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Sample records for fluorescent multiplex linkage

  1. Fluorescent multiplex linkage analysis and carrier detection for Duchenne/Becker muscular dystrophy

    SciTech Connect

    Schwartz, L.S.; Hoffman, E.P. ); Tarleton, J. ); Popovich, B. ); Seltzer, W.K. )

    1992-10-01

    The authors have developed a fast and accurate PCR-based linkage and carrier detection protocol for families of Duchenne muscular dystrophy (DMD)/Becker muscular dystrophy (BMD) patients with or without detectable deletions of the dystrophin gene, using fluorescent PCR products analyzed on an automated sequencer. When a deletion is found in the affected male DMD/BMD patient by standard multiplex PCR, fluorescently labeled primers specific for the deleted and nondeleted exon(s) are used to amplify the DNA of at-risk female relatives by using multiplex PCR at low cycle number (20 cycles). The products are then quantitatively analyzed on an automatic sequencer to determine whether they are heterozygous for the deletion and thus are carriers. As a confirmation of the deletion data, and in cases in which a deletion is not found in the proband, fluorescent multiplex PCR linkage is done by using four previously described polymorphic dinucleotide sequences. The four (CA)[sub n] repeats are located throughout the dystrophin gene, making the analysis highly informative and accurate. The authors present the successful application of this protocol in families who proved refractory to more traditional analyses. 22 refs., 3 figs.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Microgels for multiplex and direct fluorescence detection

    NASA Astrophysics Data System (ADS)

    Causa, Filippo; Aliberti, Anna; Cusano, Angela M.; Battista, Edmondo; Netti, Paolo A.

    2015-05-01

    Blood borne oligonucleotides fragments contain useful clinical information whose detection and monitoring represent the new frontier in liquid biopsy as they can transform the current diagnosis procedure. For instance, recent studies have identified a new class of circulating biomarkers such as s miRNAs, and demonstrated that changes in their concentration are closely associated with the development of cancer and other pathologies. However, direct detection of miRNAs in body fluids is particularly challenging and demands high sensitivity -concentration range between atto to femtomolarspecificity, and multiplexing Here we report on engineered multifunctional microgels and innovative probe design for a direct and multiplex detection of relevant clinical miRNAs in fluorescence by single particle assay. Polyethyleneglycol-based microgels have a coreshell architecture with two spectrally encoded fluorescent dyes for multiplex analyses and are endowed with fluorescent probes for miRNA detection. Encoding and detection fluorescence signals are distinguishable by not overlapping emission spectra. Tuneable fluorescence probe conjugation and corresponding emission confinement on single microgel allows for enhanced target detection. Such suspension array has indeed high selectivity and sensitivity with a detection limit of 10-15 M and a dynamic range from 10-9 to 10-15 M. We believe that sensitivity in the fM concentration range, signal background minimization, multiplexed capability and direct measurement of such microgels will translate into diagnostic benefits opening up new roots toward liquid biopsy in the context of point-of-care testing through an easy and fast detection of sensitive diagnostic biomarkers directly in serum.

  7. Optimal estimator for tomographic fluorescence lifetime multiplexing

    PubMed Central

    Hou, Steven S.; Bacskai, Brian J.; Kumar, Anand T. N.

    2016-01-01

    We use the model resolution matrix to analytically derive an optimal Bayesian estimator for multiparameter inverse problems that simultaneously minimizes inter-parameter cross talk and the total reconstruction error. Application of this estimator to time-domain diffuse fluorescence imaging shows that the optimal estimator for lifetime multiplexing is identical to a previously developed asymptotic time-domain (ATD) approach, except for the inclusion of a diagonal regularization term containing decay amplitude uncertainties. We show that, while the optimal estimator and ATD provide zero cross talk, the optimal estimator provides lower reconstruction error, while ATD results in superior relative quantitation. The framework presented here is generally applicable to other multiplexing problems where the simultaneous and accurate relative quantitation of multiple parameters is of interest. PMID:27192234

  8. Multiplex Detection and SNP Genotyping in a Single Fluorescence Channel

    PubMed Central

    Fu, Guoliang; Miles, Andrea; Alphey, Luke

    2012-01-01

    Probe-based PCR is widely used for SNP (single nucleotide polymorphism) genotyping and pathogen nucleic acid detection due to its simplicity, sensitivity and cost-effectiveness. However, the multiplex capability of hydrolysis probe-based PCR is normally limited to one target (pathogen or allele) per fluorescence channel. Current fluorescence PCR machines typically have 4–6 channels. We present a strategy permitting the multiplex detection of multiple targets in a single detection channel. The technique is named Multiplex Probe Amplification (MPA). Polymorphisms of the CYP2C9 gene (cytochrome P450, family 2, subfamily C, polypeptide 9, CYP2C9*2) and human papillomavirus sequences HPV16, 18, 31, 52 and 59 were chosen as model targets for testing MPA. The allele status of the CYP2C9*2 determined by MPA was entirely concordant with the reference TaqMan® SNP Genotyping Assays. The four HPV strain sequences could be independently detected in a single fluorescence detection channel. The results validate the multiplex capacity, the simplicity and accuracy of MPA for SNP genotyping and multiplex detection using different probes labeled with the same fluorophore. The technique offers a new way to multiplex in a single detection channel of a closed-tube PCR. PMID:22272339

  9. Multiplex detection and SNP genotyping in a single fluorescence channel.

    PubMed

    Fu, Guoliang; Miles, Andrea; Alphey, Luke

    2012-01-01

    Probe-based PCR is widely used for SNP (single nucleotide polymorphism) genotyping and pathogen nucleic acid detection due to its simplicity, sensitivity and cost-effectiveness. However, the multiplex capability of hydrolysis probe-based PCR is normally limited to one target (pathogen or allele) per fluorescence channel. Current fluorescence PCR machines typically have 4-6 channels. We present a strategy permitting the multiplex detection of multiple targets in a single detection channel. The technique is named Multiplex Probe Amplification (MPA). Polymorphisms of the CYP2C9 gene (cytochrome P450, family 2, subfamily C, polypeptide 9, CYP2C9*2) and human papillomavirus sequences HPV16, 18, 31, 52 and 59 were chosen as model targets for testing MPA. The allele status of the CYP2C9*2 determined by MPA was entirely concordant with the reference TaqMan® SNP Genotyping Assays. The four HPV strain sequences could be independently detected in a single fluorescence detection channel. The results validate the multiplex capacity, the simplicity and accuracy of MPA for SNP genotyping and multiplex detection using different probes labeled with the same fluorophore. The technique offers a new way to multiplex in a single detection channel of a closed-tube PCR. PMID:22272339

  10. Automated hybridization/imaging device for fluorescent multiplex DNA sequencing

    DOEpatents

    Weiss, Robert B.; Kimball, Alvin W.; Gesteland, Raymond F.; Ferguson, F. Mark; Dunn, Diane M.; Di Sera, Leonard J.; Cherry, Joshua L.

    1995-01-01

    A method is disclosed for automated multiplex sequencing of DNA with an integrated automated imaging hybridization chamber system. This system comprises an hybridization chamber device for mounting a membrane containing size-fractionated multiplex sequencing reaction products, apparatus for fluid delivery to the chamber device, imaging apparatus for light delivery to the membrane and image recording of fluorescence emanating from the membrane while in the chamber device, and programmable controller apparatus for controlling operation of the system. The multiplex reaction products are hybridized with a probe, then an enzyme (such as alkaline phosphatase) is bound to a binding moiety on the probe, and a fluorogenic substrate (such as a benzothiazole derivative) is introduced into the chamber device by the fluid delivery apparatus. The enzyme converts the fluorogenic substrate into a fluorescent product which, when illuminated in the chamber device with a beam of light from the imaging apparatus, excites fluorescence of the fluorescent product to produce a pattern of hybridization. The pattern of hybridization is imaged by a CCD camera component of the imaging apparatus to obtain a series of digital signals. These signals are converted by the controller apparatus into a string of nucleotides corresponding to the nucleotide sequence an automated sequence reader. The method and apparatus are also applicable to other membrane-based applications such as colony and plaque hybridization and Southern, Northern, and Western blots.

  11. Automated hybridization/imaging device for fluorescent multiplex DNA sequencing

    DOEpatents

    Weiss, R.B.; Kimball, A.W.; Gesteland, R.F.; Ferguson, F.M.; Dunn, D.M.; Di Sera, L.J.; Cherry, J.L.

    1995-11-28

    A method is disclosed for automated multiplex sequencing of DNA with an integrated automated imaging hybridization chamber system. This system comprises an hybridization chamber device for mounting a membrane containing size-fractionated multiplex sequencing reaction products, apparatus for fluid delivery to the chamber device, imaging apparatus for light delivery to the membrane and image recording of fluorescence emanating from the membrane while in the chamber device, and programmable controller apparatus for controlling operation of the system. The multiplex reaction products are hybridized with a probe, the enzyme (such as alkaline phosphatase) is bound to a binding moiety on the probe, and a fluorogenic substrate (such as a benzothiazole derivative) is introduced into the chamber device by the fluid delivery apparatus. The enzyme converts the fluorogenic substrate into a fluorescent product which, when illuminated in the chamber device with a beam of light from the imaging apparatus, excites fluorescence of the fluorescent product to produce a pattern of hybridization. The pattern of hybridization is imaged by a CCD camera component of the imaging apparatus to obtain a series of digital signals. These signals are converted by the controller apparatus into a string of nucleotides corresponding to the nucleotide sequence an automated sequence reader. The method and apparatus are also applicable to other membrane-based applications such as colony and plaque hybridization and Southern, Northern, and Western blots. 9 figs.

  12. Multiplexing Bioluminescent and Fluorescent Reporters to Monitor Live Cells

    PubMed Central

    Haugwitz, Michael; Nourzaie, Omar; Garachtchenko, Tatiana; Hu, Lanrong; Gandlur, Suvarna; Olsen, Cathy; Farmer, Andrew; Chaga, Grigoriy; Sagawa, Hiroaki

    2008-01-01

    Reporter proteins are valuable tools to monitor promoter activities and characterize signal transduction pathways. Many of the currently available promoter reporters have drawbacks that compromise their performance. Enzyme-based reporter systems using cytosolic luciferases are highly sensitive, but require a cell lysis step that prevents their use in long-term monitoring. By contrast, secreted bioluminescent reporters like Metridia luciferase and Secreted Alkaline Phosphatase can be assayed repeatedly, using supernatant from the same live cell population to produce many sets of data over time. This is crucial for studies with limited amounts of cells, as in the case of stem cells. The use of secreted bioluminescent reporters also enables broader applications to provide more detailed information using live cells; for example, multiplexing with fluorescent proteins. Here, data is presented describing the characteristics of secreted Metridia luciferase and its use in multiplexing applications with either Secreted Alkaline Phosphatase or a fluorescent protein. PMID:20161823

  13. Multiplexing bioluminescent and fluorescent reporters to monitor live cells.

    PubMed

    Haugwitz, Michael; Nourzaie, Omar; Garachtchenko, Tatiana; Hu, Lanrong; Gandlur, Suvarna; Olsen, Cathy; Farmer, Andrew; Chaga, Grigoriy; Sagawa, Hiroaki

    2008-01-01

    Reporter proteins are valuable tools to monitor promoter activities and characterize signal transduction pathways. Many of the currently available promoter reporters have drawbacks that compromise their performance. Enzyme-based reporter systems using cytosolic luciferases are highly sensitive, but require a cell lysis step that prevents their use in long-term monitoring. By contrast, secreted bioluminescent reporters like Metridia luciferase and Secreted Alkaline Phosphatase can be assayed repeatedly, using supernatant from the same live cell population to produce many sets of data over time. This is crucial for studies with limited amounts of cells, as in the case of stem cells. The use of secreted bioluminescent reporters also enables broader applications to provide more detailed information using live cells; for example, multiplexing with fluorescent proteins. Here, data is presented describing the characteristics of secreted Metridia luciferase and its use in multiplexing applications with either Secreted Alkaline Phosphatase or a fluorescent protein. PMID:20161823

  14. DNA-templated silver nanoclusters for multiplexed fluorescent DNA detection.

    PubMed

    Zhang, Ying; Zhu, Changfeng; Zhang, Lei; Tan, Chaoliang; Yang, Jian; Chen, Bo; Wang, Lianhui; Zhang, Hua

    2015-03-25

    Novel label-free/conjugation-free molecular beacons are designed based on DNA templated-silver nanoclusters for multiplexed DNA detection. The assay is implemented in solution, which makes it easy for the in-situ and real-time analysis. This study demonstrates a new method for multiplexd detection of biological molecules by using fluorescent Ag nanocluster-based molecular beacon probes. PMID:25491417

  15. Frequency Division Multiplexed Multichannel High-Speed Fluorescence Confocal Microscope

    PubMed Central

    Wu, Fei; Zhang, Xueqian; Cheung, Joseph Y.; Shi, Kebin; Liu, Zhiwen; Luo, Claire; Yin, Stuart; Ruffin, Paul

    2006-01-01

    In this article, we report a new type of fluorescence confocal microscope: frequency division multiplexed multichannel fluorescence confocal microscope, in which we encode the spatial location information into the frequency domain. In this microscope, the exciting laser beam is first split into multiple beams and each beam is modulated at a different frequency. These multiple beams are focused at different locations of the target to form multiple focal points, which further generate multiple fluorescent emission spots. The fluorescent emissions from different focal points are also modulated at different frequencies, because the exciting beams are modulated at different frequencies (or difference carrier frequency). Then, all the fluorescent emissions (modulated at different frequencies) are collected together and detected by a highly sensitive, large-dynamic-range photomultiplier tube. By demodulating the detected signal (i.e., via the Fourier transform), we can distinguish the fluorescent light emitted from the different locations by the corresponding carrier frequencies. The major advantage of this unique fluorescence confocal microscope is that it not only has a high sensitivity because of the use of photomultiplier tube but also can get multiple-point data simultaneously, which is crucial to study the dynamic behavior of many biological process. As an initial step, to verify the feasibility of the proposed multichannel confocal microscope, we have developed a two-channel confocal fluorescence microscope and applied it to study the dynamic behavior of the changes of the calcium ion concentration during the single cardiac myocyte contraction. Our preliminary experimental results demonstrated that we could indeed realize multichannel confocal fluorescence microscopy by utilizing the frequency division multiplexed microscope, which could become an effective tool to study the dynamic behavior of many biological processes. PMID:16815894

  16. Detection of Microsatellite Instability by Fluorescence Multiplex Polymerase Chain Reaction

    PubMed Central

    Berg, Karin D.; Glaser, Cynthia L.; Thompson, Richard E.; Hamilton, Stanley R.; Griffin, Constance A.; Eshleman, James R.

