were the most commonly involved chromosomes in balanced translocations. Of the 13 cases with fetal balanced translocations, 8 (61.5%) were inherited from a paternal chromosome, 3 (23.1%) from a maternal chromosome, and 2 (15.4%) cases were de novo. The incidence of balanced translocation at amniocentesis was 0.42%. Male carriers of reciprocal chromosome translocation appear to have a higher chance of becoming a parent of a child born by normal childbirth than female carriers.

  14. 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.

  15. 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.

  16. Detection of unbalanced chromosome segregations in preimplantation genetic diagnosis of translocations by short comparative genomic hibridization.

    Science.gov (United States)

    Rius, Mariona; Obradors, Albert; Daina, Gemma; Ramos, Laia; Pujol, Aïda; Martínez-Passarell, Olga; Marquès, Laura; Oliver-Bonet, Maria; Benet, Jordi; Navarro, Joaquima

    2011-07-01

    To apply a comprehensive chromosomal screening through short comparative genomic hybridization (CGH) in the preimplantation genetic diagnosis (PGD) of translocations. Clinical research study. A PGD laboratory and two IVF clinics. Three Robertsonian translocation carriers, two reciprocal translocation carriers, and a double-translocation carrier. After using the short-CGH approach in the reanalysis of two unbalanced embryos, discarded from a PGD for a reciprocal translocation carrier, the same method was applied in the PGD of day-3 embryos of translocation carriers. Ability of short CGH to detect partial chromosomal abnormalities in unbalanced embryos, translocation segregation proportions, and proportion of embryos carrying chromosomal abnormalities not related to the translocations. The short-CGH technique detected errors resulting from the meiotic segregation of the chromosomes involved in the translocations and other abnormalities affecting the remaining chromosomes. Alternate segregation was detected most frequently among Robertsonian translocation cases, whereas unbalanced chromosome segregations were found predominantly in reciprocal ones. Aneuploidy and structural chromosome errors were found more frequently in Robertsonian than in reciprocal translocation carriers. Application of short-CGH PGD achieved pregnancy in two cases. Short CGH is a reliable approach for PGD of translocations, as it is capable of detecting partial chromosome errors caused by unbalanced segregations simultaneously to the screening of all chromosomes, and it may improve the results after PGD for translocation carriers. Copyright © 2011 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  17. The future role of genetic screening to detect newborns at risk of childhood-onset hearing loss

    Science.gov (United States)

    2013-01-01

    Objective: To explore the future potential of genetic screening to detect newborns at risk of childhood-onset hearing loss. Design: An expert led discussion of current and future developments in genetic technology and the knowledge base of genetic hearing loss to determine the viability of genetic screening and the implications for screening policy. Results and Discussion: Despite increasing pressure to adopt genetic technologies, a major barrier for genetic screening in hearing loss is the uncertain clinical significance of the identified mutations and their interactions. Only when a reliable estimate of the future risk of hearing loss can be made at a reasonable cost, will genetic screening become viable. Given the speed of technological advancement this may be within the next 10 years. Decision-makers should start to consider how genetic screening could augment current screening programmes as well as the associated data processing and storage requirements. Conclusion: In the interim, we suggest that decision makers consider the benefits of (1) genetically testing all newborns and children with hearing loss, to determine aetiology and to increase knowledge of the genetic causes of hearing loss, and (2) consider screening pregnant women for the m.1555A> G mutation to reduce the risk of aminoglycoside antibiotic-associated hearing loss. PMID:23131088

  18. 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

  19. 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...... applied to generate biochip layouts with integrated on-chip pneumatic control....

  20. 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 intr

  1. A run-time reconfigurable Network-on-Chip for streaming DSP applications

    NARCIS (Netherlands)

    Kavaldjiev, N.K.; Kavaldjiev, Nikolay Krasimirov

    2007-01-01

    With the advance of semiconductor technology, global on-chip wiring is becoming a limiting factor for the overall performance of large System-on-Chip (SoC) designs. In this thesis we propose a global communication architecture that avoids this limitation by structuring and shortening of the global

  2. Rational design of on-chip refractive index sensors based on lattice plasmon resonances (Presentation Recording)

    Science.gov (United States)

    Lin, Linhan; Zheng, Yuebing

    2015-08-01

    Lattice plasmon resonances (LPRs), which originate from the plasmonic-photonic coupling in gold or silver nanoparticle arrays, possess ultra-narrow linewidth by suppressing the radiative damping and provide the possibility to develop the plasmonic sensors with high figure of merit (FOM). However, the plasmonic-photonic coupling is greatly suppressed when the nanoparticles are immobilized on substrates because the diffraction orders are cut off at the nanoparticle-substrate interfaces. Here, we develop the rational design of LPR structures for the high-performance, on-chip plasmonic sensors based on both orthogonal and parallel coupling. Our finite-difference time-domain simulations in the core/shell SiO2/Au nanocylinder arrays (NCAs) reveal that new modes of localized surface plasmon resonances (LSPRs) show up when the aspect ratio of the NCAs is increased. The height-induced LSPRs couple with the superstrate diffraction orders to generate the robust LPRs in asymmetric environment. The high wavelength sensitivity and narrow linewidth in these LPRs lead to the plasmonic sensors with high FOM and high signal-to-noise ratio (SNR). Wide working wavelengths from visible to near-infrared are also achieved by tuning the parameters of the NCAs. Moreover, the wide detection range of refractive index is obtained in the parallel LPR structure. The electromagnetic field distributions in the NCAs demonstrate the height-enabled tunability of the plasmonic "hot spots" at the sub-nanoparticles resolution and the coupling between these "hot spots" with the superstrate diffraction waves, which are responsible for the high performance LPRs-based on-chip refractive index sensors.

  3. Fiber free plug and play on-chip scattering cytometer module – for implementation in microfluidic point of care devices

    DEFF Research Database (Denmark)

    Jensen, Thomas Glasdam; Kutter, Jörg Peter

    2010-01-01

    In this paper, we report on recent progress toward the development of a plug and play on-chip cytometer based on light scattering. By developing a device that does not depend on the critical alignment and cumbersome handling of fragile optical fibers, we approach a device that is suitable for non......-expert users and Point-Of-Care (POC) applications. It has been demonstrated that this device is capable of detecting and counting particles down to 1 μm at 100 particles per second. This device only depends on a single microfluidic channel. Hence, the device is easy to implement, or to use on its own....

  4. 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.

  5. Advances in molecular techniques for the detection and quantification of genetically modified organisms.

    Science.gov (United States)

    Elenis, Dimitrios S; Kalogianni, Despina P; Glynou, Kyriaki; Ioannou, Penelope C; Christopoulos, Theodore K

    2008-10-01

    Progress in genetic engineering has led to the introduction of genetically modified organisms (GMOs) whose genomes have been altered by the integration of a novel sequence conferring a new trait. To allow consumers an informed choice, many countries require food products to be labeled if the GMO content exceeds a certain threshold. Consequently, the development of analytical methods for GMO screening and quantification is of great interest. Exponential amplification by the polymerase chain reaction (PCR) remains a central step in molecular methods of GMO detection and quantification. In order to meet the challenge posed by the continuously increasing number of GMOs, various multiplex assays have been developed for the simultaneous amplification and/or detection of several GMOs. Classical agarose gel electrophoresis is being replaced by capillary electrophoresis (CE) systems, including CE chips, for the rapid and automatable separation of amplified fragments. Microtiter well-based hybridization assays allow high-throughput analysis of many samples in a single plate. Microarrays have been introduced in GMO screening as a technique for the simultaneous multianalyte detection of amplified sequences. Various types of biosensors, including surface plasmon resonance sensors, quartz crystal microbalance piezoelectric sensors, thin-film optical sensors, dry-reagent dipstick-type sensors and electrochemical sensors were introduced in GMO screening because they offer simplicity and lower cost. GMO quantification is performed by real-time PCR (rt-QPCR) and competitive PCR. New endogenous reference genes have been validated. rt-QPCR is the most widely used approach. Multiplexing is another trend in this field. Strategies for high-throughput multiplex competitive quantitative PCR have been reported.

  6. 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.

  7. Frequency domain processing of on-chip biphoton frequency comb

    CERN Document Server

    Jaramillo-Villegas, Jose A; Odele, Ogaga D; Leaird, Daniel E; Ou, Zhe-Yu; Qi, Minghao; Weiner, Andrew M

    2016-01-01

    Quantum information processing (QIP) promises to improve the security of our communications as well as to solve some algorithms with exponential complexity in polynomial time. Biphotons have been demonstrated as one of the most promising platforms for real implementations of QIP systems. In particular, time-bin entangled photons have been used for implementations of quantum gates which require highly stable interferometers. On the other hand, frequency-bin entanglement has been proposed to avoid the use of interferometers and the complexity of their stabilization, which potentially makes the implementation of quantum gates highly scalable. Through Fourier transform pulse shaping and electro-optic modulation, there has been a wide range of experiments that show control of entangled photons in the frequency domain. In addition, biphoton frequency combs (BFC) have also been generated using bulk optics and frequency filtering of broadband continuous biphoton spectra. However, on-chip entangled photon pair generat...

  8. Semiconductor plasmonic gas sensor using on-chip infrared spectroscopy

    Science.gov (United States)

    Elsayed, Mohamed Y.; Ismail, Yehea; Swillam, Mohamed A.

    2017-01-01

    In this paper, we take a novel approach in on-chip optical sensing of gases. Gases have conventionally been optically sensed using refractive index, which is a non-ideal method because of the difficulty in differentiating gases with very similar refractive indices. Infrared (IR) absorption spectra on the other hand have characteristic peaks in the fingerprint region that allow identifying the analyte. Highly doped n-type Indium Arsenide was used to design a plasmonic slot waveguide, and a dispersion analysis was carried out using the finite element method to study the effect of dopant concentration and waveguide geometry on the guided modes. Finite-difference time domain was used to simulate the transmission spectrum of the waveguide with air, methane and octane and the characteristic peaks in the IR spectra showed up strongly. This is a promising versatile method that can sense any IR-active gas.

  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. On-chip data exchange for mode division multiplexed signals.

    Science.gov (United States)

    Ye, Mengyuan; Yu, Yu; Sun, Chunlei; Zhang, Xinliang

    2016-01-11

    Data exchange is an important function for flexible optical network, and it has been extensively investigated for the time and wavelength domains. The mode division multiplexing (MDM) has been proposed to further increase the transmission capacity by carrying information on different modes with only single wavelength carrier. We propose and experimentally demonstrate a novel on-chip data exchange circuit for the MDM signals by utilizing two micro-ring resonator (MRR) based mode converters. For demonstration, single and four wavelengths non-return-to-zero on-off-keying (NRZ-OOK) signals at 10 Gb/s carried on different modes are successfully processed, with open and clear eye diagrams. Measured bit error ratio (BER) results show reasonable power penalties. The proposed circuit can be potentially used in advanced and flexible MDM optical networks.

