Multiplex detection of agricultural pathogens

DOEpatents

Siezak, Thomas R.; Gardner, Shea; Torres, Clinton; Vitalis, Elizabeth; Lenhoff, Raymond J.

2013-01-15

Described are kits and methods useful for detection of agricultural pathogens in a sample. Genomic sequence information from agricultural pathogens was analyzed to identify signature sequences, e.g., polynucleotide sequences useful for confirming the presence or absence of a pathogen in a sample. Primer and probe sets were designed and optimized for use in a PCR based, multiplexed Luminex assay and/or an array assay to successfully identify the presence or absence of pathogens in a sample.

Multiplex real-time PCR assay for detection of pathogenic Vibrio parahaemolyticus strains.

PubMed

He, Peiyan; Chen, Zhongwen; Luo, Jianyong; Wang, Henghui; Yan, Yong; Chen, Lixia; Gao, Wenjie

2014-01-01

Foodborne disease caused by pathogenic Vibrio parahaemolyticus has become a serious public health problem in many countries. Rapid diagnosis and the identification of pathogenic V. parahaemolyticus are very important in the context of public health. In this study, an EvaGreen-based multiplex real-time PCR assay was established for the detection of pathogenic V. parahaemolyticus. This assay targeted three genetic markers of V. parahaemolyticus (species-specific gene toxR and virulence genes tdh and trh). The assay could unambiguously identify pathogenic V. parahaemolyticus with a minimum detection limit of 1.4 pg genomic DNA per reaction (concentration giving a positive multiplex real-time PCR result in 95% of samples). The specificity of the assay was evaluated using 72 strains of V. parahaemolyticus and other bacteria. A validation of the assay with clinical samples confirmed its sensitivity and specificity. Our data suggest the newly established multiplex real-time PCR assay is practical, cost-effective, specific, sensitive and capable of high-throughput detection of pathogenic V. parahaemolyticus. Copyright © 2014. Published by Elsevier Ltd.

Multiplex detection of agricultural pathogens

DOEpatents

McBride, Mary Teresa; Slezak, Thomas Richard; Messenger, Sharon Lee

2010-09-14

Described are kits and methods useful for detection of seven agricultural pathogens (BPSV; BHV; BVD; FMDV; BTV; SVD; and VESV) in a sample. Genomic sequence information from 7 agricultural pathogens was analyzed to identify signature sequences, e.g., polynucleotide sequences useful for confirming the presence or absence of a pathogen in a sample. Primer and probe sets were designed and optimized for use in a PCR based, multiplexed Luminex assay to successfully identify the presence or absence of pathogens in a sample.

Demonstration of Time Domain Multiplexed Readout for Magnetically Coupled Calorimeters

NASA Technical Reports Server (NTRS)

Porst, J.-P.; Adams, J. S.; Balvin, M.; Bandler, S.; Beyer, J.; Busch, S. E.; Drung, D.; Seidel, G. M.; Smith, S. J.; Stevenson, T. R.

2012-01-01

Magnetically coupled calorimeters (MCC) have extremely high potential for x-ray applications due to the inherent high energy resolution capability and being non-dissipative. Although very high energy-resolution has been demonstrated, until now there has been no demonstration of multiplexed read-out. We report on the first realization of a time domain multiplexed (TDM) read-out. While this has many similarities with TDM of transition-edge-sensors (TES), for MGGs the energy resolution is limited by the SQUID read-out noise and requires the well established scheme to be altered in order to minimize degradation due to noise aliasing effects. In cur approach, each pixel is read out by a single first stage SQUID (SQ1) that is operated in open loop. The outputs of the SQ1 s are low-pass filtered with an array of low cross-talk inductors, then fed into a single-stage SQUID TD multiplexer. The multiplexer is addressed from room temperature and read out through a single amplifier channel. We present results achieved with a new detector platform. Noise performance is presented and compared to expectations. We have demonstrated multiplexed X-ray spectroscopy at 5.9keV with delta_FWHM=10eV. In an optimized setup, we show it is possible to multiplex 32 detectors without significantly degrading the Intrinsic detector resolution.

Microwave SQUID Multiplexer for the Readout of Metallic Magnetic Calorimeters

NASA Astrophysics Data System (ADS)

Kempf, S.; Gastaldo, L.; Fleischmann, A.; Enss, C.

2014-06-01

We have realized a frequency-domain multiplexing technique for the readout of large metallic magnetic calorimeter detector arrays. It is based on non-hysteretic single-junction SQUIDs and allows for a simultaneous readout of hundreds or thousands of detectors by using a single cryogenic high electron mobility transistor amplifier and two coaxial cables that are routed from room-temperature to the detector array. We discuss the working principle of the multiplexer and present details about our prototype multiplexer design. We show that fabricated devices are fully operational and that characteristic SQUID parameters such as the input sensitivity of the SQUID or the resonance frequency of the readout circuit can be predicted with confidence. Our best device so far has shown a magnetic flux white noise level of 1.4 m which can in future be reduced by an optimization of the fabrication processes as well as an improved microwave readout system.

Performance of the SBRC 190, a cryogenic multiplexer for photoconductor arrays

NASA Technical Reports Server (NTRS)

Dotson, Jessie L.; Koerber, C. T.; Mason, C. G.; Simpson, J. P.; Moore, E. M.; Witteborn, F. C.; Farhoomand, J.; Erickson, E. F.; DeVincenzi, D. (Technical Monitor)

2002-01-01

The SBRC 190 cryogenic readouts were developed for use with far-infrared arrays of Ge:Sb and Ge:Ga photoconductor detectors. The SBRC 190 provides an AC-coupled CTIA (capacitance transimpedance amplifier) unit cell for each detector and multiplexes up to 32 detectors. This paper presents our test results characterizing and optimizing the performance of these novel devices. We will discuss their basic behavior in addition to describing the trade-offs inherent in different sampling strategies.

Lithographed Superconducting Resonator Development for Next-Generation Frequency Multiplexing Readout of Transition-Edge Sensors

NASA Astrophysics Data System (ADS)

Faramarzi, F.; De Haan, T.; Kusaka, A.; Lee, A.; Neuhauser, B.; Plambeck, R.; Raum, C.; Suzuki, A.; Westbrook, B.

2018-03-01

Ground-based cosmic microwave background (CMB) experiments are undergoing a period of exponential growth. Current experiments are observing with 1000-10,000 detectors, and the next-generation experiment (CMB stage 4) is proposing to deploy approximately 500,000 detectors. This order of magnitude increase in detector count will require a new approach for readout electronics. We have developed superconducting resonators for next-generation frequency-domain multiplexing (fMUX) readout architecture. Our goal is to reduce the physical size of resonators, such that resonators and detectors can eventually be integrated on a single wafer. To reduce the size of these resonators, we have designed spiral inductors and interdigitated capacitors that resonate around 10-100 MHz, an order of magnitude higher frequency compared to current fMUX readout systems. The higher frequency leads to a wider bandwidth and would enable higher multiplexing factor than the current ˜ 50 detectors per readout channel. We will report on the simulation, fabrication method, characterization technique, and measurement of quality factor of these resonators.

Highly multiplexed signal readout for a time-of-flight positron emission tomography detector based on silicon photomultipliers.

PubMed

Cates, Joshua W; Bieniosek, Matthew F; Levin, Craig S

2017-01-01

Maintaining excellent timing resolution in the generation of silicon photomultiplier (SiPM)-based time-of-flight positron emission tomography (TOF-PET) systems requires a large number of high-speed, high-bandwidth electronic channels and components. To minimize the cost and complexity of a system's back-end architecture and data acquisition, many analog signals are often multiplexed to fewer channels using techniques that encode timing, energy, and position information. With progress in the development SiPMs having lower dark noise, after pulsing, and cross talk along with higher photodetection efficiency, a coincidence timing resolution (CTR) well below 200 ps FWHM is now easily achievable in single pixel, bench-top setups using 20-mm length, lutetium-based inorganic scintillators. However, multiplexing the output of many SiPMs to a single channel will significantly degrade CTR without appropriate signal processing. We test the performance of a PET detector readout concept that multiplexes 16 SiPMs to two channels. One channel provides timing information with fast comparators, and the second channel encodes both position and energy information in a time-over-threshold-based pulse sequence. This multiplexing readout concept was constructed with discrete components to process signals from a [Formula: see text] array of SensL MicroFC-30035 SiPMs coupled to [Formula: see text] Lu 1.8 Gd 0.2 SiO 5 (LGSO):Ce (0.025 mol. %) scintillators. This readout method yielded a calibrated, global energy resolution of 15.3% FWHM at 511 keV with a CTR of [Formula: see text] FWHM between the 16-pixel multiplexed detector array and a [Formula: see text] LGSO-SiPM reference detector. In summary, results indicate this multiplexing scheme is a scalable readout technique that provides excellent coincidence timing performance.

Integrating IR detector imaging systems

NASA Technical Reports Server (NTRS)

Bailey, G. C. (Inventor)

1984-01-01

An integrating IR detector array for imaging is provided in a hybrid circuit with InSb mesa diodes in a linear array, a single J-FET preamplifier for readout, and a silicon integrated circuit multiplexer. Thin film conductors in a fan out pattern deposited on an Al2O3 substrate connect the diodes to the multiplexer, and thick film conductors also connect the reset switch and preamplifier to the multiplexer. Two phase clock pulses are applied with a logic return signal to the multiplexer through triax comprised of three thin film conductors deposited between layers. A lens focuses a scanned image onto the diode array for horizontal read out while a scanning mirror provides vertical scan.

Si:Bi switched photoconducttor infrared detector array

NASA Technical Reports Server (NTRS)

Eakin, C. E.

1983-01-01

A multiplexed infrared detector array is described. The small demonstration prototype consisted of two cryogenically cooled, bismuth doped silicon, extrinsic photoconductor pixels multiplexed onto a single output channel using an on focal plane switch integration sampling technique. Noise levels of the order of 400 to 600 rms electrons per sample were demonstrated for this chip and wire hybrid version.

Multispectral computational ghost imaging with multiplexed illumination

NASA Astrophysics Data System (ADS)

Huang, Jian; Shi, Dongfeng

2017-07-01

Computational ghost imaging has attracted wide attention from researchers in many fields over the last two decades. Multispectral imaging as one application of computational ghost imaging possesses spatial and spectral resolving abilities, and is very useful for surveying scenes and extracting detailed information. Existing multispectral imagers mostly utilize narrow band filters or dispersive optical devices to separate light of different wavelengths, and then use multiple bucket detectors or an array detector to record them separately. Here, we propose a novel multispectral ghost imaging method that uses one single bucket detector with multiplexed illumination to produce a colored image. The multiplexed illumination patterns are produced by three binary encoded matrices (corresponding to the red, green and blue colored information, respectively) and random patterns. The results of the simulation and experiment have verified that our method can be effective in recovering the colored object. Multispectral images are produced simultaneously by one single-pixel detector, which significantly reduces the amount of data acquisition.

Array-on-a-disk? How Blu-ray technology can be applied to molecular diagnostics.

PubMed

Morais, Sergi; Tortajada-Genaro, Luis; Maquieira, Angel

2014-09-01

This editorial comments on the balance and perspectives of compact disk technology applied to molecular diagnostics. The development of sensitive, rapid and multiplex assays using Blu-ray technology for the determination of biomarkers, drug allergens, pathogens and detection of infections would have a direct impact on diagnostics. Effective tests for use in clinical, environmental and food applications require versatile and low-cost platforms as well as cost-effective detectors. Blu-ray technology accomplishes those requirements and advances on the concept of high density arrays for massive screening to achieve the demands of point of care or in situ analysis.

Statistical approaches to developing a multiplex immunoassay for determining human exposure to environmental pathogens.

EPA Science Inventory

This paper describes the application and method performance parameters of a Luminex xMAP™ bead-based, multiplex immunoassay for measuring specific antibody responses in saliva samples (n=5438) to antigens of six common waterborne pathogens (Campylobacter jejuni, Helicobacter pylo...

Field Demonstration of a Multiplexed Point-of-Care Diagnostic Platform for Plant Pathogens.

PubMed

Lau, Han Yih; Wang, Yuling; Wee, Eugene J H; Botella, Jose R; Trau, Matt

2016-08-16

Effective disease management strategies to prevent catastrophic crop losses require rapid, sensitive, and multiplexed detection methods for timely decision making. To address this need, a rapid, highly specific and sensitive point-of-care method for multiplex detection of plant pathogens was developed by taking advantage of surface-enhanced Raman scattering (SERS) labeled nanotags and recombinase polymerase amplification (RPA), which is a rapid isothermal amplification method with high specificity. In this study, three agriculturally important plant pathogens (Botrytis cinerea, Pseudomonas syringae, and Fusarium oxysporum) were used to demonstrate potential translation into the field. The RPA-SERS method was faster, more sensitive than polymerase chain reaction, and could detect as little as 2 copies of B. cinerea DNA. Furthermore, multiplex detection of the three pathogens was demonstrated for complex systems such as the Arabidopsis thaliana plant and commercial tomato crops. To demonstrate the potential for on-site field applications, a rapid single-tube RPA/SERS assay was further developed and successfully performed for a specific target outside of a laboratory setting.

Design, development and evaluation of a resistor-based multiplexing circuit for a 20×20 SiPM array

NASA Astrophysics Data System (ADS)

Wang, Zhonghai; Sun, Xishan; Lou, Kai; Meier, Joseph; Zhou, Rong; Yang, Chaowen; Zhu, Xiaorong; Shao, Yiping

2016-04-01

One technical challenge in developing a large-size scintillator detector with multiple Silicon Photomultiplier (SiPM) arrays is to read out a large number of detector output channels. To achieve this, different signal multiplexing circuits have been studied and applied with different performances and cost-effective tradeoffs. Resistor-based multiplexing circuits exhibit simplicity and signal integrity, but also present the disadvantage of timing shift among different channels. In this study, a resistor-based multiplexing circuit for a large-sized SiPM array readout was developed and evaluated by simulation and experimental studies. Similarly to a multiplexing circuit used for multi-anode PMT, grounding and branching resistors were connected to each SiPM output channel. The grounding resistor was used to simultaneously reduce the signal crosstalk among different channels and to improve timing performance. Both grounding and branching resistor values were optimized to maintain a balanced performance of the event energy, timing, and positioning. A multiplexing circuit was implemented on a compact PCB and applied for a flat-panel detector which consisted of a 32×32 LYSO scintillator crystals optically coupled to 5×5 SiPM arrays for a total 20×20 output channels. Test results showed excellent crystal identification for all 1024 LYSO crystals (each with 2×2×30 mm3 size) with 22Na flood-source irradiation. The measured peak-to-valley ratio from typical crystal map profile is around 3:1 to 6.6:1, an average single crystal energy resolution of about 17.3%, and an average single crystal timing resolution of about 2 ns. Timing shift among different crystals, as reported in some other resistor-based multiplexing circuit designs, was not observed. In summary, we have designed and implemented a practical resistor-based multiplexing circuit that can be readily applied for reading out a large SiPM array with good detector performance.

xMAP Technology: Applications in Detection of Pathogens

PubMed Central

Reslova, Nikol; Michna, Veronika; Kasny, Martin; Mikel, Pavel; Kralik, Petr

2017-01-01

xMAP technology is applicable for high-throughput, multiplex and simultaneous detection of different analytes within a single complex sample. xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. As an open architecture platform, the xMAP technology is beneficial to end users and therefore it is used in various pharmaceutical, clinical and research laboratories. The main aim of this review is to summarize the latest findings and applications in the field of pathogen detection using microsphere-based multiplex assays. PMID:28179899

Detection of respiratory bacterial pathogens causing atypical pneumonia by multiplex Lightmix® RT-PCR.

PubMed

Wagner, Karoline; Springer, Burkard; Imkamp, Frank; Opota, Onya; Greub, Gilbert; Keller, Peter M

2018-04-01

Pneumonia is a severe infectious disease. In addition to common viruses and bacterial pathogens (e.g. Streptococcus pneumoniae), fastidious respiratory pathogens like Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella spp. can cause severe atypical pneumonia. They do not respond to penicillin derivatives, which may cause failure of antibiotic empirical therapy. The same applies for infections with B. pertussis and B. parapertussis, the cause of pertussis disease, that may present atypically and need to be treated with macrolides. Moreover, these fastidious bacteria are difficult to identify by culture or serology, and therefore often remain undetected. Thus, rapid and accurate identification of bacterial pathogens causing atypical pneumonia is crucial. We performed a retrospective method evaluation study to evaluate the diagnostic performance of the new, commercially available Lightmix ® multiplex RT-PCR assay that detects these fastidious bacterial pathogens causing atypical pneumonia. In this retrospective study, 368 clinical respiratory specimens, obtained from patients suffering from atypical pneumonia that have been tested negative for the presence of common agents of pneumonia by culture and viral PCR, were investigated. These clinical specimens have been previously characterized by singleplex RT-PCR assays in our diagnostic laboratory and were used to evaluate the diagnostic performance of the respiratory multiplex Lightmix ® RT-PCR. The multiplex RT-PCR displayed a limit of detection between 5 and 10 DNA copies for different in-panel organisms and showed identical performance characteristics with respect to specificity and sensitivity as in-house singleplex RT-PCRs for pathogen detection. The Lightmix ® multiplex RT-PCR assay represents a low-cost, time-saving and accurate diagnostic tool with high throughput potential. The time-to-result using an automated DNA extraction device for respiratory specimens followed by multiplex RT-PCR detection was below 4 h, which is expected to significantly improve diagnostics for atypical pneumonia-associated bacterial pathogens. Copyright © 2018 The Authors. Published by Elsevier GmbH.. All rights reserved.

Preliminary Assessment of Microwave Readout Multiplexing Factor

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

Croce, Mark Philip; Koehler, Katrina Elizabeth; Rabin, Michael W.

2017-01-23

Ultra-high resolution microcalorimeter gamma spectroscopy is a new non-destructive assay technology for measurement of plutonium isotopic composition, with the potential to reduce total measurement uncertainty to a level competitive with destructive analysis methods [1-4]. Achieving this level of performance in practical applications requires not only the energy resolution now routinely achieved with transition-edge sensor microcalorimeter arrays (an order of magnitude better than for germanium detectors) but also high throughput. Microcalorimeter gamma spectrometers have not yet achieved detection efficiency and count rate capability that is comparable to germanium detectors, largely because of limits from existing readout technology. Microcalorimeter detectors must bemore » operated at low temperature to achieve their exceptional energy resolution. Although the typical 100 mK operating temperatures can be achieved with reliable, cryogen-free systems, the cryogenic complexity and heat load from individual readout channels for large sensor arrays is prohibitive. Multiplexing is required for practical systems. The most mature multiplexing technology at present is time-division multiplexing (TDM) [3, 5-6]. In TDM, the sensor outputs are switched by applying bias current to one SQUID amplifier at a time. Transition-edge sensor (TES) microcalorimeter arrays as large as 256 pixels have been developed for X-ray and gamma-ray spectroscopy using TDM technology. Due to bandwidth limits and noise scaling, TDM is limited to a maximum multiplexing factor of approximately 32-40 sensors on one readout line [8]. Increasing the size of microcalorimeter arrays above the kilopixel scale, required to match the throughput of germanium detectors, requires the development of a new readout technology with a much higher multiplexing factor.« less

[A review of mixed gas detection system based on infrared spectroscopic technique].

PubMed

Dang, Jing-Min; Fu, Li; Yan, Zi-Hui; Zheng, Chuan-Tao; Chang, Yu-Chun; Chen, Chen; Wang, Yi-Din

2014-10-01

In order to provide the experiences and references to the researchers who are working on infrared (IR) mixed gas detection field. The proposed manuscript reviews two sections of the aforementioned field, including optical multiplexing structure and detection method. At present, the coherent light sources whose representative are quantum cascade laser (QCL) and inter-band cascade laser(ICL) become the mainstream light source in IR mixed gas detection, which replace the traditional non-coherent light source, such as IR radiation source and IR light emitting diode. In addition, the photon detector which has a super high detectivity and very short response time is gradually beyond thermal infrared detector, dominant in the field of infrared detector. The optical multiplexing structure is the key factor of IR mixed gas detection system, which consists of single light source multi-plexing detection structure and multi light source multiplexing detection structure. Particularly, single light source multiplexing detection structure is advantages of small volume and high integration, which make it a plausible candidate for the portable mixed gas detection system; Meanwhile, multi light source multiplexing detection structure is embodiment of time division multiplex, frequency division multiplexing and wavelength division multiplexing, and become the leading structure of the mixed gas detection system because of its wider spectral range, higher spectral resolution, etc. The detection method applied to IR mixed gas detection includes non-dispersive infrared (NDIR) spectroscopy, wavelength and frequency-modulation spectroscopy, cavity-enhanced spectroscopy and photoacoustic spectroscopy, etc. The IR mixed gas detection system designed by researchers after recognizing the whole sections of the proposed system, which play a significant role in industrial and agricultural production, environmental monitoring, and life science, etc.

Frequency multiplexed superconducting quantum interference device readout of large bolometer arrays for cosmic microwave background measurements.

PubMed

Dobbs, M A; Lueker, M; Aird, K A; Bender, A N; Benson, B A; Bleem, L E; Carlstrom, J E; Chang, C L; Cho, H-M; Clarke, J; Crawford, T M; Crites, A T; Flanigan, D I; de Haan, T; George, E M; Halverson, N W; Holzapfel, W L; Hrubes, J D; Johnson, B R; Joseph, J; Keisler, R; Kennedy, J; Kermish, Z; Lanting, T M; Lee, A T; Leitch, E M; Luong-Van, D; McMahon, J J; Mehl, J; Meyer, S S; Montroy, T E; Padin, S; Plagge, T; Pryke, C; Richards, P L; Ruhl, J E; Schaffer, K K; Schwan, D; Shirokoff, E; Spieler, H G; Staniszewski, Z; Stark, A A; Vanderlinde, K; Vieira, J D; Vu, C; Westbrook, B; Williamson, R

2012-07-01

A technological milestone for experiments employing transition edge sensor bolometers operating at sub-Kelvin temperature is the deployment of detector arrays with 100s-1000s of bolometers. One key technology for such arrays is readout multiplexing: the ability to read out many sensors simultaneously on the same set of wires. This paper describes a frequency-domain multiplexed readout system which has been developed for and deployed on the APEX-SZ and South Pole Telescope millimeter wavelength receivers. In this system, the detector array is divided into modules of seven detectors, and each bolometer within the module is biased with a unique ∼MHz sinusoidal carrier such that the individual bolometer signals are well separated in frequency space. The currents from all bolometers in a module are summed together and pre-amplified with superconducting quantum interference devices operating at 4 K. Room temperature electronics demodulate the carriers to recover the bolometer signals, which are digitized separately and stored to disk. This readout system contributes little noise relative to the detectors themselves, is remarkably insensitive to unwanted microphonic excitations, and provides a technology pathway to multiplexing larger numbers of sensors.

[Do Multiplex PCR techniques displace classical cultures in microbiology?].

PubMed

Auckenthaler, Raymond; Risch, Martin

2015-02-01

Multiplex PCR technologies progressively find their way in clinical microbiology. This technique allows the simultaneous amplification of multiple DNA targets in a single test run for the identification of pathogens up to the species level. Various pathogens of infectious diseases can be detected by a symptom-oriented approach clearly and quickly with high reliability. Essentially multiplex PCR panels are available for clarification of gastrointestinal, respiratory, sexually transmitted infections and meningitis. Today's offer from industry, university hospitals and large private laboratories of Switzerland is tabulated and commented.

Multiplexed lateral flow microarray assay for detection of citrus pathogens Xylella fastidiosa and Xanthomonas axonopodis pv citri

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

Cary,; Bruce, R; Stubben, Christopher J

The invention provides highly sensitive and specific assays for the major citrus pathogens Xylella fastidiosa and Xanthomonas axonopodis, including a field deployable multiplexed assay capable of rapidly assaying for both pathogens simultaneously. The assays are directed at particular gene targets derived from pathogenic strains that specifically cause the major citrus diseases of citrus variegated chlorosis (Xylella fastidiosa 9a5c) and citrus canker (Xanthomonas axonopodis pv citri). The citrus pathogen assays of the invention offer femtomole sensitivity, excellent linear dynamic range, and rapid and specific detection.

Multiplex detection of respiratory pathogens

DOEpatents

McBride, Mary [Brentwood, CA; Slezak, Thomas [Livermore, CA; Birch, James M [Albany, CA

2012-07-31

Described are kits and methods useful for detection of respiratory pathogens (influenza A (including subtyping capability for H1, H3, H5 and H7 subtypes) influenza B, parainfluenza (type 2), respiratory syncytial virus, and adenovirus) in a sample. Genomic sequence information from the respiratory pathogens was analyzed to identify signature sequences, e.g., polynucleotide sequences useful for confirming the presence or absence of a pathogen in a sample. Primer and probe sets were designed and optimized for use in a PCR based, multiplexed Luminex assay to successfully identify the presence or absence of pathogens in a sample.

Indium Hybridization of Large Format TES Bolometer Arrays to Readout Multiplexers for Far-Infrared Astronomy

NASA Technical Reports Server (NTRS)

Miller, Timothy M.; Costen, Nick; Allen, Christine

2007-01-01

This conference poster reviews the Indium hybridization of the large format TES bolometer arrays. We are developing a key technology to enable the next generation of detectors. That is the Hybridization of Large Format Arrays using Indium bonded detector arrays containing 32x40 elements which conforms to the NIST multiplexer readout architecture of 1135 micron pitch. We have fabricated and hybridized mechanical models with the detector chips bonded after being fully back-etched. The mechanical support consists of 30 micron walls between elements Demonstrated electrical continuity for each element. The goal is to hybridize fully functional array of TES detectors to NIST readout.

Far infrared through millimeter backshort-under-grid arrays

NASA Astrophysics Data System (ADS)

Allen, Christine A.; Abrahams, John; Benford, Dominic J.; Chervenak, James A.; Chuss, David T.; Staguhn, Johannes G.; Miller, Timothy M.; Moseley, S. Harvey; Wollack, Edward J.

2006-06-01

We are developing a large-format, versatile, bolometer array for a wide range of infrared through millimeter astronomical applications. The array design consists of three key components - superconducting transition edge sensor bolometer arrays, quarter-wave reflective backshort grids, and Superconducting Quantum Interference Device (SQUID) multiplexer readouts. The detector array is a filled, square grid of bolometers with superconducting sensors. The backshort arrays are fabricated separately and are positioned in the etch cavities behind the detector grid. The grids have unique three-dimensional interlocking features micromachined into the walls for positioning and mechanical stability. The ultimate goal of the program is to produce large-format arrays with background-limited sensitivity, suitable for a wide range of wavelengths and applications. Large-format (kilopixel) arrays will be directly indium bump bonded to a SQUID multiplexer circuit. We have produced and tested 8×8 arrays of 1 mm detectors to demonstrate proof of concept. 8×16 arrays of 2 mm detectors are being produced for a new Goddard Space Flight Center instrument. We have also produced models of a kilopixel detector grid and dummy multiplexer chip for bump bonding development. We present detector design overview, several unique fabrication highlights, and assembly technologies.

Rapid, portable, multiplexed detection of bacterial pathogens directly from clinical sample matrices

DOE PAGES

Phaneuf, Christopher R.; Mangadu, Betty Lou Bosano; Piccini, Matthew E.; ...

2016-09-23

Enteric and diarrheal diseases are a major cause of childhood illness and death in countries with developing economies. Each year, more than half of a million children under the age of five die from these diseases. We have developed a portable, microfluidic platform capable of simultaneous, multiplexed detection of several of the bacterial pathogens that cause these diseases. Furthermore, this platform can perform fast, sensitive immunoassays directly from relevant, complex clinical matrices such as stool without extensive sample cleanup or preparation. Using only 1 µL of sample per assay, we demonstrate simultaneous multiplexed detection of four bacterial pathogens implicated inmore » diarrheal and enteric diseases in less than 20 min.« less

Rapid, portable, multiplexed detection of bacterial pathogens directly from clinical sample matrices

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

Phaneuf, Christopher R.; Mangadu, Betty Lou Bosano; Piccini, Matthew E.

Enteric and diarrheal diseases are a major cause of childhood illness and death in countries with developing economies. Each year, more than half of a million children under the age of five die from these diseases. We have developed a portable, microfluidic platform capable of simultaneous, multiplexed detection of several of the bacterial pathogens that cause these diseases. Furthermore, this platform can perform fast, sensitive immunoassays directly from relevant, complex clinical matrices such as stool without extensive sample cleanup or preparation. Using only 1 µL of sample per assay, we demonstrate simultaneous multiplexed detection of four bacterial pathogens implicated inmore » diarrheal and enteric diseases in less than 20 min.« less

Performance of Multiplexed XY Resistive Micromegas detectors in a high intensity beam

NASA Astrophysics Data System (ADS)

Banerjee, D.; Burtsev, V.; Chumakov, A.; Cooke, D.; Depero, E.; Dermenev, A. V.; Donskov, S. V.; Dubinin, F.; Dusaev, R. R.; Emmenegger, S.; Fabich, A.; Frolov, V. N.; Gardikiotis, A.; Gninenko, S. N.; Hösgen, M.; Karneyeu, A. E.; Ketzer, B.; Kirsanov, M. M.; Konorov, I. V.; Kramarenko, V. A.; Kuleshov, S. V.; Levchenko, E.; Lyubovitskij, V. E.; Lysan, V.; Mamon, S.; Matveev, V. A.; Mikhailov, Yu. V.; Myalkovskiy, V. V.; Peshekhonov, V. D.; Peshekhonov, D. V.; Polyakov, V. A.; Radics, B.; Rubbia, A.; Samoylenko, V. D.; Tikhomirov, V. O.; Tlisov, D. A.; Toropin, A. N.; Vasilishin, B.; Arenas, G. Vasquez; Ulloa, P.; Crivelli, P.

2018-02-01

We present the performance of multiplexed XY resistive Micromegas detectors tested in the CERN SPS 100 GeV/c electron beam at intensities up to 3 . 3 × 105e- /(s ṡcm2) . So far, all studies with multiplexed Micromegas have only been reported for tests with radioactive sources and cosmic rays. The use of multiplexed modules in high intensity environments was not explored due to the effect of ambiguities in the reconstruction of the hit point caused by the multiplexing feature. For the specific mapping and beam intensities analyzed in this work with a multiplexing factor of five, more than 50% level of ambiguity is introduced due to particle pile-up as well as fake clusters due to the mapping feature. Our results prove that by using the additional information of cluster size and integrated charge from the signal clusters induced on the XY strips, the ambiguities can be reduced to a level below 2%. The tested detectors are used in the CERN NA64 experiment for tracking the incoming particles bending in a magnetic field in order to reconstruct their momentum. The average hit detection efficiency of each module was found to be ∼96% at the highest beam intensities. By using four modules a tracking resolution of 1.1% was obtained with ∼85% combined tracking efficiency.

PbS-PbSe IR detector arrays

NASA Technical Reports Server (NTRS)

Barrett, John R. (Inventor)

1986-01-01

A silicon wafer is provided which does not employ individually bonded leads between the IR sensitive elements and the input stages of multiplexers. The wafer is first coated with lead selenide in a first detector array area and is thereafter coated with lead sulfide within a second detector array area. The described steps result in the direct chemical deposition of lead selenide and lead sulfide upon the silicon wafer to eliminate individual wire bonding, bumping, flip chipping, planar interconnecting methods of connecting detector array elements to silicon chip circuitry, e.g., multiplexers, to enable easy fabrication of very long arrays. The electrode structure employed, produces an increase in the electrical field gradient between the electrodes for a given volume of detector material, relative to conventional electrode configurations.

Automated methods for multiplexed pathogen detection.

PubMed

Straub, Timothy M; Dockendorff, Brian P; Quiñonez-Díaz, Maria D; Valdez, Catherine O; Shutthanandan, Janani I; Tarasevich, Barbara J; Grate, Jay W; Bruckner-Lea, Cynthia J

2005-09-01

Detection of pathogenic microorganisms in environmental samples is a difficult process. Concentration of the organisms of interest also co-concentrates inhibitors of many end-point detection methods, notably, nucleic acid methods. In addition, sensitive, highly multiplexed pathogen detection continues to be problematic. The primary function of the BEADS (Biodetection Enabling Analyte Delivery System) platform is the automated concentration and purification of target analytes from interfering substances, often present in these samples, via a renewable surface column. In one version of BEADS, automated immunomagnetic separation (IMS) is used to separate cells from their samples. Captured cells are transferred to a flow-through thermal cycler where PCR, using labeled primers, is performed. PCR products are then detected by hybridization to a DNA suspension array. In another version of BEADS, cell lysis is performed, and community RNA is purified and directly labeled. Multiplexed detection is accomplished by direct hybridization of the RNA to a planar microarray. The integrated IMS/PCR version of BEADS can successfully purify and amplify 10 E. coli O157:H7 cells from river water samples. Multiplexed PCR assays for the simultaneous detection of E. coli O157:H7, Salmonella, and Shigella on bead suspension arrays was demonstrated for the detection of as few as 100 cells for each organism. Results for the RNA version of BEADS are also showing promising results. Automation yields highly purified RNA, suitable for multiplexed detection on microarrays, with microarray detection specificity equivalent to PCR. Both versions of the BEADS platform show great promise for automated pathogen detection from environmental samples. Highly multiplexed pathogen detection using PCR continues to be problematic, but may be required for trace detection in large volume samples. The RNA approach solves the issues of highly multiplexed PCR and provides "live vs. dead" capabilities. However, sensitivity of the method will need to be improved for RNA analysis to replace PCR.

Automated Methods for Multiplexed Pathogen Detection

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

Straub, Tim M.; Dockendorff, Brian P.; Quinonez-Diaz, Maria D.

2005-09-01

Detection of pathogenic microorganisms in environmental samples is a difficult process. Concentration of the organisms of interest also co-concentrates inhibitors of many end-point detection methods, notably, nucleic acid methods. In addition, sensitive, highly multiplexed pathogen detection continues to be problematic. The primary function of the BEADS (Biodetection Enabling Analyte Delivery System) platform is the automated concentration and purification of target analytes from interfering substances, often present in these samples, via a renewable surface column. In one version of BEADS, automated immunomagnetic separation (IMS) is used to separate cells from their samples. Captured cells are transferred to a flow-through thermal cyclermore » where PCR, using labeled primers, is performed. PCR products are then detected by hybridization to a DNA suspension array. In another version of BEADS, cell lysis is performed, and community RNA is purified and directly labeled. Multiplexed detection is accomplished by direct hybridization of the RNA to a planar microarray. The integrated IMS/PCR version of BEADS can successfully purify and amplify 10 E. coli O157:H7 cells from river water samples. Multiplexed PCR assays for the simultaneous detection of E. coli O157:H7, Salmonella, and Shigella on bead suspension arrays was demonstrated for the detection of as few as 100 cells for each organism. Results for the RNA version of BEADS are also showing promising results. Automation yields highly purified RNA, suitable for multiplexed detection on microarrays, with microarray detection specificity equivalent to PCR. Both versions of the BEADS platform show great promise for automated pathogen detection from environmental samples. Highly multiplexed pathogen detection using PCR continues to be problematic, but may be required for trace detection in large volume samples. The RNA approach solves the issues of highly multiplexed PCR and provides ''live vs. dead'' capabilities. However, sensitivity of the method will need to be improved for RNA analysis to replace PCR.« less

Development of a unit cell for a Ge:Ga detector array

NASA Technical Reports Server (NTRS)

1988-01-01

Two modules of gallium-doped germanium (Ge:Ga) infrared detectors with integrated multiplexing readouts and supporting drive electronics were designed and tested. This development investigated the feasibility of producing two-dimensional Ge:Ga arrays by stacking linear modules in a housing capable of providing uniaxial stress for enhanced long-wavelength response. Each module includes 8 detectors (1x1x2 mm) mounted to a sapphire board. The element spacing is 12 microns. The back faces of the detector elements are beveled with an 18 deg angle, which was proved to significantly enhance optical absorption. Each module includes a different silicon metal-oxide semiconductor field effect transistor (MOSFET) readout. The first circuit was built from discrete MOSFET components; the second incorporated devices taken from low-temperature integrated circuit multiplexers. The latter circuit exhibited much lower stray capacitance and improved stability. Using these switched-FET circuits, it was demonstrated that burst readout, with multiplexer active only during the readout period, could successfully be implemented at approximately 3.5 K.

Rapid and simultaneous detection of Salmonella spp., Escherichia coli O157, and Listeria monocytogenes by magnetic capture hybridization and multiplex real-time PCR.

PubMed

Carloni, Elisa; Rotundo, Luca; Brandi, Giorgio; Amagliani, Giulia

2018-05-25

The application of rapid, specific, and sensitive methods for pathogen detection and quantification is very advantageous in diagnosis of human pathogens in several applications, including food analysis. The aim of this study was the evaluation of a method for the multiplexed detection and quantification of three significant foodborne pathogenic species (Escherichia coli O157, Salmonella spp., and Listeria monocytogenes). The assay combines specific DNA extraction by multiplex magnetic capture hybridization (mMCH) with multiplex real-time PCR. The amplification assay showed linearity in the range 10 6 -10 genomic units (GU)/PCR for each co-amplified species. The sensitivity corresponded to 1 GU/PCR for E. coli O157 and L. monocytogenes, and 10 GU/PCR for Salmonella spp. The immobilization process and the hybrid capture of the MCH showed good efficiency and reproducibility for all targets, allowing the combination in equal amounts of the different nanoparticle types in mMCH. MCH and mMCH efficiencies were similar. The detection limit of the method was 10 CFU in samples with individual pathogens and 10 2  CFU in samples with combination of the three pathogens in unequal amounts (amount's differences of 2 or 3 log). In conclusion, this multiplex molecular platform can be applied to determine the presence of target species in food samples after culture enrichment. In this way, this method could be a time-saving and sensitive tool to be used in routine diagnosis.

Highly multiplexed signal readout for a time-of-flight positron emission tomography detector based on silicon photomultipliers

PubMed Central

Cates, Joshua W.; Bieniosek, Matthew F.; Levin, Craig S.

2017-01-01

Abstract. Maintaining excellent timing resolution in the generation of silicon photomultiplier (SiPM)-based time-of-flight positron emission tomography (TOF-PET) systems requires a large number of high-speed, high-bandwidth electronic channels and components. To minimize the cost and complexity of a system’s back-end architecture and data acquisition, many analog signals are often multiplexed to fewer channels using techniques that encode timing, energy, and position information. With progress in the development SiPMs having lower dark noise, after pulsing, and cross talk along with higher photodetection efficiency, a coincidence timing resolution (CTR) well below 200 ps FWHM is now easily achievable in single pixel, bench-top setups using 20-mm length, lutetium-based inorganic scintillators. However, multiplexing the output of many SiPMs to a single channel will significantly degrade CTR without appropriate signal processing. We test the performance of a PET detector readout concept that multiplexes 16 SiPMs to two channels. One channel provides timing information with fast comparators, and the second channel encodes both position and energy information in a time-over-threshold-based pulse sequence. This multiplexing readout concept was constructed with discrete components to process signals from a 4×4 array of SensL MicroFC-30035 SiPMs coupled to 2.9×2.9×20  mm3 Lu1.8Gd0.2SiO5 (LGSO):Ce (0.025 mol. %) scintillators. This readout method yielded a calibrated, global energy resolution of 15.3% FWHM at 511 keV with a CTR of 198±2  ps FWHM between the 16-pixel multiplexed detector array and a 2.9×2.9×20  mm3 LGSO-SiPM reference detector. In summary, results indicate this multiplexing scheme is a scalable readout technique that provides excellent coincidence timing performance. PMID:28382312

Updates on the Transition-Edge Sensors and Multiplexed Readout for HOLMES

NASA Astrophysics Data System (ADS)

Puiu, A.; Becker, D.; Bennett, D.; Biasotti, M.; Borghesi, M.; Ceriale, V.; De Gerone, M.; Faverzani, M.; Ferri, E.; Fowler, J.; Gallucci, G.; Gard, J.; Hays-Wehle, J.; Hilton, G.; Giachero, A.; Mates, J.; Nucciotti, A.; Orlando, A.; Pessina, G.; Schmidt, D.; Swetz, D.; Ullom, J.; Vale, L.

2018-05-01

Measuring the neutrino mass is one of the most compelling issues in particle physics. HOLMES is an experiment for a direct measurement of the neutrino mass. HOLMES will perform a precise measurement of the end point of the electron capture decay spectrum of ^{163}Ho in order to extract information on the neutrino mass with a sensitivity as low as 1 eV. HOLMES, in its final configuration, will deploy a 1000-pixel array of low-temperature microcalorimeters: each calorimeter is made of an absorber, where the Ho atoms will be implanted, coupled to a transition-edge sensor (TES) thermometer. The detectors will be operated at the working temperature of 100 mK provided by a dilution refrigerator. In order to read out the 1000-detector array of HOLMES, a multiplexing system is necessary: the choice is to couple the transition-edge sensors to a multiplexed rf-SQUID. In this contribution we outline the progress made towards the final configuration of HOLMES regarding both the performances of the TES detectors and the characteristics of the multiplexing system.

Multi-channel detector readout method and integrated circuit

DOEpatents

Moses, William W.; Beuville, Eric; Pedrali-Noy, Marzio

2006-12-12

An integrated circuit which provides multi-channel detector readout from a detector array. The circuit receives multiple signals from the elements of a detector array and compares the sampled amplitudes of these signals against a noise-floor threshold and against one another. A digital signal is generated which corresponds to the location of the highest of these signal amplitudes which exceeds the noise floor threshold. The digital signal is received by a multiplexing circuit which outputs an analog signal corresponding the highest of the input signal amplitudes. In addition a digital control section provides for programmatic control of the multiplexer circuit, amplifier gain, amplifier reset, masking selection, and test circuit functionality on each input thereof.

Multi-channel detector readout method and integrated circuit

DOEpatents

Moses, William W.; Beuville, Eric; Pedrali-Noy, Marzio

2004-05-18

An integrated circuit which provides multi-channel detector readout from a detector array. The circuit receives multiple signals from the elements of a detector array and compares the sampled amplitudes of these signals against a noise-floor threshold and against one another. A digital signal is generated which corresponds to the location of the highest of these signal amplitudes which exceeds the noise floor threshold. The digital signal is received by a multiplexing circuit which outputs an analog signal corresponding the highest of the input signal amplitudes. In addition a digital control section provides for programmatic control of the multiplexer circuit, amplifier gain, amplifier reset, masking selection, and test circuit functionality on each input thereof.

Prevalence of Listeria monocytogenes, Yersinia enterocolitica, Staphylococcus aureus, and Salmonella enterica Typhimurium in meat and meat products using multiplex polymerase chain reaction

PubMed Central

Latha, C.; Anu, C. J.; Ajaykumar, V. J.; Sunil, B.

2017-01-01

Aim: The objective of the study was to investigate the occurrence of Listeria monocytogenes, Yersinia enterocolitica, Staphylococcus aureus, and Salmonella enterica Typhimurium in meat and meat products using the multiplex polymerase chain reaction (PCR) method. Materials and Methods: The assay combined an enrichment step in tryptic soy broth with yeast extract formulated for the simultaneous growth of target pathogens, DNA isolation and multiplex PCR. A total of 1134 samples including beef (n=349), chicken (n=325), pork (n=310), chevon (n=50), and meat products (n=100) were collected from different parts of Kerala, India. All the samples were subjected to multiplex PCR analysis and culture-based detection for the four pathogens in parallel. Results: Overall occurrence of L. monocytogenes was 0.08 % by cultural method. However, no L. monocytogenes was obtained by multiplex PCR method. Yersinia enterocolitica was obtained from beef and pork samples. A high prevalence of S. aureus (46.7%) was found in all types of meat samples tested. None of the samples was positive for S. Typhimurium. Conclusion: Multiplex PCR assay used in this study can detect more than one pathogen simultaneously by amplifying more than one target gene in a single reaction, which can save time and labor cost. PMID:28919685

Multiplex PCR for simultaneous identification of E. coli O157:H7, Salmonella spp. and L. monocytogenes in food.

PubMed

Nguyen, Thuy Trang; Van Giau, Vo; Vo, Tuong Kha

2016-12-01

The rapid detection of pathogens in food is becoming increasingly critical for ensuring the safety of consumers, since the majority of food-borne illnesses and deaths are caused by pathogenic bacteria. Hence, rapid, sensitive, inexpensive and convenient approaches to detect food-borne pathogenic bacteria is essential in controlling food safety. In this study, a multiplex PCR assay for the rapid and simultaneous detection of Escherichia coli O157:H7, Salmonella spp. and Listeria monocytogenes was established. The invA, stx and hlyA genes specifically amplified DNA fragments of 284, 404 and 510 bp from Salmonella spp., L. monocytogenes and E. coli O157:H7, respectively. The 16S rRNA gene was targeted as an internal control gene in the presence of bacterial DNA. The specificity and sensitivity of the multiplex PCR were performed by testing different strains. The multiplex PCR assay was able to specifically simultaneously detect ten colony-forming unit/mL of each pathogen in artificially inoculated samples after enrichment for 12 h. The whole process took less than 24 h to complete, indicating that the assay is suitable for reliable and rapid identification of these three food-borne pathogens, which could be suitable in microbial epidemiology investigation.

The prevalence of the honeybee brood pathogens Ascosphaera apis, Paenibacillus larvae and Melissococcus plutonius in Spanish apiaries determined with a new multiplex PCR assay

PubMed Central

Garrido-Bailón, Encarna; Higes, Mariano; Martínez-Salvador, Amparo; Antúnez, Karina; Botías, Cristina; Meana, Aránzazu; Prieto, Lourdes; Martín-Hernández, Raquel

2013-01-01

The microorganisms Ascosphaera apis, Paenibacillus larvae and Melissococcus plutonius are the three most important pathogens that affect honeybee brood. The aim of the present study was to evaluate the prevalence of these pathogens in honeybee colonies and to elucidate their role in the honeybee colony losses in Spain. In order to get it, a multiplex polymerase chain reaction (PCR) assay was developed to simultaneously amplify the16S ribosomal ribonucleic acid (rRNA) gene of P. larvae and M. plutonius, and the 5.8S rRNA gene of A. apis. The multiplex PCR assay provides a quick and specific tool that successfully detected the three infectious pathogens (P. larvae, M. plutonius and A. apis) in brood and adult honeybee samples without the need for microbiological culture. This technique was then used to evaluate the prevalence of these pathogens in Spanish honeybee colonies in 2006 and 2007, revealing our results a low prevalence of these pathogens in most of the geographic areas studied. PMID:23919248

Chopped molecular beam multiplexing system

NASA Technical Reports Server (NTRS)

Adams, Billy R. (Inventor)

1986-01-01

The integration of a chopped molecular beam mass spectrometer with a time multiplexing system is described. The chopping of the molecular beam is synchronized with the time intervals by a phase detector and a synchronous motor. Arithmetic means are generated for phase shifting the chopper with respect to the multiplexer. A four channel amplifier provides the capacity to independently vary the baseline and amplitude in each channel of the multiplexing system.

Method of fabricating a PbS-PbSe IR detector array

NASA Technical Reports Server (NTRS)

Barrett, John R. (Inventor)

1987-01-01

A silicon wafer is provided which does not employ individually bonded leads between the IR sensitive elements and the input stages of multiplexers. The wafer is first coated with lead selenide in a first detector array area and is thereafter coated with lead sulfide within a second detector array area. The described steps result in the direct chemical deposition of lead selenide and lead sulfide upon the silicon wafer to eliminate individual wire bonding, bumping, flip chiping, planar interconnecting methods of connecting detector array elements to silicon chip circuitry, e.g., multiplexers, to enable easy fabrication of very long arrays. The electrode structure employed, produces an increase in the electrical field gradient between the electrodes for a given volume of detector material, relative to conventional electrode configurations.

Frequency-multiplexed bias and readout of a 16-pixel superconducting nanowire single-photon detector array

NASA Astrophysics Data System (ADS)

Doerner, S.; Kuzmin, A.; Wuensch, S.; Charaev, I.; Boes, F.; Zwick, T.; Siegel, M.

2017-07-01

We demonstrate a 16-pixel array of microwave-current driven superconducting nanowire single-photon detectors with an integrated and scalable frequency-division multiplexing architecture, which reduces the required number of bias and readout lines to a single microwave feed line. The electrical behavior of the photon-sensitive nanowires, embedded in a resonant circuit, as well as the optical performance and timing jitter of the single detectors is discussed. Besides the single pixel measurements, we also demonstrate the operation of a 16-pixel array with a temporal, spatial, and photon-number resolution.

A PDMS/paper/glass hybrid microfluidic biochip integrated with aptamer-functionalized graphene oxide nano-biosensors for one-step multiplexed pathogen detection.

PubMed

Zuo, Peng; Li, XiuJun; Dominguez, Delfina C; Ye, Bang-Ce

2013-10-07

Infectious pathogens often cause serious public health concerns throughout the world. There is an increasing demand for simple, rapid and sensitive approaches for multiplexed pathogen detection. In this paper we have developed a polydimethylsiloxane (PDMS)/paper/glass hybrid microfluidic system integrated with aptamer-functionalized graphene oxide (GO) nano-biosensors for simple, one-step, multiplexed pathogen detection. The paper substrate used in this hybrid microfluidic system facilitated the integration of aptamer biosensors on the microfluidic biochip, and avoided complicated surface treatment and aptamer probe immobilization in a PDMS or glass-only microfluidic system. Lactobacillus acidophilus was used as a bacterium model to develop the microfluidic platform with a detection limit of 11.0 cfu mL(-1). We have also successfully extended this method to the simultaneous detection of two infectious pathogens - Staphylococcus aureus and Salmonella enterica. This method is simple and fast. The one-step 'turn on' pathogen assay in a ready-to-use microfluidic device only takes ~10 min to complete on the biochip. Furthermore, this microfluidic device has great potential in rapid detection of a wide variety of different other bacterial and viral pathogens.

A PDMS/paper/glass hybrid microfluidic biochip integrated with aptamer-functionalized graphene oxide nano-biosensors for one-step multiplexed pathogen detection

PubMed Central

Zuo, Peng; Dominguez, Delfina C.; Ye, Bang-Ce

2014-01-01

Infectious pathogens often cause serious public health concerns throughout the world. There is an increasing demand for simple, rapid and sensitive approaches for multiplexed pathogen detection. In this paper we have developed a polydimethylsiloxane (PDMS)/paper/glass hybrid microfluidic system integrated with aptamer-functionalized graphene oxide (GO) nano-biosensors for simple, one-step, multiplexed pathogen detection. The paper substrate used in this hybrid microfluidic system facilitated the integration of aptamer biosensors on the microfluidic biochip, and avoided complicated surface treatment and aptamer probe immobilization in a PDMS or glass-only microfluidic system. Lactobacillus acidophilus was used as a bacterium model to develop the microfluidic platform with a detection limit of 11.0 cfu mL−1. We have also successfully extended this method to the simultaneous detection of two infectious pathogens - Staphylococcus aureus and Salmonella enterica. This method is simple and fast. The one-step ‘turn on’ pathogen assay in a ready-to-use microfluidic device only takes ~10 min to complete on the biochip. Furthermore, this microfluidic device has great potential in rapid detection of a wide variety of different other bacterial and viral pathogens. PMID:23929394

Immunoprevalence to Six Waterborne Pathogens in Beachgoers at Boquerón Beach, Puerto Rico: Application of a Microsphere-Based Salivary Antibody Multiplex Immunoassay

PubMed Central

Augustine, Swinburne A. J.; Simmons, Kaneatra J.; Eason, Tarsha N.; Curioso, Clarissa L.; Griffin, Shannon M.; Wade, Timothy J.; Dufour, Alfred; Fout, G. Shay; Grimm, Ann C.; Oshima, Kevin H.; Sams, Elizabeth A.; See, Mary Jean; Wymer, Larry J.

2017-01-01

Waterborne infectious diseases are a major public health concern worldwide. Few methods have been established that are capable of measuring human exposure to multiple waterborne pathogens simultaneously using non-invasive samples such as saliva. Most current methods measure exposure to only one pathogen at a time, require large volumes of individual samples collected using invasive procedures, and are very labor intensive. In this article, we applied a multiplex bead-based immunoassay capable of measuring IgG antibody responses to six waterborne pathogens simultaneously in human saliva to estimate immunoprevalence in beachgoers at Boquerón Beach, Puerto Rico. Further, we present approaches for determining cutoff points to assess immunoprevalence to the pathogens in the assay. For the six pathogens studied, our results show that IgG antibodies against antigens from noroviruses GI.I and GII.4 were more prevalent (60 and 51.6%, respectively) than Helicobacter pylori (21.4%), hepatitis A virus (20.2%), Campylobacter jejuni (8.7%), and Toxoplasma gondii (8%) in the saliva of the study participants. The salivary antibody multiplex immunoassay can be used to examine immunoprevalence of specific pathogens in human populations. PMID:28507984

Multiplexed Molecular Diagnostics for Respiratory, Gastrointestinal, and Central Nervous System Infections.

PubMed

Hanson, Kimberly E; Couturier, Marc Roger

2016-11-15

The development and implementation of highly multiplexed molecular diagnostic tests have allowed clinical microbiology laboratories to more rapidly and sensitively detect a variety of pathogens directly in clinical specimens. Current US Food and Drug Administration-approved multiplex panels target multiple different organisms simultaneously and can identify the most common pathogens implicated in respiratory viral, gastrointestinal, or central nervous system infections. This review summarizes the test characteristics of available assays, highlights the advantages and limitations of multiplex technology for infectious diseases, and discusses potential utilization of these new tests in clinical practice. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Helicase dependent OnChip-amplification and its use in multiplex pathogen detection.

PubMed

Andresen, Dennie; von Nickisch-Rosenegk, Markus; Bier, Frank F

2009-05-01

The need for fast, specific and sensitive multiparametric detection methods is an ever growing demand in molecular diagnostics. Here we report on a newly developed method, the helicase dependent OnChip amplification (OnChip-HDA). This approach integrates the analysis and detection in one single reaction thus leading to time and cost savings in multiparametric analysis. HDA is an isothermal amplification method that is not depending on thermocycling as known from PCR due to the helicases' ability to unwind DNA double-strands. We have combined the HDA with microarray based detection, making it suitable for multiplex detection. As an example we used the OnChip HDA in single and multiplex amplifications for the detection of the two pathogens N. gonorrhoeae and S. aureus directly on surface bound primers. We have successfully shown the OnChip-HDA and applied it for single- and duplex-detection of the pathogens N. gonorrhoeae and S. aureus. We have developed a new method, the OnChip-HDA for the multiplex detection of pathogens. Its simplicity in reaction setup and potential for miniaturization and multiparametric analysis is advantageous for the integration in miniaturized Lab on Chip systems, e.g. needed in point of care diagnostics.

Task-based design of a synthetic-collimator SPECT system used for small animal imaging.

PubMed

Lin, Alexander; Kupinski, Matthew A; Peterson, Todd E; Shokouhi, Sepideh; Johnson, Lindsay C

2018-05-07

In traditional multipinhole SPECT systems, image multiplexing - the overlapping of pinhole projection images - may occur on the detector, which can inhibit quality image reconstructions due to photon-origin uncertainty. One proposed system to mitigate the effects of multiplexing is the synthetic-collimator SPECT system. In this system, two detectors, a silicon detector and a germanium detector, are placed at different distances behind the multipinhole aperture, allowing for image detection to occur at different magnifications and photon energies, resulting in higher overall sensitivity while maintaining high resolution. The unwanted effects of multiplexing are reduced by utilizing the additional data collected from the front silicon detector. However, determining optimal system configurations for a given imaging task requires efficient parsing of the complex parameter space, to understand how pinhole spacings and the two detector distances influence system performance. In our simulation studies, we use the ensemble mean-squared error of the Wiener estimator (EMSE W ) as the figure of merit to determine optimum system parameters for the task of estimating the uptake of an 123 I-labeled radiotracer in three different regions of a computer-generated mouse brain phantom. The segmented phantom map is constructed by using data from the MRM NeAt database and allows for the reduction in dimensionality of the system matrix which improves the computational efficiency of scanning the system's parameter space. To contextualize our results, the Wiener estimator is also compared against a region of interest estimator using maximum-likelihood reconstructed data. Our results show that the synthetic-collimator SPECT system outperforms traditional multipinhole SPECT systems in this estimation task. We also find that image multiplexing plays an important role in the system design of the synthetic-collimator SPECT system, with optimal germanium detector distances occurring at maxima in the derivative of the percent multiplexing function. Furthermore, we report that improved task performance can be achieved by using an adaptive system design in which the germanium detector distance may vary with projection angle. Finally, in our comparative study, we find that the Wiener estimator outperforms the conventional region of interest estimator. Our work demonstrates how this optimization method has the potential to quickly and efficiently explore vast parameter spaces, providing insight into the behavior of competing factors, which are otherwise very difficult to calculate and study using other existing means. © 2018 American Association of Physicists in Medicine.

Large resistive 2D Micromegas with genetic multiplexing and some imaging applications

NASA Astrophysics Data System (ADS)

Bouteille, S.; Attié, D.; Baron, P.; Calvet, D.; Magnier, P.; Mandjavidze, I.; Procureur, S.; Riallot, M.

2016-10-01

The performance of the first large resistive Micromegas detectors with 2D readout and genetic multiplexing is presented. These detectors have a 50 × 50cm2 active area and are equipped with 1024 strips both in X- and Y-directions. The same genetic multiplexing pattern is applied on both coordinates, resulting in the compression of signals on 2 × 61 readout channels. Four such detectors have been built at CERN, and extensively tested with cosmics. The resistive strip film allows for very high gain operation, compensating for the charge spread on the 2 dimensions as well as the S / N loss due to the huge, 1 nF input capacitance. This film also creates a significantly different signal shape in the X- and Y-coordinates due to the charge evacuation along the resistive strips. All in all a detection efficiency above 95% is achieved with a 1 cm drift gap. Though not yet optimal, the measured 300 μm spatial resolution allows for very precise imaging in the field of muon tomography, and some applications of these detectors are presented.

Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop-Mediated Isothermal Amplification (TEC-LAMP) Assay for the Detection of Bacterial Meningitis Pathogens

PubMed Central

Clancy, Eoin; Cormican, Martin; Boo, Teck Wee; Cunney, Robert

2018-01-01

Bacterial meningitis infection is a leading global health concern for which rapid and accurate diagnosis is essential to reduce associated morbidity and mortality. Loop-mediated isothermal amplification (LAMP) offers an effective low-cost diagnostic approach; however, multiplex LAMP is difficult to achieve, limiting its application. We have developed novel real-time multiplex LAMP technology, TEC-LAMP, using Tth endonuclease IV and a unique LAMP primer/probe. This study evaluates the analytical specificity, limit of detection (LOD) and clinical application of an internally controlled multiplex TEC-LAMP assay for detection of leading bacterial meningitis pathogens: Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae. Analytical specificities were established by testing 168 bacterial strains, and LODs were determined using Probit analysis. The TEC-LAMP assay was 100% specific, with LODs for S. pneumoniae, N. meningitidis and H. influenzae of 39.5, 17.3 and 25.9 genome copies per reaction, respectively. Clinical performance was evaluated by testing 65 archived PCR-positive samples. Compared to singleplex real-time PCR, the multiplex TEC-LAMP assay demonstrated diagnostic sensitivity and specificity of 92.3% and 100%, respectively. This is the first report of a single-tube internally controlled multiplex LAMP assay for bacterial meningitis pathogen detection, and the first report of Tth endonuclease IV incorporation into nucleic acid amplification diagnostic technology. PMID:29425124

Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop-Mediated Isothermal Amplification (TEC-LAMP) Assay for the Detection of Bacterial Meningitis Pathogens.

PubMed

Higgins, Owen; Clancy, Eoin; Cormican, Martin; Boo, Teck Wee; Cunney, Robert; Smith, Terry J

2018-02-09

Bacterial meningitis infection is a leading global health concern for which rapid and accurate diagnosis is essential to reduce associated morbidity and mortality. Loop-mediated isothermal amplification (LAMP) offers an effective low-cost diagnostic approach; however, multiplex LAMP is difficult to achieve, limiting its application. We have developed novel real-time multiplex LAMP technology, TEC-LAMP, using Tth endonuclease IV and a unique LAMP primer/probe. This study evaluates the analytical specificity, limit of detection (LOD) and clinical application of an internally controlled multiplex TEC-LAMP assay for detection of leading bacterial meningitis pathogens: Streptococcus pneumoniae , Neisseria meningitidis and Haemophilus influenzae . Analytical specificities were established by testing 168 bacterial strains, and LODs were determined using Probit analysis. The TEC-LAMP assay was 100% specific, with LODs for S. pneumoniae , N. meningitidis and H. influenzae of 39.5, 17.3 and 25.9 genome copies per reaction, respectively. Clinical performance was evaluated by testing 65 archived PCR-positive samples. Compared to singleplex real-time PCR, the multiplex TEC-LAMP assay demonstrated diagnostic sensitivity and specificity of 92.3% and 100%, respectively. This is the first report of a single-tube internally controlled multiplex LAMP assay for bacterial meningitis pathogen detection, and the first report of Tth endonuclease IV incorporation into nucleic acid amplification diagnostic technology.

Detection of sexually transmitted infection and human papillomavirus in negative cytology by multiplex-PCR

PubMed Central

2010-01-01

Background The aim of this study was to determine the prevalence of human papillomavirus (HPV) and 15 species that cause sexually transmitted infections (STIs) in negative cytology. In addition, we compared the diagnostic performance of multiplex polymerase chain reaction (PCR) with widely available techniques used to detect HPV. Methods We recruited 235 women of reproductive age who had negative cytology findings in a liquid-based cervical smear. STIs were identified by multiplex PCR, and HPV genotypes by multiplex PCR, hybrid capture 2, and DNA microaray; discordant results were analyzed by direct sequencing. Results Approximately 96.6% of patients with negative cytology results were positive for pathogens that cause STIs. The pathogens most frequently detected were Gardnerella vaginalis, Ureaplasma urealyticum. The incidence of HPV in negative cytology was 23.3%. Low-risk HPV infection was significantly correlated with Chalmaydia trachomatis, and high-risk HPV infection was significantly correlated with Group β streptococcus. The analytical sensitivities of the multiplex PCR and DNA microarray were higher than 80%, and the analytical specificity was nearly 100% for all tests. Conclusions Multiplex PCR yielded results that most of patients with negative cytology were positive for pathogens that cause STIs, and were more similar to that of DNA microarray, than that of hybrid capture 2 in terms of analytical sensitivity and prediction value of HPV infection. PMID:20920170

Digital frequency domain multiplexing readout electronics for the next generation of millimeter telescopes

NASA Astrophysics Data System (ADS)

Bender, Amy N.; Cliche, Jean-François; de Haan, Tijmen; Dobbs, Matt A.; Gilbert, Adam J.; Montgomery, Joshua; Rowlands, Neil; Smecher, Graeme M.; Smith, Ken; Wilson, Andrew

2014-07-01

Frequency domain multiplexing (fMux) is an established technique for the readout of transition-edge sensor (TES) bolometers in millimeter-wavelength astrophysical instrumentation. In fMux, the signals from multiple detectors are read out on a single pair of wires reducing the total cryogenic thermal loading as well as the cold component complexity and cost of a system. The current digital fMux system, in use by POLARBEAR, EBEX, and the South Pole Telescope, is limited to a multiplexing factor of 16 by the dynamic range of the Superconducting Quantum Interference Device pre-amplifier and the total system bandwidth. Increased multiplexing is key for the next generation of large format TES cameras, such as SPT-3G and POLARBEAR2, which plan to have on the of order 15,000 detectors. Here, we present the next generation fMux readout, focusing on the warm electronics. In this system, the multiplexing factor increases to 64 channels per module (2 wires) while maintaining low noise levels and detector stability. This is achieved by increasing the system bandwidth, reducing the dynamic range requirements though active feedback, and digital synthesis of voltage biases with a novel polyphase filter algorithm. In addition, a version of the new fMux readout includes features such as low power consumption and radiation-hard components making it viable for future space-based millimeter telescopes such as the LiteBIRD satellite.

Design, Fabrication, and Testing of Lumped Element Kinetic inductance Detectors for 3 mm CMB Observations

NASA Technical Reports Server (NTRS)

Lowitz, Amy E.; Brown, Ari David; Stevenson, Thomas R.; Timbie, Peter T.; Wollack, Edward J.

2014-01-01

Kinetic inductance detectors (KIDs) are a promising technology for low-noise, highly-multiplexible mm- and submm-wave detection. KIDs have a number of advantages over other detector technologies, which make them an appealing option in the cosmic microwave background B-mode anisotropy search, including passive frequency domain multiplexing and relatively simple fabrication, but have suffered from challenges associated with noise control. Here we describe design and fabrication of a 20-pixel prototype array of lumped element molybdenum KIDs. We show Q, frequency and temperature measurements from the array under dark conditions. We also present evidence for a double superconducting gap in molybdenum.

Reliable detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis by using multiplex qPCR including internal controls for nucleic acid extraction and amplification.

PubMed

Janse, Ingmar; Hamidjaja, Raditijo A; Bok, Jasper M; van Rotterdam, Bart J

2010-12-08

Several pathogens could seriously affect public health if not recognized timely. To reduce the impact of such highly pathogenic micro-organisms, rapid and accurate diagnostic tools are needed for their detection in various samples, including environmental samples. Multiplex real-time PCRs were designed for rapid and reliable detection of three major pathogens that have the potential to cause high morbidity and mortality in humans: B. anthracis, F. tularensis and Y. pestis. The developed assays detect three pathogen-specific targets, including at least one chromosomal target, and one target from B. thuringiensis which is used as an internal control for nucleic acid extraction from refractory spores as well as successful DNA amplification. Validation of the PCRs showed a high analytical sensitivity, specificity and coverage of diverse pathogen strains. The multiplex qPCR assays that were developed allow the rapid detection of 3 pathogen-specific targets simultaneously, without compromising sensitivity. The application of B. thuringiensis spores as internal controls further reduces false negative results. This ensures highly reliable detection, while template consumption and laboratory effort are kept at a minimum.

Reliable detection of Bacillus anthracis, Francisella tularensis and Yersinia pestis by using multiplex qPCR including internal controls for nucleic acid extraction and amplification

PubMed Central

2010-01-01

Background Several pathogens could seriously affect public health if not recognized timely. To reduce the impact of such highly pathogenic micro-organisms, rapid and accurate diagnostic tools are needed for their detection in various samples, including environmental samples. Results Multiplex real-time PCRs were designed for rapid and reliable detection of three major pathogens that have the potential to cause high morbidity and mortality in humans: B. anthracis, F. tularensis and Y. pestis. The developed assays detect three pathogen-specific targets, including at least one chromosomal target, and one target from B. thuringiensis which is used as an internal control for nucleic acid extraction from refractory spores as well as successful DNA amplification. Validation of the PCRs showed a high analytical sensitivity, specificity and coverage of diverse pathogen strains. Conclusions The multiplex qPCR assays that were developed allow the rapid detection of 3 pathogen-specific targets simultaneously, without compromising sensitivity. The application of B. thuringiensis spores as internal controls further reduces false negative results. This ensures highly reliable detection, while template consumption and laboratory effort are kept at a minimum PMID:21143837

The microfluidic bioagent autonomous networked detector (M-BAND): an update. Fully integrated, automated, and networked field identification of airborne pathogens

NASA Astrophysics Data System (ADS)

Sanchez, M.; Probst, L.; Blazevic, E.; Nakao, B.; Northrup, M. A.

2011-11-01

We describe a fully automated and autonomous air-borne biothreat detection system for biosurveillance applications. The system, including the nucleic-acid-based detection assay, was designed, built and shipped by Microfluidic Systems Inc (MFSI), a new subsidiary of PositiveID Corporation (PSID). Our findings demonstrate that the system and assay unequivocally identify pathogenic strains of Bacillus anthracis, Yersinia pestis, Francisella tularensis, Burkholderia mallei, and Burkholderia pseudomallei. In order to assess the assay's ability to detect unknown samples, our team also challenged it against a series of blind samples provided by the Department of Homeland Security (DHS). These samples included natural occurring isolated strains, near-neighbor isolates, and environmental samples. Our results indicate that the multiplex assay was specific and produced no false positives when challenged with in house gDNA collections and DHS provided panels. Here we present another analytical tool for the rapid identification of nine Centers for Disease Control and Prevention category A and B biothreat organisms.

Synovial fluid multiplex PCR is superior to culture for detection of low-virulent pathogens causing periprosthetic joint infection.

PubMed

Morgenstern, Christian; Cabric, Sabrina; Perka, Carsten; Trampuz, Andrej; Renz, Nora

2018-02-01

Analysis of joint aspirate is the standard preoperative investigation for diagnosis of periprosthetic joint infection (PJI). We compared the diagnostic performance of culture and multiplex polymerase chain reaction (PCR) of synovial fluid for diagnosis of PJI. Patients in whom aspiration of the prosthetic hip or knee joint was performed before revision arthroplasty were prospectively included. The performance of synovial fluid culture and multiplex PCR was compared by McNemar's chi-squared test. A total of 142 patients were included, 82 with knee and 60 with hip prosthesis. PJI was diagnosed in 77 patients (54%) and aseptic failure in 65 patients (46%). The sensitivity of synovial fluid culture and PCR was 52% and 60%, respectively, showing concordant results in 116 patients (82%). In patients with PJI, PCR missed 6 high-virulent pathogens (S. aureus, streptococci, E. faecalis, E. coli) which grew in synovial fluid culture, whereas synovial fluid culture missed 12 pathogens detected by multiplex PCR, predominantly low-virulent pathogens (Cutibacterium acnes and coagulase-negative staphylococci). In patients with aseptic failure, PCR detected 6 low-virulent organisms (predominantly C. acnes). While the overall performance of synovial fluid PCR was comparable to culture, PCR was superior for detection of low-virulent bacteria such as Cutibacterium spp. and coagulase-negative staphylococci. In addition, synovial fluid culture required several days for growth, whereas multiplex PCR provided results within 5hours in an automated manner. Copyright © 2017 Elsevier Inc. All rights reserved.

The Microwave SQUID Multiplexer

NASA Astrophysics Data System (ADS)

Mates, John Arthur Benson

2011-12-01

This thesis describes a multiplexer of Superconducting Quantum Interference Devices (SQUIDs) with low-noise, ultra-low power dissipation, and great scalability. The multiplexer circuit measures the magnetic flux in a large number of unshunted rf SQUIDs by coupling each SQUID to a superconducting microwave resonator tuned to a unique resonance frequency and driving the resonators from a common feedline. A superposition of microwave tones measures each SQUID simultaneously using only two coaxial cables between the cryogenic device and room temperature. This multiplexer will enable the instrumentation of arrays with hundreds of thousands of low-temperature detectors for new applications in cosmology, materials analysis, and nuclear non-proliferation. The driving application of the Microwave SQUID Multiplexer is the readout of large arrays of superconducting transition-edge sensors, by some figures of merit the most sensitive detectors of electromagnetic signals over a span of more than nine orders of magnitude in energy, from 40 GHz microwaves to 200 keV gamma rays. Modern transition-edge sensors have noise-equivalent power as low as 10-20 W / Hz1/2 and energy resolution as good as 2 eV at 6 keV. These per-pixel sensitivities approach theoretical limits set by the underlying signals, motivating a rapid increase in pixel count to access new science. Compelling applications, like the non-destructive assay of nuclear material for treaty verification or the search for primordial gravity waves from inflation use arrays of these detectors to increase collection area or tile a focal plane. We developed three generations of SQUID multiplexers, optimizing the first for flux noise 0.17 muPhi0 / Hz1/2, the second for input current noise 19 pA / Hz1/2, and the last for practical multiplexing of large arrays of cosmic microwave background polarimeters based on transition-edge sensors. Using the last design we demonstrated multiplexed readout of prototype polarimeters with the performance required for the future development of a large-scale astronomical instrument.

Detection of pathogenic Vibrio spp. in shellfish by using multiplex PCR and DNA microarrays.

PubMed

Panicker, Gitika; Call, Douglas R; Krug, Melissa J; Bej, Asim K

2004-12-01

This study describes the development of a gene-specific DNA microarray coupled with multiplex PCR for the comprehensive detection of pathogenic vibrios that are natural inhabitants of warm coastal waters and shellfish. Multiplex PCR with vvh and viuB for Vibrio vulnificus, with ompU, toxR, tcpI, and hlyA for V. cholerae, and with tlh, tdh, trh, and open reading frame 8 for V. parahaemolyticus helped to ensure that total and pathogenic strains, including subtypes of the three Vibrio spp., could be detected and discriminated. For DNA microarrays, oligonucleotide probes for these targeted genes were deposited onto epoxysilane-derivatized, 12-well, Teflon-masked slides by using a MicroGrid II arrayer. Amplified PCR products were hybridized to arrays at 50 degrees C and detected by using tyramide signal amplification with Alexa Fluor 546 fluorescent dye. Slides were imaged by using an arrayWoRx scanner. The detection sensitivity for pure cultures without enrichment was 10(2) to 10(3) CFU/ml, and the specificity was 100%. However, 5 h of sample enrichment followed by DNA extraction with Instagene matrix and multiplex PCR with microarray hybridization resulted in the detection of 1 CFU in 1 g of oyster tissue homogenate. Thus, enrichment of the bacterial pathogens permitted higher sensitivity in compliance with the Interstate Shellfish Sanitation Conference guideline. Application of the DNA microarray methodology to natural oysters revealed the presence of V. vulnificus (100%) and V. parahaemolyticus (83%). However, V. cholerae was not detected in natural oysters. An assay involving a combination of multiplex PCR and DNA microarray hybridization would help to ensure rapid and accurate detection of pathogenic vibrios in shellfish, thereby improving the microbiological safety of shellfish for consumers.

Detection of Pathogenic Vibrio spp. in Shellfish by Using Multiplex PCR and DNA Microarrays

PubMed Central

Panicker, Gitika; Call, Douglas R.; Krug, Melissa J.; Bej, Asim K.

2004-01-01

This study describes the development of a gene-specific DNA microarray coupled with multiplex PCR for the comprehensive detection of pathogenic vibrios that are natural inhabitants of warm coastal waters and shellfish. Multiplex PCR with vvh and viuB for Vibrio vulnificus, with ompU, toxR, tcpI, and hlyA for V. cholerae, and with tlh, tdh, trh, and open reading frame 8 for V. parahaemolyticus helped to ensure that total and pathogenic strains, including subtypes of the three Vibrio spp., could be detected and discriminated. For DNA microarrays, oligonucleotide probes for these targeted genes were deposited onto epoxysilane-derivatized, 12-well, Teflon-masked slides by using a MicroGrid II arrayer. Amplified PCR products were hybridized to arrays at 50°C and detected by using tyramide signal amplification with Alexa Fluor 546 fluorescent dye. Slides were imaged by using an arrayWoRx scanner. The detection sensitivity for pure cultures without enrichment was 102 to 103 CFU/ml, and the specificity was 100%. However, 5 h of sample enrichment followed by DNA extraction with Instagene matrix and multiplex PCR with microarray hybridization resulted in the detection of 1 CFU in 1 g of oyster tissue homogenate. Thus, enrichment of the bacterial pathogens permitted higher sensitivity in compliance with the Interstate Shellfish Sanitation Conference guideline. Application of the DNA microarray methodology to natural oysters revealed the presence of V. vulnificus (100%) and V. parahaemolyticus (83%). However, V. cholerae was not detected in natural oysters. An assay involving a combination of multiplex PCR and DNA microarray hybridization would help to ensure rapid and accurate detection of pathogenic vibrios in shellfish, thereby improving the microbiological safety of shellfish for consumers. PMID:15574946

Development of a multiplexed readout with high position resolution for positron emission tomography

NASA Astrophysics Data System (ADS)

Lee, Sangwon; Choi, Yong; Kang, Jihoon; Jung, Jin Ho

2017-04-01

Detector signals for positron emission tomography (PET) are commonly multiplexed to reduce the number of digital processing channels so that the system can remain cost effective while also maintaining imaging performance. In this work, a multiplexed readout combining Anger position estimation algorithm and position decoder circuit (PDC) was developed to reduce the number of readout channels by a factor of 24, 96-to-4. The data acquisition module consisted of a TDC (50 ps resolution), 4-channel ADCs (12 bit, 105 MHz sampling rate), 2 GB SDRAM and USB3.0. The performance of the multiplexed readout was assessed with a high-resolution PET detector block composed of 2×3 detector modules, each consisting of an 8×8 array of 1.52×1.52×6 mm3 LYSO, a 4×4 array of 3×3 mm2 silicon photomultiplier (SiPM) and 13.4×13.4 mm2 light guide with 0.7 mm thickness. The acquired flood histogram showed that all 384 crystals could be resolved. The average energy resolution at 511 keV was 13.7±1.6% full-width-at-half-maximum (FWHM) and the peak-to-valley ratios of the flood histogram on the horizontal and vertical lines were 18.8±0.8 and 22.8±1.3, respectively. The coincidence resolving time of a pair of detector blocks was 6.2 ns FWHM. The reconstructed phantom image showed that rods down to a diameter of 1.6 mm could be resolved. The results of this study indicate that the multiplexed readout would be useful in developing a PET with a spatial resolution less than the pixel size of the photosensor, such as a SiPM array.