    2000-01-01

    We have created a clinical molecular diagnostic assay to test for microsatellite instability (MSI) at multiple loci simultaneously in paraffin-embedded surgical pathology colon resection specimens. This fluorescent multiplex polymerase chain reaction (PCR) assay analyzes the five primary microsatellite loci recommended at the 1997 National Cancer Institute-sponsored conference on MSI for the identification of MSI or replication errors in colorectal cancer: Bat-25, Bat-26, D2S123, D5S346, and D17S250. Amplicon detection is accomplished by capillary electrophoresis using the ABI 310 Genetic Analyzer. Assay validation compared 18 specimens previously assessed by radioactive PCR and polyacrylamide gel electrophoresis detection to results generated by the reported assay. Germline and tumor DNA samples were amplified in separate multiplex PCR reactions, sized in separate capillary electrophoresis runs, and compared directly to identify novel length alleles in tumor tissue. A concordance of 100% between the two modalities was achieved. The multiplex assay routinely detected a subpopulation of 10% tumor alleles in the presence of 90% normal alleles. A novel statistical model was generated that corroborates the validity of using results generated by analysis of five independent microsatellites to achieve a single overall MSI diagnosis. The assay presented is superior to standard radioactive monoplex PCR, polyacrylamide gel electrophoretic analysis, primarily due to the multiplex PCR format. PMID:11272898

  17. Setting up Multiplex Panels for Genetic Testing of Familial Hypertrophic Cardiomyopathy Based on Linkage Analysis

    PubMed Central

    SAGHAFI, Hoorieh; HAGHJOO, Majid; SABBAGH, Sima; SAMIEE, Niloofar; VAKILIAN, Farve; SALEHI OMRAN, Mohammad Taghi; DADASHI, Masoomeh; AMIN, Ahmad; KERAMATIPOUR, Mohammad

    2016-01-01

    Background: Familial hypertrophic cardiomyopathy (HCM) is caused by mutations in genes encoding cardiac sarcomere proteins. Nowadays genetic testing of HCM plays an important role in clinical practice by contributing to the diagnosis, prognosis, and screening of high-risk individuals. The aim of this study was developing a reliable testing strategy for HCM based on linkage analysis and appropriate for Iranian population. Methods: Six panels of four microsatellite markers surrounding MYH7, MYBPC3, TNNT2, TNNI3, TPM1, and MYL2 genes (24 markers in total) were selected for multiplex PCR and fragment length analysis. Characteristics of markers and informativeness of the panels were evaluated in 50 unrelated Iranians. The efficacy of the strategy was verified in a family with HCM. Results: All markers were highly polymorphic. The panels were informative in 96–100% of samples. Multipoint linkage analysis excluded the linkage between the disease and all six genes by obtaining maximum LOD score ≤−2. Conclusion: This study suggests a reliable genetic testing method based on linkage analysis between 6 sarcomere genes and familial HCM. It could be applied for diagnostic, predictive, or screening testing in clinical setting. PMID:27141495

  18. Enhanced speed in fluorescence imaging using beat frequency multiplexing

    NASA Astrophysics Data System (ADS)

    Mikami, Hideharu; Kobayashi, Hirofumi; Wang, Yisen; Hamad, Syed; Ozeki, Yasuyuki; Goda, Keisuke

    2016-03-01

    Fluorescence imaging using radiofrequency-tagged emission (FIRE) is an emerging technique that enables higher imaging speed (namely, temporal resolution) in fluorescence microscopy compared to conventional fluorescence imaging techniques such as confocal microscopy and wide-field microscopy. It works based on the principle that it uses multiple intensity-modulated fields in an interferometric setup as excitation fields and applies frequency-division multiplexing to fluorescence signals. Unfortunately, despite its high potential, FIRE has limited imaging speed due to two practical limitations: signal bandwidth and signal detection efficiency. The signal bandwidth is limited by that of an acousto-optic deflector (AOD) employed in the setup, which is typically 100-200 MHz for the spectral range of fluorescence excitation (400-600 nm). The signal detection efficiency is limited by poor spatial mode-matching between two interfering fields to produce a modulated excitation field. Here we present a method to overcome these limitations and thus to achieve higher imaging speed than the prior version of FIRE. Our method achieves an increase in signal bandwidth by a factor of two and nearly optimal mode matching, which enables the imaging speed limited by the lifetime of the target fluorophore rather than the imaging system itself. The higher bandwidth and better signal detection efficiency work synergistically because higher bandwidth requires higher signal levels to avoid the contribution of shot noise and amplifier noise to the fluorescence signal. Due to its unprecedentedly high-speed performance, our method has a wide variety of applications in cancer detection, drug discovery, and regenerative medicine.

  19. RNA Imaging with Multiplexed Error Robust Fluorescence in situ Hybridization

    PubMed Central

    Moffitt, Jeffrey R.; Zhuang, Xiaowei

    2016-01-01

    Quantitative measurements of both the copy number and spatial distribution of large fractions of the transcriptome in single-cells could revolutionize our understanding of a variety of cellular and tissue behaviors in both healthy and diseased states. Single-molecule Fluorescence In Situ Hybridization (smFISH)—an approach where individual RNAs are labeled with fluorescent probes and imaged in their native cellular and tissue context—provides both the copy number and spatial context of RNAs but has been limited in the number of RNA species that can be measured simultaneously. Here we describe Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH), a massively parallelized form of smFISH that can image and identify hundreds to thousands of different RNA species simultaneously with high accuracy in individual cells in their native spatial context. We provide detailed protocols on all aspects of MERFISH, including probe design, data collection, and data analysis to allow interested laboratories to perform MERFISH measurements themselves. PMID:27241748

  20. Multicolor fluorescent biosensor for multiplexed detection of DNA.

    PubMed

    Hu, Rong; Liu, Tao; Zhang, Xiao-Bing; Huan, Shuang-Yan; Wu, Cuichen; Fu, Ting; Tan, Weihong

    2014-05-20

    Development of efficient methods for highly sensitive and rapid screening of specific oligonucleotide sequences is essential to the early diagnosis of serious diseases. In this work, an aggregated cationic perylene diimide (PDI) derivative was found to efficiently quench the fluorescence emission of a variety of anionic oligonucleotide-labeled fluorophores that emit at wavelengths from the visible to NIR region. This broad-spectrum quencher was then adopted to develop a multicolor biosensor via a label-free approach for multiplexed fluorescent detection of DNA. The aggregated perylene derivative exhibits a very high quenching efficiency on all ssDNA-labeled dyes associated with biosensor detection, having efficiency values of 98.3 ± 0.9%, 97 ± 1.1%, and 98.2 ± 0.6% for FAM, TAMRA, and Cy5, respectively. An exonuclease-assisted autocatalytic target recycling amplification was also integrated into the sensing system. High quenching efficiency combined with autocatalytic target recycling amplification afforded the biosensor with high sensitivity toward target DNA, resulting in a detection limit of 20 pM, which is about 50-fold lower than that of traditional unamplified homogeneous fluorescent assay methods. The quencher did not interfere with the catalytic activity of nuclease, and the biosensor could be manipulated in either preaddition or postaddition manner with similar sensitivity. Moreover, the proposed sensing system allows for simultaneous and multicolor analysis of several oligonucleotides in homogeneous solution, demonstrating its potential application in the rapid screening of multiple biotargets. PMID:24731194

  1. Robust normalization protocols for multiplexed fluorescence bioimage analysis.

    PubMed

    Ahmed Raza, Shan E; Langenkämper, Daniel; Sirinukunwattana, Korsuk; Epstein, David; Nattkemper, Tim W; Rajpoot, Nasir M

    2016-01-01

    study of mapping and interaction of co-localized proteins at a sub-cellular level is important for understanding complex biological phenomena. One of the recent techniques to map co-localized proteins is to use the standard immuno-fluorescence microscopy in a cyclic manner (Nat Biotechnol 24:1270-8, 2006; Proc Natl Acad Sci 110:11982-7, 2013). Unfortunately, these techniques suffer from variability in intensity and positioning of signals from protein markers within a run and across different runs. Therefore, it is necessary to standardize protocols for preprocessing of the multiplexed bioimaging (MBI) data from multiple runs to a comparable scale before any further analysis can be performed on the data. In this paper, we compare various normalization protocols and propose on the basis of the obtained results, a robust normalization technique that produces consistent results on the MBI data collected from different runs using the Toponome Imaging System (TIS). Normalization results produced by the proposed method on a sample TIS data set for colorectal cancer patients were ranked favorably by two pathologists and two biologists. We show that the proposed method produces higher between class Kullback-Leibler (KL) divergence and lower within class KL divergence on a distribution of cell phenotypes from colorectal cancer and histologically normal samples. PMID:26949415

  2. Molecular analysis and test of linkage between the FMR-I gene and infantile autism in multiplex families

    SciTech Connect

    Hallmayer, J.; Pintado, E.; Lotspeich, L.; Spiker, D.; Kraemer, H.C.; Lee Wong, D.; Lin, A.; Herbert, J.; Cavalli-Sforza, L.L.; Ciaranello, R.D.

    1994-11-01

    Approximately 2%-5% of autistic children show cytogenetic evidence of the fragile X syndrome. This report tests whether infantile autism in multiplex autism families arises from an unusual manifestion of the fragile X syndrome. This could arise either by expansion of the (CGG)n trinucleotide repeat in FMR-1 or from a mutation elsewhere in the gene. We studied 35 families that met stringent criteria for multiplex autism. Amplification of the trinucleotide repeat and analysis of methylation status were performed in 79 autistic children and in 31 of their unaffected siblings by Southern blot analysis. No examples of amplified repeats were seen in the autistic or control children or in their parents or grandparents. We next examined the hypothesis that there was a mutation elsewhere in the FMR-1 gene, by linkage analysis in 32 of these families. We tested four different dominant models and a recessive model. Linkage to FMR-1 could be excluded (lod score between -24 and -62) in all models by using probes DXS548, FRAXAC1, and FRAXAC2 and the CGG repeat itself. Tests for heterogeneity in this sample were negative, and the occurrence of positive lod scores in this data set could be attributed to chance. Analysis of the data by the affected-sib method also did not show evidence for linkage of any marker to autism. These results enable us to reject the hypothesis that multiplex autism arises from expansion of the (CGG)n trinucleotide repeat in FMR-1. Further, because the overall lod scores for all probes in all models tested were highly negative, linkage to FMR-1 can also be ruled out in multiplex autistic families. 35 refs., 2 figs., 5 tabs.

  3. Parallel excitation-emission multiplexed fluorescence lifetime confocal microscopy for live cell imaging

    PubMed Central

    Zhao, Ming; Li, Yu; Peng, Leilei

    2014-01-01

    We present a novel excitation-emission multiplexed fluorescence lifetime microscopy (FLIM) method that surpasses current FLIM techniques in multiplexing capability. The method employs Fourier multiplexing to simultaneously acquire confocal fluorescence lifetime images of multiple excitation wavelength and emission color combinations at 44,000 pixels/sec. The system is built with low-cost CW laser sources and standard PMTs with versatile spectral configuration, which can be implemented as an add-on to commercial confocal microscopes. The Fourier lifetime confocal method allows fast multiplexed FLIM imaging, which makes it possible to monitor multiple biological processes in live cells. The low cost and compatibility with commercial systems could also make multiplexed FLIM more accessible to biological research community. PMID:24921725

  4. In vivo simultaneous multispectral fluorescence imaging with spectral multiplexed volume holographic imaging system

    NASA Astrophysics Data System (ADS)

    Lv, Yanlu; Zhang, Jiulou; Zhang, Dong; Cai, Wenjuan; Chen, Nanguang; Luo, Jianwen

    2016-06-01

    A simultaneous multispectral fluorescence imaging system incorporating multiplexed volume holographic grating (VHG) is developed to acquire multispectral images of an object in one shot. With the multiplexed VHG, the imaging system can provide the distribution and spectral characteristics of multiple fluorophores in the scene. The implementation and performance of the simultaneous multispectral imaging system are presented. Further, the system's capability in simultaneously obtaining multispectral fluorescence measurements is demonstrated with in vivo experiments on a mouse. The demonstrated imaging system has the potential to obtain multispectral images fluorescence simultaneously.

  5. Development of a Time Domain Fluorimeter for Fluorescent Lifetime Multiplexing Analysis

    PubMed Central

    Weissleder, Ralph; Mahmood, Umar

    2009-01-01

    We show that a portable, inexpensive USB-powered time domain fluorimeter (TDF) and analysis scheme were developed for use in evaluating a new class of fluorescent lifetime multiplexed dyes. Fluorescent proteins, organic dyes, and quantum dots allow the labeling of more and more individual features within biological systems, but the wide absorption and emission spectra of these fluorophores limit the number of distinct processes which may be simultaneously imaged using spectral separation alone. By additionally separating reporters in a second dimension, fluorescent lifetime multiplexing provides a means to multiply the number of available imaging channels. PMID:19830273

  6. Fluorescence-Raman Dual Modal Endoscopic System for Multiplexed Molecular Diagnostics

    NASA Astrophysics Data System (ADS)

    Jeong, Sinyoung; Kim, Yong-Il; Kang, Homan; Kim, Gunsung; Cha, Myeong Geun; Chang, Hyejin; Jung, Kyung Oh; Kim, Young-Hwa; Jun, Bong-Hyun; Hwang, Do Won; Lee, Yun-Sang; Youn, Hyewon; Lee, Yoon-Sik; Kang, Keon Wook; Lee, Dong Soo; Jeong, Dae Hong

    2015-03-01

    Optical endoscopic imaging, which was recently equipped with bioluminescence, fluorescence, and Raman scattering, allows minimally invasive real-time detection of pathologies on the surface of hollow organs. To characterize pathologic lesions in a multiplexed way, we developed a dual modal fluorescence-Raman endomicroscopic system (FRES), which used fluorescence and surface-enhanced Raman scattering nanoprobes (F-SERS dots). Real-time, in vivo, and multiple target detection of a specific cancer was successful, based on the fast imaging capability of fluorescence signals and the multiplex capability of simultaneously detected SERS signals using an optical fiber bundle for intraoperative endoscopic system. Human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR) on the breast cancer xenografts in a mouse orthotopic model were successfully detected in a multiplexed way, illustrating the potential of FRES as a molecular diagnostic instrument that enables real-time tumor characterization of receptors during routine endoscopic procedures.

  7. Fluorescence-Raman Dual Modal Endoscopic System for Multiplexed Molecular Diagnostics

    PubMed Central

    Jeong, Sinyoung; Kim, Yong-il; Kang, Homan; Kim, Gunsung; Cha, Myeong Geun; Chang, Hyejin; Jung, Kyung Oh; Kim, Young-Hwa; Jun, Bong-Hyun; Hwang, Do Won; Lee, Yun-Sang; Youn, Hyewon; Lee, Yoon-Sik; Kang, Keon Wook; Lee, Dong Soo; Jeong, Dae Hong

    2015-01-01

    Optical endoscopic imaging, which was recently equipped with bioluminescence, fluorescence, and Raman scattering, allows minimally invasive real-time detection of pathologies on the surface of hollow organs. To characterize pathologic lesions in a multiplexed way, we developed a dual modal fluorescence-Raman endomicroscopic system (FRES), which used fluorescence and surface-enhanced Raman scattering nanoprobes (F-SERS dots). Real-time, in vivo, and multiple target detection of a specific cancer was successful, based on the fast imaging capability of fluorescence signals and the multiplex capability of simultaneously detected SERS signals using an optical fiber bundle for intraoperative endoscopic system. Human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR) on the breast cancer xenografts in a mouse orthotopic model were successfully detected in a multiplexed way, illustrating the potential of FRES as a molecular diagnostic instrument that enables real-time tumor characterization of receptors during routine endoscopic procedures. PMID:25820115

  8. Exclusion of linkage between alcoholism and the MNS blood group region on chromosome 4q in multiplex families

    SciTech Connect

    Neiswanger, K.; Kaplan, B.; Hill, S.Y.