  11. 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

    2016-01-01

    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. PMID:27775062

  12. On-chip Inter-modal Brillouin Scattering

    CERN Document Server

    Kittlaus, Eric A; Rakich, Peter T

    2016-01-01

    Stimulated Brillouin interactions mediate nonlinear coupling between photons and acoustic phonons through an optomechanical three-wave interaction. Though these nonlinearities were previously very weak in silicon photonic systems, the recent emergence of new optomechanical waveguide structures have transformed Brillouin processes into one of the strongest and most tailorable on-chip nonlinear interactions. New technologies based on Brillouin couplings have formed a basis for amplification, filtering, and nonreciprocal signal processing techniques. In this paper, we demonstrate strong guided-wave Brillouin scattering between light fields guided in distinct spatial modes of a silicon waveguide for the first time. This inter-modal coupling creates dispersive symmetry breaking between Stokes and anti-Stokes processes, permitting single-sideband amplification and wave dynamics that permit near-unity power conversion. Combining these physics with integrated mode-multiplexers enables novel device topologies and elim...

  13. An on-chip colloidal magneto-optical grating

    Science.gov (United States)

    Prikockis, M.; Wijesinghe, H.; Chen, A.; VanCourt, J.; Roderick, D.; Sooryakumar, R.

    2016-04-01

    Interacting nano- and micro-particles provide opportunities to create a wide range of useful colloidal and soft matter constructs. In this letter, we examine interacting superparamagnetic polymeric particles residing on designed permalloy (Ni0.8 Fe0.2) shapes that are subject to weak time-orbiting magnetic fields. The precessing field and magnetic barriers that ensue along the outer perimeter of the shapes allow for containment concurrent with independent field-tunable ordering of the dipole-coupled particles. These remotely activated arrays with inter-particle spacing comparable to the wavelength of light yield microscopic on-chip surface gratings for beam steering and magnetically regulated light diffraction applications.

  14. On-chip magnetometer for characterization of superparamagnetic nanoparticles.

    Science.gov (United States)

    Kim, Kun Woo; Reddy, Venu; Torati, Sri Ramulu; Hu, Xing Hao; Sandhu, Adarsh; Kim, Cheol Gi

    2015-02-07

    An on-chip magnetometer was fabricated by integrating a planar Hall magnetoresistive (PHR) sensor with microfluidic channels. The measured in-plane field sensitivities of an integrated PHR sensor with NiFe/Cu/IrMn trilayer structure were extremely high at 8.5 μV Oe(-1). The PHR signals were monitored during the oscillation of 35 pL droplets of magnetic nanoparticles, and reversed profiles for the positive and negative z-fields were measured, where magnitudes increased with the applied z-field strength. The measured PHR signals for 35 pL droplets of magnetic nanoparticles versus applied z-fields showed excellent agreement with magnetization curves measured by a vibrating sample magnetometer (VSM) of 3 μL volume, where a PHR voltage of 1 μV change is equivalent to 0.309 emu cc(-1) of the volume magnetization with a magnetic moment resolution of ~10(-10) emu.

  15. On-chip photonic Fourier transform with surface plasmon polaritons

    Institute of Scientific and Technical Information of China (English)

    Shan Shan Kou; Guanghui Yuan; Qian wang; Luping Du; Eugeniu Balaur; Daohua Zhang; Dingyuan Tang

    2016-01-01

    The Fourier transform (FT),a cornerstone of optical processing,enables rapid evaluation of fundamental mathematical operations,such as derivatives and integrals.Conventionally,a converging lens performs an optical FT in free space when light passes through it.The speed of the transformation is limited by the thickness and the focal length of the lens.By usingthe wave nature of surface plasmon polaritons (SPPs),here we demonstrate that the FT can be implemented in a planar configuration with a minimal propagation distance of around 10 μm,resulting in an increase of speed by four to five orders of magnitude.The photonic FT was tested by synthesizing intricate SPP waves with their Fourier components.The reduced dimensionality in the minuscule device allows the future development of an ultrafast on-chip photonic information processing platform for large-scale optical computing.

  16. Magnetic Tunnel Junction as an On-Chip Temperature Sensor.

    Science.gov (United States)

    Sengupta, Abhronil; Liyanagedera, Chamika Mihiranga; Jung, Byunghoo; Roy, Kaushik

    2017-09-18

    Temperature sensors are becoming an increasingly important component in System-on-Chip (SoC) designs with increasing transistor scaling, power density and associated heating effects. This work explores a compact nanoelectronic temperature sensor based on a Magnetic Tunnel Junction (MTJ) structure. The MTJ switches probabilistically depending on the operating temperature in the presence of thermal noise. Performance evaluation of the proposed MTJ temperature sensor, based on experimentally measured device parameters, reveals that the sensor is able to achieve a conversion rate of 2.5K samples/s with energy consumption of 8.8 nJ per conversion (1-2 orders of magnitude lower than state-of-the-art CMOS sensors) for a linear sensing regime of 200-400 K.

  17. 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.

  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. 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

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

    Science.gov (United States)

    Abebe, Abiye Shenkut; Mikko, Sofia; Johansson, Anna M

    2015-01-01

    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 -6.723%. The results

  2. Fluorescent detection of Southern blots and PCR-based genetic typing tests

    Energy Technology Data Exchange (ETDEWEB)

    Mansfield, E.S.; Worley, J.M. [Molecular Dynamics, Inc., Sunnyvale, CA (United States); Zimmerman, P.A. [Laboratory of Parasitic Diseases, Bethesda, MD (United States)] [and others

    1994-09-01

    The Southern blot is used to study gene organization, to identify disease-causing genomic rearrangements, or for typing RFLP markers in forensic, paternity, or prenatal diagnostic testing. Fluorescence offers a much greater dynamic range and a more linear response than film used in radioactive or chemiluminescent detection of RFLPs. We therefore investigated using the Fluorimager{trademark} 575 (Molecular Dynamics, Inc.) for analyzing Southern blots. Using a single-locus probe to D2S44 (YNH24) (Promega Corp.), we detect as little as 100 ng (0.05 attomole) genomic DNA. The alkaline phosphatase-labeled probe is detected using AttoPhos (JBL Scientific), and the developed membrane is scanned with the Fluorimager. Biotinylated hybridization probes can also be developed using a streptavidin-alkaline phosphatase conjugate and AttoPhos. The instrument scan parameters can be adjusted to prevent overexposure and accompanying loss of resolution in images of blots, gels, or 96-well microplates. We have used these other sample formats in PCR-based genetic typing assays. We use FluorKit DQS (Molecular Dynamics) to accurately quantify PCR template DNA (1-500 ng) in 96-well microplates scanned using the same instrument. Mutation detection assays run include heteroduplex gels (5% polyacrylamide, 2.7 M urea), short tandem repeat (STR) markers, amplified fragment length polymorphisms (AmpFLP), competitive priming PCR, and allele-specific oligotyping. These assays are run using either 1- or 2-color labeling. We detect unlabeled PCR products, such as the AmpFLP marker D1S80 (Perkin-Elmer) by post-staining gels for 10 minutes with SYBR Green 1 (Molecular Probes) and scanning the wet gel. The Fluorimager scans a 20 x 25 cm sample within three minutes, allowing rapid optimization of fluorescent protocols and high sample throughput.

  3. Segmentation and detection of breast cancer in mammograms combining wavelet analysis and genetic algorithm.

    Science.gov (United States)

    Pereira, Danilo Cesar; Ramos, Rodrigo Pereira; do Nascimento, Marcelo Zanchetta

    2014-04-01

    In Brazil, the National Cancer Institute (INCA) reports more than 50,000 new cases of the disease, with risk of 51 cases per 100,000 women. Radiographic images obtained from mammography equipments are one of the most frequently used techniques for helping in early diagnosis. Due to factors related to cost and professional experience, in the last two decades computer systems to support detection (Computer-Aided Detection - CADe) and diagnosis (Computer-Aided Diagnosis - CADx) have been developed in order to assist experts in detection of abnormalities in their initial stages. Despite the large number of researches on CADe and CADx systems, there is still a need for improved computerized methods. Nowadays, there is a growing concern with the sensitivity and reliability of abnormalities diagnosis in both views of breast mammographic images, namely cranio-caudal (CC) and medio-lateral oblique (MLO). This paper presents a set of computational tools to aid segmentation and detection of mammograms that contained mass or masses in CC and MLO views. An artifact removal algorithm is first implemented followed by an image denoising and gray-level enhancement method based on wavelet transform and Wiener filter. Finally, a method for detection and segmentation of masses using multiple thresholding, wavelet transform and genetic algorithm is employed in mammograms which were randomly selected from the Digital Database for Screening Mammography (DDSM). The developed computer method was quantitatively evaluated using the area overlap metric (AOM). The mean ± standard deviation value of AOM for the proposed method was 79.2 ± 8%. The experiments demonstrate that the proposed method has a strong potential to be used as the basis for mammogram mass segmentation in CC and MLO views. Another important aspect is that the method overcomes the limitation of analyzing only CC and MLO views. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  4. 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.

  5. Land Cover Change Detection Based on Genetically Feature Aelection and Image Algebra Using Hyperion Hyperspectral Imagery

    Science.gov (United States)

    Seydi, S. T.; Hasanlou, M.

    2015-12-01

    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.

  6. Optimal Parameter Exploration for Online Change-Point Detection in Activity Monitoring Using Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Naveed Khan

    2016-10-01

    Full Text Available In recent years, smart phones with inbuilt sensors have become popular devices to facilitate activity recognition. The sensors capture a large amount of data, containing meaningful events, in a short period of time. The change points in this data are used to specify transitions to distinct events and can be used in various scenarios such as identifying change in a patient’s vital signs in the medical domain or requesting activity labels for generating real-world labeled activity datasets. Our work focuses on change-point detection to identify a transition from one activity to another. Within this paper, we extend our previous work on multivariate exponentially weighted moving average (MEWMA algorithm by using a genetic algorithm (GA to identify the optimal set of parameters for online change-point detection. The proposed technique finds the maximum accuracy and F_measure by optimizing the different parameters of the MEWMA, which subsequently identifies the exact location of the change point from an existing activity to a new one. Optimal parameter selection facilitates an algorithm to detect accurate change points and minimize false alarms. Results have been evaluated based on two real datasets of accelerometer data collected from a set of different activities from two users, with a high degree of accuracy from 99.4% to 99.8% and F_measure of up to 66.7%.

  7. The genetic-algorithm-enhanced blind system identification for water distribution pipeline leak detection

    Science.gov (United States)

    Yang, Jin; Wen, Yumei; Li, Ping

    2007-07-01

    The conventional leak location is based on the correlation of leak acoustic signals acquired spatially separately. By correlation, the time lag is estimated for localizing the leakage. In these methods, the detection distance is a prerequisite that has to be known beforehand. However, in practice, this prerequisite is not always satisfied. In this case, the correlation-based methods are not feasible. Actually, the acquired signals contain the characteristics related to the acoustic propagation channels; thus the blind system identification strategy is applied to estimate the transmission performances of acoustic channels. Then the times due to the propagation of the leak source signal travelling from the leak point to sensors are determined. In this way, for leak location, the detection distance is no longer a prerequisite. In blind system identification, due to the long impulse responses of the leak acoustic channels, the channels are inevitably ill conditioned and sensitive to the initial values. To overcome the ill conditions, the overlap-save and cross-correlation fitting techniques are utilized to identify the long impulse sequences under a built constraint. In order to avoid converging to the local minima, the genetic algorithm is used to minimize the cost functions. The practical detection results show the validity of the proposed scheme.