Using the Wiener estimator to determine optimal imaging parameters in a synthetic-collimator SPECT system used for small animal imaging

NASA Astrophysics Data System (ADS)

Lin, Alexander; Johnson, Lindsay C.; Shokouhi, Sepideh; Peterson, Todd E.; Kupinski, Matthew A.

2015-03-01

In synthetic-collimator SPECT imaging, two detectors are placed at different distances behind a multi-pinhole aperture. This configuration allows for image detection at different magnifications and photon energies, resulting in higher overall sensitivity while maintaining high resolution. Image multiplexing the undesired overlapping between images due to photon origin uncertainty may occur in both detector planes and is often present in the second detector plane due to greater magnification. However, artifact-free image reconstruction is possible by combining data from both the front detector (little to no multiplexing) and the back detector (noticeable multiplexing). When the two detectors are used in tandem, spatial resolution is increased, allowing for a higher sensitivity-to-detector-area ratio. Due to variability in detector distances and pinhole spacings found in synthetic-collimator SPECT systems, a large parameter space must be examined to determine optimal imaging configurations. We chose to assess image quality based on the task of estimating activity in various regions of a mouse brain. Phantom objects were simulated using mouse brain data from the Magnetic Resonance Microimaging Neurological Atlas (MRM NeAt) and projected at different angles through models of a synthetic-collimator SPECT system, which was developed by collaborators at Vanderbilt University. Uptake in the different brain regions was modeled as being normally distributed about predetermined means and variances. We computed the performance of the Wiener estimator for the task of estimating activity in different regions of the mouse brain. Our results demonstrate the utility of the method for optimizing synthetic-collimator system design.

Superconducting Bolometer Array Architectures

NASA Technical Reports Server (NTRS)

Benford, Dominic; Chervenak, Jay; Irwin, Kent; Moseley, S. Harvey; Shafer, Rick; Staguhn, Johannes; Wollack, Ed; Oegerle, William (Technical Monitor)

2002-01-01

The next generation of far-infrared and submillimeter instruments require large arrays of detectors containing thousands of elements. These arrays will necessarily be multiplexed, and superconducting bolometer arrays are the most promising present prospect for these detectors. We discuss our current research into superconducting bolometer array technologies, which has recently resulted in the first multiplexed detections of submillimeter light and the first multiplexed astronomical observations. Prototype arrays containing 512 pixels are in production using the Pop-Up Detector (PUD) architecture, which can be extended easily to 1000 pixel arrays. Planar arrays of close-packed bolometers are being developed for the GBT (Green Bank Telescope) and for future space missions. For certain applications, such as a slewed far-infrared sky survey, feedhorncoupling of a large sparsely-filled array of bolometers is desirable, and is being developed using photolithographic feedhorn arrays. Individual detectors have achieved a Noise Equivalent Power (NEP) of -10(exp 17) W/square root of Hz at 300mK, but several orders of magnitude improvement are required and can be reached with existing technology. The testing of such ultralow-background detectors will prove difficult, as this requires optical loading of below IfW. Antenna-coupled bolometer designs have advantages for large format array designs at low powers due to their mode selectivity.

Detection of pathogenic bacteria in shellfish using multiplex PCR followed by CovaLink NH microwell plate sandwich hybridization.

PubMed

Lee, Chi-Ying; Panicker, Gitika; Bej, Asim K

2003-05-01

Outbreak of diseases associated with consumption of raw shellfish especially oysters is a major concern to the seafood industry and public health agencies. A multiplex PCR amplification of targeted gene segments followed by DNA-DNA sandwich hybridization was optimized to detect the etiologic agents. First, a multiplex PCR amplification of hns, spvB, vvh, ctx and tl was developed enabling simultaneous detection of total Salmonella enterica serotype Typhimurium, Vibrio vulnificus, Vibrio cholerae and Vibrio parahaemolyticus from both pure cultures and seeded oysters. Amplicons were then subjected to a colorimetric CovaLink NH microwell plate sandwich hybridization using phosphorylated and biotinlylated oligonucleotide probes, the nucleotide sequences of which were located internal to the amplified DNA. The results from the hybridization with the multiplexed PCR amplified DNA exhibited a high signal/noise ratio ranging between 14.1 and 43.2 measured at 405 nm wavelength. The sensitivity of detection for each pathogen was 10(2) cells/g of oyster tissue homogenate. The results from this study showed that the combination of the multiplex PCR with a colorimetric microwell plate sandwich hybridization assay permits a specific, sensitive, and reproducible system for the detection of the microbial pathogens in shellfish, thereby improving the microbiological safety of shellfish to consumers.

Impact of Aerosol Dust on xMAP Multiplex Detection of Different Class Pathogens

PubMed Central

Kleymenov, Denis A.; Gushchin, Vladimir A.; Gintsburg, Alexander L.; Tkachuk, Artem P.

2017-01-01

Environmental or city-scale bioaerosol surveillance can provide additional value for biodefense and public health. Efficient bioaerosol monitoring should rely on multiplex systems capable of detecting a wide range of biologically hazardous components potentially present in air (bacteria, viruses, toxins and allergens). xMAP technology from LuminexTM allows multiplex bead-based detection of antigens or nucleic acids, but its use for simultaneous detection of different classes of pathogens (bacteria, virus, toxin) is questionable. Another problem is the detection of pathogens in complex matrices, e.g., in the presence of dust. In the this research, we developed the model xMAP multiplex test-system aiRDeTeX 1.0, which enables detection of influenza A virus, Adenovirus type 6 Salmonella typhimurium, and cholera toxin B subunit representing RNA virus, DNA virus, gram-negative bacteria and toxin respectively as model organisms of biologically hazardous components potentially present in or spreadable through the air. We have extensively studied the effect of matrix solution (PBS, distilled water), environmental dust and ultrasound treatment for monoplex and multiplex detection efficiency of individual targets. All targets were efficiently detectable in PBS and in the presence of dust. Ultrasound does not improve the detection except for bacterial LPS. PMID:29238328

Exploring target-specific primer extension in combination with a bead-based suspension array for multiplexed detection and typing using Streptococcus suis as a model pathogen

PubMed Central

van der Wal, Fimme J.; Achterberg, René P.; van Solt-Smits, Conny; Bergervoet, Jan H. W.; de Weerdt, Marjanne; Wisselink, Henk J.

2017-01-01

We investigated the feasibility of an assay based on target-specific primer extension, combined with a suspension array, for the multiplexed detection and typing of a veterinary pathogen in animal samples, using Streptococcus suis as a model pathogen. A procedure was established for simultaneous detection of 6 S. suis targets in pig tonsil samples (i.e., 4 genes associated with serotype 1, 2, 7, or 9, the generic S. suis glutamate dehydrogenase gene [gdh], and the gene encoding the extracellular protein factor [epf]). The procedure was set up as a combination of protocols: DNA isolation from porcine tonsils, a multiplex PCR, a multiplex target-specific primer extension, and finally a suspension array as the readout. The resulting assay was compared with a panel of conventional PCR assays. The proposed multiplex assay can correctly identify the serotype of isolates and is capable of simultaneous detection of multiple targets in porcine tonsillar samples. The assay is not as sensitive as the current conventional PCR assays, but with the correct sampling strategy, the assay can be useful for screening pig herds to establish which S. suis serotypes are circulating in a pig population. PMID:28980519

A 90GHz Bolometer Camera Detector System for the Green Bank Telescope

NASA Technical Reports Server (NTRS)

Benford, Dominic J.; Allen, Christine A.; Buchanan, Ernest D.; Chen, Tina C.; Chervenak, James A.; Devlin, Mark J.; Dicker, Simon R.; Forgione, Joshua B.

2004-01-01

We describe a close-packed, two-dimensional imaging detector system for operation at 90GHz (3.3mm) for the 100 m Green Bank Telescope (GBT) This system will provide high sensitivity (<1mjy in 1s rapid imaging (15'x15' to 250 microJy in 1 hr) at the world's largest steerable aperture. The heart of this camera is an 8x8 close packed, Nyquist-sampled array of superconducting transition edge sensor bolometers. We have designed and are producing a functional superconducting bolometer array system using a monolithic planar architecture and high-speed multiplexed readout electronics. With an NEP of approx. 2.10(exp 17) W/square root Hz, the TES bolometers will provide fast linear sensitive response for high performance imaging. The detectors are read out by and 8x8 time domain SQUID multiplexer. A digital/analog electronics system has been designed to enable read out by SQUID multiplexers. First light for this instrument on the GBT is expected within a year.

A 90GHz Bolometer Camera Detector System for the Green

NASA Technical Reports Server (NTRS)

Benford, Dominic J.; Allen, Christine A.; Buchanan, Ernest; Chen, Tina C.; Chervenak, James A.; Devlin, Mark J.; Dicker, Simon R.; Forgione, Joshua B.

2004-01-01

We describe a close-packed, two-dimensional imaging detector system for operation at 90GHz (3.3 mm) for the 100m Green Bank Telescope (GBT). This system will provide high sensitivity (less than 1mJy in 1s) rapid imaging (15'x15' to 150 micron Jy in 1 hr) at the world's largest steerable aperture. The heart of this camera is an 8x8 close-packed, Nyquist-sampled array of superconducting transition edge sensor (TES) bolometers. We have designed and are producing a functional superconducting bolometer array system using a monolithic planar architecture and high-speed multiplexed readout electronics. With an NEP of approximately 2 x 10(exp -17) W/square root of Hz, the TES bolometers will provide fast, linear, sensitive response for high performance imaging. The detectors are read out by an 8x8 time domain SQUID multiplexer. A digital/analog electronics system has been designed to enable read out by SQUID multiplexers. First light for this instrument on the GBT is expected within a year.

Electrical delay line multiplexing for pulsed mode radiation detectors

NASA Astrophysics Data System (ADS)

Vinke, Ruud; Yeom, Jung Yeol; Levin, Craig S.

2015-04-01

Medical imaging systems are composed of a large number of position sensitive radiation detectors to provide high resolution imaging. For example, whole-body Positron Emission Tomography (PET) systems are typically composed of thousands of scintillation crystal elements, which are coupled to photosensors. Thus, PET systems greatly benefit from methods to reduce the number of data acquisition channels, in order to reduce the system development cost and complexity. In this paper we present an electrical delay line multiplexing scheme that can significantly reduce the number of readout channels, while preserving the signal integrity required for good time resolution performance. We experimented with two 4 × 4 LYSO crystal arrays, with crystal elements having 3 mm × 3 mm × 5 mm and 3 mm × 3 mm × 20 mm dimensions, coupled to 16 Hamamatsu MPPC S10931-050P SiPM elements. Results show that each crystal could be accurately identified, even in the presence of scintillation light sharing and inter-crystal Compton scatter among neighboring crystal elements. The multiplexing configuration degraded the coincidence timing resolution from ∼243 ps FWHM to ∼272 ps FWHM when 16 SiPM signals were combined into a single channel for the 4 × 4 LYSO crystal array with 3 mm × 3 mm × 20 mm crystal element dimensions, in coincidence with a 3 mm × 3 mm × 5 mm LYSO crystal pixel. The method is flexible to allow multiplexing configurations across different block detectors, and is scalable to an entire ring of detectors.

Pathogen Identification by Multiplex LightMix Real-Time PCR Assay in Patients with Meningitis and Culture-Negative Cerebrospinal Fluid Specimens

PubMed Central

Wagner, Karoline; Springer, Burkard; Pires, Valeria P.

2017-01-01

ABSTRACT Acute bacterial meningitis is a medical emergency, and delays in initiating effective antimicrobial therapy result in increased morbidity and mortality. Culture-based methods, thus far considered the “gold standard” for identifying bacterial microorganisms, require 24 to 48 h to provide a diagnosis. In addition, antimicrobial therapy is often started prior to clinical sample collection, thereby decreasing the probability of confirming the bacterial pathogen by culture-based methods. To enable a fast and accurate detection of the most important bacterial pathogens causing meningitis, namely, Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, Streptococcus agalactiae, and Listeria monocytogenes, we evaluated a commercially available multiplex LightMix real-time PCR (RT-PCR) in 220 cerebrospinal fluid (CSF) specimens. The majority of CSF samples were collected by lumbar puncture, but we also included some CSF samples from patients with symptoms of meningitis from the neurology department that were recovered from shunts. CSF samples were analyzed by multiplex RT-PCR enabling a first diagnosis within a few hours after sample arrival at our institute. In contrast, bacterial identification took between 24 and 48 h by culture. Overall, a high agreement of bacterial identification between culture and multiplex RT-PCR was observed (99%). Moreover, multiplex RT-PCR enabled the detection of pathogens, S. pneumoniae (n = 2), S. agalactiae (n = 1), and N. meningitidis (n = 1), in four culture-negative samples. As a complement to classical bacteriological CSF culture, the LightMix RT-PCR assay proved to be valuable by improving the rapidity and accuracy of the diagnosis of bacterial meningitis. PMID:29237781

Detection of Gastrointestinal Pathogens from Stool Samples on Hemoccult Cards by Multiplex PCR.

PubMed

Alberer, Martin; Schlenker, Nicklas; Bauer, Malkin; Helfrich, Kerstin; Mengele, Carolin; Löscher, Thomas; Nothdurft, Hans Dieter; Bretzel, Gisela; Beissner, Marcus

2017-01-01

Purpose . Up to 30% of international travelers are affected by travelers' diarrhea (TD). Reliable data on the etiology of TD is lacking. Sufficient laboratory capacity at travel destinations is often unavailable and transporting conventional stool samples to the home country is inconvenient. We evaluated the use of Hemoccult cards for stool sampling combined with a multiplex PCR for the detection of model viral, bacterial, and protozoal TD pathogens. Methods . Following the creation of serial dilutions for each model pathogen, last positive dilution steps (LPDs) and thereof calculated last positive sample concentrations (LPCs) were compared between conventional stool samples and card samples. Furthermore, card samples were tested after a prolonged time interval simulating storage during a travel duration of up to 6 weeks. Results . The LPDs/LPCs were comparable to testing of conventional stool samples. After storage on Hemoccult cards, the recovery rate was 97.6% for C. jejuni , 100% for E . histolytica , 97.6% for norovirus GI, and 100% for GII. Detection of expected pathogens was possible at weekly intervals up to 42 days. Conclusion . Stool samples on Hemoccult cards stored at room temperature can be used in combination with a multiplex PCR as a reliable tool for testing of TD pathogens.

Design and performance of dual-polarization lumped-element kinetic inductance detectors for millimeter-wave polarimetry

NASA Astrophysics Data System (ADS)

McCarrick, H.; Jones, G.; Johnson, B. R.; Abitbol, M. H.; Ade, P. A. R.; Bryan, S.; Day, P.; Essinger-Hileman, T.; Flanigan, D.; Leduc, H. G.; Limon, M.; Mauskopf, P.; Miller, A.; Tucker, C.

2018-02-01

Aims: Lumped-element kinetic inductance detectors (LEKIDs) are an attractive technology for millimeter-wave observations that require large arrays of extremely low-noise detectors. We designed, fabricated and characterized 64-element (128 LEKID) arrays of horn-coupled, dual-polarization LEKIDs optimized for ground-based CMB polarimetry. Our devices are sensitive to two orthogonal polarizations in a single spectral band centered on 150 GHz with Δν/ν = 0.2. The 65 × 65 mm square arrays are designed to be tiled into the focal plane of an optical system. We demonstrate the viability of these dual-polarization LEKIDs with laboratory measurements. Methods: The LEKID modules are tested with an FPGA-based readout system in a sub-kelvin cryostat that uses a two-stage adiabatic demagnetization refrigerator. The devices are characterized using a blackbody and a millimeter-wave source. The polarization properties are measured with a cryogenic stepped half-wave plate. We measure the resonator parameters and the detector sensitivity, noise spectrum, dynamic range, and polarization response. Results: The resonators have internal quality factors approaching 1 × 106. The detectors have uniform response between orthogonal polarizations and a large dynamic range. The detectors are photon-noise limited above 1 pW of absorbed power. The noise-equivalent temperatures under a 3.4 K blackbody load are <100 μK √s. The polarization fractions of detectors sensitive to orthogonal polarizations are >80%. The entire array is multiplexed on a single readout line, demonstrating a multiplexing factor of 128. The array and readout meet the requirements for 4 arrays to be read out simultaneously for a multiplexing factor of 512. Conclusions: This laboratory study demonstrates the first dual-polarization LEKID array optimized specifically for CMB polarimetry and shows the readiness of the detectors for on-sky observations.

Microwave SQUID Multiplexing of Metallic Magnetic Calorimeters: Status of Multiplexer Performance and Room-Temperature Readout Electronics Development

NASA Astrophysics Data System (ADS)

Wegner, M.; Karcher, N.; Krömer, O.; Richter, D.; Ahrens, F.; Sander, O.; Kempf, S.; Weber, M.; Enss, C.

2018-02-01

To our present best knowledge, microwave SQUID multiplexing (μ MUXing) is the most suitable technique for reading out large-scale low-temperature microcalorimeter arrays that consist of hundreds or thousands of individual pixels which require a large readout bandwidth per pixel. For this reason, the present readout strategy for metallic magnetic calorimeter (MMC) arrays combining an intrinsic fast signal rise time, an excellent energy resolution, a large energy dynamic range, a quantum efficiency close to 100% as well as a highly linear detector response is based on μ MUXing. Within this paper, we summarize the state of the art in MMC μ MUXing and discuss the most recent results. This particularly includes the discussion of the performance of a 64-pixel detector array with integrated, on-chip microwave SQUID multiplexer, the progress in flux ramp modulation of MMCs as well as the status of the development of a software-defined radio-based room-temperature electronics which is specifically optimized for MMC readout.

Multiplexed Activity-based Protein Profiling of the Human Pathogen Aspergillus fumigatus Reveals Large Functional Changes upon Exposure to Human Serum*

PubMed Central

Wiedner, Susan D.; Burnum, Kristin E.; Pederson, LeeAnna M.; Anderson, Lindsey N.; Fortuin, Suereta; Chauvigné-Hines, Lacie M.; Shukla, Anil K.; Ansong, Charles; Panisko, Ellen A.; Smith, Richard D.; Wright, Aaron T.

2012-01-01

Environmental adaptability is critical for survival of the fungal human pathogen Aspergillus fumigatus in the immunocompromised host lung. We hypothesized that exposure of the fungal pathogen to human serum would lead to significant alterations to the organism's physiology, including metabolic activity and stress response. Shifts in functional pathway and corresponding enzyme reactivity of A. fumigatus upon exposure to the human host may represent much needed prognostic indicators of fungal infection. To address this, we employed a multiplexed activity-based protein profiling (ABPP) approach coupled to quantitative mass spectrometry-based proteomics to measure broad enzyme reactivity of the fungus cultured with and without human serum. ABPP showed a shift from aerobic respiration to ethanol fermentation and utilization over time in the presence of human serum, which was not observed in serum-free culture. Our approach provides direct insight into this pathogen's ability to survive, adapt, and proliferate. Additionally, our multiplexed ABPP approach captured a broad swath of enzyme reactivity and functional pathways and provides a method for rapid assessment of the A. fumigatus response to external stimuli. PMID:22865858

Multiplexed activity-based protein profiling of the human pathogen Aspergillus fumigatus reveals large functional changes upon exposure to human serum.

PubMed

Wiedner, Susan D; Burnum, Kristin E; Pederson, LeeAnna M; Anderson, Lindsey N; Fortuin, Suereta; Chauvigné-Hines, Lacie M; Shukla, Anil K; Ansong, Charles; Panisko, Ellen A; Smith, Richard D; Wright, Aaron T

2012-09-28

Environmental adaptability is critical for survival of the fungal human pathogen Aspergillus fumigatus in the immunocompromised host lung. We hypothesized that exposure of the fungal pathogen to human serum would lead to significant alterations to the organism's physiology, including metabolic activity and stress response. Shifts in functional pathway and corresponding enzyme reactivity of A. fumigatus upon exposure to the human host may represent much needed prognostic indicators of fungal infection. To address this, we employed a multiplexed activity-based protein profiling (ABPP) approach coupled to quantitative mass spectrometry-based proteomics to measure broad enzyme reactivity of the fungus cultured with and without human serum. ABPP showed a shift from aerobic respiration to ethanol fermentation and utilization over time in the presence of human serum, which was not observed in serum-free culture. Our approach provides direct insight into this pathogen's ability to survive, adapt, and proliferate. Additionally, our multiplexed ABPP approach captured a broad swath of enzyme reactivity and functional pathways and provides a method for rapid assessment of the A. fumigatus response to external stimuli.

Final Report Nucleic Acid System - Hybrid PCR and Multiplex Assay Project Phase 2

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

Koopman, R P; Langlois, R G; Nasarabadi, S

2002-04-17

This report covers phase 2 (year 2) of the Nucleic Acid System--Hybrid PCR and Multiplex Assay project. The objective of the project is to reduce to practice the detection and identification of biological warfare pathogens by the nucleic acid recognition technique of PCR (polymerase chain reaction) in a multiplex mode using flow cytometry. The Hybrid instrument consists of a flow-through PCR module capable of handling a multiplexed PCR assay, a hybridizing module capable of hybridizing multiplexed PCR amplicons and beads, and a flow cytometer module for bead-based identification, all controlled by a single computer. Multiplex immunoassay using bead-based Luminex flowmore » cytometry is available, allowing rapid screening for many agents. PCR is highly specific and complements and verifies immunoassay. It can also be multiplexed and detection provided using the bead-based Luminex flow cytometer. This approach allows full access to the speed and 100-fold multiplex capability of flow cytometry for rapid screening as well as the accuracy and specificity of PCR. This project has two principal activities: (1) Design, build and test a prototype hybrid PCR/flow cytometer with the basic capabilities for rapid, broad spectrum detection and identification, and (2) Develop and evaluate multiplex flow analysis assay protocols and reagents for the simultaneous detection of PCR products. This project requires not only building operationally functional instrumentation but also developing the chemical assays for detection of priority pathogens. This involves development and evaluation of multiplex flow analysis assay protocols and reagents for the simultaneous detection of PCR products.« less

Clinical utility of an optimised multiplex real-time PCR assay for the identification of pathogens causing sepsis in Vietnamese patients.

PubMed

Tat Trung, Ngo; Van Tong, Hoang; Lien, Tran Thi; Van Son, Trinh; Thanh Huyen, Tran Thi; Quyen, Dao Thanh; Hoan, Phan Quoc; Meyer, Christian G; Song, Le Huu

2018-02-01

For the identification of bacterial pathogens, blood culture is still the gold standard diagnostic method. However, several disadvantages apply to blood cultures, such as time and rather large volumes of blood sample required. We have previously established an optimised multiplex real-time PCR method in order to diagnose bloodstream infections. In the present study, we evaluated the diagnostic performance of this optimised multiplex RT-PCR in blood samples collected from 110 septicaemia patients enrolled at the 108 Military Central Hospital, Hanoi, Vietnam. Positive results were obtained by blood culture, the Light Cylcler-based SeptiFast ® assay and our multiplex RT-PCR in 35 (32%), 31 (28%), and 31 (28%) samples, respectively. Combined use of the three methods confirmed 50 (45.5%) positive cases of bloodstream infection, a rate significantly higher compared to the exclusive use of one of the three methods (P=0.052, 0.012 and 0.012, respectively). The sensitivity, specificity and area under the curve (AUC) of our assay were higher compared to that of the SeptiFast ® assay (77.4%, 86.1% and 0.8 vs. 67.7%, 82.3% and 0.73, respectively). Combined use of blood culture and multiplex RT-PCR assay showed a superior diagnostic performance, as the sensitivity, specificity, and AUC reached 83.3%, 100%, and 0.95, respectively. The concordance between blood culture and the multiplex RT-PCR assay was highest for Klebsiella pneumonia (100%), followed by Streptococcus spp. (77.8%), Escherichia coli (66.7%), Staphylococcus spp. (50%) and Salmonella spp. (50%). In addition, the use of the newly established multiplex RT-PCR assay increased the spectrum of identifiable agents (Acintobacter baumannii, 1/32; Proteus mirabilis, 1/32). The combination of culture and the multiplex RT-PCR assay provided an excellent diagnostic accomplishment and significantly supported the identification of causative pathogens in clinical samples obtained from septic patients. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Development of a chip-based multiplexed immunoassay using liposomal nanovesicles and its application in the detection of pathogens causing female lower genital tract infections.

PubMed

Su, Wen-Hsiang; Ho, Tien-Yu; Tsou, Tsung-Shan; Lee, Wen-Ling; Wang, Kuan-Chin; Yu, Yuan-Yi; Chen, Tien-Jui; Tan, Chia-Hsuan; Kuo, Cheng-Deng; Chen, Chien-Sheng; Wang, Peng-Hui

2013-03-01

Cervicovaginitis is a highly prevalent disease that is a burden on healthcare globally. Immediate and adequate treatment can eradicate the infection and block subsequent complications. The feasibility of achip-based multiplexed immunoassay using liposomal nanovesicles was tested. A multiplexed immunoassay chip containing five antibodies for five pathogens (Chlamydia trachomatis, Escherichia coli, Neisseria gonorrhoeae, Streptococcus agalactiae, and Candida albicans) was established and tested. Four patients with spiking of candidiasis were enrolled. The difference between positive and negative readings was evaluated using the paired Student t test. The detection threshold of Candida in this microarray was 100,000 CFU/mL in a vaginal sample, and the time required for the whole procedure was 3 hours. The testing of the four patients showed 100% for both sensitivity and specificity. This microarray chip was a rapid, easy, inexpensive and sensitive tool for detecting female lower genital tract Candida infection in a one-time vaginal sampling process, although the data on the four other pathogens were still unavailable. A larger population study is encouraged to test the validity of this multiplexed immunoassay chip. Copyright © 2013. Published by Elsevier B.V.

The readout chain for the bar PANDA MVD strip detector

NASA Astrophysics Data System (ADS)

Schnell, R.; Brinkmann, K.-Th.; Di Pietro, V.; Kleines, H.; Goerres, A.; Riccardi, A.; Rivetti, A.; Rolo, M. D.; Sohlbach, H.; Zaunick, H.-G.

2015-02-01

The bar PANDA (antiProton ANnihilation at DArmstadt) experiment will study the strong interaction in annihilation reactions between an antiproton beam and a stationary gas jet target. The detector will comprise different sub-detectors for tracking, particle identification and calorimetry. The Micro-Vertex Detector (MVD) as the innermost part of the tracking system will allow precise tracking and detection of secondary vertices. For the readout of the double-sided silicon strip sensors a custom-made ASIC is being developed, employing the Time-over-Threshold (ToT) technique for digitization and utilize time-to-digital converters (TDC) to provide a high-precision time stamp of the hit. A custom-made Module Data Concentrator ASIC (MDC) will multiplex the data of all front-ends of one sensor towards the CERN-developed GBT chip set (GigaBit Transceiver). The MicroTCA-based MVD Multiplexer Board (MMB) at the off-detector site will receive and concentrate the data from the GBT links and transfer it to FPGA-based compute nodes for global event building.

Progress Towards High-Sensitivity Arrays of Detectors of Sub-mm Radiation using Superconducting Tunnel Junctions with Radio-Frequency Single-Electron Transistors

NASA Technical Reports Server (NTRS)

Stevenson, T. R.; Hsieh, W.-T.; Li, M. J.; Stahle, C. M.; Wollack, E. J.; Schoelkopf, R. J.; Krebs, Carolyn (Technical Monitor)

2002-01-01

The science drivers for the SPIRIT/SPECS missions demand sensitive, fast, compact, low-power, large-format detector arrays for high resolution imaging and spectroscopy in the far infrared and submillimeter. Detector arrays with 10,000 pixels and sensitivity less than 10(exp 20)-20 W/Hz(exp 20)0.5 are needed. Antenna-coupled superconducting tunnel junction detectors with integrated rf single-electron transistor readout amplifiers have the potential for achieving this high level of sensitivity, and can take advantage of an rf multiplexing technique when forming arrays. The device consists of an antenna structure to couple radiation into a small superconducting volume and cause quasiparticle excitations, and a single-electron transistor to measure currents through tunnel junction contacts to the absorber volume. We will describe optimization of device parameters, and recent results on fabrication techniques for producing devices with high yield for detector arrays. We will also present modeling of expected saturation power levels, antenna coupling, and rf multiplexing schemes.

Multiplexed electronically programmable multimode ionization detector for chromatography

DOEpatents

Wise, M.B.; Buchanan, M.V.

1988-05-19

Method and apparatus for detecting and differentiating organic compounds based on their electron affinity. An electron capture detector cell (ECD) is operated in a plurality of multiplexed electronically programmable operating modes to alter the detector response during a single sampling cycle to acquire multiple simultaneous chromatograms corresponding to each of the different operating modes. The cell is held at a constant subatmospheric pressure while the electron collection bias voltage applied to the cell is modulated electronically to allow acquisition of multiple chromatograms for a single sample elution from a chromatograph representing three distinctly different response modes. A system is provided which automatically controls the programmed application of bias pulses at different intervals and/or amplitudes to switch the detector from an ionization mode to the electron capture mode and various degrees therebetween to provide an improved means of tuning an ECD for multimode detection and improved specificity. 6 figs.

Multiplexed electronically programmable multimode ionization detector for chromatography

DOEpatents

Wise, Marcus B.; Buchanan, Michelle V.

1989-01-01

Method and apparatus for detecting and differentiating organic compounds based on their electron affinity. An electron capture detector cell (ECD) is operated in a plurality of multiplexed electroncially programmable operating modes to alter the detector response during a single sampling cycle to acquire multiple simultaneous chromatograms corresponding to each of the different operating modes. The cell is held at a constant subatmospheric pressure while the electron collection bias voltage applied to the cell is modulated electronically to allow acquisition of multiple chromatograms for a single sample elution from a chromatograph representing three distinctly different response modes. A system is provided which automatically controls the programmed application of bias pulses at different intervals and/or amplitudes to switch the detector from an ionization mode to the electron capture mode and various degrees therebetween to provide an improved means of tuning an ECD for multimode detection and improved specificity.

Detector arrays for low-background space infrared astronomy

NASA Technical Reports Server (NTRS)

Mccreight, C. R.; Mckelvey, M. E.; Goebel, J. H.; Anderson, G. M.; Lee, J. H.

1986-01-01

The status of development and characterization tests of integrated infrared detector array technology for astronomy applications is described. The devices under development include intrinsic, extrinsic silicon, and extrinsic germanium detectors, with hybrid silicon multiplexers. Laboratory test results and successful astronomy imagery have established the usefulness of integrated arrays in low-background astronomy applications.

Detector arrays for low-background space infrared astronomy

NASA Technical Reports Server (NTRS)

Mccreight, C. R.; Mckelvey, M. E.; Goebel, J. H.; Anderson, G. M.; Lee, J. H.

1986-01-01

The status of development and characterization tests of integrated infrared detector array technology for astronomy applications is described. The devices under development include intrinsic, extrinsic silicon, and extrinsic germanium detectors, with hybrid silicon multiplexers. Laboratary test results and successful astronomy imagery have established the usefulness of integrated arrays in low-background astronomy applications.

Multiplex Polymerase Chain Reaction for Detection of Gastrointestinal Pathogens in Migrant Workers in Qatar.

PubMed

Humphrey, John M; Ranbhise, Sanjay; Ibrahim, Emad; Al-Romaihi, Hamad E; Farag, Elmoubasher; Abu-Raddad, Laith J; Glesby, Marshall J

2016-12-07

The causes of infectious diarrhea among the migrant worker population in Qatar are not well understood. We conducted a prospective observational study to understand the demographic and clinical characteristics and infectious causes of diarrhea among migrant workers in Doha, Qatar. A total of 126 male workers presenting to the Qatar Red Crescent Worker's Health Center outpatient clinic or emergency department were studied over a 5-month period in 2015-2016. Epidemiologic surveys were administered to all subjects and the prevalence of 22 different stool pathogens was determined using multiplex polymerase chain reaction (PCR) (FilmArray ® Gastrointestinal PCR). A target pathogen was identified in 62.7% of subjects. Enteropathogenic Escherichia coli was the most prevalent pathogen and was detected in 24.6% of subjects, followed by Salmonella (22.2%), enteroaggregative E. coli (15.1%), Giardia lamblia (9.5%), and enterotoxigenic E. coli (8.7%). Multiple pathogens were identified in 49.3% of positive stool samples. In a multivariable analysis, the presence of a heart rate ≥ 90 (adjusted odds ratio [OR] = 3.7, 95% confidence interval [CI] = 1.4-10.0) and > 5 fecal leukocytes/high-power field (adjusted OR = 2.8, 95% CI = 1.2-7.0) were significant predictors of detecting an acute inflammatory pathogen by PCR. Use of multiplex PCR enabled the detection of gastrointestinal pathogens in a high proportion of cases, illustrating the utility of this diagnostic tool in epidemiologic studies of infectious diarrhea. © The American Society of Tropical Medicine and Hygiene.

Design and Construction of a Single-Tube, LATE-PCR, Multiplex Endpoint Assay with Lights-On/Lights-Off Probes for the Detection of Pathogens Associated with Sepsis

PubMed Central

Carver-Brown, Rachel K.; Reis, Arthur H.; Rice, Lisa M.; Czajka, John W.; Wangh, Lawrence J.

2012-01-01

Aims. The goal of this study was to construct a single tube molecular diagnostic multiplex assay for the detection of microbial pathogens commonly associated with septicemia, using LATE-PCR and Lights-On/Lights-Off probe technology. Methods and Results. The assay described here identified pathogens associated with sepsis by amplification and analysis of the 16S ribosomal DNA gene sequence for bacteria and specific gene sequences for fungi. A sequence from an unidentified gene in Lactococcus lactis subsp. cremoris served as a positive control for assay function. LATE-PCR was used to generate single-stranded amplicons that were then analyzed at endpoint over a wide temperature range in a specific fluorescent color. Each bacterial target was identified by its pattern of hybridization to Lights-On/Lights-Off probes derived from molecular beacons. Complex mixtures of targets were also detected. Conclusions. All microbial targets were identified in samples containing low starting copy numbers of pathogen genomic DNA, both as individual targets and in complex mixtures. Significance and Impact of the Study. This assay uses new technology to achieve an advance in the field of molecular diagnostics: a single-tube multiplex assay for identification of pathogens commonly associated with sepsis. PMID:23326668

Detection of Gastrointestinal Pathogens from Stool Samples on Hemoccult Cards by Multiplex PCR

PubMed Central

Schlenker, Nicklas; Bauer, Malkin; Helfrich, Kerstin; Mengele, Carolin; Löscher, Thomas; Nothdurft, Hans Dieter; Bretzel, Gisela; Beissner, Marcus

2017-01-01

Purpose. Up to 30% of international travelers are affected by travelers' diarrhea (TD). Reliable data on the etiology of TD is lacking. Sufficient laboratory capacity at travel destinations is often unavailable and transporting conventional stool samples to the home country is inconvenient. We evaluated the use of Hemoccult cards for stool sampling combined with a multiplex PCR for the detection of model viral, bacterial, and protozoal TD pathogens. Methods. Following the creation of serial dilutions for each model pathogen, last positive dilution steps (LPDs) and thereof calculated last positive sample concentrations (LPCs) were compared between conventional stool samples and card samples. Furthermore, card samples were tested after a prolonged time interval simulating storage during a travel duration of up to 6 weeks. Results. The LPDs/LPCs were comparable to testing of conventional stool samples. After storage on Hemoccult cards, the recovery rate was 97.6% for C. jejuni, 100% for E. histolytica, 97.6% for norovirus GI, and 100% for GII. Detection of expected pathogens was possible at weekly intervals up to 42 days. Conclusion. Stool samples on Hemoccult cards stored at room temperature can be used in combination with a multiplex PCR as a reliable tool for testing of TD pathogens. PMID:28408937

Rapid diagnosis of sepsis with TaqMan-Based multiplex real-time PCR.

PubMed

Liu, Chang-Feng; Shi, Xin-Ping; Chen, Yun; Jin, Ye; Zhang, Bing

2018-02-01

The survival rate of septic patients mainly depends on a rapid and reliable diagnosis. A rapid, broad range, specific and sensitive quantitative diagnostic test is the urgent need. Thus, we developed a TaqMan-Based Multiplex real-time PCR assays to identify bloodstream pathogens within a few hours. Primers and TaqMan probes were designed to be complementary to conserved regions in the 16S rDNA gene of different kinds of bacteria. To evaluate accurately, sensitively, and specifically, the known bacteria samples (Standard strains, whole blood samples) are determined by TaqMan-Based Multiplex real-time PCR. In addition, 30 blood samples taken from patients with clinical symptoms of sepsis were tested by TaqMan-Based Multiplex real-time PCR and blood culture. The mean frequency of positive for Multiplex real-time PCR was 96% at a concentration of 100 CFU/mL, and it was 100% at a concentration greater than 1000 CFU/mL. All the known blood samples and Standard strains were detected positively by TaqMan-Based Multiplex PCR, no PCR products were detected when DNAs from other bacterium were used in the multiplex assay. Among the 30 patients with clinical symptoms of sepsis, 18 patients were confirmed positive by Multiplex real-time PCR and seven patients were confirmed positive by blood culture. TaqMan-Based Multiplex real-time PCR assay with highly sensitivity, specificity and broad detection range, is a rapid and accurate method in the detection of bacterial pathogens of sepsis and should have a promising usage in the diagnosis of sepsis. © 2017 Wiley Periodicals, Inc.

Integrated detector array technology for infrared astronomy

NASA Technical Reports Server (NTRS)

Mccreight, c. R.; Goebel, J. H.; Mckelvey, M. E.; Stafford, P. S.; Lee, J. H.

1984-01-01

The status of laboratory and telescope tests of integrated infrared detector array technology for astronomical applications is described. The devices tested represent a number of extrinsic and intrinsic detector materials and various multiplexer designs. Infrared arrays have now been used in successful astronomical applications. These have shown that device sensitivities can be comparable to those of discrete detector systems and excellent astronomical imagery can be produced.

Multiplexing readout channels in proportional counters

NASA Technical Reports Server (NTRS)

Caristi, James

1991-01-01

Proportional counters are important instruments used in sensing hard x-rays. The possibility is described of doubling the number of readout channels in the detector without increasing the electronics needed to amplify channel signals. This suggests that it should be possible, conversely, to reduce the number of amplifiers, thereby reducing the weight and energy budget of the instrument. Various numerical multiplexing schemes are analyzed, and a computer program is presented that can reconstruct multiplexed channel outputs with very good accuracy.

Fiber optic wavelength division multiplexing: Principles and applications in telecommunications and spectroscopy

NASA Technical Reports Server (NTRS)

Erdmann, R. K.; Walton, B. D.

1988-01-01

Design and fabrication tradeoffs of wavelength division multiplexers are discussed and performance parameters are given. The same multiplexer construction based on prism gratings has been used in spectroscopic applications, in the wavelength region from 450 to 1600 nm. For shorter wavelengths down to 200 nm, a similar instrument based on longer fibers (500 to 1000 micrometer) has been constructed and tested with both a fiber array and a photodiode detector array at the output.

Global stability and optimal control of epidemic spreading on multiplex networks with nonlinear mutual interaction

NASA Astrophysics Data System (ADS)

Jia, Nan; Ding, Li; Liu, Yu-Jing; Hu, Ping

2018-07-01

In this paper, we consider two interacting pathogens spreading on multiplex networks. Each pathogen spreads only on its single layer, and different layers have the same individuals but different network topology. A state-dependent infectious rate is proposed to describe the nonlinear mutual interaction during the propagation of two pathogens. Then a novel epidemic spreading model incorporating treatment control strategy is established. We investigate the global asymptotic stability of the equilibrium points by using Dulac's criterion, Poincaré-Bendixson theorem and Lyapunov method. Furthermore, we discuss an optimal strategy to minimize the total number of the infected individuals and the cost associated with treatment control for both spreading of two pathogens. Finally, numerical simulations are presented to show the validity and efficiency of our results.

Multiplex Molecular Panels for Diagnosis of Gastrointestinal Infection: Performance, Result Interpretation, and Cost-Effectiveness.

PubMed

Binnicker, Matthew J

2015-12-01

Gastrointestinal disease is a major cause of morbidity and mortality worldwide, especially among young children and immunocompromised patients. Diarrhea may result from infection with a variety of microbial pathogens, including bacteria, viruses, or parasites. Historically, the diagnosis of infectious diarrhea has been made using microscopy, antigen tests, culture, and real-time PCR. A combination of these traditional tests is often required due to the inability to distinguish between infectious etiologies based on the clinical presentation alone. Recently, several multiplex molecular assays have been developed for the detection of gastrointestinal pathogens directly from clinical stool samples. These panels allow for the detection and identification of up to 20 pathogens in as little as 1 h. This review will focus on the multiplex molecular panels that have received clearance from the FDA for the diagnosis of diarrheal disease and will highlight issues related to test performance, result interpretation, and cost-effectiveness of these new molecular diagnostic tools.

A novel multiplex PCR assay for simultaneous detection of nine clinically significant bacterial pathogens associated with bovine mastitis.

PubMed

Ashraf, Aqeela; Imran, Muhammad; Yaqub, Tahir; Tayyab, Muhammad; Shehzad, Wasim; Thomson, Peter C

2017-06-01

For rapid and simultaneous detection of nine bovine mastitic pathogens, a sensitive and specific multiplex PCR assay was developed. The assay was standardized using reference strains and validated on mastitic milk cultures which were identified to species level based on 16S rRNA sequencing. Multiplex PCR assay also efficiently detected the target bacterial strains directly from milk. The detection limit of the assay was up to 50 pg for DNA isolated from pure cultures and 10 4  CFU/ml for spiked milk samples. As estimated by latent class analysis, the assay was sensitive up to 88% and specific up to 98% for targeted mastitic pathogens, compared with the bacterial culture method and the 16S rRNA sequence analysis. This novel molecular assay could be useful for monitoring and maintaining the bovine udder health, ensuring the bacteriological safety of milk, and conducting epidemiological studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multiplex quantification of Escherichia coli, Salmonella typhi and Vibrio cholera with three DNA targets in single reaction assay.

PubMed

Jangampalli Adi, Pradeepkiran; Naidu, Jagadish R; Matcha, Bhaskar

2017-09-01

Escherichia coli (E. coli), Salmonella typhi and Vibrio cholera harmful pathogens, which causes various diseases in humans. Rapid diagnosis of bacterial infection is an important for patient management and appropriate therapy during the early phase of the bacterial infected diseases. Among the existing techniques for identifying pathogens were less sensitive and time-consuming processes. In the present study total, 48 clinical 31 blood and 17 urine samples of patients suspected with the infections were collected from SVRR Hospital and used to detect the pathogens. Multiplex polymerase chain reaction (PCR) assay was set to design for the identification of Escherichia coli, Salmonella typhi and Vibrio cholera from the different clinical samples. Rapid diagnosis of Escherichia coli (E. coli), Salmonella and Vibrio cholera pathogens can be done with simultaneously in a single multiplex PCR assay by using specific primers with adjusted PCR conditions. Through this approach, the results represented with out of 31 blood samples 1-15 shows the positive with E. coli and remaining 14 only 11 were correlated with multiplex results of Vibrio cholera, remaining the urine samples all are positive with 17 samples correlate with the Salmonella typhi. Through the high specificity benefits of excellent sensitivity, with high resolution and reproducibility. This method of results proved and illustrates the best potential system for diagnosing the infectious disease with modern trendy. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multiplex identification of sepsis-causing Gram-negative pathogens from the plasma of infected blood.

PubMed

Chung, Boram; Park, Chulmin; Cho, Sung-Yeon; Shin, Juyoun; Shin, Sun; Yim, Seon-Hee; Lee, Dong-Gun; Chung, Yeun-Jung

2018-02-01

Early and accurate detection of bacterial pathogens in the blood is the most crucial step for sepsis management. Gram-negative bacteria are the most common organisms causing severe sepsis and responsible for high morbidity and mortality. We aimed to develop a method for rapid multiplex identification of clinically important Gram-negative pathogens and also validated whether our system can identify Gram-negative pathogens with the cell-free plasm DNA from infected blood. We designed five MLPA probe sets targeting the genes specific to major Gram-negative pathogens (uidA and lacY for E. coli, ompA for A. baumannii, phoE for K. pneumoniae, and ecfX for P. aeruginosa) and one set targeting the CTX-M group 1 to identify the ESBL producing Gram-negative pathogens. All six target-specific peaks were clearly separated without any non-specific peaks in a multiplex reaction condition. The minimum detection limit was 100 fg of pathogen DNA. When we tested 28 Gram-negative clinical isolates, all of them were successfully identified without any non-specific peaks. To evaluate the clinical applicability, we tested seven blood samples from febrile patients. Three blood culture positive cases showed E. coli specific peaks, while no peak was detected in the other four culture negative samples. This technology can be useful for detection of major sepsis-causing, drug-resistant Gram-negative pathogens and also the major ESBL producing Gram-negatives from the blood of sepsis patients in a clinical setting. This system can help early initiation of effective antimicrobial treatment against Gram-negative pathogens for sepsis patients, which is very crucial for better treatment outcomes. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Engineered nanoconstructs for the multiplexed and sensitive detection of high-risk pathogens

NASA Astrophysics Data System (ADS)

Seo, Youngmin; Kim, Ji-Eun; Jeong, Yoon; Lee, Kwan Hong; Hwang, Jangsun; Hong, Jongwook; Park, Hansoo; Choi, Jonghoon

2016-01-01

Many countries categorize the causative agents of severe infectious diseases as high-risk pathogens. Given their extreme infectivity and potential to be used as biological weapons, a rapid and sensitive method for detection of high-risk pathogens (e.g., Bacillus anthracis, Francisella tularensis, Yersinia pestis, and Vaccinia virus) is highly desirable. Here, we report the construction of a novel detection platform comprising two units: (1) magnetic beads separately conjugated with multiple capturing antibodies against four different high-risk pathogens for simple and rapid isolation, and (2) genetically engineered apoferritin nanoparticles conjugated with multiple quantum dots and detection antibodies against four different high-risk pathogens for signal amplification. For each high-risk pathogen, we demonstrated at least 10-fold increase in sensitivity compared to traditional lateral flow devices that utilize enzyme-based detection methods. Multiplexed detection of high-risk pathogens in a sample was also successful by using the nanoconstructs harboring the dye molecules with fluorescence at different wavelengths. We ultimately envision the use of this novel nanoprobe detection platform in future applications that require highly sensitive on-site detection of high-risk pathogens.

Simultaneous Detection of 13 Key Bacterial Respiratory Pathogens by Combination of Multiplex PCR and Capillary Electrophoresis.

PubMed

Jiang, Lu Xi; Ren, Hong Yu; Zhou, Hai Jian; Zhao, Si Hong; Hou, Bo Yan; Yan, Jian Ping; Qin, Tian; Chen, Yu

2017-08-01

Lower respiratory tract infections continue to pose a significant threat to human health. It is important to accurately and rapidly detect respiratory bacteria. To compensate for the limits of current respiratory bacteria detection methods, we developed a combination of multiplex polymerase chain reaction (PCR) and capillary electrophoresis (MPCE) assay to detect thirteen bacterial pathogens responsible for lower respiratory tract infections, including Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Mycoplasma pneumoniae, Legionella spp., Bordetella pertussis, Mycobacterium tuberculosis complex, Corynebacterium diphtheriae, and Streptococcus pyogenes. Three multiplex PCR reactions were built, and the products were analyzed by capillary electrophoresis using the high-throughput DNA analyzer. The specificity of the MPCE assay was examined and the detection limit was evaluated using DNA samples from each bacterial strain and the simulative samples of each strain. This assay was further evaluated using 152 clinical specimens and compared with real-time PCR reactions. For this assay, three nested-multiplex-PCRs were used to detect these clinical specimens. The detection limits of the MPCE assay for the 13 pathogens were very low and ranged from 10-7 to 10-2 ng/μL. Furthermore, analysis of the 152 clinical specimens yielded a specificity ranging from 96.5%-100.0%, and a sensitivity of 100.0% for the 13 pathogens. This study revealed that the MPCE assay is a rapid, reliable, and high-throughput method with high specificity and sensitivity. This assay has great potential in the molecular epidemiological survey of respiratory pathogens. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Multimode fiber optic wavelength division multiplexing

NASA Technical Reports Server (NTRS)

Spencer, J. L.

1982-01-01

Optical wavelength division multiplexing (WDM) systems, with signals transmitted on different wavelengths through a single optical fiber, can have increased bandwidth and fault isolation properties over single wavelength optical systems. Two WDM system designs that might be used with multimode fibers are considered and a general description of the components which could be used to implement the system are given. The components described are sources, multiplexers, demultiplexers, and detectors. Emphasis is given to the demultiplexer technique which is the major developmental component in the WDM system.

Reduced γ-γ time walk to below 50 ps using the multiplexed-start and multiplexed-stop fast-timing technique with LaBr3(Ce) detectors

NASA Astrophysics Data System (ADS)

Régis, J.-M.; Saed-Samii, N.; Rudigier, M.; Ansari, S.; Dannhoff, M.; Esmaylzadeh, A.; Fransen, C.; Gerst, R.-B.; Jolie, J.; Karayonchev, V.; Müller-Gatermann, C.; Stegemann, S.

2016-07-01

The electronic γ-γ fast-timing technique using arrays consisting of many LaBr3(Ce) detectors is a powerful method to determine lifetimes of nuclear excited states with a lower limit of about 5 ps. This method requires the determination of the energy-dependent time walk of the zero time which is represented by the centroid of a prompt γ-γ time distribution. The full-energy peak versus full-energy peak prompt response difference which represents the linearly combined mean γ-γ time walk of a fast-timing array consisting of 8 LaBr3(Ce) detectors was measured using a standard 152Eu γ-ray source for the energy region of 40-1408 keV. The data were acquired using a "multiplexed-start and multiplexed-stop" analogue electronics circuitry and analysed by employing the generalized centroid difference method. Concerning the cylindrical 1.5 in.×1.5 in. LaBr3(Ce) crystals which are coupled to the Hamamatsu R9779 photomultiplier tubes, the best fast-timing array time resolution of 202(3) ps is obtained for the two prompt γ lines of 60Co by using the leading-edge timing principle. When using the zero-crossover timing principle the time resolution is degraded by up to 30%, dependent on the energy and the shaping delay time of the constant fraction discriminator model Ortec 935. The smallest γ-γ time walk to below 50 ps is obtained by using a shaping delay time of about 17 ns and an optimum "time-walk adjustment" needed for detector output pulses with amplitudes smaller than 400 mV.

Simultaneous Detection of Four Foodborne Viruses in Food Samples Using a One-Step Multiplex Reverse Transcription PCR.

PubMed

Lee, Shin-Young; Kim, Mi-Ju; Kim, Hyun-Joong; Jeong, KwangCheol Casey; Kim, Hae-Yeong

2018-02-28

A one-step multiplex reverse transcription PCR (RT-PCR) method comprising six primer sets (for the detection of norovirus GI and GII, hepatitis A virus, rotavirus, and astrovirus) was developed to simultaneously detect four kinds of pathogenic viruses. The size of the PCR products for norovirus GI and GII, hepatitis A virus (VP3/VP1 and P2A regions), rotavirus, and astrovirus were 330, 164, 244, 198, 629, and 449 bp, respectively. The RT-PCR with the six primer sets showed specificity for the pathogenic viruses. The detection limit of the developed multiplex RT-PCR, as evaluated using serially diluted viral RNAs, was comparable to that of one-step single RT-PCR. Moreover, this multiplex RT-PCR was evaluated using food samples such as water, oysters, lettuce, and vegetable product. These food samples were artificially spiked with the four kinds of viruses in diverse combinations, and the spiked viruses in all food samples were detected successfully.

Molecular serotyping, virulence gene profiling and pathogenicity of Streptococcus agalactiae isolated from tilapia farms in Thailand by multiplex PCR.

PubMed

Kannika, K; Pisuttharachai, D; Srisapoome, P; Wongtavatchai, J; Kondo, H; Hirono, I; Unajak, S; Areechon, N

2017-06-01

This study aimed to biotype Streptococcus agalactiae isolated from tilapia farms in Thailand based on molecular biotyping methods and to determine the correlation between the serotype and virulence of bacteria. In addition to a biotyping (serotyping) technique based on multiplex PCR of cps genes, in this study, we developed multiplex PCR typing of Group B streptococcus (GBS) virulence genes to examine three clusters of virulence genes and their correlation with the pathogenicity of S. agalactiae. The epidemiology of S. agalactiae in Thailand was analysed to provide bacterial genetic information towards a future rational vaccine strategy for tilapia culture systems. Streptococcus agalactiae were isolated from diseased tilapia from different areas of Thailand. A total of 124 S. agalactiae isolates were identified by phenotypic analysis and confirmed by 16S rRNA PCR. Bacterial genotyping was conducted based on (i) molecular serotyping of the capsular polysaccharide (cps) gene cluster and (ii) virulence gene profiling using multiplex PCR analysis of 14 virulence genes (lmb, scpB, pavA, cspA, spb1, cyl, bca, rib, fbsA, fbsB, cfb, hylB, bac and pbp1A/ponA). Only serotypes Ia and III were found in this study; serotype Ia lacks the lmb, scpB and spb1 genes, whereas serotype III lacks only the bac gene. Virulence tests in juvenile Nile tilapia demonstrated a correlation between the pathogenicity of the bacteria and their virulence gene profile, with serotype III showing higher virulence than serotype Ia. Epidemiological analysis showed an almost equal distribution in all regions of Thailand, except serotype III was found predominantly in the southern areas. Only two serotypes of S. agalactiae were isolated from diseased tilapia in Thailand. Serotype Ia showed fewer virulence genes and lower virulence than serotype III. Both serotypes showed a similar distribution throughout Thailand. We identified two major serotypes of S. agalactiae isolates associated with the outbreak in tilapia culture in Thailand. We developed multiplex PCR assays for 14 virulence genes, which may be used to predict the pathogenicity of the isolates and track future infections. Multiplex PCR typing of the GBS virulence genes was developed and might be further used to predict the pathogenicity of S. agalactiae. © 2017 The Society for Applied Microbiology.

Two-wavelength quadrature multipoint detection of partial discharge in power transformers using fiber Fabry-Perot acoustic sensors

NASA Astrophysics Data System (ADS)

Dong, Bo; Han, Ming; Wang, Anbo

2012-06-01

A reliable and low-cost two-wavelength quadrature interrogating method has been developed to demodulate optical signals from diaphragm-based Fabry-Perot interferometric fiber optic sensors for multipoint partial discharge detection in power transformers. Commercial available fused-silica parts (a wafer, a fiber ferrule, and a mating sleeve) and a cleaved optical single mode fiber were bonded together to form an extrinsic Fabry-Perot acoustic sensor. Two lasers with center wavelengths separated by a quarter of the period of sensor interference fringes were used to probe acousticwave- induced diaphragm vibration. A coarse wavelength-division multiplexing (CWDM) add/drop multiplexer was used to separate the reflected two wavelengths before two photo detectors. Optical couplers were used to distribute mixed laser light to each sensor-detector module for multiplexing purpose. Sensor structure, detection system design and experiment results are presented.

Capsular typing of Streptococcus agalactiae (Lancefield group B streptococci) from fish using multiplex PCR and serotyping

USDA-ARS?s Scientific Manuscript database

Streptococcus spp. including Streptococcus agalactiae (Lancefield group B streptococci) are considered emerging pathogens responsible for approximately $1 billion USD in annual losses to the global tilapia (Oreochromis sp.) aquaculture industry. This study evaluated a published multiplex PCR capsul...

One-Step Multiplex RT-qPCR Assay for the Detection of Peste des petits ruminants virus, Capripoxvirus, Pasteurella multocida and Mycoplasma capricolum subspecies (ssp.) capripneumoniae.

PubMed

Settypalli, Tirumala Bharani Kumar; Lamien, Charles Euloge; Spergser, Joachim; Lelenta, Mamadou; Wade, Abel; Gelaye, Esayas; Loitsch, Angelika; Minoungou, Germaine; Thiaucourt, Francois; Diallo, Adama

2016-01-01

Respiratory infections, although showing common clinical symptoms like pneumonia, are caused by bacterial, viral or parasitic agents. These are often reported in sheep and goats populations and cause huge economic losses to the animal owners in developing countries. Detection of these diseases is routinely done using ELISA or microbiological methods which are being reinforced or replaced by molecular based detection methods including multiplex assays, where detection of different pathogens is carried out in a single reaction. In the present study, a one-step multiplex RT-qPCR assay was developed for simultaneous detection of Capripoxvirus (CaPV), Peste de petits ruminants virus (PPRV), Pasteurella multocida (PM) and Mycoplasma capricolum ssp. capripneumonia (Mccp) in pathological samples collected from small ruminants with respiratory disease symptoms. The test performed efficiently without any cross-amplification. The multiplex PCR efficiency was 98.31%, 95.48%, 102.77% and 91.46% whereas the singleplex efficiency was 93.43%, 98.82%, 102.55% and 92.0% for CaPV, PPRV, PM and Mccp, respectively. The correlation coefficient was greater than 0.99 for all the targets in both multiplex and singleplex. Based on cycle threshold values, intra and inter assay variability, ranged between the limits of 2%-4%, except for lower concentrations of Mccp. The detection limits at 95% confidence interval (CI) were 12, 163, 13 and 23 copies/reaction for CaPV, PPRV, PM and Mccp, respectively. The multiplex assay was able to detect CaPVs from all genotypes, PPRV from the four lineages, PM and Mccp without amplifying the other subspecies of mycoplasmas. The discriminating power of the assay was proven by accurate detection of the targeted pathogen (s) by screening 58 viral and bacterial isolates representing all four targeted pathogens. Furthermore, by screening 81 pathological samples collected from small ruminants showing respiratory disease symptoms, CaPV was detected in 17 samples, PPRV in 45, and PM in six samples. In addition, three samples showed a co-infection of PPRV and PM. Overall, the one-step multiplex RT-qPCR assay developed will be a valuable tool for rapid detection of individual and co-infections of the targeted pathogens with high specificity and sensitivity.

Backshort-Under-Grid arrays for infrared astronomy

NASA Astrophysics Data System (ADS)

Allen, C. A.; Benford, D. J.; Chervenak, J. A.; Chuss, D. T.; Miller, T. M.; Moseley, S. H.; Staguhn, J. G.; Wollack, E. J.

2006-04-01

We are developing a kilopixel, filled bolometer array for space infrared astronomy. The array consists of three individual components, to be merged into a single, working unit; (1) a transition edge sensor bolometer array, operating in the milliKelvin regime, (2) a quarter-wave backshort grid, and (3) superconducting quantum interference device multiplexer readout. The detector array is designed as a filled, square grid of suspended, silicon bolometers with superconducting sensors. The backshort arrays are fabricated separately and will be positioned in the cavities created behind each detector during fabrication. The grids have a unique interlocking feature machined into the walls for positioning and mechanical stability. The spacing of the backshort beneath the detector grid can be set from ˜30 300 μm, by independently adjusting two process parameters during fabrication. The ultimate goal is to develop a large-format array architecture with background-limited sensitivity, suitable for a wide range of wavelengths and applications, to be directly bump bonded to a multiplexer circuit. We have produced prototype two-dimensional arrays having 8×8 detector elements. We present detector design, fabrication overview, and assembly technologies.

Iterative color-multiplexed, electro-optical processor.

PubMed

Psaltis, D; Casasent, D; Carlotto, M

1979-11-01

A noncoherent optical vector-matrix multiplier using a linear LED source array and a linear P-I-N photodiode detector array has been combined with a 1-D adder in a feedback loop. The resultant iterative optical processor and its use in solving simultaneous linear equations are described. Operation on complex data is provided by a novel color-multiplexing system.

Frequency Domain Multiplexing for Use With NaI[Tl] Detectors

NASA Astrophysics Data System (ADS)

Belling, Samuel; Coherent Collaboration

2017-09-01

A process used in many forms of signal communication known as multiplexing is adapted for the purpose of combining signals from NaI[Tl] detectors so that fewer digitizer channels can be used to process the signal information from large experiments within the COHERENT collaboration. Each signal is passed through a ringing circuit to modulate it with a characteristic frequency. Information about the signal can be extracted from its amplitude, frequency, and phase. Simulations in LTSpice show that an operational amplifier circuit with a parallel LRC feedback loop can serve as the modulating circuit. Several such circuits can be constructed and housed compactly in a unit, and fed to an inverting, summing amplifier with tunable gain, such that the signals are carried by one cable. The signals are analyzed based on a Fourier transform after being digitized. The results show that the energy, channel, and time of the original interaction can be recovered by this process. In some cases it is possible through filtering and deconvolution to recover the shape of the original signal. The effort is ongoing, but with the design presented it is possible to multiplex 10 detectors into a single digitizer channel. NSF REU Program at Duke University.

Toward Large FOV High-Resolution X-Ray Imaging Spectrometer: Microwave Multiplexed Readout of 32 TES Microcalorimeters

NASA Technical Reports Server (NTRS)

Yoon, Wonsik; Adams, Joseph S.; Bandler, Simon R.; Chervenak, James A.; Datesman, Aaron M.; Eckart, Megan E.; Finkbeiner, Fred M.; Kelley, Richard L.; Kilbourne, Caroline A.; Miniussi, Antoine R.;

Clinical Relevance of Pathogens Detected by Multiplex PCR in Blood of Very-Low-Birth Weight Infants with Suspected Sepsis - Multicentre Study of the German Neonatal Network.

PubMed

Tröger, Birte; Härtel, Christoph; Buer, Jan; Dördelmann, Michael; Felderhoff-Müser, Ursula; Höhn, Thomas; Hepping, Nico; Hillebrand, Georg; Kribs, Angela; Marissen, Janina; Olbertz, Dirk; Rath, Peter-Michael; Schmidtke, Susanne; Siegel, Jens; Herting, Egbert; Göpel, Wolfgang; Steinmann, Joerg; Stein, Anja

2016-01-01

In the German Neonatal Network (GNN) 10% of very-low-birth weight infants (VLBWI) suffer from blood-culture confirmed sepsis, while 30% of VLBWI develop clinical sepsis. Diagnosis of sepsis is a difficult task leading to potential over-treatment with antibiotics. This study aims to investigate whether the results of blood multiplex-PCR (SeptiFast®) for common sepsis pathogens are relevant for clinical decision making when sepsis is suspected in VLBWI. We performed a prospective, multi-centre study within the GNN including 133 VLBWI with 214 episodes of suspected late onset sepsis (LOS). In patients with suspected sepsis a multiplex-PCR (LightCycler SeptiFast MGRADE-test®) was performed from 100 μl EDTA blood in addition to center-specific laboratory biomarkers. The attending neonatologist documented whether the PCR-result, which was available after 24 to 48 hrs, had an impact on the choice of antibiotic drugs and duration of therapy. PCR was positive in 110/214 episodes (51%) and blood culture (BC) was positive in 55 episodes (26%). Both methods yielded predominantly coagulase-negative staphylococci (CoNS) followed by Escherichia coli and Staphylococcus aureus. In 214 BC-PCR paired samples concordant results were documented in 126 episodes (59%; n = 32 were concordant pathogen positive results, n = 94 were negative in both methods). In 65 episodes (30%) we found positive PCR results but negative BCs, with CoNS being identified in 43 (66%) of these samples. Multiplex-PCR results influenced clinical decision making in 30% of episodes, specifically in 18% for the choice of antimicrobial therapy and in 22% for the duration of antimicrobial therapy. Multiplex-PCR results had a moderate impact on clinical management in about one third of LOS-episodes. The main advantage of multiplex-PCR was the rapid detection of pathogens from micro-volume blood samples. In VLBWI limitations include risk of contamination, lack of resistance testing and high costs. The high rate of positive PCR results in episodes of negative BC might lead to overtreatment of infants which is associated with risk of mortality, antibiotic resistance, fungal sepsis and NEC.

Horn-coupled, commercially-fabricated aluminum lumped-element kinetic inductance detectors for millimeter wavelengths

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

McCarrick, H., E-mail: hlm2124@columbia.edu; Flanigan, D.; Jones, G.

We discuss the design, fabrication, and testing of prototype horn-coupled, lumped-element kinetic inductance detectors (LEKIDs) designed for cosmic microwave background studies. The LEKIDs are made from a thin aluminum film deposited on a silicon wafer and patterned using standard photolithographic techniques at STAR Cryoelectronics, a commercial device foundry. We fabricated 20-element arrays, optimized for a spectral band centered on 150 GHz, to test the sensitivity and yield of the devices as well as the multiplexing scheme. We characterized the detectors in two configurations. First, the detectors were tested in a dark environment with the horn apertures covered, and second, themore » horn apertures were pointed towards a beam-filling cryogenic blackbody load. These tests show that the multiplexing scheme is robust and scalable, the yield across multiple LEKID arrays is 91%, and the measured noise-equivalent temperatures for a 4 K optical load are in the range 26±6 μK√(s)« less

Multiplex and label-free screening of foodborne pathogens using surface plasmon resonance imaging

USDA-ARS?s Scientific Manuscript database

In order to protect outbreaks caused by foodborne pathogens, more rapid and efficient methods are needed for pathogen screening from food samples. Surface plasmon resonance imaging (SPRi) is an emerging optical technique, which allows for label-free screening of multiple targets simultaneously with ...

A multiplexed reverse transcriptase PCR assay for identification of viral respiratory pathogens at point-of-care

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

Letant, S E; .Ortiz, J I; Tammero, L

2007-04-11

We have developed a nucleic acid-based assay that is rapid, sensitive, specific, and can be used for the simultaneous detection of 5 common human respiratory pathogens including influenza A, influenza B, parainfluenza type 1 and 3, respiratory syncytial virus, and adenovirus group B, C, and E. Typically, diagnosis on an un-extracted clinical sample can be provided in less than 3 hours, including sample collection, preparation, and processing, as well as data analysis. Such a multiplexed panel would enable rapid broad-spectrum pathogen testing on nasal swabs, and therefore allow implementation of infection control measures, and timely administration of antiviral therapies. Thismore » article presents a summary of the assay performance in terms of sensitivity and specificity. Limits of detection are provided for each targeted respiratory pathogen, and result comparisons are performed on clinical samples, our goal being to compare the sensitivity and specificity of the multiplexed assay to the combination of immunofluorescence and shell vial culture currently implemented at the UCDMC hospital. Overall, the use of the multiplexed RT-PCR assay reduced the rate of false negatives by 4% and reduced the rate of false positives by up to 10%. The assay correctly identified 99.3% of the clinical negatives, 97% of adenovirus, 95% of RSV, 92% of influenza B, and 77% of influenza A without any extraction performed on the clinical samples. The data also showed that extraction will be needed for parainfluenza virus, which was only identified correctly 24% of the time on un-extracted samples.« less

A multiplex PCR assay for simultaneous detection of Escherichia coli O157:H7, Bacillus cereus, Vibrio parahaemolyticus, Salmonella spp., Listeria monocytogenes, and Staphylococcus aureus in Korean ready-to-eat food.

PubMed

Lee, Nari; Kwon, Kyung Yoon; Oh, Su Kyung; Chang, Hyun-Joo; Chun, Hyang Sook; Choi, Sung-Wook

2014-07-01

A multiplex polymerase chain reaction (PCR) assay was developed for simultaneous detection of Escherichia coli O157:H7, Bacillus cereus, Vibrio parahaemolyticus, Salmonella spp., Listeria monocytogenes, and Staphylococcus aureus in various Korean ready-to-eat foods. The six specific primer pairs for multiplex PCR were selected based on the O157 antigen (rfbE) gene of E. coli O157:H7, the DNA gyrase subunit B (gyrB) gene of B. cereus, the toxin regulatory protein (toxR) gene of V. parahaemolyticus, the invasion protein A (invA) gene of Salmonella spp., the hemolysin (hly) gene of L. monocytogenes, and the thermonuclease (nuc) gene of S. aureus. The 16S rRNA gene was targeted as an internal control gene in the presence of bacterial DNA. The specificity and sensitivity assays for multiplex primer pairs were investigated by testing different strains. When this multiplex PCR assay was applied to evaluate the validity of detecting six foodborne pathogens in artificially inoculated several ready-to-eat food samples, the assay was able to specifically simultaneously detect as few as 1 colony-forming unit/mL of each pathogen after enrichment for 12 h. Their presence in naturally contaminated samples also indicates that the developed multiplex PCR assay is an effective and informative supplement for practical use.

A SIMPLE AND EFFECTIVE MULTIPLEX PCR TECHNIQUE FOR DETECTING HUMAN PATHOGENIC TAENIA EGGS IN HOUSEFLIES.

PubMed

Pornruseetriratn, Siritavee; Maipanich, Wanna; Sa-nguankiat, Surapol; Pubampen, Somchit; Poodeepiyasawat, Akkarin; Thaenkham, Urusa

2017-01-01

Taenia solium, T. saginata, and T. asiatica are cestode pathogens causing taeniasis in humans. Houseflies can transfer Taenia eggs to food. However, houseflies are thought to carry only small numbers of Taenia eggs, sometimes fewer than 10. Although several PCR-based methods have been developed to detect Taenia DNA, these require more than 10 eggs for adequate detection. We developed a multiplex PCR method with high specificity for the discrimination among the eggs of the three Taenia species, T. solium, T. saginata, and T. asiatica, using 18S ribosomal DNA (rDNA) as a genetic marker. This technique was found to be highly sensitive, capable of identifying the Taenia species from only one egg. This multiplex PCR technique using 18S rDNA specific primers should be suitable to diagnose Taenia eggs.

State-of-the-art survey of multimode fiber optic wavelength division multiplexing

NASA Astrophysics Data System (ADS)

Spencer, J. L.

1983-05-01

Optical wavelength division multiplexing (WDM) systems, with signals transmitted on different wavelengths through a single fiber, can have increased information capacity and fault isolation properties over single wavelength optical systems. This paper describes a typical WDM system. Also, a state-of-the-art survey of optical multimode components which could be used to implement the system is made. The components to be surveyed are sources, multiplexers, and detectors. Emphasis is given to the demultiplexer techniques which are the major development components in the WDM system.

Integrated multiplexed capillary electrophoresis system

DOEpatents

Yeung, Edward S.; Tan, Hongdong

2002-05-14

The present invention provides an integrated multiplexed capillary electrophoresis system for the analysis of sample analytes. The system integrates and automates multiple components, such as chromatographic columns and separation capillaries, and further provides a detector for the detection of analytes eluting from the separation capillaries. The system employs multiplexed freeze/thaw valves to manage fluid flow and sample movement. The system is computer controlled and is capable of processing samples through reaction, purification, denaturation, pre-concentration, injection, separation and detection in parallel fashion. Methods employing the system of the invention are also provided.

Combination of microbiological culture and multiplex PCR increases the range of vaginal microorganisms identified in cervical cancer patients at high risk for bacterial vaginosis and vaginitis.

PubMed

Schmidt, Katarzyna; Cybulski, Zefiryn; Roszak, Andrzej; Grabiec, Alicja; Talaga, Zofia; Urbański, Bartosz; Odważna, Joanna; Wojciechowicz, Jacek

2015-05-01

Bacterial vaginosis (BV) and vaginitis in cervical cancer patients might becaused by mixed aerobic, anaerobic, and atypical bacteria. Since genital tract infections can be complicated, early and accurate identification of causal pathogens is vital. The purpose of this study was i) to determinate if currently used aerobic culture methods are sufficiently sensitive to identify pathogens that can appear in the cervix of women after cancer treatment; ii) to investigate if molecular methods can improve the diagnostic process of BV and vaginitis, as well as broaden the range of detectable pathogens that would otherwise be difficult to cultivate. A one-year hospital-based study was conducted in 2011/2012. Cervical swabs from 130 patients were examined by microbiological culture and multiplex PCR. Swab samples were positive for 107 and 93 women by microbiological culture and multiplex PCR, respectively The most common bacteria isolated from culture were: Escherichia coli, Enterococcus faecalis, Streptococcus agalactiae, and Staphylococcus aureus, and using the molecular technique were: Gardnerella vaginalis, Bacteroides fragilis, Ureoplasma ureoliticum/parvum, Mobiluncus curtisii and Atopobium vaginae. Multiplex PCR might contribute to the diagnosis of genital tract infections and it broadens the number of detectable microorganisms responsible for BV. Combination of these two methods may become the basis for standardized diagnosis of BV and vaginitis.

Phage-protease-peptide: a novel trifecta enabling multiplex detection of viable bacterial pathogens.

PubMed

Alcaine, S D; Tilton, L; Serrano, M A C; Wang, M; Vachet, R W; Nugen, S R

2015-10-01

Bacteriophages represent rapid, readily targeted, and easily produced molecular probes for the detection of bacterial pathogens. Molecular biology techniques have allowed researchers to make significant advances in the bioengineering of bacteriophage to further improve speed and sensitivity of detection. Despite their host specificity, bacteriophages have not been meaningfully leveraged in multiplex detection of bacterial pathogens. We propose a proof-of-principal phage-based scheme to enable multiplex detection. Our scheme involves bioengineering bacteriophage to carry a gene for a specific protease, which is expressed during infection of the target cell. Upon lysis, the protease is released to cleave a reporter peptide, and the signal detected. Here we demonstrate the successful (i) modification of T7 bacteriophage to carry tobacco etch virus (TEV) protease; (ii) expression of TEV protease by Escherichia coli following infection by our modified T7, an average of 2000 units of protease per phage are produced during infection; and (iii) proof-of-principle detection of E. coli in 3 h after a primary enrichment via TEV protease activity using a fluorescent peptide and using a designed target peptide for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (MALDI-TOF MS) analysis. This proof-of-principle can be translated to other phage-protease-peptide combinations to enable multiplex bacterial detection and readily adopted on multiple platforms, like MALDI-TOF MS or fluorescent readers, commonly found in labs.