    1995-02-27

    Polymorphic DNA markers on the long arm of chromosome 4 were used to examine linkage to alcoholism in 20 multiplex pedigrees. Fifteen loci were determined for 124 individuals. Lod scores were calculated assuming both dominant and recessive disease modes of inheritance, utilizing incidence data by age and gender that allow for correction for variable age of onset and frequency of the disorder by gender. Under the assumption that alcoholism is homogeneous in this set of pedigrees, and that a recessive mode with age and gender correction is the most appropriate, the total lod scores for all families combined were uniformly lower than -2.0. This suggests an absence of linkage between the putative alcoholism susceptibility gene and markers in the region of the MNS blood group (4q28-31), a region for which we had previously found suggestive evidence of linkage to alcoholism. The 100 cM span of chromosome 4 studied includes the class I alcohol dehydrogenase (ADH) loci. Using the recessive mode, no evidence for linkage to alcoholism was found for the markers tested, which spanned almost the entire long arm of chromosome 4. Under the dominant mode, no evidence for linkage could be found for several of the markers. 36 refs., 1 fig., 3 tabs.

  9. Clinical Application of an Innovative Multiplex-Fluorescent-Labeled STRs Assay for Prader-Willi Syndrome and Angelman Syndrome.

    PubMed

    Zhang, Kaihui; Liu, Shu; Feng, Bing; Yang, Yali; Zhang, Haiyan; Dong, Rui; Liu, Yi; Gai, Zhongtao

    2016-01-01

    Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are two clinically distinct neurodevelopmental disorders caused by absence of paternally or maternally expressed imprinted genes on chr15q11.2-q13.3. Three mechanisms are known to be involved in the pathogenesis: microdeletions, uniparental disomy (UPD) and imprinting defects. Both disorders are difficult to be definitely diagnosed at early age if no available molecular cytogenetic tests. In this study, we identified 5 AS patients with the maternal deletion and 26 PWS patients with paternal deletion on chr15q11-q13 by using an innovative multiplex-fluorescent-labeled short tandem repeats (STRs) assay based on linkage analysis, and validated by the methylation-specific PCR and array comparative genomic hybridization techniques. More interesting, one of these PWS patients was confirmed as maternal uniparental isodisomy by the STR linkage analysis. The phenotypic and genotypic characteristics of these individuals were also presented. Our results indicate that the new linkage analysis is much faster and easier for large-scale screening deletion and uniparental disomy, thus providing a valuable method for early diagnosis of PWS/AS patients, which is critical for genetic diagnosis, management and improvement of prognosis. PMID:26841067

  10. Clinical Application of an Innovative Multiplex-Fluorescent-Labeled STRs Assay for Prader-Willi Syndrome and Angelman Syndrome

    PubMed Central

    Feng, Bing; Yang, Yali; Zhang, Haiyan; Dong, Rui; Liu, Yi; Gai, Zhongtao

    2016-01-01

    Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are two clinically distinct neurodevelopmental disorders caused by absence of paternally or maternally expressed imprinted genes on chr15q11.2-q13.3. Three mechanisms are known to be involved in the pathogenesis: microdeletions, uniparental disomy (UPD) and imprinting defects. Both disorders are difficult to be definitely diagnosed at early age if no available molecular cytogenetic tests. In this study, we identified 5 AS patients with the maternal deletion and 26 PWS patients with paternal deletion on chr15q11-q13 by using an innovative multiplex-fluorescent-labeled short tandem repeats (STRs) assay based on linkage analysis, and validated by the methylation-specific PCR and array comparative genomic hybridization techniques. More interesting, one of these PWS patients was confirmed as maternal uniparental isodisomy by the STR linkage analysis. The phenotypic and genotypic characteristics of these individuals were also presented. Our results indicate that the new linkage analysis is much faster and easier for large-scale screening deletion and uniparental disomy, thus providing a valuable method for early diagnosis of PWS/AS patients, which is critical for genetic diagnosis, management and improvement of prognosis. PMID:26841067

  11. Tunable fluorescence lifetime of Eu-PMMA films with plasmonic nanostructures for multiplexing.

    PubMed

    Zhang, Jun; Song, Feng; Lin, Shangxin; Liu, Shujing; Liu, Yanling

    2016-04-18

    A method to tune fluorescence lifetime of Eu-PMMA films is proposed, which consists of self-assembled gold nanorods on glass substrate covered by Eu-PMMA shell. The fluorescence lifetime is tunable in a wide range, and depends on aspect ratio and mutual distance of gold nanorods. In a single red color emission channel, more than six distinct fluorescence lifetime populations ranging from 356 to 513 μs are obtained. Through theoretical calculation, we attribute tunable fluorescence lifetime to the change of radiative and nonradiative decay rate and density of photon states. In addition, we use these as-prepared Eu-PMMA films for security data storage to demonstrate optical multiplexing applications. The optical multiplexing experiments show an interesting pseudo-information "8" and conceal the real messages "2" and "6". PMID:27137261

  12. 4D phase-space multiplexing for fluorescent microscopy

    NASA Astrophysics Data System (ADS)

    Liu, Hsiou-Yuan; Zhong, Jingshan; Waller, Laura

    2016-03-01

    Phase-space measurements enable characterization of second-order spatial coherence properties and can be used for digital aberration removal or 3D position reconstruction. Previous methods use a scanning aperture to measure the phase space spectrogram, which is slow and light inefficient, while also attenuating information about higher-order correlations. We demonstrate a significant improvement of speed and light throughput by incorporating multiplexing techniques into our phase-space imaging system. The scheme implements 2D coded aperture patterning in the Fourier (pupil) plane of a microscope using a Spatial Light Modulator (SLM), while capturing multiple intensity images in real space. We compare various multiplexing schemes to scanning apertures and show that our phase-space reconstructions are accurate for experimental data with biological samples containing many 3D fluorophores.

  13. Erratum: Colorectal Cancer Cell Surface Protein Profiling Using an Antibody Microarray and Fluorescence Multiplexing.

    PubMed

    2015-01-01

    The author's email has been corrected in the publication of Colorectal Cancer Cell Surface Protein Profiling Using an Antibody Microarray and Fluorescence Multiplexing. There was an error with the author, Jerry Zhou's, email. The author's email has been updated to: j.zhou@uws.edu.au from: jzho7551@mail.usyd.edu.au. PMID:26167960

  14. Genome-wide linkage scan of quantitative traits representing symptom dimensions in multiplex schizophrenia families.

    PubMed

    Ryu, Seunghyong; Won, Hong-Hee; Oh, Sohee; Kim, Jong-Won; Park, Taesung; Cho, Eun-Young; Cho, Youngah; Park, Dong Yeon; Lee, Yu-Sang; Kwon, Jun Soo; Hong, Kyung Sue

    2013-12-30

    Symptom dimensions of schizophrenia are likely to be the intermediate phenotypes under the control of disease-susceptibility genes, or separate traits related to disease-modifier genes. This study aimed to identify chromosomal loci linked to symptom dimensions of schizophrenia through genome-wide quantitative trait locus (QTL) linkage analysis. The study subjects consisted of 56 families with 183 members including 123 affected individuals. Symptom evaluations were performed on lifetime basis. Through principal component factor analysis, eight quantitative phenotypes representing symptom dimensions were identified. Genotyping was done for 6008 SNP markers, and genome-wide QTL linkage analysis was performed. No symptom dimension showed a significant linkage attaining genome-wide empirical thresholds. We observed seven regions yielding linkage signals attaining genome-wide empirical thresholds for suggestive linkage (NPL Z score = 2.78-3.49); chromosome 15q26.1 for 'non-paranoid delusion factor', 2p24.3 and 7q31.1 for 'prodromal impairment factor', 1q32.1, 9p21.3, and 9q31.2 for 'negative symptom factor', and 10p13 for 'disorganization factor'. Among these loci, chromosome 2p24.3 and 1q32.1 overlap with susceptibility loci of schizophrenia identified in our previous linkage studies. This study suggests the existence of genetic loci related to various clinical features of schizophrenia. Further genetic analyses for these dimensional phenotypes are warranted. PMID:24035701

  15. Multiplexed Spectral Imaging of 120 Different Fluorescent Labels

    PubMed Central

    Valm, Alex M.; Oldenbourg, Rudolf; Borisy, Gary G.

    2016-01-01

    The number of fluorescent labels that can unambiguously be distinguished in a single image when acquired through band pass filters is severely limited by the spectral overlap of available fluorophores. The recent development of spectral microscopy and the application of linear unmixing algorithms to spectrally recorded image data have allowed simultaneous imaging of fluorophores with highly overlapping spectra. However, the number of distinguishable fluorophores is still limited by the unavoidable decrease in signal to noise ratio when fluorescence signals are fractionated over multiple wavelength bins. Here we present a spectral image analysis algorithm to greatly expand the number of distinguishable objects labeled with binary combinations of fluorophores. Our algorithm utilizes a priori knowledge about labeled specimens and imposes a binary label constraint on the unmixing solution. We have applied our labeling and analysis strategy to identify microbes labeled by fluorescence in situ hybridization and here demonstrate the ability to distinguish 120 differently labeled microbes in a single image. PMID:27391327

  16. Exploiting fluorescence for multiplex immunoassays on protein microarrays

    NASA Astrophysics Data System (ADS)

    Herbáth, Melinda; Papp, Krisztián; Balogh, Andrea; Matkó, János; Prechl, József

    2014-09-01

    Protein microarray technology is becoming the method of choice for identifying protein interaction partners, detecting specific proteins, carbohydrates and lipids, or for characterizing protein interactions and serum antibodies in a massively parallel manner. Availability of the well-established instrumentation of DNA arrays and development of new fluorescent detection instruments promoted the spread of this technique. Fluorescent detection has the advantage of high sensitivity, specificity, simplicity and wide dynamic range required by most measurements. Fluorescence through specifically designed probes and an increasing variety of detection modes offers an excellent tool for such microarray platforms. Measuring for example the level of antibodies, their isotypes and/or antigen specificity simultaneously can offer more complex and comprehensive information about the investigated biological phenomenon, especially if we take into consideration that hundreds of samples can be measured in a single assay. Not only body fluids, but also cell lysates, extracted cellular components, and intact living cells can be analyzed on protein arrays for monitoring functional responses to printed samples on the surface. As a rapidly evolving area, protein microarray technology offers a great bulk of information and new depth of knowledge. These are the features that endow protein arrays with wide applicability and robust sample analyzing capability. On the whole, protein arrays are emerging new tools not just in proteomics, but glycomics, lipidomics, and are also important for immunological research. In this review we attempt to summarize the technical aspects of planar fluorescent microarray technology along with the description of its main immunological applications.

  17. Genome-wide multipoint linkage analyses of multiplex schizophrenia pedigrees from the oceanic nation of Palau.

    PubMed

    Devlin, B; Bacanu, S-A; Roeder, K; Reimherr, F; Wender, P; Galke, B; Novasad, D; Chu, A; TCuenco, K; Tiobek, S; Otto, C; Byerley, W

    2002-01-01

    The oceanic nation of Palau has been geographically and culturally isolated over most of its 2000 year history. As part of a study of the genetic basis of schizophrenia in Palau, we genotyped five large, multigenerational schizophrenia pedigrees using markers every 10 cM (CHLC/Weber screening set 6). The number of affected/unaffected individuals genotyped per family ranged from 11/21 to 5/5. Thus the pedigrees varied in their information for linkage, but each was capable of producing a substantial LOD score. We fitted a simple dominant and recessive model to these data using multipoint linkage analysis implemented by Simwalk2. Predictably, the most informative pedigrees produced the best linkage results. After genotyping additional markers in the region, one pedigree produced a LOD = 3.4 (5q distal) under the dominant model. Seven of nine schizophrenics in the pedigree, mostly 3rd-4th degree relatives, share a 15-cM, 7-marker haplotype. For a different pedigree, another promising signal occurred on distal 3q, LOD = 2.6, for the recessive model. For two other pedigrees, the best LODs were modest, slightly better than 2.0 on 5q and 9p, while the fifth pedigree produced no noteworthy linkage signal. Similar to the results for other populations, our results suggest there are multiple genes conferring liability to schizophrenia even in the small population of Palau (roughly 21,000 individuals) in remote Oceania. PMID:12192612

  18. The Statistical Value of Raw Fluorescence Signal in Luminex xMAP Based Multiplex Immunoassays

    PubMed Central

    Breen, Edmond J.; Tan, Woei; Khan, Alamgir

    2016-01-01

    Tissue samples (plasma, saliva, serum or urine) from 169 patients classified as either normal or having one of seven possible diseases are analysed across three 96-well plates for the presences of 37 analytes using cytokine inflammation multiplexed immunoassay panels. Censoring for concentration data caused problems for analysis of the low abundant analytes. Using fluorescence analysis over concentration based analysis allowed analysis of these low abundant analytes. Mixed-effects analysis on the resulting fluorescence and concentration responses reveals a combination of censoring and mapping the fluorescence responses to concentration values, through a 5PL curve, changed observed analyte concentrations. Simulation verifies this, by showing a dependence on the mean florescence response and its distribution on the observed analyte concentration levels. Differences from normality, in the fluorescence responses, can lead to differences in concentration estimates and unreliable probabilities for treatment effects. It is seen that when fluorescence responses are normally distributed, probabilities of treatment effects for fluorescence based t-tests has greater statistical power than the same probabilities from concentration based t-tests. We add evidence that the fluorescence response, unlike concentration values, doesn’t require censoring and we show with respect to differential analysis on the fluorescence responses that background correction is not required. PMID:27243383

  19. SERS-fluorescence joint spectral encoded magnetic nanoprobes for multiplex cancer cell separation.

    PubMed

    Wang, Zhuyuan; Zong, Shenfei; Chen, Hui; Wang, Chunlei; Xu, Shuhong; Cui, Yiping

    2014-11-01

    A new kind of cancer cell separation method is demonstrated, using surface-enhanced Raman scattering (SERS) and fluorescence dual-encoded magnetic nanoprobes. The designed nanoprobes can realize SERS-fluorescence joint spectral encoding (SFJSE) and greatly improve the multiplexing ability. The nanoprobes have four main components, that is, the magnetic core, SERS generator, fluorescent agent, and targeting antibody. These components are assembled with a multi-layered structure to form the nanoprobes. Specifically, silica-coated magnetic nanobeads (MBs) are used as the inner core. Au core-Ag shell nanorods (Au@Ag NRs) are employed as the SERS generators and attached on the silica-coated MBs. After burying these Au@Ag NRs with another silica layer, CdTe quantum dots (QDs), that is, the fluorescent agent, are anchored onto the silica layer. Finally, antibodies are covalently linked to CdTe QDs. SFJSE is fulfilled by using different Raman molecules and QDs with different emission wavelengths. By utilizing four human cancer cell lines and one normal cell line as the model cells, the nanoprobes can specifically and simultaneously separate target cancer cells from the normal ones. This SFJSE-based method greatly facilitates the multiplex, rapid, and accurate cancer cell separation, and has a prosperous potential in high-throughput analysis and cancer diagnosis. PMID:24862088

  20. Fabrication of SERS-fluorescence dual modal nanoprobes and application to multiplex cancer cell imaging

    NASA Astrophysics Data System (ADS)

    Lee, Sangyeop; Chon, Hyangah; Yoon, Soo-Young; Lee, Eun Kyu; Chang, Soo-Ik; Lim, Dong Woo; Choo, Jaebum

    2011-12-01

    We report a highly sensitive optical imaging technology using surface-enhanced Raman scattering (SERS)-fluorescence dual modal nanoprobes (DMNPs). Fluorescence microscopy is a well-known imaging technique that shows specific protein distributions within cells. However, most currently available fluorescent organic dyes have relatively weak emission intensities and are rapidly photo-bleached. Thus more sensitive and stable probes are needed. In this work we develop DMNPs, which can be used for both SERS and fluorescence detection. SERS detection is a powerful technique that allows ultrasensitive chemical or biochemical analysis through unlimited multiplexing and single molecule sensitivity. Combining advantages of fluorescence and SERS allows these dual modal nanostructures to be used as powerful probes for novel biomedical imaging. In this work, the fabrication and characterization of the SERS-fluorescence DMNPs and application to biological imaging were investigated using markers CD24 and CD44, which are co-expressed in MDA-MB-231 breast cancer cells, as a model system. SERS imaging with DMNPs was found to be a powerful tool to determine the co-localization of CD24 and CD44 in the cell.We report a highly sensitive optical imaging technology using surface-enhanced Raman scattering (SERS)-fluorescence dual modal nanoprobes (DMNPs). Fluorescence microscopy is a well-known imaging technique that shows specific protein distributions within cells. However, most currently available fluorescent organic dyes have relatively weak emission intensities and are rapidly photo-bleached. Thus more sensitive and stable probes are needed. In this work we develop DMNPs, which can be used for both SERS and fluorescence detection. SERS detection is a powerful technique that allows ultrasensitive chemical or biochemical analysis through unlimited multiplexing and single molecule sensitivity. Combining advantages of fluorescence and SERS allows these dual modal nanostructures to be used

  1. Signal reduction in fluorescence imaging using radio frequency-multiplexed excitation by compressed sensing

    NASA Astrophysics Data System (ADS)

    Chan, Antony C. S.; Lam, Edmund Y.; Tsia, Kevin K.