  8. A multi-agent genetic algorithm for community detection in complex networks

    Science.gov (United States)

    Li, Zhangtao; Liu, Jing

    2016-05-01

    Complex networks are popularly used to represent a lot of practical systems in the domains of biology and sociology, and the structure of community is one of the most important network attributes which has received an enormous amount of attention. Community detection is the process of discovering the community structure hidden in complex networks, and modularity Q is one of the best known quality functions measuring the quality of communities of networks. In this paper, a multi-agent genetic algorithm, named as MAGA-Net, is proposed to optimize modularity value for the community detection. An agent, coded by a division of a network, represents a candidate solution. All agents live in a lattice-like environment, with each agent fixed on a lattice point. A series of operators are designed, namely split and merging based neighborhood competition operator, hybrid neighborhood crossover, adaptive mutation and self-learning operator, to increase modularity value. In the experiments, the performance of MAGA-Net is validated on both well-known real-world benchmark networks and large-scale synthetic LFR networks with 5000 nodes. The systematic comparisons with GA-Net and Meme-Net show that MAGA-Net outperforms these two algorithms, and can detect communities with high speed, accuracy and stability.

  9. 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.

  10. 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.

  11. 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.

  12. 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

    2017-05-09

    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.

  13. On-chip laser-induced DNA dehybridization.

    Science.gov (United States)

    Wheeler, E K; Baker, B R; Piggott, W T; Mabery, S L; Hara, C A; DeOtte, J; Benett, W; Mukerjee, E V; Dzenitis, J; Beer, N R

    2013-07-07

    Detection of pathogens and relevant genetic markers using their nucleic acid signatures is extremely common due to the inherent specificity genomic sequences provide. One approach for assaying a sample simultaneously for many different targets is the DNA microarray, which consists of several million short nucleic acid sequences (probes) bound to an inexpensive transparent substrate. Typically, complex samples hybridize to the microarray and the pattern of fluorescing probes on the microarray's surface identifies the detected targets. In the case of evolving or newly emergent organisms, a hybridization pattern can occur that differs from any previously known sources. When this happens it can be useful to recover the hybridized DNA from the binding locations of interest for sequencing. Here we present the novel utilization of a focused Infrared (IR) laser to heat user-selected spots on the DNA microarray surface, causing only localized dehybridization and recovery of the desired DNA into an elution buffer where it is available for subsequent amplification or sequencing. The introduction of a focused dehybridization method for spots of interest suppresses the amount of background DNA to be analyzed from downstream processes, and should reduce subsequent sequence assembly errors. This technique could also be applied to high-density protein microarrays where the desire to locally heat spots for release of bound molecules is desired.

  14. 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...

  15. Genetic variation and RNA binding proteins: tools and techniques to detect functional polymorphisms.

    Science.gov (United States)

    Soemedi, Rachel; Vega, Hugo; Belmont, Judson M; Ramachandran, Sohini; Fairbrother, William G

    2014-01-01

    At its most fundamental level the goal of genetics is to connect genotype to phenotype. This question is asked at a basic level evaluating the role of genes and pathways in genetic model organism. Increasingly, this question is being asked in the clinic. Genomes of individuals and populations are being sequenced and compared. The challenge often comes at the stage of analysis. The variant positions are analyzed with the hope of understanding human disease. However after a genome or exome has been sequenced, the researcher is often deluged with hundreds of potentially relevant variations. Traditionally, amino-acid changing mutations were considered the tractable class of disease-causing mutations; however, mutations that disrupt noncoding elements are the subject of growing interest. These noncoding changes are a major avenue of disease (e.g., one in three hereditary disease alleles are predicted to affect splicing). Here, we review some current practices of medical genetics, the basic theory behind biochemical binding and functional assays, and then explore technical advances in how variations that alter RNA protein recognition events are detected and studied. These advances are advances in scale-high-throughput implementations of traditional biochemical assays that are feasible to perform in any molecular biology laboratory. This chapter utilizes a case study approach to illustrate some methods for analyzing polymorphisms. The first characterizes a functional intronic SNP that deletes a high affinity PTB site using traditional low-throughput biochemical and functional assays. From here we demonstrate the utility of high-throughput splicing and spliceosome assembly assays for screening large sets of SNPs and disease alleles for allelic differences in gene expression. Finally we perform three pilot drug screens with small molecules (G418, tetracycline, and valproic acid) that illustrate how compounds that rescue specific instances of differential pre-mRNA processing

  16. 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.

  17. Intrusion detection: a novel approach that combines boosting genetic fuzzy classifier and data mining techniques

    Science.gov (United States)

    Ozyer, Tansel; Alhajj, Reda; Barker, Ken

    2005-03-01

    This paper proposes an intelligent intrusion detection system (IDS) which is an integrated approach that employs fuzziness and two of the well-known data mining techniques: namely classification and association rule mining. By using these two techniques, we adopted the idea of using an iterative rule learning that extracts out rules from the data set. Our final intention is to predict different behaviors in networked computers. To achieve this, we propose to use a fuzzy rule based genetic classifier. Our approach has two main stages. First, fuzzy association rule mining is applied and a large number of candidate rules are generated for each class. Then the rules pass through pre-screening mechanism in order to reduce the fuzzy rule search space. Candidate rules obtained after pre-screening are used in genetic fuzzy classifier to generate rules for the specified classes. Classes are defined as Normal, PRB-probe, DOS-denial of service, U2R-user to root and R2L- remote to local. Second, an iterative rule learning mechanism is employed for each class to find its fuzzy rules required to classify data each time a fuzzy rule is extracted and included in the system. A Boosting mechanism evaluates the weight of each data item in order to help the rule extraction mechanism focus more on data having relatively higher weight. Finally, extracted fuzzy rules having the corresponding weight values are aggregated on class basis to find the vote of each class label for each data item.

  18. Trichophyton tonsurans strains from Brazil: phenotypic heterogeneity, genetic homology, and detection of virulence genes.

    Science.gov (United States)

    Sidrim, José Julio Costa; Rocha, Marcos Fábio Gadelha; Leite, João Jaime Giffoni; Maranhão, Fernanda Cristina de Albuquerque; Lima, Rita Amanda Chaves; Castelo-Branco, Débora de Souza Collares Maia; Bandeira, Tereza de Jesus Pinheiro Gomes; Cordeiro, Rossana de Aguiar; Brilhante, Raimunda Sâmia Nogueira

    2013-11-01

    The objective of this study was to establish the phenotypical and molecular patterns of clinical isolates of Trichophyton tonsurans circulating in the state of Ceará, northeastern Brazil. For this purpose, 25 T. tonsurans strains isolated from independent cases of tinea capitis in children were phenotypically evaluated regarding their macro- and micro-morphological characteristics, vitamin requirements, urease production, and antifungal susceptibility. The molecular characterization was carried out with random amplified polymorphic DNA molecular markers and M13 fingerprinting. The presence of the genes CarbM14, Sub2, CER, URE, ASP, PBL, and LAC, which encode enzymes related to fungal virulence, was also evaluated. Finally, melanin production was assessed through specific staining. The data obtained demonstrated that these T. tonsurans strains have considerable phenotypical variation, although they showed a low degree of genetic polymorphism according to the markers used. The genes CarbM14, Sub2, CER, and URE were detected in all the analyzed strains. The gene LAC was also identified in all the strains, and melanin synthesis was phenotypically confirmed. The strains were susceptible to antifungals, especially itraconazole (GM = 0.06 μg/mL) and ketoconazole (GM = 0.24 μg/mL). Therefore, T. tonsurans strains can present great phenotypical heterogeneity, even in genetically similar isolates. Moreover, the presence of the LAC gene indicates the possible participation of melanin in the pathogenesis of these dermatophytes.

  19. 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.

  20. 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.

  1. Anjozorobe hantavirus, a new genetic variant of Thailand virus detected in rodents from Madagascar.

    Science.gov (United States)

    Reynes, Jean-Marc; Razafindralambo, Nadia Kaloina; Lacoste, Vincent; Olive, Marie-Marie; Barivelo, Tony Andrianaivo; Soarimalala, Voahangy; Heraud, Jean-Michel; Lavergne, Anne

    2014-03-01

    Until now, there was only serological evidence that hantaviruses were circulating in rodents and infecting humans from Madagascar. To assess the presence of a hantavirus on the island, between October, 2008, and March, 2010, we sampled 585 rodents belonging to seven species in the Anjozorobe-Angavo forest corridor, 70 km north from the capital city Antananarivo. A hantavirus was detected from organs of the ubiquist roof rat (Rattus rattus) and of the endemic Major's tufted-tailed rat (Eliurus majori). Amazingly, sequence analysis of the S (small), M (medium), and L (large) coding DNA sequence of this virus showed that the Anjozorobe strain (proposed name) was a new genetic variant of Thailand virus (THAIV) that comprises other variants found in Southeast Asia. Because THAIV is suspected of causing hemorrhagic fever with renal syndrome in humans, ongoing studies are addressing the risk of infection by this new variant in the Malagasy population.

  2. Using genetic markers in unpedigreed populations to detect a heritable trait

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Before a breeder invests selection pressure on a trait of interest, it needs to be established whether that trait is actually heritable. Some traits may not have been measured widely in pedigreed populations, for example, a disease or deformity may become more prevalent than previously, but is still relatively rare. One approach to detect inheritance would be to screen a commercial population to obtain a sample of "affecteds" (the test group) and to also obtain a random control group. These individuals are then genotyped with a set of genetic markers and the relationships between individuals within each group estimated. If the relatedness is higher in the test group than in the control group, this provides initial evidence for the trait being heritable. A power simulation shows that this approach is feasible with moderate resources.

  3. 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.

  4. Breast cancer genetic risk profile is differentially associated with interval and screen-detected breast cancers.

    Science.gov (United States)

    Li, J; Holm, J; Bergh, J; Eriksson, M; Darabi, H; Lindström, L S; Törnberg, S; Hall, P; Czene, K

    2015-03-01

    Polygenic risk profiles computed from multiple common susceptibility alleles for breast cancer have been shown to identify women at different levels of breast cancer risk. We evaluated whether this genetic risk stratification can also be applied to discriminate between screen-detected and interval cancers, which are usually associated with clinicopathological and survival differences. A 77 single-nucleotide polymorphism polygenic risk score (PRS) was constructed for breast cancer overall and by estrogen receptor (ER) status. PRS was inspected as a continuous (per standard deviation increment) variable in a case-only design. Modification of the PRS by mammographic density was evaluated by fitting an additional interaction term. PRS weighted by breast cancer overall estimates was found to be differentially associated with 1865 screen-detected and 782 interval cancers in the LIBRO-1 study {age-adjusted odds ratio (OR)perSD [95% confidence interval (CI)] 0.91 [0.83-0.99], P = 0.023}. The association was found to be more significant for PRS weighted by ER-positive breast cancer estimates [ORperSD = 0.90 (0.82-0.98), P = 0.011]. This result was corroborated by two independent studies [combined ORperSD = 0.87 (0.76-1.00), P = 0.058] with no evidence of heterogeneity. When enriched for 'true' interval cancers among nondense breasts, the difference in the association with PRS in screen-detected and interval cancers became more pronounced [ORperSD = 0.74 (0.62-0.89), P = 0.001], with a significant interaction effect between PRS and mammographic density (Pinteraction = 0.017). To our knowledge, this is the first report looking into the genetic differences between screen-detected and interval cancers. It is an affirmation that the two types of breast cancer may have unique underlying biology. © The Author 2014. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  5. Molybdenum disulfide catalyzed tungsten oxide for on-chip acetone sensing

    Science.gov (United States)

    Li, Hong; Ahn, Sung Hoon; Park, Sangwook; Cai, Lili; Zhao, Jiheng; He, Jiajun; Zhou, Minjie; Park, Joonsuk; Zheng, Xiaolin

    2016-09-01

    Acetone sensing is critical for acetone leak detection and holds a great promise for the noninvasive diagnosis of diabetes. It is thus highly desirable to develop a wearable acetone sensor that has low cost, miniature size, sub-ppm detection limit, great selectivity, as well as low operating temperature. In this work, we demonstrate a cost-effective on-chip acetone sensor with excellent sensing performances at 200 °C using molybdenum disulfide (MoS2) catalyzed tungsten oxide (WO3). The WO3 based acetone sensors are first optimized via combined mesoscopic nanostructuring and silicon doping. Under the same testing conditions, our optimized mesoporous silicon doped WO3 [Si:WO3(meso)] sensor shows 2.5 times better sensitivity with ˜1000 times smaller active device area than the state-of-art WO3 based acetone sensor. Next, MoS2 is introduced to catalyze the acetone sensing reactions for Si:WO3(meso), which reduces the operating temperature by 100 °C while retaining its high sensing performances. Our miniaturized acetone sensor may serve as a wearable acetone detector for noninvasive diabetes monitoring or acetone leakage detection. Moreover, our work demonstrates that MoS2 can be a promising nonprecious catalyst for catalytic sensing applications.