Indium Hybridization of Large Format TES Bolometer Arrays to Readout Multiplexers for Far-Infrared Astronomy

NASA Technical Reports Server (NTRS)

Miller, Timothy M.; Costen, Nick; Allen, Christine

2007-01-01

The advance of new detector technologies combined with enhanced fabrication methods has resulted in an increase in development of large format arrays. The next generation of scientific instruments will utilize detectors containing hundreds to thousands of elements providing a more efficient means to conduct large area sky surveys. Some notable detectors include a 32x32 x-ray microcalorimeter for Constellation-X, an infrared bolometer called SAFIRE to fly on the airborne observatory SOFIA, and the sub-millimeter bolometer SCUBA-2 to be deployed at the JCMT which will use more than 10,000 elements for two colors, each color using four 32x40 arrays. Of these detectors, SCUBA-2 is farthest along in development and uses indium hybridization to multiplexers for readout of the large number of elements, a technology that will be required to enable the next generation of large format arrays. Our current efforts in working toward large format arrays have produced GISMO, the Goddard IRAM Superconducting 2-Millimeter observer. GISMO is a far infrared instrument to be field tested later this year at the IRAM 30 meter telescope in Spain. GISMO utilizes transition edge sensor (TES) technology in an 8x16 filled array format that allows for typical fan-out wiring and wire-bonding to four 1x32 NIST multiplexers. GISMO'S electrical wiring is routed along the tops of 30 micron walls which also serve as the mechanical framework for the array. This architecture works well for the 128 element array, but is approaching the limit for routing the necessary wires along the surface while maintaining a high fill factor. Larger format arrays will benefit greatly from making electrical connections through the wafer to the backside, where they can be hybridized to a read-out substrate tailored to handling the wiring scheme. The next generation array we are developing is a 32x40 element array on a pitch of 1135 microns that conforms to the NIST multiplexer, already developed for the SCUBA-2 instrument This architecture will utilize electrical connections that route from the TES to the support frame and through the wafer. The detector chip will then be hybridized to the NIST multiplexer via indium bump bonding. In our development scheme we are using substrates that allow for diagnostic testing of electrical continuity across the entire array and we are testing our process to minimize or eliminate any contact resistance at metal interfaces. Our goal is hybridizing a fully functional 32x40 array of TES bolometers to a NIST multiplexer. The following work presents our current progress toward enabling this technology.

Optimising the multiplex factor of the frequency domain multiplexed readout of the TES-based microcalorimeter imaging array for the X-IFU instrument on the Athena x-ray observatory

NASA Astrophysics Data System (ADS)

van der Kuur, J.; Gottardi, L. G.; Akamatsu, H.; van Leeuwen, B. J.; den Hartog, R.; Haas, D.; Kiviranta, M.; Jackson, B. J.

2016-07-01

Athena is a space-based X-ray observatory intended for exploration of the hot and energetic universe. One of the science instruments on Athena will be the X-ray Integrated Field Unit (X-IFU), which is a cryogenic X-ray spectrometer, based on a large cryogenic imaging array of Transition Edge Sensors (TES) based microcalorimeters operating at a temperature of 100mK. The imaging array consists of 3800 pixels providing 2.5 eV spectral resolution, and covers a field of view with a diameter of of 5 arc minutes. Multiplexed readout of the cryogenic microcalorimeter array is essential to comply with the cooling power and complexity constraints on a space craft. Frequency domain multiplexing has been under development for the readout of TES-based detectors for this purpose, not only for the X-IFU detector arrays but also for TES-based bolometer arrays for the Safari instrument of the Japanese SPICA observatory. This paper discusses the design considerations which are applicable to optimise the multiplex factor within the boundary conditions as set by the space craft. More specifically, the interplay between the science requirements such as pixel dynamic range, pixel speed, and cross talk, and the space craft requirements such as the power dissipation budget, available bandwidth, and electromagnetic compatibility will be discussed.

Development of a multiplex microsphere immunoassay for the quantitation of salivary antibody responses to selected waterborne pathogens

EPA Science Inventory

Saliva has an important advantage over serum as a medium for antibody detection due to non-invasive sampling, which is critical for community-based epidemiological surveys. The development of a Luminex multiplex immunoassay for measurement of salivary IgG and IgA responses to pot...

Visible and infrared linear detector arrays for the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS)

NASA Technical Reports Server (NTRS)

Bailey, Gary C.

1987-01-01

The Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) instrument uses four separate focal plane assemblies consisting of line array detectors that are multiplexed to a common J-FET preamp using a FET switch multiplexing (MUX) technique. A 32-element silicon line array covers the spectral range from 0.41 to 0.70 microns. Three additional 64-element indium antimonide (InSb) line arrays cover the spectral range from 0.68 to 2.45 microns. The spectral sampling interval per detector element is nominally 9.8 nm, giving a total of 224 spectral channels. All focal planes operate at liquid nitrogen temperature and are housed in separate dewars. Electrical performance characteristics include a read noise of less than 1000 e(-) in all channels, response and dark nonuniformity of 5 percent peak to peak, and quantum efficiency of greater than 60 percent.

Progress Towards High-Sensitivity Arrays of Detectors of Sub-mm Radiation Using Superconducting Tunnel Junctions with Integrated Radio Frequency Single-Electron Transistors

NASA Technical Reports Server (NTRS)

Stevenson, T. R.; Hsieh, W.-T.; Li, M. J.; Prober, D. E.; Rhee, K. W.; Schoelkopf, R. J.; Stahle, C. M.; Teufel, J.; Wollack, E. J.

2004-01-01

For high resolution imaging and spectroscopy in the FIR and submillimeter, space observatories will demand sensitive, fast, compact, low-power detector arrays with 104 pixels and sensitivity less than 10(exp -20) W/Hz(sup 0.5). Antenna-coupled superconducting tunnel junctions with integrated rf single-electron transistor readout amplifiers have the potential for achieving this high level of sensitivity, and can take advantage of an rf multiplexing technique. The device consists of an antenna to couple radiation into a small superconducting volume and cause quasiparticle excitations, and a single-electron transistor to measure current through junctions contacting the absorber. We describe optimization of device parameters, and results on fabrication techniques for producing devices with high yield for detector arrays. We also present modeling of expected saturation power levels, antenna coupling, and rf multiplexing schemes.

Optimized MOL-PCR for Characterization of Microbial Pathogens.

PubMed

Wuyts, Véronique; Roosens, Nancy H C; Bertrand, Sophie; Marchal, Kathleen; De Keersmaecker, Sigrid C J

2016-01-06

Characterization of microbial pathogens is necessary for surveillance, outbreak detection, and tracing of outbreak sources. This unit describes a multiplex oligonucleotide ligation-PCR (MOL-PCR) optimized for characterization of microbial pathogens. With MOL-PCR, different types of markers, like unique sequences, single-nucleotide polymorphisms (SNPs) and indels, can be simultaneously analyzed in one assay. This assay consists of a multiplex ligation for detection of the markers, a singleplex PCR for signal amplification, and hybridization to MagPlex-TAG beads for readout on a Luminex platform after fluorescent staining. The current protocol describes the MOL-PCR, as well as methods for DNA isolation, probe design, and data interpretation and it is based on an optimized MOL-PCR assay for subtyping of Salmonella Typhimurium. Copyright © 2016 John Wiley & Sons, Inc.

Broadband Direct Detection Submillimeter Spectrometer with Multiplexed Superconducting Transition Edge Thermometer Bolometers

NASA Technical Reports Server (NTRS)

Benford, D. J.; Ames, T. A.; Chervenak, J. A.; Moseley, S. H.; Shafer, R. A.; Staguhn, J. G.; Voellmer, G. M.; Pajot, F.; Rioux, C.; Phillips, T. G.;

Enhancements to a Superconducting Quantum Interference Device (SQUID) Multiplexer Readout and Control System

NASA Technical Reports Server (NTRS)

Forgione, J.; Benford, D. J.; Buchanan, E. D.; Moseley, S. H.; Rebar, J.; Shafer, R. A.

2004-01-01

Far-infrared detector arrays such as the 16x32 superconducting bolometer array for the SAFIRE instrument (flying on the SOFIA airborne observatory) require systems of readout and control electronics to provide translation between a user-driven, digital PC and the cold, analog world of the cryogenic detector. In 2001, the National Institute of Standards and Technology (NIST) developed their Mark III electronics for purposes of control and readout of their 1x32 SQUID Multiplexer chips. We at NASA s Goddard Space Flight Center acquired a Mark 111 system and subsequently designed upgrades to suit our and our collaborators purposes. We developed an arbitrary, programmable multiplexing system that allows the user to cycle through rows in a SQUID array in an infinite number of combinations. We provided hooks in the Mark III system to allow readout of signals from outside the Mark 111 system, such as telescope status information. Finally, we augmented the heart of the system with a new feedback algorithm implementation, flexible diagnostic tools, and informative telemetry.

Enhancements to a superconducting quantum interference device (SQUID) multiplexer readout and control system

NASA Astrophysics Data System (ADS)

Forgione, Joshua B.; Benford, Dominic J.; Buchanan, Ernest D.; Moseley, S. H., Jr.; Rebar, Joyce; Shafer, Richard A.

2004-10-01

Far-infrared detector arrays such as the 16x32 superconducting bolometer array for the SAFIRE instrument (flying on the SOFIA airborne observatory) require systems of readout and control electronics to provide translation between a user-driven, digital PC and the cold, analog world of the cryogenic detector. In 2001, the National Institute of Standards and Technology (NIST) developed their Mark III electronics for purposes of control and readout of their 1x32 SQUID Multiplexer chips. We at NASA's Goddard Space Flight Center acquired a Mark III system and subsequently designed upgrades to suit our and our collaborators' purposes. We developed an arbitrary, programmable multiplexing system that allows the user to cycle through rows in a SQUID array in an infinite number of combinations. We provided 'hooks' in the Mark III system to allow readout of signals from outside the Mark III system, such as telescope status information. Finally, we augmented the heart of the system with a new feedback algorithm implementation, flexible diagnostic tools, and informative telemetry.

Development of capacitive multiplexing circuit for SiPM-based time-of-flight (TOF) PET detector

NASA Astrophysics Data System (ADS)

Choe, Hyeok-Jun; Choi, Yong; Hu, Wei; Yan, Jianhua; Jung, Jin Ho

2017-04-01

There has been great interest in developing a time-of-flight (TOF) PET to improve the signal-to-noise ratio of PET image relative to that of non-TOF PET. Silicon photomultiplier (SiPM) arrays have attracted attention for use as a fast TOF PET photosensor. Since numerous SiPM arrays are needed to construct a modern human PET, a multiplexing method providing both good timing performance and high channel reduction capability is required to develop a SiPM-based TOF PET. The purpose of this study was to develop a capacitive multiplexing circuit for the SiPM-based TOF PET. The proposed multiplexing circuit was evaluated by measuring the coincidence resolving time (CRT) and the energy resolution as a function of the overvoltage using three different capacitor values of 15, 30, and 51 pF. A flood histogram was also obtained and quantitatively assessed. Experiments were performed using a 4× 4 array of 3× 3 mm2 SiPMs. Regarding the capacitor values, the multiplexing circuit using a smaller capacitor value showed the best timing performance. On the other hand, the energy resolution and flood histogram quality of the multiplexing circuit deteriorated as the capacitor value became smaller. The proposed circuit was able to achieve a CRT of 260+/- 4 ps FWHM and an energy resolution of 17.1 % with a pair of 2× 2× 20 mm3 LYSO crystals using a capacitor value of 30 pF at an overvoltage of 3.0 V. It was also possible to clearly resolve a 6× 6 array of LYSO crystals in the flood histogram using the multiplexing circuit. The experiment results indicate that the proposed capacitive multiplexing circuit is useful to obtain an excellent timing performance and a crystal-resolving capability in the flood histogram with a minimal degradation of the energy resolution, as well as to reduce the number of the readout channels of the SiPM-based TOF PET detector.

Hole-Impeded-Doping-Superlattice LWIR Detectors

NASA Technical Reports Server (NTRS)

Maserjian, Joseph

1991-01-01

Hole-Impeded-Doping-Superlattice (HIDS) InAs devices proposed for use as photoconductive or photovoltaic detectors of radiation in long-wavelength infrared (LWIR) range of 8 to 17 micrometers. Array of HIDS devices fabricated on substrates GaAs or Si. Radiation incident on black surface, metal contacts for picture elements serve as reactors, effectively doubling optical path and thereby increasing absorption of photons. Photoconductive detector offers advantages of high gain and high impedance; photovoltaic detector offers lower noise and better interface to multiplexer readouts.

NASA AMES infrared detector assemblies

NASA Technical Reports Server (NTRS)

1979-01-01

Silicon: Gallium infrared detector assemblies were designed, fabricated, and tested using techniques representative of those employed for hybrid arrays to determine the suitability of this candidate technology for infrared astronomical detector array applications. Both the single channel assembly and the assembly using a 32 channel CMOS multiplexer are considered. The detector material was certified to have a boron background of less than 10 to the 13th power atoms/sq cm counter doped with phosphorus. The gallium concentration is 2 x 10 to the 16th power atoms/cu cm.

Demonstration of a scalable frequency-domain readout of metallic magnetic calorimeters by means of a microwave SQUID multiplexer

NASA Astrophysics Data System (ADS)

Kempf, Sebastian; Wegner, Mathias; Fleischmann, Andreas; Gastaldo, Loredana; Herrmann, Felix; Papst, Maximilian; Richter, Daniel; Enss, Christian

2017-01-01

We report on the first demonstration of a scalable GHz frequency-domain readout of metallic magnetic calorimeters (MMCs) using a 64 pixel detector array that is read out by an integrated, on-chip microwave SQUID multiplexer. The detector array is optimized for detecting soft X-ray photons and the multiplexer is designed to provide a signal rise time τrise<400 ns and an intrinsic energy sensitivity ɛ <30 h . This results in an expected energy resolution Δ EFWHM <10 eV . We measured a signal rise time τrise as low as 90 ns and an energy resolution Δ EFWHM as low as 50 eV for 5.9 keV photons. The rise time is about an order of magnitude faster compared to other multiplexed low-temperature microcalorimeters and close to the intrinsic value set by the coupling between electron and spins. The energy resolution is degraded with respect to our design value due to a rather low intrinsic quality factor of the microwave resonators that is caused by the quality of the Josephson junction of the associated rf-SQUID as well as an elevated chip temperature as compared to the heat bath. Though the achieved energy resolution is not yet compatible with state-of-the-art single-channel MMCs, this demonstration of a scalable readout approach for MMCs in combination with the full understanding of the device performance showing ways how to improve represents an important milestone for the development of future large-scale MMC detector arrays.

Rapid, sensitive, and simultaneous detection of three foodborne pathogens using magnetic nanobead-based immunoseparation and quantum dot-based multiplex immunoassay.

PubMed

Wang, Hong; Li, Yanbin; Wang, Andrew; Slavik, Michael

2011-12-01

Losses caused by foodborne diseases are enormous in terms of human life, illness, medical costs, and food product recalls. Rapid detection of multiple bacterial pathogens in foods is extremely important to ensure food safety. The objective of this research was to develop a multiplex immunoassay by integrating magnetic nanobeads (MNBs) for immunoseparation with quantum dots (QDs) as fluorescent labels for rapid, sensitive, and simultaneous detection of three major pathogenic bacteria, Salmonella Typhimurium, Escherichia coli O157:H7, and Listeria monocytogenes, in food products. In this research, both streptavidin-conjugated MNBs (30- and 150-nm diameter) and QDs (530-, 580-, and 620-nm emission wavelength) were separately coated with biotinylated anti-Salmonella, anti-E. coli, and anti-Listeria antibodies. The immuno-MNBs were mixed with a food sample to capture the three target bacteria. After being magnetically separated from the sample, the MNB-cell conjugates were mixed with the immuno-QDs to form the MNB-cell-QD complexes, and unattached QDs were removed. The fluorescence intensity of the MNB-cell-QD complexes was measured at wavelengths of 530, 580, and 620 nm to determine the populations of Salmonella Typhimurium, E. coli O157:H7, and L. monocytogenes, respectively. This multiplex immunoassay simultaneously detected Salmonella Typhimurium, E. coli O157:H7, and L. monocytogenes at levels as low as 20 to 50 CFU/ml in food samples in less than 2 h without enrichment. The change in fluorescence intensity was linearly correlated (R(2) > 0.96) with the logarithmic value of bacterial level in the range of 10 to 10(3) CFU/ml. More than 85% of the three target pathogens could be simultaneously separated from food samples. The multiplex immunoassay could be expanded to detect more target pathogens, depending on the availability of specific antibodies and QDs with different emission wavelengths.

Externally-Modulated Electro-Optically Coupled Detector Architecture for Nuclear Physics Instrumentation

NASA Astrophysics Data System (ADS)

Xi, Wenze; McKisson, J. E.; Weisenberger, Andrew G.; Zhang, Shukui; Zorn, Carl

2014-06-01

A new laser-based externally-modulated electro-optically coupled detector (EOCD) architecture is being developed to enable high-density readout for radiation detectors with accurate analog radiation pulse shape and timing preservation. Unlike digital conversion before electro-optical modulation, the EOCD implements complete analog optical signal modulation and multiplexing in its detector front-end. The result is a compact, high performance detector readout that can be both radiation tolerant and immune to magnetic fields. In this work, the feasibility of EOCD was explored by constructing a two-wavelength laser-based externally-modulated EOCD, and testing analog pulse shape preservation and wavelength-division multiplexing (WDM) crosstalk. Comparisons were first made between the corresponding initial pulses and the electro-optically coupled analog pulses. This confirmed an excellent analog pulse preservation over 29% of the modulator's switching voltage range. Optical spectrum analysis revealed less than -14 dB crosstalk with 1.2 nm WDM wavelength bandgap, and provided insight on experimental conditions that could lead to increased inter-wavelength crosstalk. Further discussions and previous research on the radiation tolerance and magnetic field immunity of the candidate materials were also given, and quantitative device testing is proposed in the future.

Multiplexed fluorescence detector system for capillary electrophoresis

DOEpatents

Yeung, E.S.; Taylor, J.A.

1996-03-12

A fluorescence detection system for capillary electrophoresis is provided wherein the detection system can simultaneously excite fluorescence and substantially simultaneously monitor separations in multiple capillaries. This multiplexing approach involves laser irradiation of a sample in a plurality of capillaries through optical fibers that are coupled individually with the capillaries. The array is imaged orthogonally through a microscope onto a charge-coupled device camera for signal analysis. 14 figs.

Multiplexed fluorescence detector system for capillary electrophoresis

DOEpatents

Yeung, E.S.; Taylor, J.A.

1994-06-28

A fluorescence detection system for capillary electrophoresis is provided wherein the detection system can simultaneously excite fluorescence and substantially simultaneously monitor separations in multiple capillaries. This multiplexing approach involves laser irradiation of a sample in a plurality of capillaries through optical fibers that are coupled individually with the capillaries. The array is imaged orthogonally through a microscope onto a charge-coupled device camera for signal analysis. 14 figures.

Multiplexed fluorescence detector system for capillary electrophoresis

DOEpatents

Yeung, Edward S.; Taylor, John A.

1996-03-12

A fluorescence detection system for capillary electrophoresis is provided wherein the detection system can simultaneously excite fluorescence and substantially simultaneously monitor separations in multiple capillaries. This multiplexing approach involves laser irradiation of a sample in a plurality of capillaries through optical fibers that are coupled individually with the capillaries. The array is imaged orthogonally through a microscope onto a charge-coupled device camera for signal analysis.

Multiplexed fluorescence detector system for capillary electrophoresis

DOEpatents

Yeung, Edward S.; Taylor, John A.

1994-06-28

A fluorescence detection system for capillary electrophoresis is provided wherein the detection system can simultaneously excite fluorescence and substantially simultaneously monitor separations in multiple capillaries. This multiplexing approach involves laser irradiation of a sample in a plurality of capillaries through optical fibers that are coupled individually with the capillaries. The array is imaged orthogonally through a microscope onto a charge-coupled device camera for signal analysis.

Quantitative multiplex detection of pathogen biomarkers

DOEpatents

Mukundan, Harshini; Xie, Hongzhi; Swanson, Basil I.; Martinez, Jennifer; Grace, Wynne K.

2016-02-09

The present invention addresses the simultaneous detection and quantitative measurement of multiple biomolecules, e.g., pathogen biomarkers through either a sandwich assay approach or a lipid insertion approach. The invention can further employ a multichannel, structure with multi-sensor elements per channel.

Quantitative multiplex detection of pathogen biomarkers

DOEpatents

Mukundan, Harshini; Xie, Hongzhi; Swanson, Basil I; Martinez, Jennifer; Grace, Wynne K

2014-10-14

The present invention addresses the simultaneous detection and quantitative measurement of multiple biomolecules, e.g., pathogen biomarkers through either a sandwich assay approach or a lipid insertion approach. The invention can further employ a multichannel, structure with multi-sensor elements per channel.

Development of a multiplex PCR assay for rapid and simultaneous detection of four genera of fish pathogenic bacteria.

PubMed

Zhang, D F; Zhang, Q Q; Li, A H

2014-11-01

Species of genus Aeromonas, Vibrio, Edwardsiella and Streptococcus are the most common fish pathogenic bacteria that cause economically devastating losses in aquaculture. A multiplex polymerase chain reaction (mPCR) was developed for the simultaneous detection and differentiation of the four genera of fish pathogenic bacteria. Through the use of genus-specific primers instead of species-specific ones, the current mPCR covered much more target bacterial species compared with previously reported species-specific mPCR methods. The specificity of the four putative genus-specific primers was validated experimentally while used exclusively (uniplex PCR) or combined (mPCR) against bacterial genomic DNA templates of the target bacteria and nontarget bacteria. The PCR amplicons for the following genera were obtained as expected: Aeromonas (875 bp), Vibrio (524 bp), Edwardsiella (302 bp) and Streptococcus (197 bp), and the fragments could be separated clearly on the agarose gel electrophoresis. The mPCR did not produce nonspecific amplification products when used to amplify 21 nontarget species of bacteria. The mPCR detection limits for each target bacterial genera were 50 colony-forming units (CFU) in pure culture and 100 CFU in fish tissue samples. In conclusion, the mPCR assay was proven to be a powerful alternative to the conventional culture-based method, given its rapid, specific, sensitive and reliable detection of target pathogens. The fish pathogenic bacteria of genus Aeromonas, Vibrio, Edwardsiella and Streptococcus frequently cause severe outbreaks of diseases in cultured fish, and the genus-specific multiplex PCR assay developed in this study can detect the bacteria of the four genera when present in the samples either alone or mixed. The mPCR assay is expected to identify the causative agents more efficiently than uniplex PCR or species-specific multiplex PCR for clinical diagnosis, resulting in the earlier implementation of control measures. This mPCR assay provides a rapid, specific and sensitive tool for the detection or identification of common fish pathogenic bacteria in aquaculture practice. © 2014 The Society for Applied Microbiology.

Fiber optics for the future - wavelength division multiplexing

NASA Technical Reports Server (NTRS)

Spencer, J. L.

1982-01-01

Optical wavelength division multiplexing (WDM) systems, with signals transmitted on different wavelengths through a single fiber, can have increased information capacity and fault isolation properties over single wavelength optical systems. This paper describes a typical WDM system. The applicability of future standards to such a system are discussed. Also, a state-of-the-art survey of optical multimode components which could be used to implement the system are made. The components to be surveyed are sources, multiplexers, and detectors. Emphasis is given to the demultiplexer techniques which are the major developmental components in the WDM system.

High speed, long distance, data transmission multiplexing circuit

DOEpatents

Mariotti, Razvan

1991-01-01

A high speed serial data transmission multiplexing circuit, which is operable to accurately transmit data over long distances (up to 3 Km), and to multiplex, select and continuously display real time analog signals in a bandwidth from DC to 100 Khz. The circuit is made fault tolerant by use of a programmable flywheel algorithm, which enables the circuit to tolerate one transmission error before losing synchronization of the transmitted frames of data. A method of encoding and framing captured and transmitted data is used which has a low overhead and prevents some particular transmitted data patterns from locking an included detector/decoder circuit.

Superconducting Digital Multiplexers for Sensor Arrays

NASA Technical Reports Server (NTRS)

Kadin, Alan M.; Brock, Darren K.; Gupta, Deepnarayan

2004-01-01

Arrays of cryogenic microbolometers and other cryogenic detectors are being developed for infrared imaging. If the signal from each sensor is amplified, multiplexed, and digitized using superconducting electronics, then this data can be efficiently read out to ambient temperature with a minimum of noise and thermal load. HYPRES is developing an integrated system based on SQUID amplifiers, a high-resolution analog-to-digital converter (ADC) based on RSFQ (rapid single flux quantum) logic, and a clocked RSFQ multiplexer. The ADC and SQUIDs have already been demonstrated for other projects, so this paper will focus on new results of a digital multiplexer. Several test circuits have been fabricated using Nb Josephson technology and are about to be tested at T = 4.2 K, with a more complete prototype in preparation.

[Investigation of bacterial and viral etiology in community acquired central nervous system infections with molecular methods].

PubMed

Kahraman, Hasip; Tünger, Alper; Şenol, Şebnem; Gazi, Hörü; Avcı, Meltem; Örmen, Bahar; Türker, Nesrin; Atalay, Sabri; Köse, Şükran; Ulusoy, Sercan; Işıkgöz Taşbakan, Meltem; Sipahi, Oğuz Reşat; Yamazhan, Tansu; Gülay, Zeynep; Alp Çavuş, Sema; Pullukçu, Hüsnü

2017-07-01

In this multicenter prospective cohort study, it was aimed to evaluate the bacterial and viral etiology in community-acquired central nervous system infections by standart bacteriological culture and multiplex polymerase chain reaction (PCR) methods. Patients hospitalized with central nervous system infections between April 2012 and February 2014 were enrolled in the study. Demographic and clinical information of the patients were collected prospectively. Cerebrospinal fluid (CSF) samples of the patients were examined by standart bacteriological culture methods, bacterial multiplex PCR (Seeplex meningitis-B ACE Detection (Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Listeria monocytogenes, Group B streptococci) and viral multiplex PCR (Seeplex meningitis-V1 ACE Detection kits herpes simplex virus-1 (HSV1), herpes simplex virus-2 (HSV2), varicella zoster virus (VZV), cytomegalovirus (CMV), Epstein Barr virus (EBV) and human herpes virus 6 (HHV6)) (Seeplex meningitis-V2 ACE Detection kit (enteroviruses)). Patients were classified as purulent meningitis, aseptic meningitis and encephalitis according to their clinical, CSF (leukocyte level, predominant cell type, protein and glucose (blood/CSF) levels) and cranial imaging results. Patients who were infected with a pathogen other than the detection of the kit or diagnosed as chronic meningitis and other diseases during the follow up, were excluded from the study. A total of 79 patients (28 female, 51 male, aged 42.1 ± 18.5) fulfilled the study inclusion criteria. A total of 46 patients were classified in purulent meningitis group whereas 33 were in aseptic meningitis/encephalitis group. Pathogens were detected by multiplex PCR in 41 patients. CSF cultures were positive in 10 (21.7%) patients (nine S.pneumoniae, one H.influenzae) and PCR were positive for 27 (58.6%) patients in purulent meningitis group. In this group one type of bacteria were detected in 18 patients (14 S.pneumoniae, two N.meningitidis, one H.influenzae, one L.monocytogenes). Besides, it is noteworthy that multiple pathogens were detected such as bacteria-virus combination in eight patients and two different bacteria in one patient. In the aseptic meningitis/encephalitis group, pathogens were detected in 14 out of 33 patients; single type of viruses in 11 patients (seven enterovirus, two HSV1, one HSV2, one VZV) and two different viruses were determined in three patients. These data suggest that multiplex PCR methods may increase the isolation rate of pathogens in central nervous system infections. Existence of mixed pathogen growth is remarkable in our study. Further studies are needed for the clinical relevance of this result.

Prevalence of Trichomonas vaginalis in Women Visiting 2 Obstetrics and Gynecology Clinics in Daegu, South Korea.

PubMed

Goo, Youn-Kyoung; Shin, Won-Sik; Yang, Hye-Won; Joo, So-Young; Song, Su-Min; Ryu, Jae-Sook; Lee, Won-Myung; Kong, Hyun-Hee; Lee, Won-Ki; Lee, Sang-Eun; Lee, Won-Ja; Chung, Dong-Il; Hong, Yeonchul

2016-02-01

This study explored epidemiological trends in trichomoniasis in Daegu, South Korea. Wet mount microscopy, PCR, and multiplex PCR were used to test for Trichomonas vaginalis in vaginal swab samples obtained from 621 women visiting 2 clinics in Daegu. Of the 621 women tested, microscopy detected T. vaginalis in 4 (0.6%) patients, PCR detected T. vaginalis in 19 (3.0%) patients, and multiplex PCR detected T. vaginalis in 12 (1.9%) patients. Testing via PCR demonstrated high sensitivity and high negative predictive value for T. vaginalis. Among the 19 women who tested positive for T. vaginalis according to PCR, 94.7% (18/19) reported vaginal signs and symptoms. Notably, more than 50% of T. vaginalis infections occurred in females younger than 30 years old, and 58% were unmarried. Multiplex PCR, which simultaneously detects pathogens from various sexually transmitted infections, revealed that 91.7% (11/12) of patients were infected with 2 or more pathogens. Mycoplasma hominis was the most prevalent co-infection pathogen with T. vaginalis, followed by Ureaplasma urealyticum and Chlamydia trachomatis. Our results indicate that PCR and multiplex PCR are the most sensitive tools for T. vaginalis diagnosis, rather than microscopy which has been routinely used to detect T. vaginalis infections in South Korea. Therefore, clinicians should take note of the high prevalence of T. vaginalis infections among adolescent and young women in order to prevent persistent infection and transmission of this disease.

Fully integrated multiplexed lab-on-a-card assay for enteric pathogens

NASA Astrophysics Data System (ADS)

Weigl, B. H.; Gerdes, J.; Tarr, P.; Yager, P.; Dillman, L.; Peck, R.; Ramachandran, S.; Lemba, M.; Kokoris, M.; Nabavi, M.; Battrell, F.; Hoekstra, D.; Klein, E. J.; Denno, D. M.

2006-01-01

Under this NIH-funded project, we are developing a lab-on-a-card platform to identify enteric bacterial pathogens in patients presenting with acute diarrhea, with special reference to infections that might be encountered in developing countries. Component functions that are integrated on this platform include on-chip immunocapture of live or whole pathogens, multiplexed nucleic acid amplification and on-chip detection, sample processing to support direct use of clinical specimens, and dry reagent storage and handling. All microfluidic functions are contained on the lab card. This new diagnostic test will be able to rapidly identify and differentiate Shigella dysenteriae serotype 1, Shigella toxin-producing Escherichia coli, E. coli 0157, Campylobacter jejuni, and Salmonella and Shigella species. This presentation will report on progress to date on sample and bacteria processing methodologies, identification and validation of capture antibodies and strategy for organism immunocapture, identification and validation of specific polymerase chain reaction (PCR) primer sequences for over 200 clinical isolates of enteric pathogens, and implementation of on-chip nucleic acid extraction for a subset of those pathogens.

Surface elastic wave detectors

NASA Technical Reports Server (NTRS)

Lawson, R. L.

1971-01-01

The potential applications of acoustic surface wave technology to multiplex communication systems such as data-bus, are examined. The goals are primarily to characterize certain aspects of surface wave trapped delay lines, surface wave modulation techniques, and surface wave applications that are relevant to the evaluation of surface wave devices in multiplex systems. The results indicate that there is a potential for the application of surface wave technology in data-bus type systems.

Massively multiplexed microbial identification using resequencing DNA microarrays for outbreak investigation

NASA Astrophysics Data System (ADS)

Leski, T. A.; Ansumana, R.; Jimmy, D. H.; Bangura, U.; Malanoski, A. P.; Lin, B.; Stenger, D. A.

2011-06-01

Multiplexed microbial diagnostic assays are a promising method for detection and identification of pathogens causing syndromes characterized by nonspecific symptoms in which traditional differential diagnosis is difficult. Also such assays can play an important role in outbreak investigations and environmental screening for intentional or accidental release of biothreat agents, which requires simultaneous testing for hundreds of potential pathogens. The resequencing pathogen microarray (RPM) is an emerging technological platform, relying on a combination of massively multiplex PCR and high-density DNA microarrays for rapid detection and high-resolution identification of hundreds of infectious agents simultaneously. The RPM diagnostic system was deployed in Sierra Leone, West Africa in collaboration with Njala University and Mercy Hospital Research Laboratory located in Bo. We used the RPM-Flu microarray designed for broad-range detection of human respiratory pathogens, to investigate a suspected outbreak of avian influenza in a number of poultry farms in which significant mortality of chickens was observed. The microarray results were additionally confirmed by influenza specific real-time PCR. The results of the study excluded the possibility that the outbreak was caused by influenza, but implicated Klebsiella pneumoniae as a possible pathogen. The outcome of this feasibility study confirms that application of broad-spectrum detection platforms for outbreak investigation in low-resource locations is possible and allows for rapid discovery of the responsible agents, even in cases when different agents are suspected. This strategy enables quick and cost effective detection of low probability events such as outbreak of a rare disease or intentional release of a biothreat agent.

A novel, multiplex, real-time PCR-based approach for the detection of the commonly occurring pathogenic fungi and bacteria.

PubMed

Horváth, Ádám; Pető, Zoltán; Urbán, Edit; Vágvölgyi, Csaba; Somogyvári, Ferenc

2013-12-23

Polymerase chain reaction (PCR)-based techniques are widely used to identify fungal and bacterial infections. There have been numerous reports of different, new, real-time PCR-based pathogen identification methods although the clinical practicability of such techniques is not yet fully clarified.The present study focuses on a novel, multiplex, real-time PCR-based pathogen identification system developed for rapid differentiation of the commonly occurring bacterial and fungal causative pathogens of bloodstream infections. A multiplex, real-time PCR approach is introduced for the detection and differentiation of fungi, Gram-positive (G+) and Gram-negative (G-) bacteria. The Gram classification is performed with the specific fluorescence resonance energy transfer (FRET) probes recommended for LightCycler capillary real-time PCR. The novelty of our system is the use of a non-specific SYBR Green dye instead of labelled anchor probes or primers, to excite the acceptor dyes on the FRET probes. In conjunction with this, the use of an intercalating dye allows the detection of fungal amplicons.With the novel pathogen detection system, fungi, G + and G- bacteria in the same reaction tube can be differentiated within an hour after the DNA preparation via the melting temperatures of the amplicons and probes in the same tube. This modified FRET technique is specific and more rapid than the gold-standard culture-based methods. The fact that fungi, G + and G- bacteria were successfully identified in the same tube within an hour after the DNA preparation permits rapid and early evidence-based management of bloodstream infections in clinical practice.

A multiplex PCR assay for determination of mating type in isolates of the honey bee fungal pathogen, Ascosphaera apis

USDA-ARS?s Scientific Manuscript database

In this study we developed a multiplex PCR for identification of mating type idiomorphs in the filamentous fungus, Ascosphaera apis, the causative agent of chalkbrood disease in the honey bee (Apis melliffera). A combination of gene-specific primers was designed to amplify Mat1-1 and Mat1-2 gene fra...

Developing a Salivary Antibody Multiplex Immunoassay to Measure Human Exposure to Environmental Pathogens

EPA Science Inventory

The etiology and impacts of human exposure to environmental pathogens are of major concern worldwide and, thus, the ability to assess exposure and infections using cost effective, high-throughput approaches would be indispensable. The principal objective of this work is to devel...

Development of Multiplex Reverse Transcription-Polymerase Chain Reaction for Simultaneous Detection of Influenza A, B and Adenoviruses

PubMed Central

Nakhaie, Mohsen; Soleimanjahi, Hoorieh; Mollaie, Hamid Reza; Arabzadeh, Seyed Mohamad Ali

2018-01-01

Background and objective: Millions of people in developing countries lose their lives due to acute respiratory infections, such as Influenza A & B and Adeno viruses. Given the importance of rapid identification of the virus, in this study the researchers attempted to design a method that enables detection of influenza A, B, and adenoviruses, quickly and simultaneously. The Multiplex RT PCR method was the preferred method for the detection of influenza A, B, and adenoviruses in clinical specimens because it is rapid, sensitive, specific, and more cost-effective than alternative methods Methods: After collecting samples from patients with respiratory disease, virus genome was extracted, then Monoplex PCR was used on positive samples and Multiplex RT-PCR on clinical specimens. Finally, by comparing the bands of these samples, the type of virus in the clinical samples was determined. Results: Performing Multiplex RT-PCR on 50 samples of respiratory tract led to following results; flu A: 12.5%, fluB: 50%, adeno: 27.5%, negative: 7.5%, and 2.5% contamination. Conclusion: Reverse transcription-multiplex Polymerase Chain Reaction (PCR) technique, a rapid diagnostic tool, has potential for high-throughput testing. This method has a significant advantage, which provides simultaneous amplification of numerous viruses in a single reaction. This study concentrates on multiplex molecular technologies and their clinical application for the detection and quantification of respiratory pathogens. The improvement in diagnostic testing for viral respiratory pathogens effects patient management, and leads to more cost-effective delivery of care. It limits unnecessary antibiotic use and improves clinical management by use of suitable treatment. PMID:29731796

Direct PCR - A rapid method for multiplexed detection of different serotypes of Salmonella in enriched pork meat samples.

PubMed

Chin, Wai Hoe; Sun, Yi; Høgberg, Jonas; Quyen, Than Linh; Engelsmann, Pia; Wolff, Anders; Bang, Dang Duong

2017-04-01

Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture method is time consuming. In response to the demand for rapid on line or at site detection of pathogens, in this study, we developed a multiplex Direct PCR method for rapid detection of different Salmonella serotypes directly from pork meat samples without any DNA purification steps. An inhibitor-resistant Phusion Pfu DNA polymerase was used to overcome PCR inhibition. Four pairs of primers including a pair of newly designed primers targeting Salmonella spp. at subtype level were incorporated in the multiplex Direct PCR. To maximize the efficiency of the Direct PCR, the ratio between sample and dilution buffer was optimized. The sensitivity and specificity of the multiplex Direct PCR were tested using naturally contaminated pork meat samples for detecting and subtyping of Salmonella spp. Conventional bacterial culture methods were used as reference to evaluate the performance of the multiplex Direct PCR. Relative accuracy, sensitivity and specificity of 98.8%; 97.6% and 100%, respectively, were achieved by the method. Application of the multiplex Direct PCR to detect Salmonella in pork meat at slaughter reduces the time of detection from 5 to 6 days by conventional bacterial culture and serotyping methods to 14 h (including 12 h enrichment time). Furthermore, the method poses a possibility of miniaturization and integration into a point-of-need Lab-on-a-chip system for rapid online pathogen detection. Copyright © 2016 Elsevier Ltd. All rights reserved.

Specification and Design of the SBRC-190: A Cryogenic Multiplexer for Far Infrared Photoconductor Detectors

NASA Technical Reports Server (NTRS)

Erickson, E. F.; Young, E. T.; Wolf, J.; Asbrock, J. F.; Lum, N.; DeVincenzi, D. (Technical Monitor)

2002-01-01

Arrays of far-infrared photoconductor detectors operate at a few degrees Kelvin and require electronic amplifiers in close proximity. For the electronics, a cryogenic multiplexer is ideal to avoid the large number of wires associated with individual amplifiers for each pixel, and to avoid adverse effects of thermal and radiative heat loads from the circuitry. For low background applications, the 32 channel CRC 696 CMOS device was previously developed for SIRTF, the cryogenic Space Infrared Telescope Facility. For higher background applications, we have developed a similar circuit, featuring several modifications: (a) an AC coupled, capacitive feedback transimpedence unit cell, to minimize input offset effects, thereby enabling low detector biases, (b) selectable feedback capacitors to enable operation over a wide range of backgrounds, and (c) clamp and sample & hold output circuits to improve sampling efficiency, which is a concern at the high readout rates required. We describe the requirements for and design of the new device.

Method and apparatus for signal processing in a sensor system for use in spectroscopy

DOEpatents

O'Connor, Paul [Bellport, NY; DeGeronimo, Gianluigi [Nesconset, NY; Grosholz, Joseph [Natrona Heights, PA

2008-05-27

A method for processing pulses arriving randomly in time on at least one channel using multiple peak detectors includes asynchronously selecting a non-busy peak detector (PD) in response to a pulse-generated trigger signal, connecting the channel to the selected PD in response to the trigger signal, and detecting a pulse peak amplitude. Amplitude and time of arrival data are output in first-in first-out (FIFO) sequence. An apparatus includes trigger comparators to generate the trigger signal for the pulse-receiving channel, PDs, a switch for connecting the channel to the selected PD, and logic circuitry which maintains the write pointer. Also included, time-to-amplitude converters (TACs) convert time of arrival to analog voltage and an analog multiplexer provides FIFO output. A multi-element sensor system for spectroscopy includes detector elements, channels, trigger comparators, PDs, a switch, and a logic circuit with asynchronous write pointer. The system includes TACs, a multiplexer and analog-to-digital converter.

Multiplexed single-mode wavelength-to-time mapping of multimode light

PubMed Central

Chandrasekharan, Harikumar K; Izdebski, Frauke; Gris-Sánchez, Itandehui; Krstajić, Nikola; Walker, Richard; Bridle, Helen L.; Dalgarno, Paul A.; MacPherson, William N.; Henderson, Robert K.; Birks, Tim A.; Thomson, Robert R.

2017-01-01

When an optical pulse propagates along an optical fibre, different wavelengths travel at different group velocities. As a result, wavelength information is converted into arrival-time information, a process known as wavelength-to-time mapping. This phenomenon is most cleanly observed using a single-mode fibre transmission line, where spatial mode dispersion is not present, but the use of such fibres restricts possible applications. Here we demonstrate that photonic lanterns based on tapered single-mode multicore fibres provide an efficient way to couple multimode light to an array of single-photon avalanche detectors, each of which has its own time-to-digital converter for time-correlated single-photon counting. Exploiting this capability, we demonstrate the multiplexed single-mode wavelength-to-time mapping of multimode light using a multicore fibre photonic lantern with 121 single-mode cores, coupled to 121 detectors on a 32 × 32 detector array. This work paves the way to efficient multimode wavelength-to-time mapping systems with the spectral performance of single-mode systems. PMID:28120822

Frequency division multiplexed readout of TES detectors with baseband feedback

NASA Astrophysics Data System (ADS)

den Hartog, R.; Audley, M. D.; Beyer, J.; Bruijn, M. P.; de Korte, P.; Gottardi, L.; Hijmering, R.; Jackson, B.; Nieuwenhuizen, A.; van der Kuur, J.; van Leeuwen, B.-J.; Van Loon, D.

2012-09-01

SRON is developing an electronic system for the multiplexed read-out of an array of transition edge sensors (TES) by combining the techniques of frequency domain multiplexing (FDM) with base-band feedback (BBFB). The astronomical applications are the read-out of soft X-ray microcalorimeters and the far-infrared bolometers for the SAFARI instrument on the Japanese mission SPICA. In this paper we derive the requirements for the read-out system regarding noise and dynamic range in the context of the SAFARI instrument, and demonstrate that the current experimental prototype is capable of simultaneously locking 57 channels and complies with these requirements.

Sensitive multiplex PCR assay to differentiate Lyme spirochetes and emerging pathogens Anaplasma phagocytophilum and Babesia microti.

PubMed

Chan, Kamfai; Marras, Salvatore A E; Parveen, Nikhat

2013-12-20

The infection with Borrelia burgdorferi can result in acute to chronic Lyme disease. In addition, coinfection with tick-borne pathogens, Babesia species and Anaplasma phagocytophilum has been increasing in endemic regions of the USA and Europe. The currently used serological diagnostic tests are often difficult to interpret and, moreover, antibodies against the pathogens persist for a long time making it difficult to confirm the cure of the disease. In addition, these tests cannot be used for diagnosis of early disease state before the adaptive immune response is established. Since nucleic acids of the pathogens do not persist after the cure, DNA-based diagnostic tests are becoming highly useful for detecting infectious diseases. In this study, we describe a real-time multiplex PCR assay to detect the presence of B. burgdorferi, B. microti and A. phagocytophilum simultaneously even when they are present in very low copy numbers. Interestingly, this quantitative PCR technique is also able to differentiate all three major Lyme spirochete species, B. burgdorferi, B. afzelii, and B. garinii by utilizing a post-PCR denaturation profile analysis and a single molecular beacon probe. This could be very useful for diagnosis and discrimination of various Lyme spirochetes in European countries where all three Lyme spirochete species are prevalent. As proof of the principle for patient samples, we detected the presence of low number of Lyme spirochetes spiked in the human blood using our assay. Finally, our multiplex assay can detect all three tick-borne pathogens in a sensitive and specific manner irrespective of the level of each pathogen present in the sample. We anticipate that this novel diagnostic method will be able to simultaneously diagnose early to chronic stages of Lyme disease, babesiosis and anaplasmosis using the patients' blood samples. Real-time quantitative PCR using specific primers and molecular beacon probes for the selected amplicon described in this study can detect three tick-borne pathogens simultaneously in an accurate manner.

Sensitive multiplex PCR assay to differentiate Lyme spirochetes and emerging pathogens Anaplasma phagocytophilum and Babesia microti

PubMed Central

2013-01-01

Background The infection with Borrelia burgdorferi can result in acute to chronic Lyme disease. In addition, coinfection with tick-borne pathogens, Babesia species and Anaplasma phagocytophilum has been increasing in endemic regions of the USA and Europe. The currently used serological diagnostic tests are often difficult to interpret and, moreover, antibodies against the pathogens persist for a long time making it difficult to confirm the cure of the disease. In addition, these tests cannot be used for diagnosis of early disease state before the adaptive immune response is established. Since nucleic acids of the pathogens do not persist after the cure, DNA-based diagnostic tests are becoming highly useful for detecting infectious diseases. Results In this study, we describe a real-time multiplex PCR assay to detect the presence of B. burgdorferi, B. microti and A. phagocytophilum simultaneously even when they are present in very low copy numbers. Interestingly, this quantitative PCR technique is also able to differentiate all three major Lyme spirochete species, B. burgdorferi, B. afzelii, and B. garinii by utilizing a post-PCR denaturation profile analysis and a single molecular beacon probe. This could be very useful for diagnosis and discrimination of various Lyme spirochetes in European countries where all three Lyme spirochete species are prevalent. As proof of the principle for patient samples, we detected the presence of low number of Lyme spirochetes spiked in the human blood using our assay. Finally, our multiplex assay can detect all three tick-borne pathogens in a sensitive and specific manner irrespective of the level of each pathogen present in the sample. We anticipate that this novel diagnostic method will be able to simultaneously diagnose early to chronic stages of Lyme disease, babesiosis and anaplasmosis using the patients’ blood samples. Conclusion Real-time quantitative PCR using specific primers and molecular beacon probes for the selected amplicon described in this study can detect three tick-borne pathogens simultaneously in an accurate manner. PMID:24359556

Application of a multiplex PCR assay for Campylobacter fetus detection and subspecies differentiation in uncultured samples of aborted bovine fetuses.

PubMed

Iraola, Gregorio; Hernández, Martín; Calleros, Lucía; Paolicchi, Fernando; Silveyra, Silvia; Velilla, Alejandra; Carretto, Luis; Rodríguez, Eliana; Pérez, Ruben

2012-12-01

Campylobacter (C.) fetus (epsilonproteobacteria) is an important veterinary pathogen. This species is currently divided into C. fetus subspecies (subsp.) fetus (Cff) and C. fetus subsp. venerealis (Cfv). Cfv is the causative agent of bovine genital Campylobacteriosis, an infectious disease that leads to severe reproductive problems in cattle worldwide. Cff is a more general pathogen that causes reproductive problems mainly in sheep although cattle can also be affected. Here we describe a multiplex PCR method to detect C. fetus and differentiate between subspecies in a single step. The assay was standardized using cultured strains and successfully used to analyze the abomasal liquid of aborted bovine fetuses without any pre-enrichment step. Results of our assay were completely consistent with those of traditional bacteriological diagnostic methods. Furthermore, the multiplex PCR technique we developed may be easily adopted by any molecular diagnostic laboratory as a complementary tool for detecting C. fetus subspecies and obtaining epidemiological information about abortion events in cattle.

Application of a multiplex immunoassay for detection of salivary antibody responses to selected potentially waterborne pathogens

EPA Science Inventory

Although this work was reviewed by EPA and approved for publication, it may not necessarily reflect official Agency policy. Pathogen-specific antibodies in saliva can be used as bioindicators of recent or ongoing infection. Because collection of saliva is easy and painless, i...

Surface plasmon resonance imaging for label-free detection of foodborne pathogens and toxins

USDA-ARS?s Scientific Manuscript database

More rapid and efficient detection methods for foodborne pathogenic bacteria and toxins are needed to address the long assay time and limitations in multiplex capacity. Surface plasmon resonance imaging (SPRi) is an emerging optical technique, which allows for rapid and label-free screening of multi...

Single-Tube Multiplexed Molecular Detection of Endemic Porcine Viruses in Combination with Background Screening for Transboundary Diseases

PubMed Central

Wernike, Kerstin; Hoffmann, Bernd

2013-01-01

Detection of several pathogens with multiplexed real-time quantitative PCR (qPCR) assays in a one-step setup allows the simultaneous detection of two endemic porcine and four different selected transboundary viruses. Reverse transcription (RT)-qPCR systems for the detection of porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2), two of the most economically important pathogens of swine worldwide, were combined with a screening system for diseases notifiable to the World Organization of Animal Health, namely, classical and African swine fever, foot-and-mouth disease, and Aujeszky's disease. Background screening was implemented using the identical fluorophore for all four different RT-qPCR assays. The novel multiplex RT-qPCR system was validated with a large panel of different body fluids and tissues from pigs and other animal species. Both reference samples and clinical specimens were used for a complete evaluation. It could be demonstrated that a highly sensitive and specific parallel detection of the different viruses was possible. The assays for the notifiable diseases were even not affected by the simultaneous amplification of very high loads of PRRSV- and PCV2-specific sequences. The novel broad-spectrum multiplex assay allows in a unique form the routine investigation for endemic porcine pathogens with exclusion diagnostics of the most important transboundary diseases in samples from pigs with unspecific clinical signs, such as fever or hemorrhages. The new system could significantly improve early detection of the most important notifiable diseases of swine and could lead to a new approach in syndromic surveillance. PMID:23303496

Rapid Multiplex PCR Assay To Identify Respiratory Viral Pathogens: Moving Forward Diagnosing The Common Cold

PubMed Central

Gordon, Sarah M; Elegino-Steffens, Diane U; Agee, Willie; Barnhill, Jason; Hsue, Gunther

2013-01-01

Upper respiratory tract infections (URIs) can be a serious burden to the healthcare system. The majority of URIs are viral in etiology, but definitive diagnosis can prove difficult due to frequently overlapping clinical presentations of viral and bacterial infections, and the variable sensitivity, and lengthy turn-around time of viral culture. We tested new automated nested multiplex PCR technology, the FilmArray® system, in the TAMC department of clinical investigations, to determine the feasibility of replacing the standard viral culture with a rapid turn-around system. We conducted a feasibility study using a single-blinded comparison study, comparing PCR results with archived viral culture results from a convenience sample of cryopreserved archived nasopharyngeal swabs from acutely ill ED patients who presented with complaints of URI symptoms. A total of 61 archived samples were processed. Viral culture had previously identified 31 positive specimens from these samples. The automated nested multiplex PCR detected 38 positive samples. In total, PCR was 94.5% concordant with the previously positive viral culture results. However, PCR was only 63.4% concordant with the negative viral culture results, owing to PCR detection of 11 additional viral pathogens not recovered on viral culture. The average time to process a sample was 75 minutes. We determined that an automated nested multiplex PCR is a feasible alternative to viral culture in an acute clinical setting. We were able to detect at least 94.5% as many viral pathogens as viral culture is able to identify, with a faster turn-around time. PMID:24052914

Determination of foodborne pathogenic bacteria by multiplex PCR-microchip capillary electrophoresis with genetic algorithm-support vector regression optimization.

PubMed

Li, Yongxin; Li, Yuanqian; Zheng, Bo; Qu, Lingli; Li, Can

2009-06-08

A rapid and sensitive method based on microchip capillary electrophoresis with condition optimization of genetic algorithm-support vector regression (GA-SVR) was developed and applied to simultaneous analysis of multiplex PCR products of four foodborne pathogenic bacteria. Four pairs of oligonucleotide primers were designed to exclusively amplify the targeted gene of Vibrio parahemolyticus, Salmonella, Escherichia coli (E. coli) O157:H7, Shigella and the quadruplex PCR parameters were optimized. At the same time, GA-SVR was employed to optimize the separation conditions of DNA fragments in microchip capillary electrophoresis. The proposed method was applied to simultaneously detect the multiplex PCR products of four foodborne pathogenic bacteria under the optimal conditions within 8 min. The levels of detection were as low as 1.2 x 10(2) CFU mL(-1) of Vibrio parahemolyticus, 2.9 x 10(2) CFU mL(-1) of Salmonella, 8.7 x 10(1) CFU mL(-1) of E. coli O157:H7 and 5.2 x 10(1) CFU mL(-1) of Shigella, respectively. The relative standard deviation of migration time was in the range of 0.74-2.09%. The results demonstrated that the good resolution and less analytical time were achieved due to the application of the multivariate strategy. This study offers an efficient alternative to routine foodborne pathogenic bacteria detection in a fast, reliable, and sensitive way.

Superconducting Detector Arrays for Astrophysics

NASA Technical Reports Server (NTRS)

Chervenak, James

2008-01-01

The next generation of astrophysics instruments will feature an order of magnitude more photon sensors or sensors that have an order of magnitude greater sensitivity. Since detector noise scales with temperature, a number of candidate technologies have been developed that use the intrinsic advantages of detector systems that operate below 1 Kelvin. Many of these systems employ of the superconducting phenomena that occur in metals at these temperatures to build ultrasensitive detectors and low-noise, low-power readout architectures. I will present one such system in use today to meet the needs of the astrophysics community at millimeter and x-ray wavelengths. Our group at NASA in collaboration with Princeton, NIST, Boulder and a number of other groups is building large format arrays of superconducting transition edge sensors (TES) read out with multiplexed superconducting quantum interference devices (SQUID). I will present the high sensitivity we have achieved in multiplexed x-ray sensors with the TES technology and describe the construction of a 1000-sensor TES/SQUID array for microwave measurements. With our collaboration's deployment of a kilopixel TES array for 2 mm radiation at the Atacarna Cosmology Telescope in November 2007, we have first images of the lensed Cosmic Microwave Background at fine angular scales.

An Integrated Quantum Dot Barcode Smartphone Optical Device for Wireless Multiplexed Diagnosis of Infected Patients

NASA Astrophysics Data System (ADS)

Ming, Kevin

Integrating mobile-cellular devices with multiplex molecular diagnostics can potentially provide the most powerful platform for tracking, managing and preventing the transmission of infectious diseases. With over 6.9 billion subscriptions globally, handheld mobile-cellular devices can be programmed to spatially map, temporally track, and transmit information on infections over wide geographical space and boundaries. Current cell phone diagnostic technologies have poor limit of detection, dynamic range, and cannot detect multiple pathogen targets simultaneously, limiting their utility to single infections with high load. Here we combined recent advances in quantum dot barcode technology for molecular detection with smartphones to engineer a simple and low-cost chip-based wireless multiplex diagnostic device. We validated our device using a variety of synthetic genomic targets for the respiratory virus and blood-borne pathogens, and demonstrated that it could detect clinical samples after simple amplification. More importantly, we confirmed that the device is capable of detecting patients infected with a single or multiple infectious pathogens (e.g., HIV and hepatitis B) in a single test. This device advances the capacity for global surveillance of infectious diseases and has the potential to accelerate knowledge exchange-transfer of emerging or exigent disease threats with healthcare and military organizations in real-time.

A single-electrode electrochemical system for multiplex electrochemiluminescence analysis based on a resistance induced potential difference.

PubMed

Gao, Wenyue; Muzyka, Kateryna; Ma, Xiangui; Lou, Baohua; Xu, Guobao

2018-04-28

Developing low-cost and simple electrochemical systems is becoming increasingly important but still challenged for multiplex experiments. Here we report a single-electrode electrochemical system (SEES) using only one electrode not only for a single experiment but also for multiplex experiments based on a resistance induced potential difference. SEESs for a single experiment and multiplex experiments are fabricated by attaching a self-adhesive label with a hole and multiple holes onto an ITO electrode, respectively. This enables multiplex electrochemiluminescence analysis with high sensitivity at a very low safe voltage using a smartphone as a detector. For the multiplex analysis, the SEES using a single electrode is much simpler, cheaper and more user-friendly than conventional electrochemical systems and bipolar electrochemical systems using electrode arrays. Moreover, SEESs are free from the electrochemiluminescent background problem from driving electrodes in bipolar electrochemical systems. Since numerous electrodes and cover materials can be used to fabricate SEESs readily and electrochemistry is being extensively used, SEESs are very promising for broad applications, such as drug screening and high throughput analysis.

Molecular testing for viral and bacterial enteric pathogens: gold standard for viruses, but don't let culture go just yet?

PubMed

Bloomfield, Maxim G; Balm, Michelle N D; Blackmore, Timothy K

2015-04-01

Contemporary diagnostic microbiology is increasingly adopting molecular methods as front line tests for a variety of samples. This trend holds true for detection of enteric pathogens (EP), where nucleic acid amplification tests (NAAT) for viruses are well established as the gold standard, and an increasing number of commercial multi-target assays are now available for bacteria and parasites. NAAT have significant sensitivity and turnaround time advantages over traditional methods, potentially returning same-day results. Multiplex panels offer an attractive 'one-stop shop' that may provide workflow and cost advantages to laboratories processing large sample volumes. However, there are a number of issues which need consideration. Reflex culture is required for antibiotic susceptibility testing and strain typing when needed for food safety and other epidemiological investigations. Surveillance systems will need to allow for differences in disease incidence due to the enhanced sensitivity of NAAT. Laboratories should be mindful of local epidemiology when selecting which pathogens to include in multiplex panels, and be thoughtful regarding which pathogens will not be detected. Multiplex panels may not be appropriate in certain situations, such as hospital-onset diarrhoea, where Clostridium difficile testing might be all that is required, and laboratories may wish to retain the flexibility to run single tests in such situations. The clinical impact of rapid results is also likely to be relatively minor, as infective diarrhoea is a self-limiting illness in the majority of cases. Laboratories will require strategies to assist users in the interpretation of the results produced by NAAT, particularly where pathogens are detected at low levels with uncertain clinical significance. These caveats aside, faecal NAAT are increasingly being used and introduce a new era of diagnosis of gastrointestinal infection.

How Well Does Physician Selection of Microbiologic Tests Identify Clostridium difficile and other Pathogens in Paediatric Diarrhoea? Insights Using Multiplex PCR-Based Detection

PubMed Central

Stockmann, Chris; Rogatcheva, Margarita; Harrel, Brian; Vaughn, Mike; Crisp, Rob; Poritz, Mark; Thatcher, Stephanie; Korgenski, Ernest K; Barney, Trenda; Daly, Judy; Pavia, Andrew T

2014-01-01

The objective of this study was to compare the aetiologic yield of standard of care microbiologic testing ordered by physicians with that of a multiplex PCR platform. Stool specimens obtained from children and young adults with gastrointestinal illness were evaluated by standard laboratory methods and a developmental version of the FilmArray Gastrointestinal Diagnostic System (FilmArray GI Panel), a rapid multiplex PCR platform that detects 23 bacterial, viral, and protozoal agents. Results were classified according to the microbiologic tests requested by the treating physician. A median of 3 (range 1-10) microbiologic tests were performed by the clinical laboratory during 378 unique diarrhoeal episodes. A potential aetiologic agent was identified in 46% of stool specimens by standard laboratory methods and in 65% of specimens tested using the FilmArray GI Panel (P<0.001). For those patients who only had Clostridium difficile testing requested, an alternative pathogen was identified in 29% of cases with the FilmArray GI Panel. Notably, 11 (12%) cases of norovirus were identified among children who only had testing for C. difficile ordered. Among those who had C. difficile testing ordered in combination with other tests, an additional pathogen was identified in 57% of stool specimens with the FilmArray GI Panel. For patients who had no C. difficile testing performed, the FilmArray GI Panel identified a pathogen in 63% of cases, including C. difficile in 8%. Physician-specified laboratory testing may miss important diarrhoeal pathogens. Additionally, standard laboratory testing is likely to underestimate co-infections with multiple infectious diarrhoeagenic agents. PMID:25599941

Highly sensitive and quantitative detection of rare pathogens through agarose droplet microfluidic emulsion PCR at the single-cell level.

PubMed

Zhu, Zhi; Zhang, Wenhua; Leng, Xuefei; Zhang, Mingxia; Guan, Zhichao; Lu, Jiangquan; Yang, Chaoyong James

2012-10-21

Genetic alternations can serve as highly specific biomarkers to distinguish fatal bacteria or cancer cells from their normal counterparts. However, these mutations normally exist in very rare amount in the presence of a large excess of non-mutated analogs. Taking the notorious pathogen E. coli O157:H7 as the target analyte, we have developed an agarose droplet-based microfluidic ePCR method for highly sensitive, specific and quantitative detection of rare pathogens in the high background of normal bacteria. Massively parallel singleplex and multiplex PCR at the single-cell level in agarose droplets have been successfully established. Moreover, we challenged the system with rare pathogen detection and realized the sensitive and quantitative analysis of a single E. coli O157:H7 cell in the high background of 100,000 excess normal K12 cells. For the first time, we demonstrated rare pathogen detection through agarose droplet microfluidic ePCR. Such a multiplex single-cell agarose droplet amplification method enables ultra-high throughput and multi-parameter genetic analysis of large population of cells at the single-cell level to uncover the stochastic variations in biological systems.

Randomized controlled clinical trial evaluating multiplex polymerase chain reaction for pathogen identification and therapy adaptation in critical care patients with pulmonary or abdominal sepsis.

PubMed

Tafelski, Sascha; Nachtigall, Irit; Adam, Thomas; Bereswill, Stefan; Faust, Jana; Tamarkin, Andrey; Trefzer, Tanja; Deja, Maria; Idelevich, Evgeny A; Wernecke, Klaus-Dieter; Becker, Karsten; Spies, Claudia

2015-06-01

To determine whether a multiplex polymerase chain reaction (PCR)-based test could reduce the time required for initial pathogen identification in patients in an intensive care unit (ICU) setting. This double-blind, parallel-group randomized controlled trial** enrolled adults with suspected pulmonary or abdominal sepsis caused by an unknown pathogen. Both the intervention and control groups underwent the standard blood culture (BC) testing, but additional pathogen identification, based on the results of a LightCycler® SeptiFast PCR test, were provided in the intervention group. The study enrolled 37 patients in the control group and 41 in the intervention group. Baseline clinical and demographic characteristics were similar in both groups. The PCR-based test identified a pathogen in 10 out of 41 (24.4%) patients in the intervention group, with a mean duration from sampling to providing the information to the ICU of 15.9 h. In the control group, BC results were available after a significantly longer period (38.1 h). The LightCycler® SeptiFast PCR test demonstrated a significant reduction in the time required for initial pathogen identification, compared with standard BC. © The Author(s) 2015 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Piglet colibacillosis diagnosis based on multiplex polymerase chain reaction and immunohistochemistry of paraffin-embedded tissues

PubMed Central

de Andrade, Caroline P.; Machado, Verônica S. L.; Bianchi, Matheus V.; Rolim, Veronica M.; Cruz, Raquel A. S.; Driemeier, David

2018-01-01

Enterotoxigenic Escherichia coli (ETEC) causes diarrhea in pigs, referred to as colibacillosis. The aim of this study was to optimize multiplex polymerase chain reaction (PCR) and immunohistochemistry (IHC) analyses of paraffin-embedded material to detect pathogenic E. coli strains causing colibacillosis in pigs. Multiplex PCR was optimized for fimbriae (F18, F4, F6, F5, and F41) and toxins (types A and B heat-stable toxins [STaP and STb], heat-labile toxin [LT], and type 2 Shiga toxin [STx2e]), and IHC was optimized for an anti-E. coli polyclonal antibody. Samples (132) from pigs received between 2006 and 2014 with clinical and histopathological diagnoses of colibacillosis were analyzed. E. coli was detected by IHC in 78.7%, and at least one virulence factor gene was detected in 71.2%. Pathogenic strains of ETEC with at least one fimbria and one toxin were detected in 40% of the samples in multiplex PCR. The most frequent virulence types were F18-STaP (7.5%), F18-STaP-STb (5.7%), and F4-STaP (3.8%). A statistically significant association was noted between virulence factors F4, F18, STaP, and STb and positive immunostaining results. Colibacillosis diagnosis through multiplex PCR and IHC of paraffin-embedded tissues is a practical approach, as samples can be fixed and stored for long periods before analysis. PMID:28693311

Hybrid charge division multiplexing method for silicon photomultiplier based PET detectors

NASA Astrophysics Data System (ADS)

Park, Haewook; Ko, Guen Bae; Lee, Jae Sung

2017-06-01

Silicon photomultiplier (SiPM) is widely utilized in various positron emission tomography (PET) detectors and systems. However, the individual recording of SiPM output signals is still challenging owing to the high granularity of the SiPM; thus, charge division multiplexing is commonly used in PET detectors. Resistive charge division method is well established for reducing the number of output channels in conventional multi-channel photosensors, but it degrades the timing performance of SiPM-based PET detectors by yielding a large resistor-capacitor (RC) constant. Capacitive charge division method, on the other hand, yields a small RC constant and provides a faster timing response than the resistive method, but it suffers from an output signal undershoot. Therefore, in this study, we propose a hybrid charge division method which can be implemented by cascading the parallel combination of a resistor and a capacitor throughout the multiplexing network. In order to compare the performance of the proposed method with the conventional methods, a 16-channel Hamamatsu SiPM (S11064-050P) was coupled with a 4  ×  4 LGSO crystal block (3  ×  3  ×  20 mm3) and a 9  ×  9 LYSO crystal block (1.2  ×  1.2  ×  10 mm3). In addition, we tested a time-over-threshold (TOT) readout using the digitized position signals to further demonstrate the feasibility of the time-based readout of multiplexed signals based on the proposed method. The results indicated that the proposed method exhibited good energy and timing performance, thus inheriting only the advantages of conventional resistive and capacitive methods. Moreover, the proposed method showed excellent pulse shape uniformity that does not depend on the position of the interacted crystal. Accordingly, we can conclude that the hybrid charge division method is useful for effectively reducing the number of output channels of the SiPM array.

A capillary-based multiplexed isothermal nucleic acid-based test for sexually transmitted diseases in patients.

PubMed

Xu, Gaolian; Zhao, Hang; Cooper, Jonathan M; Reboud, Julien

2016-10-06

We demonstrate a multiplexed loop mediated isothermal amplification (LAMP) assay for infectious disease diagnostics, where the analytical process flow of target pathogens genomic DNA is performed manually by moving magnetic beads through a series of plugs in a capillary. Heat is provided by a water bath and the results are read by the naked eye, enabling applications in low resource settings.

Homologous Recombination and Xylella fastidiosa Host-Pathogen Associations in South America.

PubMed

Coletta-Filho, Helvécio D; Francisco, Carolina S; Lopes, João R S; Muller, Christiane; Almeida, Rodrigo P P

2017-03-01

Homologous recombination affects the evolution of bacteria such as Xylella fastidiosa, a naturally competent plant pathogen that requires insect vectors for dispersal. This bacterial species is taxonomically divided into subspecies, with phylogenetic clusters within subspecies that are host specific. One subspecies, pauca, is primarily limited to South America, with the exception of recently reported strains in Europe and Costa Rica. Despite the economic importance of X. fastidiosa subsp. pauca in South America, little is known about its genetic diversity. Multilocus sequence typing (MLST) has previously identified six sequence types (ST) among plant samples collected in Brazil (both subsp. pauca and multiplex). Here, we report on a survey of X. fastidiosa genetic diversity (MLST based) performed in six regions in Brazil and two in Argentina, by sampling five different plant species. In addition to the six previously reported ST, seven new subsp. pauca and two new subsp. multiplex ST were identified. The presence of subsp. multiplex in South America is considered to be the consequence of a single introduction from its native range in North America more than 80 years ago. Different phylogenetic approaches clustered the South American ST into four groups, with strains infecting citrus (subsp. pauca); coffee and olive (subsp. pauca); coffee, hibiscus, and plum (subsp. pauca); and plum (subsp. multiplex). In areas where these different genetic clusters occurred sympatrically, we found evidence of homologous recombination in the form of bidirectional allelic exchange between subspp. pauca and multiplex. In fact, the only strain of subsp. pauca isolated from a plum host had an allele that originated from subsp. multiplex. These signatures of bidirectional homologous recombination between endemic and introduced ST indicate that gene flow occurs in short evolutionary time frames in X. fastidiosa, despite the ecological isolation (i.e., host plant species) of genotypes.

Immunoprevalence to Six Waterborne Pathogens in Beachgoers at Boquerón Beach, Puerto Rico: Application of a Microsphere-Based Salivary Antibody Multiplex Immunoassay

EPA Science Inventory

Waterborne infectious diseases are a major public health concern worldwide. Few methods have been established that are capable of measuring human exposure to multiple waterborne pathogens simultaneously using non-invasive samples such as saliva. Most current methods measure expos...

Portable Microfluidic Integrated Plasmonic Platform for Pathogen Detection

PubMed Central

Tokel, Onur; Yildiz, Umit Hakan; Inci, Fatih; Durmus, Naside Gozde; Ekiz, Okan Oner; Turker, Burak; Cetin, Can; Rao, Shruthi; Sridhar, Kaushik; Natarajan, Nalini; Shafiee, Hadi; Dana, Aykutlu; Demirci, Utkan

2015-01-01

Timely detection of infectious agents is critical in early diagnosis and treatment of infectious diseases. Conventional pathogen detection methods, such as enzyme linked immunosorbent assay (ELISA), culturing or polymerase chain reaction (PCR) require long assay times, and complex and expensive instruments, which are not adaptable to point-of-care (POC) needs at resource-constrained as well as primary care settings. Therefore, there is an unmet need to develop simple, rapid, and accurate methods for detection of pathogens at the POC. Here, we present a portable, multiplex, inexpensive microfluidic-integrated surface plasmon resonance (SPR) platform that detects and quantifies bacteria, i.e., Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) rapidly. The platform presented reliable capture and detection of E. coli at concentrations ranging from ~105 to 3.2 × 107 CFUs/mL in phosphate buffered saline (PBS) and peritoneal dialysis (PD) fluid. The multiplexing and specificity capability of the platform was also tested with S. aureus samples. The presented platform technology could potentially be applicable to capture and detect other pathogens at the POC and primary care settings. PMID:25801042

Recent advances in superconducting nanowire single photon detectors for single-photon imaging

NASA Astrophysics Data System (ADS)

Verma, V. B.; Allman, M. S.; Stevens, M.; Gerrits, T.; Horansky, R. D.; Lita, A. E.; Marsili, F.; Beyer, A.; Shaw, M. D.; Stern, J. A.; Mirin, R. P.; Nam, S. W.

2016-05-01

We demonstrate a 64-pixel free-space-coupled array of superconducting nanowire single photon detectors optimized for high detection efficiency in the near-infrared range. An integrated, readily scalable, multiplexed readout scheme is employed to reduce the number of readout lines to 16. The cryogenic, optical, and electronic packaging to read out the array, as well as characterization measurements are discussed.

Development of a Multiplex PCR Method to Detect Fungal Pathogens for Quarantine on Exported Cacti

PubMed Central

Cho, Hyun ji; Hong, Seong Won; Kim, Hyun-ju; Kwak, Youn-Sig

2016-01-01

Major diseases in grafted cacti have been reported and Fusarium oxysporum, Bipolaris cactivora, Phytophthora spp. and Collectotrichum spp. are known as causal pathogens. These pathogens can lead to plant death after infection. Therefore, some European countries have quarantined imported cacti that are infected with specific fungal pathogens. Consequently, we developed PCR detection methods to identify four quarantined fungal pathogens and reduce export rejection rates of Korean grafted cacti. The pathogen specific primer sets F.oF-F.oR, B.CF-B.CR, P.nF-P.nR, and P.cF-P.CR were tested for F. oxysporum, B. cactivora, P. nicotinae, and P. cactorum, respectively. The F.oF-F.oR primer set was designed from the Fusarium ITS region; the B.CF-B.CR and P.nF-P.nR primers respectively from Bipolaris and Phytophthora ITS1; and the P.cF-P.CR primer set from the Ypt1protein gene region. The quarantine fungal pathogen primer pairs were amplified to the specific number of base pairs in each of the following fungal pathogens: 210-bp (F. oxysporum), 510-bp (B. cactivora), 313-bp (P. nicotinae), and 447-bp (P. cactorum). The detection limit for the mono- and multiplex PCR primer sets was 0.1 ng of template DNA under in vitro conditions. Therefore, each primer set successfully diagnosed contamination of quarantine pathogens in export grafted cacti. Consequently, our methodology is a viable tool to screen contamination of the fungal pathogen in exported grafted cacti. PMID:26889115

Integrated infrared detector arrays for low-background astronomy

NASA Technical Reports Server (NTRS)

Mccreight, C. R.

1979-01-01

Existing integrated infrared detector array technology is being evaluated under low-background conditions to determine its applicability in orbiting astronomical applications where extended integration times and photometric accuracy are of interest. Preliminary performance results of a 1 x 20 elements InSb CCD array under simulated astronomical conditions are presented. Using the findings of these tests, improved linear- and area-array technology will be developed for use in NASA programs such as the Shuttle Infrared Telescope Facility. For wavelengths less than 30 microns, extrinsic silicon and intrinsic arrays with CCD readout will be evaluated and improved as required, while multiplexed arrays of Ge:Ga for wavelengths in the range 30 to 120 microns will be developed as fundamental understanding of this material improves. Future efforts will include development of improved drive and readout circuitry, and consideration of alternate multiplexing schemes.

Single line-of-sight dual energy backlighter for mix width experiments

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

Baker, K. L., E-mail: baker7@llnl.gov; Glendinning, S. G.; Martinez, D.

2014-11-15

We present a diagnostic technique used to spatially multiplex two x-ray radiographs of an object onto a detector along a single line-of-sight. This technique uses a thin, <2 μm, cosputtered backlighter target to simultaneously produce both Ni and Zn He{sub α} emission. A Ni picket fence filter, 500 μm wide bars and troughs, is then placed in front of the detector to pass only the Ni He{sub α} emission in the bar region and both energies in the trough region thereby spatially multiplexing the two radiographs on a single image. Initial experimental results testing the backlighter spectrum are presented alongmore » with simulated images showing the calculated radiographic images though the nickel picket fence filter which are used to measure the mix width in an accelerated nickel foam.« less

Development of a Massive, Highly Multiplexible, Phonon-Mediated Particle Detector Using Kinetic Inductance Detectors

NASA Astrophysics Data System (ADS)

Chang, Y.-Y.; Cornell, B.; Aralis, T.; Bumble, B.; Golwala, S. R.

2018-04-01

We present a status update on the development of a phonon-mediated particle detector using kinetic inductance detector (KID). The design is intended for O(1) kg substrate, using O(102) KIDs on a single readout line, to image the athermal phonon distribution at < 1 mm position resolution and O(10) eV energy resolution. The design specification is set by the need to improve position reconstruction fidelity while maintaining low energy threshold for future rare-event searches such as for low-mass dark matter. We report on the design, which shows negligible crosstalk and > 95% inductor current uniformity, using the coplanar waveguide feedline, ground shield, and a new class of KIDs with symmetric coplanar stripline (sCPS) inductor. The multiplexing is designed upon the frequency-geometry relation we develop for the sCPS KIDs. We introduce the fabrications of the Nb RF assessment prototypes and the high phonon collection efficiency Al-Nb devices. We achieve ≲ 0.07% frequency displacement on a 80-KID RF assessment prototype, and the result indicates that we may place more than 180 resonances in our 0.4 GHz readout band with minimal frequency misordering. The coupling quality factors are ˜ 105 as designed. Finally, we update our work in progress in fabricating the O(102) KID, bi-material, O(1) kg detectors, and the expected position and energy resolutions.