    2014-11-01

    Fluorescence imaging using radio frequency-multiplexed excitation (FIRE) has emerged to enable an order-of-magnitude higher frame rate than the current technologies. Similar to all high-speed realtime imaging modalities, FIRE inherently generates massive image data continuously. While this technology entails high-throughput data sampling, processing, and storage in real-time, strategies in data compression on the fly is also beneficial. We here report that it is feasible to exploit the radio frequency-multiplexed excitation scheme in FIRE for implementing compressed sensing (CS) without any modification of the FIRE system. We numerically demonstrate that CS-FIRE can reduce the effective data rate by 95% without severe degradation of image quality.

  2. Multiplexed miRNA Fluorescence In Situ Hybridization for Formalin-Fixed Paraffin-Embedded Tissues

    PubMed Central

    Renwick, Neil; Cekan, Pavol; Bognanni, Claudia; Tuschl, Thomas

    2015-01-01

    Multiplexed miRNA fluorescence in situ hybridization (miRNA FISH) is an advanced method for visualizing differentially expressed miRNAs, together with other reference RNAs, in archival tissues. Some miRNAs are excellent disease biomarkers due to their abundance and cell-type specificity. However, these short RNA molecules are difficult to visualize due to loss by diffusion, probe mishybridization, and signal detection and signal amplification issues. Here, we describe a reliable and adjustable method for visualizing and normalizing miRNA signals in formalin-fixed paraffin-embedded (FFPE) tissue sections. PMID:25218385

  3. Rapid detection of mitochondrial sequence polymorphisms using multiplex solid-phase fluorescent minisequencing

    SciTech Connect

    Tully, G.; Sullivan, K.M.; Nixon, P.

    1996-05-15

    This work describes a novel method, multiplex solidphase fluorescent minisequencing, for the simultaneous detection of several point mutations and/or small deletions and insertions. The method is applied to the analysis of mitochondrial DNA polymorphisms for the purposes of individual identification. A database of 152 British Caucasians and 103 British Afro-Caribbeans has been constructed, and the probability of a chance match between two unrelated individuals is calculated as 0.054 for Caucasians and 0.026 for Afro-Caribbeans. 36 refs., 4 figs., 2 tabs.

  4. Linkage analysis of chromosome 22q12-13 in a United Kingdom/Icelandic sample of 23 multiplex schizophrenia families

    SciTech Connect

    Kalsi, G.; Read, T.; Butler, R.

    1995-08-14

    A possible linkage to a genetic subtype of schizophrenia and related disorders has been reported on the long arm of chromosome 22 at q12-13. However formal statistical tests in a combined sample could not reject homogeneity and prove that there was linked subgroup of families. We have studied 23 schizophrenia pedigrees to test whether some multiplex schizophrenia families may be linked to the microsatellite markers D22S274 and D22S283 which span the 22q12-13 region. Two point followed by multipoint lod and non-parametric linkage analyses under the assumption of heterogeneity provided no evidence for linkage over the relevant region. 16 refs., 4 tabs.

  5. Fluorescence of Dendrons based on Donors and Accepter with Different Linkages

    NASA Astrophysics Data System (ADS)

    Park, J. H.; Wu, Y.; Modarelli, D. A.; Parquette, J. R.; Epstein, A. J.

    2007-03-01

    Earlier indirect studies utilizing wavelength and bias spectra of photocurrent in simple photovoltaic cells demonstrated charge transfer (CT) in 1st generation dendritic macromolecules prepared using two different donor (tetraphenylporphyrin) groups bound to an accepter (naphthalenediimide) group. We report here fluorescence for solid-state films and solutions of these donor and dendrons. Using 460nm excitation, fluorescence (660nm, 715nm) in solution samples can be observed for both donor and dendron but fluorescence in the solid state can be observable only in donor sample due to fluorescence quenching within the dendron. This demonstrates intermolecular CT from donor to accepter. Fluorescence lifetime measurements (460nm 1.5nsec FWHM pulse excitation) of donor and dendron solutions show that it depends on length of the linkage between donor and accepter. This shows a direct relaxation path from donor to accepter (intramolecular CT). The separation of the exciton to separate electron and on the donor and acceptor portions of the dendron would open the potential for its use in photovoltaic application. Supported in part by DOE #DE-FG02-01ER45931

  6. Wide-Range Tunable Fluorescence Lifetime and Ultrabright Luminescence of Eu-Grafted Plasmonic Core-Shell Nanoparticles for Multiplexing.

    PubMed

    Zhang, Jun; Song, Feng; He, Zhubing; Liu, Yanling; Chen, Zhanyao; Lin, Shangxin; Huang, Ling; Huang, Wei

    2016-01-20

    Wide-range, well-separated, and tunable lifetime nanocomposites with ultrabright fluorescence are highly desirable for applications in optical multiplexing such as multiplexed biological detection, data storage, and security printing. Here, a synthesis of tunable fluorescence lifetime nanocomposites is reported featuring europium chelate grafted onto the surface of plasmonic core-shell nanoparticles, and systematically investigated their optical performance. In a single red color emission channel, more than 12 distinct fluorescence lifetime populations with high fluorescence efficiency (up to 73%) are reported. The fluorescence lifetime of Eu-grafted core-shell nanoparticles exhibits a wider tunable range, possesses larger lifetime interval and is more sensitive to separation distance than that of ordinary Eu-doping core-shell type. These superior performances are attributed to the unique nanostructure of Eu-grafed type. In addition, these as-prepared nanocomposites are used for security printing to demonstrate optical multiplexing applications. The optical multiplexing experiments show an interesting pseudo-information "a rabbit in a well" and conceal the real message "NKU." PMID:26618616

  7. Micro fluorescence in situ hybridization (μFISH) for spatially multiplexed analysis of a cell monolayer.

    PubMed

    Huber, D; Autebert, J; Kaigala, G V

    2016-04-01

    We here present a micrometer-scale implementation of fluorescence in situ hybridization that we term μFISH. This μFISH implementation makes use of a non-contact scanning probe technology, namely, a microfluidic probe (MFP) that hydrodynamically shapes nanoliter volumes of liquid on a surface with micrometer resolution. By confining FISH probes at the tip of this microfabricated scanning probe, we locally exposed approximately 1000 selected MCF-7 cells of a monolayer to perform incubation of probes - the rate-limiting step in conventional FISH. This method is compatible with the standard workflow of conventional FISH, allows re-budgeting of the sample for various tests, and results in a ~ 15-fold reduction in probe consumption. The continuous flow of probes and shaping liquid on these selected cells resulted in a 120-fold reduction of the hybridization time compared with the standard protocol (3 min vs. 6 h) and efficient rinsing, thereby shortening the total FISH assay time for centromeric probes. We further demonstrated spatially multiplexed μFISH, enabling the use of spectrally equivalent probes for detailed and real-time analysis of a cell monolayer, which paves the way towards rapid and automated multiplexed FISH on standard cytological supports. PMID:27138995

  8. Fluorescent silver nanocluster DNA probes for multiplexed detection using microfluidic capillary electrophoresis.

    PubMed

    Del Bonis-O'Donnell, Jackson Travis; Fygenson, Deborah K; Pennathur, Sumita

    2015-03-01

    DNA-stabilized fluorescent silver nanoclusters (AgNC DNA) are a new class of fluorophore that are formed by sequence specific interactions between silver and single-stranded DNA. By incorporating both target-binding and fluorescent-reporting sequences into a single synthetic DNA oligomer, AgNC DNA probes eliminate the need to conjugate dye or quencher molecules. In this study, we modify a AgNC DNA probe to demonstrate single-color multiplexed detection of DNA targets. We show that appending different lengths of poly-dT to the probe sequences tunes the electrophoretic mobility of AgNC DNA probes without affecting their fluorescence spectra. We use this to introduce a set of AgNC DNA probes selective for Hepatitis A, B and C target sequences that can be processed together in a simple, single-step protocol and distinguished with a resolution of 3.47 and signal to noise ratio of 17.23 in under 10 seconds by microfluidic capillary electrophoresis. PMID:25601044

  9. Multiplexed fluorescence tomography with spectral and temporal data: demixing with intrinsic regularization.

    PubMed

    Pera, Vivian; Brooks, Dana H; Niedre, Mark

    2016-01-01

    We consider the joint use of spectral and temporal data for multiplexed fluorescence molecular tomography to enable high-throughput imaging of multiple fluorescent targets in bulk tissue. This is a challenging problem due to the narrow near-infrared diagnostic window and relatively broad emission spectra of common fluorophores, and the distortion ("redshift") that the fluorophore signals undergo as they propagate through tissue. We show through a Cramér-Rao lower bound analysis that demixing with spectral-temporal data could result in an order of magnitude improvement in performance over either modality alone. To cope with the resulting large data set, we propose a novel two-stage algorithm that decouples the demixing and tomographic reconstruction operations. In this work we concentrate on the demixing stage. We introduce an approach which incorporates ideas from sparse subspace clustering and compressed sensing and does not require a regularization parameter. We report on simulations in which we simultaneously demixed four fluorophores with closely overlapping spectral and temporal profiles in a 25 mm diameter cross-sectional area with a root-mean-square error of less than 3% per fluorophore, as well as on studies of sensitivity of the method to model mismatch. PMID:26819822

  10. Identification of olive pollen allergens using a fluorescence-based 2D multiplex method.

    PubMed

    Zienkiewicz, Krzysztof; Alché, Juan de Dios; Zienkiewicz, Agnieszka; Tormo, Alejandro; Castro, Antonio Jesús

    2015-04-01

    Olive (Olea europaea L.) pollen is a major health concern in the Mediterranean countries and some olive growing regions in America and Australia. The molecular variability of pollen allergens constitutes a handicap for commercial extract standardization, which is the base of current diagnosis and vaccination procedures. In this paper, we report a time-saving and plant material saving multiplex detection method for the rapid and simultaneous analysis of Ole e 1, Ole e 2, and Ole e 5 allergen polymorphism on a single blot. This method combines high-resolution 2DE techniques with high-sensitive fluorescence-based detection methods. Using this strategy, we were capable to identify a higher number of allergen forms compared with classical 1D approach. The use of fluorescent probes and the increased resolution of 2D blots avoided overlapping effects, and allow estimating the amount of individual allergen forms. In addition, the pattern and identity of the IgE-reactive proteins of either a population or individual patients allergic to olive pollen was also effortlessly determined in a single additional step. This flexible method might be extended to a higher number of olive allergens and cultivars, and is also applicable to other allergogenic plant species and sources. PMID:25640071

  11. Two-Beam multiplexed laser-induced fluorescence measurements of an argon arcjet plume

    NASA Technical Reports Server (NTRS)

    Ruyten, Wilhelmus M.; Keefer, Dennis

    1993-01-01

    We describe a multiplexed, laser-induced fluorescence (LIF) technique with which radial and axial profiles of vector velocities of excited propellant species were obtained in the exhaust plume from a 300-W argon arcjet. Although the arcjet is a prototype, and although argon is not an interesting propellant from a propulsion perspective, the technique clearly demonstrates how a narrowband, frequency-stabilized ring-dye laser can be used to obtain simultaneous measurements of two velocity components in an arcjet plume and how a third signal from an optogalvanic cell can be used as a frequency reference. We also show that much information on the flow can be obtained by analyzing the Doppler widths and fluorescence intensities of the LIF data. Specifically, the data identify a boundary layer in the radial direction of the plume and a shock in the downstream region of the flow. Also, some flow anisotropy is observed, consistent with the assumption that the magnitude of the mean flow velocity fluctuates. The peak velocity on centerline remains roughly constant at 3 km/s throughout the expansion.

  12. Multiplexed fluorescence tomography with spectral and temporal data: demixing with intrinsic regularization

    PubMed Central

    Pera, Vivian; Brooks, Dana H.; Niedre, Mark

    2015-01-01

    We consider the joint use of spectral and temporal data for multiplexed fluorescence molecular tomography to enable high-throughput imaging of multiple fluorescent targets in bulk tissue. This is a challenging problem due to the narrow near-infrared diagnostic window and relatively broad emission spectra of common fluorophores, and the distortion (“redshift”) that the fluorophore signals undergo as they propagate through tissue. We show through a Cramér-Rao lower bound analysis that demixing with spectral-temporal data could result in an order of magnitude improvement in performance over either modality alone. To cope with the resulting large data set, we propose a novel two-stage algorithm that decouples the demixing and tomographic reconstruction operations. In this work we concentrate on the demixing stage. We introduce an approach which incorporates ideas from sparse subspace clustering and compressed sensing and does not require a regularization parameter. We report on simulations in which we simultaneously demixed four fluorophores with closely overlapping spectral and temporal profiles in a 25 mm diameter cross-sectional area with a root-mean-square error of less than 3% per fluorophore, as well as on studies of sensitivity of the method to model mismatch. PMID:26819822

  13. First demonstration of multiplexed X-ray fluorescence computed tomography (XFCT) imaging.

    PubMed

    Kuang, Yu; Pratx, Guillem; Bazalova, Magdalena; Meng, Bowen; Qian, Jianguo; Xing, Lei

    2013-02-01

    Simultaneous imaging of multiple probes or biomarkers represents a critical step toward high specificity molecular imaging. In this work, we propose to utilize the element-specific nature of the X-ray fluorescence (XRF) signal for imaging multiple elements simultaneously (multiplexing) using XRF computed tomography (XFCT). A 5-mm-diameter pencil beam produced by a polychromatic X-ray source (150 kV, 20 mA) was used to stimulate emission of XRF photons from 2% (weight/volume) gold (Au), gadolinium (Gd), and barium (Ba) embedded within a water phantom. The phantom was translated and rotated relative to the stationary pencil beam in a first-generation CT geometry. The X-ray energy spectrum was collected for 18 s at each position using a cadmium telluride detector. The spectra were then used to isolate the K shell XRF peak and to generate sinograms for the three elements of interest. The distribution and concentration of the three elements were reconstructed with the iterative maximum likelihood expectation maximization algorithm. The linearity between the XFCT intensity and the concentrations of elements of interest was investigated. We found that measured XRF spectra showed sharp peaks characteristic of Au, Gd, and Ba. The narrow full-width at half-maximum (FWHM) of the peaks strongly supports the potential of XFCT for multiplexed imaging of Au, Gd, and Ba ( FWHM(Au,Kα1) = 0.619 keV, FWHM(Au,Kα2)=1.371 keV , FWHM(Gd,Kα)=1.297 keV, FWHM(Gd,Kβ)=0.974 keV , FWHM(Ba,Kα)=0.852 keV, and FWHM(Ba,Kβ)=0.594 keV ). The distribution of Au, Gd, and Ba in the water phantom was clearly identifiable in the reconstructed XRF images. Our results showed linear relationships between the XRF intensity of each tested element and their concentrations ( R(2)(Au)=0.944 , R(Gd)(2)=0.986, and R(Ba)(2)=0.999), suggesting that XFCT is capable of quantitative imaging. Finally, a transmission CT image was obtained to show the potential of the approach for providing attenuation correction

  14. Erratum to: Automated Sample Preparation Method for Suspension Arrays using Renewable Surface Separations with Multiplexed Flow Cytometry Fluorescence Detection

    SciTech Connect

    Grate, Jay W.; Bruckner-Lea, Cindy J.; Jarrell, Ann E.; Chandler, Darrell P.