  6. On-chip electrochemical microsystems for measurements of copper and conductivity in artificial seawater.

    Science.gov (United States)

    Herzog, Grégoire; Moujahid, Waleed; Twomey, Karen; Lyons, Conor; Ogurtsov, Vladimir I

    2013-11-15

    The fabrication and characterisation of microelectrochemical sensors for Cu(2+) and conductivity suitable for operation in the marine environment are presented. The impact of the designs on sensor performance and their adequacy to operate in real conditions are discussed. The sensors, tailored to voltammetric and impedimetric measurements, are fabricated on silicon using photolithographic and thin film deposition techniques. The impedimetric sensor is made of Pt interdigitated electrodes which are used for the measurement of conductivity. The voltammetric sensors are based on a three electrode electrochemical cell with on-chip Ag|AgCl reference and Pt counter and working electrodes, used for detection of copper by underpotential deposition-stripping voltammetry at microelectrode array. The sensors operated in the Cu(2+) concentrations ranging from 0.48 to 3.97 µM with a limit of detection of 0.115 μM. The impact of the temperature, the pH and the salinity of the artificial seawater on the sensitivity for Cu(2+) detection are also considered. Measurements of copper concentration and conductivity are validated using certified reference materials and standard solutions.

  7. 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.

  8. Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Olli-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

    2008-09-09

    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 analyses. 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), retinoblastoma, ovarian and uterine cancers, 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.

  9. Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Joe W. (San Francisco, CA); Pinkel, Daniel (Lafayette, CA); Kallioniemi, Olli-Pekka (Turku, FI); Kallioniemi, Anne (Tampere, FI); Sakamoto, Masaru (Tokyo, JP)

    2009-10-06

    Methods and compositions for staining based upon nucleic acid sequence that employ .[.nudeic.]. .Iadd.nucleic .Iaddend.acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. 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), retinoblastoma, ovarian and uterine cancers, 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.

  10. Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Joe W. (Livermore, CA); Pinkel, Daniel (Walnut Creek, CA); Kallioniemi, Olli-Pekka (Tampere, FI); Kallioniemi, Anne (Tampere, FI); Sakamoto, Masaru (Tokyo, JP)

    2002-01-01

    Methods and compositions for staining based upon nucleic acid sequence that employ nudeic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. 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), retinoblastoma, ovarian and uterine cancers, 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.

  11. Chromosome-Specific Staining To Detect Genetic Rearrangements Associated With Chromosome 3 And/Or Chromosone 17

    Energy Technology Data Exchange (ETDEWEB)

    Gray; Joe W. (Livermore, CA); Pinkel; Daniel (Walnut Creek, CA); Kallioniemi; Olli-Pekka (Tampere, FI); Kallioniemi; Anne (Tampere, FI); Sakamoto; Masaru (Tokyo, JP)

    2002-02-05

    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 analyses. 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), retinoblastoma, ovarian and uterine cancers, 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.

  12. Genetically encoded green fluorescent Ca2+ indicators with improved detectability for neuronal Ca2+ signals.

    Science.gov (United States)

    Ohkura, Masamichi; Sasaki, Takuya; Sadakari, Junko; Gengyo-Ando, Keiko; Kagawa-Nagamura, Yuko; Kobayashi, Chiaki; Ikegaya, Yuji; Nakai, Junichi

    2012-01-01

    Imaging the activities of individual neurons with genetically encoded Ca(2+) indicators (GECIs) is a promising method for understanding neuronal network functions. Here, we report GECIs with improved neuronal Ca(2+) signal detectability, termed G-CaMP6 and G-CaMP8. Compared to a series of existing G-CaMPs, G-CaMP6 showed fairly high sensitivity and rapid kinetics, both of which are suitable properties for detecting subtle and fast neuronal activities. G-CaMP8 showed a greater signal (F(max)/F(min) = 38) than G-CaMP6 and demonstrated kinetics similar to those of G-CaMP6. Both GECIs could detect individual spikes from pyramidal neurons of cultured hippocampal slices or acute cortical slices with 100% detection rates, demonstrating their superior performance to existing GECIs. Because G-CaMP6 showed a higher sensitivity and brighter baseline fluorescence than G-CaMP8 in a cellular environment, we applied G-CaMP6 for Ca(2+) imaging of dendritic spines, the putative postsynaptic sites. By expressing a G-CaMP6-actin fusion protein for the spines in hippocampal CA3 pyramidal neurons and electrically stimulating the granule cells of the dentate gyrus, which innervate CA3 pyramidal neurons, we found that sub-threshold stimulation triggered small Ca(2+) responses in a limited number of spines with a low response rate in active spines, whereas supra-threshold stimulation triggered large fluorescence responses in virtually all of the spines with a 100% activity rate.

  13. A programmable and configurable multi-port System-on-Chip for stimulating electrokinetically-driven microfluidic devices.

    Science.gov (United States)

    Lopez, Martha Salome; Gerstlauer, Andreas; Avila, Alfonso; Martinez-Chapa, Sergio O

    2011-01-01

    Recent research has demonstrated the use of microfluidic devices and electro-kinetics in areas such as medicine, genetics, embryology, epidemiology and pollution analysis, where manipulation of particles suspended in liquid media is required. Micro-fabrication technology has made it possible to increase system complexity and functionality by allowing integration of different processing and analysis stages in a single chip. However, fully integrated and autonomous microfluidic systems supporting ad-hoc stimulation have yet to be developed. This paper presents a flexible, configurable and programmable stimulator for electro-kinetically driven microfluidic devices. The stimulator is a dedicated System-on-Chip (SoC) architecture that generates sine, triangle, and sawtooth signals within a frequency range of 1 Hz to 20 MHz, capable of delivering single, dual, and superimposed waveforms, in a user defined test sequence for a selected time period. The system is designed to be integrated into complete, autonomous Lab-on-Chip, portable or implantable devices. As such, it is expected to help significantly advance current and future research on particle manipulation.

  14. 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.

  15. A Software Framework for Rapid Application-Specific Hybrid Photonic Network-on-Chip Synthesis

    Directory of Open Access Journals (Sweden)

    Shirish Bahirat

    2016-05-01

    Full Text Available Network on Chip (NoC architectures have emerged in recent years as scalable communication fabrics to enable high bandwidth data transfers in chip multiprocessors (CMPs. These interconnection architectures still need to conquer many challenges, e.g., significant power consumption and high data transfer latencies. Hybrid electro-photonic NoCs have been recently proposed as a solution to mitigate some of these challenges. However, with increasing application complexity, hardware dependencies, and performance variability, optimization of hybrid photonic NoCs requires traversing a massive design space. To date, prior work on software tools for rapid automated NoC synthesis have mainly focused on electrical NoCs. In this article, we propose a novel suite of software tools for effectively synthesizing hybrid photonic NoCs. We formulate and solve the synthesis problem using four search-based optimization heuristics: (1 Ant Colony Optimization (ACO; (2 Particle Swarm Optimization (PSO; (3 Genetic Algorithm (GA; and (4 Simulated Annealing (SA. Our experimental results show significant promise for the ACO and PSO based heuristics. Our novel implementation of PSO achieves an average of 64% energy-delay product improvements over GA and 53% improvement over SA; while our novel ACO implementation achieves 107% energy-delay product improvements over GA and 62% improvement over SA.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Crack detection in a beam with an arbitrary number of transverse cracks using genetic algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Khaji, N. [Tarbiat Modares University, Tehran (Iran, Islamic Republic of); Mehrjoo, M. [Islamic Azad University, Tehran (Iran, Islamic Republic of)

    2014-03-15

    In this paper, a crack detection approach is presented for detecting depth and location of cracks in beam-like structures. For this purpose, a new beam element with an arbitrary number of embedded transverse edge cracks, in arbitrary positions of beam element with any depth, is derived. The components of the stiffness matrix for the cracked element are computed using the conjugate beam concept and Betti's theorem, and finally represented in closed-form expressions. The proposed beam element is efficiently employed for solving forward problem (i.e., to gain precise natural frequencies and mode shapes of the beam knowing the cracks' characteristics). To validate the proposed element, results obtained by new element are compared with two-dimensional (2D) finite element results and available experimental measurements. Moreover, by knowing the natural frequencies and mode shapes, an inverse problem is established in which the location and depth of cracks are determined. In the inverse approach, an optimization problem based on the new finite element and genetic algorithms (GAs) is solved to search the solution. It is shown that the present algorithm is able to identify various crack configurations in a cracked beam. The proposed approach is verified through a cracked beam containing various cracks with different depths.

  2. Object detection via feature synthesis using MDL-based genetic programming.

    Science.gov (United States)

    Lin, Yingqiang; Bhanu, Bir

    2005-06-01

    In this paper, we use genetic programming (GP) to synthesize composite operators and composite features from combinations of primitive operations and primitive features for object detection. The motivation for using GP is to overcome the human experts' limitations of focusing only on conventional combinations of primitive image processing operations in the feature synthesis. GP attempts many unconventional combinations that in some cases yield exceptionally good results. To improve the efficiency of GP and prevent its well-known code bloat problem without imposing severe restriction on the GP search, we design a new fitness function based on minimum description length principle to incorporate both the pixel labeling error and the size of a composite operator into the fitness evaluation process. To further improve the efficiency of GP, smart crossover, smart mutation and a public library ideas are incorporated to identify and keep the effective components of composite operators. Our experiments, which are performed on selected training regions of a training image to reduce the training time, show that compared to normal GP, our GP algorithm finds effective composite operators more quickly and the learned composite operators can be applied to the whole training image and other similar testing images. Also, compared to a traditional region-of-interest extraction algorithm, the composite operators learned by GP are more effective and efficient for object detection.