Performance studies of X3 silicon detectors for the future ELISSA array at ELI-NP

NASA Astrophysics Data System (ADS)

Chesnevskaya, S.; Balabanski, D. L.; Choudhury, D.; Constantin, P.; Filipescu, D. M.; Ghita, D. G.; Guardo, G. L.; Lattuada, D.; Matei, C.; Rotaru, A.; State, A.

2018-05-01

ELISSA is an array of silicon strip detectors under construction at the ELI-NP facility for measurements of photodissociation reactions using high-brilliance, quasi monoenergetic gamma beams. The detection system consists of 35 single-sided position-sensitive X3 detectors arranged in a cylindrical configuration and eight QQQ3 detectors as end-caps. A batch of forty X3 detectors have been tested at ELI-NP. The energy and position resolution, ballistic deficit, leakage currents, and depletion voltage were measured and analyzed. Measurements of the energy resolution were carried out using two read-out electronic chains, one based on multichannel preamplifiers and another based on multiplexers.

Comparison of NxTAG Respiratory Pathogen Panel and Anyplex II RV16 Tests for Multiplex Detection of Respiratory Pathogens in Hospitalized Children

PubMed Central

Brotons, Pedro; Henares, Desiree; Latorre, Irene; Cepillo, Antonio; Launes, Cristian

2016-01-01

Multiplex molecular techniques can detect a diversity of respiratory viruses and bacteria that cause childhood acute respiratory infection rapidly and conveniently. However, currently available techniques show high variation in performance. We sought to compare the diagnostic accuracy of the novel multiplex NxTAG respiratory pathogen panel (RPP) RUO test versus a routine multiplex Anyplex II RV16 assay in respiratory specimens collected from children <18 years of age hospitalized with nonspecific symptoms of acute lower respiratory infection. Parallel testing was performed on nasopharyngeal aspirates prospectively collected at referral Children's Hospital Sant Joan de Déu (Barcelona, Spain) between June and November 2015. Agreement values between the two tests and kappa coefficients were assessed. Bidirectional sequencing was performed for the resolution of discordant results. A total of 319 samples were analyzed by both techniques. A total of 268 (84.0%) of them yielded concordant results. Positive percent agreement values ranged from 83.3 to 100%, while the negative percent agreement was more than 99% for all targets except for enterovirus/rhinovirus (EV/RV; 94.4%). Kappa coefficients ranged from 0.83 to 1.00. Discrepancy analysis confirmed 66.0% of NxTAG RPP RUO results. A total of 260 viruses were detected, with EV/RV (n = 105, 40.4%) being the most prevalent target. Viral coinfections were found in 44 (14.2%) samples. In addition, NxTAG RPP RUO detected single bacterial and mixed viral-bacterial infections in seven samples. NxTAG RPP RUO showed high positive and negative agreement with Anyplex II RV16 for main viruses that cause acute respiratory infections in children, coupled with an additional capability to detect some respiratory bacteria. PMID:27629904

Performance of automated multiplex PCR using sonication fluid for diagnosis of periprosthetic joint infection: a prospective cohort.

PubMed

Renz, Nora; Feihl, Susanne; Cabric, Sabrina; Trampuz, Andrej

2017-12-01

Sonication of explanted prostheses improved the microbiological diagnosis of periprosthetic joint infections (PJI). We evaluated the performance of automated multiplex polymerase chain reaction (PCR) using sonication fluid for the microbiological diagnosis of PJI. In a prospective cohort using uniform definition criteria for PJI, explanted joint prostheses were investigated by sonication and the resulting sonication fluid was analyzed by culture and multiplex PCR. McNemar's Chi-squared test was used to compare the performance of diagnostic tests. Among 111 patients, PJI was diagnosed in 78 (70%) and aseptic failure in 33 (30%). For the diagnosis of PJI, the sensitivity and specificity of periprosthetic tissue culture was 51 and 100%, of sonication fluid culture 58 and 100%, and of sonication fluid PCR 51 and 94%, respectively. Among 70 microorganisms, periprosthetic tissue culture grew 52 (74%), sonication fluid culture grew 50 (71%) and sonication fluid PCR detected 37 pathogens (53%). If only organisms are considered, for which primers are included in the test panel, PCR detected 37 of 58 pathogens (64%). The sonication fluid PCR missed 19 pathogens (predominantly oral streptococci and anaerobes), whereas 7 additional microorganisms were detected only by PCR (including Cutibacterium spp. and coagulase-negative staphylococci). The performance of multiplex PCR using sonication fluid is comparable to culture of periprosthetic tissue or sonication fluid. The advantages of PCR are short processing time (< 5 h) and fully automated procedure. However, culture technique is still needed due to the low sensitivity and the need of comprehensive susceptibility testing. Modification of primers or inclusion of additional ones may improve the performance of PCR, especially of low-virulent organisms.

Frequency-domain cascading microwave superconducting quantum interference device multiplexers; beyond limitations originating from room-temperature electronics

NASA Astrophysics Data System (ADS)

Kohjiro, Satoshi; Hirayama, Fuminori

2018-07-01

A novel approach, frequency-domain cascading microwave multiplexers (MW-Mux), has been proposed and its basic operation has been demonstrated to increase the number of pixels multiplexed in a readout line U of MW-Mux for superconducting detector arrays. This method is an alternative to the challenging development of wideband, large power, and spurious-free room-temperature (300 K) electronics. The readout system for U pixels consists of four main parts: (1) multiplexer chips connected in series those contain U superconducting resonators in total. (2) A cryogenic high-electron-mobility transistor amplifier (HEMT). (3) A 300 K microwave frequency comb generator based on N(≡U/M) parallel units of digital-to-analog converters (DAC). (4) N parallel units of 300 K analog-to-digital converters (ADC). Here, M is the number of tones each DAC produces and each ADC handles. The output signal of U detectors multiplexed at the cryogenic stage is transmitted through a cable to the room temperature and divided into N processors where each handles M pixels. Due to the reduction factor of 1/N, U is not anymore dominated by the 300 K electronics but can be increased up to the potential value determined by either the bandwidth or the spurious-free power of the HEMT. Based on experimental results on the prototype system with N = 2 and M = 3, neither excess inter-pixel crosstalk nor excess noise has been observed in comparison with conventional MW-Mux. This indicates that the frequency-domain cascading MW-Mux provides the full (100%) usage of the HEMT band by assigning N 300 K bands on the frequency axis without inter-band gaps.

Read-noise characterization of focal plane array detectors via mean-variance analysis.

PubMed

Sperline, R P; Knight, A K; Gresham, C A; Koppenaal, D W; Hieftje, G M; Denton, M B

2005-11-01

Mean-variance analysis is described as a method for characterization of the read-noise and gain of focal plane array (FPA) detectors, including charge-coupled devices (CCDs), charge-injection devices (CIDs), and complementary metal-oxide-semiconductor (CMOS) multiplexers (infrared arrays). Practical FPA detector characterization is outlined. The nondestructive readout capability available in some CIDs and FPA devices is discussed as a means for signal-to-noise ratio improvement. Derivations of the equations are fully presented to unify understanding of this method by the spectroscopic community.

Molecular detection of Xanthomonas oryzae pv. oryzae, Xanthomonas oryzae pv. oryzicola, and Burkholderia glumae in infected rice seeds and leaves

USDA-ARS?s Scientific Manuscript database

Polymerase chain reaction (PCR) is particularly useful for plant pathogen detection. In the present study, multiplex PCR and SYBR green real-time PCR were developed to facilitate simultaneous detection of three important rice pathogens, Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, and Bur...

Detection of Neisseria meningitidis in cerebrospinal fluid using a multiplex PCR and the Luminex detection technology.

PubMed

Møller, Jens Kjølseth

2012-01-01

Rapid clinical and laboratory diagnoses are the foundation for a successful management of serious infections with Neisseria meningitidis. A species-specific multiplex polymerase chain reaction (PCR) coupled with fluidic microarrays using microbeads (the Luminex xMAP™ Technology) can detect pathogens most frequently found in the cerebrospinal fluid of patients. The Luminex suspension array system uniquely combines flow cytometry, microspheres, laser technology, digital signal processing, and traditional chemistry. In this method, the reaction is carried out in one vessel, in which distinctly color-coded bead sets, each conjugated with a different specific nucleic acid reactant, are hybridized with the PCR products, and a reporter molecule is used to quantify the interaction. The flow-based Luminex array reader identifies each reaction (bead set) after excitation by a red classification laser. Reporter signals from each reaction are simultaneously quantified by fluorescence generated by a green reporter laser. This nonculture, multiplex assay may prove to be an important tool for optimal laboratory diagnosis, not only of meningococcal meningitis, but also of meningitis caused by other bacterial or viral pathogens.

Multiplex Real-Time PCR for Monitoring Heterobasidion annosum Colonization in Norway Spruce Clones That Differ in Disease Resistance

PubMed Central

Hietala, Ari M.; Eikenes, Morten; Kvaalen, Harald; Solheim, Halvor; Fossdal, Carl G.

2003-01-01

A multiplex real-time PCR assay was developed to monitor the dynamics of the Picea abies-Heterobasidion annosum pathosystem. Tissue cultures and 32-year-old trees with low or high resistance to this pathogen were used as the host material. Probes and primers were based on a laccase gene for the pathogen and a polyubiquitin gene for the host. The real-time PCR procedure was compared to an ergosterol-based quantification method in a tissue culture experiment, and there was a strong correlation (product moment correlation coefficient, 0.908) between the data sets. The multiplex real-time PCR procedure had higher resolution and sensitivity during the early stages of colonization and also could be used to monitor the host. In the tissue culture experiment, host DNA was degraded more rapidly in the clone with low resistance than in the clone with high resistance. In the field experiment, the lesions elicited were not strictly proportional to the area colonized by the pathogen. Fungal colonization was more restricted and localized in the lesion in the clone with high resistance, whereas in the clone with low resistance, the fungus could be detected until the visible end of the lesion. Thus, the real-time PCR assay gives better resolution than does the traditionally used lesion length measurement when screening host clones for resistance. PMID:12902224

Roles of the spreading scope and effectiveness in spreading dynamics on multiplex networks

NASA Astrophysics Data System (ADS)

Li, Ming; Liu, Run-Ran; Peng, Dan; Jia, Chun-Xiao; Wang, Bing-Hong

2018-02-01

Comparing with single networks, the multiplex networks bring two main effects on the spreading process among individuals. First, the pathogen or information can be transmitted to more individuals through different layers at one time, which enlarges the spreading scope. Second, through different layers, an individual can also transmit the pathogen or information to the same individuals more than once at one time, which makes the spreading more effective. To understand the different roles of the spreading scope and effectiveness, we propose an epidemic model on multiplex networks with link overlapping, where the spreading effectiveness of each interaction as well as the variety of channels (spreading scope) can be controlled by the number of overlapping links. We find that for Poisson degree distribution, increasing the epidemic scope (the first effect) is more efficient than enhancing epidemic probability (the second effect) to facilitate the spreading process. However, for power-law degree distribution, the effects of the two factors on the spreading dynamics become complicated. Enhancing epidemic probability makes pathogen or rumor easier to outbreak in a finite system. But after that increasing epidemic scopes is still more effective for a wide spreading. Theoretical results along with reasonable explanation for these phenomena are all given in this paper, which indicates that the epidemic scope could play an important role in the spreading dynamics.

Lead sulfide - Silicon MOSFET infrared focal plane development

NASA Technical Reports Server (NTRS)

Barrett, J. R.; Jhabvala, M. D.

1983-01-01

A process for directly integrating photoconductive lead sulfide (PbS) infrared detector material with silicon MOS integrated circuits has been developed primarily for application in long (greater than 10,000 detector elements) linear arrays for pushbroom scanning applications. The processing technology is based on the conventional PMOS and CMOS technologies with a variation in the metallization. Results and measurements on a fully integrated eight-element multiplexer are shown.

Detection and treatment of chemical weapons and/or biological pathogens

DOEpatents

Mariella Jr., Raymond P.

2004-09-07

A system for detection and treatment of chemical weapons and/or biological pathogens uses a detector system, an electrostatic precipitator or scrubber, a circulation system, and a control. The precipitator or scrubber is activated in response to a signal from the detector upon the detection of chemical weapons and/or biological pathogens.

Parallel multiplex laser feedback interferometry

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

Zhang, Song; Tan, Yidong; Zhang, Shulian, E-mail: zsl-dpi@mail.tsinghua.edu.cn

2013-12-15

We present a parallel multiplex laser feedback interferometer based on spatial multiplexing which avoids the signal crosstalk in the former feedback interferometer. The interferometer outputs two close parallel laser beams, whose frequencies are shifted by two acousto-optic modulators by 2Ω simultaneously. A static reference mirror is inserted into one of the optical paths as the reference optical path. The other beam impinges on the target as the measurement optical path. Phase variations of the two feedback laser beams are simultaneously measured through heterodyne demodulation with two different detectors. Their subtraction accurately reflects the target displacement. Under typical room conditions, experimentalmore » results show a resolution of 1.6 nm and accuracy of 7.8 nm within the range of 100 μm.« less

Measuring changes in transmission of neglected tropical diseases, malaria, and enteric pathogens from quantitative antibody levels.

PubMed

Arnold, Benjamin F; van der Laan, Mark J; Hubbard, Alan E; Steel, Cathy; Kubofcik, Joseph; Hamlin, Katy L; Moss, Delynn M; Nutman, Thomas B; Priest, Jeffrey W; Lammie, Patrick J

2017-05-01

Serological antibody levels are a sensitive marker of pathogen exposure, and advances in multiplex assays have created enormous potential for large-scale, integrated infectious disease surveillance. Most methods to analyze antibody measurements reduce quantitative antibody levels to seropositive and seronegative groups, but this can be difficult for many pathogens and may provide lower resolution information than quantitative levels. Analysis methods have predominantly maintained a single disease focus, yet integrated surveillance platforms would benefit from methodologies that work across diverse pathogens included in multiplex assays. We developed an approach to measure changes in transmission from quantitative antibody levels that can be applied to diverse pathogens of global importance. We compared age-dependent immunoglobulin G curves in repeated cross-sectional surveys between populations with differences in transmission for multiple pathogens, including: lymphatic filariasis (Wuchereria bancrofti) measured before and after mass drug administration on Mauke, Cook Islands, malaria (Plasmodium falciparum) before and after a combined insecticide and mass drug administration intervention in the Garki project, Nigeria, and enteric protozoans (Cryptosporidium parvum, Giardia intestinalis, Entamoeba histolytica), bacteria (enterotoxigenic Escherichia coli, Salmonella spp.), and viruses (norovirus groups I and II) in children living in Haiti and the USA. Age-dependent antibody curves fit with ensemble machine learning followed a characteristic shape across pathogens that aligned with predictions from basic mechanisms of humoral immunity. Differences in pathogen transmission led to shifts in fitted antibody curves that were remarkably consistent across pathogens, assays, and populations. Mean antibody levels correlated strongly with traditional measures of transmission intensity, such as the entomological inoculation rate for P. falciparum (Spearman's rho = 0.75). In both high- and low transmission settings, mean antibody curves revealed changes in population mean antibody levels that were masked by seroprevalence measures because changes took place above or below the seropositivity cutoff. Age-dependent antibody curves and summary means provided a robust and sensitive measure of changes in transmission, with greatest sensitivity among young children. The method generalizes to pathogens that can be measured in high-throughput, multiplex serological assays, and scales to surveillance activities that require high spatiotemporal resolution. Our results suggest quantitative antibody levels will be particularly useful to measure differences in exposure for pathogens that elicit a transient antibody response or for monitoring populations with very high- or very low transmission, when seroprevalence is less informative. The approach represents a new opportunity to conduct integrated serological surveillance for neglected tropical diseases, malaria, and other infectious diseases with well-defined antigen targets.

Measuring changes in transmission of neglected tropical diseases, malaria, and enteric pathogens from quantitative antibody levels

PubMed Central

van der Laan, Mark J.; Hubbard, Alan E.; Steel, Cathy; Kubofcik, Joseph; Hamlin, Katy L.; Moss, Delynn M.; Nutman, Thomas B.; Priest, Jeffrey W.; Lammie, Patrick J.

2017-01-01

Background Serological antibody levels are a sensitive marker of pathogen exposure, and advances in multiplex assays have created enormous potential for large-scale, integrated infectious disease surveillance. Most methods to analyze antibody measurements reduce quantitative antibody levels to seropositive and seronegative groups, but this can be difficult for many pathogens and may provide lower resolution information than quantitative levels. Analysis methods have predominantly maintained a single disease focus, yet integrated surveillance platforms would benefit from methodologies that work across diverse pathogens included in multiplex assays. Methods/Principal findings We developed an approach to measure changes in transmission from quantitative antibody levels that can be applied to diverse pathogens of global importance. We compared age-dependent immunoglobulin G curves in repeated cross-sectional surveys between populations with differences in transmission for multiple pathogens, including: lymphatic filariasis (Wuchereria bancrofti) measured before and after mass drug administration on Mauke, Cook Islands, malaria (Plasmodium falciparum) before and after a combined insecticide and mass drug administration intervention in the Garki project, Nigeria, and enteric protozoans (Cryptosporidium parvum, Giardia intestinalis, Entamoeba histolytica), bacteria (enterotoxigenic Escherichia coli, Salmonella spp.), and viruses (norovirus groups I and II) in children living in Haiti and the USA. Age-dependent antibody curves fit with ensemble machine learning followed a characteristic shape across pathogens that aligned with predictions from basic mechanisms of humoral immunity. Differences in pathogen transmission led to shifts in fitted antibody curves that were remarkably consistent across pathogens, assays, and populations. Mean antibody levels correlated strongly with traditional measures of transmission intensity, such as the entomological inoculation rate for P. falciparum (Spearman’s rho = 0.75). In both high- and low transmission settings, mean antibody curves revealed changes in population mean antibody levels that were masked by seroprevalence measures because changes took place above or below the seropositivity cutoff. Conclusions/Significance Age-dependent antibody curves and summary means provided a robust and sensitive measure of changes in transmission, with greatest sensitivity among young children. The method generalizes to pathogens that can be measured in high-throughput, multiplex serological assays, and scales to surveillance activities that require high spatiotemporal resolution. Our results suggest quantitative antibody levels will be particularly useful to measure differences in exposure for pathogens that elicit a transient antibody response or for monitoring populations with very high- or very low transmission, when seroprevalence is less informative. The approach represents a new opportunity to conduct integrated serological surveillance for neglected tropical diseases, malaria, and other infectious diseases with well-defined antigen targets. PMID:28542223

Multiplex PCR detection of problematic pathogens of clinically heterogeneous bacterial vaginosis in Bulgarian women

PubMed

Tosheva-Daskalova, Konstantsa; Strateva, Tanya Vasileva; Mitov, Ivan Gergov; Gergova, Raina Tzvetanova

2017-11-13

Background/aim: This study aimed to investigate the correlation between the prevalence of problematic pathogens and the clinical status of women with bacterial vaginosis (BV). Materials and methods: Gardnerella vaginalis, Atopobium vaginae, and Mobiluncus spp. were detected using a multiplex PCR assay, and their role in the infection of Bulgarian women with clinically heterogeneous BV was evaluated. Results: The predominant BV-associated pathogen identified was G. vaginalis with an incidence of 98.39%, followed by A. vaginae (68.05%) and Mobiluncus spp. at 17.01%. The coexistence of A. vaginae and G. vaginalis was more common in women with discharge (in 72.04%) and in patients with chronic recurrent BV than among asymptomatic or newly diagnosed BV cases (P < 0.05). Mobiluncus spp. was detected mostly in coinfections, in association with Trichomonas vaginalis. The coinfections were predominantly related to recurrent BV and with complications (P < 0.05). Conclusion: This is the first study about the correlation between problematic pathogens and clinically heterogeneous BV in Bulgarian women. High frequency of infection with key BV-related pathogens was observed in childbearing women. The incidence was shown to often correlate with coexistent T. vaginalis, with severity of infection, and with complicated and recurrent BV after unsuccessful treatments. Screening should be considered in reproductive health programs.

Simultaneous detection of antibodies to five Actinobacillus pleuropneumoniae serovars using bead-based multiplex analysis.

PubMed

Berger, Sanne Schou; Lauritsen, Klara Tølbøll; Boas, Ulrik; Lind, Peter; Andresen, Lars Ole

2017-11-01

We developed and made a preliminary validation of a bead-based multiplexed immunoassay for simultaneous detection of porcine serum antibodies to Actinobacillus pleuropneumoniae serovars 1, 2, 6, 7, and 12. Magnetic fluorescent beads were coupled with A. pleuropneumoniae antigens and tested with a panel of serum samples from experimentally infected pigs and with serum samples from uninfected and naturally infected pigs. The multiplex assay was compared to in-house ELISAs and complement fixation (CF) tests, which have been used for decades as tools for herd classification in the Danish Specific Pathogen Free system. Assay specificities and sensitivities as well as the corresponding cutoff values were determined using receiver operating characteristic (ROC) curve analysis, and the A. pleuropneumoniae multiplex assay showed good correlation with the in-house ELISAs and CF tests with areas under ROC curves ≥ 0.988. Benefits of multiplexed assays compared to ELISAs and CF tests include reduced serum sample volumes needed for analysis, less labor, and shorter assay time.

Blocked impurity band hybrid infrared focal plane arrays for astronomy

NASA Technical Reports Server (NTRS)

Reynolds, D. B.; Seib, D. H.; Stetson, S. B.; Herter, T.; Rowlands, N.

1989-01-01

High-performance infrared hybrid focal plane arrays using 10- x 50-element Si:As blocked-impurity-band (BIB) detectors (cutoff wavelength = 28 microns) and matching switched MOSFET multiplexers have been developed and characterized for space astronomy. Use of impurity-band-conduction technology provides detectors which are nuclear-radiation-hard and free of the many anomalies associated with conventional silicon photoconductive detectors. Emphasis in the present work is on recent advances in detector material quality which have led to significantly improved detector and hybrid characteristics. Results demonstrating increased quantum efficiency (particularly at short-wavelength infrared), obtained by varying the BIB detector properties (infrared active layer thickness and arsenic doping profile), are summarized. Measured read noise and dark current for different temperatures are reported. The hybrid array performance achieved demonstrates that BIB detectors are well suited for use in astronomical instrumentation.

Development of a novel depth of interaction PET detector using highly multiplexed G-APD cross-strip encoding

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

Kolb, A., E-mail: armin.kolb@med.uni-tuebingen.de; Parl, C.; Liu, C. C.

Purpose: The aim of this study was to develop a prototype PET detector module for a combined small animal positron emission tomography and magnetic resonance imaging (PET/MRI) system. The most important factor for small animal imaging applications is the detection sensitivity of the PET camera, which can be optimized by utilizing longer scintillation crystals. At the same time, small animal PET systems must yield a high spatial resolution. The measured object is very close to the PET detector because the bore diameter of a high field animal MR scanner is limited. When used in combination with long scintillation crystals, thesemore » small-bore PET systems generate parallax errors that ultimately lead to a decreased spatial resolution. Thus, we developed a depth of interaction (DoI) encoding PET detector module that has a uniform spatial resolution across the whole field of view (FOV), high detection sensitivity, compactness, and insensitivity to magnetic fields. Methods: The approach was based on Geiger mode avalanche photodiode (G-APD) detectors with cross-strip encoding. The number of readout channels was reduced by a factor of 36 for the chosen block elements. Two 12 × 2 G-APD strip arrays (25μm cells) were placed perpendicular on each face of a 12 × 12 lutetium oxyorthosilicate crystal block with a crystal size of 1.55 × 1.55 × 20 mm. The strip arrays were multiplexed into two channels and used to calculate the x, y coordinates for each array and the deposited energy. The DoI was measured in step sizes of 1.8 mm by a collimated {sup 18}F source. The coincident resolved time (CRT) was analyzed at all DoI positions by acquiring the waveform for each event and applying a digital leading edge discriminator. Results: All 144 crystals were well resolved in the crystal flood map. The average full width half maximum (FWHM) energy resolution of the detector was 12.8% ± 1.5% with a FWHM CRT of 1.14 ± 0.02 ns. The average FWHM DoI resolution over 12 crystals was 2.90 ± 0.15 mm. Conclusions: The novel DoI PET detector, which is based on strip G-APD arrays, yielded a DoI resolution of 2.9 mm and excellent timing and energy resolution. Its high multiplexing factor reduces the number of electronic channels. Thus, this cross-strip approach enables low-cost, high-performance PET detectors for dedicated small animal PET and PET/MRI and potentially clinical PET/MRI systems.« less

Identification of nonclassical properties of light with multiplexing layouts

NASA Astrophysics Data System (ADS)

Sperling, J.; Eckstein, A.; Clements, W. R.; Moore, M.; Renema, J. J.; Kolthammer, W. S.; Nam, S. W.; Lita, A.; Gerrits, T.; Walmsley, I. A.; Agarwal, G. S.; Vogel, W.

2017-07-01

In Sperling et al. [Phys. Rev. Lett. 118, 163602 (2017), 10.1103/PhysRevLett.118.163602], we introduced and applied a detector-independent method to uncover nonclassicality. Here, we extend those techniques and give more details on the performed analysis. We derive a general theory of the positive-operator-valued measure that describes multiplexing layouts with arbitrary detectors. From the resulting quantum version of a multinomial statistics, we infer nonclassicality probes based on a matrix of normally ordered moments. We discuss these criteria and apply the theory to our data which are measured with superconducting transition-edge sensors. Our experiment produces heralded multiphoton states from a parametric down-conversion light source. We show that the known notions of sub-Poisson and sub-binomial light can be deduced from our general approach, and we establish the concept of sub-multinomial light, which is shown to outperform the former two concepts of nonclassicality for our data.

Identification of nonclassical properties of light with multiplexing layouts

PubMed Central

Sperling, J.; Eckstein, A.; Clements, W. R.; Moore, M.; Renema, J. J.; Kolthammer, W. S.; Nam, S. W.; Lita, A.; Gerrits, T.; Walmsley, I. A.; Agarwal, G. S.; Vogel, W.

2018-01-01

In Sperling et al. [Phys. Rev. Lett. 118, 163602 (2017)], we introduced and applied a detector-independent method to uncover nonclassicality. Here, we extend those techniques and give more details on the performed analysis. We derive a general theory of the positive-operator-valued measure that describes multiplexing layouts with arbitrary detectors. From the resulting quantum version of a multinomial statistics, we infer nonclassicality probes based on a matrix of normally ordered moments. We discuss these criteria and apply the theory to our data which are measured with superconducting transition-edge sensors. Our experiment produces heralded multiphoton states from a parametric down-conversion light source. We show that the known notions of sub-Poisson and sub-binomial light can be deduced from our general approach, and we establish the concept of sub-multinomial light, which is shown to outperform the former two concepts of nonclassicality for our data. PMID:29670949

Pilot-multiplexed continuous-variable quantum key distribution with a real local oscillator

NASA Astrophysics Data System (ADS)

Wang, Tao; Huang, Peng; Zhou, Yingming; Liu, Weiqi; Zeng, Guihua

2018-01-01

We propose a pilot-multiplexed continuous-variable quantum key distribution (CVQKD) scheme based on a local local oscillator (LLO). Our scheme utilizes time-multiplexing and polarization-multiplexing techniques to dramatically isolate the quantum signal from the pilot, employs two heterodyne detectors to separately detect the signal and the pilot, and adopts a phase compensation method to almost eliminate the multifrequency phase jitter. In order to analyze the performance of our scheme, a general LLO noise model is constructed. Besides the phase noise and the modulation noise, the photon-leakage noise from the reference path and the quantization noise due to the analog-to-digital converter (ADC) are also considered, which are first analyzed in the LLO regime. Under such general noise model, our scheme has a higher key rate and longer secure distance compared with the preexisting LLO schemes. Moreover, we also conduct an experiment to verify our pilot-multiplexed scheme. Results show that it maintains a low level of the phase noise and is expected to obtain a 554-Kbps secure key rate within a 15-km distance under the finite-size effect.

An improved method to simultaneously detect Salmonella enteritidis, Escherichia coli O157 and Listeria monocytogenes in ground black pepper using multiplex real-time PCR

USDA-ARS?s Scientific Manuscript database

Introduction: The three common foodborne pathogens implicated in foodborne outbreaks are Salmonella spp., Escherichia coli O157:H7 and Listeria monocytogenes. Hence, it is important to identify these pathogens in contaminated foods so that they can be eliminated from the marketplace. At present, the...

A nested multiplex polymerase chain reaction assay for the differential identification of three zooanthroponotic chlamydial strains in porcine swab samples.

PubMed

Li, Yingguo; Wang, Yu; Nie, Fuping; Xiao, Jinwen; Wang, Guoming; Yuan, Ling; Li, Zhengguo

2011-07-01

Porcine chlamydial infection is an enzootic infectious disease caused by multiple members of the family Chlamydiaceae (e.g. Chlamydophila abortus, Chlamydia suis, and Chlamydophila pneumoniae). Rapid and accurate differentiation of these pathogens is critical in the control and prevention of disease. The aim of the current study was to develop a nested multiplex polymerase chain reaction (nmPCR) assay to simultaneously detect the 3 chlamydial pathogens in clinical samples. In the first round of the nmPCR, 1 pair of family-specific primers were used to amplify the 1,100 base pair (bp) fragment of chlamydial ompA gene. In the second round of the nmPCR, 4 inner primers were designed for Ch. abortus, C. suis, and Ch. pneumoniae. Each pathogen produced a specific amplicon with a size of 340 bp, 526 bp, and 267 bp respectively. The assay was sensitive and specific for detecting target pathogens in both cell cultures and clinical specimens. The results, incorporated with the improved rapid DNA extraction protocol, suggest that the nmPCR could be a promising assay for differential identification of different chlamydial strains in pigs.

Feasibility Study of an Axially Extendable Multiplex Cylinder PET

NASA Astrophysics Data System (ADS)

Yoshida, Eiji; Hirano, Yoshiyuki; Tashima, Hideaki; Inadama, Naoko; Nishikido, Fumihiko; Murayama, Hideo; Ito, Hiroshi; Yamaya, Taiga

2013-10-01

Current clinical PET scanners have a 15-22 cm axial field-of-view (FOV). These scanners image the whole body using six or more bed positions. We designed an axially extendable multiplex cylinder (AEMC) PET scanner to provide high versatility for clinical and research studies using semiconductor photo-sensor based, depth-of-interaction (DOI) detectors. Since silicon-photomultipliers (Si-PMs) have high gain like conventional photomultiplier tubes and a compact design, the Si-PM-based detector is particularly expected to enable various new detector arrangements. The AEMC-PET scanner consists of multiple independent and laminated detector rings using the DOI detectors. The AEMC-PET scanner can extend the axial FOV as each stacked detector ring can be slid sideways. When this PET scanner is used for the four-layer DOI detector, its minimum axial FOV is 24 cm and its maximum crystal thickness is 3 cm. On the other hand, the axial FOV can be extended to 96 cm when laminated detector rings are slid sideways, but the crystal thickness must be 1/4 of 3 cm. In this work, we evaluated performance characteristics of the PET scanner with a variable axial FOV using Monte Carlo simulation. From the simulation of the 180-cm line source, the 96-cm axial FOV was found to have two-fold better sensitivity compared to the 24-cm axial FOV. For extension of the axial FOV, scatter and attenuation of oblique lines-of-response reduced the yield of true coincidences, but effects of scatter and attenuation were small. Conclusive results were obtained showing the 52.8-cm axial FOV yielded an increase in the noise equivalent count rate of approximately 30% relative to the 24-cm axial FOV. We expect the designed AEMC-PET scanner will provide high versatility in applications such as for measuring whole-body tracer uptakes while keeping the continuous axial FOV; as well, the scan time for static images will be reduced for a comparable number of detectors as conventional PET scanners.

Development of a Multiplex Real-Time PCR Assay with an Internal Amplification Control for the Detection of Total and Pathogenic Vibrio parahaemolyticus Bacteria in Oysters▿

PubMed Central

Nordstrom, Jessica L.; Vickery, Michael C. L.; Blackstone, George M.; Murray, Shelley L.; DePaola, Angelo

2007-01-01

Vibrio parahaemolyticus is an estuarine bacterium that is the leading cause of shellfish-associated cases of bacterial gastroenteritis in the United States. Our laboratory developed a real-time multiplex PCR assay for the simultaneous detection of the thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and thermostable-related hemolysin (trh) genes of V. parahaemolyticus. The tlh gene is a species-specific marker, while the tdh and trh genes are pathogenicity markers. An internal amplification control (IAC) was incorporated to ensure PCR integrity and eliminate false-negative reporting. The assay was tested for specificity against >150 strains representing eight bacterial species. Only V. parahaemolyticus strains possessing the appropriate target genes generated a fluorescent signal, except for a late tdh signal generated by three strains of V. hollisae. The multiplex assay detected <10 CFU/reaction of pathogenic V. parahaemolyticus in the presence of >104 CFU/reaction of total V. parahaemolyticus bacteria. The real-time PCR assay was utilized with a most-probable-number format, and its results were compared to standard V. parahaemolyticus isolation methodology during an environmental survey of Alaskan oysters. The IAC was occasionally inhibited by the oyster matrix, and this usually corresponded to negative results for V. parahaemolyticus targets. V. parahaemolyticus tlh, tdh, and trh were detected in 44, 44, and 52% of the oyster samples, respectively. V. parahaemolyticus was isolated from 33% of the samples, and tdh+ and trh+ strains were isolated from 19 and 26%, respectively. These results demonstrate the utility of the real-time PCR assay in environmental surveys and its possible application to outbreak investigations for the detection of total and pathogenic V. parahaemolyticus. PMID:17644647

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

Hsia, Chu Chieh; Chizhikov, Vladimir E.; Yang, Amy X.

Hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus type-1 (HIV-1) are transfusion-transmitted human pathogens that have a major impact on blood safety and public health worldwide. We developed a microarray multiplex assay for the simultaneous detection and discrimination of these three viruses. The microarray consists of 16 oligonucleotide probes, immobilized on a silylated glass slide. Amplicons from multiplex PCR were labeled with Cy-5 and hybridized to the microarray. The assay detected 1 International Unit (IU), 10 IU, 20 IU of HBV, HCV, and HIV-1, respectively, in a single multiplex reaction. The assay also detected and discriminatedmore » the presence of two or three of these viruses in a single sample. Our data represent a proof-of-concept for the possible use of highly sensitive multiplex microarray assay to screen and confirm the presence of these viruses in blood donors and patients.« less

Effective characterization of Salmonella Enteritidis by most probable number (MPN) followed by multiplex polymerase chain reaction (PCR) methods.

PubMed

Zappelini, Lincohn; Martone-Rocha, Solange; Dropa, Milena; Matté, Maria Helena; Tiba, Monique Ribeiro; Breternitz, Bruna Suellen; Razzolini, Maria Tereza Pepe

2017-02-01

Nontyphoidal Salmonella (NTS) is a relevant pathogen involved in gastroenteritis outbreaks worldwide. In this study, we determined the capacity to combine the most probable number (MPN) and multiplex polymerase chain reaction (PCR) methods to characterize the most important Salmonella serotypes in raw sewage. A total of 499 isolates were recovered from 27 raw sewage samples and screened using two previously described multiplex PCR methods. From those, 123 isolates were selected based on PCR banding pattern-identical or similar to Salmonella Enteritidis and Salmonella Typhimurium-and submitted to conventional serotyping. Results showed that both PCR assays correctly serotyped Salmonella Enteritidis, however, they presented ambiguous results for Salmonella Typhimurium identification. These data highlight that MPN and multiplex PCR can be useful methods to describe microbial quality in raw sewage and suggest two new PCR patterns for Salmonella Enteritidis identification.

Delay grid multiplexing: simple time-based multiplexing and readout method for silicon photomultipliers

NASA Astrophysics Data System (ADS)

Won, Jun Yeon; Ko, Guen Bae; Lee, Jae Sung

2016-10-01

In this paper, we propose a fully time-based multiplexing and readout method that uses the principle of the global positioning system. Time-based multiplexing allows simplifying the multiplexing circuits where the only innate traces that connect the signal pins of the silicon photomultiplier (SiPM) channels to the readout channels are used as the multiplexing circuit. Every SiPM channel is connected to the delay grid that consists of the traces on a printed circuit board, and the inherent transit times from each SiPM channel to the readout channels encode the position information uniquely. Thus, the position of each SiPM can be identified using the time difference of arrival (TDOA) measurements. The proposed multiplexing can also allow simplification of the readout circuit using the time-to-digital converter (TDC) implemented in a field-programmable gate array (FPGA), where the time-over-threshold (ToT) is used to extract the energy information after multiplexing. In order to verify the proposed multiplexing method, we built a positron emission tomography (PET) detector that consisted of an array of 4  ×  4 LGSO crystals, each with a dimension of 3  ×  3  ×  20 mm3, and one- to-one coupled SiPM channels. We first employed the waveform sampler as an initial study, and then replaced the waveform sampler with an FPGA-TDC to further simplify the readout circuits. The 16 crystals were clearly resolved using only the time information obtained from the four readout channels. The coincidence resolving times (CRTs) were 382 and 406 ps FWHM when using the waveform sampler and the FPGA-TDC, respectively. The proposed simple multiplexing and readout methods can be useful for time-of-flight (TOF) PET scanners.

High throughput, multiplexed pathogen detection authenticates plague waves in medieval Venice, Italy.

PubMed

Tran, Thi-Nguyen-Ny; Signoli, Michel; Fozzati, Luigi; Aboudharam, Gérard; Raoult, Didier; Drancourt, Michel

2011-03-10

Historical records suggest that multiple burial sites from the 14th-16th centuries in Venice, Italy, were used during the Black Death and subsequent plague epidemics. High throughput, multiplexed real-time PCR detected DNA of seven highly transmissible pathogens in 173 dental pulp specimens collected from 46 graves. Bartonella quintana DNA was identified in five (2.9%) samples, including three from the 16th century and two from the 15th century, and Yersinia pestis DNA was detected in three (1.7%) samples, including two from the 14th century and one from the 16th century. Partial glpD gene sequencing indicated that the detected Y. pestis was the Orientalis biotype. These data document for the first time successive plague epidemics in the medieval European city where quarantine was first instituted in the 14th century.

Simultaneous aptasensor for multiplex pathogenic bacteria detection based on multicolor upconversion nanoparticles labels.

PubMed

Wu, Shijia; Duan, Nuo; Shi, Zhao; Fang, Congcong; Wang, Zhouping

2014-03-18

A highly sensitive and specific multiplex method for the simultaneous detection of three pathogenic bacteria was fabricated using multicolor upconversion nanoparticles (UCNPs) as luminescence labels coupled with aptamers as the molecular recognition elements. Multicolor UCNPs were synthesized via doping with various rare-earth ions to obtain well-separated emission peaks. The aptamer sequences were selected using the systematic evolution of ligands by exponential enrichment (SELEX) strategy for Staphylococcus aureus, Vibrio parahemolyticus, and Salmonella typhimurium. When applied in this method, aptamers can be used for the specific recognition of the bacteria from complex mixtures, including those found in real food matrixes. Aptamers and multicolor UCNPs were employed to selectively capture and simultaneously quantify the three target bacteria on the basis of the independent peaks. Under optimal conditions, the correlation between the concentration of three bacteria and the luminescence signal was found to be linear from 50-10(6) cfu mL(-1). Improved by the magnetic separation and concentration effect of Fe3O4 magnetic nanoparticles, the limits of detection of the developed method were found to be 25, 10, and 15 cfu mL(-1) for S. aureus, V. parahemolyticus, and S. typhimurium, respectively. The capability of the bioassay in real food samples was also investigated, and the results were consistent with experimental results obtained from plate-counting methods. This proposed method for the detection of various pathogenic bacteria based on multicolor UCNPs has great potential in the application of food safety and multiplex nanosensors.

Rapid detection of Shigella and enteroinvasive Escherichia coli in produce enrichments by a conventional multiplex PCR assay.

PubMed

Binet, Rachel; Deer, Deanne M; Uhlfelder, Samantha J

2014-06-01

Faster detection of contaminated foods can prevent adulterated foods from being consumed and minimize the risk of an outbreak of foodborne illness. A sensitive molecular detection method is especially important for Shigella because ingestion of as few as 10 of these bacterial pathogens can cause disease. The objectives of this study were to compare the ability of four DNA extraction methods to detect Shigella in six types of produce, post-enrichment, and to evaluate a new and rapid conventional multiplex assay that targets the Shigella ipaH, virB and mxiC virulence genes. This assay can detect less than two Shigella cells in pure culture, even when the pathogen is mixed with background microflora, and it can also differentiate natural Shigella strains from a control strain and eliminate false positive results due to accidental laboratory contamination. The four DNA extraction methods (boiling, PrepMan Ultra [Applied Biosystems], InstaGene Matrix [Bio-Rad], DNeasy Tissue kit [Qiagen]) detected 1.6 × 10(3)Shigella CFU/ml post-enrichment, requiring ∼18 doublings to one cell in 25 g of produce pre-enrichment. Lower sensitivity was obtained, depending on produce type and extraction method. The InstaGene Matrix was the most consistent and sensitive and the multiplex assay accurately detected Shigella in less than 90 min, outperforming, to the best of our knowledge, molecular assays currently in place for this pathogen. Published by Elsevier Ltd.

MO-F-CAMPUS-J-03: Development of a Human Brain PET for On-Line Proton Beam-Range Verification

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

Shao, Yiping

Purpose: To develop a prototype PET for verifying proton beam-range before each fractionated therapy that will enable on-line re-planning proton therapy. Methods: Latest “edge-less” silicon photomultiplier arrays and customized ASIC readout electronics were used to develop PET detectors with depth-of-interaction (DOI) measurement capability. Each detector consists of one LYSO array with each end coupled to a SiPM array. Multiple detectors can be seamlessly tiled together to form a large detector panel. Detectors with 1.5×1.5 and 2.0×2.0 mm crystals at 20 or 30 mm lengths were studied. Readout of individual SiPM or signal multiplexing was used to transfer 3D interaction position-codedmore » analog signals through flexible-print-circuit cables or PCB board to dedicated ASIC front-end electronics to output digital timing pulses that encode interaction information. These digital pulses can be transferred to, through standard LVDS cables, and decoded by a FPGA-based data acquisition of coincidence events and data transfer. The modular detector and scalable electronics/data acquisition will enable flexible PET system configuration for different imaging geometry. Results: Initial detector performance measurement shows excellent crystal identification even with 30 mm long crystals, ∼18% and 2.8 ns energy and timing resolutions, and around 2–3 mm DOI resolution. A small prototype PET scanner with one detector ring has been built and evaluated, validating the technology and design. A large size detector panel has been fabricated by scaling up from modular detectors. Different designs of resistor and capacitor based signal multiplexing boards were tested and selected based on optimal crystal identification and timing performance. Stackable readout electronics boards and FPGA-based data acquisition boards were developed and tested. A brain PET is under construction. Conclusion: Technology of large-size DOI detector based on SiPM array and advanced readout has been developed. PET imaging performance and initial phantom studies of on-line proton beam-range measurement will be conducted and reported. NIH grant R21CA187717; Cancer Prevention and Research Institute of Texas grant RP120326.« less

First Tests of Prototype SCUBA-2 Superconducting Bolometer Array

NASA Astrophysics Data System (ADS)

Woodcraft, Adam L.; Ade, Peter A. R.; Bintley, Dan; Hunt, Cynthia L.; Sudiwala, Rashmi V.; Hilton, Gene C.; Irwin, Kent D.; Reintsema, Carl D.; Audley, Michael D.; Holland, Wayne S.; MacIntosh, Mike

2006-09-01

We present results of the first tests on a 1280 pixel superconducting bolometer array, a prototype for SCUBA-2, a sub-mm camera being built for the James Clerk Maxwell Telescope in Hawaii. The bolometers are TES (transition edge sensor) detectors; these take advantage of the large variation of resistance with temperature through the superconducting transition. To keep the number of wires reasonable, a multiplexed read-out is used. Each pixel is read out through an individual DC SQUID; room temperature electronics switch between rows in the array by biasing the appropriate SQUIDs in turn. Arrays of 100 SQUIDs in series for each column then amplify the output. Unlike previous TES arrays, the multiplexing elements are located beneath each pixel, making large arrays possible, but construction more challenging. The detectors are constructed from Mo/Cu bi-layers; this technique enables the transition temperature to be tuned using the proximity effect by choosing the thickness of the normal and superconducting materials. To achieve the required performance, the detectors are operated at a temperature of approximately 120 mK. We describe the results of a basic characterisation of the array, demonstrating that it is fully operational, and give the results of signal to noise measurements.

A novel, multiplexed, probe-based quantitative PCR assay for the soybean root- and stem-rot pathogen, Phytophthora sojae, utilizes its transposable element

USDA-ARS?s Scientific Manuscript database

Phytophthora root rot of soybean (Glycine max Merr.) is caused by the oomycete Phytophthora sojae (Kaufm. and Gerd.). P. sojae has a narrow host range, consisting primarily of soybean, and it is a serious pathogen worldwide. It exists in root and stem tissues as mycelium, wherein it can form oospo...

Multiplexed Oversampling Digitizer in 65 nm CMOS for Column-Parallel CCD Readout

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

Grace, Carl; Walder, Jean-Pierre; von der Lippe, Henrik

2012-04-10

A digitizer designed to read out column-parallel charge-coupled devices (CCDs) used for high-speed X-ray imaging is presented. The digitizer is included as part of the High-Speed Image Preprocessor with Oversampling (HIPPO) integrated circuit. The digitizer module comprises a multiplexed, oversampling, 12-bit, 80 MS/s pipelined Analog-to-Digital Converter (ADC) and a bank of four fast-settling sample-and-hold amplifiers to instrument four analog channels. The ADC multiplexes and oversamples to reduce its area to allow integration that is pitch-matched to the columns of the CCD. Novel design techniques are used to enable oversampling and multiplexing with a reduced power penalty. The ADC exhibits 188more » ?V-rms noise which is less than 1 LSB at a 12-bit level. The prototype is implemented in a commercially available 65 nm CMOS process. The digitizer will lead to a proof-of-principle 2D 10 Gigapixel/s X-ray detector.« less

APDS: the autonomous pathogen detection system.

PubMed

Hindson, Benjamin J; Makarewicz, Anthony J; Setlur, Ujwal S; Henderer, Bruce D; McBride, Mary T; Dzenitis, John M

2005-04-15

We have developed and tested a fully autonomous pathogen detection system (APDS) capable of continuously monitoring the environment for airborne biological threat agents. The system was developed to provide early warning to civilians in the event of a bioterrorism incident and can be used at high profile events for short-term, intensive monitoring or in major public buildings or transportation nodes for long-term monitoring. The APDS is completely automated, offering continuous aerosol sampling, in-line sample preparation fluidics, multiplexed detection and identification immunoassays, and nucleic acid-based polymerase chain reaction (PCR) amplification and detection. Highly multiplexed antibody-based and duplex nucleic acid-based assays are combined to reduce false positives to a very low level, lower reagent costs, and significantly expand the detection capabilities of this biosensor. This article provides an overview of the current design and operation of the APDS. Certain sub-components of the ADPS are described in detail, including the aerosol collector, the automated sample preparation module that performs multiplexed immunoassays with confirmatory PCR, and the data monitoring and communications system. Data obtained from an APDS that operated continuously for 7 days in a major U.S. transportation hub is reported.

Implementing a Multiplexed System of Detectors for Higher Photon Counting Rates

DTIC Science & Technology

2007-01-01

D1 D2 Fig. 3. (a) Setup for testing different arrangements of InGaAs SPAD assemblies; (b) three different InGaAs SPAD assemblies; ( c ) schematic of...presently available, either commercial or prototype, the deadtimes range from ≈50 ns for actively quenched single photon avalanche detectors ( SPADs ...to ≈10 µs for passively quenched SPADs , although even actively quenched SPADs sometimes employ µs deadtimes to avoid excessive afterpulsing rates. In

Laser-Based Measurements of OH, Temperature, and Water Vapor Concentration in a Hydrocarbon-Fueled Scramjet (POSTPRINT)

DTIC Science & Technology

2008-07-01

hours. The detector signals are post-processed with a software lock-in amplifier to recover the WMS-1f and WMS-2f signals. The TDLAS sensor utilizes...Figure 6. Schematic of TDLAS sensor for temperature and water vapor concentration. Fiber Diode lasers Grating Fiber Detectors Demultiplexer Multiplexer...within the combustor. Tunable diode laser- based absorption spectroscopy ( TDLAS ) is used to measure water vapor concentration and static temperature near

Heterojunction-Internal-Photoemission Infrared Detectors

NASA Technical Reports Server (NTRS)

Maserjian, Joseph

1991-01-01

New type of photodetector adds options for design of imaging devices. Heterojunction-internal-photoemission (HIP) infrared photodetectors proposed for incorporation into planar arrays in imaging devices required to function well at wavelengths from 8 to 17 micrometers and at temperatures above 65 K. Photoexcited electrons cross energy barrier at heterojunction and swept toward collection layer. Array of such detectors made by etching mesa structures. HIP layers stacked to increase quantum efficiency. Also built into integrated circuits including silicon multiplexer/readout circuits.

A Silicon SPECT System for Molecular Imaging of the Mouse Brain.

PubMed

Shokouhi, Sepideh; Fritz, Mark A; McDonald, Benjamin S; Durko, Heather L; Furenlid, Lars R; Wilson, Donald W; Peterson, Todd E

2007-01-01

We previously demonstrated the feasibility of using silicon double-sided strip detectors (DSSDs) for SPECT imaging of the activity distribution of iodine-125 using a 300-micrometer thick detector. Based on this experience, we now have developed fully customized silicon DSSDs and associated readout electronics with the intent of developing a multi-pinhole SPECT system. Each DSSD has a 60.4 mm × 60.4 mm active area and is 1 mm thick. The strip pitch is 59 micrometers, and the readout of the 1024 strips on each side gives rise to a detector with over one million pixels. Combining four high-resolution DSSDs into a SPECT system offers an unprecedented space-bandwidth product for the imaging of single-photon emitters. The system consists of two camera heads with two silicon detectors stacked one behind the other in each head. The collimator has a focused pinhole system with cylindrical-shaped pinholes that are laser-drilled in a 250 μm tungsten plate. The unique ability to collect projection data at two magnifications simultaneously allows for multiplexed data at high resolution to be combined with lower magnification data with little or no multiplexing. With the current multi-pinhole collimator design, our SPECT system will be capable of offering high spatial resolution, sensitivity and angular sampling for small field-of-view applications, such as molecular imaging of the mouse brain.

Operation and performance of new NIR detectors from SELEX

NASA Astrophysics Data System (ADS)

Atkinson, D.; Bezawada, N.; Hipwood, L. G.; Shorrocks, N.; Milne, H.

2012-07-01

The European Space Agency (ESA) has funded SELEX Galileo, Southampton, UK to develop large format near infrared (NIR) detectors for its future space and ground based programmes. The UKATC has worked in collaboration with SELEX Galileo to test and characterise the new detectors produced during phase-1 of the development. In order to demonstrate the detector material performance, the HgCdTe (MCT) detector diodes (grown on GaAs substrate through MOVPE process in small 320×256, 24μm pixel format) are hybridised to the existing SELEX Galileo SWALLOW CMOS readout chip. The substrate removed and MCT thinned detector arrays were then tested and evaluated at the UKATC following screening tests at SELEX. This paper briefly describes the test setup, the operational aspects of the readout multiplexer and presents the performance parameters of the detector arrays including: conversion gain, detector dark current, read noise, linearity, quantum efficiency and persistence for various detector temperatures between 80K and 140K.

The increasing application of multiplex nucleic acid detection tests to the diagnosis of syndromic infections.

PubMed

Gray, J; Coupland, L J

2014-01-01

On 14 January 2013, the US Food and Drug Administration (FDA) announced permission for a multiplex nucleic acid test, the xTAG® Gastrointestinal Pathogen Panel (GPP) (Luminex Corporation, USA), which simultaneously detects 11 common viral, bacterial and parasitic causes of infectious gastroenteritis, to be marketed in the USA. This announcement reflects the current move towards the development and commercialization of detection technologies based on nucleic acid amplification techniques for diagnosis of syndromic infections. We discuss the limitations and advantages of nucleic acid amplification techniques and the recent advances in Conformité Européene - in-vitro diagnostic (CE-IVD)-approved multiplex real-time PCR kits for the simultaneous detection of multiple targets within the clinical diagnostics market.

Multiplex polymerase chain reaction assay for the detection of minute virus of mice and mouse parvovirus infections in laboratory mice.

PubMed

Wang, K W; Chueh, L L; Wang, M H; Huang, Y T; Fang, B H; Chang, C Y; Fang, M C; Chou, J Y; Hsieh, S C; Wan, C H

2013-04-01

Mouse parvoviruses are among the most prevalent infectious pathogens in contemporary mouse colonies. To improve the efficiency of routine screening for mouse parvovirus infections, a multiplex polymerase chain reaction (PCR) assay targeting the VP gene was developed. The assay detected minute virus of mice (MVM), mouse parvovirus (MPV) and a mouse housekeeping gene (α-actin) and was able to specifically detect MVM and MPV at levels as low as 50 copies. Co-infection with the two viruses with up to 200-fold differences in viral concentrations can easily be detected. The multiplex PCR assay developed here could be a useful tool for monitoring mouse health and the viral contamination of biological materials.

Measuring the electron neutrino mass with improved sensitivity: the HOLMES experiment

NASA Astrophysics Data System (ADS)

Giachero, A.; Alpert, B. K.; Becker, D. T.; Bennett, D. A.; Biasotti, M.; Brofferio, C.; Ceriale, V.; Ceruti, G.; Corsini, D.; Day, P. K.; De Gerone, M.; Dressler, R.; Faverzani, M.; Ferri, E.; Fowler, J. W.; Fumagalli, E.; Gallucci, G.; Gard, J. D.; Gatti, F.; Hays-Wehle, J. P.; Heinitz, S.; Hilton, G. C.; Köster, U.; Lusignoli, M.; Mates, J. A. B.; Nisi, S.; Nucciotti, A.; Orlando, A.; Parodi, L.; Pessina, G.; Pizzigoni, G.; Puiu, A.; Ragazzi, S.; Reintsema, C. D.; Ribeiro Gomes, M.; Schmidt, D. R.; Schumann, D.; Siccardi, F.; Sisti, M.; Swetz, D. S.; Terranova, F.; Ullom, J. N.; Vale, L. R.

2017-02-01

HOLMES is a new experiment aiming at directly measuring the neutrino mass with a sensitivity below 2 eV . HOLMES will perform a calorimetric measurement of the energy released in the decay of 163Ho. The calorimetric measurement eliminates systematic uncertainties arising from the use of external beta sources, as in experiments with spectrometers. This measurement was proposed in 1982 by A. De Rujula and M. Lusignoli, but only recently the detector technological progress has allowed to design a sensitive experiment. HOLMES will deploy a 1000 pixels array of low temperature microcalorimeters with implanted 163Ho nuclei. HOLMES, besides being an important step forward in the direct neutrino mass measurement with a calorimetric approach, will also establish the potential of this approach to extend the sensitivity down to 0.1 eV and lower. The detectors used for the HOLMES experiment will be Mo/Cu bilayers TESs (Transition Edge Sensors) on SiNx membrane with gold absorbers. Microwave multiplexed rf-SQUIDs are the best available technique to read out large array of such detectors. An extensive R&D activity is in progress in order to maximize the multiplexing factor while preserving the performances of the individual detectors. To embed the 163Ho into the gold absorbers a custom mass separator ion implanter is being developed. The current activities are focused on the the single detector performances optimization and on the 163Ho isotope production and embedding. A preliminary measurement of a sub-array of 4× 16 detectors is planned late in 2017. In this contribution we present the HOLMES project with its technical challenges, its status and perspectives.

A kilo-pixel imaging system for future space based far-infrared observatories using microwave kinetic inductance detectors

NASA Astrophysics Data System (ADS)

Baselmans, J. J. A.; Bueno, J.; Yates, S. J. C.; Yurduseven, O.; Llombart, N.; Karatsu, K.; Baryshev, A. M.; Ferrari, L.; Endo, A.; Thoen, D. J.; de Visser, P. J.; Janssen, R. M. J.; Murugesan, V.; Driessen, E. F. C.; Coiffard, G.; Martin-Pintado, J.; Hargrave, P.; Griffin, M.

2017-05-01

Aims: Future astrophysics and cosmic microwave background space missions operating in the far-infrared to millimetre part of the spectrum will require very large arrays of ultra-sensitive detectors in combination with high multiplexing factors and efficient low-noise and low-power readout systems. We have developed a demonstrator system suitable for such applications. Methods: The system combines a 961 pixel imaging array based upon Microwave Kinetic Inductance Detectors (MKIDs) with a readout system capable of reading out all pixels simultaneously with only one readout cable pair and a single cryogenic amplifier. We evaluate, in a representative environment, the system performance in terms of sensitivity, dynamic range, optical efficiency, cosmic ray rejection, pixel-pixel crosstalk and overall yield at an observation centre frequency of 850 GHz and 20% fractional bandwidth. Results: The overall system has an excellent sensitivity, with an average detector sensitivity < NEPdet> =3×10-19 WHz measured using a thermal calibration source. At a loading power per pixel of 50 fW we demonstrate white, photon noise limited detector noise down to 300 mHz. The dynamic range would allow the detection of 1 Jy bright sources within the field of view without tuning the readout of the detectors. The expected dead time due to cosmic ray interactions, when operated in an L2 or a similar far-Earth orbit, is found to be <4%. Additionally, the achieved pixel yield is 83% and the crosstalk between the pixels is <-30 dB. Conclusions: This demonstrates that MKID technology can provide multiplexing ratios on the order of a 1000 with state-of-the-art single pixel performance, and that the technology is now mature enough to be considered for future space based observatories and experiments.

Experimental study of a depth-encoding PET detector inserting horizontal-striped glass between crystal layers

NASA Astrophysics Data System (ADS)

Yang, J.; Kim, K. B.; Choi, Y.; Kang, J.

2018-04-01

A depth-encoding positron emission tomography (PET) detector inserting a horizontal-striped glass between pixilated scintillation crystal layers was developed and experimentally evaluated. The detector consists of 2-layers of 4×4 LYSO array arranged with a 3.37 mm pitch. Horizontal-striped glasses with 1×4 array with different thickness of 3, 4 and 5 mm were inserted between top- and bottom-crystal layers. Bottom surface of bottom-layer was optically coupled to a 4×4 GAPD array. Sixteen output signals from DOI-PET detector were multiplexed by modified resistive charge division (RCD) networks and multiplexed signals were fed into custom-made charge-sensitive preamplifiers. The four amplified signals were digitized and recorded by the custom-made DAQ system based on FPGA. The four digitized outputs were post-processed and converted to flood histograms for each interaction event. Experimental results revealed that all crystal pixels were clearly identified on the 2D flood histogram without overlapping. Patterns of the 2D flood histogram were constituted with arrangements of [bottom–top–bottom–top–\\ldots–top–bottom–top–bottom] crystal responses in X-direction. These could be achieved by employing horizontal-striped glass that controlled the extent of light dispersion towards the X-direction in crystal layers for generation of a different position mapping for each layer and the modified RCD network that controls degree of charge sharing in readout electronics for reduction of identification error. This study demonstrated the proposed DOI-PET detector can extract the 3D γ-ray interaction position without considerable performance degradation of PET detector from the 2D flood histogram.

Holmes

NASA Astrophysics Data System (ADS)

Faverzani, M.; HOLMES Collaboration

2017-09-01

The experiment HOLMES, founded by the European Research Council, will perform a calorimetric measurement of the energy released in the electron capture of 163Ho to directly measure the neutrino mass with a sensitivity of ˜ 1 eV. This approach allows to eliminate the problematics connected to the use of external sources and the systematic uncertainties arising from decays on excited states. Such measurement will be performed with low temperature thermal detectors, where the decay energy is converted into a temperature signal measured by sensitive thermometers. HOLMES, besides of being an important step forward in the direct neutrino mass measurement with a calorimetric approach, will also establish the potential of this approach to extend the sensitivity down to 0.1 eV and lower. The best configuration has been defined with Monte Carlo simulations: HOLMES will collect about 3 × 1013 decays with 1000 detectors characterized by an instrumental energy resolution of the order of the eV and a time resolution of few microseconds. For a measuring time of 3 years, this translates in a total required 163Ho activity of about 300 kBq, equivalent to about 6.5 × 1016 163Ho nuclei, or 18 µg. The HOLMES detectors will have 163Ho implanted into Gold absorber coupled to Transition Edge Sensors, which will be read using microwave multiplexed rf-SQUIDs in combination with a ROACH2 based acquisition system. An extensive R&D activity is in progress in order to maximize the multiplexing factor while preserving the performances of the individual detectors. R&D activities aimed at optimizing the single detector performances, the 163Ho isotope production and embedding are in progress and will converge in a preliminary measurement of an array of 16 detectors planned by the end of 2016. We outline here the HOLMES project with its technical challenges, its status and perspectives.

Advanced DNA-Based Point-of-Care Diagnostic Methods for Plant Diseases Detection.

PubMed

Lau, Han Yih; Botella, Jose R

2017-01-01

Diagnostic technologies for the detection of plant pathogens with point-of-care capability and high multiplexing ability are an essential tool in the fight to reduce the large agricultural production losses caused by plant diseases. The main desirable characteristics for such diagnostic assays are high specificity, sensitivity, reproducibility, quickness, cost efficiency and high-throughput multiplex detection capability. This article describes and discusses various DNA-based point-of care diagnostic methods for applications in plant disease detection. Polymerase chain reaction (PCR) is the most common DNA amplification technology used for detecting various plant and animal pathogens. However, subsequent to PCR based assays, several types of nucleic acid amplification technologies have been developed to achieve higher sensitivity, rapid detection as well as suitable for field applications such as loop-mediated isothermal amplification, helicase-dependent amplification, rolling circle amplification, recombinase polymerase amplification, and molecular inversion probe. The principle behind these technologies has been thoroughly discussed in several review papers; herein we emphasize the application of these technologies to detect plant pathogens by outlining the advantages and disadvantages of each technology in detail.

Advanced DNA-Based Point-of-Care Diagnostic Methods for Plant Diseases Detection

PubMed Central

Lau, Han Yih; Botella, Jose R.

2017-01-01

Diagnostic technologies for the detection of plant pathogens with point-of-care capability and high multiplexing ability are an essential tool in the fight to reduce the large agricultural production losses caused by plant diseases. The main desirable characteristics for such diagnostic assays are high specificity, sensitivity, reproducibility, quickness, cost efficiency and high-throughput multiplex detection capability. This article describes and discusses various DNA-based point-of care diagnostic methods for applications in plant disease detection. Polymerase chain reaction (PCR) is the most common DNA amplification technology used for detecting various plant and animal pathogens. However, subsequent to PCR based assays, several types of nucleic acid amplification technologies have been developed to achieve higher sensitivity, rapid detection as well as suitable for field applications such as loop-mediated isothermal amplification, helicase-dependent amplification, rolling circle amplification, recombinase polymerase amplification, and molecular inversion probe. The principle behind these technologies has been thoroughly discussed in several review papers; herein we emphasize the application of these technologies to detect plant pathogens by outlining the advantages and disadvantages of each technology in detail. PMID:29375588

Multiplex detection of pathogen biomarkers in human blood, serum, and saliva using silicon photonic microring resonators

NASA Astrophysics Data System (ADS)

Estrada, I. A.; Burlingame, R. W.; Wang, A. P.; Chawla, K.; Grove, T.; Wang, J.; Southern, S. O.; Iqbal, M.; Gunn, L. C.; Gleeson, M. A.

2015-05-01

Genalyte has developed a multiplex silicon photonic chip diagnostics platform (MaverickTM) for rapid detection of up to 32 biological analytes from a drop of sample in just 10 to 20 minutes. The chips are manufactured with waveguides adjacent to ring resonators, and probed with a continuously variable wavelength laser. A shift in the resonant wavelength as mass binds above the ring resonators is measured and is directly proportional to the amount of bound macromolecules. We present here the ability to multiplex the detection of hemorrhagic fever antigens in whole blood, serum, and saliva in a 16 minute assay. Our proof of concept testing of a multiplex antigencapture chip has the ability to detect Zaire Ebola (ZEBOV) recombinant soluble glycoprotein (rsGP), Marburg virus (MARV) Angola recombinant glycoprotein (rGP) and dengue nonstructural protein I (NS1). In parallel, detection of 2 malaria antigens has proven successful, but has yet to be incorporated into multiplex with the others. Each assay performs with sensitivity ranging from 1.6 ng/ml to 39 ng/ml depending on the antigen detected, and with minimal cross-reactivity.

Single transmission-line readout method for silicon photomultiplier based time-of-flight and depth-of-interaction PET

NASA Astrophysics Data System (ADS)

Ko, Guen Bae; Lee, Jae Sung

2017-03-01

We propose a novel single transmission-line readout method for whole-body time-of-flight positron emission tomography applications, without compromising on performance. The basic idea of the proposed multiplexing method is the addition of a specially prepared tag signal ahead of the scintillation pulse. The tag signal is a square pulse that encodes photon arrival time and channel information. The 2D position of a silicon photomultiplier (SiPM) array is encoded by the specific width and height of the tag signal. A summing amplifier merges the tag and scintillation signals of each channel, and the final output signal can be acquired with a one-channel digitizer. The feasibility and performance of the proposed method were evaluated using a 1:1 coupled detector consisting of 4  ×  4 array of LGSO crystals and 16 channel SiPM. The sixteen 3 mm LGSO crystals were clearly separated in the crystal-positioning map with high reliability. The average energy resolution and coincidence resolving time were 11.31  ±  0.55% and 264.7  ±  10.7 ps, respectively. We also proved that the proposed method does not degrade timing performance with increasing multiplexing ratio. The two types of LGSO crystals (L0.95GSO and L0.20GSO) in phoswich detector were also clearly identified with the high-reliability using pulse shape discrimination, thanks to the well-preserved pulse shape information. In conclusion, the proposed multiplexing method allows decoding of the 3D interaction position of gamma rays in the scintillation detector with single-line readout.

Single transmission-line readout method for silicon photomultiplier based time-of-flight and depth-of-interaction PET.

PubMed

Ko, Guen Bae; Lee, Jae Sung

2017-03-21

We propose a novel single transmission-line readout method for whole-body time-of-flight positron emission tomography applications, without compromising on performance. The basic idea of the proposed multiplexing method is the addition of a specially prepared tag signal ahead of the scintillation pulse. The tag signal is a square pulse that encodes photon arrival time and channel information. The 2D position of a silicon photomultiplier (SiPM) array is encoded by the specific width and height of the tag signal. A summing amplifier merges the tag and scintillation signals of each channel, and the final output signal can be acquired with a one-channel digitizer. The feasibility and performance of the proposed method were evaluated using a 1:1 coupled detector consisting of 4  ×  4 array of LGSO crystals and 16 channel SiPM. The sixteen 3 mm LGSO crystals were clearly separated in the crystal-positioning map with high reliability. The average energy resolution and coincidence resolving time were 11.31  ±  0.55% and 264.7  ±  10.7 ps, respectively. We also proved that the proposed method does not degrade timing performance with increasing multiplexing ratio. The two types of LGSO crystals (L 0.95 GSO and L 0.20 GSO) in phoswich detector were also clearly identified with the high-reliability using pulse shape discrimination, thanks to the well-preserved pulse shape information. In conclusion, the proposed multiplexing method allows decoding of the 3D interaction position of gamma rays in the scintillation detector with single-line readout.

Fabrication of the pinhole aperture for AdaptiSPECT

PubMed Central

Kovalsky, Stephen; Kupinski, Matthew A.; Barrett, Harrison H.; Furenlid, Lars R.

2015-01-01

AdaptiSPECT is a pre-clinical pinhole SPECT imaging system under final construction at the Center for Gamma-Ray Imaging. The system is designed to be able to autonomously change its imaging configuration. The system comprises 16 detectors mounted on translational stages to move radially away and towards the center of the field-of-view. The system also possesses an adaptive pinhole aperture with multiple collimator diameters and pinhole sizes, as well as the possibility to switch between multiplexed and non-multiplexed imaging configurations. In this paper, we describe the fabrication of the AdaptiSPECT pinhole aperture and its controllers. PMID:26146443

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

Liu, R.; Lu, R.; Gong, S.

We demonstrate a room-temperature semiconductor-based photodetector where readout is achieved using a resonant radio-frequency (RF) circuit consisting of a microstrip split-ring resonator coupled to a microstrip busline, fabricated on a semiconductor substrate. The RF resonant circuits are characterized at RF frequencies as function of resonator geometry, as well as for their response to incident IR radiation. The detectors are modeled analytically and using commercial simulation software, with good agreement to our experimental results. Though the detector sensitivity is weak, the detector architecture offers the potential for multiplexing arrays of detectors on a single read-out line, in addition to high speedmore » response for either direct coupling of optical signals to RF circuitry, or alternatively, carrier dynamics characterization of semiconductor, or other, material systems.« less

Multiplex cytokine profiling with highly pathogenic material: use of formalin solution in luminex analysis.

PubMed

Dowall, Stuart D; Graham, Victoria A; Tipton, Thomas R W; Hewson, Roger

2009-08-31

Work with highly pathogenic material mandates the use of biological containment facilities, involving microbiological safety cabinets and specialist laboratory engineering structures typified by containment level 3 (CL3) and CL4 laboratories. Consequences of working in high containment are the practical difficulties associated with containing specialist assays and equipment often essential for experimental analyses. In an era of increased interest in biodefence pathogens and emerging diseases, immunological analysis has developed rapidly alongside traditional techniques in virology and molecular biology. For example, in order to maximise the use of small sample volumes, multiplexing has become a more popular and widespread approach to quantify multiple analytes simultaneously, such as cytokines and chemokines. The luminex microsphere system allows for the detection of many cytokines and chemokines in a single sample, but the detection method of using aligned lasers and fluidics means that samples often have to be analysed in low containment facilities. In order to perform cytokine analysis in materials from high containment (CL3 and CL4 laboratories), we have developed an appropriate inactivation methodology after staining steps, which although results in a reduction of median fluorescent intensity, produces statistically comparable outcomes when judged against non-inactivated samples. This methodology thus extends the use of luminex technology for material that contains highly pathogenic biological agents.

CALDER: Cryogenic light detectors for background-free searches

NASA Astrophysics Data System (ADS)

Di Domizio, S.; Bellini, F.; Cardani, L.; Casali, N.; Castellano, M. G.; Colantoni, I.; Cosmelli, C.; Cruciani, A.; D'Addabbo, A.; Martinez, M.; Minutolo, L.; Tomei, C.; Vignati, M.

2018-01-01

CALDER is a R&D project for the development of cryogenic light detectors with an active surface of 5x5cm2 and an energy resolution of 20 eV RMS for visible and UV photons. These devices can enhance the sensitivity of next generation large mass bolometric detectors for rare event searches, providing an active background rejection method based on particle discrimination. A CALDER detector is composed by a large area Si absorber substrate with superconducting kinetic inductance detectors (KIDs) deposited on it. The substrate converts the incoming light into athermal phonons, that are then sensed by the KIDs. KID technology combine fabrication simplicity with natural attitude to frequency-domain multiplexing, making it an ideal candidate for a large scale bolometric experiments. We will give an overview of the CALDER project and show the performances obtained with prototype detectors both in terms of energy resolution and efficiency.

Development of a Crosstalk Suppression Algorithm for KID Readout

NASA Astrophysics Data System (ADS)

Lee, Kyungmin; Ishitsuka, H.; Oguri, S.; Suzuki, J.; Tajima, O.; Tomita, N.; Won, Eunil; Yoshida, M.

2018-06-01

The GroundBIRD telescope aims to detect B-mode polarization of the cosmic microwave background radiation using the kinetic inductance detector array as a polarimeter. For the readout of the signal from detector array, we have developed a frequency division multiplexing readout system based on a digital down converter method. These techniques in general have the leakage problems caused by the crosstalks. The window function was applied in the field programmable gate arrays to mitigate the effect of these problems and tested it in algorithm level.

Sensors with centroid-based common sensing scheme and their multiplexing

NASA Astrophysics Data System (ADS)

Berkcan, Ertugrul; Tiemann, Jerome J.; Brooksby, Glen W.

1993-03-01

The ability to multiplex sensors with different measurands but with a common sensing scheme is of importance in aircraft and aircraft engine applications; this unification of the sensors into a common interface has major implications for weight, cost, and reliability. A new class of sensors based on a common sensing scheme and their E/O Interface has been developed. The approach detects the location of the centroid of a beam of light; the set of fiber optic sensors with this sensing scheme include linear and rotary position, temperature, pressure, as well as duct Mach number. The sensing scheme provides immunity to intensity variations of the source or due to environmental effects on the fiber. A detector spatially multiplexed common electro-optic interface for the sensors has been demonstrated with a position and a temperature sensor.

Multi-pinhole SPECT Imaging with Silicon Strip Detectors

PubMed Central

Peterson, Todd E.; Shokouhi, Sepideh; Furenlid, Lars R.; Wilson, Donald W.

2010-01-01

Silicon double-sided strip detectors offer outstanding instrinsic spatial resolution with reasonable detection efficiency for iodine-125 emissions. This spatial resolution allows for multiple-pinhole imaging at low magnification, minimizing the problem of multiplexing. We have conducted imaging studies using a prototype system that utilizes a detector of 300-micrometer thickness and 50-micrometer strip pitch together with a 23-pinhole collimator. These studies include an investigation of the synthetic-collimator imaging approach, which combines multiple-pinhole projections acquired at multiple magnifications to obtain tomographic reconstructions from limited-angle data using the ML-EM algorithm. Sub-millimeter spatial resolution was obtained, demonstrating the basic validity of this approach. PMID:20953300

Ultrasensitive multiplex optical quantification of bacteria in large samples of biofluids

PubMed Central

Pazos-Perez, Nicolas; Pazos, Elena; Catala, Carme; Mir-Simon, Bernat; Gómez-de Pedro, Sara; Sagales, Juan; Villanueva, Carlos; Vila, Jordi; Soriano, Alex; García de Abajo, F. Javier; Alvarez-Puebla, Ramon A.

2016-01-01

Efficient treatments in bacterial infections require the fast and accurate recognition of pathogens, with concentrations as low as one per milliliter in the case of septicemia. Detecting and quantifying bacteria in such low concentrations is challenging and typically demands cultures of large samples of blood (~1 milliliter) extending over 24–72 hours. This delay seriously compromises the health of patients. Here we demonstrate a fast microorganism optical detection system for the exhaustive identification and quantification of pathogens in volumes of biofluids with clinical relevance (~1 milliliter) in minutes. We drive each type of bacteria to accumulate antibody functionalized SERS-labelled silver nanoparticles. Particle aggregation on the bacteria membranes renders dense arrays of inter-particle gaps in which the Raman signal is exponentially amplified by several orders of magnitude relative to the dispersed particles. This enables a multiplex identification of the microorganisms through the molecule-specific spectral fingerprints. PMID:27364357

Development of a novel hexa-plex PCR method for identification and serotyping of Salmonella species.