    2003-04-10

    In this paper we describe a new method of automated sample preparation for multiplexed biological analysis systems that use flow cytometry fluorescence detection. In this approach, color-encoded microspheres derivatized to capture particular biomolecules are temporarily trapped in a renewable surface separation column to enable perfusion with sample and reagents prior to delivery to the detector. This method provides for separation of the biomolecules of interest from other sample matrix components as well as from labeling solutions.

  15. Multiplexed visualization of dynamic signaling networks using genetically encoded fluorescent protein-based biosensors

    PubMed Central

    Depry, Charlene; Mehta, Sohum; Zhang, Jin

    2012-01-01

    Cells rely on a complex, interconnected network of signaling pathways to sense and interpret changes in their extracellular environment. The development of genetically encoded fluorescent protein (FP)-based biosensors has made it possible for researchers to directly observe and characterize the spatiotemporal dynamics of these intracellular signaling pathways in living cells. However, detailed information regarding the precise temporal and spatial relationships between intersecting pathways is often lost when individual signaling events are monitored in isolation. As the development of biosensor technology continues to advance, it is becoming increasingly feasible to image multiple FP-based biosensors concurrently, permitting greater insights into the intricate coordination of intracellular signaling networks by enabling parallel monitoring of distinct signaling events within the same cell. In this review, we discuss several strategies for multiplexed imaging of FP-based biosensors, while also underscoring some of the challenges associated with these techniques and highlighting additional avenues that could lead to further improvements in parallel monitoring of intracellular signaling events. PMID:23138230

  16. Multiplex Fluorescent Immunoassay for Detection of Mice Infected with Lactate Dehydrogenase Elevating Virus

    PubMed Central

    Adams, Veronica; Myles, Matthew H

    2013-01-01

    Commercially available diagnostic tools for the detection of lactate dehydrogenase elevating virus (LDV) infection have been restricted to measurement of serum lactate dehydrogenase (LDH) activity levels and detection of the viral genome by RT-PCR assays. Serologic diagnosis of LDV infection has not been widely adopted due to the belief that the formation of antigen–antibody complexes and B-cell polyclonal activation may confound interpretation of results. In the current study, we inoculated BALB/c, C57BL/6, and Swiss Webster mice with LDV to compare the diagnostic reliability of a commercially available multiplex fluorescent immunoassay for the detection of antiLDV antibodies with that of the LDH enzyme assay. The serologic assay was vastly more sensitive and specific than was the LDH enzyme assay. Moreover, the serologic assay detected antiviral antibodies throughout the 3-mo time course of this study. These results suggest that antigen–antibody complex formation and polyclonal B-cell activation had little effect on assay performance. PMID:23849407

  17. In-situ fluorescent immunomagnetic multiplex detection of foodborne pathogens in very low numbers.

    PubMed

    Cho, Il-Hoon; Mauer, Lisa; Irudayaraj, Joseph

    2014-07-15

    Consumption of foods contaminated with pathogenic bacteria is a major public health concern. Foods contain microorganisms, the overwhelming majority of which are nonpathogenic, some are responsible for food spoilage, and some cause serious illness leading to death or a variety of diseases in humans. The key challenge in food safety is to rapidly screen foods to determine the presence of pathogens so that appropriate intervention protocols can be pursued. A simple fluorometric immunological method in combination with a magnetic concentration step was developed for rapid detection of target bacteria with high sensitivity and specificity in less than 2h without enumeration. The method constitutes performing an in-situ immunoassay on a magnetic bead through the formation of a sandwich complex of the target bacteria and the probe (detection antibody-denatured BSA labelled with fluorophores) followed by the release of fluorophores by means of enzymatic digestion with proteinase K. The limit of detection (LOD) was <5 CFU/mL of the tested pathogens (Escherichia coli O157:H7, Salmonella typhimurium, and Listeria monocytogenes) in buffer. When the pathogens were inoculated in foods (spinach, chicken, and milk), the LOD was under 5 CFU/mL for E. coli O157:H7, S. typhimurium and L. monocytogenes. Furthermore, the method was highly specific in detecting the target pathogens in a multiplex format. The developed in-situ fluorescent immunomagnetic sensor approach offers distinct advantages because it is rapid, highly sensitive, and easy to use and could therefore be potentially used as a pathogen screening tool. PMID:24583684

  18. A universal multi-wavelength fluorescence polarization immunoassay for multiplexed detection of mycotoxins in maize.

    PubMed

    Li, Chenglong; Wen, Kai; Mi, Tiejun; Zhang, Xiya; Zhang, Huiyan; Zhang, Suxia; Shen, Jianzhong; Wang, Zhanhui

    2016-05-15

    Multi-analyte immunoassays have attracted increasing attention due to their short assay times, low sample consumption, and reduced detection costs per assay. In this work, we describe a homologous and high-throughput multi-wavelength fluorescence polarization immunoassay (MWFPIA) for the multiplexed detection of mycotoxins. Three typical Fusarium mycotoxins, deoxynivalenol (DON), T-2 toxin and fumonisin B1 (FB1), were labeled with different dyes. Tracers and specific monoclonal antibodies (mAbs) were employed in the MWFPIA to simultaneously detect the three mycotoxins. Under optimal conditions, the limits of detection using MWFPIA were 242.0 μg kg(-1) for DON, 17.8 μg kg(-1) for T-2 toxin and 331.5 μg kg(-1) for FB1, providing sufficient sensitivity to meet the action levels of these three contaminants in maize as set by the European Union. The use of a methanol/water (2:3, v/v) mixture for sample pretreatment allowed recoveries ranging from 76.5-106.3%, with coefficients of variation less than 21.7%. The total time of analysis, including sample preparation, was less than 30 min. Twenty naturally contaminated maize samples were tested using MWFPIA and HPLC-MS/MS, with correlation coefficients (R(2)) of 0.97 for DON and 0.99 for FB1. By changing the targets of interest, homologous MWFPIA, a method with high sensitivity, a simple procedure and a short analysis time, can easily be extended to other chemical contaminants. Thus, MWFPIA represents a versatile strategy for food safety analysis. PMID:26720917

  19. Multiplex fluorescence in situ hybridization (M-FISH) and confocal laser scanning microscopy (CLSM) to analyze multispecies oral biofilms.

    PubMed

    Karygianni, Lamprini; Hellwig, Elmar; Al-Ahmad, Ali

    2014-01-01

    Multiplex fluorescence in situ hybridization (M-FISH) constitutes a favorable microbiological method for the analysis of spatial distribution of highly variable phenotypes found in multispecies oral biofilms. The combined use of confocal laser scanning microscopy (CLSM) produces high-resolution three-dimensional (3D) images of individual bacteria in their natural environment. Here, we describe the application of M-FISH on early (Streptococcus spp., Actinomyces naeslundii) and late colonizers (Fusobacterium nucleatum, Veillonella spp.) of in situ-formed oral biofilms, the acquisition of CLSM images, as well as the qualitative and quantitative analysis of these digitally obtained and processed images. PMID:24664826

  20. Multiplexed detection of protein cancer markers on Au/Ag-barcoded nanorods using fluorescent-conjugated polymers.

    PubMed

    Zheng, Weiming; He, Lin

    2010-07-01

    Integration of fluorescent-conjugated polymers as detection moiety with metallic striped nanorods for multiplexed detection of clinically important cancer marker proteins in an immunoassay format was demonstrated in this report. Specifically, cationic conjugated polymers were introduced to protein complexes through electrostatic binding to negatively charged double-stranded DNA, which was tagged on detection antibodies prior to antigen recognition. The intense fluorescence emission of conjugated polymers resulted in highly sensitive detection of cancer marker proteins wherein an undiluted bovine serum sample as low as approximately 25 target molecules captured on each particle was detectable. Meanwhile, the use of polymer molecules as the detection probe did not obscure the optical pattern of underlying nanorods, i.e., the encoding capability of barcoded nanorods was preserved, which allowed simultaneous detection of three cancer marker proteins with good specificity. PMID:20496173

  1. Colorectal Cancer Cell Surface Protein Profiling Using an Antibody Microarray and Fluorescence Multiplexing

    PubMed Central

    Zhou, Jerry; Belov, Larissa; Solomon, Michael J.; Chan, Charles; Clarke, Stephen J.; Christopherson, Richard I.

    2011-01-01

    . Cells are captured only on antibodies for which they express the corresponding antigen. The cell density per dot, determined by optical scanning, reflects the proportion of cells expressing that antigen, the level of expression of the antigen and affinity of the antibody6. For CRC tissue or normal intestinal mucosa, optical scans reflect the immunophenotype of mixed populations of cells. Fluorescence multiplexing can then be used to profile selected sub-populations of cells of interest captured on the array. For example, Alexa 647-anti-epithelial cell adhesion molecule (EpCAM; CD326), is a pan-epithelial differentiation antigen that was used to detect CRC cells and also epithelial cells of normal intestinal mucosa, while Phycoerythrin-anti-CD3, was used to detect infiltrating T-cells7. The DotScan CRC microarray should be the prototype for a diagnostic alternative to the anatomically-based CRC staging system. PMID:21968569

  2. A multicolor time-resolved fluorescence aptasensor for the simultaneous detection of multiplex Staphylococcus aureus enterotoxins in the milk.

    PubMed

    Huang, Yukun; Zhang, Hui; Chen, Xiujuan; Wang, Xiaole; Duan, Nuo; Wu, Shijia; Xu, Baocai; Wang, Zhouping

    2015-12-15

    Food safety is one of the most important public health issues worldwide. Foodborne illnesses caused by Staphylococcus aureus enterotoxins (SEs) commonly occur, affecting both developing and developed countries. In this study, multicolor lanthanide-doped time-resolved fluorescence nanoparticles labeled with aptamers were used as bioprobes, and graphene oxide (GO) was employed as a resonance energy acceptor. Based on the "turn down" strategy, the simultaneous detection of multiplex SEs was realized in a homogeneous solution. Under the optimal conditions, the developed method exhibited high sensitivity and selectivity to three serological types of enterotoxins, including type A, B, C1, with limits of detection below 1 ng mL(-1). The application of this bioassay in milk analysis with no sample dilution was also investigated, and the results of recovery rates covered from 92.76% to 114.58%, revealing that the developed method was accurate. Therefore, this detection aptasnesor can be a good candidate for multiplex analysis and screening with simple and effective operations. PMID:26141103

  3. Development and Validation of a Fluorescent Multiplexed Immunoassay for Measurement of Transgenic Proteins in Cotton (Gossypium hirsutum).

    PubMed

    Yeaman, Grant R; Paul, Sudakshina; Nahirna, Iryna; Wang, Yongcheng; Deffenbaugh, Andrew E; Liu, Zi Lucy; Glenn, Kevin C

    2016-06-22

    In order to provide farmers with better and more customized alternatives to improve yields, combining multiple genetically modified (GM) traits into a single product (called stacked trait crops) is becoming prevalent. Trait protein expression levels are used to characterize new GM products and establish exposure limits, two important components of safety assessment. Developing a multiplexed immunoassay capable of measuring all trait proteins in the same sample allows for higher sample throughput and savings in both time and expense. Fluorescent (bead-based) multiplexed immunoassays (FMI) have gained wide acceptance in mammalian research and in clinical applications. In order to facilitate the measurement of stacked GM traits, we have developed and validated an FMI assay that can measure five different proteins (β-glucuronidase, neomycin phosphotransferase II, Cry1Ac, Cry2Ab2, and CP4 5-enolpyruvyl-shikimate-3-phosphate synthase) present in cotton leaf from a stacked trait product. Expression levels of the five proteins determined by FMI in cotton leaf tissues have been evaluated relative to expression levels determined by enzyme-linked immunosorbent assays (ELISAs) of the individual proteins and shown to be comparable. The FMI met characterization requirements similar to those used for ELISA. Therefore, it is reasonable to conclude that FMI results are equivalent to those determined by conventional individual ELISAs to measure GM protein expression levels in stacked trait products but with significantly higher throughput, reduced time, and more efficient use of resources. PMID:27177195

  4. Evaluation of quantum dot-based concentric FRET configurations with a fluorescent dye and dark quencher for multiplexed bioanalyses

    NASA Astrophysics Data System (ADS)

    Conroy, Erin M.; Algar, W. Russ

    2014-03-01

    Semiconductor quantum dots (QDs) continue to emerge as a highly advantageous platform for bioanalysis. Their unique physical and optical properties are especially well suited for Förster resonance energy transfer (FRET)-based bioprobes. Concentric FRET configurations are a recent development in this area of research and are best described as QD bioconjugates where multiple energy transfer pathways have been assembled around the central QD. Concentric FRET configurations permit multiplexed bioanalysis using one type of QD vector, but require more sophisticated analyses than conventional FRET pairs. In this paper, we describe the design and characterization of a new concentric FRET configuration that assembles both a fluorescent dye, Alexa Fluor 555 or Alexa Fluor 647, and a dark quencher, QSY9, at different ratios around a central CdSeS/ZnS QD. It was found that the magnitudes of the total photoluminescence (PL) intensity and either the A555/QD or A647/QD PL ratio can be related to the number of QSY9 and A555 or A647 per QD. The trends in these parameters with changes in the number of each dye molecule per QD have both similarities and differences between configurations with A555 and A647. In each case, a system of equations can be defined to permit calculation of the number of each dye molecule per QD from PL measurements. Both of these dark quencher-based concentric FRET configurations are therefore good candidates for quantitative, multiplexed bioanalysis.

  5. Two-color widefield fluorescence microendoscopy enables multiplexed molecular imaging in the alveolar space of human lung tissue

    NASA Astrophysics Data System (ADS)

    Krstajić, Nikola; Akram, Ahsan R.; Choudhary, Tushar R.; McDonald, Neil; Tanner, Michael G.; Pedretti, Ettore; Dalgarno, Paul A.; Scholefield, Emma; Girkin, John M.; Moore, Anne; Bradley, Mark; Dhaliwal, Kevin

    2016-04-01

    We demonstrate a fast two-color widefield fluorescence microendoscopy system capable of simultaneously detecting several disease targets in intact human ex vivo lung tissue. We characterize the system for light throughput from the excitation light emitting diodes, fluorescence collection efficiency, and chromatic focal shifts. We demonstrate the effectiveness of the instrument by imaging bacteria (Pseudomonas aeruginosa) in ex vivo human lung tissue. We describe a mechanism of bacterial detection through the fiber bundle that uses blinking effects of bacteria as they move in front of the fiber core providing detection of objects smaller than the fiber core and cladding (˜3 μm). This effectively increases the measured spatial resolution of 4 μm. We show simultaneous imaging of neutrophils, monocytes, and fungus (Aspergillus fumigatus) in ex vivo human lung tissue. The instrument has 10 nM and 50 nM sensitivity for fluorescein and Cy5 solutions, respectively. Lung tissue autofluorescence remains visible at up to 200 fps camera acquisition rate. The optical system lends itself to clinical translation due to high-fluorescence sensitivity, simplicity, and the ability to multiplex several pathological molecular imaging targets simultaneously.