  3. Designing multilayered nanoplatforms for SERS-based detection of genetically modified organisms

    Energy Technology Data Exchange (ETDEWEB)

    Uluok, Saadet [Dumlupinar University, Department of Chemistry, Faculty of Arts and Sciences (Turkey); Guven, Burcu [Hacettepe University, Department of Food Engineering, Faculty of Engineering (Turkey); Eksi, Haslet [Hacettepe University, Food Research Center (Turkey); Ustundag, Zafer [Dumlupinar University, Department of Chemistry, Faculty of Arts and Sciences (Turkey); Tamer, Ugur [Gazi University, Department of Analytical Chemistry, Faculty of Pharmacy (Turkey); Boyaci, Ismail Hakki, E-mail: ihb@hacettepe.edu.tr [Hacettepe University, Department of Food Engineering, Faculty of Engineering (Turkey)

    2015-01-15

    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 Au{sub rod} and Au{sub spherical} nanoparticles to form multilayered constructions on the gold (Au){sub 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 Au{sub rod} nanoparticles and Au{sub slide} 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.

  4. Behavioural and genetic evidence for C. elegans' ability to detect volatile chemicals associated with explosives.

    Science.gov (United States)

    Liao, Chunyan; Gock, Andrew; Michie, Michelle; Morton, Bethany; Anderson, Alisha; Trowell, Stephen

    2010-09-07

    Automated standoff detection and classification of explosives based on their characteristic vapours would be highly desirable. Biologically derived odorant receptors have potential as the explosive recognition element in novel biosensors. Caenorhabditis elegans' genome contains over 1,000 uncharacterised candidate chemosensory receptors. It was not known whether any of these respond to volatile chemicals derived from or associated with explosives. We assayed C. elegans for chemotactic responses to chemical vapours of explosives and compounds associated with explosives. C. elegans failed to respond to many of the explosive materials themselves but showed strong chemotaxis with a number of compounds associated with commercial or homemade explosives. Genetic mutant strains were used to identify the likely neuronal location of a putative receptor responding to cyclohexanone, which is a contaminant of some compounded explosives, and to identify the specific transduction pathway involved. Upper limits on the sensitivity of the nematode were calculated. A sensory adaptation protocol was used to estimate the receptive range of the receptor. The results suggest that C. elegans may be a convenient source of highly sensitive, narrowly tuned receptors to detect a range of explosive-associated volatiles.

  5. 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.

  6. Microbead-assisted PDA sensor for the detection of genetically modified organisms.

    Science.gov (United States)

    Lim, Min-Cheol; Shin, Yeo-Jae; Jeon, Tae-Joon; Kim, Hae-Yeong; Kim, Young-Rok

    2011-05-01

    A simple and sensitive approach for the detection of marker protein, phosphinothricin acetyltransferase, from genetically modified crops was developed based on the colorimetric transition of polydiacetylene (PDA) vesicles in combination with silica microbeads. PDAs have attracted a great deal of interests as a transducing material due to their special features that allow colorimetric response to sensory signals, as well as their inherent simplicity. However, most PDA-based biosensors require additional analytical equipment such as a fluorescence microscope or UV-Vis spectrometer. In this study, we report a new approach to increase the degree of color transition by coupling antibody-conjugated PDA vesicles with silica microbeads in an effort to monitor the results with the unaided eye or simple RGB analysis. By immobilizing PDA vesicles on silica microbeads, we were able to overcome the disadvantages of colloidal PDA-based sensors and increase the degree of colorimetric changes in response to target molecules to a concentration as low as 20 nM. The additional stresses were given to PDA vesicles by antigen-antibody bridging of PDA vesicles coupled with microbeads, resulting in enhanced blue-red color transition. All the results showed that PDA vesicles in conjunction with silica microbeads will be a promising transducing material for the detection of target proteins in diagnostic and biosensing applications.

  7. Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA.

    Science.gov (United States)

    Glushakova, Lyudmyla G; Sharma, Nidhi; Hoshika, Shuichi; Bradley, Andrea C; Bradley, Kevin M; Yang, Zunyi; Benner, Steven A

    2015-11-15

    Nucleic acid (NA)-targeted tests detect and quantify viral DNA and RNA (collectively xNA) to support epidemiological surveillance and, in individual patients, to guide therapy. They commonly use polymerase chain reaction (PCR) and reverse transcription PCR. Although these all have rapid turnaround, they are expensive to run. Multiplexing would allow their cost to be spread over multiple targets, but often only with lower sensitivity and accuracy, noise, false positives, and false negatives; these arise by interactions between the multiple nucleic acid primers and probes in a multiplexed kit. Here we offer a multiplexed assay for a panel of respiratory viruses that mitigates these problems by combining several nucleic acid analogs from the emerging field of synthetic biology: (i) self-avoiding molecular recognition systems (SAMRSs), which facilitate multiplexing, and (ii) artificially expanded genetic information systems (AEGISs), which enable low-noise PCR. These are supplemented by "transliteration" technology, which converts standard nucleotides in a target to AEGIS nucleotides in a product, improving hybridization. The combination supports a multiplexed Luminex-based respiratory panel that potentially differentiates influenza viruses A and B, respiratory syncytial virus, severe acute respiratory syndrome coronavirus (SARS), and Middle East respiratory syndrome (MERS) coronavirus, detecting as few as 10 MERS virions in a 20-μl sample. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. A lab-on-chip cell-based biosensor for label-free sensing of water toxicants.

    Science.gov (United States)

    Liu, F; Nordin, A N; Li, F; Voiculescu, I

    2014-04-07

    This paper presents a lab-on-chip biosensor containing an enclosed fluidic cell culturing well seeded with live cells for rapid screening of toxicants in drinking water. The sensor is based on the innovative placement of the working electrode for the electrical cell-substrate impedance sensing (ECIS) technique as the top electrode of a quartz crystal microbalance (QCM) resonator. Cell damage induced by toxic water will cause a decrease in impedance, as well as an increase in the resonant frequency. For water toxicity tests, the biosensor's unique capabilities of performing two complementary measurements simultaneously (impedance and mass-sensing) will increase the accuracy of detection while decreasing the false-positive rate. Bovine aortic endothelial cells (BAECs) were used as toxicity sensing cells. The effects of the toxicants, ammonia, nicotine and aldicarb, on cells were monitored with both the QCM and the ECIS technique. The lab-on-chip was demonstrated to be sensitive to low concentrations of toxicants. The responses of BAECs to toxic samples occurred during the initial 5 to 20 minutes depending on the type of chemical and concentrations. Testing the multiparameter biosensor with aldicarb also demonstrated the hypothesis that using two different sensors to monitor the same cell monolayer provides cross validation and increases the accuracy of detection. For low concentrations of aldicarb, the variations in impedance measurements are insignificant in comparison with the shifts of resonant frequency monitored using the QCM resonator. A highly linear correlation between signal shifts and chemical concentrations was demonstrated for each toxicant.

  9. On-Chip Micro-Electro-Mechanical System Fourier Transform Infrared (MEMS FT-IR) Spectrometer-Based Gas Sensing.

    Science.gov (United States)

    Erfan, Mazen; Sabry, Yasser M; Sakr, Mohammad; Mortada, Bassem; Medhat, Mostafa; Khalil, Diaa

    2016-05-01

    In this work, we study the detection of acetylene (C2H2), carbon dioxide (CO2) and water vapor (H2O) gases in the near-infrared (NIR) range using an on-chip silicon micro-electro-mechanical system (MEMS) Fourier transform infrared (FT-IR) spectrometer in the wavelength range 1300-2500 nm (4000-7692 cm(-1)). The spectrometer core engine is a scanning Michelson interferometer micro-fabricated using a deep-etching technology producing self-aligned components. The light is free-space propagating in-plane with respect to the silicon chip substrate. The moving mirror of the interferometer is driven by a relatively large stroke electrostatic comb-drive actuator corresponding to about 30 cm(-1) resolution. Multi-mode optical fibers are used to connect light between the wideband light source, the interferometer, the 10 cm gas cell, and the optical detector. A wide dynamic range of gas concentration down to 2000 parts per million (ppm) in only 10 cm length gas cell is demonstrated. Extending the wavelength range to the mid-infrared (MIR) range up to 4200 nm (2380 cm(-1)) is also experimentally demonstrated, for the first time, using a bulk micro-machined on-chip MEMS FT-IR spectrometer. The obtained results open the door for an on-chip optical gas sensor for many applications including environmental sensing and industrial process control in the NIR/MIR spectral ranges.

  10. Status of SuperSpec: A Broadband, On-Chip Millimeter-Wave Spectrometer

    CERN Document Server

    Hailey-Dunsheath, S; Barry, P S; Bradford, C M; Chattopadhyay, G; Day, P; Doyle, S; Hollister, M; Kovacs, A; LeDuc, H G; Mauskopf, P; McKenney, C M; Monroe, R; O'Brient, R; Padin, S; Reck, T; Swenson, L; Tucker, C E; Zmuidzinas, J

    2015-01-01

    SuperSpec is a novel on-chip spectrometer we are developing for multi-object, moderate resolution (R = 100 - 500), large bandwidth (~1.65:1) submillimeter and millimeter survey spectroscopy of high-redshift galaxies. The spectrometer employs a filter bank architecture, and consists of a series of half-wave resonators formed by lithographically-patterned superconducting transmission lines. The signal power admitted by each resonator is detected by a lumped element titanium nitride (TiN) kinetic inductance detector (KID) operating at 100-200 MHz. We have tested a new prototype device that is more sensitive than previous devices, and easier to fabricate. We present a characterization of a representative R=282 channel at f = 236 GHz, including measurements of the spectrometer detection efficiency, the detector responsivity over a large range of optical loading, and the full system optical efficiency. We outline future improvements to the current system that we expect will enable construction of a photon-noise-lim...

  11. 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.

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

    Science.gov (United States)

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

    2015-04-01

    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.

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

    Science.gov (United States)

    Papireddy Vinayaka, Poornachandra; van den Driesche, Sander; Blank, Roland; Tahir, Muhammad Waseem; Frodl, Mathias; Lang, Walter; Vellekoop, Michael J

    2016-09-28

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Rizzi, Giovanni, E-mail: giori@nanotech.dtu.dk; Østerberg, Frederik W.; Henriksen, Anders D.; Dufva, Martin; Hansen, Mikkel F., E-mail: mikkel.hansen@nanotech.dtu.dk

    2015-04-15

    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.

  16. Fully integrated system-on-chip for pixel-based 3D depth and scene mapping

    Science.gov (United States)

    Popp, Martin; De Coi, Beat; Thalmann, Markus; Gancarz, Radoslav; Ferrat, Pascal; Dürmüller, Martin; Britt, Florian; Annese, Marco; Ledergerber, Markus; Catregn, Gion-Pol

    2012-03-01

    We present for the first time a fully integrated system-on-chip (SoC) for pixel-based 3D range detection suited for commercial applications. It is based on the time-of-flight (ToF) principle, i.e. measuring the phase difference of a reflected pulse train. The product epc600 is fabricated using a dedicated process flow, called Espros Photonic CMOS. This integration makes it possible to achieve a Quantum Efficiency (QE) of >80% in the full wavelength band from 520nm up to 900nm as well as very high timing precision in the sub-ns range which is needed for exact detection of the phase delay. The SoC features 8x8 pixels and includes all necessary sub-components such as ToF pixel array, voltage generation and regulation, non-volatile memory for configuration, LED driver for active illumination, digital SPI interface for easy communication, column based 12bit ADC converters, PLL and digital data processing with temporary data storage. The system can be operated at up to 100 frames per second.