PubMed

Li, Ruichao; Wang, Yang; Shen, Jianzhong; Wu, Congming

2014-01-01

Salmonella is one of the most important foodborne pathogens, which causes a huge economic burden worldwide. To detect Salmonella rapidly is very meaningful in preventing salmonellosis and decreasing economic losses. Currently, isolation of Salmonella is confirmed by biochemical and serobased serotyping methods, which are time consuming, labor intensive, and complicated. To solve this problem, a hexa-plex polymerase chain reaction (PCR) method was developed using comparative genomics analysis and multiplex PCR technology to detect Salmonella and Salmonella Typhimurium, Salmonella Enteritidis, Salmonella Agona, Salmonella Choleraesuis, and Salmonella Pullorum simultaneously. The accuracy of this method was tested by a collection of 142 Salmonella. Furthermore, the strategy described in this article to mine serovar-specific fragments for Salmonella could be used to find specific fragments for other Salmonella serotypes and bacteria. The combination of this strategy and multiplex PCR is promising in the rapid identification of foodborne pathogens.

[Combined G-banded karyotyping and multiplex ligation-dependent probe amplification for the detection of chromosomal abnormalities in fetuses with congenital heart defects].

PubMed

Liu, Yang; Xie, Jiansheng; Geng, Qian; Xu, Zhiyong; Wu, Weiqin; Luo, Fuwei; Li, Suli; Wang, Qin; Chen, Wubin; Tan, Hongxi; Zhang, Hu

2017-02-10

To assess the value of G-banded karyotyping in combination with multiplex ligation-dependent probe amplification (MLPA) as a tool for the detection of chromosomal abnormalities in fetuses with congenital heart defects. The combined method was used to analyze 104 fetuses with heart malformations identified by ultrasonography. Abnormal findings were confirmed with chromosomal microarray analysis (CMA). Nineteen (18%) fetuses were found to harbor chromosomal aberrations by G-banded karyotyping and MLPA. For 93 cases, CMA has detected abnormalities in 14 cases including 10 pathogenic copy number variations (CNVs) and 4 CNVs of uncertain significance (VOUS). MLPA was able to detect all of the pathogenic CNVs and 1 VOUS CNV. Combined use of G-banded karyotyping and MLPA is a rapid, low-cost and effective method to detect chromosomal abnormalities in fetuses with various heart malformations.

Detection of Multiple Pathogens in Serum Using Silica-Encapsulated Nanotags in a Surface-Enhanced Raman Scattering-Based Immunoassay.

PubMed

Neng, Jing; Li, Yina; Driscoll, Ashley J; Wilson, William C; Johnson, Patrick A

2018-06-06

A robust immunoassay based on surface-enhanced Raman scattering (SERS) has been developed to simultaneously detect trace quantities of multiple pathogenic antigens from West Nile virus, Rift Valley fever virus, and Yersinia pestis in fetal bovine serum. Antigens were detected by capture with silica-encapsulated nanotags and magnetic nanoparticles conjugated with polyclonal antibodies. The magnetic pull-down resulted in aggregation of the immune complexes, and the silica-encapsulated nanotags provided distinct spectra corresponding to each antigen captured. The limit of detection was ∼10 pg/mL in 20% fetal bovine serum, a significant improvement over previous studies in terms of sensitivity, level of multiplexing, and medium complexity. This highly sensitive multiplex immunoassay platform provides a promising method to detect various antigens directly in crude serum samples without the tedious process of sample preparation, which is desirable for on-site diagnostic testing and real-time disease monitoring.

Zika Virus and Chikungunya Virus CoInfections: A Series of Three Cases from a Single Center in Ecuador

PubMed Central

Zambrano, Hector; Waggoner, Jesse J.; Almeida, Cristina; Rivera, Lisette; Benjamin, Juan Quintana; Pinsky, Benjamin A.

2016-01-01

Zika virus (ZIKV) and chikungunya virus (CHIKV) cocirculate throughout much of the tropical Western Hemisphere; however, few cases of coinfection with these two pathogens have been reported. Herein, we describe three cases of ZIKV–CHIKV coinfection detected at a single center in Ecuador: a patient who developed symptoms on postoperative day 5 from an orthopedic procedure, a woman who had traveled to Ecuador for fertility treatment, and a woman who was admitted for Guillain–Barré syndrome and had ZIKV and CHIKV detected in serum and cerebrospinal fluid. All cases were diagnosed using a multiplex real-time reverse transcription polymerase chain reaction, and ZIKV viremia was detected as late as 16 days after symptom onset. These cases demonstrate the varied clinical presentation of ZIKV–CHIKV coinfections as well as the importance of multiplexed arboviral testing for these pathogens. PMID:27402518

Zika Virus and Chikungunya Virus CoInfections: A Series of Three Cases from a Single Center in Ecuador.

PubMed

Zambrano, Hector; Waggoner, Jesse J; Almeida, Cristina; Rivera, Lisette; Benjamin, Juan Quintana; Pinsky, Benjamin A

2016-10-05

Zika virus (ZIKV) and chikungunya virus (CHIKV) cocirculate throughout much of the tropical Western Hemisphere; however, few cases of coinfection with these two pathogens have been reported. Herein, we describe three cases of ZIKV-CHIKV coinfection detected at a single center in Ecuador: a patient who developed symptoms on postoperative day 5 from an orthopedic procedure, a woman who had traveled to Ecuador for fertility treatment, and a woman who was admitted for Guillain-Barré syndrome and had ZIKV and CHIKV detected in serum and cerebrospinal fluid. All cases were diagnosed using a multiplex real-time reverse transcription polymerase chain reaction, and ZIKV viremia was detected as late as 16 days after symptom onset. These cases demonstrate the varied clinical presentation of ZIKV-CHIKV coinfections as well as the importance of multiplexed arboviral testing for these pathogens. © The American Society of Tropical Medicine and Hygiene.

High Throughput, Multiplexed Pathogen Detection Authenticates Plague Waves in Medieval Venice, Italy

PubMed Central

Tran, Thi-Nguyen-Ny; Signoli, Michel; Fozzati, Luigi; Aboudharam, Gérard; Raoult, Didier; Drancourt, Michel

2011-01-01

Background Historical records suggest that multiple burial sites from the 14th–16th centuries in Venice, Italy, were used during the Black Death and subsequent plague epidemics. Methodology/Principal Findings High throughput, multiplexed real-time PCR detected DNA of seven highly transmissible pathogens in 173 dental pulp specimens collected from 46 graves. Bartonella quintana DNA was identified in five (2.9%) samples, including three from the 16th century and two from the 15th century, and Yersinia pestis DNA was detected in three (1.7%) samples, including two from the 14th century and one from the 16th century. Partial glpD gene sequencing indicated that the detected Y. pestis was the Orientalis biotype. Conclusions These data document for the first time successive plague epidemics in the medieval European city where quarantine was first instituted in the 14th century. PMID:21423736

Solution-based circuits enable rapid and multiplexed pathogen detection.

PubMed

Lam, Brian; Das, Jagotamoy; Holmes, Richard D; Live, Ludovic; Sage, Andrew; Sargent, Edward H; Kelley, Shana O

2013-01-01

Electronic readout of markers of disease provides compelling simplicity, sensitivity and specificity in the detection of small panels of biomarkers in clinical samples; however, the most important emerging tests for disease, such as infectious disease speciation and antibiotic-resistance profiling, will need to interrogate samples for many dozens of biomarkers. Electronic readout of large panels of markers has been hampered by the difficulty of addressing large arrays of electrode-based sensors on inexpensive platforms. Here we report a new concept--solution-based circuits formed on chip--that makes highly multiplexed electrochemical sensing feasible on passive chips. The solution-based circuits switch the information-carrying signal readout channels and eliminate all measurable crosstalk from adjacent, biomolecule-specific microsensors. We build chips that feature this advance and prove that they analyse unpurified samples successfully, and accurately classify pathogens at clinically relevant concentrations. We also show that signature molecules can be accurately read 2  minutes after sample introduction.

Assessment of illumination conditions in a single-pixel imaging configuration

NASA Astrophysics Data System (ADS)

Garoi, Florin; Udrea, Cristian; Damian, Cristian; Logofǎtu, Petre C.; Colţuc, Daniela

2016-12-01

Single-pixel imaging based on multiplexing is a promising technique, especially in applications where 2D detectors or raster scanning imaging are not readily applicable. With this method, Hadamard masks are projected on a spatial light modulator to encode an incident scene and a signal is recorded at the photodiode detector for each of these masks. Ultimately, the image is reconstructed on the computer by applying the inverse transform matrix. Thus, various algorithms were optimized and several spatial light modulators already characterized for such a task. This work analyses the imaging quality of such a single-pixel arrangement, when various illumination conditions are used. More precisely, the main comparison is made between coherent and incoherent ("white light") illumination and between two multiplexing methods, namely Hadamard and Scanning. The quality of the images is assessed by calculating their SNR, using two relations. The results show better images are obtained with "white light" illumination for the first method and coherent one for the second.

Multiplex families with epilepsy

PubMed Central

Afawi, Zaid; Oliver, Karen L.; Kivity, Sara; Mazarib, Aziz; Blatt, Ilan; Neufeld, Miriam Y.; Helbig, Katherine L.; Goldberg-Stern, Hadassa; Misk, Adel J.; Straussberg, Rachel; Walid, Simri; Mahajnah, Muhammad; Lerman-Sagie, Tally; Ben-Zeev, Bruria; Kahana, Esther; Masalha, Rafik; Kramer, Uri; Ekstein, Dana; Shorer, Zamir; Wallace, Robyn H.; Mangelsdorf, Marie; MacPherson, James N.; Carvill, Gemma L.; Mefford, Heather C.; Jackson, Graeme D.; Scheffer, Ingrid E.; Bahlo, Melanie; Gecz, Jozef; Heron, Sarah E.; Corbett, Mark; Mulley, John C.; Dibbens, Leanne M.; Korczyn, Amos D.

2016-01-01

Objective: To analyze the clinical syndromes and inheritance patterns of multiplex families with epilepsy toward the ultimate aim of uncovering the underlying molecular genetic basis. Methods: Following the referral of families with 2 or more relatives with epilepsy, individuals were classified into epilepsy syndromes. Families were classified into syndromes where at least 2 family members had a specific diagnosis. Pedigrees were analyzed and molecular genetic studies were performed as appropriate. Results: A total of 211 families were ascertained over an 11-year period in Israel. A total of 169 were classified into broad familial epilepsy syndrome groups: 61 generalized, 22 focal, 24 febrile seizure syndromes, 33 special syndromes, and 29 mixed. A total of 42 families remained unclassified. Pathogenic variants were identified in 49/211 families (23%). The majority were found in established epilepsy genes (e.g., SCN1A, KCNQ2, CSTB), but in 11 families, this cohort contributed to the initial discovery (e.g., KCNT1, PCDH19, TBC1D24). We expand the phenotypic spectrum of established epilepsy genes by reporting a familial LAMC3 homozygous variant, where the predominant phenotype was epilepsy with myoclonic-atonic seizures, and a pathogenic SCN1A variant in a family where in 5 siblings the phenotype was broadly consistent with Dravet syndrome, a disorder that usually occurs sporadically. Conclusion: A total of 80% of families were successfully classified, with pathogenic variants identified in 23%. The successful characterization of familial electroclinical and inheritance patterns has highlighted the value of studying multiplex families and their contribution towards uncovering the genetic basis of the epilepsies. PMID:26802095

Thermally multiplexed polymerase chain reaction.

PubMed

Phaneuf, Christopher R; Pak, Nikita; Saunders, D Curtis; Holst, Gregory L; Birjiniuk, Joav; Nagpal, Nikita; Culpepper, Stephen; Popler, Emily; Shane, Andi L; Jerris, Robert; Forest, Craig R

2015-07-01

Amplification of multiple unique genetic targets using the polymerase chain reaction (PCR) is commonly required in molecular biology laboratories. Such reactions are typically performed either serially or by multiplex PCR. Serial reactions are time consuming, and multiplex PCR, while powerful and widely used, can be prone to amplification bias, PCR drift, and primer-primer interactions. We present a new thermocycling method, termed thermal multiplexing, in which a single heat source is uniformly distributed and selectively modulated for independent temperature control of an array of PCR reactions. Thermal multiplexing allows amplification of multiple targets simultaneously-each reaction segregated and performed at optimal conditions. We demonstrate the method using a microfluidic system consisting of an infrared laser thermocycler, a polymer microchip featuring 1 μl, oil-encapsulated reactions, and closed-loop pulse-width modulation control. Heat transfer modeling is used to characterize thermal performance limitations of the system. We validate the model and perform two reactions simultaneously with widely varying annealing temperatures (48 °C and 68 °C), demonstrating excellent amplification. In addition, to demonstrate microfluidic infrared PCR using clinical specimens, we successfully amplified and detected both influenza A and B from human nasopharyngeal swabs. Thermal multiplexing is scalable and applicable to challenges such as pathogen detection where patients presenting non-specific symptoms need to be efficiently screened across a viral or bacterial panel.

Development of a Multiplexed Bead-Based Suspension Array for the Detection and Discrimination of Pospiviroid Plant Pathogens

PubMed Central

van Brunschot, Sharon L.; Bergervoet, Jan H. W.; Pagendam, Daniel E.; de Weerdt, Marjanne; Geering, Andrew D. W.; Drenth, André; van der Vlugt, René A. A.

2014-01-01

Efficient and reliable diagnostic tools for the routine indexing and certification of clean propagating material are essential for the management of pospiviroid diseases in horticultural crops. This study describes the development of a true multiplexed diagnostic method for the detection and identification of all nine currently recognized pospiviroid species in one assay using Luminex bead-based suspension array technology. In addition, a new data-driven, statistical method is presented for establishing thresholds for positivity for individual assays within multiplexed arrays. When applied to the multiplexed array data generated in this study, the new method was shown to have better control of false positives and false negative results than two other commonly used approaches for setting thresholds. The 11-plex Luminex MagPlex-TAG pospiviroid array described here has a unique hierarchical assay design, incorporating a near-universal assay in addition to nine species-specific assays, and a co-amplified plant internal control assay for quality assurance purposes. All assays of the multiplexed array were shown to be 100% specific, sensitive and reproducible. The multiplexed array described herein is robust, easy to use, displays unambiguous results and has strong potential for use in routine pospiviroid indexing to improve disease management strategies. PMID:24404188

Detection of enteropathogens associated with travelers’ diarrhea using a multiplex Luminex-based assay performed on stool samples smeared on Whatman FTA Elute cards

PubMed Central

Lalani, Tahaniyat; Tisdale, Michele D; Maguire, Jason D; Wongsrichanalai, Chansuda; Riddle, Mark S; Tribble, David R

2015-01-01

We evaluated the limits of detection (LoD) for an 11-plex PCR-Luminex assay performed on Whatman FTA Elute cards smeared with stool containing pathogens associated with travelers’ diarrhea. LoDs ranged between 102-105 CFU, PFU or cysts/g for most pathogens except Cryptosporidium. Campylobacter and norovirus LoD increased with prolonged storage of cards. PMID:26072151

Energy resolution and efficiency of phonon-mediated kinetic inductance detectors for light detection

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

Cardani, L., E-mail: laura.cardani@roma1.infn.it; Physics Department, Princeton University, Washington Road, 08544, Princeton, New Jersey; Colantoni, I.

The development of sensitive cryogenic light detectors is of primary interest for bolometric experiments searching for rare events like dark matter interactions or neutrino-less double beta decay. Thanks to their good energy resolution and the natural multiplexed read-out, Kinetic Inductance Detectors (KIDs) are particularly suitable for this purpose. To efficiently couple KIDs-based light detectors to the large crystals used by the most advanced bolometric detectors, active surfaces of several cm{sup 2} are needed. For this reason, we are developing phonon-mediated detectors. In this paper, we present the results obtained with a prototype consisting of four 40 nm thick aluminum resonators patternedmore » on a 2 × 2 cm{sup 2} silicon chip, and calibrated with optical pulses and X-rays. The detector features a noise resolution σ{sub E} = 154 ± 7 eV and an (18 ± 2)% efficiency.« less

A multiplexed TOF and DOI capable PET detector using a binary position sensitive network.

PubMed

Bieniosek, M F; Cates, J W; Levin, C S

2016-11-07

Time of flight (TOF) and depth of interaction (DOI) capabilities can significantly enhance the quality and uniformity of positron emission tomography (PET) images. Many proposed TOF/DOI PET detectors require complex readout systems using additional photosensors, active cooling, or waveform sampling. This work describes a high performance, low complexity, room temperature TOF/DOI PET module. The module uses multiplexed timing channels to significantly reduce the electronic readout complexity of the PET detector while maintaining excellent timing, energy, and position resolution. DOI was determined using a two layer light sharing scintillation crystal array with a novel binary position sensitive network. A 20 mm effective thickness LYSO crystal array with four 3 mm  ×  3 mm silicon photomultipliers (SiPM) read out by a single timing channel, one energy channel and two position channels achieved a full width half maximum (FWHM) coincidence time resolution of 180  ±  2 ps with 10 mm of DOI resolution and 11% energy resolution. With sixteen 3 mm  ×  3 mm SiPMs read out by a single timing channel, one energy channel and four position channels a coincidence time resolution 204  ±  1 ps was achieved with 10 mm of DOI resolution and 15% energy resolution. The methods presented here could significantly simplify the construction of high performance TOF/DOI PET detectors.

Relevancies of multiple-interaction events and signal-to-noise ratio for Anger-logic based PET detector designs

NASA Astrophysics Data System (ADS)

Peng, Hao

2015-10-01

A fundamental challenge for PET block detector designs is to deploy finer crystal elements while limiting the number of readout channels. The standard Anger-logic scheme including light sharing (an 8 by 8 crystal array coupled to a 2×2 photodetector array with an optical diffuser, multiplexing ratio: 16:1) has been widely used to address such a challenge. Our work proposes a generalized model to study the impacts of two critical parameters on spatial resolution performance of a PET block detector: multiple interaction events and signal-to-noise ratio (SNR). The study consists of the following three parts: (1) studying light output profile and multiple interactions of 511 keV photons within crystal arrays of different crystal widths (from 4 mm down to 1 mm, constant height: 20 mm); (2) applying the Anger-logic positioning algorithm to investigate positioning/decoding uncertainties (i.e., "block effect") in terms of peak-to-valley ratio (PVR), with light sharing, multiple interactions and photodetector SNR taken into account; and (3) studying the dependency of spatial resolution on SNR in the context of modulation transfer function (MTF). The proposed model can be used to guide the development and evaluation of a standard Anger-logic based PET block detector including: (1) selecting/optimizing the configuration of crystal elements for a given photodetector SNR; and (2) predicting to what extent additional electronic multiplexing may be implemented to further reduce the number of readout channels.

Multiplexing 32,000 spectra onto 8 detectors: the HARMONI field splitting, image slicing, and wavelength selecting optics

NASA Astrophysics Data System (ADS)

Tecza, Matthias; Thatte, Niranjan; Clarke, Fraser; Freeman, David; Kosmalski, Johan

2012-09-01

HARMONI, the High Angular Resolution Monolithic Optical & Near-infrared Integral field spectrograph is one of two first-light instruments for the European Extremely Large Telescope. Over a 256x128 pixel field-of-view HARMONI will simultaneously measure approximately 32,000 spectra. Each spectrum is about 4000 spectral pixels long, and covers a selectable part of the 0.47-2.45 μm wavelength range at resolving powers of either R≍4000, 10000, or 20000. All 32,000 spectra are imaged onto eight HAWAII4RG detectors using a multiplexing scheme that divides the input field into four sub-fields, each imaged onto one image slicer that in turn re-arranges a single sub-field into two long exit slits feeding one spectrograph each. In total we require eight spectrographs, each with one HAWAII4RG detector. A system of articulated and exchangeable fold-mirrors and VPH gratings allows one to select different spectral resolving powers and wavelength ranges of interest while keeping a fixed geometry between the spectrograph collimator and camera avoiding the need for an articulated grating and camera. In this paper we describe both the field splitting and image slicing optics as well as the optics that will be used to select both spectral resolving power and wavelength range.

Dual-excitation upconverting nanoparticle and quantum dot aptasensor for multiplexed food pathogen detection.

PubMed

Kurt, Hasan; Yüce, Meral; Hussain, Babar; Budak, Hikmet

2016-07-15

In this report, a dual-excitation sensing method was developed using aptamer-functionalized quantum dots and upconverting nanoparticles, exhibiting Stokes and anti-Stokes type excitation profiles, respectively. Conjugation of the aptamer-functionalized luminescent nanoparticles with the magnetic beads, comprising short DNA sequences that were partially complementary to the aptamer sequences, enabled facile separation of the analyte-free conjugates for fluorescent measurement. UV-Visible spectroscopy, Circular Dichroism spectroscopy, Dynamic Light Scattering and Polyacrylamide Gel Electrophoresis techniques were used to characterize the aptamer probes developed. The target-specific luminescent conjugates were applied for multiplex detection of model food pathogens, Salmonella typhimurium, and Staphylococcus aureus, in which the fluorescent emission spectra were obtained under UV excitation at 325nm for quantum dots and NIR excitation at 980nm for upconverting nanoparticles, respectively. The dual-excitation strategy was aimed to minimize cross-talk between the luminescent signals for multiplexed detection, and yielded limit of detection values of 16 and 28cfumL(-1) for Staphylococcus aureus, and Salmonella typhimurium, respectively. By employing a greater number of quantum dots and upconverting nanoparticles with non-overlapping fluorescent emissions, the proposed methodology might be exploited further to detect several analytes, simultaneously. Copyright © 2016 Elsevier B.V. All rights reserved.

Surveillance for Emerging Diseases with Multiplexed Point-of-Care Diagnostics

DOE PAGES

Deshpande, Alina; McMahon, Benjamin; Daughton, Ashlynn Rae; ...

2016-06-17

Here, we present an analysis of the diagnostic technologies that were used to identify historical outbreaks of ebola virus disease and consider systematic surveillance strategies that may greatly reduce the peak size of future epidemics. We observe that clinical signs and symptoms alone are often insufficient to recognize index cases of diseases of global concern against the considerable background infectious disease burden that is present throughout the developing world. We propose a simple sampling strategy to enrich in especially dangerous pathogens with a low background for molecular diagnostics by targeting blood borne pathogens in the healthiest age groups. With existingmore » multiplexed diagnostic technologies, such a system could be combined with existing public health screening and reference laboratory systems for malaria, dengue, and common bacteremia or be used to develop such an infrastructure in less-developed locations. Because the needs for valid samples and accurate recording of patient attributes are aligned with needs for global biosurveillance, local public health needs, and improving patient care, co-development of these capabilities appears to be quite natural, flexible, and extensible as capabilities, technologies, and needs evolve over time. Furthermore, implementation of multiplexed diagnostic technologies to enhance fundamental clinical lab capacity will increase public health monitoring and biosurveillance as a natural extension.« less

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.

PubMed

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. Copyright © 2016 Elsevier B.V. All rights reserved.

Surveillance for Emerging Diseases with Multiplexed Point-of-Care Diagnostics

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

Deshpande, Alina; McMahon, Benjamin; Daughton, Ashlynn Rae

Here, we present an analysis of the diagnostic technologies that were used to identify historical outbreaks of ebola virus disease and consider systematic surveillance strategies that may greatly reduce the peak size of future epidemics. We observe that clinical signs and symptoms alone are often insufficient to recognize index cases of diseases of global concern against the considerable background infectious disease burden that is present throughout the developing world. We propose a simple sampling strategy to enrich in especially dangerous pathogens with a low background for molecular diagnostics by targeting blood borne pathogens in the healthiest age groups. With existingmore » multiplexed diagnostic technologies, such a system could be combined with existing public health screening and reference laboratory systems for malaria, dengue, and common bacteremia or be used to develop such an infrastructure in less-developed locations. Because the needs for valid samples and accurate recording of patient attributes are aligned with needs for global biosurveillance, local public health needs, and improving patient care, co-development of these capabilities appears to be quite natural, flexible, and extensible as capabilities, technologies, and needs evolve over time. Furthermore, implementation of multiplexed diagnostic technologies to enhance fundamental clinical lab capacity will increase public health monitoring and biosurveillance as a natural extension.« less

Multiplexed Lateral Flow Test for Detection and Differentiation of Cronobacter sakazakii Serotypes O1 and O2

PubMed Central

Scharinger, Eva J.; Dietrich, Richard; Wittwer, Tobias; Märtlbauer, Erwin; Schauer, Kristina

2017-01-01

The ubiquitous and opportunistic pathogen Cronobacter sakazakii is responsible for severe meningitis, sepsis, and necrotizing enterocolitis in neonates and infants associated with ingestion of contaminated powdered infant formula (PIF). The current ISO method for isolation and detection of Cronobacter spp. is laborious, time-consuming and expensive. In this study, a multiplexed lateral flow test strip was developed to rapidly detect and simultaneously serotype O1 and O2 C. sakazakii serotypes. The assay is based on two monoclonal antibodies (MAb) that specifically bind to the lipopolysaccharides (LPS) of these pathogens. The test strip provides results very quickly; C. sakazakii could be detected in pure culture within 15 min with a sensitivity of 107 CFU/ml. After non-selective enrichment for 18 h as low as one Cronobacter cell per g PIF could be detected. Moreover, the established lateral flow assay (LFA) offers excellent specificity showing no cross-reactivity with other C. sakazakii serotypes, Cronobacter species or Enterobacteriaceae tested. These characteristics, together with several advantages such as speed, simplicity in performance, low analysis cost, and no requirement of specialized skills or sophisticated equipment make the developed multiplexed LFA suitable for reliable detection and serotyping of C. sakazakii serotypes O1 and O2. PMID:28979257

Multiplexed Lateral Flow Test for Detection and Differentiation of Cronobacter sakazakii Serotypes O1 and O2.

PubMed

Scharinger, Eva J; Dietrich, Richard; Wittwer, Tobias; Märtlbauer, Erwin; Schauer, Kristina

2017-01-01

The ubiquitous and opportunistic pathogen Cronobacter sakazakii is responsible for severe meningitis, sepsis, and necrotizing enterocolitis in neonates and infants associated with ingestion of contaminated powdered infant formula (PIF). The current ISO method for isolation and detection of Cronobacter spp. is laborious, time-consuming and expensive. In this study, a multiplexed lateral flow test strip was developed to rapidly detect and simultaneously serotype O1 and O2 C. sakazakii serotypes. The assay is based on two monoclonal antibodies (MAb) that specifically bind to the lipopolysaccharides (LPS) of these pathogens. The test strip provides results very quickly; C. sakazakii could be detected in pure culture within 15 min with a sensitivity of 10 7 CFU/ml. After non-selective enrichment for 18 h as low as one Cronobacter cell per g PIF could be detected. Moreover, the established lateral flow assay (LFA) offers excellent specificity showing no cross-reactivity with other C. sakazakii serotypes, Cronobacter species or Enterobacteriaceae tested. These characteristics, together with several advantages such as speed, simplicity in performance, low analysis cost, and no requirement of specialized skills or sophisticated equipment make the developed multiplexed LFA suitable for reliable detection and serotyping of C. sakazakii serotypes O1 and O2.

Molecular identification of common Salmonella serovars using multiplex DNA sensor-based suspension array.

PubMed

Aydin, Muhsin; Carter-Conger, Jacqueline; Gao, Ning; Gilmore, David F; Ricke, Steven C; Ahn, Soohyoun

2018-04-01

Salmonella is one of major foodborne pathogens and the leading cause of foodborne illness-related hospitalizations and deaths. It is critical to develop a sensitive and rapid detection assay that can identify Salmonella to ensure food safety. In this study, a DNA sensor-based suspension array system of high multiplexing ability was developed to identify eight Salmonella serovars commonly associated with foodborne outbreaks to the serotype level. Each DNA sensor was prepared by activating pre-encoded microspheres with oligonucleotide probes that are targeting virulence genes and serovar-specific regions. The mixture of 12 different types of DNA sensors were loaded into a 96-well microplate and used as a 12-plex DNA sensor array platform. DNA isolated from Salmonella was amplified by multiplex polymerase chain reaction (mPCR), and the presence of Salmonella was determined by reading fluorescent signals from hybridization between probes on DNA sensors and fluorescently labeled target DNA using the Bio-Plex® system. The developed multiplex array was able to detect synthetic DNA at the concentration as low as 100 fM and various Salmonella serovars as low as 100 CFU/mL within 1 h post-PCR. Sensitivity of this assay was further improved to 1 CFU/mL with 6-h enrichment. The array system also correctly and specifically identified serotype of tested Salmonella strains without any cross-reactivity with other common foodborne pathogens. Our results indicate the developed DNA sensor suspension array can be a rapid and reliable high-throughput method for simultaneous detection and molecular identification of common Salmonella serotypes.

Charging YOYO-1 on Capillary Wall for Online DNA Intercalation and Integrating This Approach with Multiplex PCR and Bare Narrow Capillary–Hydrodynamic Chromatography for Online DNA Analysis

PubMed Central

2016-01-01

Multiplex polymerase chain reaction (PCR) has been widely utilized for high-throughput pathogen identification. Often, a dye is used to intercalate the amplified DNA fragments, and identifications of the pathogens are carried out by DNA melting curve analysis or gel electrophoresis. Integrating DNA amplification and identification is a logic path toward maximizing the benefit of multiplex PCR. Although PCR and gel electrophoresis have been integrated, replenishing the gels after each run is tedious and time-consuming. In this technical note, we develop an approach to address this issue. We perform multiplex PCR inside a capillary, transfer the amplified fragments to a bare narrow capillary, and measure their lengths online using bare narrow capillary–hydrodynamic chromatography (BaNC-HDC), a new technique recently developed in our laboratory for free-solution DNA separation. To intercalate the DNA with YOYO-1 (a fluorescent dye) for BaNC-HDC, we flush the capillary column with a YOYO-1 solution; positively charged YOYO-1 is adsorbed (or charged) onto the negatively charged capillary wall. As DNA molecules are driven down the column for separation, they react with the YOYO-1 stored on the capillary wall and are online-intercalated with the dye. With a single YOYO-1 charging, the column can be used for more than 40 runs, although the fluorescence signal intensities of the DNA peaks decrease gradually. Although the dye-DNA intercalation occurs during the separation, it does not affect the retention times, separation efficiencies, or resolutions. PMID:25555111

First Astronomical Use of Multiplexed Transition Edge Sensor Bolometers

NASA Technical Reports Server (NTRS)

Staguhn, J. G.; Ames, T. A.; Benford, D. J.; Chervenak, J. A.; Grossman, E. N.; Irwin, K. D.; Khan, S. A.; Maffei, B.; Moseley, S. H.; Pajot, F.

2004-01-01

We present performance results based on the first astronomical use of multiplexed superconducting bolometers. The Fabry-Perot Interferometer Bolometer Research Experiment (FIBRE) is a broadband submillimeter spectrometer that achieved first light in June 2001 at the Caltech Submillimeter Observatory (CSO). FIBRE's detectors are superconducting transition edge sensor (TES) bolometers read out by a SQUID multiplexer. The Fabry-Perot uses a low resolution grating to order sort the incoming light. A linear bolometer array consisting of 16 elements detects this dispersed light, capturing 5 orders simultaneously from one position on the sky. With tuning of the Fabry-Perot over one free spectral range, a spectrum covering Delta lambda/lambda = 1/7 at a resolution of delta lambda/lambda approx. 1/1200 can be acquired. This spectral resolution is sufficient to resolve Doppler-broadened line emission from external galaxies. FIBRE operates in the 350 m and 450 m bands. These bands cover line emission from the important star formation tracers neutral carbon (CI) and carbon monoxide (CO). We have verified that the multiplexed bolometers are photon noise limited even with the low power present in moderate resolution spectrometry.

A valveless rotary microfluidic device for multiplex point mutation identification based on ligation-rolling circle amplification.

PubMed

Heo, Hyun Young; Chung, Soyi; Kim, Yong Tae; Kim, Do Hyun; Seo, Tae Seok

2016-04-15

Genetic variations such as single nucleotide polymorphism (SNP) and point mutations are important biomarkers to monitor disease prognosis and diagnosis. In this study, we developed a novel rotary microfluidic device which can perform multiplex SNP typing on the mutation sites of TP53 genes. The microdevice consists of three glass layers: a channel wafer, a Ti/Pt electrode-patterned resistance temperature detector (RTD) wafer, and a rotary plate in which twelve reaction chambers were fabricated. A series of sample injection, ligation-rolling circle amplification (L-RCA) reaction, and fluorescence detection of the resultant amplicons could be executed by rotating the top rotary plate, identifying five mutation points related with cancer prognosis. The use of the rotary plate eliminates the necessity of microvalves and micropumps to control the microfluidic flow in the channel, simplifying the chip design and chip operation for multiplex SNP detection. The proposed microdevice provides an advanced genetic analysis platform in terms of multiplexity, simplicity, and portability in the fields of biomedical diagnostics. Copyright © 2015 Elsevier B.V. All rights reserved.

First Astronomical Use Of Multiplexed Transition Edge Bolometers

NASA Technical Reports Server (NTRS)

Benford, D. J.; Chervenak, J. A.; Grossman, E. N.; Irwin, K. D.; DeKotwara, S. A.; Maffei, B.; Moseley, S. H.; Pajot, F.; Phillips, T. G.; Reintsema, C. D.

2001-01-01

We present performance results based on the first astronomical use of multiplexed superconducting bolometers. The Fabry-Perot Interferometer Bolometer Research Experiment (FIBRE) is a broadband submillimeter spectrometer that achieved first light in June 2001 at the Caltech Submillimeter Observatory (CSO). FIBRE's detectors are superconducting transition edge sensor (TES) bolometers read out by a SQUID multiplexer. The Fabry-Perot uses a low resolution grating to order sort the incoming light. A linear bolometer array consisting of 16 elements detects this dispersed light, capturing five orders simultaneously from one position on the sky. With tuning of the Fabry-Perot over one free spectral range, a spectrum covering delta-lamda/lamda = 1/7 at a resolution of delta-lamda/lamda = 1/1200 can be acquired. This spectral resolution is sufficient to resolve doppler broadened line emission from external galaxies. FIBRE operates in the 350 micrometer and 450 micrometer bands. These bands cover line emission from the important PDR tracers neutral carbon [CI] and carbon monoxide (CO). We have verified that the multiplexed bolometers are photon noise limited even with the low power present in moderate resolution spectrometry.

Multiplex Real-Time PCR Assay for Rapid Detection of Methicillin-Resistant Staphylococci Directly from Positive Blood Cultures

PubMed Central

Wang, Hye-young; Kim, Sunghyun; Kim, Jungho; Park, Soon-Deok

2014-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) is the most prevalent cause of bloodstream infections (BSIs) and is recognized as a major nosocomial pathogen. This study aimed to evaluate a newly designed multiplex real-time PCR assay capable of the simultaneous detection of mecA, S. aureus, and coagulase-negative staphylococci (CoNS) in blood culture specimens. The Real-MRSA and Real-MRCoNS multiplex real-time PCR assays (M&D, Republic of Korea) use the TaqMan probes 16S rRNA for Staphylococcus spp., the nuc gene for S. aureus, and the mecA gene for methicillin resistance. The detection limit of the multiplex real-time PCR assay was 103 CFU/ml per PCR for each gene target. The multiplex real-time PCR assay was evaluated using 118 clinical isolates from various specimen types and a total of 350 positive blood cultures from a continuous monitoring blood culture system. The results obtained with the multiplex real-time PCR assay for the three targets were in agreement with those of conventional identification and susceptibility testing methods except for one organism. Of 350 positive bottle cultures, the sensitivities of the multiplex real-time PCR kit were 100% (166/166 cultures), 97.2% (35/36 cultures), and 99.2% (117/118 cultures) for the 16S rRNA, nuc, and mecA genes, respectively, and the specificities for all three targets were 100%. The Real-MRSA and Real-MRCoNS multiplex real-time PCR assays are very useful for the rapid accurate diagnosis of staphylococcal BSIs. In addition, the Real-MRSA and Real-MRCoNS multiplex real-time PCR assays could have an important impact on the choice of appropriate antimicrobial therapy, based on detection of the mecA gene. PMID:24648566

Spectroscopic optical coherence tomography based on wavelength de-multiplexing and smart pixel array detection

NASA Astrophysics Data System (ADS)

Laubscher, Markus; Bourquin, Stéphane; Froehly, Luc; Karamata, Boris; Lasser, Theo

2004-07-01

Current spectroscopic optical coherence tomography (OCT) methods rely on a posteriori numerical calculation. We present an experimental alternative for accessing spectroscopic information in OCT without post-processing based on wavelength de-multiplexing and parallel detection using a diffraction grating and a smart pixel detector array. Both a conventional A-scan with high axial resolution and the spectrally resolved measurement are acquired simultaneously. A proof-of-principle demonstration is given on a dynamically changing absorbing sample. The method's potential for fast spectroscopic OCT imaging is discussed. The spectral measurements obtained with this approach are insensitive to scan non-linearities or sample movements.

The LiteBIRD Satellite Mission: Sub-Kelvin Instrument

NASA Astrophysics Data System (ADS)

Suzuki, A.; Ade, P. A. R.; Akiba, Y.; Alonso, D.; Arnold, K.; Aumont, J.; Baccigalupi, C.; Barron, D.; Basak, S.; Beckman, S.; Borrill, J.; Boulanger, F.; Bucher, M.; Calabrese, E.; Chinone, Y.; Cho, S.; Crill, B.; Cukierman, A.; Curtis, D. W.; de Haan, T.; Dobbs, M.; Dominjon, A.; Dotani, T.; Duband, L.; Ducout, A.; Dunkley, J.; Duval, J. M.; Elleflot, T.; Eriksen, H. K.; Errard, J.; Fischer, J.; Fujino, T.; Funaki, T.; Fuskeland, U.; Ganga, K.; Goeckner-Wald, N.; Grain, J.; Halverson, N. W.; Hamada, T.; Hasebe, T.; Hasegawa, M.; Hattori, K.; Hattori, M.; Hayes, L.; Hazumi, M.; Hidehira, N.; Hill, C. A.; Hilton, G.; Hubmayr, J.; Ichiki, K.; Iida, T.; Imada, H.; Inoue, M.; Inoue, Y.; Irwin, K. D.; Ishino, H.; Jeong, O.; Kanai, H.; Kaneko, D.; Kashima, S.; Katayama, N.; Kawasaki, T.; Kernasovskiy, S. A.; Keskitalo, R.; Kibayashi, A.; Kida, Y.; Kimura, K.; Kisner, T.; Kohri, K.; Komatsu, E.; Komatsu, K.; Kuo, C. L.; Kurinsky, N. A.; Kusaka, A.; Lazarian, A.; Lee, A. T.; Li, D.; Linder, E.; Maffei, B.; Mangilli, A.; Maki, M.; Matsumura, T.; Matsuura, S.; Meilhan, D.; Mima, S.; Minami, Y.; Mitsuda, K.; Montier, L.; Nagai, M.; Nagasaki, T.; Nagata, R.; Nakajima, M.; Nakamura, S.; Namikawa, T.; Naruse, M.; Nishino, H.; Nitta, T.; Noguchi, T.; Ogawa, H.; Oguri, S.; Okada, N.; Okamoto, A.; Okamura, T.; Otani, C.; Patanchon, G.; Pisano, G.; Rebeiz, G.; Remazeilles, M.; Richards, P. L.; Sakai, S.; Sakurai, Y.; Sato, Y.; Sato, N.; Sawada, M.; Segawa, Y.; Sekimoto, Y.; Seljak, U.; Sherwin, B. D.; Shimizu, T.; Shinozaki, K.; Stompor, R.; Sugai, H.; Sugita, H.; Suzuki, J.; Tajima, O.; Takada, S.; Takaku, R.; Takakura, S.; Takatori, S.; Tanabe, D.; Taylor, E.; Thompson, K. L.; Thorne, B.; Tomaru, T.; Tomida, T.; Tomita, N.; Tristram, M.; Tucker, C.; Turin, P.; Tsujimoto, M.; Uozumi, S.; Utsunomiya, S.; Uzawa, Y.; Vansyngel, F.; Wehus, I. K.; Westbrook, B.; Willer, M.; Whitehorn, N.; Yamada, Y.; Yamamoto, R.; Yamasaki, N.; Yamashita, T.; Yoshida, M.

2018-05-01

Inflation is the leading theory of the first instant of the universe. Inflation, which postulates that the universe underwent a period of rapid expansion an instant after its birth, provides convincing explanation for cosmological observations. Recent advancements in detector technology have opened opportunities to explore primordial gravitational waves generated by the inflation through "B-mode" (divergent-free) polarization pattern embedded in the cosmic microwave background anisotropies. If detected, these signals would provide strong evidence for inflation, point to the correct model for inflation, and open a window to physics at ultra-high energies. LiteBIRD is a satellite mission with a goal of detecting degree-and-larger-angular-scale B-mode polarization. LiteBIRD will observe at the second Lagrange point with a 400 mm diameter telescope and 2622 detectors. It will survey the entire sky with 15 frequency bands from 40 to 400 GHz to measure and subtract foregrounds. The US LiteBIRD team is proposing to deliver sub-Kelvin instruments that include detectors and readout electronics. A lenslet-coupled sinuous antenna array will cover low-frequency bands (40-235 GHz) with four frequency arrangements of trichroic pixels. An orthomode-transducer-coupled corrugated horn array will cover high-frequency bands (280-402 GHz) with three types of single frequency detectors. The detectors will be made with transition edge sensor (TES) bolometers cooled to a 100 milli-Kelvin base temperature by an adiabatic demagnetization refrigerator. The TES bolometers will be read out using digital frequency multiplexing with Superconducting QUantum Interference Device (SQUID) amplifiers. Up to 78 bolometers will be multiplexed with a single SQUID amplifier. We report on the sub-Kelvin instrument design and ongoing developments for the LiteBIRD mission.

Kinetic inductance detectors for far-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Barlis, Alyssa; Aguirre, James; Stevenson, Thomas

2016-07-01

The star formation mechanisms at work in the early universe remain one of the major unsolved problems of modern astrophysics. Many of the luminous galaxies present during the period of peak star formation (between redshifts 1 and 3) were heavily enshrouded in dust, which makes observing their properties difficult at optical wavelengths. However, many spectral lines exist at far-infrared wavelengths that serve as tracers of star formation during that period, in particular fine structure lines of nitrogen, carbon, and oxygen, as well as the carbon monoxide molecule. Using an observation technique known as intensity mapping, it would be possible to observe the total line intensity for a given redshift range even without detecting individual sources. Here, we describe a detector system suitable for a balloonborne spectroscopic intensity mapping experiment at far-infrared wavelengths. The experiment requires an "integralfield" type spectrograph, with modest spectral resolution (R 100) for each of a number of spatial pixels spanning several octaves in wavelength. The detector system uses lumped-element kinetic inductance detectors (LEKIDs), which have the potential to achieve the high sensitivity, low noise, and high multiplexing factor required for this experiment. We detail the design requirements and considerations, and the fabrication process for a prototype LEKID array of 1600 pixels. The pixel design is driven by the need for high responsivity, which requires a small physical volume for the LEKID inductor. In order to minimize two-level system noise, the resonators include large-area interdigitated capacitors. High quality factor resonances are required for a large frequency multiplexing factor. Detectors were fabricated using both trilayer TiN/Ti/TiN recipes and thin-film Al, and are operated at base temperatures near 250 mK.

Code-division-multiplexed readout of large arrays of TES microcalorimeters

NASA Astrophysics Data System (ADS)

Morgan, K. M.; Alpert, B. K.; Bennett, D. A.; Denison, E. V.; Doriese, W. B.; Fowler, J. W.; Gard, J. D.; Hilton, G. C.; Irwin, K. D.; Joe, Y. I.; O'Neil, G. C.; Reintsema, C. D.; Schmidt, D. R.; Ullom, J. N.; Swetz, D. S.

2016-09-01

Code-division multiplexing (CDM) offers a path to reading out large arrays of transition edge sensor (TES) X-ray microcalorimeters with excellent energy and timing resolution. We demonstrate the readout of X-ray TESs with a 32-channel flux-summed code-division multiplexing circuit based on superconducting quantum interference device (SQUID) amplifiers. The best detector has energy resolution of 2.28 ± 0.12 eV FWHM at 5.9 keV and the array has mean energy resolution of 2.77 ± 0.02 eV over 30 working sensors. The readout channels are sampled sequentially at 160 ns/row, for an effective sampling rate of 5.12 μs/channel. The SQUID amplifiers have a measured flux noise of 0.17 μΦ0/√Hz (non-multiplexed, referred to the first stage SQUID). The multiplexed noise level and signal slew rate are sufficient to allow readout of more than 40 pixels per column, making CDM compatible with requirements outlined for future space missions. Additionally, because the modulated data from the 32 SQUID readout channels provide information on each X-ray event at the row rate, our CDM architecture allows determination of the arrival time of an X-ray event to within 275 ns FWHM with potential benefits in experiments that require detection of near-coincident events.

Flow cytometer acquisition and detection system

DOEpatents

Casstevens, Martin K.; Burzynski, Ryszard; Weibel, John; Kachynski, Alexander

2010-05-04

A flow cytometer has a flow cell through which a sample flows and at least one laser emitting an excitation beam for illuminating a corresponding interrogation region in the flow cell. Scattered and fluorescence light from each interrogation region is collected by one or more input fibers for that region, and the input fiber(s) are fed to a dispersion module for that interrogation region that disperses the incoming light into different spectral regions. The dispersed light is conveyed, such as by a plurality of output fibers, to one or more photosensitive detectors. Thus, time multiplexed light signals may be delivered to a detector whereby several unique light signals can be measured by a single detector.

Novel Multiplexing Technique for Detector and Mixer Arrays

NASA Technical Reports Server (NTRS)

Karasik, Boris S.; McGrath, William R.

2001-01-01

Future submillimeter and far-infrared space telescopes will require large-format (many 1000's of elements) imaging detector arrays to perform state-of-the-art astronomical observations. A crucial issue related to a focal plane array is a readout scheme which is compatible with large numbers of cryogenically-cooled (typically < 1 K) detectors elements. When the number of elements becomes of the order of thousands, the physical layout for individual readout amplifiers becomes nearly impossible to realize for practical systems. Another important concern is the large number of wires leading to a 0.1-0.3 K platform. In the case of superconducting transition edge sensors (TES), a scheme for time-division multiplexing of SQUID read-out amplifiers has been recently demonstrated. In this scheme the number of SQUIDs is equal to the number (N) of the detectors, but only one SQUID is turned on at a time. The SQUIDs are connected in series in each column of the array, so the number of wires leading to the amplifiers can be reduced, but it is still of the order of N. Another approach uses a frequency domain multiplexing scheme of the bolometer array. The bolometers are biased with ac currents whose frequencies are individual for each element and are much higher than the bolometer bandwidth. The output signals are connected in series in a summing loop which is coupled to a single SQUID amplifier. The total number of channels depends on the ratio between the SQUID bandwidth and the bolometer bandwidth and can be at least 100 according to the authors. An important concern about this technique is a contribution of the out-of-band Johnson noise which multiplies by factor N(exp 1/2) for each frequency channel. We propose a novel solution for large format arrays based on the Hadamard transform coding technique which requires only one amplifier to read out the entire array of potentially many 1000's of elements and uses approximately 10 wires between the cold stage and room temperature electronics. This can significantly reduce the complexity of the readout circuits.

A TaqMan-Based Multiplex qPCR Assay and DNA Extraction Method for Phylotype IIB Sequevars 1&2 (Select Agent) Strains of Ralstonia solanacearum

PubMed Central

Stulberg, Michael J.; Huang, Qi

2015-01-01

Ralstonia solanacearum race 3 biovar 2 strains belonging to phylotype IIB, sequevars 1 and 2 (IIB-1&2) cause brown rot of potato in temperate climates, and are quarantined pathogens in Canada and Europe. Since these strains are not established in the U.S. and because of their potential risk to the potato industry, the U.S. government has listed them as select agents. Cultivated geraniums are also a host and have the potential to spread the pathogen through trade, and its extracts strongly inhibits DNA-based detection methods. We designed four primer and probe sets for an improved qPCR method that targets stable regions of DNA. RsSA1 and RsSA2 recognize IIB-1&2 strains, RsII recognizes the current phylotype II (the newly proposed R. solanacearum species) strains (and a non-plant associated R. mannitolilytica), and Cox1 recognizes eight plant species including major hosts of R. solanacearum such as potato, tomato and cultivated geranium as an internal plant control. We multiplexed the RsSA2 with the RsII and Cox1 sets to provide two layers of detection of a positive IIB-1&2 sample, and to validate plant extracts and qPCR reactions. The TaqMan-based uniplex and multiplex qPCR assays correctly identified 34 IIB-1&2 and 52 phylotype II strains out of 90 R. solanacearum species complex strains. Additionally, the multiplex qPCR assay was validated successfully using 169 artificially inoculated symptomatic and asymptomatic plant samples from multiple plant hosts including geranium. Furthermore, we developed an extraction buffer that allowed for a quick and easy DNA extraction from infected plants including geranium for detection of R. solanacearum by qPCR. Our multiplex qPCR assay, especially when coupled with the quick extraction buffer method, allows for quick, easy and reliable detection and differentiation of the IIB-1&2 strains of R. solanacearum. PMID:26426354

Evaluation of a shortened QIAsymphony DNA extraction protocol for stool samples using a multiplex real-time PCR for the detection of enteric pathogens.

PubMed

van Zanten, E; Wisselink, G J; Stoll, S; Alvarez, R; Kooistra-Smid, A M D

2011-02-01

A shortened DNA extraction protocol for the QIAsymphony SP was evaluated by quantitative and qualitative comparison of real-time PCR results of 150 co-extracted stool samples. The average ∆Cycle threshold value for positive pathogenic targets was 0.28 Ct. A consensus of 96.91%, with a correlation coefficient of 0.9880 was recorded. Copyright © 2010 Elsevier B.V. All rights reserved.

Large-Format AlGaN PIN Photodiode Arrays for UV Images

NASA Technical Reports Server (NTRS)

Aslam, Shahid; Franz, David

2010-01-01

A large-format hybridized AlGaN photodiode array with an adjustable bandwidth features stray-light control, ultralow dark-current noise to reduce cooling requirements, and much higher radiation tolerance than previous technologies. This technology reduces the size, mass, power, and cost of future ultraviolet (UV) detection instruments by using lightweight, low-voltage AlGaN detectors in a hybrid detector/multiplexer configuration. The solar-blind feature eliminates the need for additional visible light rejection and reduces the sensitivity of the system to stray light that can contaminate observations.

A sub-millimeter resolution PET detector module using a multi-pixel photon counter array

NASA Astrophysics Data System (ADS)

Song, Tae Yong; Wu, Heyu; Komarov, Sergey; Siegel, Stefan B.; Tai, Yuan-Chuan

2010-05-01

A PET block detector module using an array of sub-millimeter lutetium oxyorthosilicate (LSO) crystals read out by an array of surface-mount, semiconductor photosensors has been developed. The detector consists of a LSO array, a custom acrylic light guide, a 3 × 3 multi-pixel photon counter (MPPC) array (S10362-11-050P, Hamamatsu Photonics, Japan) and a readout board with a charge division resistor network. The LSO array consists of 100 crystals, each measuring 0.8 × 0.8 × 3 mm3 and arranged in 0.86 mm pitches. A Monte Carlo simulation was used to aid the design and fabrication of a custom light guide to control distribution of scintillation light over the surface of the MPPC array. The output signals of the nine MPPC are multiplexed by a charge division resistor network to generate four position-encoded analog outputs. Flood image, energy resolution and timing resolution measurements were performed using standard NIM electronics. The linearity of the detector response was investigated using gamma-ray sources of different energies. The 10 × 10 array of 0.8 mm LSO crystals was clearly resolved in the flood image. The average energy resolution and standard deviation were 20.0% full-width at half-maximum (FWHM) and ±5.0%, respectively, at 511 keV. The timing resolution of a single MPPC coupled to a LSO crystal was found to be 857 ps FWHM, and the value for the central region of detector module was 1182 ps FWHM when ±10% energy window was applied. The nonlinear response of a single MPPC when used to read out a single LSO was observed among the corner crystals of the proposed detector module. However, the central region of the detector module exhibits significantly less nonlinearity (6.5% for 511 keV). These results demonstrate that (1) a charge-sharing resistor network can effectively multiplex MPPC signals and reduce the number of output signals without significantly degrading the performance of a PET detector and (2) a custom light guide to permit light sharing among multiple MPPC and to diffuse and direct scintillation light can reduce the nonlinearity of the detector response within the limited dynamic range of a typical MPPC. As a result, the proposed PET detector module has the potential to be refined for use in high-resolution PET insert applications.

A sub-millimeter resolution PET detector module using a multi-pixel photon counter array.

PubMed

Song, Tae Yong; Wu, Heyu; Komarov, Sergey; Siegel, Stefan B; Tai, Yuan-Chuan

2010-05-07

A PET block detector module using an array of sub-millimeter lutetium oxyorthosilicate (LSO) crystals read out by an array of surface-mount, semiconductor photosensors has been developed. The detector consists of a LSO array, a custom acrylic light guide, a 3 x 3 multi-pixel photon counter (MPPC) array (S10362-11-050P, Hamamatsu Photonics, Japan) and a readout board with a charge division resistor network. The LSO array consists of 100 crystals, each measuring 0.8 x 0.8 x 3 mm(3) and arranged in 0.86 mm pitches. A Monte Carlo simulation was used to aid the design and fabrication of a custom light guide to control distribution of scintillation light over the surface of the MPPC array. The output signals of the nine MPPC are multiplexed by a charge division resistor network to generate four position-encoded analog outputs. Flood image, energy resolution and timing resolution measurements were performed using standard NIM electronics. The linearity of the detector response was investigated using gamma-ray sources of different energies. The 10 x 10 array of 0.8 mm LSO crystals was clearly resolved in the flood image. The average energy resolution and standard deviation were 20.0% full-width at half-maximum (FWHM) and +/-5.0%, respectively, at 511 keV. The timing resolution of a single MPPC coupled to a LSO crystal was found to be 857 ps FWHM, and the value for the central region of detector module was 1182 ps FWHM when +/-10% energy window was applied. The nonlinear response of a single MPPC when used to read out a single LSO was observed among the corner crystals of the proposed detector module. However, the central region of the detector module exhibits significantly less nonlinearity (6.5% for 511 keV). These results demonstrate that (1) a charge-sharing resistor network can effectively multiplex MPPC signals and reduce the number of output signals without significantly degrading the performance of a PET detector and (2) a custom light guide to permit light sharing among multiple MPPC and to diffuse and direct scintillation light can reduce the nonlinearity of the detector response within the limited dynamic range of a typical MPPC. As a result, the proposed PET detector module has the potential to be refined for use in high-resolution PET insert applications.

A sub-millimeter resolution PET detector module using a multi-pixel photon counter array

PubMed Central

Song, Tae Yong; Wu, Heyu; Komarov, Sergey; Siegel, Stefan B; Tai, Yuan-Chuan

2010-01-01

A PET block detector module using an array of sub-millimeter lutetium oxyorthosilicate (LSO) crystals read out by an array of surface-mount, semiconductor photosensors has been developed. The detector consists of a LSO array, a custom acrylic light guide, a 3 × 3 multi-pixel photon counter (MPPC) array (S10362-11-050P, Hamamatsu Photonics, Japan) and a readout board with a charge division resistor network. The LSO array consists of 100 crystals, each measuring 0.8 × 0.8 × 3 mm3 and arranged in 0.86 mm pitches. A Monte Carlo simulation was used to aid the design and fabrication of a custom light guide to control distribution of scintillation light over the surface of the MPPC array. The output signals of the nine MPPC are multiplexed by a charge division resistor network to generate four position-encoded analog outputs. Flood image, energy resolution and timing resolution measurements were performed using standard NIM electronics. The linearity of the detector response was investigated using gamma-ray sources of different energies. The 10 × 10 array of 0.8 mm LSO crystals was clearly resolved in the flood image. The average energy resolution and standard deviation were 20.0% full-width at half-maximum (FWHM) and ±5.0%, respectively, at 511 keV. The timing resolution of a single MPPC coupled to a LSO crystal was found to be 857 ps FWHM, and the value for the central region of detector module was 1182 ps FWHM when ±10% energy window was applied. The nonlinear response of a single MPPC when used to read out a single LSO was observed among the corner crystals of the proposed detector module. However, the central region of the detector module exhibits significantly less nonlinearity (6.5% for 511 keV). These results demonstrate that (1) a charge-sharing resistor network can effectively multiplex MPPC signals and reduce the number of output signals without significantly degrading the performance of a PET detector and (2) a custom light guide to permit light sharing among multiple MPPC and to diffuse and direct scintillation light can reduce the nonlinearity of the detector response within the limited dynamic range of a typical MPPC. As a result, the proposed PET detector module has the potential to be refined for use in high-resolution PET insert applications. PMID:20393236

Bolometric kinetic inductance detector technology for sub-millimeter radiometric imaging

NASA Astrophysics Data System (ADS)

Hassel, Juha; Timofeev, Andrey V.; Vesterinen, Visa; Sipola, Hannu; Helistö, Panu; Aikio, Mika; Mäyrä, Aki; Grönberg, Leif; Luukanen, Arttu

2015-10-01

Radiometric sub-millimeter imaging is a candidate technology especially in security screening applications utilizing the property of radiation in the band of 0.2 - 1.0 THz to penetrate through dielectric substances such as clothing. The challenge of the passive technology is the fact that the irradiance corresponding to the blackbody radiation is very weak in this spectral band: about two orders of magnitude below that of the infrared band. Therefore the role of the detector technology is of ultimate importance to achieve sufficient sensitivity. In this paper we present results related to our technology relying on superconducting kinetic inductance detectors operating in a thermal (bolometric) mode. The detector technology is motivated by the fact that it is naturally suitable for scalable multiplexed readout systems, and operates with relatively simple cryogenics. We will review the basic concepts of the detectors, and provide experimental figures of merit. Furthermore, we will discuss the issues related to the scale-up of our detector technology into large 2D focal plane arrays.

Multiplex molecular testing for management of infectious gastroenteritis in a hospital setting: a comparative diagnostic and clinical utility study.

PubMed

Halligan, E; Edgeworth, J; Bisnauthsing, K; Bible, J; Cliff, P; Aarons, E; Klein, J; Patel, A; Goldenberg, S

2014-08-01

Laboratory diagnosis and clinical management of inpatients with diarrhoea is complex and time consuming. Tests are often requested sequentially and undertaken in different laboratories. This causes prolonged unnecessary presumptive isolation of patients, because most cases are non-infectious. A molecular multiplex test (Luminex(®) Gastrointestinal Pathogen Panel (GPP)) was compared with conventional testing over 8 months to determine diagnostic accuracy, turnaround times, laboratory costs, use of isolation facilities and user acceptability. A total of 262 (12%) patients had a pathogen detected by conventional methods compared with 483 (22.1%) by GPP. Most additional cases were detected in patients developing symptoms in the first 4 days of admission. Additional cases were detected because of presumed improved diagnostic sensitivity but also because clinicians had not requested the correct pathogen. Turnaround time (41.8 h) was faster than bacterial culture (66.5 h) and parasite investigation (66.5 h) but slower than conventional testing for Clostridium difficile (17.3 h) and viruses (27 h). The test could allow simplified requesting by clinicians and a consolidated laboratory workflow, reducing the overall number of specimens received by the laboratory. A total of 154 isolation days were saved at an estimated cost of £30 800. Consumables and labour were estimated at £150 641 compared with £63 431 for conventional testing. Multiplex molecular testing using a panel of targets allowed enhanced detection and a consolidated laboratory workflow. This is likely to be of greater benefit to cases that present within the first 4 days of hospital admission. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

A novel, multiplexed, probe-based quantitative PCR assay for the soybean root- and stem-rot pathogen, Phytophthora sojae, utilizes its transposable element

PubMed Central

Haudenshield, James S.; Song, Jeong Y.; Hartman, Glen L.

2017-01-01

Phytophthora root rot of soybean [Glycine max (L.) Merr.] is caused by the oomycete Phytophthora sojae (Kaufm. & Gerd.). P. sojae has a narrow host range, consisting primarily of soybean, and it is a serious pathogen worldwide. It exists in root and stem tissues as mycelium, wherein it can form oospores which subsequently germinate to release motile, infectious zoospores. Molecular assays detecting DNA of P. sojae are useful in disease diagnostics, and for determining the presence of the organism in host tissues, soils, and runoff or ponded water from potentially infested fields. Such assays as published have utilized ITS sequences from the nuclear ribosomal RNA genes in conventional PCR or dye-binding quantitative PCR (Q-PCR) but are not amenable to multiplexing, and some of these assays did not utilize control strategies for type I or type II errors. In this study, we describe primers and a bifunctional probe with specificity to a gypsy-like retroelement in the P. sojae genome to create a fluorogenic 5’-exonuclease linear hydrolysis assay, with a multiplexed internal control reaction detecting an exogenous target to validate negative calls, and with uracil-deglycosylase-mediated protection against carryover contamination. The assay specifically detected 13 different P. sojae isolates, and excluded 17 other Phytophthora species along with 20 non-Phytophthora fungal and oomycete species pathogenic on soybean. A diagnostic limit of detection of 34 fg total P. sojae DNA was observed in serial dilutions, equivalent to 0.3 genome, and a practical detection sensitivity of four zoospores per sample was achieved, despite losses during DNA extraction. PMID:28441441

Detection of Pneumonia Associated Pathogens Using a Prototype Multiplexed Pneumonia Test in Hospitalized Patients with Severe Pneumonia

PubMed Central

Schulte, Berit; Eickmeyer, Holm; Heininger, Alexandra; Juretzek, Stephanie; Karrasch, Matthias; Denis, Olivier; Roisin, Sandrine; Pletz, Mathias W.; Klein, Matthias; Barth, Sandra; Lüdke, Gerd H.; Thews, Anne; Torres, Antoni; Cillóniz, Catia; Straube, Eberhard; Autenrieth, Ingo B.; Keller, Peter M.

2014-01-01

Severe pneumonia remains an important cause of morbidity and mortality. Polymerase chain reaction (PCR) has been shown to be more sensitive than current standard microbiological methods – particularly in patients with prior antibiotic treatment – and therefore, may improve the accuracy of microbiological diagnosis for hospitalized patients with pneumonia. Conventional detection techniques and multiplex PCR for 14 typical bacterial pneumonia-associated pathogens were performed on respiratory samples collected from adult hospitalized patients enrolled in a prospective multi-center study. Patients were enrolled from March until September 2012. A total of 739 fresh, native samples were eligible for analysis, of which 75 were sputa, 421 aspirates, and 234 bronchial lavages. 276 pathogens were detected by microbiology for which a valid PCR result was generated (positive or negative detection result by Curetis prototype system). Among these, 120 were identified by the prototype assay, 50 pathogens were not detected. Overall performance of the prototype for pathogen identification was 70.6% sensitivity (95% confidence interval (CI) lower bound: 63.3%, upper bound: 76.9%) and 95.2% specificity (95% CI lower bound: 94.6%, upper bound: 95.7%). Based on the study results, device cut-off settings were adjusted for future series production. The overall performance with the settings of the CE series production devices was 78.7% sensitivity (95% CI lower bound: 72.1%) and 96.6% specificity (95% CI lower bound: 96.1%). Time to result was 5.2 hours (median) for the prototype test and 43.5 h for standard-of-care. The Pneumonia Application provides a rapid and moderately sensitive assay for the detection of pneumonia-causing pathogens with minimal hands-on time. Trial Registration Deutsches Register Klinischer Studien (DRKS) DRKS00005684 PMID:25397673

Microtiter plate-based antibody microarrays for bacteria and toxins

USDA-ARS?s Scientific Manuscript database

Research has focused on the development of rapid biosensor-based, high-throughput, and multiplexed detection of pathogenic bacteria in foods. Specifically, antibody microarrays in 96-well microtiter plates have been generated for the purpose of selective detection of Shiga toxin-producing E. coli (...

Analyses of Xylella whole genome sequences and proposal of Xylella taiwanensis sp. nov.

USDA-ARS?s Scientific Manuscript database

Xylella fastidiosa is a Gram negative, xylem limited and nutritionally fastidious plant pathogenic bacterium that cause disease in many economically important plants. A single species, fastidiosa, with three subspecies (fastidiosa, multiplex, and pauca) have been described. Most Xylella strains were...

Occurrence of Vibrio parahaemolyticus and Vibrio vulnificus in retail raw oysters from the eastern coast of Thailand.

PubMed

Changchai, Nuttawee; Saunjit, Sudarat

2014-05-01

Occurrence, population density and virulence of Vibrio parahaemolyticus and V. vulnificus in 240 retail raw oysters collected monthly between March 2010 and February 2011 from Ang Sila coast, Chon Buri Province, Thailand were determined using most probable number (MPN) multiplex PCR. Multiplex PCR detected V. parahaemolyticus in 219 raw oyster samples, of which 29 samples contained the virulence tdh. MPN values for V. parahaemolyticus and pathogenic strains in most samples ranged from 10 to 10(2) and from 3 to 10 MPN/g, respectively. The presence of V. vulnificus was found in 53 oyster samples in amounts between 10 and 10(2) MPN/g. Of 1,087 V. parahaemolyticus isolates, 14 and 2 isolates carried tdh and virulence trh, respectively but none with both genes. However, none of the presumptive isolates was shown to be V. vulnificus. The detection of pathogenic V. parahaemolyticus and V. vulnificus in raw oysters has rendered high awareness of risk in consumption of raw or undercooked oysters.

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

Allman, M. S., E-mail: shane.allman@boulder.nist.gov; Verma, V. B.; Stevens, M.

We demonstrate a 64-pixel free-space-coupled array of superconducting nanowire single photon detectors optimized for high detection efficiency in the near-infrared range. An integrated, readily scalable, multiplexed readout scheme is employed to reduce the number of readout lines to 16. The cryogenic, optical, and electronic packaging to read out the array as well as characterization measurements are discussed.

A multiplex PCR/LDR assay for simultaneous detection and identification of the NIAID category B bacterial food and water-borne pathogens.

PubMed

Rundell, Mark S; Pingle, Maneesh; Das, Sanchita; Hussain, Aashiq; Ocheretina, Oksana; Charles, Macarthur; Larone, Davise H; Spitzer, Eric D; Golightly, Linnie; Barany, Francis

2014-06-01

Enteric pathogens that cause gastroenteritis remain a major global health concern. The goal of this study was to develop a multiplex PCR/ligation detection reaction (LDR) assay for the detection of all NIAID category B bacterial food and water-borne pathogens directly from stool specimens. To validate the PCR/LDR assay, clinical isolates of Campylobacter spp., Vibrio spp., Shigella spp., Salmonella spp., Listeria monocytogenes, Yersinia enterocolitica, and diarrheagenic Escherichia coli were tested. The sensitivity and specificity of the assay were assessed using a large number of seeded culture-negative stool specimens and a smaller set of clinical specimens from Haiti. The overall sensitivity ranged from 91% to 100% (median 100%) depending on the species. For the majority of organisms, the sensitivity was 100%. The overall specificity based on initial testing ranged from 98% to 100% depending on the species. After additional testing of discordant samples, the lowest specificity was 99.4%. PCR/LDR detected additional category B agents (particularly diarrheagenic E. coli) in 11/40 specimens from Haiti that were culture-positive for V. cholerae and in approximately 1% of routine culture-negative stool specimens from a hospital in New York. This study demonstrated the ability of the PCR/LDR assay to detect a large comprehensive panel of category B enteric bacterial pathogens as well as mixed infections. This type of assay has the potential to provide earlier warnings of possible public health threats and more accurate surveillance of food and water-borne pathogens. Copyright © 2014 Elsevier Inc. All rights reserved.

A Multiplex PCR/LDR Assay for Simultaneous Detection and Identification of the NIAID Category B Bacterial Food and Water-borne Pathogens

PubMed Central

Rundell, Mark S.; Pingle, Maneesh; Das, Sanchita; Hussain, Aashiq; Ocheretina, Oksana; Charles, Macarthur; Larone, Davise H.; Spitzer, Eric D.; Golightly, Linnie; Barany, Francis

2014-01-01

Enteric pathogens that cause gastroenteritis remain a major global health concern. The goal of this study was to develop a multiplex PCR/LDR assay for the detection of all NIAID category B bacterial food and water-borne pathogens directly from stool specimens. To validate the PCR/LDR assay, clinical isolates of Campylobacter spp., Vibrio spp., Shigella spp., Salmonella spp., Listeria monocytogenes, Yersinia enterocolitica, and diarrheagenic Escherichia coli were tested. The sensitivity and specificity of the assay was assessed using a large number of seeded culture-negative stool specimens and a smaller set of clinical specimens from Haiti. The overall sensitivity ranged from 91 to 100% (median 100%) depending on the species. For the majority of organisms the sensitivity was 100%. The overall specificity based on initial testing ranged from 98% to 100% depending on the species. After additional testing of discordant samples the lowest specificity was 99.4%. PCR/LDR detected additional category B agents (particularly diarrheagenic E. coli) in 11/40 specimens from Haiti that were culture-positive for V. cholerae and in approximately 1% of routine culture-negative stool specimens from a hospital in New York. This study demonstrated the ability of the PCR/LDR assay to detect a large comprehensive panel of category B enteric bacterial pathogens as well as mixed infections. This type of assay has the potential to provide earlier warnings of possible public health threats and more accurate surveillance of food and water-borne pathogens. PMID:24709368

HgCdTe 256x256 NWIR FPA

NASA Technical Reports Server (NTRS)

Vural, Kadri; Blessinger, Michael; Chen, Jenkon; Kleinhans, William

1989-01-01

Researchers developed a HgCdTe 256x256 focal plane array (FPA) which operates in the 1 to 5 micron band. This is presently the largest demonstrated HgCdTe FPA. The detector material is HgCdTe on sapphire (PACE-1 technology) which has a low thermal expansion mismatch with silicon. The multiplexer is a CMOS FET-switch device processed through a commercial silicon foundry. The multiplexer input is direct injection and the charge capacity is about 2 times 10 to the 7th power electrons. The kTC limited read noise is 400 electrons. Researchers demonstrated high background imaging using the device. The broadband quantum efficiency is measured to be 59 percent. Dark currents less than 0.1 pA were measured at 77 K for detectors processed on PACE-1 material with 4.9 microns cutoff. The dark currents decrease as the temperature is lowered, and researchers are presently studying the T less than 77 K characteristics. The interconnect yield is greater than 95 percent. The devices are available for astronomical applications.

Advanced ACTPol Cryogenic Detector Arrays and Readout

NASA Astrophysics Data System (ADS)

Henderson, S. W.; Allison, R.; Austermann, J.; Baildon, T.; Battaglia, N.; Beall, J. A.; Becker, D.; De Bernardis, F.; Bond, J. R.; Calabrese, E.; Choi, S. K.; Coughlin, K. P.; Crowley, K. T.; Datta, R.; Devlin, M. J.; Duff, S. M.; Dunkley, J.; Dünner, R.; van Engelen, A.; Gallardo, P. A.; Grace, E.; Hasselfield, M.; Hills, F.; Hilton, G. C.; Hincks, A. D.; Hloẑek, R.; Ho, S. P.; Hubmayr, J.; Huffenberger, K.; Hughes, J. P.; Irwin, K. D.; Koopman, B. J.; Kosowsky, A. B.; Li, D.; McMahon, J.; Munson, C.; Nati, F.; Newburgh, L.; Niemack, M. D.; Niraula, P.; Page, L. A.; Pappas, C. G.; Salatino, M.; Schillaci, A.; Schmitt, B. L.; Sehgal, N.; Sherwin, B. D.; Sievers, J. L.; Simon, S. M.; Spergel, D. N.; Staggs, S. T.; Stevens, J. R.; Thornton, R.; Van Lanen, J.; Vavagiakis, E. M.; Ward, J. T.; Wollack, E. J.

2016-08-01

Advanced ACTPol is a polarization-sensitive upgrade for the 6 m aperture Atacama Cosmology Telescope, adding new frequencies and increasing sensitivity over the previous ACTPol receiver. In 2016, Advanced ACTPol will begin to map approximately half the sky in five frequency bands (28-230 GHz). Its maps of primary and secondary cosmic microwave background anisotropies—imaged in intensity and polarization at few arcminute-scale resolution—will enable precision cosmological constraints and also a wide array of cross-correlation science that probes the expansion history of the universe and the growth of structure via gravitational collapse. To accomplish these scientific goals, the Advanced ACTPol receiver will be a significant upgrade to the ACTPol receiver, including four new multichroic arrays of cryogenic, feedhorn-coupled AlMn transition edge sensor polarimeters (fabricated on 150 mm diameter wafers); a system of continuously rotating meta-material silicon half-wave plates; and a new multiplexing readout architecture which uses superconducting quantum interference devices and time division to achieve a 64-row multiplexing factor. Here we present the status and scientific goals of the Advanced ACTPol instrument, emphasizing the design and implementation of the Advanced ACTPol cryogenic detector arrays.

Advanced ACTPol Cryogenic Detector Arrays and Readout

NASA Technical Reports Server (NTRS)

Henderson, S.W.; Allison, R.; Austermann, J.; Baildon, T.; Battaglia, N.; Beall, J. A.; Becker, D.; De Bernardis, F.; Bond, J. R.; Wollack, E. J.

2016-01-01

Advanced ACTPol is a polarization-sensitive upgrade for the 6 m aperture Atacama Cosmology Telescope, adding new frequencies and increasing sensitivity over the previous ACTPol receiver. In 2016, Advanced ACTPol will begin to map approximately half the sky in five frequency bands (28-230 GHz). Its maps of primary and secondary cosmic microwave background anisotropies-imaged in intensity and polarization at few arcminute-scale resolution-will enable precision cosmological constraints and also awide array of cross-correlation science that probes the expansion history of the universe and the growth of structure via gravitational collapse. To accomplish these scientific goals, the AdvancedACTPol receiver will be a significant upgrade to the ACTPol receiver, including four new multichroic arrays of cryogenic, feedhorn-coupled AlMn transition edge sensor polarimeters (fabricated on 150 mm diameter wafers); a system of continuously rotating meta-material silicon half-wave plates; and a new multiplexing readout architecture which uses superconducting quantum interference devices and time division to achieve a 64-row multiplexing factor. Here we present the status and scientific goals of the Advanced ACTPol instrument, emphasizing the design and implementation of the AdvancedACTPol cryogenic detector arrays.

Demonstrating Enabling Technologies for the High-Resolution Imaging Spectrometer of the Next NASA X-ray Astronomy Mission

NASA Astrophysics Data System (ADS)

Kilbourne, Caroline; Adams, J. S.; Bandler, S.; Chervenak, J.; Chiao, M.; Doriese, R.; Eckart, M.; Finkbeiner, F.; Fowler, J. W.; Hilton, G.; Irwin, K.; Kelley, R. L.; Moseley, S. J.; Porter, F. S.; Reintsema, C.; Sadleir, J.; Smith, S. J.; Swetz, D.; Ullom, J.

2014-01-01

NASA/GSFC and NIST-Boulder are collaborating on a program to advance superconducting transition-edge sensor (TES) microcalorimeter technology toward Technology Readiness Level (TRL) 6. The technology development for a TES imaging X-ray microcalorimeter spectrometer (TES microcalorimeter arrays and time-division multiplexed SQUID readout) is now at TRL 4, as evaluated by both NASA and the European Space Agency (ESA) during mission formulation for the International X-ray Observatory (IXO). We will present the status of the development program. The primary goal of the current project is to advance the core X-ray Microcalorimeter Spectrometer (XMS) detector-system technologies to a demonstration of TRL 5 in 2014. Additional objectives are to develop and demonstrate two important related technologies to at least TRL 4: position-sensitive TES devices and code-division multiplexing (CDM). These technologies have the potential to expand significantly the range of possible instrument optimizations; together they allow an expanded focal plane and higher per-pixel count rates without greatly increasing mission resources. The project also includes development of a design concept and critical technologies needed for the thermal, electrical, and mechanical integration of the detector and readout components into the focal-plane assembly. A verified design concept for the packaging of the focal-plane components will be needed for the detector system eventually to advance to TRL 6. Thus, the current project is a targeted development and demonstration program designed to make significant progress in advancing the XMS detector system toward TRL 6, establishing its readiness for a range of possible mission implementations.