  6. Fluorescent Protein Nanowire-Mediated Protein Microarrays for Multiplexed and Highly Sensitive Pathogen Detection.

    PubMed

    Men, Dong; Zhou, Juan; Li, Wei; Leng, Yan; Chen, Xinwen; Tao, Shengce; Zhang, Xian-En

    2016-07-13

    Protein microarrays are powerful tools for high-throughput and simultaneous detection of different target molecules in complex biological samples. However, the sensitivity of conventional fluorescence-labeling protein detection methods is limited by the availability of signal molecules for binding to the target molecule. Here, we built a multifunctional fluorescent protein nanowire (FNw) by harnessing self-assembly of yeast amyloid protein. The FNw integrated a large number of fluorescent molecules, thereby enhancing the fluorescent signal output in target detection. The FNw was then combined with protein microarray technology to detect proteins derived from two pathogens, including influenza virus (hemagglutinin 1, HA1) and human immunodeficiency virus (p24 and gp120). The resulting detection sensitivity achieved a 100-fold improvement over a commercially available detection reagent. PMID:27315221

  7. Multiplex immunoassay using fluorescent-surface enhanced Raman spectroscopic dots for the detection of bronchioalveolar stem cells in murine lung.

    PubMed

    Woo, Min-Ah; Lee, Sang-Myung; Kim, Gunsung; Baek, JongHo; Noh, Mi Suk; Kim, Ji Eun; Park, Sung Jin; Minai-Tehrani, Arash; Park, Se-Chang; Seo, Yeong Tai; Kim, Yong-Kwon; Lee, Yoon-Sik; Jeong, Dae Hong; Cho, Myung-Haing

    2009-02-01

    Immunoassays using nanomaterials have been rapidly developed for the analysis of multiple biomolecules. Highly sensitive and biocompatible surface enhanced Raman spectroscopy-active nanomaterials have been used for biomolecule analysis by many research groups in order to overcome intrinsic problems of conventional immunoassays. We used fluorescent surface-enhanced Raman spectroscopic dots (F-SERS dots) to detect biomolecules in this study. The F-SERS dots are composed of silver nanoparticle-embedded silica nanospheres, organic Raman tagging materials, and fluorescent dyes. The F-SERS dots demonstrated highly sensitive, selective, and multifunctional characteristics for multiplex targeting, tracking, and imaging of cellular and molecular events in the living organism. We successfully applied F-SERS dots for the detection of three cellular proteins, including CD34, Sca-1, and SP-C. These proteins are simultaneously expressed in bronchioalveolar stem cells (BASCs) in the murine lung. We analyzed the relative expression ratios of each protein in BASCs since external standards were used to evaluate SERS intensity in tissue. Quantitative comparisons of multiple protein expression in tissue were first attempted using SERS-encoded nanoprobes. Our results suggested that immunoassays using F-SERS dots offered significant increases in sensitivity and selectivity. Such immunoassays may serve as the primary next-generation labeling technologies for the simultaneous analysis of multiple biomolecules. PMID:19117480

  8. One-step, multiplexed fluorescence detection of microRNAs based on duplex-specific nuclease signal amplification.

    PubMed

    Yin, Bin-Cheng; Liu, Yu-Qiang; Ye, Bang-Ce

    2012-03-21

    Traditional molecular beacons, widely applied for detection of nucleic acids, have an intrinsic limitation on sensitivity, as one target molecule converts only one beacon molecule to its fluorescent form. Herein, we take advantage of the duplex-specific nuclease (DSN) to create a new signal-amplifying mechanism, duplex-specific nuclease signal amplification (DSNSA), to increase the detection sensitivity of molecular beacons (Taqman probes). DSN nuclease is employed to recycle the process of target-assisted digestion of Taqman probes, thus, resulting in a significant fluorescence signal amplification through which one target molecule cleaves thousands of probe molecules. We further demonstrate the efficiency of this DSNSA strategy for rapid direct quantification of multiple miRNAs in biological samples. Our experimental results showed a quantitative measurement of sequence-specific miRNAs with the detection limit in the femtomolar range, nearly 5 orders of magnitude lower than that of conventional molecular beacons. This amplification strategy also demonstrated a high selectivity for discriminating differences between miRNA family members. Considering the superior sensitivity and specificity, as well as the multiplex and simple-to-implement features, this method promises a great potential of becoming a routine tool for simultaneously quantitative analysis of multiple miRNAs in tissues or cells, and supplies valuable information for biomedical research and clinical early diagnosis. PMID:22394262

  9. Multiplexed fluorescent microarray for human salivary protein analysis using polymer microspheres and fiber-optic bundles.

    PubMed

    Nie, Shuai; Benito-Peña, Elena; Zhang, Huaibin; Wu, Yue; Walt, David R

    2013-01-01

    Herein, we describe a protocol for simultaneously measuring six proteins in saliva using a fiber-optic microsphere-based antibody array. The immuno-array technology employed combines the advantages of microsphere-based suspension array fabrication with the use of fluorescence microscopy. As described in the video protocol, commercially available 4.5 μm polymer microspheres were encoded into seven different types, differentiated by the concentration of two fluorescent dyes physically trapped inside the microspheres. The encoded microspheres containing surface carboxyl groups were modified with monoclonal capture antibodies through EDC/NHS coupling chemistry. To assemble the protein microarray, the different types of encoded and functionalized microspheres were mixed and randomly deposited in 4.5 μm microwells, which were chemically etched at the proximal end of a fiber-optic bundle. The fiber-optic bundle was used as both a carrier and for imaging the microspheres. Once assembled, the microarray was used to capture proteins in the saliva supernatant collected from the clinic. The detection was based on a sandwich immunoassay using a mixture of biotinylated detection antibodies for different analytes with a streptavidin-conjugated fluorescent probe, R-phycoerythrin. The microarray was imaged by fluorescence microscopy in three different channels, two for microsphere registration and one for the assay signal. The fluorescence micrographs were then decoded and analyzed using a homemade algorithm in MATLAB. PMID:24145242

  10. Multiplexed biomarker detection using x-ray fluorescence of composition-encoded nanoparticles

    SciTech Connect

    Hossain, Mainul; Wang Chaoming; Su Ming

    2010-12-27

    Multiple DNA and protein biomarkers have been detected based on characteristic x-ray fluorescence of a panel of metal and alloy nanoparticles, which are modified with ligands of biomarkers to create a one-to-one correspondence and immobilized on ligand-modified substrates after forming complexes with target biomarkers in three-strand or sandwich configuration. By determining the presence and concentration of nanoparticles using x-ray fluorescence, the nature and amount of biomarkers can be detected with limits of 1 nM for DNA and 1 ng/ml for protein. By combining high penetrating ability of x-rays, this method allows quantitative imaging of multiple biomarkers.

  11. Protecting Quantum Dot Fluorescence from Quenching to Achieve a Reliable Automated Multiplex Fluorescence In Situ Hybridization Assay.

    PubMed

    Zhang, Wenjun; Hubbard, Antony; Pang, Lizhen; Parkinson, Leslie Baca; Brunhoeber, Patrick; Wang, Yixin; Tang, Lei

    2015-09-01

    Quantum dots (QD) are novel inorganic fluorochromes that are ultra-bright, photo-stable, and available in multiple, highly-resolvable colors. QDs represent an ideal detection material for in situ hybridization (ISH) because they may provide unprecedented resolution and strong signal intensities that are not attainable with traditional fluorophores. Unfortunately, lack of reliability has been an impediment to widespread adoption of QD-based fluorescence in situ hybridization (QD FISH) technology. By optimizing QD-to-target accessibility, we have developed a QD FISH staining procedure that dramatically improves the reliability of an automated ERG/PTEN QD FISH assay (91% 1st pass rate). Here, we report improvements to the assay that protects QD fluorescence from quenching due to trace amounts of heavy metals and minimizes QD background signals. When using this method, highly-consistent staining was observed with the ERG/PTEN QD FISH assay in prostate tissue. Successful staining of several other clinically-relevant genetic markers was also possible. We further demonstrated improved reliability for determining HER2 gene status in breast cancer, identifying anaplastic lymphoma kinase (ALK) gene break-apart in non-small cell lung cancer, and detecting human papillomavirus 16 (HPV16) in cervical intraepithelial neoplasia. The enhanced QD FISH assay allows for examining complicated genetic aberrances without use of enzymatic amplification. Our optimized methods now demonstrate reliability sufficient for QD FISH technology to be a diagnostic tool in a clinical setting. PMID:26485928

  12. Development and potential applications of microarrays based on fluorescent nanocrystal-encoded beads for multiplexed cancer diagnostics

    NASA Astrophysics Data System (ADS)

    Brazhnik, Kristina; Grinevich, Regina; Efimov, Anton E.; Nabiev, Igor; Sukhanova, Alyona

    2014-05-01

    Advanced multiplexed assays have recently become an indispensable tool for clinical diagnostics. These techniques provide simultaneous quantitative determination of multiple biomolecules in a single sample quickly and accurately. The development of multiplex suspension arrays is currently of particular interest for clinical applications. Optical encoding of microparticles is the most available and easy-to-use technique. This technology uses fluorophores incorporated into microbeads to obtain individual optical codes. Fluorophore-encoded beads can be rapidly analyzed using classical flow cytometry or microfluidic techniques. We have developed a new generation of highly sensitive and specific diagnostic systems for detection of cancer antigens in human serum samples based on microbeads encoded with fluorescent quantum dots (QDs). The designed suspension microarray system was validated for quantitative detection of (1) free and total prostate specific antigen (PSA) in the serum of patients with prostate cancer and (2) carcinoembryonic antigen (CEA) and cancer antigen 15-3 (CA 15-3) in the serum of patients with breast cancer. The serum samples from healthy donors were used as a control. The antigen detection is based on the formation of an immune complex of a specific capture antibody (Ab), a target antigen (Ag), and a detector Ab on the surface of the encoded particles. The capture Ab is bound to the polymer shell of microbeads via an adapter molecule, for example, protein A. Protein A binds a monoclonal Ab in a highly oriented manner due to specific interaction with the Fc-region of the Ab molecule. Each antigen can be recognized and detected due to a specific microbead population carrying the unique fluorescent code. 100 and 231 serum samples from patients with different stages of prostate cancer and breast cancer, respectively, and those from healthy donors were examined using the designed suspension system. The data were validated by comparing with the results of

  13. Silica-coated liposomes loaded with quantum dots as labels for multiplex fluorescent immunoassay.

    PubMed

    Beloglazova, N V; Goryacheva, O A; Speranskaya, E S; Aubert, T; Shmelin, P S; Kurbangaleev, V R; Goryacheva, I Yu; De Saeger, S

    2015-03-01

    This manuscript describes synthesis and followed application of silica-coated liposomes loaded with quantum dots as a perspective label for immunoaasay. The hollow spherical structure of liposomes makes them an attractive package material for encapsulation of multiple water-insoluble quantum dots and amplifying the analytical signal. Silica coverage ensures the stability of the loaded liposomes against fusion and internal leakage during storage, transporting, application and also provides groups for bioconugation. For the first time these nanostructures were employed for the sensitive multiplex immunochemical determination of two analytes. As a model system mycotoxins zearalenone and aflatoxin B1 were detected in cereals. For simplification of multiassay results' evaluation the silanized liposomed loaded with QDs of different colors were used. The IC50 values for the simultaneous determination of zearalenone and aflatoxin B1 were 16.2 and 18 µg kg(-1) for zearalenone and 2.2 and 2.6 µg kg(-1) for aflatoxin B1 in wheat and maize, respectively. As confirmatory method, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was used. PMID:25618647

  14. Species specificities among primates probed with commercially available fluorescence-based multiplex PCR typing kits.

    PubMed

    Hiroshige, Yuuji; Ohtaki, Hiroyuki; Yoshimoto, Takashi; Ogawa, Hisae; Ishii, Akira; Yamamoto, Toshimichi

    2015-09-01

    To assess species specificities among primates of signals from short tandem repeat (STR) loci included in two commercially available kits, mainly the AmpFlSTR Identifiler kit and additionally the GenePrint PowerPlex 16 system, we analyzed 69 DNA samples from 22 nonhuman primate species representing apes, Old World Monkeys (OWMs), New World Monkeys (NWMs), and prosimians. Each prosimian species and the NWM cotton-top tamarin apparently lacked all STR loci probed. Only one peak, the amelogenin-X peak, was evident in samples from all other NWMs, except the owl monkey. In contrast, several loci, including the amelogenin-X peak, was evident in samples from each OWM species. Notably, for each ape sample, the amelogenin peaks were concordant with morphological gender of the individual. Among the primates, especially in apes, the numbers of alleles for STR loci were increasing according to their phylogenetic order: prosimiansmultiplex STR kits examined in this study would contribute to forensic examinations. PMID:25899252

  15. Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes.

    PubMed

    Bray, Mark-Anthony; Singh, Shantanu; Han, Han; Davis, Chadwick T; Borgeson, Blake; Hartland, Cathy; Kost-Alimova, Maria; Gustafsdottir, Sigrun M; Gibson, Christopher C; Carpenter, Anne E

    2016-09-01

    In morphological profiling, quantitative data are extracted from microscopy images of cells to identify biologically relevant similarities and differences among samples based on these profiles. This protocol describes the design and execution of experiments using Cell Painting, which is a morphological profiling assay that multiplexes six fluorescent dyes, imaged in five channels, to reveal eight broadly relevant cellular components or organelles. Cells are plated in multiwell plates, perturbed with the treatments to be tested, stained, fixed, and imaged on a high-throughput microscope. Next, an automated image analysis software identifies individual cells and measures ∼1,500 morphological features (various measures of size, shape, texture, intensity, and so on) to produce a rich profile that is suitable for the detection of subtle phenotypes. Profiles of cell populations treated with different experimental perturbations can be compared to suit many goals, such as identifying the phenotypic impact of chemical or genetic perturbations, grouping compounds and/or genes into functional pathways, and identifying signatures of disease. Cell culture and image acquisition takes 2 weeks; feature extraction and data analysis take an additional 1-2 weeks. PMID:27560178

  16. Multiplex Ligation-Dependent Probe Amplification Versus Multiprobe Fluorescence in Situ Hybridization To Detect Genomic Aberrations in Chronic Lymphocytic Leukemia

    PubMed Central

    Al Zaabi, Eiman A.; Fernandez, Louis A.; Sadek, Irene A.; Riddell, D. Christie; Greer, Wenda L.