  17. 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.

  18. On-chip dual comb source for spectroscopy

    CERN Document Server

    Dutt, Avik; 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 combs on the same chip from a single laser. The combs span a broad bandwidth of 51 THz around a wavelength of 1.56 $\\mu$m. We demonstrate low-noise operation of both frequency combs by deterministically tuning into soliton mode-locked states using integrated microheaters, resulting in narrow ($<$ 10 kHz) microwave beatnotes. We further use one mode-locked comb as a reference to probe the formation dynamics of the other comb, thus introducing a technique to investigate comb evolution without auxiliary lasers or microwave os...

  19. 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.

  20. Micromechanical Characterization of Polysilicon Films through On-Chip Tests

    Directory of Open Access Journals (Sweden)

    Ramin Mirzazadeh

    2016-07-01

    Full Text Available When the dimensions of polycrystalline structures become comparable to the average grain size, some reliability issues can be reported for the moving parts of inertial microelectromechanical systems (MEMS. Not only the overall behavior of the device turns out to be affected by a large scattering, but also the sensitivity to imperfections gets enhanced. In this work, through on-chip tests, we experimentally investigate the behavior of thin polysilicon samples using standard electrostatic actuation/sensing. The discrepancy between the target and actual responses of each sample has then been exploited to identify: (i the overall stiffness of the film and, according to standard continuum elasticity, a morphology-based value of its Young’s modulus; (ii the relevant over-etch induced by the fabrication process. To properly account for the aforementioned stochastic features at the micro-scale, the identification procedure has been based on particle filtering. A simple analytical reduced-order model of the moving structure has been also developed to account for the nonlinearities in the electrical field, up to pull-in. Results are reported for a set of ten film samples of constant slenderness, and the effects of different actuation mechanisms on the identified micromechanical features are thoroughly discussed.

  1. Pipelined multiprocessor system-on-chip for multimedia

    CERN Document Server

    Javaid, Haris

    2014-01-01

    This book describes analytical models and estimation methods to enhance performance estimation of pipelined multiprocessor systems-on-chip (MPSoCs).  A framework is introduced for both design-time and run-time optimizations. For design space exploration, several algorithms are presented to minimize the area footprint of a pipelined MPSoC under a latency or a throughput constraint.  A novel adaptive pipelined MPSoC architecture is described, where idle processors are transitioned into low-power states at run-time to reduce energy consumption. Multi-mode pipelined MPSoCs are introduced, where multiple pipelined MPSoCs optimized separately are merged into a single pipelined MPSoC, enabling further reduction of the area footprint by sharing the processors and communication buffers. Readers will benefit from the authors’ combined use of analytical models, estimation methods and exploration algorithms and will be enabled to explore billions of design points in a few minutes.   ·         Describes the ...

  2. Micromechanical Characterization of Polysilicon Films through On-Chip Tests.

    Science.gov (United States)

    Mirzazadeh, Ramin; Eftekhar Azam, Saeed; Mariani, Stefano

    2016-07-28

    When the dimensions of polycrystalline structures become comparable to the average grain size, some reliability issues can be reported for the moving parts of inertial microelectromechanical systems (MEMS). Not only the overall behavior of the device turns out to be affected by a large scattering, but also the sensitivity to imperfections gets enhanced. In this work, through on-chip tests, we experimentally investigate the behavior of thin polysilicon samples using standard electrostatic actuation/sensing. The discrepancy between the target and actual responses of each sample has then been exploited to identify: (i) the overall stiffness of the film and, according to standard continuum elasticity, a morphology-based value of its Young's modulus; (ii) the relevant over-etch induced by the fabrication process. To properly account for the aforementioned stochastic features at the micro-scale, the identification procedure has been based on particle filtering. A simple analytical reduced-order model of the moving structure has been also developed to account for the nonlinearities in the electrical field, up to pull-in. Results are reported for a set of ten film samples of constant slenderness, and the effects of different actuation mechanisms on the identified micromechanical features are thoroughly discussed.

  3. Near-infrared Spectral Detection of the Content of Soybean Fat Acids Based on Genetic Multilayer Feed forward Neural Network

    Institute of Scientific and Technical Information of China (English)

    CHAI Yu-hua; PAN Wei; NING Hai-long

    2005-01-01

    In the paper, a method of building mathematic model employing genetic multilayer feed forward neural network is presented, and the quantitative relationship of chemical measured values and near-infrared spectral data is established. In the paper, quantitative mathematic model related chemical assayed values and near-infrared spectral data is established by means of genetic multilayer feed forward neural network, acquired near-infrared spectral data are taken as input of network with the content of five kinds of fat acids tested from chemical method as output,weight values of multilayer feed forward neural network are trained by genetic algorithms and detection model of neural network of soybean is built. A kind of multilayer feed forward neural network trained by genetic algorithms is designed in the paper. Through experiments, all the related coefficients of five fat acids can approach 0.9 which satisfies the preliminary test of soybean breeding.

  4. Genetic Diversity and Evolutionary Tendency Detected by Isozyme, RFLP and RAPD Markers in the Wild and Cultivated Soybean in China

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A large numbers of samples of wild soybean accessions and cultivated soybean landraces from various areas in China were analyzed by isozyrme, cytoplasmic DNA RFLP and nuclear DNA RAPD markers in order to reveal their genetic diversity. Greater comprehensive genetic diversity was detected in wild soybean than in cultivated soybean. The genetic plentifulness and the genetic dispersion of wild soybean were 180 (95. 2%) and 0. 2891 while those of cultivated soybean were 154(81.5%) and 0. 2091,respectively. On the most loci, especially on isozyme loci Idh1, Aph, Idh2,and Dia, cytoplasmic DNA RFLP loci cp Ⅰ , cp Ⅲ, mt Ⅳ a and mt Ⅳ b, and nuclear RAPD loci OPAP4-8, OPAP5-1, OPAP9-8 and OPAP20-8, the wild soybeans djffered remarkably from the cultivated ones in allele frequency. These markers could be used in further study on the evolution and origin of the cultivated soybean.

  5. Genetic Diversity and Evolutionary Tendency Detected by Isozyme, RFLP and RAPD Markers in the Wild and Cultivated Soybean in China

    Institute of Scientific and Technical Information of China (English)

    Xu Donghe; Gao Zhong; Gai Junyi; Zhang Zhiyong; Chen Shouyi; Fukushi Hirofurm; Kitajirma Shunji; Abe Jun; Shimamoto Yoshiya

    2000-01-01

    A large numbers of samples of wild soybean accessions and cultivated soybean landraces from various areas in China were analyzed by isozyrme, cytoplasmic DNA RFLP and nuclear DNA RAPD markers in order to reveal their genetic diversity. Greater comprehensive genetic diversity was detected in wild soybean than in cultivated soybean. The genetic plentifulness and the genetic dispersion of wild soybean were 180 (95. 2%) and 0. 2891 while those of cultivated soybean were 154(81.5%) and 0. 2091,respectively. On the most loci, especially on isozyme loci Idh1, Aph, Idh2,and Dia, cytoplasmic DNA RFLP loci cp Ⅰ , cp Ⅲ, mt Ⅳ a and mt Ⅳ b, and nuclear RAPD loci OPAP4-8, OPAP5-1, OPAP9-8 and OPAP20-8, the wild soybeans djffered remarkably from the cultivated ones in allele frequency. These markers could be used in further study on the evolution and origin of the cultivated soybean.

  6. 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.

  7. Bioinformatics' approaches to detect genetic variation in whole genome sequencing data

    NARCIS (Netherlands)

    Kerstens, H.H.D.

    2010-01-01

    Current genetic marker repositories are not sufficient or even are completely lacking for most farm animals. However, genetic markers are essential for the development of a research tool facilitating discovery of genetic factors that contribute to resistance to disease and the overall welfare and pe

  8. A Quality-of-Service Mechanism for Interconnection Networks in System-on-Chips

    CERN Document Server

    Weber, Wolf-Dietrich; Swarbrick, Ian; Wingard, Drew

    2011-01-01

    As Moore's Law continues to fuel the ability to build ever increasingly complex system-on-chips (SoCs), achieving performance goals is rising as a critical challenge to completing designs. In particular, the system interconnect must efficiently service a diverse set of data flows with widely ranging quality-of-service (QoS) requirements. However, the known solutions for off-chip interconnects such as large-scale networks are not necessarily applicable to the on-chip environment. Latency and memory constraints for on-chip interconnects are quite different from larger-scale interconnects. This paper introduces a novel on-chip interconnect arbitration scheme. We show how this scheme can be distributed across a chip for high-speed implementation. We compare the performance of the arbitration scheme with other known interconnect arbitration schemes. Existing schemes typically focus heavily on either low latency of service for some initiators, or alternatively on guaranteed bandwidth delivery for other initiators. ...

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

    DEFF Research Database (Denmark)

    Bjerregaard, Tobias; Sparsø, Jens

    2006-01-01

    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......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...... (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...

  10. 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.

  11. Note: Wide-range and high-resolution on-chip delay measurement circuit with low supply-voltage sensitivity for SoC applications

    Science.gov (United States)

    Sheng, Duo; Hung, Yu-Chan

    2016-11-01

    This paper presents an on-chip delay measurement (OCDM) circuit with a wide delay-measurement range, a high delay-measurement resolution and low supply-voltage sensitivity for efficient detection, and diagnosis in the high-performance system-on-chip (SoC). The proposed cascade-stage measurement structure can simultaneously achieve a delay-measurement range of several nanoseconds and a quantization resolution of several picoseconds. The proposed delay-measurement circuit has a high immunity to supply voltage variations without any additional calibration or self-biasing circuit. The delay-measurement range is 5.25 ns with 6 ps resolution; and the average delay resolution variation is 0.41% with ±10% supply voltage variations.

  12. Photonic-Networks-on-Chip for High Performance Radiation Survivable Multi-Core Processor Systems

    Science.gov (United States)

    2013-12-01

    TR-14-7 Photonic-Networks-on-Chip for High Performance Radiation Survivable Multi-Core Processor Systems Approved for public release...Networks-on-Chip for High Performance Radiation Survivable Multi-Core Processor Systems DTRA01-03-D-0026 Prof. Luke Lester and Prof. Ganesh...release; distribution is unlimited. The University of New Mexico has undertaken a study to determine the effects of radiation on Quantum Dot Photonic

  13. 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...... are discussed. We also evaluate performance analysis techniques. The research shows that NoC constitutes a unification of current trends of intrachip communication rather than an explicit new alternative....