Detection of enteropathogens associated with travelers' diarrhea using a multiplex Luminex-based assay performed on stool samples smeared on Whatman FTA Elute cards.

PubMed

Lalani, Tahaniyat; Tisdale, Michele D; Maguire, Jason D; Wongsrichanalai, Chansuda; Riddle, Mark S; Tribble, David R

2015-09-01

We evaluated the limits of detection (LoD) for an 11-plex PCR-Luminex assay performed on Whatman(™) FTA Elute cards smeared with stool containing pathogens associated with travelers' diarrhea. LoDs ranged from 10(2) to 10(5)CFU, PFU, or cysts/g for most pathogens except Cryptosporidium. Campylobacter and norovirus LoDs increased with prolonged storage of cards. Copyright © 2015 Elsevier Inc. All rights reserved.

Portable pathogen detection system

DOEpatents

Colston, Billy W.; Everett, Matthew; Milanovich, Fred P.; Brown, Steve B.; Vendateswaran, Kodumudi; Simon, Jonathan N.

2005-06-14

A portable pathogen detection system that accomplishes on-site multiplex detection of targets in biological samples. The system includes: microbead specific reagents, incubation/mixing chambers, a disposable microbead capture substrate, and an optical measurement and decoding arrangement. The basis of this system is a highly flexible Liquid Array that utilizes optically encoded microbeads as the templates for biological assays. Target biological samples are optically labeled and captured on the microbeads, which are in turn captured on an ordered array or disordered array disposable capture substrate and then optically read.

Multiplex Touchdown PCR for Rapid Typing of the Opportunistic Pathogen Propionibacterium acnes

PubMed Central

Barnard, Emma; Nagy, István; Hunyadkürti, Judit; Patrick, Sheila

2015-01-01

The opportunistic human pathogen Propionibacterium acnes is composed of a number of distinct phylogroups, designated types IA1, IA2, IB, IC, II, and III, which vary in their production of putative virulence factors, their inflammatory potential, and their biochemical, aggregative, and morphological characteristics. Although multilocus sequence typing (MLST) currently represents the gold standard for unambiguous phylogroup classification and individual strain identification, it is a labor-intensive and time-consuming technique. As a consequence, we developed a multiplex touchdown PCR assay that in a single reaction can confirm the species identity and phylogeny of an isolate based on its pattern of reaction with six primer sets that target the 16S rRNA gene (all isolates), ATPase (types IA1, IA2, and IC), sodA (types IA2 and IB), atpD (type II), and recA (type III) housekeeping genes, as well as a Fic family toxin gene (type IC). When applied to 312 P. acnes isolates previously characterized by MLST and representing types IA1 (n = 145), IA2 (n = 20), IB (n = 65), IC (n = 7), II (n = 45), and III (n = 30), the multiplex displayed 100% sensitivity and 100% specificity for detecting isolates within each targeted phylogroup. No cross-reactivity with isolates from other bacterial species was observed. This multiplex assay will provide researchers with a rapid, high-throughput, and technically undemanding typing method for epidemiological and phylogenetic investigations. It will facilitate studies investigating the association of lineages with various infections and clinical conditions, and it will serve as a prescreening tool to maximize the number of genetically diverse isolates selected for downstream higher-resolution sequence-based analyses. PMID:25631794

Toward Large Field-of-View High-Resolution X-ray Imaging Spectrometers: Microwave Multiplexed Readout of 28 TES Microcalorimeters

NASA Astrophysics Data System (ADS)

Yoon, W.; Adams, J. S.; Bandler, S. R.; Becker, D.; Bennett, D. A.; Chervenak, J. A.; Datesman, A. M.; Eckart, M. E.; Finkbeiner, F. M.; Fowler, J. W.; Gard, J. D.; Hilton, G. C.; Kelley, R. L.; Kilbourne, C. A.; Mates, J. A. B.; Miniussi, A. R.; Moseley, S. H.; Noroozian, O.; Porter, F. S.; Reintsema, C. D.; Sadleir, J. E.; Sakai, K.; Smith, S. J.; Stevenson, T. R.; Swetz, D. S.; Ullom, J. N.; Vale, L. R.; Wakeham, N. A.; Wassell, E. J.; Wollack, E. J.

2018-04-01

We performed small-scale demonstrations at GSFC of high-resolution X-ray TES microcalorimeters read out using a microwave SQUID multiplexer. This work is part of our effort to develop detector and readout technologies for future space-based X-ray instruments such as the microcalorimeter spectrometer envisaged for Lynx, a large mission concept under development for the Astro 2020 Decadal Survey. In this paper we describe our experiment, including details of a recently designed, microwave-optimized low-temperature setup that is thermally anchored to the 55 mK stage of our laboratory ADR. Using a ROACH2 FPGA at room temperature, we read out pixels of a GSFC-built detector array via a NIST-built multiplexer chip with Nb coplanar waveguide resonators coupled to rf-SQUIDs. The resonators are spaced 6 MHz apart (at ˜ 5.9 GHz) and have quality factors of ˜ 15,000. In our initial demonstration, we used flux-ramp modulation frequencies of 125 kHz to read out 5 pixels simultaneously and achieved spectral resolutions of 2.8-3.1 eV FWHM at 5.9 keV. Our subsequent work is ongoing: to-date we have achieved a median spectral resolution of 3.4 eV FWHM at 5.9 keV while reading out 28 pixels simultaneously with flux-ramp frequencies of 160 kHz. We present the measured system-level noise and maximum slew rates and briefly describe our future development work.

Quantitation of Marek's disease and chicken anemia viruses in organs of experimentally infected chickens and commercial chickens by multiplex real-time PCR.

PubMed

Davidson, Irit; Raibshtein, I; Al-Touri, A

2013-06-01

The worldwide distribution of chicken anemia virus (CAV) and Marek's disease virus (MDV) is well documented. In addition to their economic significance in single- or dual-virus infections, the two viruses can often accompany various other pathogens and affect poultry health either directly, by causing tumors, anemia, and delayed growth, or indirectly, by aggravating other diseases, as a result of their immunosuppressive effects. After a decade of employing the molecular diagnosis of those viruses, which replaced conventional virus isolation, we present the development of a real-time multiplex PCR for the simultaneous detection of both viruses. The real-time PCRs for MDV and for CAV alone are more sensitive than the respective end-point PCRs. In addition, the multiplex real-time shows a similar sensitivity when compared to the single real-time PCR for each virus. The newly developed real-time multiplex PCR is of importance in terms of the diagnosis and detection of low copies of each virus, MDV and CAV in single- and in multiple-virus infections, and its applicability will be further evaluated.

A frequency and sensitivity tunable microresonator array for high-speed quantum processor readout

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

Whittaker, J. D., E-mail: jwhittaker@dwavesys.com; Swenson, L. J.; Volkmann, M. H.

Superconducting microresonators have been successfully utilized as detection elements for a wide variety of applications. With multiplexing factors exceeding 1000 detectors per transmission line, they are the most scalable low-temperature detector technology demonstrated to date. For high-throughput applications, fewer detectors can be coupled to a single wire but utilize a larger per-detector bandwidth. For all existing designs, fluctuations in fabrication tolerances result in a non-uniform shift in resonance frequency and sensitivity, which ultimately limits the efficiency of bandwidth utilization. Here, we present the design, implementation, and initial characterization of a superconducting microresonator readout integrating two tunable inductances per detector. Wemore » demonstrate that these tuning elements provide independent control of both the detector frequency and sensitivity, allowing us to maximize the transmission line bandwidth utilization. Finally, we discuss the integration of these detectors in a multilayer fabrication stack for high-speed readout of the D-Wave quantum processor, highlighting the use of control and routing circuitry composed of single-flux-quantum loops to minimize the number of control wires at the lowest temperature stage.« less

Noise, fluctuation, and HADAMARD-transform spectrometry

NASA Astrophysics Data System (ADS)

Nitzsche, Guenter; Riesenberg, Rainer

2003-05-01

The HADAMARD principle is known in optics as a multiplex technique. It describes the mode with the most advantageous increase of the signal-to-noise ratio (SNR) in terms of scanning (Fellget advantage). The maximum increase of SNR, we call it gain, is (n+1)/(2On), where n is the number of multiplexing. It is valid in the case of pure detector noise. The multiplex encoding Hadamard pattern in case of n = 7 is 1110100, whereby 1 stands for a switched on channel performed by a field selector. The signals of all (switched on) channels are detected by a single detector. n measurement steps with a cyclic change of the pattern is necessary to perform the Hadamard transformation and to get the result of each individual channel. In case of n = 7 the theoretical gain is 1.51. For all possible multiplex pattern (1100000, 1110000 and so on) the gain is theoretically investigated. A multiplexing advantage (gain > 1) is reached only by the Hadamard pattern, the inverse Hadamard pattern and for (0111111)-pattern (gain=1.08). Most of the multiplex pattern are disadvantageous. The reason for maximum gain of the HADAMARD transformation is analysed theoretically. Signal fluctuations during the measurement caused by fluctuations of the illumination or by the object under test, reduce the multiplex gain, too. So the limits for realizing a gain are estimated theoretically. Essential is the transformation procedure and its influence on the error propagation. The results could be verified by experiments with array spectrometeres. Requirements are derived by numerical simulation concerning the stability of the signals to be multiplexed. It is simulated the needed stability of the signals with increasing order of multiplexing. So the increase of the multiplex gain is limited by signal fluctuations. A realized 96 channel spectral reader is presented as a modern application of an optical multiplexing arrangement. ! M. Harvid, N. J. A. Sloane, Hadamard Transform Optics, Academic Press, 1979 ! R.A. De Verse, R.M. Hammaker, W. G. Fately, J.A.Graham, J.D.Tate, "Spectrometry and imaging using a digital micromirror array" American Laboratory, Vol. 30, 21, pp. 112-120, 1998 ! R. Riesenberg, A. Wuttig, B. Harnisch, "Optical MEMS Technology for Multiplexing in High-End Micro-Scpectrometers", Proc. SPIE 4928, 6-14, 2002 ! A. Wuttig, R. Riesenberg, "Hyperspectral imager with a facile MEMS", Proc. SPIE 4881A, 2002, to be published ! R. Riesenberg, G. Nitzsche, W. Voigt, 'HADAMARD Encoding and other optical Multiplexing', VDI-Berichte 1694, pp. 345-350, 2002 ! A. Wuttig, R. Riesenberg, G. Nitzsche, "Subpixel Analysis of Double Array Grating Spectrometer", Proc. SPIE 4480, pp. 334-344, 2002 ! A. Wuttig, R. Riesenberg, G. Nitzsche, "Integral Field and Multi Object Spectrometry with MEMS", Proc. SPIE 4480, pp. 367-376, 2002 ! R. Riesenberg, G. Nitzsche, A. Wuttig, B. Harnisch, "Micro Spectrometer and MEMS for Space" in "Smaller Satellites: Bigger Business?", edited by M. Rycroft, N. Crosby, Kluwer Academic Publisher, pp. 403-406, 2002 ! R. Riesenberg, A. Wuttig, "Optical sensors with MEMS, slit masks and micromechanical devices", Proc. SPIE 4561, pp. 315-322, 2001 ! R. Riesenberg, "MicroMechanical Slit Positioning System as a transmissive spatial Light Modulator", Proc. SPIE 4457, pp.197-203, 2001 ! R. Riesenberg, J. Lonschinski, "HADAMARD-Minispectrometer made by a Micro Device", Proc. "3rd Round Table on Micro/NanoTechnologies for Space", ESTEC, Noordwijk, The Netherlands, pp. 291 - 297, 2000 ! R. Riesenberg, U. Dillner, "HADAMARD Imaging Spectrometers", Proc. SPIE 3753, pp. 203-213, 1999 ! R. Riesenberg, Th. Seifert, "Design of spatial Light Modulator Microdevices - Micro Slit Arrays", Proc. SPIE 3680, Part One, pp. 406-414, 1999 ! R. Riesenberg, W. Voigt, J. Schoneich, "Compact Spectrometers made by Micro System Technology", Sensor 97, Proc. Vol. 2, pp. 145-150,1997

High-speed wavelength-division multiplexing quantum key distribution system.

PubMed

Yoshino, Ken-ichiro; Fujiwara, Mikio; Tanaka, Akihiro; Takahashi, Seigo; Nambu, Yoshihiro; Tomita, Akihisa; Miki, Shigehito; Yamashita, Taro; Wang, Zhen; Sasaki, Masahide; Tajima, Akio

2012-01-15

A high-speed quantum key distribution system was developed with the wavelength-division multiplexing (WDM) technique and dedicated key distillation hardware engines. Two interferometers for encoding and decoding are shared over eight wavelengths to reduce the system's size, cost, and control complexity. The key distillation engines can process a huge amount of data from the WDM channels by using a 1 Mbit block in real time. We demonstrated a three-channel WDM system that simultaneously uses avalanche photodiodes and superconducting single-photon detectors. We achieved 12 h continuous key generation with a secure key rate of 208 kilobits per second through a 45 km field fiber with 14.5 dB loss.

Continuous-variable quantum key distribution with 1 Mbps secure key rate.

PubMed

Huang, Duan; Lin, Dakai; Wang, Chao; Liu, Weiqi; Fang, Shuanghong; Peng, Jinye; Huang, Peng; Zeng, Guihua

2015-06-29

We report the first continuous-variable quantum key distribution (CVQKD) experiment to enable the creation of 1 Mbps secure key rate over 25 km standard telecom fiber in a coarse wavelength division multiplexers (CWDM) environment. The result is achieved with two major technological advances: the use of a 1 GHz shot-noise-limited homodyne detector and the implementation of a 50 MHz clock system. The excess noise due to noise photons from local oscillator and classical data channels in CWDM is controlled effectively. We note that the experimental verification of high-bit-rate CVQKD in the multiplexing environment is a significant step closer toward large-scale deployment in fiber networks.

Analog bus driver and multiplexer

NASA Technical Reports Server (NTRS)

Pain, Bedabrata (Inventor); Hancock, Bruce (Inventor); Cunningham, Thomas J. (Inventor)

2012-01-01

For a source-follower signal chain, the ohmic drop in the selection switch causes unacceptable voltage offset, non-linearity, and reduced small signal gain. For an op amp signal chain, the required bias current and the output noise rises rapidly with increasing the array format due to a rapid increase in the effective capacitance caused by the Miller effect boosting up the contribution of the bus capacitance. A new switched source-follower signal chain circuit overcomes limitations of existing op-amp based or source follower based circuits used in column multiplexers and data readout. This will improve performance of CMOS imagers, and focal plane read-out integrated circuits for detectors of infrared or ultraviolet light.

Gallium arsenide quantum well-based far infrared array radiometric imager

NASA Technical Reports Server (NTRS)

Forrest, Kathrine A.; Jhabvala, Murzy D.

1991-01-01

We have built an array-based camera (FIRARI) for thermal imaging (lambda = 8 to 12 microns). FIRARI uses a square format 128 by 128 element array of aluminum gallium arsenide quantum well detectors that are indium bump bonded to a high capacity silicon multiplexer. The quantum well detectors offer good responsivity along with high response and noise uniformity, resulting in excellent thermal images without compensation for variation in pixel response. A noise equivalent temperature difference of 0.02 K at a scene temperature of 290 K was achieved with the array operating at 60 K. FIRARI demonstrated that AlGaAS quantum well detector technology can provide large format arrays with performance superior to mercury cadmium telluride at far less cost.

Rapid Identification of Pathogens from Positive Blood Cultures by Multiplex PCR using the FilmArray System

PubMed Central

Blaschke, Anne J.; Heyrend, Caroline; Byington, Carrie L.; Fisher, Mark A.; Barker, Elizabeth; Garrone, Nicholas F.; Thatcher, Stephanie A.; Pavia, Andrew T.; Barney, Trenda; Alger, Garrison D.; Daly, Judy A.; Ririe, Kirk M.; Ota, Irene; Poritz, Mark A.

2012-01-01

Sepsis is a leading cause of death. Rapid and accurate identification of pathogens and antimicrobial resistance directly from blood culture could improve patient outcomes. The FilmArray® (FA; Idaho Technology, Inc., Salt Lake City, UT) Blood Culture (BC) panel can identify > 25 pathogens and 4 antibiotic resistance genes from positive blood cultures in 1 hour. We compared a development version of the panel to conventional culture and susceptibility testing on 102 archived blood cultures from adults and children with bacteremia. Of 109 pathogens identified by culture, 95% were identified by FA. Among 111 prospectively collected blood cultures, the FA identified 84 of 92 pathogens (91%) covered by the panel. Among 25 Staphylococcus aureus and 21 Enterococcus species detected, FA identified all culture-proven MRSA and VRE. The FA BC panel is an accurate method for the rapid identification of pathogens and resistance genes from blood culture. PMID:22999332

Identification of agents effective against multiple toxins and viruses by host-oriented cell targeting.

PubMed

Zilbermintz, Leeor; Leonardi, William; Jeong, Sun-Young; Sjodt, Megan; McComb, Ryan; Ho, Chi-Lee C; Retterer, Cary; Gharaibeh, Dima; Zamani, Rouzbeh; Soloveva, Veronica; Bavari, Sina; Levitin, Anastasia; West, Joel; Bradley, Kenneth A; Clubb, Robert T; Cohen, Stanley N; Gupta, Vivek; Martchenko, Mikhail

2015-08-27

A longstanding and still-increasing threat to the effective treatment of infectious diseases is resistance to antimicrobial countermeasures. Potentially, the targeting of host proteins and pathways essential for the detrimental effects of pathogens offers an approach that may discover broad-spectrum anti-pathogen countermeasures and circumvent the effects of pathogen mutations leading to resistance. Here we report implementation of a strategy for discovering broad-spectrum host-oriented therapies against multiple pathogenic agents by multiplex screening of drugs for protection against the detrimental effects of multiple pathogens, identification of host cell pathways inhibited by the drug, and screening for effects of the agent on other pathogens exploiting the same pathway. We show that a clinically used antimalarial drug, Amodiaquine, discovered by this strategy, protects host cells against infection by multiple toxins and viruses by inhibiting host cathepsin B. Our results reveal the practicality of discovering broadly acting anti-pathogen countermeasures that target host proteins exploited by pathogens.

Multiplex PCR for the detection and differentiation of Vibrio parahaemolyticus strains using the groEL, tdh and trh genes.

PubMed

Hossain, Muhammad Tofazzal; Kim, Young-Ok; Kong, In-Soo

2013-01-01

Vibrio parahaemolyticus is a significant cause of human gastrointestinal disorders worldwide, transmitted primarily by ingestion of raw or undercooked contaminated seafood. In this study, a multiplex PCR assay for the detection and differentiation of V. parahaemolyticus strains was developed using primer sets for a species-specific marker, groEL, and two virulence markers, tdh and trh. Multiplex PCR conditions were standardised, and extracted genomic DNA of 70 V. parahaemolyticus strains was used for identification. The sensitivity and efficacy of this method were validated using artificially inoculated shellfish and seawater. The expected sizes of amplicons were 510 bp, 382 bp, and 171 bp for groEL, tdh and trh, respectively. PCR products were sufficiently different in size, and the detection limits of the multiplex PCR for groEL, tdh and trh were each 200 pg DNA. Specific detection and differentiation of virulent from non-virulent strains in shellfish homogenates and seawater was also possible after artificial inoculation with various V. parahaemolyticus strains. This newly developed multiplex PCR is a rapid assay for detection and differentiation of pathogenic V. parahaemolyticus strains, and could be used to prevent disease outbreaks and protect public health by helping the seafood industry maintain a safe shellfish supply. Copyright © 2013 Elsevier Ltd. All rights reserved.

Development of a multiplex PCR assay for detection and discrimination of Theileria annulata and Theileria sergenti in cattle.

PubMed

Junlong, Liu; Li, Youquan; Liu, Aihong; Guan, Guiquan; Xie, Junren; Yin, Hong; Luo, Jianxun

2015-07-01

Aim to construct a simple and efficient diagnostic assay for Theileria annulata and Theileria sergenti, a multiplex polymerase chain reaction (PCR) method was developed in this study. Following the alignment of the related sequences, two primer sets were designed specific targeting on T. annulata cytochrome b (COB) gene and T. sergenti internal transcribed spacer (ITS) sequences. It was found that the designed primers could react in one PCR system and generating amplifications of 818 and 393 base pair for T. sergenti and T. annulata, respectively. The standard genomic DNA of both species Theileria was serial tenfold diluted for testing the sensitivity, while specificity test confirmed both primer sets have no cross-reaction with other Theileria and Babesia species. In addition, 378 field samples were used for evaluation of the utility of the multiplex PCR assay for detection of the pathogens infection. The detection results were compared with the other two published PCR methods which targeting on T. annulata COB gene and T. sergenti major piroplasm surface protein (MPSP) gene, respectively. The developed multiplex PCR assay has similar efficient detection with COB and MPSP PCR, which indicates this multiplex PCR may be a valuable assay for the epidemiological studies for T. annulata and T. sergenti.

Multiplex real-time PCR detection and differentiation of Colletotrichum species infecting soybean

USDA-ARS?s Scientific Manuscript database

Colletotrichum species are fungal plant pathogens of worldwide significance. We isolated Colletotrichum species from soybean [Glycine max (L.) Merr.] with anthracnose symptoms in the U.S. states of Alabama, Arkansas, Illinois, Mississippi, and North Dakota from 2009 to 2013. Thirty-five strains from...

Optical performance of prototype horn-coupled TES bolometer arrays for SAFARI

NASA Astrophysics Data System (ADS)

Audley, Michael D.; de Lange, Gert; Gao, Jian-Rong; Khosropanah, Pourya; Hijmering, Richard; Ridder, Marcel L.

2016-07-01

The SAFARI Detector Test Facility is an ultra-low background optical testbed for characterizing ultra-sensitive prototype horn-coupled TES bolmeters for SAFARI, the grating spectrometer on board the proposed SPICA satellite. The testbed contains internal cold and hot black-body illuminators and a light-pipe for illumination with an external source. We have added reimaging optics to facilitate array optical measurements. The system is now being used for optical testing of prototype detector arrays read out with frequency-domain multiplexing. We present our latest optical measurements of prototype arrays and discuss these in terms of the instrument performance.

Antenna-Coupled Superconducting Tunnel Junctions with Single-Electron Transistor Readout for Detection of Sub-mm Radiation

NASA Technical Reports Server (NTRS)

Stevenson, T. R.; Hsieh, W.-T.; Li, M. J.; Stahle, C. M.; Wollack, E. J.; Schoelkopf, R. J.; Teufel, J.; Krebs, Carolyn (Technical Monitor)

2002-01-01

Antenna-coupled superconducting tunnel junction detectors have the potential for photon-counting sensitivity at sub-mm wavelengths. The device consists of an antenna structure to couple radiation into a small superconducting volume and cause quasiparticle excitations, and a single-electron transistor to measure currents through tunnel junction contacts to the absorber volume. We will describe optimization of device parameters, and recent results on fabrication techniques for producing devices with high yield for detector arrays. We will also present modeling of expected saturation power levels, antenna coupling, and rf multiplexing schemes.

Variant Interpretation: Functional Assays to the Rescue.

PubMed

Starita, Lea M; Ahituv, Nadav; Dunham, Maitreya J; Kitzman, Jacob O; Roth, Frederick P; Seelig, Georg; Shendure, Jay; Fowler, Douglas M

2017-09-07

Classical genetic approaches for interpreting variants, such as case-control or co-segregation studies, require finding many individuals with each variant. Because the overwhelming majority of variants are present in only a few living humans, this strategy has clear limits. Fully realizing the clinical potential of genetics requires that we accurately infer pathogenicity even for rare or private variation. Many computational approaches to predicting variant effects have been developed, but they can identify only a small fraction of pathogenic variants with the high confidence that is required in the clinic. Experimentally measuring a variant's functional consequences can provide clearer guidance, but individual assays performed only after the discovery of the variant are both time and resource intensive. Here, we discuss how multiplex assays of variant effect (MAVEs) can be used to measure the functional consequences of all possible variants in disease-relevant loci for a variety of molecular and cellular phenotypes. The resulting large-scale functional data can be combined with machine learning and clinical knowledge for the development of "lookup tables" of accurate pathogenicity predictions. A coordinated effort to produce, analyze, and disseminate large-scale functional data generated by multiplex assays could be essential to addressing the variant-interpretation crisis. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Detection of Anaplasma phagocytophilum, Babesia microti, Borrelia burgdorferi, Borrelia miyamotoi, and Powassan Virus in Ticks by a Multiplex Real-Time Reverse Transcription-PCR Assay

PubMed Central

Tagliafierro, Teresa; Cucura, D. Moses; Rochlin, Ilia; Sameroff, Stephen; Lipkin, W. Ian

2017-01-01

ABSTRACT Ixodes scapularis ticks are implicated in transmission of Anaplasma phagocytophilum, Borrelia burgdorferi, Borrelia miyamotoi, Babesia microti, and Powassan virus. We describe the establishment and implementation of the first multiplex real-time PCR assay with the capability to simultaneously detect and differentiate all five pathogens in a single reaction. The application of this assay for analysis of ticks at sites in New York and Connecticut revealed a high prevalence of B. microti in ticks from Suffolk County, NY. These findings are consistent with reports of a higher incidence of babesiosis from clinicians managing the care of patients with tick-borne diseases in this region. IMPORTANCE The understanding of pathogen prevalence is an important factor in the determination of human risks for tick-borne diseases and can help guide diagnosis and treatment. The implementation of our assay addresses a critical need in surveillance of tick-borne diseases, through generation of a comprehensive assessment of pathogen prevalence in I. scapularis. Our finding of a high frequency of ticks infected with Babesia microti in Suffolk County, NY, implicates this agent as a probable frequent cause of non-Lyme tick-borne disease in this area. PMID:28435891

Detection of Anaplasma phagocytophilum, Babesia microti, Borrelia burgdorferi, Borrelia miyamotoi, and Powassan Virus in Ticks by a Multiplex Real-Time Reverse Transcription-PCR Assay.

PubMed

Tokarz, Rafal; Tagliafierro, Teresa; Cucura, D Moses; Rochlin, Ilia; Sameroff, Stephen; Lipkin, W Ian

2017-01-01

Ixodes scapularis ticks are implicated in transmission of Anaplasma phagocytophilum , Borrelia burgdorferi , Borrelia miyamotoi , Babesia microti , and Powassan virus. We describe the establishment and implementation of the first multiplex real-time PCR assay with the capability to simultaneously detect and differentiate all five pathogens in a single reaction. The application of this assay for analysis of ticks at sites in New York and Connecticut revealed a high prevalence of B. microti in ticks from Suffolk County, NY. These findings are consistent with reports of a higher incidence of babesiosis from clinicians managing the care of patients with tick-borne diseases in this region. IMPORTANCE The understanding of pathogen prevalence is an important factor in the determination of human risks for tick-borne diseases and can help guide diagnosis and treatment. The implementation of our assay addresses a critical need in surveillance of tick-borne diseases, through generation of a comprehensive assessment of pathogen prevalence in I. scapularis . Our finding of a high frequency of ticks infected with Babesia microti in Suffolk County, NY, implicates this agent as a probable frequent cause of non-Lyme tick-borne disease in this area.

The detection and differentiation of canine respiratory pathogens using oligonucleotide microarrays.

PubMed

Wang, Lih-Chiann; Kuo, Ya-Ting; Chueh, Ling-Ling; Huang, Dean; Lin, Jiunn-Horng

2017-05-01

Canine respiratory diseases are commonly seen in dogs along with co-infections with multiple respiratory pathogens, including viruses and bacteria. Virus infections in even vaccinated dogs were also reported. The clinical signs caused by different respiratory etiological agents are similar, which makes differential diagnosis imperative. An oligonucleotide microarray system was developed in this study. The wild type and vaccine strains of canine distemper virus (CDV), influenza virus, canine herpesvirus (CHV), Bordetella bronchiseptica and Mycoplasma cynos were detected and differentiated simultaneously on a microarray chip. The detection limit is 10, 10, 100, 50 and 50 copy numbers for CDV, influenza virus, CHV, B. bronchiseptica and M. cynos, respectively. The clinical test results of nasal swab samples showed that the microarray had remarkably better efficacy than the multiplex PCR-agarose gel method. The positive detection rate of microarray and agarose gel was 59.0% (n=33) and 41.1% (n=23) among the 56 samples, respectively. CDV vaccine strain and pathogen co-infections were further demonstrated by the microarray but not by the multiplex PCR-agarose gel. The oligonucleotide microarray provides a highly efficient diagnosis alternative that could be applied to clinical usage, greatly assisting in disease therapy and control. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed Central

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

2011-01-01

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

Multiplex polymerase chain reaction assay developed to diagnose adult bacterial meningitis in Taiwan.

PubMed

Lee, Chi-Tsung; Hsiao, Kuang-Ming; Chen, Jin-Cherng; Su, Cheng-Chuan

2015-11-01

Acute bacterial meningitis causes high morbidity and mortality; the associated clinical symptoms often are insensitive or non-specific; and the pathogenic bacteria are geographically diverse. Clinical diagnosis requires a rapid and accurate methodology. This study aimed to develop a new multiplex polymerase chain reaction (mPCR) assay to detect simultaneously six major bacteria that cause adult bacterial meningitis in Taiwan: Klebsiella pneumoniae, Pseudomonas aeruginosa, Streptococcus pneumoniae, Staphylococcus aureus, Escherichia coli, and Acinetobacter baumannii. Species-specific primers for the six bacteria were developed using reference strains. The specificities of the mPCRs for these bacteria were validated, and the sensitivities were evaluated via serial dilutions. The mPCR assay specifically detected all of the six pathogens, particularly with sensitivities of 12 colony forming units (CFU)/mL, 90 CFU/mL, and 390 CFU/mL for E. coli, S. pneumoniae, and K. pneumoniae, respectively. This mPCR assay is a rapid and specific tool to detect the six major bacterial pathogens that cause acute adult meningitis in Taiwan, particularly sensitive for detecting E. coli, S. pneumoniae, and K. pneumoniae. The assay may facilitate early diagnosis and guidance for antimicrobial therapy for adult patients with this deadly disease in Taiwan. © 2015 APMIS. Published by John Wiley & Sons Ltd.

The DCU: the detector control unit for SPICA-SAFARI

NASA Astrophysics Data System (ADS)

Clénet, Antoine; Ravera, Laurent; Bertrand, Bernard; den Hartog, Roland H.; Jackson, Brian D.; van Leeuven, Bert-Joost; van Loon, Dennis; Parot, Yann; Pointecouteau, Etienne; Sournac, Anthony

2014-08-01

IRAP is developing the warm electronic, so called Detector Control Unit" (DCU), in charge of the readout of the SPICA-SAFARI's TES type detectors. The architecture of the electronics used to readout the 3 500 sensors of the 3 focal plane arrays is based on the frequency domain multiplexing technique (FDM). In each of the 24 detection channels the data of up to 160 pixels are multiplexed in frequency domain between 1 and 3:3 MHz. The DCU provides the AC signals to voltage-bias the detectors; it demodulates the detectors data which are readout in the cold by a SQUID; and it computes a feedback signal for the SQUID to linearize the detection chain in order to optimize its dynamic range. The feedback is computed with a specific technique, so called baseband feedback (BBFB) which ensures that the loop is stable even with long propagation and processing delays (i.e. several µs) and with fast signals (i.e. frequency carriers at 3:3 MHz). This digital signal processing is complex and has to be done at the same time for the 3 500 pixels. It thus requires an optimisation of the power consumption. We took the advantage of the relatively reduced science signal bandwidth (i.e. 20 - 40 Hz) to decouple the signal sampling frequency (10 MHz) and the data processing rate. Thanks to this method we managed to reduce the total number of operations per second and thus the power consumption of the digital processing circuit by a factor of 10. Moreover we used time multiplexing techniques to share the resources of the circuit (e.g. a single BBFB module processes 32 pixels). The current version of the firmware is under validation in a Xilinx Virtex 5 FPGA, the final version will be developed in a space qualified digital ASIC. Beyond the firmware architecture the optimization of the instrument concerns the characterization routines and the definition of the optimal parameters. Indeed the operation of the detection and readout chains requires to properly define more than 17 500 parameters (about 5 parameters per pixel). Thus it is mandatory to work out an automatic procedure to set up these optimal values. We defined a fast algorithm which characterizes the phase correction to be applied by the BBFB firmware and the pixel resonance frequencies. We also defined a technique to define the AC-carrier initial phases in such a way that the amplitude of their sum is minimized (for a better use of the DAC dynamic range).

Effect of Shot Noise on Simultaneous Sensing in Frequency Division Multiplexed Diffuse Optical Tomographic Imaging Process.

PubMed

Jang, Hansol; Lim, Gukbin; Hong, Keum-Shik; Cho, Jaedu; Gulsen, Gultekin; Kim, Chang-Seok

2017-11-28

Diffuse optical tomography (DOT) has been studied for use in the detection of breast cancer, cerebral oxygenation, and cognitive brain signals. As optical imaging studies have increased significantly, acquiring imaging data in real time has become increasingly important. We have developed frequency-division multiplexing (FDM) DOT systems to analyze their performance with respect to acquisition time and imaging quality, in comparison with the conventional time-division multiplexing (TDM) DOT. A large tomographic area of a cylindrical phantom 60 mm in diameter could be successfully reconstructed using both TDM DOT and FDM DOT systems. In our experiment with 6 source-detector (S-D) pairs, the TDM DOT and FDM DOT systems required 6.18 and 1 s, respectively, to obtain a single tomographic data set. While the absorption coefficient of the reconstruction image was underestimated in the case of the FDM DOT, we experimentally confirmed that the abnormal region can be clearly distinguished from the background phantom using both methods.

Large Format, Background Limited Arrays of Kinetic Inductance Detectors for Sub-mm Astronomy

NASA Astrophysics Data System (ADS)

Baselmans, Jochem

2018-01-01

We present the development of large format imaging arrays for sub-mm astronomy based upon microwave Kinetic Inductance detectors and their read-out. In particular we focus on the arrays developed for the A-MKID instrument for the APEX telescope. AMKID contains 2 focal plane arrays, covering a field of view of 15?x15?. One array is optimized for the 350 GHz telluric window, the other for the 850 GHz window. Both arrays are constructed from four 61 x 61 mm detector chips, each of which contains up to 3400 detectors and up to 880 detectors per readout line. The detectors are lens antenna coupled MKIDs made from NbTiN and Aluminium that reach photon noise limited sensitivity in combination with a high optical coupling. The lens-antenna radiation coupling enables the use of 4K optics and Lyot stop due to the intrinsic directivity of the detector beam, allowing a simple cryogenic architecture. We discuss the pixel design and verification, detector packaging and the array performance. We will also discuss the readout system, which is a combination of a digital and analog back-end that can read-out up to 4000 pixels simultaneously using frequency division multiplexing.

A Rapid Turnaround Cryogenic Detector Characterization System

NASA Technical Reports Server (NTRS)

Benford, Dominic j.; Dipirro, Michael J.; Forgione, Joshua B.; Jackson, Clifton E.; Jackson, Michael L.; Kogut, Al; Moseley, S. Harvey; Shirron, Peter J.

2004-01-01

Upcoming major NASA missions such as the Einstein Inflation Probe and the Single Aperture Far-Infrared Observatory require arrays of detectors with thousands of elements, operating at temperatures near l00 mK and sensitive to wavelengths from approx. 100 microns to approx. 3 mm. Such detectors represent a substantial enabling technology for these missions, and must be demonstrated soon in order for them to proceed. In order to make rapid progress on detector development, the cryogenic testing cycle must be made convenient and quick. We have developed a cryogenic detector characterization system capable of testing superconducting detector arrays in formats up to 8 x 32, read out by SQUID multiplexers. The system relies on the cooling of a two-stage adiabatic demagnetization refrigerator immersed in a liquid helium bath. This approach permits a detector to be cooled from 300K to 50 mK in about 4 hours, so that a test cycle begun in the morning will be over by the end of the day. Tine system is modular, with two identical immersible units, so that while one unit is cooling, the second can be reconfigured for the next battery of tests. We describe the design, construction, and performance of this cryogenic detector testing facility.

Development of a two-step, non-probed multiplex real-time PCR for surveilling Vibrio anguillarum in seawater

USDA-ARS?s Scientific Manuscript database

Vibrio anguillarum is an aggressive and halophilic bacterial pathogen commonly found in seawater. Its presence in aquaculture facilities causes significant morbidity and mortality among aquaculture species primarily from hemorrhaging of the body and skin of the infected fish that eventually leads t...

A-Salivary antibody responses as an indicator of waterborne infections: Pilot community study before and after installation of UV treatment

EPA Science Inventory

This ongoing project involves the development, validation and pilot application of a multiplex immunoassay based on Luminex microsphere technology to measure salivary antibody responses to the potentially-waterborne pathogens, noroviruses (Norwalk, VA387 and VA207), rotaviruses, ...

Multiplex surface plasmon resonance imaging platform for label-free detection of foodborne pathogens

USDA-ARS?s Scientific Manuscript database

Salmonellae are among the leading causes of foodborne outbreaks in the United States, and more rapid and efficient detection methods are needed. Surface plasmon resonance imaging (SPRi) is an emerging optical technique, which allows for rapid and label-free screening of multiple targets simultaneous...

Using multiplex-staining to study changes in the maize leaf phosphoproteome in response to mechanical wounding

USDA-ARS?s Scientific Manuscript database

Mechanical wounding of 2-week old maize (Zea mays L.) leaves, one of the first steps in both pathogen infection and herbivore attack, stimulates metabolism and activates signal transduction pathways dedicated to defense and recovery. The signaling pathways include reversible protein phosphorylation...

Practical photon number detection with electric field-modulated silicon avalanche photodiodes.

PubMed

Thomas, O; Yuan, Z L; Shields, A J

2012-01-24

Low-noise single-photon detection is a prerequisite for quantum information processing using photonic qubits. In particular, detectors that are able to accurately resolve the number of photons in an incident light pulse will find application in functions such as quantum teleportation and linear optics quantum computing. More generally, such a detector will allow the advantages of quantum light detection to be extended to stronger optical signals, permitting optical measurements limited only by fluctuations in the photon number of the source. Here we demonstrate a practical high-speed device, which allows the signals arising from multiple photon-induced avalanches to be precisely discriminated. We use a type of silicon avalanche photodiode in which the lateral electric field profile is strongly modulated in order to realize a spatially multiplexed detector. Clearly discerned multiphoton signals are obtained by applying sub-nanosecond voltage gates in order to restrict the detector current.

Distributed Antenna-Coupled TES for FIR Detectors Arrays

NASA Technical Reports Server (NTRS)

Day, Peter K.; Leduc, Henry G.; Dowell, C. Darren; Lee, Richard A.; Zmuidzinas, Jonas

2007-01-01

We describe a new architecture for a superconducting detector for the submillimeter and far-infrared. This detector uses a distributed hot-electron transition edge sensor (TES) to collect the power from a focal-plane-filling slot antenna array. The sensors lay directly across the slots of the antenna and match the antenna impedance of about 30 ohms. Each pixel contains many sensors that are wired in parallel as a single distributed TES, which results in a low impedance that readily matches to a multiplexed SQUID readout These detectors are inherently polarization sensitive, with very low cross-polarization response, but can also be configured to sum both polarizations. The dual-polarization design can have a bandwidth of 50The use of electron-phonon decoupling eliminates the need for micro-machining, making the focal plane much easier to fabricate than with absorber-coupled, mechanically isolated pixels. We discuss applications of these detectors and a hybridization scheme compatible with arrays of tens of thousands of pixels.

Conceptual design of a hybrid Ge:Ga detector array

NASA Technical Reports Server (NTRS)

Parry, C. M.

1984-01-01

For potential applications in space infrared astronomy missions such as the Space Infrared Telescope Facility and the Large Deployable Reflector, integrated arrays of long-wavelength detectors are desired. The results of a feasibility study which developed a design for applying integrated array techniques to a long-wavelength (gallium-doped germanium) material to achieve spectral coverage between 30 and 200 microns are presented. An approach which builds up a two-dimensional array by stacking linear detector modules is presented. The spectral response of the Ge:Ga detectors is extended to 200 microns by application of uniaxial stress to the stack of modules. The detectors are assembled with 1 mm spacing between the elements. Multiplexed readout of each module is accomplished with integration sampling of a metal-oxide-semiconductor (MOS) switch chip. Aspects of the overall design, including the anticipated level of particle effects on the array in the space environment, a transparent electrode design for 200 microns response, estimates of optical crosstalk, and mechanical stress design calculations are included.

Multiplexed wavelet transform technique for detection of microcalcification in digitized mammograms.

PubMed

Mini, M G; Devassia, V P; Thomas, Tessamma

2004-12-01

Wavelet transform (WT) is a potential tool for the detection of microcalcifications, an early sign of breast cancer. This article describes the implementation and evaluates the performance of two novel WT-based schemes for the automatic detection of clustered microcalcifications in digitized mammograms. Employing a one-dimensional WT technique that utilizes the pseudo-periodicity property of image sequences, the proposed algorithms achieve high detection efficiency and low processing memory requirements. The detection is achieved from the parent-child relationship between the zero-crossings [Marr-Hildreth (M-H) detector] /local extrema (Canny detector) of the WT coefficients at different levels of decomposition. The detected pixels are weighted before the inverse transform is computed, and they are segmented by simple global gray level thresholding. Both detectors produce 95% detection sensitivity, even though there are more false positives for the M-H detector. The M-H detector preserves the shape information and provides better detection sensitivity for mammograms containing widely distributed calcifications.

Label and label-free based surface-enhanced Raman scattering for pathogen bacteria detection: A review.

PubMed

Liu, Yu; Zhou, Haibo; Hu, Ziwei; Yu, Guangxia; Yang, Danting; Zhao, Jinshun

2017-08-15

Rapid, accurate detection of pathogen bacteria is a highly topical research area for the sake of food safety and public health. Surface-enhanced Raman scattering (SERS) is being considered as a powerful and attractive technique for pathogen bacteria detection, due to its sensitivity, high speed, comparatively low cost, multiplexing ability and portability. This contribution aims to give a comprehensive overview of SERS as a technique for rapid detection of pathogen bacteria based on label and label-free strategies. A brief tutorial on SERS is given first of all. Then we summarize the recent trends and developments of label and label-free based SERS applied to detection of pathogen bacteria, including the relatively complete interpretation of SERS spectra. In addition, multifunctional SERS platforms for pathogen bacteria in matrix are discussed as well. Furthermore, an outlook of the work done and a perspective on the future directions of SERS as a reliable tool for real-time pathogen bacteria detection are given. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparison of antibiotic resistance, virulence gene profiles, and pathogenicity of methicillin-resistant and methicillin-susceptible Staphylococcus aureus using a Caenorhabditis elegans infection model

PubMed Central

Thompson, Terissa; Brown, Paul D

2014-01-01

Objectives: This study compared the presence of 35 virulence genes, resistance phenotypes to 11 anti-staphylococcal antibiotics, and pathogenicity in methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible S. aureus (MSSA). Methods: Multiplex PCR analysis was used to differentiate Staphylococcus aureus isolates (n = 102) based on characterization of the Staphylococcal Cassette Chromosome mec (SCCmec). Singleplex and multiplex PCR assays targeting 35 virulence determinants were used to analyze the virulence repertoire of S. aureus. In vitro activities of the antibiotics were determined by the disk-diffusion method. The pathogenicity of representative isolates was assessed using Caenorhabditis elegans survival assays. Significance in virulence distribution and antibiotic resistance phenotypes was assessed using the Chi-squared tests. Kaplan–Meier survival estimates were used to analyze nematode survival and significance of survival rates evaluated using the log-rank test. Results: Except for sei (staphylococcal enterotoxin I) (P  =  0.027), all other virulence genes were not significantly associated with MRSA. Resistance to clindamycin (P  =  0.03), tetracycline (P  =  0.048), trimethoprim/sulfamethoxazole (P  =  0.038), and oxacillin (P  =  0.004) was significantly associated with MRSA. Survival assay showed MSSA having a lower median lifespan of 3 days than MRSA that had a median lifespan of 6 days. The difference in the killing time of MRSA and MSSA was significant (P < 0.001). Conclusion: While antibiotic resistance was significantly associated with MRSA, there was no preferential distribution of the virulence genes. The quicker killing potential of MSSA compared to MRSA suggests that carriage of virulence determinants per se does not determine pathogenicity in S. aureus. Pathogenicity is impacted by other factors, possibly antibiotic resistance. PMID:25319852

A superconducting focal plane array for ultraviolet, optical, and near-infrared astrophysics.

PubMed

Mazin, Benjamin A; Bumble, Bruce; Meeker, Seth R; O'Brien, Kieran; McHugh, Sean; Langman, Eric

2012-01-16

Microwave Kinetic Inductance Detectors, or MKIDs, have proven to be a powerful cryogenic detector technology due to their sensitivity and the ease with which they can be multiplexed into large arrays. A MKID is an energy sensor based on a photon-variable superconducting inductance in a lithographed microresonator, and is capable of functioning as a photon detector across the electromagnetic spectrum as well as a particle detector. Here we describe the first successful effort to create a photon-counting, energy-resolving ultraviolet, optical, and near infrared MKID focal plane array. These new Optical Lumped Element (OLE) MKID arrays have significant advantages over semiconductor detectors like charge coupled devices (CCDs). They can count individual photons with essentially no false counts and determine the energy and arrival time of every photon with good quantum efficiency. Their physical pixel size and maximum count rate is well matched with large telescopes. These capabilities enable powerful new astrophysical instruments usable from the ground and space. MKIDs could eventually supplant semiconductor detectors for most astronomical instrumentation, and will be useful for other disciplines such as quantum optics and biological imaging.

A TaqMan-based multiplex qPCR assay and DNA extraction method for phylotype IIB sequevars 1&2 (select agent) strains of Ralstonia solanacearum

DOE PAGES

Stulberg, Michael J.; Huang, Qi

2015-10-01

Ralstonia solanacearum race 3 biovar 2 strains belonging to phylotype IIB, sequevars 1 and 2 (IIB-1&2) cause brown rot of potato in temperate climates, and are quarantined pathogens in Canada and Europe. Since these strains are not established in the U.S. and because of their potential risk to the potato industry, the U.S. government has listed them as select agents. Cultivated geraniums are also a host and have the potential to spread the pathogen through trade, and its extracts strongly inhibits DNA-based detection methods. We designed four primer and probe sets for an improved qPCR method that targets stable regionsmore » of DNA. RsSA1 and RsSA2 recognize IIB-1&2 strains, RsII recognizes the current phylotype II (the newly proposed R. solanacearum species) strains (and a non-plant associated R. mannitolilytica), and Cox1 recognizes eight plant species including major hosts of R. solanacearum such as potato, tomato and cultivated geranium as an internal plant control. We multiplexed the RsSA2 with the RsII and Cox1 sets to provide two layers of detection of a positive IIB-1&2 sample, and to validate plant extracts and qPCR reactions. The TaqMan-based uniplex and multiplex qPCR assays correctly identified 34 IIB-1&2 and 52 phylotype II strains out of 90 R. solanacearum species complex strains. Additionally, the multiplex qPCR assay was validated successfully using 169 artificially inoculated symptomatic and asymptomatic plant samples from multiple plant hosts including geranium. Moreover, we developed an extraction buffer that allowed for a quick and easy DNA extraction from infected plants including geranium for detection of R. solanacearum by qPCR. Our multiplex qPCR assay, especially when coupled with the quick extraction buffer method, allows for quick, easy and reliable detection and differentiation of the IIB-1&2 strains of R. solanacearum.« less

Laboratory Tests of Multiplex Detection of PCR Amplicons Using the Luminex 100 Flow Analyzer

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

Venkateswaran, K.S.; Nasarabadi, S.; Langlois, R.G.

2000-05-05

Lawrence Livermore National Laboratory (LLNL) demonstrated the power of flow cytometry in detecting the biological agents simulants at JFT III. LLNL pioneered in the development of advanced nucleic acid analyzer (ANM) for portable real time identification. Recent advances in flow cytometry provide a means for multiplexed nucleic acid detection and immunoassay of pathogenic microorganisms. We are presently developing multiplexed immunoassays for the simultaneous detection of different simulants. Our goal is to build an integrated instrument for both nucleic acid analysis and immuno detection. In this study we evaluated the Luminex LX 100 for concurrent identification of more than one PCRmore » amplified product. ANAA has real-time Taqman fluorescent detection capability for rapid identification of field samples. However, its multiplexing ability is limited by the combination of available fluorescent labels. Hence integration of ANAA with flow cytometry can give the rapidity of ANAA amplification and the multiplex capability of flow cytometry. Multiplexed flow cytometric analysis is made possible using a set of fluorescent latex microsphere that are individually identified by their red and infrared fluorescence. A green fluorochrome is used as the assay signal. Methods were developed for the identification of specific nucleic acid sequences from Bacillus globigii (Bg), Bacillus thuringensis (Bt) and Erwinia herbicola (Eh). Detection sensitivity using different reporter fluorochromes was tested with the LX 100, and also different assay formats were evaluated for their suitability for rapid testing. A blind laboratory trial was carried out December 22-27, 1999 to evaluate bead assays for multiplex identification of Bg and Bt PCR products. This report summarizes the assay development, fluorochrome comparisons, and the results of the blind trial conducted at LLNL for the laboratory evaluation of the LX 100 flow analyzer.« less

Kinetic inductance detectors for millimeter and submillimeter astronomy

NASA Astrophysics Data System (ADS)

Boudou, Nicolas; Benoit, Alain; Bourrion, Olivier; Calvo, Martino; Désert, François-Xavier; Macias-Perez, Juan; Monfardini, Alessandro; Roesch, Markus

2012-01-01

We present recent developments in Kinetic Inductance Detectors (KID) for large arrays of detectors. The main application is ground-based millimeter wave astronomy. We focus in particular, as a case study, on our own experiment: NIKA (Néel IRAM KID Arrays). NIKA is today the best in-the-field experiment using KID-based instruments, and consists of a dual-band imaging system designed for the IRAM 30 meter telescope at Pico Veleta. We describe in this article, after a general context introduction, the KID working principle and the readout electronics, crucial to take advantage of the intrinsic KID multiplexability. We conclude with a small subset of the astronomical sources observed simultaneously at 2 mm and 1.4 mm by NIKA during the last run, held in October 2010.

Large format imaging arrays for the Atacama Cosmology Telescope

NASA Technical Reports Server (NTRS)

Chervenak, J. A.; Wollack, E. J.; Marraige, T.; Staggs, S.; Niemack, M.; Doriese, B.

2006-01-01

We describe progress in the fabrication, characterization, and production of detector arrays for the Atacama Cosmology Telescope (ACT). The completed ACT instrument is specified to image simultaneously at 145, 225, and 265 GHz using three 32x32 filled arrays of superconducting transition edge sensors (TES) read out with time-division-multiplexed SQUID amplifiers. We present details of the pixel design and testing including the optimization of the electrical parameters for multiplexed readout. Using geometric noise suppression and careful tuning of operation temperature and device bias resistance, the excess noise in the TES devices is balanced with detector speed for interfacing with the ACT optics. The design also accounts for practical tolerances such as transition temperature gradients and scatter that occur in the production of multiple wafers to populate fully the kilopixel cameras. We have developed an implanted absorber layer compatible with our silicon-on-insulator process that allows for tunable optical resistance with requisite on-wafer uniformity and wafer-to-wafer reproducibility. Arrays of 32 elements have been tested in the laboratory environment including electrical, optical, and multiplexed performance. Given this pixel design, optical tests and modeling are used to predict the performance of the filled array under anticipated viewing conditions. Integration of the filled array of pixels with a tuned backshort and dielectric plate in front of the array maximize absorption and the focal plane and suppress reflections. A mechanical design for the build of the full structure is completed and we report on progress toward the construction of a prototype array for first light on the ACT.

Integrated performance of a frequency domain multiplexing readout in the SPT-3G receiver

NASA Astrophysics Data System (ADS)

Bender, A. N.; Ade, P. A. R.; Anderson, A. J.; Avva, J.; Ahmed, Z.; Arnold, K.; Austermann, J. E.; Basu Thakur, R.; Benson, B. A.; Bleem, L. E.; Byrum, K.; Carlstrom, J. E.; Carter, F. W.; Chang, C. L.; Cho, H. M.; Cliche, J. F.; Crawford, T. M.; Cukierman, A.; Czaplewski, D. A.; Ding, J.; Divan, R.; de Haan, T.; Dobbs, M. A.; Dutcher, D.; Everett, W.; Gilbert, A.; Groh, J. C.; Guyser, R.; Halverson, N. W.; Harke-Hosemann, A.; Harrington, N. L.; Hattori, K.; Henning, J. W.; Hilton, G. C.; Holzapfel, W. L.; Huang, N.; Irwin, K. D.; Jeong, O.; Khaire, T.; Korman, M.; Kubik, D.; Kuo, C. L.; Lee, A. T.; Leitch, E. M.; Lendinez, S.; Meyer, S. S.; Miller, C. S.; Montgomery, J.; Nadolski, A.; Natoli, T.; Nguyen, H.; Novosad, V.; Padin, S.; Pan, Z.; Pearson, J.; Posada, C. M.; Rahlin, A.; Reichardt, C. L.; Ruhl, J. E.; Saliwanchik, B. R.; Sayre, J. T.; Shariff, J. A.; Shirley, Ian; Shirokoff, E.; Smecher, G.; Sobrin, J.; Stan, L.; Stark, A. A.; Story, K.; Suzuki, A.; Tang, Q. Y.; Thompson, K. L.; Tucker, C.; Vanderlinde, K.; Vieira, J. D.; Wang, G.; Whitehorn, N.; Yefremenko, V.; Yoon, K. W.

2016-07-01

The third generation receiver for the South Pole Telescope, SPT-3G, will make extremely deep, arcminuteresolution maps of the temperature and polarization of the cosmic microwave background. The SPT-3G maps will enable studies of the B-mode polarization signature, constraining primordial gravitational waves as well as the effect of massive neutrinos on structure formation in the late universe. The SPT-3G receiver will achieve exceptional sensitivity through a focal plane of 16,000 transition-edge sensor bolometers, an order of magnitude more than the current SPTpol receiver. SPT-3G uses a frequency domain multiplexing (fMux) scheme to read out the focal plane, combining the signals from 64 bolometers onto a single pair of wires. The fMux readout facilitates the large number of detectors in the SPT-3G focal plane by limiting the thermal load due to readout wiring on the 250 millikelvin cryogenic stage. A second advantage of the fMux system is that the operation of each bolometer can be optimized. In addition to these benefits, the fMux readout introduces new challenges into the design and operation of the receiver. The bolometers are operated at a range of frequencies up to 5 MHz, requiring control of stray reactances over a large bandwidth. Additionally, crosstalk between multiplexed detectors will inject large false signals into the data if not adequately mitigated. SPT-3G is scheduled to deploy to the South Pole Telescope in late 2016. Here, we present the pre-deployment performance of the fMux readout system with the SPT-3G focal plane.

High-performance single cell genetic analysis using microfluidic emulsion generator arrays.

PubMed

Zeng, Yong; Novak, Richard; Shuga, Joe; Smith, Martyn T; Mathies, Richard A

2010-04-15

High-throughput genetic and phenotypic analysis at the single cell level is critical to advance our understanding of the molecular mechanisms underlying cellular function and dysfunction. Here we describe a high-performance single cell genetic analysis (SCGA) technique that combines high-throughput microfluidic emulsion generation with single cell multiplex polymerase chain reaction (PCR). Microfabricated emulsion generator array (MEGA) devices containing 4, 32, and 96 channels are developed to confer a flexible capability of generating up to 3.4 x 10(6) nanoliter-volume droplets per hour. Hybrid glass-polydimethylsiloxane diaphragm micropumps integrated into the MEGA chips afford uniform droplet formation, controlled generation frequency, and effective transportation and encapsulation of primer functionalized microbeads and cells. A multiplex single cell PCR method is developed to detect and quantify both wild type and mutant/pathogenic cells. In this method, microbeads functionalized with multiple forward primers targeting specific genes from different cell types are used for solid-phase PCR in droplets. Following PCR, the droplets are lysed and the beads are pooled and rapidly analyzed by multicolor flow cytometry. Using Escherichia coli bacterial cells as a model, we show that this technique enables digital detection of pathogenic E. coli O157 cells in a high background of normal K12 cells, with a detection limit on the order of 1/10(5). This result demonstrates that multiplex SCGA is a promising tool for high-throughput quantitative digital analysis of genetic variation in complex populations.

High-Performance Single Cell Genetic Analysis Using Microfluidic Emulsion Generator Arrays

PubMed Central

Zeng, Yong; Novak, Richard; Shuga, Joe; Smith, Martyn T.; Mathies, Richard A.

2010-01-01

High-throughput genetic and phenotypic analysis at the single cell level is critical to advance our understanding of the molecular mechanisms underlying cellular function and dysfunction. Here we describe a high-performance single cell genetic analysis (SCGA) technique that combines high-throughput microfluidic emulsion generation with single cell multiplex PCR. Microfabricated emulsion generator array (MEGA) devices containing 4, 32 and 96 channels are developed to confer a flexible capability of generating up to 3.4 × 106 nanoliter-volume droplets per hour. Hybrid glass-polydimethylsiloxane diaphragm micropumps integrated into the MEGA chips afford uniform droplet formation, controlled generation frequency, and effective transportation and encapsulation of primer functionalized microbeads and cells. A multiplex single cell PCR method is developed to detect and quantify both wild type and mutant/pathogenic cells. In this method, microbeads functionalized with multiple forward primers targeting specific genes from different cell types are used for solid-phase PCR in droplets. Following PCR, the droplets are lysed, the beads are pooled and rapidly analyzed by multi-color flow cytometry. Using E. coli bacterial cells as a model, we show that this technique enables digital detection of pathogenic E. coli O157 cells in a high background of normal K12 cells, with a detection limit on the order of 1:105. This result demonstrates that multiplex SCGA is a promising tool for high-throughput quantitative digital analysis of genetic variation in complex populations. PMID:20192178

SERS based immuno-microwell arrays for multiplexed detection of foodborne pathogenic bacteria

NASA Astrophysics Data System (ADS)

Sun, Jian; Hankus, Mikella E.; Cullum, Brian M.

2009-05-01

A novel surface enhanced Raman scattering (SERS)-based immuno-microwell array has been developed for multiplexed detection of foodborne pathogenic bacteria. The immuno-microwell array was prepared by immobilizing the optical addressable immunomagnetic beads (IMB) into the microwell array on one end of a fiber optic bundle. The IMBs, magnetic beads coated with specific antibody to specific bacteria, were used for immunomagnetic separation (IMS) of corresponding bacteria. The magnetic separation by the homemade magnetic separation system was evaluated in terms of the influences of several important parameters including the beads concentration, the sample volume and the separation time. IMS separation efficiency of the model bacteria E.coli O157:H7 was 63% in 3 minutes. The microwell array was fabricated on hydrofluoric acid etched end of a fiber optic bundle containing 30,000 fiber elements. After being coated with silver, the microwell array was used as a uniform SERS substrate with the relative standard deviation of the SERS enhancement across the microwell array < 2% and the enhancement factor as high as 2.18 x 107. The antibody modified microwell array was prepared for bacteria immobilization into the microwell array, which was characterized by a sandwich immunoassay. To demonstrate the potential of multiplexed SERS detection with the immuno-microwell array, the SERS spectra of different Raman dye labeled magnetic beads as well as mixtures were measured on the mircrowell array. In bead mixture, different beads were identified by the characteristic SERS bands of the corresponding Raman label.

New target and detection methods: active detectors

NASA Astrophysics Data System (ADS)

Mittig, W.; Savajols, H.; Demonchy, C. E.; Giot, L.; Roussel-Chomaz, P.; Wang, H.; Ter-Akopian, G.; Fomichev, A.; Golovkov, M. S.; Stepansov, S.; Wolski, R.; Alamanos, N.; Drouart, A.; Gillibert, A.; Lapoux, V.; Pollacco, E.

2003-07-01

The study of nuclei far from stability interacting with simple target nuclei, such as protons, deuterons, 3He and 4He implies the use of inverse kinematics. The very special kinematics, together with the low intensities of the beams calls for special techniques. In july 2002 we tested a new detector, in which the detector gas is the target. This allows in principle a 4π solid angle of the detection, and a big effective target thickness without loss of resolution. The detector developped, called Maya, used isobuthane C4H10 as gas in present tests, and other gases are possible. The multiplexed electronics of more than 1000channels allows the reconstruction of the events occuring between the incoming particle and the detector gas atoms in 3D. Here we were interested in the elastic scattering of 8He on protons for the study of the isobaric analogue states (IAS) of 9He. The beam, in this case, is stopped in the detector. The resonance energy is determined by the place of interaction and the energy of the recoiling proton. The design of the detector is shown, together with some preliminary results are discussed.

Xylella fastidiosa Isolates from Both subsp. multiplex and fastidiosa Cause Disease on Southern Highbush Blueberry (Vaccinium sp.) Under Greenhouse Conditions.

PubMed

Oliver, J E; Cobine, P A; De La Fuente, L

2015-07-01

Xylella fastidiosa is a xylem-limited gram-negative plant pathogen that affects numerous crop species, including grape, citrus, peach, pecan, and almond. Recently, X. fastidiosa has also been found to be the cause of bacterial leaf scorch on blueberry in the southeastern United States. Thus far, all X. fastidiosa isolates obtained from infected blueberry have been classified as X. fastidiosa subsp. multiplex; however, X. fastidiosa subsp. fastidiosa isolates are also present in the southeastern United States and commonly cause Pierce's disease of grapevines. In this study, seven southeastern U.S. isolates of X. fastidiosa, including three X. fastidiosa subsp. fastidiosa isolates from grape, one X. fastidiosa subsp. fastidiosa isolate from elderberry, and three X. fastidiosa subsp. multiplex isolates from blueberry, were used to infect the southern highbush blueberry 'Rebel'. Following inoculation, all isolates colonized blueberry, and isolates from both X. fastidiosa subsp. multiplex and X. fastidiosa subsp. fastidiosa caused symptoms, including characteristic stem yellowing and leaf scorch symptoms as well as dieback of the stem tips. Two X. fastidiosa subsp. multiplex isolates from blueberry caused more severe symptoms than the other isolates examined, and infection with these two isolates also had a significant impact on host mineral nutrient content in sap and leaves. These findings have potential implications for understanding X. fastidiosa host adaptation and expansion and the development of emerging diseases caused by this bacterium.

Efficient heralding of O-band passively spatial-multiplexed photons for noise-tolerant quantum key distribution.

PubMed

Liu, Mao Tong; Lim, Han Chuen

2014-09-22

When implementing O-band quantum key distribution on optical fiber transmission lines carrying C-band data traffic, noise photons that arise from spontaneous Raman scattering or insufficient filtering of the classical data channels could cause the quantum bit-error rate to exceed the security threshold. In this case, a photon heralding scheme may be used to reject the uncorrelated noise photons in order to restore the quantum bit-error rate to a low level. However, the secure key rate would suffer unless one uses a heralded photon source with sufficiently high heralding rate and heralding efficiency. In this work we demonstrate a heralded photon source that has a heralding efficiency that is as high as 74.5%. One disadvantage of a typical heralded photon source is that the long deadtime of the heralding detector results in a significant drop in the heralding rate. To counter this problem, we propose a passively spatial-multiplexed configuration at the heralding arm. Using two heralding detectors in this configuration, we obtain an increase in the heralding rate by 37% and a corresponding increase in the heralded photon detection rate by 16%. We transmit the O-band photons over 10 km of noisy optical fiber to observe the relation between quantum bit-error rate and noise-degraded second-order correlation function of the transmitted photons. The effects of afterpulsing when we shorten the deadtime of the heralding detectors are also observed and discussed.

Side illuminated optical fiber as a multiplexing element for spectroscopic systems

NASA Astrophysics Data System (ADS)

Egalon, Claudio O.; Matta, Michael P.; Lavezzari, Delbert C.; Insley, Robert Y.; Jaring, Carolyn C.; Quiday, Marie F.

2013-09-01

A new type of colorimeter with multiple channels was demonstrated using a side illuminated optical fiber. When different spots of a properly modified fiber are side illuminated, multiple signals are generated and guided by the waveguide: the essence of multiplexing. This configuration is simple, low cost, does not require a sensitive coating and can analyze several samples along the fiber with a single detector: the most expensive component. Since regular colorimeters use one detector per sample, our new configuration considerably lowers the cost of analyzing multiple samples. This system consists of a fiber mounted over a support, three LEDs, an LED driver, a photo diode and a read-out: to increase the signal, the fiber was tapered. For calibration purposes, six solutions of different concentrations of food dye were prepared, placed inside cuvettes along the fiber length and illuminated by the LEDs. This light passes through the solution, strikes the fiber and is guided to the detector: the darker the solution the lower the signal intensity. Several calibration curves were obtained using different light intensities: it was found that the greater the intensity, the higher the colorimeter sensitivity. This simple capability can be used to easily control the device's sensitivity and its resolution. Although built for three samples only, this device can be modified to accommodate more. With cuvettes measuring 1 cm, it is possible to accommodate one sample per cm of fiber. Also, with minor modifications, this colorimeter can be used for fluorescence, scattering and index of refraction measurements.

10Gbps monolithic silicon FTTH transceiver without laser diode for a new PON configuration.

PubMed

Zhang, Jing; Liow, Tsung-Yang; Lo, Guo-Qiang; Kwong, Dim-Lee

2010-03-01

A new passive optical network (PON) configuration and a novel silicon photonic transceiver architecture for optical network unit (ONU) are proposed, eliminating the need for an internal laser source in ONU. The Si transceiver is fully monolithic, includes integrated wavelength division multiplexing (WDM) filters, modulators (MOD) and photo-detectors (PD), and demonstrates low-cost high volume manufacturability.

A multiplex PCR assay for molecular capsular serotyping of Mannheimia haemolytica serotypes 1, 2, and 6

USDA-ARS?s Scientific Manuscript database

Mannheimia haemolytica is an important respiratory pathogen of ruminants. Of the 12 capsular serovars identified, 1 and 6 are most frequently associated with disease in cattle, while 2 is largely a commensal. Comparative analysis of 24 M. haemolytica genomes was used to identify unique genes associa...

High-throughput biosensors for multiplexed foodborne pathogen detection

USDA-ARS?s Scientific Manuscript database

Incidental contamination of foods by harmful bacteria (such as E. coli and Salmonella) and the toxins that they produce is a serious threat to public health and the economy in the United States. The presence of such bacteri and toxins in foods must be rapidly determined at various stages of food pr...

Multiplex PCR assay for the detection and quantification of Campylobacter spp., Escherichia coli O157:H7, and Salmonella serotypes in water samples

USDA-ARS?s Scientific Manuscript database

Three pathogens, Campylobacter, Salmonella, and Shiga toxin producing Escherichia coli (STEC), are leading causes of bacterial gastroenteritis in the United States and worldwide. For example, Campylobacter species are responsible for 17% of all hospitalizations related to illness, and although Campy...

A multiplexed immunofluorescence method identifies Phakopsora pachyrhizi urediniospores and determines their viability

USDA-ARS?s Scientific Manuscript database

Soybean rust, caused by Phakopsora pachyrhizi, has been reported in most tropical and subtropical countries of the world that grow soybean. After reports of its first occurrence in Brazil in 2001 and the continental United States of America in 2004, research on the disease and its pathogen has great...

Surface-enhanced Raman scattering (SERS) detection of multiple viral antigens using magnetic capture of SERS-active nanoparticles

USDA-ARS?s Scientific Manuscript database

A highly sensitive immunoassay based on surface-enhanced Raman scattering (SERS) spectroscopy has been developed for multiplex detection of surface envelope and capsid antigens of the viral zoonotic pathogens West Nile virus (WNV) and Rift Valley fever virus (RVFV). Detection was mediated by antibo...

Design and fabricate multi channel microfluidic mold on top of glass slide using SU-8

NASA Astrophysics Data System (ADS)

Azman, N. A. N.; Rajapaksha, R. D. A. A.; Uda, M. N. A.; Hashim, U.

2017-09-01

Microfluidic is the study of fluid in microscale. Microfluidics provides miniaturized fluidic networks for processing and analyzing liquids in the nanoliter to milliliter range. Microfluidic device comprises of some essential segments or structure that are micromixer, microchannel and microchamber. The SU-8 mold is known as the most used technique in microfluidic fabrication due to the characteristic of very gooey polymer that can be spread over a thickness. In this study, in order to reduce the fabrication cost, the development and fabrication of SU-8 mold is replace by using a glass plate instead of silicon wafer which is used in the previous research. We designed a microfluidic chip for use with an IDE sensors to conduct multiplex detection of multiple channels. The microfluidic chip was designed to include multiplex detection for pathogen that consists of multiple channels of simultaneous results. The multi-channel microfluidic chip was designed, including the fluid outlet and inlet. A multi-channel microfluidic chip was used for pathogen detection. This paper sum up the fabrication of lab SU-8 mold using glass slide.

Evaluation of a multiplex real-time PCR assay for detecting pathogens in cardiac valve tissue in patients with endocarditis.

PubMed

Fernández, Angel L; Varela, Eduardo; Martínez, Lucía; Martínez, Amparo; Sierra, Juan; González-Juanatey, José R; Regueiro, Benito

2010-10-01

With a novel real-time multiplex polymerase chain reaction test, the LightCycler SeptiFast® test, 25 bacterial and fungal species can be identified directly in blood. The SeptiFast® test has been used for rapid etiologic diagnosis in infectious endocarditis using blood samples but has not been evaluated directly on cardiac vegetations in patients being treated for infectious endocarditis. We prospectively analyzed 15 samples of heart valve tissue with active infectious endocarditis using the SeptiFast® test and compared the test's sensitivity with that of blood culture, valve tissue culture, and the SeptiFast® test in blood. The sensitivity of the SeptiFast test in heart valve tissue was 100%. The test results confirmed the diagnosis obtained using blood culture in 13 cases and identified the pathogen in 2 cases where blood culture tested negative. The sensitivity of the SeptiFast® test in heart valve tissue was greater than that obtained with conventional culture of vegetations or with the SeptiFast test in blood.

A BOX-SCAR fragment for the identification of Actinobacillus pleuropneumoniae.

PubMed

Rossi, Ciro C; Pereira, Monalessa F; Langford, Paul R; Bazzolli, Denise M S

2014-03-01

Bacterial respiratory diseases are responsible for considerable mortality, morbidity and economic losses in the swine industry. Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, is one of the most important disease agents, but its identification and surveillance can be impaired by the existence of many other related bacteria in normal swine microbiota. In this work, we have evaluated a BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) sequence characterised amplified region (SCAR) marker for the specific identification of A. pleuropneumoniae and its use in a multiplex PCR to detect additionally Haemophilus parasuis and Pasteurella multocida, two other major respiratory pathogens of pigs that are members of the family Pasteurellaceae. PCRs based on the BOX-SCAR fragment developed were rapid, sensitive and differentiated A. pleuropneumoniae from all swine-related members of the Pasteurellaceae family tested. Single and multiplex BOX-SCAR fragment-based PCRs can be used to identify A. pleuropneumoniae from other bacterial swine pathogens and will be useful in surveillance and epidemiological studies. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Detection systems for carbapenemase gene identification should include the SME serine carbapenemase.

PubMed

Bush, Karen; Pannell, Megan; Lock, John L; Queenan, Anne Marie; Jorgensen, James H; Lee, Ryan M; Lewis, James S; Jarrett, Deidre

2013-01-01

Carbapenemase detection has become a major problem in hospitals that encounter outbreaks of infections caused by carbapenem-resistant Gram-negative bacteria. Rapid detection systems have been reported using multiplex PCR analyses and DNA microarray assays. Major carbapenemases that are detected by these systems include the KPC and OXA serine carbapenemases, and the IMP, VIM and NDM families of metallo-β-lactamases. However, increasing numbers of the SME serine carbapenemase are being reported from Serratia marcescens, especially from North and South America. These organisms differ from many of the other carbapenemase-producing pathogens in that they are generally susceptible to the expanded-spectrum cephalosporins ceftazidime and cefepime while retaining resistance to almost all other β-lactam antibiotics. Thus, multiplex PCR assays or DNA microarray testing of carbapenem-resistant S. marcescens isolates should include analyses for production of the SME carbapenemase. Confirmation of the presence of this enzyme may provide reassurance that oxyimino-cephalosporins can be considered for treatment of infections caused by these carbapenem-resistant pathogens. Copyright © 2012 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Diagnostic Performance of a Multiplex PCR assay for meningitis in an HIV-infected population in Uganda

PubMed Central

Rhein, Joshua; Bahr, Nathan C; Hemmert, Andrew C; Cloud, Joann L; Bellamkonda, Satya; Oswald, Cody; Lo, Eric; Nabeta, Henry; Kiggundu, Reuben; Akampurira, Andrew; Musubire, Abdu; Williams, Darlisha; Meya, David B; Boulware, David R

2015-01-01

Meningitis remains a worldwide problem, and rapid diagnosis is essential to optimize survival. We evaluated the utility of a multiplex PCR test in differentiating possible etiologies of meningitis. Cerebrospinal fluid (CSF) from 69 HIV-infected Ugandan adults with meningitis was collected at diagnosis (n=51) and among persons with cryptococcal meningitis during therapeutic lumbar punctures (n=68). Cryopreserved CSF specimens were analyzed with BioFire FilmArray® Meningitis/Encephalitis panel, which targets 17 pathogens. The panel detected Cryptococcus in the CSF of patients diagnosed with a first-episode of cryptococcal meningitis by fungal culture with 100% sensitivity and specificity, and differentiated between fungal relapse and paradoxical immune reconstitution inflammatory syndrome in recurrent episodes. A negative FilmArray result was predictive of CSF sterility on follow-up lumbar punctures for cryptococcal meningitis. EBV was frequently detected in this immunosuppressed population (n=45). Other pathogens detected included: CMV (n=2), VZV (n=2), HHV-6 (n=1), and Streptococcus pneumoniae (n=1). The FilmArray Meningitis/Encephalitis panel offers a promising platform for rapid meningitis diagnosis. PMID:26711635

Analysis of Multiplexed Nanosensor Arrays Based on Near-Infrared Fluorescent Single-Walled Carbon Nanotubes.

PubMed

Dong, Juyao; Salem, Daniel P; Sun, Jessica H; Strano, Michael S

2018-04-24

The high-throughput, label-free detection of biomolecules remains an important challenge in analytical chemistry with the potential of nanosensors to significantly increase the ability to multiplex such assays. In this work, we develop an optical sensor array, printable from a single-walled carbon nanotube/chitosan ink and functionalized to enable a divalent ion-based proximity quenching mechanism for transducing binding between a capture protein or an antibody with the target analyte. Arrays of 5 × 6, 200 μm near-infrared (nIR) spots at a density of ≈300 spots/cm 2 are conjugated with immunoglobulin-binding proteins (proteins A, G, and L) for the detection of human IgG, mouse IgM, rat IgG2a, and human IgD. Binding kinetics are measured in a parallel, multiplexed fashion from each sensor spot using a custom laser scanning imaging configuration with an nIR photomultiplier tube detector. These arrays are used to examine cross-reactivity, competitive and nonspecific binding of analyte mixtures. We find that protein G and protein L functionalized sensors report selective responses to mouse IgM on the latter, as anticipated. Optically addressable platforms such as the one examined in this work have potential to significantly advance the real-time, multiplexed biomolecular detection of complex mixtures.