    2010-01-01

    Cytogenetic abnormalities play a major role in the prognosis of patients with chronic lymphocytic leukemia (CLL). Several methods have emerged to try to best identify these abnormalities. We used fluorescence in situ hybridization (FISH) to determine the frequency of cytogenetic changes in our CLL patient population. We also evaluated the effectiveness of multiplex ligation-dependent probe amplification (MLPA) in detecting these abnormalities. Sixty-two B-CLL patients and 20 healthy controls were enrolled, and FISH and MLPA analyses were performed on peripheral blood samples. Using FISH, genomic aberrations were found in 73% of patients and presented as follows: single 13q14.3 deletion (60%), trisomy 12 (7%), ATM deletion (6%), 17p13.1 deletion (2%). MLPA analyses done on 61/62 patients showed sensitivity and specificity values of 90% and 100% respectively. MLPA revealed several additional copy number changes, the most common being 19p13 (LDLR and CDKN2D). Moreover, the cost for MLPA analysis, including technical time and reagents, is 86% less than FISH. In conclusion, cytogenetic abnormalities are a common finding in CLL patients, and MLPA is a reliable approach that is more cost effective and faster than FISH. Despite MLPA limitations of sensitivity, it can be used as a first-line screen and complementary test to FISH analysis. PMID:20093390

  17. Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method

    PubMed Central

    Machado, António; Castro, Joana; Cereija, Tatiana; Almeida, Carina

    2015-01-01

    Bacterial vaginosis (BV) is one of most common vaginal infections. However, its diagnosis by classical methods reveals low specificity. Our goal was to evaluate the accuracy diagnosis of 150 vaginal samples with research gold standard methods and our Peptide Nucleic Acid (PNA) probes by Fluorescence in situ Hybridization (FISH) methodology. Also, we described the first PNA-FISH methodology for BV diagnosis, which provides results in approximately 3 h. The results showed a sensitivity of 84.6% (95% confidence interval (CI), from 64.3 to 95.0%) and a specificity of 97.6% (95% CI [92.6–99.4%]), demonstrating the higher specificity of the PNA-FISH method and showing false positive results in BV diagnosis commonly obtained by the classical methods. This methodology combines the specificity of PNA probes for Lactobacillus species and G. vaginalis visualization and the calculation of the microscopic field by Nugent score, allowing a trustful evaluation of the bacteria present in vaginal microflora and avoiding the occurrence of misleading diagnostics. Therefore, the PNA-FISH methodology represents a valuable alternative for BV diagnosis. PMID:25737820

  18. Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method.

    PubMed

    Machado, António; Castro, Joana; Cereija, Tatiana; Almeida, Carina; Cerca, Nuno

    2015-01-01

    Bacterial vaginosis (BV) is one of most common vaginal infections. However, its diagnosis by classical methods reveals low specificity. Our goal was to evaluate the accuracy diagnosis of 150 vaginal samples with research gold standard methods and our Peptide Nucleic Acid (PNA) probes by Fluorescence in situ Hybridization (FISH) methodology. Also, we described the first PNA-FISH methodology for BV diagnosis, which provides results in approximately 3 h. The results showed a sensitivity of 84.6% (95% confidence interval (CI), from 64.3 to 95.0%) and a specificity of 97.6% (95% CI [92.6-99.4%]), demonstrating the higher specificity of the PNA-FISH method and showing false positive results in BV diagnosis commonly obtained by the classical methods. This methodology combines the specificity of PNA probes for Lactobacillus species and G. vaginalis visualization and the calculation of the microscopic field by Nugent score, allowing a trustful evaluation of the bacteria present in vaginal microflora and avoiding the occurrence of misleading diagnostics. Therefore, the PNA-FISH methodology represents a valuable alternative for BV diagnosis. PMID:25737820

  19. Amplification and modulation of fluorescent signals by using hybridization chain reactions for multiplexed sensing of biomolecules in a one-pot

    NASA Astrophysics Data System (ADS)

    Nishimura, Takahiro; Ogura, Yusuke; Yamada, Kenji; Ohno, Yuko; Tanida, Jun

    2014-02-01

    Fluorescence readout of molecular information is a promising approach for biomolecular sensing. For detection of enormous biomolecules via uorescence, biomolecular information should be converted to codes that can be readout easily and simultaneously. For the purpose, we study a biomolecule uorescence color (B/F) encoders that modulate uorescence signals by control of uorescence resonance energy transfer (FRET). The B/F encoder converts biomolecular signals into uorescent color codes represented with uorescent wavelengths and intensity levels. The combination offers a great number of codes for representing the biomolecular information. In this study, we discuss multiplexed detection of target biomolecules using B/F encoders. Use of the B/F encoders would offer a multiplexed biomolecular sensing in a one-pot without micro-fabrication like DNA microarray. In the experiments, we prepared B/F encoders based on two kinds of hybridization chain reactions (HCR) that make long double-stranded DNA polymers to control positions of uorescence and quencher molecules. In the B/F encoders, target molecules trigger to start assembling the polymer structures. The uorescent molecules in the absence of the targets are near the quenchers and the output uorescence is suppressed by FRET. The polymerization process separates the uorescent and quencher dyes and the uorescent signal increase. The experimental results show that the B/F encoders based on HCRs have linear and independent response to each target, and temporal signals during the encoding reactions are usable for multiplexed readout. This result leads to the multiplexed sensing in a one-pot by uorescent ampli cation and multiple uorescent color-coding.

  20. A multiplex and straightforward aqueous phase immunoassay protocol through the combination of SERS-fluorescence dual mode nanoprobes and magnetic nanobeads.

    PubMed

    Zong, Shenfei; Wang, Zhuyuan; Zhang, Ruohu; Wang, Chunlei; Xu, Shuhong; Cui, Yiping

    2013-03-15

    A novel aqueous phase immunoassay protocol was demonstrated, using surface enhanced Raman scattering (SERS)-fluorescence dual mode nanoprobes combined with magnetic nanobeads (MBs). Here, the dual mode nanoprobes provide an excellent multiplexing ability while the MBs greatly simplify the immunoassay process. Basically, the nanoprobes were acquired by assembling the Raman reporter tagged Au@Ag core-shell nanorods and quantum dots onto the silica nanospheres. When the specific antigens are presented in the immunoassay system containing antibody modified nanoprobes and MBs, the nanoprobes are captured by the MBs and further precipitated by a magnet. Consequently, both SERS and fluorescence signals are detected in the precipitates. Sandwich type immunoassay was conducted to examine the practicability of this protocol. Experimental results confirmed that the presented immunoassay protocol can accomplish highly specific and sensitive recognition of the target antigens. The detection limit was found out to be 0.1 pg/mL. We anticipate that high throughput bioanalysis can be fulfilled using the proposed immunoassay protocol, as the dual mode nanoprobes provide a great multiplexing capability while the MBs facilitate the convenient aqueous phase detection of the analytes. PMID:23084027

  1. Development of a multiplexed fluorescent immunoassay for the quantitation of antibody responses to four Neisseria meningitidis serogroups.

    PubMed

    Martins, Thomas B; Jaskowski, Troy D; Tebo, Anne; Hill, Harry R

    2009-03-15

    Neisseria meningitidis is a gram-negative bacterium causing disease world wide with a fatality rate of 5-10%. Five serogroups, A, B, C, Y and W-135 are responsible for virtually all cases of the disease in humans. We have developed a multiplexed assay for the simultaneous quantitation of IgG antibody responses to the four most immunogenic (A, C, Y, and W-135) N. meningitidis serogroups. A simple and less manipulative method was employed for conjugation of the capsular polysaccharide antigens to the microspheres. The multiplex assay compared well with traditional individual ELISAs, but demonstrated greater than 1 log increase in dynamic range and sensitivity. Specificity studies of the multiplex assay showed greater than 95% homologous inhibition and less than 5% heterologous inhibition for all four serogroups. Intra and inter-assay CVs were generally less than 10% and the limit of detection was <600 pg/ml. The multiplexed assay proved to be reproducible as well as specific and sensitive when compared to the standardized ELISAs. Advantages included a greater dynamic range and simultaneous detection of antibody responses to the four serogroups contained in the tetravalent meningococcal polysaccharide vaccine. PMID:19159627

  2. Fluorescent Quantification of DNA Based on Core-Shell Fe3O4@SiO2@Au Nanocomposites and Multiplex Ligation-Dependent Probe Amplification.

    PubMed

    Fan, Jing; Yang, Haowen; Liu, Ming; Wu, Dan; Jiang, Hongrong; Zeng, Xin; Elingarami, Sauli; Ll, Zhiyang; Li, Song; Liu, Hongna; He, Nongyue

    2015-02-01

    In this research, a novel method for relative fluorescent quantification of DNA based on Fe3O4@SiO2@Au gold-coated magnetic nanocomposites (GMNPs) and multiplex ligation- dependent probe amplification (MLPA) has been developed. With the help of self-assembly, seed-mediated growth and chemical reduction method, core-shell Fe3O4@SiO2@Au GMNPs were synthesized. Through modified streptavidin on the GMNPs surface, we obtained a bead chip which can capture the biotinylated probes. Then we designed MLPA probes which were tagged with biotin or Cy3 and target DNA on the basis of human APP gene sequence. The products from the thermostable DNA ligase induced ligation reactions and PCR amplifications were incubated with SA-GMNPs. After washing, magnetic separation, spotting, the fluorescent scanning results showed our method can be used for the relative quantitative analysis of the target DNA in the concentration range of 03004~0.5 µM. PMID:26353621

  3. Highly sensitive and simultaneous detection of melamine and aflatoxin M1 in milk products by multiplexed planar waveguide fluorescence immunosensor (MPWFI).

    PubMed

    Guo, Hongli; Zhou, Xiaohong; Zhang, Yan; Song, Baodong; Zhang, Jingxuan; Shi, Hanchang

    2016-04-15

    Mycotoxins and industrial chemicals, such as aflatoxin M1 and melamine, now commonly exist in milk and cause potential health risks. This study presents an indirect competitive immunoassay through multiplex planar waveguide fluorescence immunosensor (MPWFI) for rapid, sensitive, and simultaneous detection and quantification of aflatoxin M1 and melamine by applying the principle of immunoreaction and total internal reflect fluorescent. Double-channel standard curves with appropriate logistic correlation (R(2)>0.99) were plotted, respectively. The working ranges (0.073-0.400 ng/mL and 26.38-270.00 ng/mL, respectively) were calculated, as well as the limit of detection (0.045 and 13.37 ng/mL, respectively), when two analytes were simultaneously detected. Both results satisfied the requirements for the maximum amount set by the WHO, which illustrated that the current method was better than some other standard methods. The recovery rates in the actual samples ranged from 85% to 103%, with relative standard deviations between 1.3% and 6.5%, which indicated high accuracy and repeatability. PMID:26616961

  4. Mononeuritis multiplex

    MedlinePlus

    Mononeuropathy multiplex; Multifocal neuropathy; Peripheral neuropathy - mononeuritis multiplex ... Shy ME. Peripheral neuropathies. In: Goldman L, Ausiello D, eds. Goldman's Cecil Medicine . 23rd ed. Philadelphia, PA: Elsevier Saunders; 2007:chap 446.

  5. FPGA-based multi-channel fluorescence lifetime analysis of Fourier multiplexed frequency-sweeping lifetime imaging

    PubMed Central

    Zhao, Ming; Li, Yu; Peng, Leilei

    2014-01-01

    We report a fast non-iterative lifetime data analysis method for the Fourier multiplexed frequency-sweeping confocal FLIM (Fm-FLIM) system [ Opt. Express22, 10221 ( 2014)24921725]. The new method, named R-method, allows fast multi-channel lifetime image analysis in the system’s FPGA data processing board. Experimental tests proved that the performance of the R-method is equivalent to that of single-exponential iterative fitting, and its sensitivity is well suited for time-lapse FLIM-FRET imaging of live cells, for example cyclic adenosine monophosphate (cAMP) level imaging with GFP-Epac-mCherry sensors. With the R-method and its FPGA implementation, multi-channel lifetime images can now be generated in real time on the multi-channel frequency-sweeping FLIM system, and live readout of FRET sensors can be performed during time-lapse imaging. PMID:25321778

  6. LINKAGE programs: linkage analysis for monogenic cardiovascular diseases.

    PubMed

    Li, Lin; Wang, Qing K; Rao, Shaoqi

    2006-01-01

    Identification of the genes for a human disease provides significant insights into the molecular mechanism underlying the pathogenesis of the disease. A human disease gene can be identified by its chromosomal location (positional cloning). Linkage analysis is a key step in positional cloning. For monogenic disorders with a known inheritance pattern, model-based linkage analysis is effective in mapping the disease location. Therefore, model-based linkage analysis can provide a powerful tool to positional cloning of some specific molecular determinants that co-segregate with disease phenotypes in the isolated samples (e.g., large and multiplex impaired pedigrees). This chapter describes model-based human genetic linkage analysis as implemented in the LINKAGE computer package. First, we introduce the basic concepts and principles for genetic analysis of monogenic disorders. Then, we demonstrate the usages of the programs by analyzing several examples of hypothetical pedigrees with the inheritance modes of autosomal-dominant, autosomal-recessive, and genetic heterogeneity. PMID:17071989

  7. Near-infrared fluorescence-based multiplex lateral flow immunoassay for the simultaneous detection of four antibiotic residue families in milk.

    PubMed

    Chen, Yiqiang; Chen, Qian; Han, Miaomiao; Liu, Jiangyang; Zhao, Peng; He, Lidong; Zhang, Yuan; Niu, Yiming; Yang, Wenjun; Zhang, Liying

    2016-05-15

    In this study, we developed a novel near-infrared fluorescence based multiplex lateral flow immunoassay by conjugating a near-infrared label to broad-specificity monoclonal antibody/receptor as detection complexes. Different antigens were dispensed onto separate test zones of nitrocellulose membrane to serve as capture reagents. This assay format allowed the simultaneous detection of four families of antibiotics (β-lactams, tetracyclines, quinolones and sulfonamides) in milk within 20 min. Qualitative and quantitative analysis of target antibiotics were realized by imaging the fluorescence intensity of the near-infrared label captured on respective test lines. For qualitative analysis, the cut-off values of β-lactams, tetracyclines, quinolones and sulfonamides were determined to be 8 ng/mL, 2 ng/mL, 4 ng/mL and 8 ng/mL respectively, which were much lower than the conventional gold nanoparticle based lateral flow immunoassay. For quantitative analysis, the detection ranges were 0.26-3.56 ng/mL for β-lactams, 0.04-0.98 ng/mL for tetracyclines, 0.08-2.0 ng/mL for quinolones, and 0.1-3.98 ng/mL for sulfonamides, with linear correlation coefficients higher than 0.97. The mean spiked recoveries ranged from 93.7% to 108.2% with coefficient of variations less than 16.3%. These results demonstrated that this novel immunoassay is a promising approach for rapidly screening the four families of antibiotic residues in milk. PMID:26741531

  8. Quantitative multiplexed quantum dot immunohistochemistry

    SciTech Connect

    Sweeney, E.; Ward, T.H.; Gray, N.; Womack, C.; Jayson, G.; Hughes, A.; Dive, C.; Byers, R.

    2008-09-19

    Quantum dots are photostable fluorescent semiconductor nanocrystals possessing wide excitation and bright narrow, symmetrical, emission spectra. These characteristics have engendered considerable interest in their application in multiplex immunohistochemistry for biomarker quantification and co-localisation in clinical samples. Robust quantitation allows biomarker validation, and there is growing need for multiplex staining due to limited quantity of clinical samples. Most reported multiplexed quantum dot staining used sequential methods that are laborious and impractical in a high-throughput setting. Problems associated with sequential multiplex staining have been investigated and a method developed using QDs conjugated to biotinylated primary antibodies, enabling simultaneous multiplex staining with three antibodies. CD34, Cytokeratin 18 and cleaved Caspase 3 were triplexed in tonsillar tissue using an 8 h protocol, each localised to separate cellular compartments. This demonstrates utility of the method for biomarker measurement enabling rapid measurement of multiple co-localised biomarkers on single paraffin tissue sections, of importance for clinical trial studies.

  9. Development of a fluorescent microsphere-based multiplexed high-throughput assay system for profiling of transcription factor activation.