  14. Detection of genetically modified DNA sequences in milk from the Italian market.

    Science.gov (United States)

    Agodi, Antonella; Barchitta, Martina; Grillo, Agata; Sciacca, Salvatore

    2006-01-01

    The possible transfer and accumulation of novel DNA and/or proteins in food for human consumption derived from animals receiving genetically modified (GM) feed is at present the object of scientific dispute. A number of studies failed to identify GM DNA in milk, meat, or eggs derived from livestock receiving GM feed ingredients. The present study was performed in order to: (i) develop a valid protocol by PCR and multicomponent analysis for the detection of specific DNA sequences in milk, focused on GM maize and GM soybean; (ii) assess the stability of transgenic DNA after pasteurization treatment and (iii) determine the presence of GM DNA sequences in milk samples collected from the Italian market. Results from the screening of 60 samples of 12 different milk brands demonstrated the presence of GM maize sequences in 15 (25%) and of GM soybean sequences in 7 samples (11.7%). Our screening methodology shows a very high sensitivity and the use of an automatic identification of the amplified products increases its specificity and reliability. Moreover, we demonstrated that the pasteurization process is not able to degrade the DNA sequences in spiked milk samples. The detection of GM DNA in milk can be interpreted as an indicator of fecal or airborne contamination, respectively, with feed DNA or feed particles, although an alternative source of contamination, possibly recognizable in the natural environment can be suggested. Further studies, performed on a larger number of milk samples, are needed to understand the likely source of contamination of milk collected from the Italian market.

  15. Genetic-algorithm-based multiple regression with fuzzy inference system for detection of nocturnal hypoglycemic episodes.

    Science.gov (United States)

    Ling, Steve S H; Nguyen, Hung T

    2011-03-01

    Hypoglycemia or low blood glucose is dangerous and can result in unconsciousness, seizures, and even death. It is a common and serious side effect of insulin therapy in patients with diabetes. Hypoglycemic monitor is a noninvasive monitor that measures some physiological parameters continuously to provide detection of hypoglycemic episodes in type 1 diabetes mellitus patients (T1DM). Based on heart rate (HR), corrected QT interval of the ECG signal, change of HR, and the change of corrected QT interval, we develop a genetic algorithm (GA)-based multiple regression with fuzzy inference system (FIS) to classify the presence of hypoglycemic episodes. GA is used to find the optimal fuzzy rules and membership functions of FIS and the model parameters of regression method. From a clinical study of 16 children with T1DM, natural occurrence of nocturnal hypoglycemic episodes is associated with HRs and corrected QT intervals. The overall data were organized into a training set (eight patients) and a testing set (another eight patients) randomly selected. The results show that the proposed algorithm performs a good sensitivity with an acceptable specificity.

  16. 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.

  17. 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.

  18. Detection of processed genetically modified food using CIM monolithic columns for DNA isolation.

    Science.gov (United States)

    Jerman, Sergej; Podgornik, Ales; Cankar, Katarina; Cadet, Neza; Skrt, Mihaela; Zel, Jana; Raspor, Peter

    2005-02-11

    The availability of sufficient quantities of DNA of adequate quality is crucial in polymerase chain reaction (PCR)-based methods for genetically modified food detection. In this work, the suitability of anion-exchange CIM (Convective Interaction Media; BIA Separations, Ljubljana, Slovenia) monolithic columns for isolation of DNA from food was studied. Maize and its derivates corn meal and thermally pretreated corn meal were chosen as model food. Two commercially available CIM disk columns were tested: DEAE (diethylaminoethyl) and QA (quaternary amine). Preliminary separations were performed with standard solution of salmon DNA at different pH values and different NaCl concentrations in mobile phase. DEAE groups and pH 8 were chosen for further isolations of DNA from a complex matrix-food extract. The quality and quantity of isolated DNA were tested on agarose gel electrophoresis, with UV-scanning spectrophotometry, and by amplification with real-time PCR. DNA isolated in this way was of suitable quality for further PCR analyses. The described method is also applicable for DNA isolation from processed foods with decreased DNA content. Furthermore, it is more effective and less time-consuming in comparison with the existing proposed methods for isolation of DNA from plant-derived foods.

  19. 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.

  20. Microarchitecture of a MultiCore SoC for Data Analysis of a Lab-on-Chip Microarray

    Directory of Open Access Journals (Sweden)

    S. Blionas

    2008-07-01

    Full Text Available This paper presents a reconfigurable architecture of a lab-on-chip (LoC microarray device capable to process data either in genotyping or in gene expression applications in a fraction of the time that is required by the usual software methods running on a standard computer. The entire LoC consists of a microfluidics part for the sample preparation and hybridization, a microsystem part including the application specific array of sensors for the electronic detection, and finally a reconfigurable processing part for the data analysis. The proposed data processing and analysis electronic module are an embedded multicore reconfigurable system-on-chip designed to analyze data from the forthcoming high-density oligonucleotide microarrays. The proposed architecture employs reconfigurable technology and has the capacity to process data from microarrays of various sizes from small size ones used in genotyping up to large-scale gene expression arrays. Additionally, the embedded processing cores feature reconfigurable circuitry for implementing the intense part of the processing, supplementing the various computational needs of the diverse applications for microarray real-time data processing and for a scalable reconfigurable architecture to handle also the future high-density microarrays.

  1. 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.

  2. SEMICONDUCTOR INTEGRATED CIRCUITS: A self-adaptive full asynchronous bi-directional transmission channel for network-on-chips

    Science.gov (United States)

    Xuguang, Guan; Yintang, Yang; Zhangming, Zhu; Duan, Zhou

    2010-08-01

    To improve two shortcomings of conventional network-on-chips, i.e. low utilization rate in channels between routers and excessive interconnection lines, this paper proposes a full asynchronous self-adaptive bi-directional transmission channel. It can utilize interconnection lines and register resources with high efficiency, and dynamically detect the data transmission state between routers through a direction regulator, which controls the sequencer to automatically adjust the transmission direction of the bi-directional channel, so as to provide a flexible data transmission environment. Null convention logic units are used to make the circuit quasi-delay insensitive and highly robust. The proposed bi-directional transmission channel is implemented based on SMIC 0.18 μm standard CMOS technology. Post-layout simulation results demonstrate that this self-adaptive bi-directional channel has better performance on throughput, transmission flexibility and channel bandwidth utilization compared to a conventional single direction channel. Moreover, the proposed channel can save interconnection lines up to 30% and can provide twice the bandwidth resources of a single direction transmission channel. The proposed channel can apply to an on-chip network which has limited resources of registers and interconnection lines.

  3. MUSE, a Lab-On-Chip System for In-Situ Analysis

    Science.gov (United States)

    Eckhard, F.; Prak, A.; van den Assem, D.

    Stork Product Engineering and 3T are working for several years on the development of an assembly technology for microsystem parts. This work has led to MATAS: Modular Assembly Technology for μTAS, a generic methodology which enables the development of very compact and highly integrated microsystems technology (MST) systems. MATAS has as great advantage that it enables the application of commercially available microsystem parts derived from different suppliers. The high degree of integration of both the MST parts with electronics enables the development of highly autonomous and intelligent systems which are suited for incorporation in planetary rovers or to support the research in ISS. For further improvement of the technology, and to show its advantages, the development of a system for on-chip capillary electrophoresis (CE) has been selected. CE, which is of old applied in the biosciences and biotechnology, is one of the key technologies for the detection and measurement of enantiomers. The study on enantiomers is an important aspect in the search to pre-biotic life. Due to the limited dimensions of Muse, the system is perfectly suited for use in a planetary rover but could also easily become part of the Astrobiology Facility of Space Station. For the measurement and detection of these enantiomers and other biomolecules, the system is equipped with a fluorescence detector. In 2002 a new project has been started to equip the system with an electrochemical detector enabling conductivity and amperometric analysis. Direct conductivity detection is especially applied in capillary ion electrophoresis, which can be used complementary, or separate to the zone electrophoresis, in which the fluorescence detector is applied. The combination of these detection technologies leads to a multi analysis system (Muse) with a very broad application area.

  4. Utilization of a genetic algorithm for the automatic detection of oil spill from RADARSAT-2 SAR satellite data.

    Science.gov (United States)

    Marghany, Maged

    2014-12-15

    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.

  5. Proof-of-concept demonstration of free-form optics enhanced confocal Raman spectroscopy in combination with optofluidic lab-on-chip

    Science.gov (United States)

    Liu, Qing; De Coster, Diane; Loterie, Damien; Van Erps, Jürgen; Vervaeke, Michael; Missinne, Jeroen; Thienpont, Hugo; Ottevaere, Heidi

    2016-07-01

    Raman spectroscopy is a powerful optical and non-destructive technique and a well-known method for analysis purposes, especially to determine the molecular fingerprint of substances. Traditionally, such analyses are done in a specialized lab, with considerable requirements in terms of equipment, time and manual sampling of substances of interest. In this paper we take a step from bulky Raman spectroscopy laboratory analyses towards lab-on-chip (LOC) analyses. We present an optofluidic lab-on-chip for confocal Raman spectroscopy, which can be used for the analysis of liquids. The confocal detection suppresses the unwanted background from the polymer material out of which the chip is fabricated. We design the free-form optical reflector using non-sequential ray-tracing combined with a mathematical code to simulate the Raman scattering behavior of the substance under test. We prototype the device in Polymethyl methacrylate (PMMA) by means of ultraprecision diamond tooling. In a proof-of-concept demonstration, we first show the confocal behavior of our Raman lab-on-chip system by measuring the Raman spectrum of ethanol. In a next step, we compare the Raman spectra measured in our lab-on-chip with spectra measured with a commercial Raman spectrometer. Finally, to calibrate the system we perform Raman measurements on urea solutions with different concentrations. We achieve a detection limit that corresponds to a noise equivalent concentration of 20mM. Apart from strongly reducing the background perturbations, our confocal Raman spectroscopy system has other advantages as well. The reflector design is robust from a mechanical point of view and has the potential for mass-manufacturing using hot embossing or injection molding.

  6. Thin film magnetostrictive sensor with on-chip readout

    Science.gov (United States)

    Lu, Yong

    We report the first successful integration of magnetostrictive Metglas2605S2 (Fesb{78}Sisb9Bsb{13}) thin film sensor system on silicon with high resolution capacitive readout. A deposition process for Metglas thin film has been developed to allow easy control of thin film composition. An amorphous microstructure has been achieved over a wide temperature range, and in-situ magnetic domain alignment can be accomplished at room temperature as the film is deposited. The thin film has been characterized by Inductively Coupled Plasma (ICP) analysis for composition, X-Ray Diffraction (XRD) spectrum for microstructure, magnetization measurement for domain alignment and capacitive measurement for magnetostriction. The thin film is suitable for any magnetostrictive sensor applications, in particular, for IC compatible microsensors and microactuators. We have demonstrated the subsequent process integration with IC fabrication technology. Here, the Metglas thin film has been successfully incorporated to micromechanical structures using surface micromachining with appropriate choice of sacrificial layer and low stress mechanical layers. In addition, we present the development of a high resolution capacitive readout circuit co-integrated with the sensor. The readout circuit is based on a floating gate MOSFET configuration, requiring just a single transistor and operated at DC or low frequencies. Using the prototype developed in-house, we have successfully demonstrated a resolution capability of 10sp{-17} F, this translates to a few A in terms of cantilever beam deflection of the sensor. The floating gate readout technique is readily applicable to any capacitive sensors with a need for on-chip readout. It is also an ideal in-situ test structure for on IC chip process characterization and parameter extraction.