The Development of a 30-125 Micron Array for Airborne Astronomy

NASA Technical Reports Server (NTRS)

Mason, C. G.; Dotson, J. L.; Erickson, E. F.; Farhoomand, J.; Haas, M. R.; Koerber, C. T.; Prasad, A.; Sisson, D.; Witteborn, F. C.; DeVincenzi, Donald (Technical Monitor)

2002-01-01

The development of a 30-125 micron Ge:Sb photoconductor array for AIRES (Airborne Infra-Red Echelle Spectrometer) is described. The prototype array is a 2x24 module which can be close-stacked to provide larger two-dimensional formats. Light is focused onto each detector using a collecting cone with a 2 mm pitch. The array is read out by two Raytheon SBRC-190 cryogenic multiplexers that also provide a CTIA (capacitive transimpedance amplifier) unit cell for each detector. We discuss our results from a test series conducted to measure the array performance and to evaluate its suitability for airborne astronomy.

The Mid-Infrared Instrument for the James Webb Space Telescope, VIII: The MIRI Focal Plane System

NASA Astrophysics Data System (ADS)

Ressler, M. E.; Sukhatme, K. G.; Franklin, B. R.; Mahoney, J. C.; Thelen, M. P.; Bouchet, P.; Colbert, J. W.; Cracraft, Misty; Dicken, D.; Gastaud, R.; Goodson, G. B.; Eccleston, Paul; Moreau, V.; Rieke, G. H.; Schneider, Analyn

2015-07-01

We describe the layout and unique features of the focal plane system for MIRI. We begin with the detector array and its readout integrated circuit (combining the amplifier unit cells and the multiplexer), the electronics, and the steps by which the data collection is controlled and the output signals are digitized and delivered to the JWST spacecraft electronics system. We then discuss the operation of this MIRI data system, including detector readout patterns, operation of subarrays, and data formats. Finally, we summarize the performance of the system, including remaining anomalies that need to be corrected in the data pipeline.

Rapid diagnostic tests apply for pediatric infections at outpatient clinic setting.

PubMed

Ushijima, Hiroshi; Thongprachum, Aksara; Tran, Dinh Nguyen; Fujimoto, Tsuguto; Hanaoka, Nozomu; Okitsu, Shoko; Takanashi, Sayaka; Mizuguchi, Masashi; Hayakawa, Satoshi

2015-01-01

Early identification of the etiology of infection is beneficial. Most infections are treated as outpatients. However, facilities for rapid diagnosis are not available in clinic settings. We applied Immunochromatography (IC) and Loop-mediated Isothermal Amplification (LAMP) methods to rapidly diagnose pathogens among 31 children with respiratory infection and 12 with gastroenteritis at a clinic in Saitama prefecture, Japan. Pathogens were then screened by multiplex conventional and real-time PCRs and bacterial culture. Respiratory pathogens were found in 64.5%. Despite the narrow spectrum, rapid tests identified pathogens in 28.6% of cases with a high agreement rate of 89.3% with PCR. Gastroenteritis pathogens were found in 66.7%. E. coli was positive in 3 cases and all were negative for verotoxin by LAMP. The agreement rate of IC and PCR assay was high, 100%. IC and LAMP are reliable and suitable methods in limited-resource settings for early pathogenic identification, which will help appropriate management, avoid unnecessary intervention, and cost saving.

Enhanced capillary electrophoretic screening of Alzheimer based on direct apolipoprotein E genotyping and one-step multiplex PCR.

PubMed

Woo, Nain; Kim, Su-Kang; Sun, Yucheng; Kang, Seong Ho

2018-01-01

Human apolipoprotein E (ApoE) is associated with high cholesterol levels, coronary artery disease, and especially Alzheimer's disease. In this study, we developed an ApoE genotyping and one-step multiplex polymerase chain reaction (PCR) based-capillary electrophoresis (CE) method for the enhanced diagnosis of Alzheimer's. The primer mixture of ApoE genes enabled the performance of direct one-step multiplex PCR from whole blood without DNA purification. The combination of direct ApoE genotyping and one-step multiplex PCR minimized the risk of DNA loss or contamination due to the process of DNA purification. All amplified PCR products with different DNA lengths (112-, 253-, 308-, 444-, and 514-bp DNA) of the ApoE genes were analyzed within 2min by an extended voltage programming (VP)-based CE under the optimal conditions. The extended VP-based CE method was at least 120-180 times faster than conventional slab gel electrophoresis methods In particular, all amplified DNA fragments were detected in less than 10 PCR cycles using a laser-induced fluorescence detector. The detection limits of the ApoE genes were 6.4-62.0pM, which were approximately 100-100,000 times more sensitive than previous Alzheimer's diagnosis methods In addition, the combined one-step multiplex PCR and extended VP-based CE method was also successfully applied to the analysis of ApoE genotypes in Alzheimer's patients and normal samples and confirmed the distribution probability of allele frequencies. This combination of direct one-step multiplex PCR and an extended VP-based CE method should increase the diagnostic reliability of Alzheimer's with high sensitivity and short analysis time even with direct use of whole blood. Copyright © 2017 Elsevier B.V. All rights reserved.

[Monitoring AIDS patients for the development of cytomegalovirus (CMV) disease using multiplex PCR].

PubMed

Terra, A P; Silva-Vergara, M L; Gomes, R A; Pereira, C L; Simpson, A J; Caballero, O L

2000-01-01

The human cytomegalovirus is an important pathogen in patients infected with the human immunodeficiency virus (HIV). The CMV viral load seems to be predictor of the development of the CMV disease in these patients. We used a multiplex PCR protocol that also provides quantitative information in those samples from which a single band is amplified and contains fewer viral genomes than those from which both targets are amplified. Monthly blood samples were collected from 270 AIDS patients. From twenty patients, two CMV targets were amplified three or more consecutive times and these patients developed CMV related disease during the study. In contrast, patients who did not result positive for both viral targets, for three or more consecutive times, or who had alternating positive and negative samples during the follow up did not present CMV related disease. The results suggest that the PCR multiplex can be used for the identification of HIV positive patients with higher risk of development of CMV disease.

Preparation of armored RNA as a control for multiplex real-time reverse transcription-PCR detection of influenza virus and severe acute respiratory syndrome coronavirus.

PubMed

Yu, Xin-Fen; Pan, Jing-Cao; Ye, Rong; Xiang, Hai-Qing; Kou, Yu; Huang, Zhi-Cheng

2008-03-01

The common respiratory viruses, including influenza A, influenza B, and newly emerging severe acute respiratory syndrome (SARS) viruses, may cause similar clinical symptoms. Therefore, differential diagnosis of these virus pathogens is frequently required for single clinical samples. In addition, there is an urgent need for noninfectious and stable RNA standards and controls for multivirus detection. In this study, reverse transcription-PCR (RT-PCR) targeting of the RNAs of influenza A and influenza B viruses and SARS coronavirus was performed, and the resulting products were spliced into a fragment which was packaged into armored RNA for use as a noninfectious, quantifiable synthetic substitute. Furthermore, in the present study we developed a multiplex real-time RT-PCR assay in which the armored RNA was used as an external positive control and the three RNA viruses could be detected simultaneously in a single reaction mix. The detection limit of the multiplex real-time PCR was 10 copies/microl of armored RNA.

Electrokinetic Stringency Control in Self-Assembled Monolayer-based Biosensors for Multiplex Urinary Tract Infection Diagnosis

PubMed Central

Liu, Tingting; Sin, Mandy L. Y.; Pyne, Jeff D.; Gau, Vincent; Liao, Joseph C.; Wong, Pak Kin

2013-01-01

Rapid detection of bacterial pathogens is critical toward judicious management of infectious diseases. Herein, we demonstrate an in situ electrokinetic stringency control approach for a self-assembled monolayer-based electrochemical biosensor toward urinary tract infection diagnosis. The in situ electrokinetic stringency control technique generates Joule heating induced temperature rise and electrothermal fluid motion directly on the sensor to improve its performance for detecting bacterial 16S rRNA, a phylogenetic biomarker. The dependence of the hybridization efficiency reveals that in situ electrokinetic stringency control is capable of discriminating single-base mismatches. With electrokinetic stringency control, the background noise due to the matrix effects of clinical urine samples can be reduced by 60%. The applicability of the system is demonstrated by multiplex detection of three uropathogenic clinical isolates with similar 16S rRNA sequences. The results demonstrate that electrokinetic stringency control can significantly improve the signal-to-noise ratio of the biosensor for multiplex urinary tract infection diagnosis. PMID:23891989

Multiplex serology for common viral infections in feral pigs (Sus scrofa) in Hawaii between 2007 and 2010.

PubMed

Stephenson, Rachel J; Trible, Benjamin R; Wang, Yu; Kerrigan, Maureen A; Goldstein, Samuel M; Rowland, Raymond R R

2015-01-01

Multiplex serology was performed for the detection of total immunoglobulin (Ig) and IgM antibodies against porcine circovirus type 2 (PCV2), porcine reproductive and respiratory syndrome virus (PRRSV), and swine influenza virus (SIV) antigens in feral swine (Sus scrofa). Serum samples were collected from the islands of Oahu (292 pigs) and Hawaii (52 pigs) between 2007 and 2010. The highest antibody prevalence was to PCV2 (63%), followed by SIV (7.8%) and PRRSV (5.8%). Antigen-specific IgM was detected at a much lower prevalence. PCR amplification and sequence analysis of PCV2 in three IgM-positive samples identified PCV2b as the only genotype. While the prevalence of PCV2 and PRRSV remained similar between 2007 and 2010, the percentage of SIV-positive samples on Oahu increased from 2% to 19%. Our results demonstrate the utility of multiplex serology for pathogen surveillance in feral pig populations.

The First Multichroic Polarimeter Array on the Atacama Cosmology Telescope: Characterization and Performance

NASA Technical Reports Server (NTRS)

Ho, S. P.; Pappas, C. G.; Austermann, J.; Beall, J. A.; Becker, D.; Choi, S. K.; Datta, R.; Duff, S. M.; Gallardo, P. A.; Grace, E.;

The First Multichroic Polarimeter Array on the Atacama Cosmology Telescope: Characterization and Performance

NASA Astrophysics Data System (ADS)

Ho, S. P.; Pappas, C. G.; Austermann, J.; Beall, J. A.; Becker, D.; Choi, S. K.; Datta, R.; Duff, S. M.; Gallardo, P. A.; Grace, E.; Hasselfield, M.; Henderson, S. W.; Hilton, G. C.; Hubmayr, J.; Koopman, B. J.; Lanen, J. V.; Li, D.; McMahon, J.; Nati, F.; Niemack, M. D.; Niraula, P.; Salatino, M.; Schillaci, A.; Schmitt, B. L.; Simon, S. M.; Staggs, S. T.; Stevens, J. R.; Ward, J. T.; Wollack, E. J.; Vavagiakis, E. M.

2016-08-01

The Atacama Cosmology Telescope Polarimeter (ACTPol) is a polarization sensitive receiver for the 6-m Atacama Cosmology Telescope (ACT) and measures the small angular scale polarization anisotropies in the cosmic microwave background (CMB). The full focal plane is composed of three detector arrays, containing over 3000 transition edge sensors (TES detectors) in total. The first two detector arrays, observing at 146 GHz, were deployed in 2013 and 2014, respectively. The third and final array is composed of multichroic pixels sensitive to both 90 and 146 GHz and saw first light in February 2015. Fabricated at NIST, this dichroic array consists of 255 pixels, with a total of 1020 polarization sensitive bolometers and is coupled to the telescope with a monolithic array of broad-band silicon feedhorns. The detectors are read out using time-division SQUID multiplexing and cooled by a dilution refrigerator at 110 mK. We present an overview of the assembly and characterization of this multichroic array in the lab, and the initial detector performance in Chile. The detector array has a TES detector electrical yield of 85 %, a total array sensitivity of less than 10 \\upmu K√{ {s}}, and detector time constants and saturation powers suitable for ACT CMB observations.

Detectors for Tomorrow's Instruments

NASA Technical Reports Server (NTRS)

Moseley, Harvey

2009-01-01

Cryogenically cooled superconducting detectors have become essential tools for a wide range of measurement applications, ranging from quantum limited heterodyne detection in the millimeter range to direct searches for dark matter with superconducting phonon detectors operating at 20 mK. Superconducting detectors have several fundamental and practical advantages which have resulted in their rapid adoption by experimenters. Their excellent performance arises in part from reductions in noise resulting from their low operating temperatures, but unique superconducting properties provide a wide range of mechanisms for detection. For example, the steep dependence of resistance with temperature on the superconductor/normal transition provides a sensitive thermometer for calorimetric and bolometric applications. Parametric changes in the properties of superconducting resonators provides a mechanism for high sensitivity detection of submillimeter photons. From a practical point of view, the use of superconducting detectors has grown rapidly because many of these devices couple well to SQUID amplifiers, which are easily integrated with the detectors. These SQUID-based amplifiers and multiplexers have matured with the detectors; they are convenient to use, and have excellent noise performance. The first generation of fully integrated large scale superconducting detection systems are now being deployed. I will discuss the prospects for a new generation of instruments designed to take full advantage of the revolution in detector technology.

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

Stulberg, Michael J.; Huang, Qi

Ralstonia solanacearum race 3 biovar 2 strains belonging to phylotype IIB, sequevars 1 and 2 (IIB-1&2) cause brown rot of potato in temperate climates, and are quarantined pathogens in Canada and Europe. Since these strains are not established in the U.S. and because of their potential risk to the potato industry, the U.S. government has listed them as select agents. Cultivated geraniums are also a host and have the potential to spread the pathogen through trade, and its extracts strongly inhibits DNA-based detection methods. We designed four primer and probe sets for an improved qPCR method that targets stable regionsmore » of DNA. RsSA1 and RsSA2 recognize IIB-1&2 strains, RsII recognizes the current phylotype II (the newly proposed R. solanacearum species) strains (and a non-plant associated R. mannitolilytica), and Cox1 recognizes eight plant species including major hosts of R. solanacearum such as potato, tomato and cultivated geranium as an internal plant control. We multiplexed the RsSA2 with the RsII and Cox1 sets to provide two layers of detection of a positive IIB-1&2 sample, and to validate plant extracts and qPCR reactions. The TaqMan-based uniplex and multiplex qPCR assays correctly identified 34 IIB-1&2 and 52 phylotype II strains out of 90 R. solanacearum species complex strains. Additionally, the multiplex qPCR assay was validated successfully using 169 artificially inoculated symptomatic and asymptomatic plant samples from multiple plant hosts including geranium. Moreover, we developed an extraction buffer that allowed for a quick and easy DNA extraction from infected plants including geranium for detection of R. solanacearum by qPCR. Our multiplex qPCR assay, especially when coupled with the quick extraction buffer method, allows for quick, easy and reliable detection and differentiation of the IIB-1&2 strains of R. solanacearum.« less

A Novel Multiplex PCR Discriminates Bacillus anthracis and Its Genetically Related Strains from Other Bacillus cereus Group Species

PubMed Central

Ogawa, Hirohito; Fujikura, Daisuke; Ohnuma, Miyuki; Ohnishi, Naomi; Hang'ombe, Bernard M.; Mimuro, Hitomi; Ezaki, Takayuki; Mweene, Aaron S.; Higashi, Hideaki

2015-01-01

Anthrax is an important zoonotic disease worldwide that is caused by Bacillus anthracis, a spore-forming pathogenic bacterium. A rapid and sensitive method to detect B. anthracis is important for anthrax risk management and control in animal cases to address public health issues. However, it has recently become difficult to identify B. anthracis by using previously reported molecular-based methods because of the emergence of B. cereus, which causes severe extra-intestinal infection, as well as the human pathogenic B. thuringiensis, both of which are genetically related to B. anthracis. The close genetic relation of chromosomal backgrounds has led to complexity of molecular-based diagnosis. In this study, we established a B. anthracis multiplex PCR that can screen for the presence of B. anthracis virulent plasmids and differentiate B. anthracis and its genetically related strains from other B. cereus group species. Six sets of primers targeting a chromosome of B. anthracis and B. anthracis-like strains, two virulent plasmids, pXO1 and pXO2, a bacterial gene, 16S rRNA gene, and a mammalian gene, actin-beta gene, were designed. The multiplex PCR detected approximately 3.0 CFU of B. anthracis DNA per PCR reaction and was sensitive to B. anthracis. The internal control primers also detected all bacterial and mammalian DNAs examined, indicating the practical applicability of this assay as it enables monitoring of appropriate amplification. The assay was also applied for detection of clinical strains genetically related to B. anthracis, which were B. cereus strains isolated from outbreaks of hospital infections in Japan, and field strains isolated in Zambia, and the assay differentiated B. anthracis and its genetically related strains from other B. cereus group strains. Taken together, the results indicate that the newly developed multiplex PCR is a sensitive and practical method for detecting B. anthracis. PMID:25774512

Fabrication of Detector Arrays for the SPT-3G Receiver

NASA Astrophysics Data System (ADS)

Posada, C. M.; Ade, P. A. R.; Ahmed, Z.; Anderson, A. J.; Austermann, J. E.; Avva, J. S.; Thakur, R. Basu; Bender, A. N.; Benson, B. A.; Carlstrom, J. E.; Carter, F. W.; Cecil, T.; Chang, C. L.; Cliche, J. F.; Cukierman, A.; Denison, E. V.; de Haan, T.; Ding, J.; Divan, R.; Dobbs, M. A.; Dutcher, D.; Everett, W.; Foster, A.; Gannon, R. N.; Gilbert, A.; Groh, J. C.; Halverson, N. W.; Harke-Hosemann, A. H.; Harrington, N. L.; Henning, J. W.; Hilton, G. C.; Holzapfel, W. L.; Huang, N.; Irwin, K. D.; Jeong, O. B.; Jonas, M.; Khaire, T.; Kofman, A. M.; Korman, M.; Kubik, D.; Kuhlmann, S.; Kuo, C. L.; Lee, A. T.; Lowitz, A. E.; Meyer, S. S.; Michalik, D.; Miller, C. S.; Montgomery, J.; Nadolski, A.; Natoli, T.; Nguyen, H.; Noble, G. I.; Novosad, V.; Padin, S.; Pan, Z.; Pearson, J.; Rahlin, A.; Ruhl, J. E.; Saunders, L. J.; Sayre, J. T.; Shirley, I.; Shirokoff, E.; Smecher, G.; Sobrin, J. A.; Stan, L.; Stark, A. A.; Story, K. T.; Suzuki, A.; Tang, Q. Y.; Thompson, K. L.; Tucker, C.; Vale, L. R.; Vanderlinde, K.; Vieira, J. D.; Wang, G.; Whitehorn, N.; Yefremenko, V.; Yoon, K. W.; Young, M. R.

2018-05-01

The South Pole Telescope third-generation (SPT-3G) receiver was installed during the austral summer of 2016-2017. It is designed to measure the cosmic microwave background across three frequency bands centered at 95, 150, and 220 GHz. The SPT-3G receiver has ten focal plane modules, each with 269 pixels. Each pixel features a broadband sinuous antenna coupled to a niobium microstrip transmission line. In-line filters define the desired band-passes before the signal is coupled to six bolometers with Ti/Au/Ti/Au transition edge sensors (three bands × two polarizations). In total, the SPT-3G receiver is composed of 16,000 detectors, which are read out using a 68× frequency-domain multiplexing scheme. In this paper, we present the process employed in fabricating the detector arrays.

Ultrasonic liquid-level detector for varying temperature and pressure environments

DOEpatents

Anderson, R.L.; Miller, G.N.

1981-10-26

An ultrasonic liquid level detector for use in varying temperature and pressure environments, such as a pressurized water nuclear reactor vessel, is provided. The detector employs ultrasonic extensional and torsional waves launched in a multiplexed alternating sequence into a common sensor. The sensor is a rectangular cross section stainless steel rod which extends into the liquid medium whose level is to be detected. The sensor temperature derived from the extensional wave velocity measurements is used to compensate for the temperature dependence of the torsional wave velocity measurements which are also level dependent. The torsional wave velocity measurements of a multiple reflection sensor then provide a measurement of liquid level over a range of several meters with a small uncertainty over a temperature range of 20 to 250/sup 0/C and pressures up to 15 MPa.

Simultaneous detection of multiple lower genital tract pathogens by an impedimetric immunochip.

PubMed

Chiriacò, Maria Serena; Primiceri, Elisabetta; De Feo, Francesco; Montanaro, Alessandro; Monteduro, Anna Grazia; Tinelli, Andrea; Megha, Marcella; Carati, Davide; Maruccio, Giuseppe

2016-05-15

Lower genital tract infections caused by both sexually and not-sexually transmitted pathogens in women are a key public health priority worldwide, especially in developing countries. Since standard analyses are time-consuming, appropriate therapeutic intervention is often neglected or delayed. Lab-on-chips and biosensors open new perspectives and offer innovative tools to simplify the diagnosis by medical staff, especially in countries with inadequate resources. Here we report a biosensing platform based on Electrochemical Impedance Spectroscopy (EIS) that allows multiplexed detection of Candida albicans, Streptococcus agalactiae and Chlamydia trachomatis with a single biochip, enabling a quick screening thanks to the presence of different immobilized antibodies, each specific for one of the different target pathogens. Copyright © 2015 Elsevier B.V. All rights reserved.

Infrared fiber optic focal plane dispersers

NASA Technical Reports Server (NTRS)

Goebel, J. H.

1981-01-01

Far infrared transmissive fiber optics as a component in the design of integrated far infrared focal plane array utilization is discussed. A tightly packed bundle of fibers is placed at the focal plane, where an array of infrared detectors would normally reside, and then fanned out in two or three dimensions to individual detectors. Subsequently, the detectors are multiplexed by cryogenic electronics for relay of the data. A second possible application is frequency up-conversion (v sub 1 + v sub 2 = v sub 3), which takes advantage of the nonlinear optical index of refraction of certain infrared transmissive materials in fiber form. Again, a fiber bundle is utilized as above, but now a laser of frequency v sub 1 is mixed with the incoming radiation of frequency v sub 1 within the nonlinear fiber material. The sum, v sub 2 is then detected by near infrared or visible detectors which are more sensitive than those available at v sub 2. Due to the geometrical size limitations of detectors such as photomultipliers, the focal plane dispersal technique is advantageous for imaging up-conversion.

HVMUX, a high voltage multiplexing for the ATLAS Tracker upgrade

NASA Astrophysics Data System (ADS)

Giulio Villani, E.; Phillips, P.; Matheson, J.; Zhang, Z.; Lynn, D.; Kuczewski, P.; Hommels, L. B. A.; Gregor, I.; Bessner, M.; Tackmann, K.; Newcomer, F. M.; Spencer, E.; Greenall, A.

2017-01-01

The HV biasing solution adopted in the current ATLAS detector uses one HV conductor for each sensor. This approach easily allows disabling of malfunctioning sensors without affecting the others, but space constraints and material budget considerations renders this approach impractical for the Upgraded detector. In fact, the increased luminosity of the Upgraded LHC will require more channels in the upgraded ATLAS Tracker, as a result of the finer detector segmentation. Different approaches to bring the HV biasing to the detectors, including the use of a shared HV line to bias several sensors and employing semiconductor switches for the HV routing (HVMUX), have been investigated. Beside the size constraints, particular attention must be paid to the radiation tolerance of any proposed solution, which, for the strips detector, requires proper operation up to fluences of the order of 2ṡ 1015 1MeV neq/cm2 and TID in excess of 300 kGy. In this paper, a description of the proposed HVMUX solution, along with electrical and radiation tests results will be presented and discussed.

Multiplexing in astrophysics with a UV multi-object spectrometer on CETUS, a probe-class mission study

NASA Astrophysics Data System (ADS)

Kendrick, Stephen E.; Woodruff, Robert A.; Hull, Tony; Heap, Sara R.; Kutyrev, Alexander; Danchi, William; Purves, Lloyd

2017-09-01

The ultraviolet multi-object spectrograph (MOS) for the Cosmic Evolution Through UV Spectroscopy (CETUS) concept1,2 is a slit-based instrument allowing multiple simultaneous observations over a wide field of view. It utilizes a next-generation micro-shutter array, an efficient aspheric Offner spectrometer design with a convex grating, and carbon nanotube light traps for suppressing unwanted wavelengths. The optical coatings are also designed to optimize the UV throughput while minimizing out-of-band signal at the detector. The UV MOS will be able to target up to 100 objects at a time without the issues of confusion with nearby sources or unwanted background like zodiacal stray light. With this multiplexing, the scientific yield of both Probe and Great Observatories will be greatly enhanced.

Compact pulse width modulation circuitry for silicon photomultiplier readout.

PubMed

Bieniosek, M F; Olcott, P D; Levin, C S

2013-08-07

The adoption of solid-state photodetectors for positron emission tomography (PET) system design and the interest in 3D interaction information from PET detectors has lead to an increasing number of readout channels in PET systems. To handle these additional readout channels, PET readout electronics should be simplified to reduce the power consumption, cost, and size of the electronics for a single channel. Pulse-width modulation (PWM), where detector pulses are converted to digital pulses with width proportional to the detected photon energy, promises to simplify PET readout by converting the signals to digital form at the beginning of the processing chain, and allowing a single time-to-digital converter to perform the data acquisition for many channels rather than routing many analogue channels and digitizing in the back end. Integrator based PWM systems, also known as charge-to-time converters (QTCs), are especially compact, reducing the front-end electronics to an op-amp integrator with a resistor discharge, and a comparator. QTCs, however, have a long dead-time during which dark count noise is integrated, reducing the output signal-to-noise ratio. This work presents a QTC based PWM circuit with a gated integrator that shows performance improvements over existing QTC based PWM. By opening and closing an analogue switch on the input of the integrator, the circuit can be controlled to integrate only the portions of the signal with a high signal-to-noise ratio. It also allows for multiplexing different detectors into the same PWM circuit while avoiding uncorrelated noise propagation between photodetector channels. Four gated integrator PWM circuits were built to readout the spatial channels of two position sensitive solid-state photomultiplier (PS-SSPM). Results show a 4 × 4 array 0.9 mm × 0.9 mm × 15 mm of LYSO crystals being identified on the 5 mm × 5 mm PS-SSPM at room temperature with no degradation for twofold multiplexing. In principle, much larger multiplexing ratios are possible, limited only by count rate issues.

Synthetic internal control sequences to increase negative call veracity in multiplexed, quantitative PCR assays for Phakopsora pachyrhizi

USDA-ARS?s Scientific Manuscript database

Quantitative PCR (Q-PCR) utilizing specific primer sequences and a fluorogenic, 5’-exonuclease linear hydrolysis probe is well established as a detection and identification method for Phakopsora pachyrhizi, the soybean rust pathogen. Because of the extreme sensitivity of Q-PCR, the DNA of a single u...

Utilization of evolutionary model, bioinformatics and heuristics for development of a multiplex Escherichia coli O157:H7 PCR assay

USDA-ARS?s Scientific Manuscript database

Introduction: Escherichia coli O157:H7 is a devastating foodborne pathogen causing many foodborne outbreaks worldwide with significant morbidity and mortality. The plasticity of the E. coli O157:H7 genome, inconsistent expression of surface antigens, and sharing of genetic elements with other non-...

Direct multiplex PCR (dmPCR) for the identification of six Phlebotomine sand fly species (Diptera: Psychodidae), including major Leishmania vectors of the Mediterranean

USDA-ARS?s Scientific Manuscript database

Sand flies (Diptera: Psychodidae, subfamily Phlebotominae) are haematophagous insects that are known to transmit several anthroponotic and zoonotic diseases. Reliable identification of sand flies at species level is crucial for their surveillance, the detection and spread of their pathogens and the ...

A dual-wavelength light-emitting diode based detector for flow-injection analysis process analysers.

PubMed

Huang, J; Liu, H; Tan, A; Xu, J; Zhao, X

1992-06-01

In this paper, a small dual-wavelength light-emitting diode (LED) based detector for FIA process analysers is designed. The detector's optical parts include a flow cell, a dual-wavelength LED and a photodiode. Neither mirrors nor lenses are used. The optical paths for the different light beams are almost the same, distinguishing it from previously reported LED based detectors. The detector's electronic components, including a signal amplifier, an A/D and D/A converter, and an Intel 8031 single-chip microcomputer, are integrated on one small board. In order to obtain response signals of approximate intensity for the two colours, the D/A converter and a multiplexer are used to adjust the emission intensity of the two colours respectively. Under microcomputer control, light beams are rapidly electronically modulated. Therefore, dark current and intensity of the light beams are measured almost simultaneously; as a result, the effect of drift is negligible. While a solution of absorbance 0.875 was measured repeatedly, an RSD (relative standard deviation) of 0.24% could be reached. Furthermore, such a detector with a red/yellow LED has been coupled with the FIA technique for the determination of 10(-6)M levels of cobalt.

Single cell analysis using surface enhanced Raman scattering (SERS) tags

PubMed Central

Nolan, John P.; Duggan, Erika; Liu, Er; Condello, Danilo; Dave, Isha; Stoner, Samuel A.

2013-01-01

Fluorescence is a mainstay of bioanalytical methods, offering sensitive and quantitative reporting, often in multiplexed or multiparameter assays. Perhaps the best example of the latter is flow cytometry, where instruments equipped with multiple lasers and detectors allow measurement of 15 or more different fluorophores simultaneously, but increases beyond this number are limited by the relatively broad emission spectra. Surface enhanced Raman scattering (SERS) from metal nanoparticles can produce signal intensities that rival fluorescence, but with narrower spectral features that allow a greater degree of multiplexing. We are developing nanoparticle SERS tags as well as Raman flow cytometers for multiparameter single cell analysis of suspension or adherent cells. SERS tags are based on plasmonically active nanoparticles (gold nanorods) whose plasmon resonance can be tuned to give optimal SERS signals at a desired excitation wavelength. Raman resonant compounds are adsorbed on the nanoparticles to confer a unique spectral fingerprint on each SERS tag, which are then encapsulated in a polymer coating for conjugation to antibodies or other targeting molecules. Raman flow cytometry employs a high resolution spectral flow cytometer capable of measuring the complete SERS spectra, as well as conventional flow cytometry measurements, from thousands of individual cells per minute. Automated spectral unmixing algorithms extract the contributions of each SERS tag from each cell to generate high content, multiparameter single cell population data. SERS-based cytometry is a powerful complement to conventional fluorescence-based cytometry. The narrow spectral features of the SERS signal enables more distinct probes to be measured in a smaller region of the optical spectrum with a single laser and detector, allowing for higher levels of multiplexing and multiparameter analysis. PMID:22498143

A Multiplexed Diagnostic Platform for Point-of-Care Pathogen Detection

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

Regan, J F; Letant, S E; Adams, K L

2008-02-04

We developed an automated point-of-care diagnostic instrument that is capable of analyzing nasal swab samples for the presence of respiratory diseases. This robust instrument, called FluIDx, performs autonomous multiplexed RT-PCR reactions that are analyzed by microsphere xMAP technology. We evaluated the performance of FluIDx, in comparison rapid tests specific for influenza and respiratory syncytial virus, in a clinical study performed at the UC Davis Medical Center. The clinical study included samples positive for RSV (n = 71), influenza A (n = 16), influenza B (n = 4), adenovirus (n = 5), parainfluenza virus (n = 2), and 44 negative samples,more » according to a composite reference method. FluIDx and the rapid tests detected 85.9% and 62.0% of the RSV positive samples, respectively. Similar sensitivities were recorded for the influenza B samples; whereas the influenza A samples were poorly detected, likely due to the utilization of an influenza A signature that did not accurately match currently circulating influenza A strains. Data for all pathogens were compiled and indicate that FluIDx is more sensitive than the rapid tests, detecting 74.2% (95% C.I. of 64.7-81.9%) of the positive samples in comparison to 53.6% (95% C.I. of 43.7-63.2%) for the rapid tests. The higher sensitivity of FluIDx was partially offset by a lower specificity, 77.3% versus 100.0%. Overall, these data suggest automated flow-through PCR-based instruments that perform multiplexed assays can successfully screen clinical samples for infectious diseases.« less

Combining Forces - The Use of Landsat TM Satellite Imagery, Soil Parameter Information, and Multiplex PCR to Detect Coccidioides immitis Growth Sites in Kern County, California

PubMed Central

Lauer, Antje; Talamantes, Jorge; Castañón Olivares, Laura Rosío; Medina, Luis Jaime; Baal, Joe Daryl Hugo; Casimiro, Kayla; Shroff, Natasha; Emery, Kirt W.

2014-01-01

Coccidioidomycosis is a fungal disease acquired through the inhalation of spores of Coccidioides spp., which afflicts primarily humans and other mammals. It is endemic to areas in the southwestern United States, including the San Joaquin Valley portion of Kern County, California, our region of interest (ROI). Recently, incidence of coccidioidomycosis, also known as valley fever, has increased significantly, and several factors including climate change have been suggested as possible drivers for this observation. Up to date details about the ecological niche of C. immitis have escaped full characterization. In our project, we chose a three-step approach to investigate this niche: 1) We examined Landsat-5-Thematic-Mapper multispectral images of our ROI by using training pixels at a 750 m×750 m section of Sharktooth Hill, a site confirmed to be a C. immitis growth site, to implement a Maximum Likelihood Classification scheme to map out the locations that could be suitable to support the growth of the pathogen; 2) We used the websoilsurvey database of the US Department of Agriculture to obtain soil parameter data; and 3) We investigated soil samples from 23 sites around Bakersfield, California using a multiplex Polymerase Chain Reaction (PCR) based method to detect the pathogen. Our results indicated that a combination of satellite imagery, soil type information, and multiplex PCR are powerful tools to predict and identify growth sites of C. immitis. This approach can be used as a basis for systematic sampling and investigation of soils to detect Coccidioides spp. PMID:25380290

Rapid and Accurate Diagnosis of Acute Pyogenic Meningitis Due to Streptococcus Pneumoniae, Haemophilus influenzae Type b and Neisseria meningitidis Using A Multiplex PCR Assay.

PubMed

Seth, Rajeev; Murthy, Peela Sree Ramchandra; Sistla, Sujatha; Subramanian, Mahadevan; Tamilarasu, Kadhiravan

2017-09-01

Acute bacterial meningitis is one of the major causes of morbidity and mortality in children and geriatric population, especially in developing countries. Methods of identification are standard culture and other phenotypic tests in many resource poor settings. To use molecular methods for the improvement of aetiological diagnosis of acute pyogenic meningitis in patients. CSF samples of 125 patients were included for the study. Gram staining and culture were performed according to standard procedures. Antigen was detected using commercial latex agglutination test kit. Multiplex PCR was performed using previously published primers and protocols. Fischer's exact test was used for finding association between presence of the disease and clinical/biochemical parameters, considering two tailed p<0.05 as statistically significant. Sensitivity, specificity, positive and negative predictive values were calculated using Graphpad QuicCalc software. A total of 39 cases (31.2%) were confirmed to be of acute pyogenic meningitis based on biochemical methods. Only 10/39 was positive for the three organisms tested. Multiplex PCR was able to detect one additional isolate each of Streptococcus pneumoniae and Haemophilus influenzae type b. When compared with multiplex PCR as the gold standard, culture and latex agglutination tests had same sensitivity (80%), specificity (100%), PPV (100%) and NPV (97.8%), whereas Gram stain had poor sensitivity (40%) and good specificity (95.6%). Detection rates were higher in multiplex PCR for the two organisms Streptococcus pneumoniae and Haemophilus influenzae type b. Multiplex PCR was more sensitive than culture or antigen detection, and employing this assay can significantly increase the speed and accuracy of identification of the pathogen.

Instrumentation for Kinetic-Inductance-Detector-Based Submillimeter Radio Astronomy

NASA Astrophysics Data System (ADS)

Duan, Ran

A substantial amount of important scientific information is contained within astronomical data at the submillimeter and far-infrared (FIR) wavelengths, including information regarding dusty galaxies, galaxy clusters, and star-forming regions; however, these wavelengths are among the least-explored fields in astronomy because of the technological difficulties involved in such research. Over the past 20 years, considerable efforts have been devoted to developing submillimeter- and millimeter-wavelength astronomical instruments and telescopes. The number of detectors is an important property of such instruments and is the subject of the current study. Future telescopes will require as many as hundreds of thousands of detectors to meet the necessary requirements in terms of the field of view, scan speed, and resolution. A large pixel count is one benefit of the development of multiplexable detectors that use kinetic inductance detector (KID) technology. This dissertation presents the development of a KID-based instrument including a portion of the millimeter-wave bandpass filters and all aspects of the readout electronics, which together enabled one of the largest detector counts achieved to date in submillimeter-/millimeter-wavelength imaging arrays: a total of 2304 detectors. The work presented in this dissertation has been implemented in the MUltiwavelength Submillimeter Inductance Camera (MUSIC), a new instrument for the Caltech Submillimeter Observatory (CSO).

Assessment of the Usefulness of Multiplex Real-Time PCR Tests in the Diagnostic and Therapeutic Process of Pneumonia in Hospitalized Children: A Single-Center Experience.

PubMed

Gowin, Ewelina; Bartkowska-Śniatkowska, Alicja; Jończyk-Potoczna, Katarzyna; Wysocka-Leszczyńska, Joanna; Bobkowski, Waldemar; Fichna, Piotr; Sobkowiak, Paulina; Mazur-Melewska, Katarzyna; Bręborowicz, Anna; Wysocki, Jacek; Januszkiewicz-Lewandowska, Danuta

2017-01-01

The aim of the study was assessment of the usefulness of multiplex real-time PCR tests in the diagnostic and therapeutic process in children hospitalized due to pneumonia and burdened with comorbidities. Methods . The study group included 97 children hospitalized due to pneumonia at the Karol Jonscher Teaching Hospital in Poznań, in whom multiplex real-time PCR tests (FTD respiratory pathogens 33; fast-track diagnostics) were used. Results . Positive test results of the test were achieved in 74 patients (76.3%). The average age in the group was 56 months. Viruses were detected in 61 samples (82% of all positive results); bacterial factors were found in 29 samples (39% of all positive results). The presence of comorbidities was established in 90 children (92.78%). On the basis of the obtained results, 5 groups of patients were established: viral etiology of infection, 34 patients; bacterial etiology, 7 patients; mixed etiology, 23 patients; pneumocystis, 9 patients; and no etiology diagnosed, 24 patients. Conclusions . Our analysis demonstrated that the participation of viruses in causing severe lung infections is significant in children with comorbidities. Multiplex real-time PCR tests proved to be more useful in establishing the etiology of pneumonia in hospitalized children than the traditional microbiological examinations.

A novel multiplex PCR for the simultaneous detection of Salmonella enterica and Shigella species.

PubMed

Radhika, M; Saugata, Majumder; Murali, H S; Batra, H V

2014-01-01

Salmonella enterica and Shigella species are commonly associated with food and water borne infections leading to gastrointestinal diseases. The present work was undertaken to develop a sensitive and reliable PCR based detection system for simultaneous detection of Salmonella enterica and Shigella at species level. For this the conserved regions of specific genes namely ipaH1, ipaH, wbgZ, wzy and invA were targeted for detection of Shigella genus, S. flexneri, S. sonnei, S. boydii and Salmonella enterica respectively along with an internal amplification control (IAC). The results showed that twenty Salmonella and eleven Shigella spp., were accurately identified by the assay without showing non-specificity against closely related other Enterobacteriaceae organisms and also against other pathogens. Further evaluation of multiplex PCR was undertaken on 50 natural samples of chicken, eggs and poultry litter and results compared with conventional culture isolation and identification procedure. The multiplex PCR identified the presence of Salmonella and Shigella strains with a short pre-enrichment step of 5 h in peptone water and the same samples were processed by conventional procedures for comparison. Therefore, this reported multiplex PCR can serve as an alternative to the tedious time-consuming procedure of culture and identification in food safety laboratories.

Centrifugal sedimentation immunoassays for multiplexed detection of enteric bacteria in ground water

DOE PAGES

Litvinov, Julia; Moen, Scott T.; Koh, Chung-Yan; ...

2016-01-01

Water-born pathogens pose significant threat to the global population and early detection plays an important role both in making drinking water safe, as well as in diagnostics and treatment of water-borne diseases. We present an innovative centrifugal microfluidic platform (SpinDx) for detection of bacterial pathogens using bead-based immunoassays. Our approach is based on binding of pathogens to antibody-functionalized capture particles followed by sedimentation of the particles through a density-media in a microfluidic disk and quantification by fluorescence microscopy. Our platform is fast (20 min), sensitive (10 3 CFU/mL), requires minimal sample preparation, and can detect multiple pathogens simultaneously with sensitivitymore » similar to that required by the EPA. We demonstrate detection of a panel of enteric bacteria (Escherichia coli, Salmonella typhimurium, Shigella, Listeria, and Campylobacter) at concentrations as low as 10 3 CFU/mL or 30 bacteria per reaction.« less

Centrifugal sedimentation immunoassays for multiplexed detection of enteric bacteria in ground water

PubMed Central

Litvinov, Julia; Moen, Scott T.; Koh, Chung-Yan; Singh, Anup K.

2016-01-01

Waterborne pathogens pose significant threat to the global population and early detection plays an important role both in making drinking water safe, as well as in diagnostics and treatment of water-borne diseases. We present an innovative centrifugal sedimentation immunoassay platform for detection of bacterial pathogens in water. Our approach is based on binding of pathogens to antibody-functionalized capture particles followed by sedimentation of the particles through a density-media in a microfluidic disk. Beads at the distal end of the disk are imaged to quantify the fluorescence and determine the bacterial concentration. Our platform is fast (20 min), can detect as few as ∼10 bacteria with minimal sample preparation, and can detect multiple pathogens simultaneously. The platform was used to detect a panel of enteric bacteria (Escherichia coli, Salmonella typhimurium, Shigella, Listeria, and Campylobacter) spiked in tap and ground water samples. PMID:26858815

Development of transition edge sensors with rf-SQUID based multiplexing system for the HOLMES experiment

NASA Astrophysics Data System (ADS)

Puiu, A.; Becker, D.; Bennett, D.; Faverzani, M.; Ferri, E.; Fowler, J.; Gard, J.; Hays-Wehle, J.; Hilton, G.; Giachero, A.; Maino, M.; Mates, J.; Nucciotti, A.; Schmidt, D.; Swetz, D.; Ullom, J.; Vale, L.

2017-09-01

Measuring the neutrino mass is one the most compelling issue in particle physics. HOLMES is an experiment funded by the European Research Council for a direct measurement of neutrino mass. HOLMES will perform a precise measurement of the end point of the Electron Capture decay spectrum of 163Ho in order to extract information on neutrino mass with a sensitivity as low as 1 eV. HOLMES, in its final configuration will deploy a 1000 pixel array of low temperature microcalorimeters: each calorimeter consists of an absorber, where the Ho atoms will be implanted, coupled to a Transition Edge Sensor thermometer. The detectors will be kept at the working temperature of ˜70 mK using a dilution refrigerator. In order to gather the required 3 × 1013 events in a three year long data taking with a pile up fraction as low as 10-4, detectors must fulfill rather high speed and resolution requirements, i.e. 10 µs rise time and 4 eV resolution. To ensure such performances with an efficient read out technique for very large detectors array kept at low temperature inside a cryostat is no trivial matter: at the moment, the most appealing read out technique applicable to large arrays of Transition Edge Sensors is rf-SQUID multiplexing. It is based on the use of rf-SQUIDs as input devices with flux ramp modulation for linearisation purposes; the rf-SQUID is then coupled to a super-conductive λ/4-wave resonator in the GHz range, and the modulated signal is finally read out using the homodyne technique.

Development of the Nano-HEB Array for Low-Background Far-IR Applications

NASA Technical Reports Server (NTRS)

Karasik, Boris S.; Pereverzev, Sergey V.; Olaya, David; Gershenson, Michael E.; Cantor, Robin; Kawamura, Jonathan H.; Day, Peter K.; Bumble, Bruce; LeDuc, Henry G.; Monacos, Steve P.;

Electrophoretically mediated microanalysis of a nicotinamide adenine dinucleotide-dependent enzyme and its facile multiplexing using an active pixel sensor UV detector.

PubMed

Urban, Pawel L; Goodall, David M; Bergström, Edmund T; Bruce, Neil C

2007-08-31

An electrophoretically mediated microanalysis (EMMA) method has been developed for yeast alcohol dehydrogenase and quantification of reactant and product cofactors, NAD and NADH. The enzyme substrate ethanol (1% (v/v)) was added to the buffer (50 mM borate, pH 8.8). Results are presented for parallel capillary electrophoresis with a novel miniature UV area detector, with an active pixel sensor imaging an array of two or six parallel capillaries connected via a manifold to a single output capillary in a commercial CE instrument, allowing conversions with five different yeast alcohol dehydrogenase concentrations to be quantified in a single experiment.

Multiplexing Readout of TES Microcalorimeters Based on Analog Baseband Feedback

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

Takei, Y.; Yamasaki, N.Y; Mitsuda, K.

2009-12-16

A TES microcalorimeter array is a promising spectrometer with excellent energy resolution and a moderate imaging capability. To realize a large format array in space, multiplexing the TES signals at the low tempersture stage is mandatory. We are developing frequency division multiplexing (FDM) based on baseband feedback technique. In FDM, each TES is AC-biased with a different carrier frequency. Signals from several pixels are summed and then read out by one SQUID. The maximum number of multiplexed pixels are limited by the frequency band in which the SQUID can be operated in a flux-locked loop, which is {approx}1 MHz withmore » standard flux-locked loop circuit. In the baseband feedback, the signal ({approx}10 kHz band) from the TES is once demodulated. Then a reconstructed copy of the modulated signal with an appropriate phase is fed back to the SQUID input coil to maintain an approximately constant magnetic flux. This can be implemented even for large cable delays and automatically suppresses the carrier. We developed a prototype electronics for the baseband feedback based on an analog phase sensitive detector (PSD) and a multiplier. Combined with Seiko 80-SSA SQUID amp, open-loop gain of 8 has been obtained for 10 kHz baseband signal at 5 MHz carrier frequency, with a moderate noise contribution of 27pA/{radical}(Hz) at input.« less

Development of the Focal Plane Detection System for the Future Gas-Filled Separator at the Cyclotron Institute

NASA Astrophysics Data System (ADS)

Bertelsen, Erin; Mayorov, Dmitriy; Folden, Charles ``Cody'', III

2015-10-01

A focal plane detection system is being developed for use with the gas-filled separator previously known as SASSYER (Small Angle Separator System at Yale for Evaporation Residues) that will be installed at the Cyclotron Institute at Texas A&M University. This system will be used to study heavy (Z >= 90) elements and features two 60×40 strip double-sided silicon detectors (DSSDs) and accompanying multiplexing read-out electronics. The DSSDs cover an area of 120×40 mm2 and are read-out by fourteen 16-channel multiplexers (Mesytec MUX-16) that perform the function of a preamplifier, shaper, and leading-edge discriminator in one unit. The multiplexers are controlled by four ``MUX drivers,'' each of which serves as a signal bus for multiple MUX-16 boards. The system allows a single 16-channel ADC to read the combined 200 strips of both DSSDs. A four peak source composed of 148Gd, 239Pu, 241Am, and 244Cm was used to characterize the performance of the system, with a preliminary energy resolution of ~ 60 keV measured for the 241Am alphas. This contribution will discuss the work performed in assembly of the test setup, optimization and performance check of the multiplexers, and the preliminary energy and position data collected with the α-source. Present address: Los Alamos National Laboratory, Los Alamos, NM 87545.

Development and first evaluation of a novel multiplex real-time PCR on whole blood samples for rapid pathogen identification in critically ill patients with sepsis.

PubMed

van de Groep, Kirsten; Bos, Martine P; Savelkoul, Paul H M; Rubenjan, Anna; Gazenbeek, Christel; Melchers, Willem J G; van der Poll, Tom; Juffermans, Nicole P; Ong, David S Y; Bonten, Marc J M; Cremer, Olaf L

2018-04-26

Molecular tests may enable early adjustment of antimicrobial therapy and be complementary to blood culture (BC) which has imperfect sensitivity in critically ill patients. We evaluated a novel multiplex real-time PCR assay to diagnose bloodstream pathogens directly in whole blood samples (BSI-PCR). BSI-PCR included 11 species- and four genus-specific PCRs, a molecular Gram-stain PCR, and two antibiotic resistance markers. We collected 5 mL blood from critically ill patients simultaneously with clinically indicated BC. Microbial DNA was isolated using the Polaris method followed by automated DNA extraction. Sensitivity and specificity were calculated using BC as reference. BSI-PCR was evaluated in 347 BC-positive samples (representing up to 50 instances of each pathogen covered by the test) and 200 BC-negative samples. Bacterial species-specific PCR sensitivities ranged from 65 to 100%. Sensitivity was 26% for the Gram-positive PCR, 32% for the Gram-negative PCR, and ranged 0 to 7% for yeast PCRs. Yeast detection was improved to 40% in a smaller set-up. There was no overall association between BSI-PCR sensitivity and time-to-positivity of BC (which was highly variable), yet Ct-values were lower for true-positive versus false-positive PCR results. False-positive results were observed in 84 (4%) of the 2200 species-specific PCRs in 200 culture-negative samples, and ranged from 0 to 6% for generic PCRs. Sensitivity of BSI-PCR was promising for individual bacterial pathogens, but still insufficient for yeasts and generic PCRs. Further development of BSI-PCR will focus on improving sensitivity by increasing input volumes and on subsequent implementation as a bedside test.

A Multiplex PCR/LDR Assay for the Simultaneous Identification of Category A Infectious Pathogens: Agents of Viral Hemorrhagic Fever and Variola Virus

PubMed Central

Das, Sanchita; Rundell, Mark S.; Mirza, Aashiq H.; Pingle, Maneesh R.; Shigyo, Kristi; Garrison, Aura R.; Paragas, Jason; Smith, Scott K.; Olson, Victoria A.; Larone, Davise H.; Spitzer, Eric D.; Barany, Francis; Golightly, Linnie M.

2015-01-01

CDC designated category A infectious agents pose a major risk to national security and require special action for public health preparedness. They include viruses that cause viral hemorrhagic fever (VHF) syndrome as well as variola virus, the agent of smallpox. VHF is characterized by hemorrhage and fever with multi-organ failure leading to high morbidity and mortality. Smallpox, a prior scourge, has been eradicated for decades, making it a particularly serious threat if released nefariously in the essentially non-immune world population. Early detection of the causative agents, and the ability to distinguish them from other pathogens, is essential to contain outbreaks, implement proper control measures, and prevent morbidity and mortality. We have developed a multiplex detection assay that uses several species-specific PCR primers to generate amplicons from multiple pathogens; these are then targeted in a ligase detection reaction (LDR). The resultant fluorescently-labeled ligation products are detected on a universal array enabling simultaneous identification of the pathogens. The assay was evaluated on 32 different isolates associated with VHF (ebolavirus, marburgvirus, Crimean Congo hemorrhagic fever virus, Lassa fever virus, Rift Valley fever virus, Dengue virus, and Yellow fever virus) as well as variola virus and vaccinia virus (the agent of smallpox and its vaccine strain, respectively). The assay was able to detect all viruses tested, including 8 sequences representative of different variola virus strains from the CDC repository. It does not cross react with other emerging zoonoses such as monkeypox virus or cowpox virus, or six flaviviruses tested (St. Louis encephalitis virus, Murray Valley encephalitis virus, Powassan virus, Tick-borne encephalitis virus, West Nile virus and Japanese encephalitis virus). PMID:26381398

Retrospective analysis of multiplex polymerase chain reaction-based molecular diagnostics (SES) in 70 patients with suspected central nervous system infections: A single-center study

PubMed Central

Ramalingam, Rama Krishnan Tiruppur Chinnappan; Chakraborty, Dipanjan

2016-01-01

Background: Central nervous system (CNS) infections present a grave health care challenge due to high morbidity and mortality. Clinical findings and conventional laboratory assessments are not sufficiently distinct for specific etiologic diagnosis. Identification of pathogens is a key to appropriate therapy. Aim: In this retrospective observational study, we evaluated the efficacy and clinical utility of syndrome evaluation system (SES) for diagnosing clinically suspected CNS infections. Materials and Methods: This retrospective analysis included inpatients in our tertiary level neurointensive care unit (NICU) and ward from February 2010 to December 2013. Cerebrospinal fluid (CSF) samples of 70 patients, clinically suspected of having CNS infections, were subjected to routine laboratory tests, culture, imaging, and SES. We analyzed the efficacy of SES in the diagnosis of CNS infections and its utility in therapeutic decision-making. Results: SES had a clinical sensitivity of 57.4% and clinical specificity of 95.6%. Streptococcus pneumoniae and Pseudomonas aeruginosa were the top two bacterial pathogens, whereas Herpes simplex virus (HSV) was the most common viral pathogen. Polymicrobial infections were detected in 32.14% of SES-positive cases. SES elicited a change in the management in 30% of the patients from initial empiric therapy. At discharge, 51 patients recovered fully while 11 patients had partial recovery. Three-month follow-up showed only six patients to have neurological deficits. Conclusion: In a tertiary care center, etiological microbial diagnosis is central to appropriate therapy and outcomes. Sensitive and accurate multiplex molecular diagnostics play a critical role in not only identifying the causative pathogen but also in helping clinicians to institute appropriate therapy, reduce overuse of antimicrobials, and ensure superior clinical outcomes. PMID:27994358

Retrospective analysis of multiplex polymerase chain reaction-based molecular diagnostics (SES) in 70 patients with suspected central nervous system infections: A single-center study.

PubMed

Ramalingam, Rama Krishnan Tiruppur Chinnappan; Chakraborty, Dipanjan

2016-01-01

Central nervous system (CNS) infections present a grave health care challenge due to high morbidity and mortality. Clinical findings and conventional laboratory assessments are not sufficiently distinct for specific etiologic diagnosis. Identification of pathogens is a key to appropriate therapy. In this retrospective observational study, we evaluated the efficacy and clinical utility of syndrome evaluation system (SES) for diagnosing clinically suspected CNS infections. This retrospective analysis included inpatients in our tertiary level neurointensive care unit (NICU) and ward from February 2010 to December 2013. Cerebrospinal fluid (CSF) samples of 70 patients, clinically suspected of having CNS infections, were subjected to routine laboratory tests, culture, imaging, and SES. We analyzed the efficacy of SES in the diagnosis of CNS infections and its utility in therapeutic decision-making. SES had a clinical sensitivity of 57.4% and clinical specificity of 95.6%. Streptococcus pneumoniae and Pseudomonas aeruginosa were the top two bacterial pathogens, whereas Herpes simplex virus (HSV) was the most common viral pathogen. Polymicrobial infections were detected in 32.14% of SES-positive cases. SES elicited a change in the management in 30% of the patients from initial empiric therapy. At discharge, 51 patients recovered fully while 11 patients had partial recovery. Three-month follow-up showed only six patients to have neurological deficits. In a tertiary care center, etiological microbial diagnosis is central to appropriate therapy and outcomes. Sensitive and accurate multiplex molecular diagnostics play a critical role in not only identifying the causative pathogen but also in helping clinicians to institute appropriate therapy, reduce overuse of antimicrobials, and ensure superior clinical outcomes.

A Multiplex PCR/LDR Assay for the Simultaneous Identification of Category A Infectious Pathogens: Agents of Viral Hemorrhagic Fever and Variola Virus.

PubMed

Das, Sanchita; Rundell, Mark S; Mirza, Aashiq H; Pingle, Maneesh R; Shigyo, Kristi; Garrison, Aura R; Paragas, Jason; Smith, Scott K; Olson, Victoria A; Larone, Davise H; Spitzer, Eric D; Barany, Francis; Golightly, Linnie M

2015-01-01

CDC designated category A infectious agents pose a major risk to national security and require special action for public health preparedness. They include viruses that cause viral hemorrhagic fever (VHF) syndrome as well as variola virus, the agent of smallpox. VHF is characterized by hemorrhage and fever with multi-organ failure leading to high morbidity and mortality. Smallpox, a prior scourge, has been eradicated for decades, making it a particularly serious threat if released nefariously in the essentially non-immune world population. Early detection of the causative agents, and the ability to distinguish them from other pathogens, is essential to contain outbreaks, implement proper control measures, and prevent morbidity and mortality. We have developed a multiplex detection assay that uses several species-specific PCR primers to generate amplicons from multiple pathogens; these are then targeted in a ligase detection reaction (LDR). The resultant fluorescently-labeled ligation products are detected on a universal array enabling simultaneous identification of the pathogens. The assay was evaluated on 32 different isolates associated with VHF (ebolavirus, marburgvirus, Crimean Congo hemorrhagic fever virus, Lassa fever virus, Rift Valley fever virus, Dengue virus, and Yellow fever virus) as well as variola virus and vaccinia virus (the agent of smallpox and its vaccine strain, respectively). The assay was able to detect all viruses tested, including 8 sequences representative of different variola virus strains from the CDC repository. It does not cross react with other emerging zoonoses such as monkeypox virus or cowpox virus, or six flaviviruses tested (St. Louis encephalitis virus, Murray Valley encephalitis virus, Powassan virus, Tick-borne encephalitis virus, West Nile virus and Japanese encephalitis virus).

Clinical Validation of Multiplex Real-Time PCR Assays for Detection of Bacterial Meningitis Pathogens

PubMed Central

Theodore, M. Jordan; Mair, Raydel; Trujillo-Lopez, Elizabeth; du Plessis, Mignon; Wolter, Nicole; Baughman, Andrew L.; Hatcher, Cynthia; Vuong, Jeni; Lott, Lisa; von Gottberg, Anne; Sacchi, Claudio; McDonald, J. Matthew; Messonnier, Nancy E.; Mayer, Leonard W.

2012-01-01

Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae are important causes of meningitis and other infections, and rapid, sensitive, and specific laboratory assays are critical for effective public health interventions. Singleplex real-time PCR assays have been developed to detect N. meningitidis ctrA, H. influenzae hpd, and S. pneumoniae lytA and serogroup-specific genes in the cap locus for N. meningitidis serogroups A, B, C, W135, X, and Y. However, the assay sensitivity for serogroups B, W135, and Y is low. We aimed to improve assay sensitivity and develop multiplex assays to reduce time and cost. New singleplex real-time PCR assays for serogroup B synD, W135 synG, and Y synF showed 100% specificity for detecting N. meningitidis species, with high sensitivity (serogroup B synD, 99% [75/76]; W135 synG, 97% [38/39]; and Y synF, 100% [66/66]). The lower limits of detection (LLD) were 9, 43, and 10 copies/reaction for serogroup B synD, W135 synG, and Y synF assays, respectively, a significant improvement compared to results for the previous singleplex assays. We developed three multiplex real-time PCR assays for detection of (i) N. meningitidis ctrA, H. influenzae hpd, and S. pneumoniae lytA (NHS assay); (ii) N. meningitidis serogroups A, W135, and X (AWX assay); and (iii) N. meningitidis serogroups B, C, and Y (BCY assay). Each multiplex assay was 100% specific for detecting its target organisms or serogroups, and the LLD was similar to that for the singleplex assay. Pairwise comparison of real-time PCR between multiplex and singleplex assays showed that cycle threshold values of the multiplex assay were similar to those for the singleplex assay. There were no substantial differences in sensitivity and specificity between these multiplex and singleplex real-time PCR assays. PMID:22170919

Clinical validation of multiplex real-time PCR assays for detection of bacterial meningitis pathogens.

PubMed

Wang, Xin; Theodore, M Jordan; Mair, Raydel; Trujillo-Lopez, Elizabeth; du Plessis, Mignon; Wolter, Nicole; Baughman, Andrew L; Hatcher, Cynthia; Vuong, Jeni; Lott, Lisa; von Gottberg, Anne; Sacchi, Claudio; McDonald, J Matthew; Messonnier, Nancy E; Mayer, Leonard W

2012-03-01

Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae are important causes of meningitis and other infections, and rapid, sensitive, and specific laboratory assays are critical for effective public health interventions. Singleplex real-time PCR assays have been developed to detect N. meningitidis ctrA, H. influenzae hpd, and S. pneumoniae lytA and serogroup-specific genes in the cap locus for N. meningitidis serogroups A, B, C, W135, X, and Y. However, the assay sensitivity for serogroups B, W135, and Y is low. We aimed to improve assay sensitivity and develop multiplex assays to reduce time and cost. New singleplex real-time PCR assays for serogroup B synD, W135 synG, and Y synF showed 100% specificity for detecting N. meningitidis species, with high sensitivity (serogroup B synD, 99% [75/76]; W135 synG, 97% [38/39]; and Y synF, 100% [66/66]). The lower limits of detection (LLD) were 9, 43, and 10 copies/reaction for serogroup B synD, W135 synG, and Y synF assays, respectively, a significant improvement compared to results for the previous singleplex assays. We developed three multiplex real-time PCR assays for detection of (i) N. meningitidis ctrA, H. influenzae hpd, and S. pneumoniae lytA (NHS assay); (ii) N. meningitidis serogroups A, W135, and X (AWX assay); and (iii) N. meningitidis serogroups B, C, and Y (BCY assay). Each multiplex assay was 100% specific for detecting its target organisms or serogroups, and the LLD was similar to that for the singleplex assay. Pairwise comparison of real-time PCR between multiplex and singleplex assays showed that cycle threshold values of the multiplex assay were similar to those for the singleplex assay. There were no substantial differences in sensitivity and specificity between these multiplex and singleplex real-time PCR assays.

A fully sealed plastic chip for multiplex PCR and its application in bacteria identification.

PubMed

Xu, Youchun; Yan, He; Zhang, Yan; Jiang, Kewei; Lu, Ying; Ren, Yonghong; Wang, Hui; Wang, Shan; Xing, Wanli

2015-07-07

Multiplex PCR is an effective tool for simultaneous multiple target detection but is limited by the intrinsic interference and competition among primer pairs when it is performed in one reaction tube. Dividing a multiplex PCR into many single PCRs is a simple strategy to overcome this issue. Here, we constructed a plastic, easy-to-use, fully sealed multiplex PCR chip based on reversible centrifugation for the simultaneous detection of 63 target DNA sequences. The structure of the chip is quite simple, which contains sine-shaped infusing channels and a number of reaction chambers connecting to one side of these channels. Primer pairs for multiplex PCR were sequentially preloaded in the different reaction chambers, and the chip was enclosed with PCR-compatible adhesive tape. For usage, the PCR master mix containing a DNA template is pipetted into the infusing channels and centrifuged into the reaction chambers, leaving the infusing channels filled with air to avoid cross-contamination of the different chambers. Then, the chip is sealed and placed on a flat thermal cycler for PCR. Finally, amplification products can be detected in situ using a fluorescence scanner or recovered by reverse centrifugation for further analyses. Therefore, our chip possesses two functions: 1) it can be used for multi-target detection based on end-point in situ fluorescence detection; and 2) it can work as a sample preparation unit for analyses that need multiplex PCR such as hybridization and target sequencing. The performance of this chip was carefully examined and further illustrated in the identification of 8 pathogenic bacterial genomic DNA samples and 13 drug-resistance genes. Due to simplicity of its structure and operation, accuracy and generality, high-throughput capacity, and versatile functions (i.e., for in situ detection and sample preparation), our multiplex PCR chip has great potential in clinical diagnostics and nucleic acid-based point-of-care testing.

A bench-top megavoltage fan-beam CT using CdWO4-photodiode detectors. I. System description and detector characterization.

PubMed

Rathee, S; Tu, D; Monajemi, T T; Rickey, D W; Fallone, B G

2006-04-01

We describe the components of a bench-top megavoltage computed tomography (MVCT) scanner that uses an 80-element detector array consisting of CdWO4 scintillators coupled to photodiodes. Each CdWO4 crystal is 2.75 x 8 x 10 mm3. The detailed design of the detector array, timing control, and multiplexer are presented. The detectors show a linear response to dose (dose rate was varied by changing the source to detector distance) with a correlation coefficient (R2) nearly unity with the standard deviation of signal at each dose being less than 0.25%. The attenuation of a 6 MV beam by solid water measured by this detector array indicates a small, yet significant spectral hardening that needs to be corrected before image reconstruction. The presampled modulation transfer function is strongly affected by the detector's large pitch and a large improvement can be obtained by reducing the detector pitch. The measured detective quantum efficiency at zero spatial frequency is 18.8% for 6 MV photons which will reduce the dose to the patient in MVCT applications. The detector shows a less than a 2% reduction in response for a dose of 24.5 Gy accumulated in 2 h; however, the lost response is recovered on the following day. A complete recovery can be assumed within the experimental uncertainty (standard deviation <0.5%); however, any smaller permanent damage could not be assessed.

A highly accurate wireless digital sun sensor based on profile detecting and detector multiplexing technologies

NASA Astrophysics Data System (ADS)

Wei, Minsong; Xing, Fei; You, Zheng

2017-01-01

The advancing growth of micro- and nano-satellites requires miniaturized sun sensors which could be conveniently applied in the attitude determination subsystem. In this work, a profile detecting technology based high accurate wireless digital sun sensor was proposed, which could transform a two-dimensional image into two-linear profile output so that it can realize a high update rate under a very low power consumption. A multiple spots recovery approach with an asymmetric mask pattern design principle was introduced to fit the multiplexing image detector method for accuracy improvement of the sun sensor within a large Field of View (FOV). A FOV determination principle based on the concept of FOV region was also proposed to facilitate both sub-FOV analysis and the whole FOV determination. A RF MCU, together with solar cells, was utilized to achieve the wireless and self-powered functionality. The prototype of the sun sensor is approximately 10 times lower in size and weight compared with the conventional digital sun sensor (DSS). Test results indicated that the accuracy of the prototype was 0.01° within a cone FOV of 100°. Such an autonomous DSS could be equipped flexibly on a micro- or nano-satellite, especially for highly accurate remote sensing applications.

Characterization of Kilopixel TES detector arrays for PIPER

NASA Astrophysics Data System (ADS)

Datta, Rahul; Ade, Peter; Benford, Dominic; Bennett, Charles; Chuss, David; Costen, Nicholas; Coughlin, Kevin; Dotson, Jessie; Eimer, Joseph; Fixsen, Dale; Gandilo, Natalie; Halpern, Mark; Essinger-Hileman, Thomas; Hilton, Gene; Hinshaw, Gary; Irwin, Kent; Jhabvala, Christine; Kimball, Mark; Kogut, Al; Lazear, Justin; Lowe, Luke; Manos, George; McMahon, Jeff; Miller, Timothy; Mirel, Paul; Moseley, Samuel Harvey; Pawlyk, Samuel; Rodriguez, Samelys; Sharp, Elmer; Shirron, Peter; Staguhn, Johannes G.; Sullivan, Dan; Switzer, Eric; Taraschi, Peter; Tucker, Carole; Walts, Alexander; Wollack, Edward

2018-01-01

The Primordial Inflation Polarization ExploreR (PIPER) is a balloon-borne instrument optimized to measure the polarization of the Cosmic Microwave Background (CMB) at large angular scales. It will map 85% of the sky in four frequency bands centered at 200, 270, 350, and 600 GHz to characterize dust foregrounds and constrain the tensor-to-scalar ratio, r. The sky is imaged on to 32x40 pixel arrays of time-domain multiplexed Transition-Edge Sensor (TES) bolometers operating at a bath temperature of 100 mK to achieve background-limited sensitivity. Each kilopixel array is indium-bump-bonded to a 2D superconducting quantum interference device (SQUID) time-domain multiplexer (MUX) chip and read out by warm electronics. Each pixel measures total incident power over a frequency band defined by bandpass filters in front of the array, while polarization sensitivity is provided by the upstream Variable-delay Polarization Modulators (VPMs) and analyzer grids. We present measurements of the detector parameters from the laboratory characterization of the first kilopixel science array for PIPER including transition temperature, saturation power, thermal conductivity, time constant, and noise performance. We also describe the testing of the 2D MUX chips, optimization of the integrated readout parameters, and the overall pixel yield of the array. The first PIPER science flight is planned for June 2018 from Palestine, Texas.

Fabrication of an Absorber-Coupled MKID Detector and Readout for Sub-Millimeter and Far-Infrared Astronomy

NASA Technical Reports Server (NTRS)

Brown, Ari-David; Hsieh, Wen-Ting; Moseley, S. Harvey; Stevenson, Thomas R.; U-yen, Kongpop; Wollack, Edward J.

2010-01-01

We have fabricated absorber-coupled microwave kinetic inductance detector (MKID) arrays for sub-millimeter and far-infrared astronomy. Each detector array is comprised of lambda/2 stepped impedance resonators, a 1.5 micrometer thick silicon membrane, and 380 micrometer thick silicon walls. The resonators consist of parallel plate aluminum transmission lines coupled to low impedance Nb microstrip traces of variable length, which set the resonant frequency of each resonator. This allows for multiplexed microwave readout and, consequently, good spatial discrimination between pixels in the array. The Al transmission lines simultaneously act to absorb optical power and are designed to have a surface impedance and filling fraction so as to match the impedance of free space. Our novel fabrication techniques demonstrate high fabrication yield of MKID arrays on large single crystal membranes and sub-micron front-to-back alignment of the microstrip circuit.

Fabrication of an Absorber-Coupled MKID Detector and Readout for Sub-Millimeter and Far-Infrared Astronomy

NASA Technical Reports Server (NTRS)

Brown, Ari-David; Hsieh, Wen-Ting; Moseley, S. Harvey; Stevenson, Thomas R.; U-yen, Kongpop; Wollack, Edward J.

2010-01-01

We have fabricated absorber-coupled microwave kinetic inductance detector (MKID) arrays for sub-millimeter and farinfrared astronomy. Each detector array is comprised of lambda/2 stepped impedance resonators, a 1.5µm thick silicon membrane, and 380µm thick silicon walls. The resonators consist of parallel plate aluminum transmission lines coupled to low impedance Nb microstrip traces of variable length, which set the resonant frequency of each resonator. This allows for multiplexed microwave readout and, consequently, good spatial discrimination between pixels in the array. The Al transmission lines simultaneously act to absorb optical power and are designed to have a surface impedance and filling fraction so as to match the impedance of free space. Our novel fabrication techniques demonstrate high fabrication yield of MKID arrays on large single crystal membranes and sub-micron front-to-back alignment of the microstrip circuit.

Demodulation Algorithms for the Ofdm Signals in the Time- and Frequency-Scattering Channels

NASA Astrophysics Data System (ADS)

Bochkov, G. N.; Gorokhov, K. V.; Kolobkov, A. V.

2016-06-01

We consider a method based on the generalized maximum-likelihood rule for solving the problem of reception of the signals with orthogonal frequency division multiplexing of their harmonic components (OFDM signals) in the time- and frequency-scattering channels. The coherent and incoherent demodulators effectively using the time scattering due to the fast fading of the signal are developed. Using computer simulation, we performed comparative analysis of the proposed algorithms and well-known signal-reception algorithms with equalizers. The proposed symbolby-symbol detector with decision feedback and restriction of the number of searched variants is shown to have the best bit-error-rate performance. It is shown that under conditions of the limited accuracy of estimating the communication-channel parameters, the incoherent OFDMsignal detectors with differential phase-shift keying can ensure a better bit-error-rate performance compared with the coherent OFDM-signal detectors with absolute phase-shift keying.

Multiplex real-time PCR assay for detection of Escherichia coli O157:H7 and screening for non-O157 Shiga toxin-producing E. coli.

PubMed

Li, Baoguang; Liu, Huanli; Wang, Weimin

2017-11-09

Shiga toxin-producing Escherichia coli (STEC), including E. coli O157:H7, are responsible for numerous foodborne outbreaks annually worldwide. E. coli O157:H7, as well as pathogenic non-O157:H7 STECs, can cause life-threating complications, such as bloody diarrhea (hemolytic colitis) and hemolytic-uremic syndrome (HUS). Previously, we developed a real-time PCR assay to detect E. coli O157:H7 in foods by targeting a unique putative fimbriae protein Z3276. To extend the detection spectrum of the assay, we report a multiplex real-time PCR assay to specifically detect E. coli O157:H7 and screen for non-O157 STEC by targeting Z3276 and Shiga toxin genes (stx1 and stx2). Also, an internal amplification control (IAC) was incorporated into the assay to monitor the amplification efficiency. The multiplex real-time PCR assay was developed using the Life Technology ABI 7500 System platform and the standard chemistry. The optimal amplification mixture of the assay contains 12.5 μl of 2 × Universal Master Mix (Life Technology), 200 nM forward and reverse primers, appropriate concentrations of four probes [(Z3276 (80 nM), stx1 (80 nM), stx2 (20 nM), and IAC (40 nM)], 2 μl of template DNA, and water (to make up to 25 μl in total volume). The amplification conditions of the assay were set as follows: activation of TaqMan at 95 °C for 10 min, then 40 cycles of denaturation at 95 °C for 10 s and annealing/extension at 60 °C for 60 s. The multiplex assay was optimized for amplification conditions. The limit of detection (LOD) for the multiplex assay was determined to be 200 fg of bacterial DNA, which is equivalent to 40 CFU per reaction which is similar to the LOD generated in single targeted PCRs. Inclusivity and exclusivity determinants were performed with 196 bacterial strains. All E. coli O157:H7 (n = 135) were detected as positive and all STEC strains (n = 33) were positive for stx1, or stx2, or stx1 and stx2 (Table 1). No cross reactivity was detected with Salmonella enterica, Shigella strains, or any other pathogenic strains tested. A multiplex real-time PCR assay that can rapidly and simultaneously detect E. coli O157:H7 and screen for non-O157 STEC strains has been developed and assessed for efficacy. The inclusivity and exclusivity tests demonstrated high sensitivity and specificity of the multiplex real-time PCR assay. In addition, this multiplex assay was shown to be effective for the detection of E. coli O157:H7 from two common food matrices, beef and spinach, and may be applied for detection of E. coli O157:H7 and screening for non-O157 STEC strains from other food matrices as well.

Molecular diagnostics: the changing culture of medical microbiology.

PubMed

Bullman, Susan; Lucey, Brigid; Sleator, Roy D

2012-01-01

Diagnostic molecular biology is arguably the fastest growing area in current laboratory-based medicine. Growth of the so called 'omics' technologies has, over the last decade, led to a gradual migration away from the 'one test, one pathogen' paradigm, toward multiplex approaches to infectious disease diagnosis, which have led to significant improvements in clinical diagnostics and ultimately improved patient care.

Multiplex assay for the quantitative assessment of Rhizoctonia solani AG2-2, AG4 and Rhizoctonia zeae from the soil

USDA-ARS?s Scientific Manuscript database

Rhizoctonia solani causes damping off and root and crown rot in sugar beets resulting in substantial losses in the field and during storage. Root rot is a difficult fungal disease to diagnose and manage, as the pathogen is usually not detected until after damage has occurred. The objective of this s...

Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens

PubMed Central

Kostić, Tanja; Sessitsch, Angela

2011-01-01

Reliable and sensitive pathogen detection in clinical and environmental (including food and water) samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i) specificity; (ii) sensitivity; (iii) multiplexing potential; (iv) robustness; (v) speed; (vi) automation potential; and (vii) low cost. Microarray technology can, through its very nature, fulfill many of these requirements directly and the remaining challenges have been tackled. In this review, we attempt to compare performance characteristics of the microbial diagnostic microarrays developed for the detection and typing of food and water pathogens, and discuss limitations, points still to be addressed and issues specific for the analysis of food, water and environmental samples. PMID:27605332

Evaluation of the Luminex xTAG Respiratory Viral Panel FAST v2 assay for detection of multiple respiratory viral pathogens in nasal and throat swabs in Vietnam

PubMed Central

Thi Ty Hang, Vu; Thi Han Ny, Nguyen; My Phuc, Tran; Thi Thanh Tam, Pham; Thao Huong, Dang; Dang Trung Nghia, Ho; Tran Anh Vu, Nguyen; Thi Hong Phuong, Pham; Van Xang, Nguyen; Dong, Nguyen; Nhu Hiep, Pham; Van Hung, Nguyen; Tinh Hien, Tran; Rabaa, Maia; Thwaites, Guy E.; Baker, Stephen; Van Tan, Le; van Doorn, H.Rogier

2018-01-01

Background: Acute respiratory infections (ARI) are among the leading causes of hospitalization in children ≤5 years old. Rapid diagnostics of viral pathogens is essential to avoid unnecessary antibiotic treatment, thereby slowing down antibiotic-resistance. We evaluated the diagnostic performance of the Luminex xTAG Respiratory Viral Panel FAST v2 against viral specific PCR as reference assays for ARI in Vietnam. Methods: Four hundred and forty two nose and throat swabs were collected in viral transport medium, and were tested with Luminex xTAG Respiratory Viral Panel FAST v2. Multiplex RT-PCR and single RT-PCR were used as references.    Results: Overall, sensitivity of the Luminex against reference assays was 91.8%, 95% CI 88.1-94.7 (270/294), whilst 112/6336 (1.8%, 95% CI, 1.4-2.1) of pathogens were detected by the Luminex, but not by reference assays. Frequency of pathogens detected by Luminex and reference assays was 379 and 292, respectively. The diagnostic yield was 66.7% (295/442, 95%CI 62.1-71.1%) for the Luminex assay and 54.1% (239/442, 95% CI, 49.3-58.8%) for reference assays. The Luminex kit had higher yields for all viruses except influenza B virus, respiratory syncytial virus, and human bocavirus. High agreements between both methods [mean (range): 0.91 (0.83-1.00)] were found for 10/15 viral agents. Conclusions: The Luminex assay is a high throughput multiplex platform for rapid detection of common viral pathogens causing ARI. Although the current high cost may prevent Luminex assays from being widely used, especially in limited resource settings where ARI are felt most, its introduction in clinical diagnostics may help reduce unnecessary use of antibiotic prescription. PMID:29503874

Development of multiplex polymerase chain reaction assay for simultaneous detection of clostero-, badna- and mandari-viruses along with huanglongbing bacterium in citrus trees.

PubMed

Meena, Ram Prasnna; Baranwal, V K

2016-09-01

Citrus trees harbor a large number of viral and bacterial pathogens. Citrus yellow vein clearing virus (CYVCV), Indian citrus ringspot virus (ICRSV), Citrus yellow mosaic virus (CYMV), Citrus tristeza virus (CTV) and a bacterium, Candidatus Liberibacter asiaticus (CLa) associated with huanglongbing (HLB) disease, the most prevalent pathogens in citrus orchards of different regions in India and are responsible for debilitating citriculture. For detection of these viral and bacterial pathogens a quick, sensitive and cost effective detection method is required. With this objective a multiplex polymerase chain reaction (mPCR) assay was developed for simultaneous detection of four viruses and a bacterium in citrus. Several sets of primers were designed for each virus based on the retrieved reference sequences from the GenBank. A primer pair published previously was used for greening bacterium. Each pair of primers was evaluated for their sensitivity and differentiation by simplex and mPCR. The constant amplified products were identified on the basis of molecular size in mPCR and were compared with standard PCR. The amplicons were cloned and results were confirmed with sequencing analysis. The mPCR assay was validated using naturally infected field samples for one or more citrus viruses and the huanglongbing bacterium. The mPCR assay developed here will aid in the production of virus free planting materials and rapid indexing for certification of citrus budwood programme. Copyright © 2016 Elsevier B.V. All rights reserved.

Surveillance of Food- and Smear-Transmitted Pathogens in European Soldiers with Diarrhea on Deployment in the Tropics: Experience from the European Union Training Mission (EUTM) Mali

PubMed Central

Frickmann, Hagen; Warnke, Philipp; Frey, Claudia; Schmidt, Salvatore; Janke, Christian; Erkens, Kay; Schotte, Ulrich; Köller, Thomas; Maaßen, Winfried; Podbielski, Andreas; Binder, Alfred; Hinz, Rebecca; Queyriaux, Benjamin; Wiemer, Dorothea; Schwarz, Norbert Georg; Hagen, Ralf Matthias

2015-01-01

Introduction. Since 2013, European soldiers have been deployed on the European Union Training Mission (EUTM) in Mali. From the beginning, diarrhea has been among the most “urgent” concerns. Diarrhea surveillance based on deployable real-time PCR equipment was conducted between December 2013 and August 2014. Material and Methods. In total, 53 stool samples were obtained from 51 soldiers with acute diarrhea. Multiplex PCR panels comprised enteroinvasive bacteria, diarrhea-associated Escherichia coli (EPEC, ETEC, EAEC, and EIEC), enteropathogenic viruses, and protozoa. Noroviruses were characterized by sequencing. Cultural screening for Enterobacteriaceae with extended-spectrum beta-lactamases (ESBL) with subsequent repetitive sequence-based PCR (rep-PCR) typing was performed. Clinical information was assessed. Results. Positive PCR results for diarrhea-associated pathogens were detected in 43/53 samples, comprising EPEC (n = 21), ETEC (n = 19), EAEC (n = 15), Norovirus (n = 10), Shigella spp./EIEC (n = 6), Cryptosporidium parvum (n = 3), Giardia duodenalis (n = 2), Salmonella spp. (n = 1), Astrovirus (n = 1), Rotavirus (n = 1), and Sapovirus (n = 1). ESBL-positive Enterobacteriaceae were grown from 13 out of 48 samples. Simultaneous infections with several enteropathogenic agents were observed in 23 instances. Symptoms were mild to moderate. There were hints of autochthonous transmission. Conclusions. Multiplex real-time PCR proved to be suitable for diarrhea surveillance on deployment. Etiological attribution is challenging in cases of detection of multiple pathogens. PMID:26525953

Simultaneous differential detection of human pathogenic and nonpathogenic Vibrio species using a multiplex PCR based on gyrB and pntA genes.

PubMed

Teh, C S J; Chua, K H; Thong, K L

2010-06-01

To develop a multiplex PCR targeting the gyrB and pntA genes for Vibrio species differentiation. Four pairs of primers targeting gyrB gene of Vibrios at genus level and pntA gene of Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus were designed. This PCR method precisely identified 250 Vibrio species and demonstrated sensitivity in the range of 4 x 10(4) CFU ml(-1) (c. 200 CFU per PCR) to 2 x 10(3) CFU ml(-1) (c. 10 CFU per PCR). Overall, the gyrB gene marker showed a higher specificity than the dnaJ gene marker for Vibrio detection and was able to distinguish Aeromonas from Vibrio species. The multiplex PCR based on combined gyrB and pntA provides a high discriminatory power in the differentiation between Vibrio alginolyticus and V. parahaemolyticus, and between V. cholerae and Vibrio mimicus. This assay will be useful for rapid differentiation of various Vibrio species from clinical and environmental sources and significantly overcomes the limitations of the conventional methods.

a Study of Multiplexing Schemes for Voice and Data.

NASA Astrophysics Data System (ADS)

Sriram, Kotikalapudi

Voice traffic variations are characterized by on/off transitions of voice calls, and talkspurt/silence transitions of speakers in conversations. A speaker is known to be in silence for more than half the time during a telephone conversation. In this dissertation, we study some schemes which exploit speaker silences for an efficient utilization of the transmission capacity in integrated voice/data multiplexing and in digital speech interpolation. We study two voice/data multiplexing schemes. In each scheme, any time slots momentarily unutilized by the voice traffic are made available to data. In the first scheme, the multiplexer does not use speech activity detectors (SAD), and hence the voice traffic variations are due to call on/off only. In the second scheme, the multiplexer detects speaker silences using SAD and transmits voice only during talkspurts. The multiplexer with SAD performs digital speech interpolation (DSI) as well as dynamic channel allocation to voice and data. The performance of the two schemes is evaluated using discrete-time modeling and analysis. The data delay performance for the case of English speech is compared with that for the case of Japanese speech. A closed form expression for the mean data message delay is derived for the single-channel single-talker case. In a DSI system, occasional speech losses occur whenever the number of speakers in simultaneous talkspurt exceeds the number of TDM voice channels. In a buffered DSI system, speech loss is further reduced at the cost of delay. We propose a novel fixed-delay buffered DSI scheme. In this scheme, speech fill-in/hangover is not required because there are no variable delays. Hence, all silences that naturally occur in speech are fully utilized. Consequently, a substantial improvement in the DSI performance is made possible. The scheme is modeled and analyzed in discrete -time. Its performance is evaluated in terms of the probability of speech clipping, packet rejection ratio, DSI advantage, and the delay.

3D imaging LADAR with linear array devices: laser, detector and ROIC

NASA Astrophysics Data System (ADS)

Kameyama, Shumpei; Imaki, Masaharu; Tamagawa, Yasuhisa; Akino, Yosuke; Hirai, Akihito; Ishimura, Eitaro; Hirano, Yoshihito

2009-07-01

This paper introduces the recent development of 3D imaging LADAR (LAser Detection And Ranging) in Mitsubishi Electric Corporation. The system consists of in-house-made key devices which are linear array: the laser, the detector and the ROIC (Read-Out Integrated Circuit). The laser transmitter is the high power and compact planar waveguide array laser at the wavelength of 1.5 micron. The detector array consists of the low excess noise Avalanche Photo Diode (APD) using the InAlAs multiplication layer. The analog ROIC array, which is fabricated in the SiGe- BiCMOS process, includes the Trans-Impedance Amplifiers (TIA), the peak intensity detectors, the Time-Of-Flight (TOF) detectors, and the multiplexers for read-out. This device has the feature in its detection ability for the small signal by optimizing the peak intensity detection circuit. By combining these devices with the one dimensional fast scanner, the real-time 3D range image can be obtained. After the explanations about the key devices, some 3D imaging results are demonstrated using the single element key devices. The imaging using the developed array devices is planned in the near future.

Large Imaging X-ray MKID Arrays for Astrophysics

NASA Astrophysics Data System (ADS)

Mazin, Benjamin

Microwave Kinetic Inductance Detectors, or MKIDs, are a relatively new type of superconducting detector with built-in frequency domain multiplexing. Like Transition Edge Sensors (TESs) microbolometers, MKIDs can count single X-ray photons over a wide energy range and determine their energy and arrival time. MKIDs allow very large pixel counts with a simple room temperature microwave readout. In this investigation we will develop a new type of detector based on a MKID called the Thermal Kinetic Inductance Detector, or TKID. A TKID changes the basic MKID architecture by placing the inductor of the MKID on a suspended SiN membrane. The capacitor will remain on the bulk Si to reduce noise. Much like a TES, the TKID will sense changes in temperature of the isolated SiN island caused by photon absorption. The advantages of a TKID include lack of positional/geometry dependence, a more tunable pulse decay time, a relaxation of the MKID resonator material requirements, and more. We have already fabricated a TKID with the best energy resolution seen to date in any KID. Here we propose to improve the energy resolution below 10 eV, develop mushroom absorbers compatible with our TKIDs, and integrate these detectors into small arrays.

Optoelectrical clock recovery with dispersion monitoring for high speed transmission

NASA Astrophysics Data System (ADS)

Wen, He; Liao, Jinxin; Zheng, Xiaoping; Zhang, Hanyi; Guo, Yili

2010-12-01

The proposed clock recovery scheme introduces electrooptical modulation to down convert the clock frequency facilitating succeeding narrow band filtering by a phase locked loop (PLL) with ordinary radio frequency (RF) devices, further, employs a quadrature phase detector in the PLL to provide an indication signal for monitoring residual dispersion. It was demonstrated in a polarization multiplexed 160-Gbit/s optical non-return to zero quadrature phase shift keying (NRZ-QPSK) transmission system.

Microwave SQUID Multiplexer Demonstration for Cosmic Microwave Background Imagers.

PubMed

Dober, B; Becker, D T; Bennett, D A; Bryan, S A; Duff, S M; Gard, J D; Hays-Wehle, J P; Hilton, G C; Hubmayr, J; Mates, J A B; Reintsema, C D; Vale, L R; Ullom, J N

2017-12-01

Key performance characteristics are demonstrated for the microwave SQUID multiplexer (µmux) coupled to transition edge sensor (TES) bolometers that have been optimized for cosmic microwave background (CMB) observations. In a 64-channel demonstration, we show that the µmux produces a white, input referred current noise level of [Formula: see text] at -77 dB microwave probe tone power, which is well below expected fundamental detector and photon noise sources for a ground-based CMB-optimized bolometer. Operated with negligible photon loading, we measure [Formula: see text] in the TES-coupled channels biased at 65% of the sensor normal resistance. This noise level is consistent with that predicted from bolometer thermal fluctuation (i.e. phonon) noise. Furthermore, the power spectral density is white over a range of frequencies down to ~ 100 mHz, which enables CMB mapping on large angular scales that constrain the physics of inflation. Additionally, we report cross-talk measurements that indicate a level below 0.3%, which is less than the level of cross-talk from multiplexed readout systems in deployed CMB imagers. These measurements demonstrate the µmux as a viable readout technique for future CMB imaging instruments.

A robust multiplex real-time PCR method for simultaneous detection of Salmonella spp., Escherichia coli O157 and Listeria monocytogenes in fresh fruits and vegetables

USDA-ARS?s Scientific Manuscript database

Introduction: On average, about 48 million people per year in the U.S. are affected by food borne diseases. A major portion of these illnesses are caused by Salmonella spp., Escherichia coli O157:H7 and Listeria monocytogenes. Hence, it is important to identify the specific pathogens in contaminate...

Development of a real-time RT-PCR assay for squash mosaic virus useful for broad spectrum detection of various serotypes and its incorporation into a multiplex seed health assay

USDA-ARS?s Scientific Manuscript database

Seed-borne pathogens pose a serious threat to modern agricultural cropping systems as they can be disseminated to many geographical regions around the world. With trends of increasing global seed production and trade, seed-health testing is an important quality control step to prevent the introduct...

Rapid multiplex PCR and Real-Time TaqMan PCR assays for detection of Salmonella enterica and the highly virulent serovars Choleraesuis and Paratyphi C

USDA-ARS?s Scientific Manuscript database

Salmonella enterica is a human pathogen with over 2,500 serovars characterized. S. enterica serovars Choleraesuis (Cs) and Paratyphi C (Pc) are two globally distributed serovars. We have developed a rapid molecular typing method to detect Cs and Pc in food samples by using a comparative genomics ap...

Prospective evaluation of SeptiFast Multiplex PCR in children with systemic inflammatory response syndrome under antibiotic treatment.

PubMed

Gies, Franziska; Tschiedel, Eva; Felderhoff-Müser, Ursula; Rath, Peter-Michael; Steinmann, Joerg; Dohna-Schwake, Christian

2016-08-08

Antimicrobially pre-treated children with systemic inflammation often pose a diagnostic challenge to the physician. We aimed to evaluate the additional use of SeptiFast multiplex polymerase chain reaction (PCR) to identify causative pathogens in children with suspected systemic bacterial or fungal infection. Prospective observational study in 39 children with systemic inflammatory response syndrome (SIRS) under empiric antibiotic treatment. Primary outcome was the rate of positive blood cultures (BC), compared to the rate of positive SeptiFast (SF) results. In total, 14 SF-samples yielded positive results, compared to 4 positive BC (p < 0.05). All blood cultures and 13 of 14 positive SF-tests were considered infection. Median time for positive BC was 2 days, and time to definite result was 6 days, compared to 12 h for SF. Antimicrobial therapy was adapted in 7 of the 14 patients with positive SeptiFast, and in 3 of the 4 patients with positive BC. Best predictive power for positive SF shown by receiver-operating characteristic was demonstrated for procalcitonin PCT (Area under the curve AUC: 0.79), compared to C-reactive protein CRP (AUC: 0.51) and leukocyte count (AUC: 0.46). A procalcitonin threshold of 0.89 ng/ml yielded a sensitivity of 0.82 and a specifity of 0.7. Children with a positive SeptiFast result on day 0 had a significantly higher risk to require treatment on the Pediatric Intensive Care Unit or to be deceased on day 30 (Odds-Ratio 8.62 (CI 1.44-51.72). The additional testing with SeptiFast in antimicrobially pre-treated children with systemic inflammation enhances the rate of pathogen detection. The influence of multiplex PCR on clinically relevant outcome parameters has to be further evaluated. ( DRKS00004694).

Analysis of sensitivity and rapid hybridization of a multiplexed Microbial Detection Microarray

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

Thissen, James B.; McLoughlin, Kevin; Gardner, Shea

Microarrays have proven to be useful in rapid detection of many viruses and bacteria. Pathogen detection microarrays have been used to diagnose viral and bacterial infections in clinical samples and to evaluate the safety of biological drug materials. A multiplexed version of the Lawrence Livermore Microbial Detection Array (LLMDA) was developed and evaluated with minimum detectable concentrations for pure unamplified DNA viruses, along with mixtures of viral and bacterial DNA subjected to different whole genome amplification protocols. In addition the performance of the array was tested when hybridization time was reduced from 17 h to 1 h. The LLMDA wasmore » able to detect unamplified vaccinia virus DNA at a concentration of 14 fM, or 100,000 genome copies in 12 μL of sample. With amplification, positive identification was made with only 100 genome copies of input material. When tested against human stool samples from patients with acute gastroenteritis, the microarray detected common gastroenteritis viral and bacterial infections such as rotavirus and E. coli. Accurate detection was found but with a 4-fold drop in sensitivity for a 1 h compared to a 17 h hybridization. The array detected 2 ng (equivalent concentration of 15.6 fM) of labeled DNA from a virus with 1 h hybridization without any amplification, and was able to identify the components of a mixture of viruses and bacteria at species and in some cases strain level resolution. Sensitivity improved by three orders of magnitude with random whole genome amplification prior to hybridization; for instance, the array detected a DNA virus with only 20 fg or 100 genome copies as input. This multiplexed microarray is an efficient tool to analyze clinical and environmental samples for the presence of multiple viral and bacterial pathogens rapidly.« less

Recent Evolutionary Radiation and Host Plant Specialization in the Xylella fastidiosa Subspecies Native to the United States

PubMed Central

Vickerman, Danel B.; Bromley, Robin E.; Russell, Stephanie A.; Hartman, John R.; Morano, Lisa D.; Stouthamer, Richard

2013-01-01

The bacterial pathogen, Xylella fastidiosa, infects many plant species in the Americas, making it a good model for investigating the genetics of host adaptation. We used multilocus sequence typing (MLST) to identify isolates of the native U.S. subsp. multiplex that were largely unaffected by intersubspecific homologous recombination (IHR) and to investigate how their evolutionary history influences plant host specialization. We identified 110 “non-IHR” isolates, 2 minimally recombinant “intermediate” ones (including the subspecific type), and 31 with extensive IHR. The non-IHR and intermediate isolates defined 23 sequence types (STs) which we used to identify 22 plant hosts (73% trees) characteristic of the subspecies. Except for almond, subsp. multiplex showed no host overlap with the introduced subspecies (subspecies fastidiosa and sandyi). MLST sequences revealed that subsp. multiplex underwent recent radiation (<25% of subspecies age) which included only limited intrasubspecific recombination (ρ/θ = 0.02); only one isolated lineage (ST50 from ash) was older. A total of 20 of the STs grouped into three loose phylogenetic clusters distinguished by nonoverlapping hosts (excepting purple leaf plum): “almond,” “peach,” and “oak” types. These host differences were not geographical, since all three types also occurred in California. ST designation was a good indicator of host specialization. ST09, widespread in the southeastern United States, only infected oak species, and all peach isolates were ST10 (from California, Florida, and Georgia). Only ST23 had a broad host range. Hosts of related genotypes were sometimes related, but often host groupings crossed plant family or even order, suggesting that phylogenetically plastic features of hosts affect bacterial pathogenicity. PMID:23354698

Large-Scale Intersubspecific Recombination in the Plant-Pathogenic Bacterium Xylella fastidiosa Is Associated with the Host Shift to Mulberry

PubMed Central

Schuenzel, Erin L.; Scally, Mark; Bromley, Robin E.; Stouthamer, Richard

2014-01-01

Homologous recombination plays an important role in the structuring of genetic variation of many bacteria; however, its importance in adaptive evolution is not well established. We investigated the association of intersubspecific homologous recombination (IHR) with the shift to a novel host (mulberry) by the plant-pathogenic bacterium Xylella fastidiosa. Mulberry leaf scorch was identified about 25 years ago in native red mulberry in the eastern United States and has spread to introduced white mulberry in California. Comparing a sequence of 8 genes (4,706 bp) from 21 mulberry-type isolates to published data (352 isolates representing all subspecies), we confirmed previous indications that the mulberry isolates define a group distinct from the 4 subspecies, and we propose naming the taxon X. fastidiosa subsp. morus. The ancestry of its gene sequences was mixed, with 4 derived from X. fastidiosa subsp. fastidiosa (introduced from Central America), 3 from X. fastidiosa subsp. multiplex (considered native to the United States), and 1 chimeric, demonstrating that this group originated by large-scale IHR. The very low within-type genetic variation (0.08% site polymorphism), plus the apparent inability of native X. fastidiosa subsp. multiplex to infect mulberry, suggests that this host shift was achieved after strong selection acted on genetic variants created by IHR. Sequence data indicate that a single ancestral IHR event gave rise not only to X. fastidiosa subsp. morus but also to the X. fastidiosa subsp. multiplex recombinant group which infects several hosts but is the only type naturally infecting blueberry, thus implicating this IHR in the invasion of at least two novel native hosts, mulberry and blueberry. PMID:24610840

High-Resolution Melting Analysis as a Powerful Tool to Discriminate and Genotype Pseudomonas savastanoi Pathovars and Strains

PubMed Central

Gori, Andrea; Cerboneschi, Matteo; Tegli, Stefania

2012-01-01

Pseudomonas savastanoi is a serious pathogen of Olive, Oleander, Ash, and several other Oleaceae. Its epiphytic or endophytic presence in asymptomatic plants is crucial for the spread of Olive and Oleander knot disease, as already ascertained for P. savastanoi pv. savastanoi (Psv) on Olive and for pv. nerii (Psn) on Oleander, while no information is available for pv. fraxini (Psf) on Ash. Nothing is known yet about the distribution on the different host plants and the real host range of these pathovars in nature, although cross-infections were observed following artificial inoculations. A multiplex Real-Time PCR assay was recently developed to simultaneously and quantitatively discriminate in vitro and in planta these P. savastanoi pathovars, for routine culture confirmation and for epidemiological and diagnostical studies. Here an innovative High-Resolution Melting Analysis (HRMA)-based assay was set up to unequivocally discriminate Psv, Psn and Psf, according to several single nucleotide polymorphisms found in their Type Three Secretion System clusters. The genetic distances among 56 P. savastanoi strains belonging to these pathovars were also evaluated, confirming and refining data previously obtained by fAFLP. To our knowledge, this is the first time that HRMA is applied to a bacterial plant pathogen, and one of the few multiplex HRMA-based assays developed so far. This protocol provides a rapid, sensitive, specific tool to differentiate and detect Psv, Psn and Psf strains, also in vivo and against other related bacteria, with lower costs than conventional multiplex Real-Time PCR. Its application is particularly suitable for sanitary certification programs for P. savastanoi, aimed at avoiding the spreading of this phytopathogen through asymptomatic plants. PMID:22295075

Analysis of sensitivity and rapid hybridization of a multiplexed Microbial Detection Microarray

DOE PAGES

Thissen, James B.; McLoughlin, Kevin; Gardner, Shea; ...

2014-06-01

Microarrays have proven to be useful in rapid detection of many viruses and bacteria. Pathogen detection microarrays have been used to diagnose viral and bacterial infections in clinical samples and to evaluate the safety of biological drug materials. A multiplexed version of the Lawrence Livermore Microbial Detection Array (LLMDA) was developed and evaluated with minimum detectable concentrations for pure unamplified DNA viruses, along with mixtures of viral and bacterial DNA subjected to different whole genome amplification protocols. In addition the performance of the array was tested when hybridization time was reduced from 17 h to 1 h. The LLMDA wasmore » able to detect unamplified vaccinia virus DNA at a concentration of 14 fM, or 100,000 genome copies in 12 μL of sample. With amplification, positive identification was made with only 100 genome copies of input material. When tested against human stool samples from patients with acute gastroenteritis, the microarray detected common gastroenteritis viral and bacterial infections such as rotavirus and E. coli. Accurate detection was found but with a 4-fold drop in sensitivity for a 1 h compared to a 17 h hybridization. The array detected 2 ng (equivalent concentration of 15.6 fM) of labeled DNA from a virus with 1 h hybridization without any amplification, and was able to identify the components of a mixture of viruses and bacteria at species and in some cases strain level resolution. Sensitivity improved by three orders of magnitude with random whole genome amplification prior to hybridization; for instance, the array detected a DNA virus with only 20 fg or 100 genome copies as input. This multiplexed microarray is an efficient tool to analyze clinical and environmental samples for the presence of multiple viral and bacterial pathogens rapidly.« less

Large-scale intersubspecific recombination in the plant-pathogenic bacterium Xylella fastidiosa is associated with the host shift to mulberry.

PubMed

Nunney, Leonard; Schuenzel, Erin L; Scally, Mark; Bromley, Robin E; Stouthamer, Richard

2014-05-01

Homologous recombination plays an important role in the structuring of genetic variation of many bacteria; however, its importance in adaptive evolution is not well established. We investigated the association of intersubspecific homologous recombination (IHR) with the shift to a novel host (mulberry) by the plant-pathogenic bacterium Xylella fastidiosa. Mulberry leaf scorch was identified about 25 years ago in native red mulberry in the eastern United States and has spread to introduced white mulberry in California. Comparing a sequence of 8 genes (4,706 bp) from 21 mulberry-type isolates to published data (352 isolates representing all subspecies), we confirmed previous indications that the mulberry isolates define a group distinct from the 4 subspecies, and we propose naming the taxon X. fastidiosa subsp. morus. The ancestry of its gene sequences was mixed, with 4 derived from X. fastidiosa subsp. fastidiosa (introduced from Central America), 3 from X. fastidiosa subsp. multiplex (considered native to the United States), and 1 chimeric, demonstrating that this group originated by large-scale IHR. The very low within-type genetic variation (0.08% site polymorphism), plus the apparent inability of native X. fastidiosa subsp. multiplex to infect mulberry, suggests that this host shift was achieved after strong selection acted on genetic variants created by IHR. Sequence data indicate that a single ancestral IHR event gave rise not only to X. fastidiosa subsp. morus but also to the X. fastidiosa subsp. multiplex recombinant group which infects several hosts but is the only type naturally infecting blueberry, thus implicating this IHR in the invasion of at least two novel native hosts, mulberry and blueberry.

Recent evolutionary radiation and host plant specialization in the Xylella fastidiosa subspecies native to the United States.

PubMed

Nunney, Leonard; Vickerman, Danel B; Bromley, Robin E; Russell, Stephanie A; Hartman, John R; Morano, Lisa D; Stouthamer, Richard

2013-04-01

The bacterial pathogen, Xylella fastidiosa, infects many plant species in the Americas, making it a good model for investigating the genetics of host adaptation. We used multilocus sequence typing (MLST) to identify isolates of the native U.S. subsp. multiplex that were largely unaffected by intersubspecific homologous recombination (IHR) and to investigate how their evolutionary history influences plant host specialization. We identified 110 "non-IHR" isolates, 2 minimally recombinant "intermediate" ones (including the subspecific type), and 31 with extensive IHR. The non-IHR and intermediate isolates defined 23 sequence types (STs) which we used to identify 22 plant hosts (73% trees) characteristic of the subspecies. Except for almond, subsp. multiplex showed no host overlap with the introduced subspecies (subspecies fastidiosa and sandyi). MLST sequences revealed that subsp. multiplex underwent recent radiation (<25% of subspecies age) which included only limited intrasubspecific recombination (ρ/θ = 0.02); only one isolated lineage (ST50 from ash) was older. A total of 20 of the STs grouped into three loose phylogenetic clusters distinguished by nonoverlapping hosts (excepting purple leaf plum): "almond," "peach," and "oak" types. These host differences were not geographical, since all three types also occurred in California. ST designation was a good indicator of host specialization. ST09, widespread in the southeastern United States, only infected oak species, and all peach isolates were ST10 (from California, Florida, and Georgia). Only ST23 had a broad host range. Hosts of related genotypes were sometimes related, but often host groupings crossed plant family or even order, suggesting that phylogenetically plastic features of hosts affect bacterial pathogenicity.

MT-PCR panel detection of canine parvovirus (CPV-2): Vaccine and wild-type CPV-2 can be difficult to differentiate in canine diagnostic fecal samples.

PubMed

Meggiolaro, Maira N; Ly, Anna; Rysnik-Steck, Benjamin; Silva, Carolina; Zhang, Joshua; Higgins, Damien P; Muscatello, Gary; Norris, Jacqueline M; Krockenberger, Mark; Šlapeta, Jan

2017-06-01

Canine parvovirus (CPV-2) remains an important cause of devastating enteritis in young dogs. It can be successfully prevented with live attenuated CPV-2 vaccines when given at the appropriate age and in the absence of maternal antibody interference. Rapid diagnosis of parvoviral enteritis in young dogs is essential to ensuring suitable barrier nursing protocols within veterinary hospitals. The current diagnostic trend is to use multiplexed PCR panels to detect an array of pathogens commonly responsible for diarrhea in dogs. The multiplexed PCR assays do not distinguish wild from vaccine CPV-2. They are highly sensitive and detect even a low level of virus shedding, such as those caused by the CPV-2 vaccine. The aim of this study was to identify the CPV-2 subtypes detected in diagnostic specimens and rule out occult shedding of CPV-2 vaccine strains. For a total of 21 samples that tested positive for CPV-2 in a small animal fecal pathogens diagnostic multiplexed tandem PCR (MT-PCR) panel during 2014-2016 we partially characterized the VP2 gene of CPV-2. Vaccine CPV-2 strain, wild type CPV-2a subtypes and vaccine-like CPV-2b subtypes were detected. High copy number was indicative of wild-type CPV-2a presence, but presence of vaccine-like CPV-2b had a variable copy number in fecal samples. A yardstick approach to a copy number or C t -value to discriminate vaccine strain from a wild type virus of CPV-2 can be, in some cases, potentially misleading. Therefore, discriminating vaccine strain from a wild type subtype of CPV-2 remains ambitious. Copyright © 2017 Elsevier Ltd. All rights reserved.

A 128 x 128 InGaAs detector array for 1.0 - 1.7 microns

NASA Technical Reports Server (NTRS)

Olsen, G.; Joshi, A.; Lange, M.; Woodruff, K.; Mykietyn, E.; Gay, D.; Ackley, D.; Erickson, G.; Ban, V.; Staller, C.

1990-01-01

A two-dimensional 128 x 128 detector array for the 1.0 - 1.7 micron spectral region has been demonstrated with indium gallium arsenide. The 30 micron square pixels had 60 micron spacing in both directions and were designed to be compatible with a 2D Reticon multiplexer. Dark currents below 100 pA, capacitance near 0.1 pF, and quantum efficiencies above 80 percent were measured. Probe maps of dark current and quantum efficiency are presented along with pixel dropout data and wafer yield which was as high as 99.89 percent (7 dropouts) in an area of 6528 pixels and 99.37 percent (103 dropouts) over an entire 128 x 128 pixel region.

A passive terahertz video camera based on lumped element kinetic inductance detectors

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

Rowe, Sam, E-mail: sam.rowe@astro.cf.ac.uk; Pascale, Enzo; Doyle, Simon

We have developed a passive 350 GHz (850 μm) video-camera to demonstrate lumped element kinetic inductance detectors (LEKIDs)—designed originally for far-infrared astronomy—as an option for general purpose terrestrial terahertz imaging applications. The camera currently operates at a quasi-video frame rate of 2 Hz with a noise equivalent temperature difference per frame of ∼0.1 K, which is close to the background limit. The 152 element superconducting LEKID array is fabricated from a simple 40 nm aluminum film on a silicon dielectric substrate and is read out through a single microwave feedline with a cryogenic low noise amplifier and room temperature frequencymore » domain multiplexing electronics.« less

Design and Performance of the Antenna-Coupled Lumped-Element Kinetic Inductance Detector

NASA Astrophysics Data System (ADS)

Barry, P. S.; Doyle, S.; Hornsby, A. L.; Kofman, A.; Mayer, E.; Nadolski, A.; Tang, Q. Y.; Vieira, J.; Shirokoff, E.

2018-05-01

Focal plane arrays consisting of low-noise, polarisation-sensitive detectors have made possible the pioneering advances in the study of the cosmic microwave background (CMB). To make further progress, the next generation of CMB experiments (e.g. CMB-S4) will require a substantial increase in the number of detectors compared to current instruments. Arrays of kinetic inductance detectors (KIDs) provide a possible path to realising such large-format arrays owing to their intrinsic multiplexing advantage and relative cryogenic simplicity. In this paper, we report on the design of a variant of the traditional KID design: the antenna-coupled lumped-element KID. A polarisation-sensitive twin-slot antenna placed behind an optimised hemispherical lens couples power onto a thin-film superconducting microstrip line. The power is then guided into the inductive section of an aluminium KID, where it is absorbed and modifies both the resonant frequency and quality factor of the KID. We present the various aspects of the design and preliminary results from the first set of seven-element prototype arrays and compare to the expected modelled performance.

High resolution muon tracking with resistive plate chambers

NASA Astrophysics Data System (ADS)

Baesso, P.; Cussans, D.; Davies, J.; Glaysher, P.; Thomay, C.; Vassallo, C.; Velthuis, J.; Quillin, S.; Robertson, S.; Steer, C.

2012-11-01

Following their introduction in the physics community in the early '80s the use of Resistive Plate Chambers (RPCs) as charged particles detectors has constantly increased. Low cost per unit area, good time resolution and easy of operation are some of the features that contributed to such large adoption and that make RPCs interesting for several applications not necessarily related to physics. We built a prototype detector to track cosmic muons and exploit the information provided by estimating the multiple coulomb scattering angle to determine the type of materials they traversed. Simulations show that the technique could be used to inspect a cargo container in a time of the order of minutes. The detector we built consists of six planes, each one providing X-Y readout over a 50 cm × 50 cm area. The readout scheme we adopted, based on multiplexing chips used in high energy physics, allowed us to use a limited amount of electronic output channels while still obtaining a spatial resolution lower than 1 mm. An overview of the detector and of the analysis performed on the data is provided.

Long-distance continuous-variable quantum key distribution using non-Gaussian state-discrimination detection

NASA Astrophysics Data System (ADS)

Liao, Qin; Guo, Ying; Huang, Duan; Huang, Peng; Zeng, Guihua

2018-02-01

We propose a long-distance continuous-variable quantum key distribution (CVQKD) with a four-state protocol using non-Gaussian state-discrimination detection. A photon subtraction operation, which is deployed at the transmitter, is used for splitting the signal required for generating the non-Gaussian operation to lengthen the maximum transmission distance of the CVQKD. Whereby an improved state-discrimination detector, which can be deemed as an optimized quantum measurement that allows the discrimination of nonorthogonal coherent states beating the standard quantum limit, is applied at the receiver to codetermine the measurement result with the conventional coherent detector. By tactfully exploiting the multiplexing technique, the resulting signals can be simultaneously transmitted through an untrusted quantum channel, and subsequently sent to the state-discrimination detector and coherent detector, respectively. Security analysis shows that the proposed scheme can lengthen the maximum transmission distance up to hundreds of kilometers. Furthermore, by taking the finite-size effect and composable security into account we obtain the tightest bound of the secure distance, which is more practical than that obtained in the asymptotic limit.

Tuning the transition temperature of WSi$$_{x}$$ alloys for use in cryogenic microcalorimeters

DOE PAGES

Cecil, T.; Gades, L.; Madden, T.; ...

2016-03-10

Here, microwave kinetic inductance detectors (MKID) provide a pathway to highly multiplexed, high-resolution, detectors. Over the past several years we have introduced the concept of the Thermal Kinetic Inductance Detector (TKID), which operates as a microcalorimeter. As with other microcalorimeters, the thermal noise of a TKID is reduced when the operating temperature is decreased. However, because the sensitivity of a TKID decreases as the operating temperature drops below 20% of T C, the T C of the resonator material must be tuned to match the desired operating temperature. We have investigated the WSimore » $$_{x}$$ alloy system as a material for these detectors. By co-sputtering from a Si andW2Si target, we have deposited WSi$$_{x}$$ films with a tunable T C that ranges from 5 K down to 500 mK. These films provide a large kinetic inductance fraction and relatively low noise levels. We provide results of these studies showing the T C, resistivity, quality factors, and noise as a function of deposition conditions. These results show that WSi$$_{x}$$ is a good candidate for TKIDs.« less

Detection of Rickettsia rickettsii, Rickettsia parkeri, and Rickettsia akari in Skin Biopsy Specimens Using a Multiplex Real-time Polymerase Chain Reaction Assay

PubMed Central

Denison, Amy M.; Amin, Bijal D.; Nicholson, William L.; Paddock, Christopher D.

2015-01-01

Background Rickettsia rickettsii, Rickettsia parkeri, and Rickettsia akari are the most common causes of spotted fever group rickettsioses indigenous to the United States. Infected patients characteristically present with a maculopapular rash, often accompanied by an inoculation eschar. Skin biopsy specimens are often obtained from these lesions for diagnostic evaluation. However, a species-specific diagnosis is achieved infrequently from pathologic specimens because immunohistochemical stains do not differentiate among the causative agents of spotted fever group rickettsiae, and existing polymerase chain reaction (PCR) assays generally target large gene segments that may be difficult or impossible to obtain from formalin-fixed tissues. Methods This work describes the development and evaluation of a multiplex real-time PCR assay for the detection of these 3 Rickettsia species from formalin-fixed, paraffin-embedded (FFPE) skin biopsy specimens. Results The multiplex PCR assay was specific at discriminating each species from FFPE controls of unrelated bacterial, viral, protozoan, and fungal pathogens that cause skin lesions, as well as other closely related spotted fever group Rickettsia species. Conclusions This multiplex real-time PCR demonstrates greater sensitivity than nested PCR assays in FFPE tissues and provides an effective method to specifically identify cases of Rocky Mountain spotted fever, rickettsialpox, and R. parkeri rickettsiosis by using skin biopsy specimens. PMID:24829214

Analysis of an all optical de-multiplexer architecture utilizing bevel design for spatially multiplexed optical fiber communication systems

NASA Astrophysics Data System (ADS)

Murshid, Syed H.; Finch, Michael F.; Lovell, Gregory L.

2014-09-01

Spatial domain multiplexing (SDM) is a system that allows multiple channels of light to traverse a single fiber, utilizing separate spatial regions inside the carrier fiber, thereby applying a new degree of photon freedom for optical fiber communications. These channels follow a helical pattern, the screen projection of which is viewable as concentric rings at the output end of the system. The MIMO nature of the SDM system implies that a typical pin-diode or APD will be unable to distinguish between these channels, as the diode will interpret the combination of the SDM signals from all channels as a single signal. As such, spatial de-multiplexing methods must be introduced to properly detect the SDM based MIMO signals. One such method utilizes a fiber consisting of multiple, concentric, hollow core fibers to route each channel independently and thereby de-mux the signals into separate fibers or detectors. These de-mux fibers consist of hollow core cylindrical structures with beveled edges on one side that gradually taper to route the circular, ring type, output energy patterns into a spot with the highest possible efficiency. This paper analyzes the beveled edge by varying its length and analyzing the total output power for each predetermined length allowing us to simulate ideal bevel length to minimize both system losses as well as total de-mux footprint. OptiBPM simulation engine is employed for these analyses.

Toward photostable multiplex analyte detection on a single mode planar optical waveguide

NASA Astrophysics Data System (ADS)

Mukundan, Harshini; Xie, Hongzhi; Anderson, Aaron; Grace, W. Kevin; Martinez, Jennifer S.; Swanson, Basil

2009-02-01

We have developed a waveguide-based optical biosensor for the sensitive and specific detection of biomarkers associated with disease. Our technology combines the superior optical properties of single-mode planar waveguides, the robust nature of functionalized self-assembled monolayer sensing films and the specificity of fluorescence sandwich immunoassays to detect biomarkers in complex biological samples such as serum, urine and sputum. We have previously reported the adaptation of our technology to the detection of biomarkers associated with breast cancer and anthrax. However, these approaches primarily used phospholipid bilayers as the functional film and organic dyes (ex: AlexaFluors) as the fluorescence reporter. Organic dyes are easily photodegraded and are not amenable to multiplexing because of their narrow Stokes' shift. Here we have developed strategies for conjugation of the detector antibodies with quantum dots for use in a multiplex detection platform. We have previously evaluated dihydroxylipoic acid quantum dots for the detection of a breast cancer biomarker. In this manuscript, we investigate the detection of the Bacillus anthracis protective antigen using antibodies conjugated with polymer-coated quantum dots. Kinetics of binding on the waveguide-based biosensor is reported. We compare the sensitivity of quantum dot labeled antibodies to those labeled with AlexaFluor and demonstrate the photostability of the former in our assay platform. In addition, we compare sulfydryl labeling of the antibody in the hinge region to that of nonspecific amine labeling. This is but the first step in developing a multiplex assay for such biomarkers on our waveguide platform.

Characterization and use of the spent beam for serial operation of LCLS

DOE PAGES

Boutet, Sébastien; Foucar, Lutz; Barends, Thomas R. M.; ...

2015-04-11

X-ray free-electron laser sources such as the Linac Coherent Light Source offer very exciting possibilities for unique research. However, beam time at such facilities is very limited and in high demand. This has led to significant efforts towards beam multiplexing of various forms. One such effort involves re-using the so-called spent beam that passes through the hole in an area detector after a weak interaction with a primary sample. This beam can be refocused into a secondary interaction region and used for a second, independent experiment operating in series. The beam profile of this refocused beam was characterized for amore » particular experimental geometry at the Coherent X-ray Imaging instrument at LCLS. A demonstration of this multiplexing capability was performed with two simultaneous serial femtosecond crystallography experiments, both yielding interpretable data of sufficient quality to produce electron density maps.« less

Characterization and use of the spent beam for serial operation of LCLS

PubMed Central

Boutet, Sébastien; Foucar, Lutz; Barends, Thomas R. M.; Botha, Sabine; Doak, R. Bruce; Koglin, Jason E.; Messerschmidt, Marc; Nass, Karol; Schlichting, Ilme; Seibert, M. Marvin; Shoeman, Robert L.; Williams, Garth J.

2015-01-01

X-ray free-electron laser sources such as the Linac Coherent Light Source offer very exciting possibilities for unique research. However, beam time at such facilities is very limited and in high demand. This has led to significant efforts towards beam multiplexing of various forms. One such effort involves re-using the so-called spent beam that passes through the hole in an area detector after a weak interaction with a primary sample. This beam can be refocused into a secondary interaction region and used for a second, independent experiment operating in series. The beam profile of this refocused beam was characterized for a particular experimental geometry at the Coherent X-ray Imaging instrument at LCLS. A demonstration of this multiplexing capability was performed with two simultaneous serial femtosecond crystallography experiments, both yielding interpretable data of sufficient quality to produce electron density maps. PMID:25931079

Multiplex coherent raman spectroscopy detector and method

NASA Technical Reports Server (NTRS)

Joyner, Candace C. (Inventor); Patrick, Sheena T. (Inventor); Chen, Peter (Inventor); Guyer, Dean R. (Inventor)

2004-01-01

A multiplex coherent Raman spectrometer (10) and spectroscopy method rapidly detects and identifies individual components of a chemical mixture separated by a separation technique, such as gas chromatography. The spectrometer (10) and method accurately identify a variety of compounds because they produce the entire gas phase vibrational Raman spectrum of the unknown gas. This is accomplished by tilting a Raman cell (20) to produce a high-intensity, backward-stimulated, coherent Raman beam of 683 nm, which drives a degenerate optical parametric oscillator (28) to produce a broadband beam of 1100-1700 nm covering a range of more than 3000 wavenumber. This broadband beam is combined with a narrowband beam of 532 nm having a bandwidth of 0.003 wavenumbers and focused into a heated windowless cell (38) that receives gases separated by a gas chromatograph (40). The Raman radiation scattered from these gases is filtered and sent to a monochromator (50) with multichannel detection.

Multiplex coherent raman spectroscopy detector and method

DOEpatents

Chen, Peter; Joyner, Candace C.; Patrick, Sheena T.; Guyer, Dean R.

2004-06-08

A multiplex coherent Raman spectrometer (10) and spectroscopy method rapidly detects and identifies individual components of a chemical mixture separated by a separation technique, such as gas chromatography. The spectrometer (10) and method accurately identify a variety of compounds because they produce the entire gas phase vibrational Raman spectrum of the unknown gas. This is accomplished by tilting a Raman cell (20) to produce a high-intensity, backward-stimulated, coherent Raman beam of 683 nm, which drives a degenerate optical parametric oscillator (28) to produce a broadband beam of 1100-1700 nm covering a range of more than 3000 wavenumber. This broadband beam is combined with a narrowband beam of 532 nm having a bandwidth of 0.003 wavenumbers and focused into a heated windowless cell (38) that receives gases separated by a gas chromatograph (40). The Raman radiation scattered from these gases is filtered and sent to a monochromator (50) with multichannel detection.

Cryogenic low noise and low dissipation multiplexing electronics, using HEMT+SiGe ASICs, for the readout of high impedance sensors: New version

NASA Astrophysics Data System (ADS)

de la Broïse, Xavier; Lugiez, Francis; Bounab, Ayoub; Le Coguie, Alain

2015-07-01

High Electron Mobility Transistors (HEMTs), optimized by CNRS/LPN laboratory for ultra-low noise at very low temperature, have demonstrated their capacity to be used in place of Si JFETs when working temperatures below 100 K are required. We associated them with specific SiGe ASICs that we developed, to implement a complete readout channel able to read highly segmented high impedance detectors within a framework of very low thermal dissipation. Our electronics is dimensioned to read 4096 detection channels, of typically 1 MΩ impedance, and performs 32:1 multiplexing and amplifying, dissipating only 6 mW at 2.5 K and 100 mW at 15 K thanks to high impedance commuting of input stage, with a typical noise of 1 nV/√Hz at 1 kHz.

TES-Based X-Ray Microcalorimeter Performances Under AC Bias and FDM for Athena

NASA Technical Reports Server (NTRS)

Akamatsu, H.; Gottardi, L.; de Vries, C. P.; Adams, J. S.; Bandler, S. R.; Bruijn, M. P.; Chervenak, J. A.; Eckart, M. E.; Finkbeiner, F. M.; Gao, J. R.;

Dual quantum cascade laser-based sensor for simultaneous NO and NO2 detection using a wavelength modulation-division multiplexing technique

NASA Astrophysics Data System (ADS)

Yu, Yajun; Sanchez, Nancy P.; Yi, Fan; Zheng, Chuantao; Ye, Weilin; Wu, Hongpeng; Griffin, Robert J.; Tittel, Frank K.

2017-05-01

A sensor system capable of simultaneous measurements of NO and NO2 was developed using a wavelength modulation-division multiplexing (WMDM) scheme and multi-pass absorption spectroscopy. A continuous wave (CW), distributed-feedback (DFB) quantum cascade laser (QCL) and a CW external-cavity (EC) QCL were employed for targeting a NO absorption doublet at 1900.075 cm-1 and a NO2 absorption line at 1630.33 cm-1, respectively. Simultaneous detection was realized by modulating both QCLs independently at different frequencies and demodulating the detector signals with LabView-programmed lock-in amplifiers. The sensor operated at a reduced pressure of 40 Torr and a data sampling rate of 1 Hz. An Allan-Werle deviation analysis indicated that the minimum detection limits of NO and NO2 can reach sub-ppbv concentration levels with averaging times of 100 and 200 s, respectively.

Viral prevalence increases with regional colony abundance in honey bee drones (Apis mellifera L).

PubMed

Forfert, Nadège; Natsopoulou, Myrsini E; Paxton, Robert J; Moritz, Robin F A

2016-10-01

Transmission among colonies is a central feature for the epidemiology of honey bee pathogens. High colony abundance may promote transmission among colonies independently of apiary layout, making colony abundance a potentially important parameter determining pathogen prevalence in populations of honey bees. To test this idea, we sampled male honey bees (drones) from seven distinct drone congregation areas (DCA), and used their genotypes to estimate colony abundance at each site. A multiplex ligation dependent probe amplification assay (MLPA) was used to assess the prevalence of ten viruses, using five common viral targets, in individual drones. There was a significant positive association between colony abundance and number of viral infections. This result highlights the potential importance of high colony abundance for pathogen prevalence, possibly because high population density facilitates pathogen transmission. Pathogen prevalence in drones collected from DCAs may be a useful means of estimating the disease status of a population of honey bees during the mating season, especially for localities with a large number of wild or feral colonies. Copyright © 2016 Elsevier B.V. All rights reserved.

T-Cell response profiling to biological threat agents including the SARS coronavirus.

PubMed

Gioia, C; Horejsh, D; Agrati, C; Martini, F; Capobianchi, M R; Ippolito, G; Poccia, F

2005-01-01

The emergence of pathogens such as SARS and the increased threat of bioterrorism has stimulated the development of novel diagnostic assays for differential diagnosis. Rather than focusing on the detection of an individual pathogen component, we have developed a T cell profiling system to monitor responses to the pathogens in an array format. Using a matrix of antigens specific for different pathogens, a specific T cell profile was generated for each individual by monitoring the intracellular production of interferon-gamma by flow cytometry. This assay allows for the testing of multiple proteins or peptides at a single time and provides a quantitative and phenotypic assessment of CD4(+) and CD8(+) responding cells. We present profiling examples for several positive individuals, including those vaccinated with the smallpox and anthrax vaccines. We also show antigen optimization for the SARS-hCoV, as studies revealed that these proteins contain peptides which cross-react with more common coronaviruses, a cause of the common cold. The T cell array is an early and sensitive multiplex measure of active infection, exposure to a pathogen, or effective, recent vaccination.

Superconducting Detectors Come of Age, or Ready to Leave the Lab

NASA Technical Reports Server (NTRS)

Moseley, Samuel H.

2008-01-01

Cryogenically cooled superconducting detectors have become essential tools for a wide range of measurement applications, ranging from quantum limited heterodyne detection in the millimeter range to direct searches for dark matter with superconducting phonon detectors operating at 20 mK. Superconducting detectors have several fundamental and practical advantages which have resulted in their rapid adoption by experimenters. Their excellent performance arises in part from reductions in noise resulting from their low operating temperatures, but unique superconducting properties provide a wide range of mechanisms for detection. For example, the steep dependence of resistance with temperature on the superconductor normal transition provides a sensitive thermometer for calorimetric and bolometric applications. Parametric changes in the properties of superconducting resonators provide a mechanism for high sensitivity detection of submillil.neter photons. From a practical point of view, the use of superconducting detectors has grown rapidly because many of these devices couple well to SQUID amplifiers, which are easily integrated with the detectors. These SQUID-based amplifiers and multiplexers have matured with the detectors; they are convenient to use, and have excellent noise performance. The first generation of fully integrated large-scale superconducting detection systems is now being deployed. Improved understanding of the operation of these detectors, combined with rapidly improving fabrication techniques, is quickly expanding the capability of these detectors. I will review the development and application of superconductor-based detectors, the ultimate limits to their performance, and consider prospects for their future applications. Continued advances promise to enable important new measurements in physics, and with appropriate advances in cryogenic infrastncturem, ay result in the use of these detectors in everyday monitoring applications.

A-7 Airborne Light Optical Fiber Technology (ALOFT) Demonstration Project

DTIC Science & Technology

1977-02-03

emitting diode; the light detector was at PIN silicon phiotodiode. The cable consisted of "high loss," glass core, glass-clad fibers in a 0.045-inch...will emphasize low weight and lost cost. They will be made of’ composite , non-metalflic, structures which;i will uffem veiny little shielding. The...TSP) and fiber-optic systems have components which are similar to equipment presently in use for multiplexed digital-data transfer sys- Stents and

Ultra-Compact, Superconducting Spectrometer-on-a-Chip at Submillimeter Wavelengths

NASA Technical Reports Server (NTRS)

Chattopadhyay, Goutam; Zmuidzinas, Jonas; Bradford, Charles M.; Leduc, Henry G.; Day, Peter K.; Swenson, Loren; Hailey-Dunsheath, Steven; O'Brient, Roger C.; Padin, Stephen; Shirokoff, Erik D.;

High-Speed Microscale Optical Tracking Using Digital Frequency-Domain Multiplexing.

PubMed

Maclachlan, Robert A; Riviere, Cameron N

2009-06-01

Position-sensitive detectors (PSDs), or lateral-effect photodiodes, are commonly used for high-speed, high-resolution optical position measurement. This paper describes the instrument design for multidimensional position and orientation measurement based on the simultaneous position measurement of multiple modulated sources using frequency-domain-multiplexed (FDM) PSDs. The important advantages of this optical configuration in comparison with laser/mirror combinations are that it has a large angular measurement range and allows the use of a probe that is small in comparison with the measurement volume. We review PSD characteristics and quantitative resolution limits, consider the lock-in amplifier measurement system as a communication link, discuss the application of FDM to PSDs, and make comparisons with time-domain techniques. We consider the phase-sensitive detector as a multirate DSP problem, explore parallels with Fourier spectral estimation and filter banks, discuss how to choose the modulation frequencies and sample rates that maximize channel isolation under design constraints, and describe efficient digital implementation. We also discuss hardware design considerations, sensor calibration, probe construction and calibration, and 3-D measurement by triangulation using two sensors. As an example, we characterize the resolution, speed, and accuracy of an instrument that measures the position and orientation of a 10 mm × 5 mm probe in 5 degrees of freedom (DOF) over a 30-mm cube with 4-μm peak-to-peak resolution at 1-kHz sampling.

Detection and Differentiation of Lyme Spirochetes and Other Tick-Borne Pathogens from Blood Using Real-Time PCR with Molecular Beacons.

PubMed

Schlachter, Samantha; Chan, Kamfai; Marras, Salvatore A E; Parveen, Nikhat

2017-01-01

Real-time PCR assays have recently been implemented in diagnostics for many bacterial pathogens, allowing rapid and accurate detection, which ultimately results in improved clinical intervention. Here, we describe a sensitive method of detection for three common tick-borne pathogens Borrelia burgdorferi, Anaplasma phagocytophilum, and Babesia microti since coinfections with these pathogens have started occurring with increasing frequency over the last several years in both North America and Europe. A shared geographic region, the same tick vectors, and similar transmission cycle all favor simultaneous transmission of these three tick-borne pathogens. Furthermore, early symptoms of the diseases are often similar and somewhat nonspecific leading to poor clinical identification. The multiplex real-time PCR assay we describe here utilizes gene-specific primers, molecular beacon probes tagged with different fluorophores, and optimized PCR conditions to detect even small amounts of specific pathogen DNA without interference. Application of this detection method will offer better diagnostics for acute and persistent infection compared to the two-tier serological tests that are currently approved in North America and Europe, which do not necessarily detect active infection.

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

Larson, Richard; Branch, Darren; Edwards, Thayne

The acoustic wave biosensor is innovative device that is a handheld, battery-powered, portable detection system capable of multiplex identification of a wide range of medically relevant pathogens and their biomolecular signatures — viruses, bacteria, proteins, and DNA — at clinically relevant levels. This detection occurs within minutes — not hours — at the point of care, whether that care is in a physician's office, a hospital bed, or at the scene of a biodefense or biomedical emergency.

Multiple advanced logic gates made of DNA-Ag nanocluster and the application for intelligent detection of pathogenic bacterial genes.

PubMed

Lin, Xiaodong; Liu, Yaqing; Deng, Jiankang; Lyu, Yanlong; Qian, Pengcheng; Li, Yunfei; Wang, Shuo

2018-02-21

The integration of multiple DNA logic gates on a universal platform to implement advance logic functions is a critical challenge for DNA computing. Herein, a straightforward and powerful strategy in which a guanine-rich DNA sequence lighting up a silver nanocluster and fluorophore was developed to construct a library of logic gates on a simple DNA-templated silver nanoclusters (DNA-AgNCs) platform. This library included basic logic gates, YES, AND, OR, INHIBIT, and XOR, which were further integrated into complex logic circuits to implement diverse advanced arithmetic/non-arithmetic functions including half-adder, half-subtractor, multiplexer, and demultiplexer. Under UV irradiation, all the logic functions could be instantly visualized, confirming an excellent repeatability. The logic operations were entirely based on DNA hybridization in an enzyme-free and label-free condition, avoiding waste accumulation and reducing cost consumption. Interestingly, a DNA-AgNCs-based multiplexer was, for the first time, used as an intelligent biosensor to identify pathogenic genes, E. coli and S. aureus genes, with a high sensitivity. The investigation provides a prototype for the wireless integration of multiple devices on even the simplest single-strand DNA platform to perform diverse complex functions in a straightforward and cost-effective way.

Genetic relationships among strains of Xanthomonas fragariae based on random amplified polymorphic DNA PCR, repetitive extragenic palindromic PCR, and enterobacterial repetitive intergenic consensus PCR data and generation of multiplexed PCR primers useful for the identification of this phytopathogen.

PubMed Central

Pooler, M R; Ritchie, D F; Hartung, J S

1996-01-01

Genetic relationships among 25 isolates of Xanthomonas fragariae from diverse geographic regions were determined by three PCR methods that rely on different amplification priming strategies: random amplified polymorphic DNA (RAPD) PCR, repetitive extragenic palindromic (REP) PCR, and enterobacterial repetitive intergenic consensus (ERIC) PCR. The results of these assays are mutually consistent and indicate that pathogenic strains are very closely related to each other. RAPD, ERIC, and REP PCR assays identified nine, four, and two genotypes, respectively, within X. fragariae isolates. A single nonpathogenic isolate of X. fragariae was not distinguishable by these methods. The results of the PCR assays were also fully confirmed by physiological tests. There was no correlation between DNA amplification product patterns and geographic sites of isolation, suggesting that this bacterium has spread largely through exchange of infected plant germ plasm. Sequences identified through the RAPD assays were used to develop three primer pairs for standard PCR assays to identify X. fragariae. In addition, we developed a stringent multiplexed PCR assay to identify X. fragariae by simultaneously using the three independently derived sets of primers specific for pathogenic strains of the bacteria. PMID:8795198

Low cost charged-coupled device (CCD) based detectors for Shiga toxins activity analysis

USDA-ARS?s Scientific Manuscript database

To improve food safety there is a need to develop simple, low-cost sensitive devices for detection of foodborne pathogens and their toxins. We describe a simple and relatively low-cost webcam-based detector which can be used for various optical detection modalities, including fluorescence, chemilumi...

A single-step polymerase chain reaction for simultaneous detection and differentiation of nontypeable and serotypeable Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pneumoniae.

PubMed

Kunthalert, Duangkamol; Henghiranyawong, Kritsada; Sistayanarain, Anchalee; Khoothiam, Krissana

2013-02-01

The critically high prevalence of bacterial otitis media worldwide has prompted a proper disease management. While vaccine development for otitis media is promising, the reliable and effective methods for diagnosis of such etiologic agents are of importance. We developed a multiplex polymerase chain reaction assay for simultaneous detection and differentiation of nontypeable and serotypeable Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pneumoniae. Five primer pairs targeting genes fumarate reductase (H. influenzae), outer membrane protein B (M. catarrhalis), major autolysin (S. pneumoniae), capsulation-associated BexA protein (all encapsulated H. influenzae) and 16S rRNA were incorporated in this single-step PCR. Validation of the multiplex PCR was also performed on clinical isolates. The developed multiplex PCR was highly specific, enabling the detection of the target pathogens in a specific manner, either individually or as a mixture of all target organisms. The assay was also found to be sensitive with the lowest detection limit of 1 ng of bacterial DNA. When applied to clinical isolates from diverse specimen sources, the multiplex PCR developed in this study correctly identified each microorganism individually or in a combination of two or more target organisms. All results matched with conventional culture identification. In addition, the ability of such assay to differentiate H. influenzae encapsulation from the study clinical isolates was 100%. Our multiplex PCR provides a rapid and accurate diagnostic tool for detection of the 4 target organisms. Such assay would serve as a useful tool for clinicians and epidemiologists in their efforts to the proper treatment and disease management caused by these organisms. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Diagnostic accuracy of two multiplex real-time polymerase chain reaction assays for the diagnosis of meningitis in children in a resource-limited setting.

PubMed

Khumalo, Jermaine; Nicol, Mark; Hardie, Diana; Muloiwa, Rudzani; Mteshana, Phindile; Bamford, Colleen

2017-01-01

Accurate etiological diagnosis of meningitis is important, but difficult in resource-limited settings due to prior administration of antibiotics and lack of viral diagnostics. We aimed to develop and validate 2 real-time multiplex PCR (RT-PCR) assays for the detection of common causes of community-acquired bacterial and viral meningitis in South African children. We developed 2 multiplex RT- PCRs for detection of S. pneumoniae, N. meningitidis, H. influenzae, enteroviruses, mumps virus and herpes simplex virus. We tested residual CSF samples from children presenting to a local paediatric hospital over a one-year period, whose CSF showed an abnormal cell count. Results were compared with routine diagnostic tests and the final discharge diagnosis. We calculated accuracy of the bacterial RT-PCR assay compared to CSF culture and using World Health Organisation definitions of laboratory-confirmed bacterial meningitis. From 292 samples, bacterial DNA was detected in 12 (4.1%) and viral nucleic acids in 94 (32%). Compared to CSF culture, the sensitivity and specificity of the bacterial RT-PCR was 100% and 97.2% with complete agreement in organism identification. None of the cases positive by viral RT-PCR had a bacterial cause confirmed on CSF culture. Only 9/90 (10%) of patients diagnosed clinically as bacterial meningitis or partially treated bacterial meningitis tested positive with the bacterial RT-PCR. In this population the use of 2 multiplex RT-PCRs targeting 6 common pathogens gave promising results. If introduced into routine diagnostic testing, these multiplex RT-PCR assays would supplement other diagnostic tests, and have the potential to limit unnecessary antibiotic therapy and hospitalisation.

Diagnostic accuracy of two multiplex real-time polymerase chain reaction assays for the diagnosis of meningitis in children in a resource-limited setting

PubMed Central

Khumalo, Jermaine; Nicol, Mark; Hardie, Diana; Muloiwa, Rudzani; Mteshana, Phindile

2017-01-01

Introduction Accurate etiological diagnosis of meningitis is important, but difficult in resource-limited settings due to prior administration of antibiotics and lack of viral diagnostics. We aimed to develop and validate 2 real-time multiplex PCR (RT-PCR) assays for the detection of common causes of community-acquired bacterial and viral meningitis in South African children. Methods We developed 2 multiplex RT- PCRs for detection of S. pneumoniae, N. meningitidis, H. influenzae, enteroviruses, mumps virus and herpes simplex virus. We tested residual CSF samples from children presenting to a local paediatric hospital over a one-year period, whose CSF showed an abnormal cell count. Results were compared with routine diagnostic tests and the final discharge diagnosis. We calculated accuracy of the bacterial RT-PCR assay compared to CSF culture and using World Health Organisation definitions of laboratory-confirmed bacterial meningitis. Results From 292 samples, bacterial DNA was detected in 12 (4.1%) and viral nucleic acids in 94 (32%). Compared to CSF culture, the sensitivity and specificity of the bacterial RT-PCR was 100% and 97.2% with complete agreement in organism identification. None of the cases positive by viral RT-PCR had a bacterial cause confirmed on CSF culture. Only 9/90 (10%) of patients diagnosed clinically as bacterial meningitis or partially treated bacterial meningitis tested positive with the bacterial RT-PCR. Discussion In this population the use of 2 multiplex RT-PCRs targeting 6 common pathogens gave promising results. If introduced into routine diagnostic testing, these multiplex RT-PCR assays would supplement other diagnostic tests, and have the potential to limit unnecessary antibiotic therapy and hospitalisation. PMID:28346504

Identification of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from burn patients by multiplex PCR.

PubMed

Montazeri, Effat Abbasi; Khosravi, Azar Dokht; Jolodar, Abbas; Ghaderpanah, Mozhgan; Azarpira, Samireh

2015-05-01

Methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative staphylococci (MRCoNS) as important human pathogens are causes of nosocomial infections worldwide. Burn patients are at a higher risk of local and systemic infections with these microorganisms. A screening method for MRSA by using a multiplex polymerase chain reaction (PCR) targeting the 16S ribosomal RNA (rRNA), mecA, and nuc genes was developed. The aim of the present study was to investigate the potential of this PCR assay for the detection of MRSA strains in samples from burn patients. During an 11-month period, 230 isolates (53.11%) of Staphylococcus spp. were collected from burn patients. The isolates were identified as S. aureus by using standard culture and biochemical tests. DNA was extracted from bacterial colonies and multiplex PCR was used to detect MRSA and MRCoNS strains. Of the staphylococci isolates, 149 (64.9%) were identified as S. aureus and 81 (35.21%) were described as CoNS. Among the latter, 51 (62.97%) were reported to be MRCoNS. From the total S. aureus isolates, 132 (88.6%) were detected as MRSA and 17 (11.4%) were methicillin-susceptible S. aureus (MSSA). The presence of the mecA gene in all isolates was confirmed by using multiplex PCR as a gold standard method. This study presented a high MRSA rate in the region under investigation. The 16S rRNA-mecA-nuc multiplex PCR is a good tool for the rapid characterization of MRSA strains. This paper emphasizes the need for preventive measures and choosing effective antimicrobials against MRSA and MRCoNS infections in the burn units. Copyright © 2014 Elsevier Ltd and ISBI. All rights reserved.

The SOFIA/SAFIRE Far-Infrared Spectrometer: Highlighting Submillimeter Astrophysics and Technology

NASA Technical Reports Server (NTRS)

Benford, Dominic J.

2009-01-01

The Submillimeter and Far-InfraRed Experiment (SAFIRE) on the SOFIA airborne observatory is an imaging spectrometer for wavelengths between 28 microns and 440 microns. Our design is a dual-band long-slit grating spectrometer, which provides broadband (approx. 4000 km/s) observations in two lines simultaneously over a field of view roughly 10" wide by 320" long. The low backgrounds in spectroscopy require very sensitive detectors with noise equivalent powers of order 10(exp -18) W/square root of Hz. We are developing a kilopixel, filled detector array for SAFIRE in a 32 x 40 format. The detector consists of a transition edge sensor (TES) bolometer array, a per-pixel broadband absorbing backshort array, and a NIST SQUID multiplexer readout array. This general type of array has been used successfully in the GISMO instrument, so we extrapolate to the sensitivity needed for airborne spectroscopy. Much of the cryogenic, electronics, and software infrastructure for SAFIRE have been developed. I provide here an overview of the progress on SAFIRE.

VMM - An ASIC for Micropattern Detectors

NASA Astrophysics Data System (ADS)

Iakovidis, George

2018-02-01

The VMM is a custom Application Specific Integrated Circuit (ASIC) that can be used in a variety of charge interpolating tracking detectors. It is designed to be used with the resistive strip micromegas and sTGC detectors in the New Small Wheel upgrade of the ATLAS Muon spectrometer. The ASIC is designed at Brookhaven National Laboratory and fabricated in the 130 nm Global Foundries 8RF-DM process. It is packaged in a Ball Grid Array with outline dimensions of 21×21 mm2. It integrates 64 channels, each providing charge amplification, discrimination, neighbour logic, amplitude and timing measurements, analog-to-digital conversions, and either direct output for trigger or multiplexed readout. The front-end amplifier can operate with a wide range of input capacitances, has adjustable polarity, gain and peaking time. The VMM1 and VMM2 are the first two versions of the VMM ASIC family fabricated in 2012 and 2014 respectively. The design, tests and qualification of the VMM1, VMM2 and roadmap to VMM3 are described.

Shortwave infrared 512 x 2 line sensor for earth resources applications

NASA Astrophysics Data System (ADS)

Tower, J. R.; Pellon, L. E.; McCarthy, B. M.; Elabd, H.; Moldovan, A. G.; Kosonocky, W. F.; Kalshoven, J. E., Jr.; Tom, D.

1985-08-01

As part of the NASA remote-sensing Multispectral Linear Array Program, an edge-buttable 512 x 2 IRCCD line image sensor with 30-micron Pd2Si Schottky-barrier detectors is developed for operation with passive cooling at 120 K in the 1.1-2.5 micron short infrared band. On-chip CCD multiplexers provide one video output for each 512 detector band. The monolithic silicon line imager performance at a 4-ms optical integration time includes a signal-to-noise ratio of 241 for irradiance of 7.2 microwatts/sq cm at 1.65 microns wavelength, a 5000 dynamic range, a modulation transfer function, greater than 60 percent at the Nyquist frequency, and an 18-milliwatt imager chip total power dissipation. Blemish-free images with three percent nonuniformity under illumination and nonlinearity of 1.25 percent are obtained. A five SWIR imager hybrid focal plane was constructed, demonstrating the feasibility of arrays with only a two-detector loss at each joint.

Prospective study of pathogens in asymptomatic travellers and those with diarrhoea: aetiological agents revisited.

PubMed

Lääveri, T; Antikainen, J; Pakkanen, S H; Kirveskari, J; Kantele, A

2016-06-01

Travellers' diarrhoea (TD) remains the most frequent health problem encountered by visitors to the (sub)tropics. Traditional stool culture identifies the pathogen in only 15% of cases. Exploiting PCR-based methods, we investigated TD pathogens with a focus on asymptomatic travellers and severity of symptoms. Pre- and post-travel stools of 382 travellers with no history of antibiotic use during travel were analysed with a multiplex quantitative PCR for Salmonella, Yersinia, Campylobacter, Shigella, Vibrio cholerae and five diarrhoeagenic Escherichia coli: enteroaggregative (EAEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), enterohaemorrhagic (EHEC) and enteroinvasive (EIEC). The participants were categorized by presence/absence of TD during travel and on return, and by severity of symptoms. A pathogen was indentified in 61% of the asymptomatic travellers, 83% of those with resolved TD, and 83% of those with ongoing TD; 25%, 43% and 53% had multiple pathogens, respectively. EPEC, EAEC, ETEC and Campylobacter associated especially with ongoing TD symptoms. EAEC and EPEC proved more common than ETEC. To conclude, modern methodology challenges our perception of stool pathogens: all pathogens were common both in asymptomatic and symptomatic travellers. TD has a multibacterial nature, but diarrhoeal symptoms mostly associate with EAEC, EPEC, ETEC and Campylobacter. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Development and Comparison of Two Assay Formats for Parallel Detection of Four Biothreat Pathogens by Using Suspension Microarrays

PubMed Central

Janse, Ingmar; Bok, Jasper M.; Hamidjaja, Raditijo A.; Hodemaekers, Hennie M.; van Rotterdam, Bart J.

2012-01-01

Microarrays provide a powerful analytical tool for the simultaneous detection of multiple pathogens. We developed diagnostic suspension microarrays for sensitive and specific detection of the biothreat pathogens Bacillus anthracis, Yersinia pestis, Francisella tularensis and Coxiella burnetii. Two assay chemistries for amplification and labeling were developed, one method using direct hybridization and the other using target-specific primer extension, combined with hybridization to universal arrays. Asymmetric PCR products for both assay chemistries were produced by using a multiplex asymmetric PCR amplifying 16 DNA signatures (16-plex). The performances of both assay chemistries were compared and their advantages and disadvantages are discussed. The developed microarrays detected multiple signature sequences and an internal control which made it possible to confidently identify the targeted pathogens and assess their virulence potential. The microarrays were highly specific and detected various strains of the targeted pathogens. Detection limits for the different pathogen signatures were similar or slightly higher compared to real-time PCR. Probit analysis showed that even a few genomic copies could be detected with 95% confidence. The microarrays detected DNA from different pathogens mixed in different ratios and from spiked or naturally contaminated samples. The assays that were developed have a potential for application in surveillance and diagnostics. PMID:22355407

Development and comparison of two assay formats for parallel detection of four biothreat pathogens by using suspension microarrays.

PubMed

Janse, Ingmar; Bok, Jasper M; Hamidjaja, Raditijo A; Hodemaekers, Hennie M; van Rotterdam, Bart J

2012-01-01

Microarrays provide a powerful analytical tool for the simultaneous detection of multiple pathogens. We developed diagnostic suspension microarrays for sensitive and specific detection of the biothreat pathogens Bacillus anthracis, Yersinia pestis, Francisella tularensis and Coxiella burnetii. Two assay chemistries for amplification and labeling were developed, one method using direct hybridization and the other using target-specific primer extension, combined with hybridization to universal arrays. Asymmetric PCR products for both assay chemistries were produced by using a multiplex asymmetric PCR amplifying 16 DNA signatures (16-plex). The performances of both assay chemistries were compared and their advantages and disadvantages are discussed. The developed microarrays detected multiple signature sequences and an internal control which made it possible to confidently identify the targeted pathogens and assess their virulence potential. The microarrays were highly specific and detected various strains of the targeted pathogens. Detection limits for the different pathogen signatures were similar or slightly higher compared to real-time PCR. Probit analysis showed that even a few genomic copies could be detected with 95% confidence. The microarrays detected DNA from different pathogens mixed in different ratios and from spiked or naturally contaminated samples. The assays that were developed have a potential for application in surveillance and diagnostics.

Development of Kilo-Pixel Arrays of Transition-Edge Sensors for X-Ray Spectroscopy

NASA Technical Reports Server (NTRS)

Adams, J. S.; Bandler, S. R.; Busch, S. E.; Chervenak, J. A.; Chiao, M. P.; Eckart, M. E.; Ewin, A. J.; Finkbeiner, F. M.; Kelley, R. L.; Kelly, D. P.;

NTD-GE Based Microcalorimeter Performance

NASA Technical Reports Server (NTRS)

Bandler, Simon; Silver, Eric; Schnopper, Herbert; Murray, Stephen; Barbera, Marco; Madden, Norm; Landis, Don; Beeman, Jeff; Haller, Eugene; Tucker, Greg

2000-01-01

Our group has been developing x-ray microcalorimeters consisting of neutron transmutation doped (NTD) germanium thermistors attached to superconducting tin absorbers. We discuss the performance of single pixel x-ray detectors, and describe an array technology. In this paper we describe the read-out circuit that allows us to measure fast signals in our detectors as this will be important in understanding the primary cause of resolution broadening. We describe briefly a multiplexing scheme that allows a number of different calorimeters to be read out using a single JFET. We list the possible causes of broadening and give a description of the experiment which best demonstrates the cause of the primary broadening source. We mention our strategy for finding a suitable solution to this problem and describe briefly a technology for building arrays of these calorimeters.

Fabrication of Antenna-Coupled KID Array for Cosmic Microwave Background Detection

NASA Astrophysics Data System (ADS)

Tang, Q. Y.; Barry, P. S.; Basu Thakur, R.; Kofman, A.; Nadolski, A.; Vieira, J.; Shirokoff, E.

2018-05-01

Kinetic inductance detectors (KIDs) have become an attractive alternative to traditional bolometers in the sub-mm and mm observing community due to their innate frequency multiplexing capabilities and simple lithographic processes. These advantages make KIDs a viable option for the O(500,000) detectors needed for the upcoming Cosmic Microwave Background-Stage 4 experiment. We have fabricated an antenna-coupled MKID array in the 150 GHz band optimized for CMB detection. Our design uses a twin-slot antenna coupled to an inverted microstrip made from a superconducting Nb/Al bilayer as the strip, a Nb ground plane and a SiN_x dielectric layer in between, which is then coupled to an Al KID grown on high-resistivity Si. We present the fabrication process and measurements of SiN_x microstrip resonators.