  7. 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 chip. The field-of-view of these computational microscopes is equal to the active-area of the sensor-array, easily reaching, for example, chips, respectively. In addition to this remarkable increase in throughput, another major 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

  8. On-chip optical trapping for atomic applications

    Science.gov (United States)

    Perez, Maximillian A.; Salim, Evan; Farkas, Daniel; Duggan, Janet; Ivory, Megan; Anderson, Dana

    2014-09-01

    To simplify applications that rely on optical trapping of cold and ultracold atoms, ColdQuanta is developing techniques to incorporate miniature optical components onto in-vacuum atom chips. The result is a hybrid atom chip that combines an in-vacuum micro-optical bench for optical control with an atom chip for magnetic control. Placing optical components on a chip inside of the vacuum system produces a compact system that can be targeted to specific experiments, in this case the generation of optical lattices. Applications that can benefit from this technology include timekeeping, inertial sensing, gravimetry, quantum information, and emulation of quantum many-body systems. ColdQuanta's GlasSi atom chip technology incorporates glass windows in the plane of a silicon atom chip. In conjunction with the in-vacuum micro-optical bench, optical lattices can be generated within a few hundred microns of an atom chip window through which single atomic lattice sites can be imaged with sub-micron spatial resolution. The result is a quantum gas microscope that allows optical lattices to be studied at the level of single lattice sites. Similar to what ColdQuanta has achieved with magneto-optical traps (MOTs) in its miniMOT system and with Bose- Einstein condensates (BECs) in its RuBECi(R) system, ColdQuanta seeks to apply the on-chip optical bench technology to studies of optical lattices in a commercially available, turnkey system. These techniques are currently being considered for lattice experiments in NASA's Cold Atom Laboratory (CAL) slated for flight on the International Space Station.

  9. Capacitance Variation Induced by Microfluidic Two-Phase Flow across Insulated Interdigital Electrodes in Lab-On-Chip Devices

    Directory of Open Access Journals (Sweden)

    Tao Dong

    2015-01-01

    Full Text Available 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.

  10. 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.

  11. VLSI architecture of leading eigenvector generation for on-chip principal component analysis spike sorting system.

    Science.gov (United States)

    Chen, Tung-Chien; Liu, Wentai; Chen, Liang-Gee

    2008-01-01

    On-chip spike detection and principal component analysis (PCA) sorting hardware in an integrated multi-channel neural recording system is highly desired to ease the bandwidth bottleneck from high-density microelectrode array implanted in the cortex. In this paper, we propose the first leading eigenvector generator, the key hardware module of PCA, to enable the whole framework. Based on the iterative eigenvector distilling algorithm, the proposed flipped structure enables the low cost and low power implementation by discarding the division and square root hardware units. Further, the proposed adaptive level shifting scheme optimizes the accuracy and area trade off by dynamically increasing the quantization parameter according to the signal level.With the specification of four principal components/channel, 32 samples/spike, and nine bits/sample, the proposed hardware can train 312 channels per minute with 1MHz operation frequency. 0.13 mm(2) silicon area and 282microW power consumption are required in 90 nm 1P9M CMOS process.

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

    Institute of Scientific and Technical Information of China (English)

    Li Jinfeng; Tang Zhen'an; Wang Jiaqi

    2009-01-01

    An on-chip microelectromechanical system was fabricated in a 0.5μm 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 105 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.

  13. Thin Film Differential Photosensor for Reduction of Temperature Effects in Lab-on-Chip Applications.

    Science.gov (United States)

    de Cesare, Giampiero; Carpentiero, Matteo; Nascetti, Augusto; Caputo, Domenico

    2016-02-20

    This paper presents a thin film structure suitable for low-level radiation measurements in lab-on-chip systems that are subject to thermal treatments of the analyte and/or to large temperature variations. The device is the series connection of two amorphous silicon/amorphous silicon carbide heterojunctions designed to perform differential current measurements. The two diodes experience the same temperature, while only one is exposed to the incident radiation. Under these conditions, temperature and light are the common and differential mode signals, respectively. A proper electrical connection reads the differential current of the two diodes (ideally the photocurrent) as the output signal. The experimental characterization shows the benefits of the differential structure in minimizing the temperature effects with respect to a single diode operation. In particular, when the temperature varies from 23 to 50 °C, the proposed device shows a common mode rejection ratio up to 24 dB and reduces of a factor of three the error in detecting very low-intensity light signals.

  14. Plasma cell treatment device Plasma-on-Chip: Monitoring plasma-generated reactive species in microwells

    Science.gov (United States)

    Oh, Jun-Seok; Kojima, Shinya; Sasaki, Minoru; Hatta, Akimitsu; Kumagai, Shinya

    2017-01-01

    We have developed a plasma cell treatment device called Plasma-on-Chip that enables the real-time monitoring of a single cell culture during plasma treatment. The device consists of three parts: 1) microwells for cell culture, 2) a microplasma device for generating reactive oxygen and nitrogen species (RONS) for use in cell treatment, and 3) through-holes (microchannels) that connect each microwell with the microplasma region for RONS delivery. Here, we analysed the delivery of the RONS to the liquid culture medium stored in the microwells. We developed a simple experimental set-up using a microdevice and applied in situ ultraviolet absorption spectroscopy with high sensitivity for detecting RONS in liquid. The plasma-generated RONS were delivered into the liquid culture medium via the through-holes fabricated into the microdevice. The RONS concentrations were on the order of 10–100 μM depending on the size of the through-holes. In contrast, we found that the amount of dissolved oxygen was almost constant. To investigate the process of RONS generation, we numerically analysed the gas flow in the through-holes. We suggest that the circulating gas flow in the through-holes promotes the interaction between the plasma (ionised gas) and the liquid, resulting in enhanced RONS concentrations. PMID:28176800

  15. Fenton fragmentation for faster electrophoretic on chip purification of amplifiable genomic DNA.

    Science.gov (United States)

    Hakenberg, S; Hügle, M; Meyer, P; Behrmann, O; Dame, G; Urban, G A

    2015-05-15

    With a rapid and simple actuation protocol electrophoretic nucleic acid extraction is easy automatable, requires no moving parts, is easy to miniaturize and furthermore possesses a size dependent cut-off filter adjustable by the pore size of the hydrogel. However electrophoretic nucleic acid extraction from bacteria has so far been applied mainly for short RNA targets. One of the reasons is that electrophoretic processing of unfragmented genomic DNA strands is time-consuming, because of the length. Here DNA fragmentation would accelerate extraction and isolation. We introduce on-chip lysis and non-enzymatic DNA cleavage directly followed by a purifying step for receiving amplifiable DNA fragments from bacteria in less than 25 min. In contrast to restriction enzymes the Fenton reaction is known to cleave DNA without nucleotide specificity. The reaction mix contains iron(II) EDTA, sodium ascorbate, hydrogen peroxide and lysozyme. The degree of fragmentation can be adjusted by the concentration of reagents. The results enable electrophoretic extraction methods to unspecifically process long genomic DNA in a short time frame, e.g. for pathogen detection in a lab-on-a-chip format. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Thin Film Differential Photosensor for Reduction of Temperature Effects in Lab-on-Chip Applications

    Science.gov (United States)

    de Cesare, Giampiero; Carpentiero, Matteo; Nascetti, Augusto; Caputo, Domenico

    2016-01-01

    This paper presents a thin film structure suitable for low-level radiation measurements in lab-on-chip systems that are subject to thermal treatments of the analyte and/or to large temperature variations. The device is the series connection of two amorphous silicon/amorphous silicon carbide heterojunctions designed to perform differential current measurements. The two diodes experience the same temperature, while only one is exposed to the incident radiation. Under these conditions, temperature and light are the common and differential mode signals, respectively. A proper electrical connection reads the differential current of the two diodes (ideally the photocurrent) as the output signal. The experimental characterization shows the benefits of the differential structure in minimizing the temperature effects with respect to a single diode operation. In particular, when the temperature varies from 23 to 50 °C, the proposed device shows a common mode rejection ratio up to 24 dB and reduces of a factor of three the error in detecting very low-intensity light signals. PMID:26907292

  17. On-chip imaging of Schistosoma haematobium eggs in urine for diagnosis by computer vision.

    Directory of Open Access Journals (Sweden)

    Ewert Linder

    Full Text Available BACKGROUND: Microscopy, being relatively easy to perform at low cost, is the universal diagnostic method for detection of most globally important parasitic infections. As quality control is hard to maintain, misdiagnosis is common, which affects both estimates of parasite burdens and patient care. Novel techniques for high-resolution imaging and image transfer over data networks may offer solutions to these problems through provision of education, quality assurance and diagnostics. Imaging can be done directly on image sensor chips, a technique possible to exploit commercially for the development of inexpensive "mini-microscopes". Images can be transferred for analysis both visually and by computer vision both at point-of-care and at remote locations. METHODS/PRINCIPAL FINDINGS: Here we describe imaging of helminth eggs using mini-microscopes constructed from webcams and mobile phone cameras. The results show that an inexpensive webcam, stripped off its optics to allow direct application of the test sample on the exposed surface of the sensor, yields images of Schistosoma haematobium eggs, which can be identified visually. Using a highly specific image pattern recognition algorithm, 4 out of 5 eggs observed visually could be identified. CONCLUSIONS/SIGNIFICANCE: As proof of concept we show that an inexpensive imaging device, such as a webcam, may be easily modified into a microscope, for the detection of helminth eggs based on on-chip imaging. Furthermore, algorithms for helminth egg detection by machine vision can be generated for automated diagnostics. The results can be exploited for constructing simple imaging devices for low-cost diagnostics of urogenital schistosomiasis and other neglected tropical infectious diseases.

  18. 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.

  19. Establishment and application of a multiplex genetic mutation-detection method of lung cancer based on MassARRAY platform

    Institute of Scientific and Technical Information of China (English)

    Hong-Xia Tian; Xu-Chao Zhang; Zhen Wang; Jian-Guang Chen; Shi-Liang Chen; Wei-Bang Guo; Yi-Long Wu

    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 LungCartaTM kit. The sensitivity and specificity of the proposed method were evaluated by directly sequencingEGFR andKRAS 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 LungCartaTM kit. However, anFGFR2 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.

  20. A hybrid color space for skin detection using genetic algorithm heuristic search and principal component analysis technique.

    Directory of Open Access Journals (Sweden)

    Mahdi Maktabdar Oghaz

    Full Text Available Color is one of the most prominent features of an image and used in many skin and face detection applications. Color space transformation is widely used by researchers to improve face and skin detection performance. Despite the substantial research efforts in this area, choosing a proper color space in terms of skin and face classification performance which can address issues like illumination variations, various camera characteristics and diversity in skin color tones has remained an open issue. This research proposes a new three-dimensional hybrid color space termed SKN by employing the Genetic Algorithm heuristic and Principal Component Analysis to find the optimal representation of human skin color in over seventeen existing color spaces. Genetic Algorithm heuristic is used to find the optimal color component combination setup in terms of skin detection accuracy while the Principal Component Analysis projects the optimal Genetic Algorithm solution to a less complex dimension. Pixel wise skin detection was used to evaluate the performance of the proposed color space. We have employed four classifiers including Random Forest, Naïve Bayes, Support Vector Machine and Multilayer Perceptron in order to generate the human skin color predictive model. The proposed color space was compared to some existing color spaces and shows superior results in terms of pixel-wise skin detection accuracy. Experimental results show that by using Random Forest classifier, the proposed SKN color space obtained an average F-score and True Positive Rate of 0.953 and False Positive Rate of 0.0482 which outperformed the existing color spaces in terms of pixel wise skin detection accuracy. The results also indicate that among the classifiers used in this study, Random Forest is the most suitable classifier for pixel wise skin detection applications.