    PubMed

    Yaoi, Takuro; Jiang, Xin; Li, Xianqiang

    2006-06-01

    Transcription factors (TFs), which play crucial roles in the regulation of gene expression in the human genome, are highly regulated by a variety of mechanisms. A single extracellular stimulus can trigger multiple signaling pathways, and these in turn can activate multiple TFs to mediate the inducible expression of target genes. Alterations in the activities of TFs are often associated with human diseases, such as altered activating factor 1, estrogen receptor, and p53 function in cancer, nuclear factor kappaB in inflammatory diseases, and peroxisome proliferator-activated receptor gamma in obesity. A systematic assay for profiling the activation of TFs will aid in elucidating the mechanisms of TF activation, reveal altered TFs associated with human diseases, and aid in developing assays for drug discovery. Here, we developed a 24-plex fluorescent microsphere-based TF activation assay system with a 96-well plate format. The assay system enabled high-throughput profiling of the DNA binding activity of TFs in multiple samples with high sensitivity. PMID:16834534

  10. Steatocystoma multiplex.

    PubMed

    Chu, David H

    2003-10-01

    A 25-year-old man with a 20-year history of asymptomatic nodules on his arms and trunk, which histopathological analysis showed to be consistent with steatocystoma multiplex, is presented. Steatocystoma multiplex is a disorder characterized by multiple, asymptomatic, dermal cysts that usually occur on the trunk and proximal aspects of the extremities. Steatocystoma multiplex with acral predominance has only recently been described. Development of steatocystomas has been hypothesized to be due to alterations in the structure of keratin 17. Treatment for lesions has included surgical excision or drainage, oral retinoids, and liquid nitrogen cryotherapy. PMID:14594591

  11. Multiplex SSR-PCR approaches for semi-automated genotyping and characterization of loci linked to blast disease resistance genes in rice.

    PubMed

    Ashkani, Sadegh; Rafii, Mohd Yusop; Shabanimofrad, Mahmoodreza; Foroughi, Majid; Azizia, Parisa; Akhtar, Mohd Sayeed; Sahebi, Mahbod; Harun, Abd Rahim; Nasehi, Abbas

    2015-11-01

    In the present study, 63 polymorphic microsatellite markers related to rice blast resistance genes were fluorescently labelled at the 5'-end with either 6-FAM or HEX using the G5 dye set and incorporated into a multiplex SSR-PCR for the detection of fragments using an automated system. For rice F3 families obtained from crosses between Pongsu Seribu 2 (Malaysian blast resistant cultivar) and Mahsuri (a susceptible rice cultivar), the genotypes for 13 designated multiplex SSR panels were determined. The genotyping assays were performed using a capillary-based ABIPRISM 3100 genetic analyser. The sizes of the SSRs alleles observed in the range from 79 to 324 bp. The observed marker segregation data were analysed using the Chi(2) test. A genetic linkage map covering ten chromosomes and comprising 63 polymorphic SSR markers was constructed, and the distorted loci were localised to linkage groups. The results indicated that distorted loci are presented on eight chromosomes. PMID:26318048

  12. Portable Multiplex Pathogen Detector

    SciTech Connect

    Visuri, S; McBride, M T; Matthews, D; Rao, R

    2002-07-15

    Tumor marker concentrations in serum provide useful information regarding clinical stage and prognosis of cancer and can thus be used for presymptomatic diagnostic purposes. Currently, detection and identification of soluble analytes in biological fluids is conducted by methods including bioassays, ELISA, PCR, DNA chip or strip tests. While these technologies are generally sensitive and specific, they are time consuming, labor intensive and cannot be multiplexed. Our goal is to develop a simple, point-of-care, portable, liquid array-based immunoassay device capable of simultaneous detection of a variety of cancer markers. Here we describe the development of assays for the detection of Serum Prostate Specific Antigen, and Ovalbumin from a single sample. The multiplexed immunoassays utilize polystyrene microbeads. The beads are imbedded with precise ratios of red and orange fluorescent dyes yielding an array of 100 beads, each with a unique spectral address (Figure 1). Each bead can be coated with capture antibodies specific for a given antigen. After antigen capture, secondary antibodies sandwich the bound antigen and are indirectly labeled by the fluorescent reporter phycoerythrin (PE). Each optically encoded and fluorescently-labeled microbead is then individually interrogated. A red laser excites the dye molecules imbedded inside the bead and classifies the bead to its unique bead set, and a green laser quantifies the assay at the bead surface. This technology has been proven to be comparable to the ELISA in terms of sensitivity and specificity. We also describe the laser-based instrumentation used to acquire fluorescent bead images Following the assay, droplets of bead suspension containing a mixture of bead classes were deposited onto filters held in place by a disposable plexiglass device and the resultant arrays viewed under the fluorescent imaging setup. Using the appropriate filter sets to extract the necessary red, orange and green fluorescence from the

  13. Multiplex Pyrosequencing.

    PubMed

    Pourmand, Nader; Elahi, Elahe; Davis, Ronald W; Ronaghi, Mostafa

    2002-04-01

    We describe here the development of a new and simple single-tube multiplex Pyrosequencing assay. Genomic DNA or cDNA was employed to PCR amplify region(s) using biotinylated and normal primer(s). Subsequent to capture of PCR products on streptavidin-coated beads, single-stranded DNA separation and hybridization of multiple sequencing primers, Pyrosequencing was performed. The obtained pyrogram resulted in a unique pattern in which the intensity of the signal determined the number of incorporated nucleotide(s). Here, we demonstrate the use of this multiplex Pyrosequencing for single nucleotide polymorphisms genotyping and microbial typing. PMID:11917037

  14. Multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, Edward S.; Li, Qingbo; Lu, Xiandan

    1998-04-21

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification ("base calling") is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations.

  15. Multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, Edward S.; Chang, Huan-Tsang; Fung, Eliza N.; Li, Qingbo; Lu, Xiandan

    1996-12-10

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification ("base calling") is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations.

  16. Multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, E.S.; Li, Q.; Lu, X.

    1998-04-21

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification (``base calling``) is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations. 19 figs.

  17. Multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, E.S.; Chang, H.T.; Fung, E.N.; Li, Q.; Lu, X.

    1996-12-10

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification (``base calling``) is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations. 19 figs.

  18. Color-Multiplexing-Based Fluorescent Test Paper: Dosage-Sensitive Visualization of Arsenic(III) with Discernable Scale as Low as 5 ppb.

    PubMed

    Zhou, Yujie; Huang, Xiaoyan; Liu, Cui; Zhang, Ruilong; Gu, Xiaoling; Guan, Guijian; Jiang, Changlong; Zhang, Liying; Du, Shuhu; Liu, Bianhua; Han, Ming-Yong; Zhang, Zhongping

    2016-06-21

    Fluorescent colorimetry test papers are promising for the assays of environments, medicines, and foods by the observation of the naked eye on the variations of fluorescence brightness and color. Unlike dye-absorption-based pH test paper, however, the fluorescent test papers with wide color-emissive variations with target dosages for accurate quantification remain unsuccessful even if the multicolorful fluorescent probes are used. Here, we report the dosage-sensitive fluorescent colorimetry test paper with a very wide/consecutive "from red to cyan" response to the presence and amount of arsenic ions, As(III). Red quantum dots (QDs) were modified with glutathione and dithiothreitol to obtain the supersensitivity to As(III) by the quenching of red fluorescence through the formation of dispersive QDs aggregates. A small amount of cyan carbon dots (CDs) with spectral blue-green components as the photostable internal standard were mixed into the QDs solution to produce a composited red fluorescence. Upon the addition of As(III) into the sensory solution, the fluorescence color could gradually be reversed from red to cyan with a detection limit of 1.7 ppb As(III). When the sensory solution was printed onto a piece of filter paper, surprisingly a serial of color evolution from peach to pink to orange to khaki to yellowish to yellow-green to final cyan with the addition of As(III) was displayed and clearly discerned the dosage scale as low as 5 ppb. The methodology reported here opens a novel pathway toward the real applications of fluorescent test papers. PMID:27230307

  19. Lifetime-based tomographic multiplexing

    NASA Astrophysics Data System (ADS)

    Raymond, Scott B.; Boas, David A.; Bacskai, Brian J.; Kumar, Anand T. N.

    2010-07-01

    Near-infrared (NIR) fluorescence tomography of multiple fluorophores has previously been limited by the bandwidth of the NIR spectral regime and the broad emission spectra of most NIR fluorophores. We describe in vivo tomography of three spectrally overlapping fluorophores using fluorescence lifetime-based separation. Time-domain images are acquired using a voltage-gated, intensified charge-coupled device (CCD) in free-space transmission geometry with 750 nm Ti:sapphire laser excitation. Lifetime components are fit from the asymptotic portion of fluorescence decay curve and reconstructed separately with a lifetime-adjusted forward model. We use this system to test the in vivo lifetime multiplexing suitability of commercially available fluorophores, and demonstrate lifetime multiplexing in solution mixtures and in nude mice. All of the fluorophores tested exhibit nearly monoexponential decays, with narrow in vivo lifetime distributions suitable for lifetime multiplexing. Quantitative separation of two fluorophores with lifetimes of 1.1 and 1.37 ns is demonstrated for relative concentrations of 1:5. Finally, we demonstrate tomographic imaging of two and three fluorophores in nude mice with fluorophores that localize to distinct organ systems. This technique should be widely applicable to imaging multiple NIR fluorophores in 3-D.

  20. Unravelling the Bacterial Vaginosis-Associated Biofilm: A Multiplex Gardnerella vaginalis and Atopobium vaginae Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes

    PubMed Central

    Hardy, Liselotte; Jespers, Vicky; Dahchour, Nassira; Mwambarangwe, Lambert; Musengamana, Viateur; Vaneechoutte, Mario; Crucitti, Tania

    2015-01-01

    Bacterial vaginosis (BV), a condition defined by increased vaginal discharge without significant inflammation, is characterized by a change in the bacterial composition of the vagina. Lactobacillus spp., associated with a healthy vaginal microbiome, are outnumbered by BV-associated organisms. These bacteria could form a polymicrobial biofilm which allows them to persist in spite of antibiotic treatment. In this study, we examined the presence of Gardnerella vaginalis and Atopobium vaginae in vaginal biofilms using Peptide Nucleic Acid (PNA) probes targeting these bacteria. For this purpose, we developed three new PNA probes for A. vaginae. The most specific A. vaginae probe, AtoITM1, was selected and then used in an assay with two existing probes, Gard162 and BacUni-1, to evaluate multiplex FISH on clinical samples. Using quantitative polymerase chain reaction (qPCR) as the gold standard, we demonstrated a sensitivity of 66.7% (95% confidence interval: 54.5% - 77.1%) and a specificity of 89.4% (95% confidence interval: 76.1% - 96%) of the new AtoITM1 probe. FISH enabled us to show the presence of a polymicrobial biofilm in bacterial vaginosis, in which Atopobium vaginae is part of a Gardnerella vaginalis-dominated biofilm. We showed that the presence of this biofilm is associated with high bacterial loads of A. vaginae and G. vaginalis. PMID:26305575

  1. Unravelling the Bacterial Vaginosis-Associated Biofilm: A Multiplex Gardnerella vaginalis and Atopobium vaginae Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes.

    PubMed

    Hardy, Liselotte; Jespers, Vicky; Dahchour, Nassira; Mwambarangwe, Lambert; Musengamana, Viateur; Vaneechoutte, Mario; Crucitti, Tania

    2015-01-01

    Bacterial vaginosis (BV), a condition defined by increased vaginal discharge without significant inflammation, is characterized by a change in the bacterial composition of the vagina. Lactobacillus spp., associated with a healthy vaginal microbiome, are outnumbered by BV-associated organisms. These bacteria could form a polymicrobial biofilm which allows them to persist in spite of antibiotic treatment. In this study, we examined the presence of Gardnerella vaginalis and Atopobium vaginae in vaginal biofilms using Peptide Nucleic Acid (PNA) probes targeting these bacteria. For this purpose, we developed three new PNA probes for A. vaginae. The most specific A. vaginae probe, AtoITM1, was selected and then used in an assay with two existing probes, Gard162 and BacUni-1, to evaluate multiplex FISH on clinical samples. Using quantitative polymerase chain reaction (qPCR) as the gold standard, we demonstrated a sensitivity of 66.7% (95% confidence interval: 54.5% - 77.1%) and a specificity of 89.4% (95% confidence interval: 76.1% - 96%) of the new AtoITM1 probe. FISH enabled us to show the presence of a polymicrobial biofilm in bacterial vaginosis, in which Atopobium vaginae is part of a Gardnerella vaginalis-dominated biofilm. We showed that the presence of this biofilm is associated with high bacterial loads of A. vaginae and G. vaginalis. PMID:26305575

  2. Establishment of a human malignant fibrous histiocytoma cell line, COMA. Characterization By conventional cytogenetics, comparative genomic hybridization, and multiplex fluorescence In situ hybridization.

    PubMed

    Mairal, A; Chibon, F; Rousselet, A; Couturier, J; Terrier, P; Aurias, A

    2000-09-01

    The human COMA cell line has been established from a storiform pleomorphic malignant fibrous histiocytoma (MFH). As expected for this tumor type, a very complex karyotype was observed after R-banding analysis. An extensive analysis by 24-color painting, comparative genomic hybridization (CGH), and fluorescence in situ hybridization (FISH) was performed. Twelve complex marker chromosomes recurrently observed were clearly identified; among them, three were systematically present in all analyzed metaphases. Amplifications detected by CGH were refined by FISH with probes specific for various candidate loci. A significant aneuploidy and numerous micronuclei were observed, which could be related to the anomalies of centriole numbers detected in a proportion of cells. Such an analysis, performed on a series of MFH cell lines, would allow the delineation of the genomic alterations specific for the oncogenesis or progression of this complex tumor type or both. PMID:11063793

  3. 5-color multiplexed microwave-accelerated metal-enhanced fluorescence: detection and analysis of multiple DNA sequences from within one sample well within a few seconds.

    PubMed

    Dragan, Anatoliy; Geddes, Chris D

    2014-11-01

    We present a potentially highly sensitive and selective bio-assay for the potential detection of any five different DNA sequences from one sample in one well. The assay is based on a DNA "rapid catch and signal" (DNA-RCS) technology developed for the detection of different DNA sequences from a sample well area. Our signal amplification utilizes the metal-enhanced fluorescence (MEF) of dyes attached to the probe-DNAs, which hybridizes with the pre-formed mixture of anchor-DNA scaffolds on silver island films (SiFs). Low-power microwave irradiation accelerates both the formation of the anchor-DNA scaffold on the SiF-surface and anchor/probe DNA hybridization, i.e. "rapid catch" of target DNAs from a bulk solution, decreasing the assay run time from hours to only a few seconds. Localization of signaling dye-labels close to the SiFs make them extremely photostable, which allows for collecting/integrating the signal over a long time period. To demonstrate a 5 color DNA assay (5-plex) we have used a range of readily available Alexa™ dyes. Advantages and perspectives of the RCS-technologies ability to detect 5 different DNA sequences from within one plate-well are discussed. PMID:25263097

  4. Optofluidic wavelength division multiplexing for single-virus detection.

    PubMed

    Ozcelik, Damla; Parks, Joshua W; Wall, Thomas A; Stott, Matthew A; Cai, Hong; Parks, Joseph W; Hawkins, Aaron R; Schmidt, Holger

    2015-10-20

    Optical waveguides simultaneously transport light at different colors, forming the basis of fiber-optic telecommunication networks that shuttle data in dozens of spectrally separated channels. Here, we reimagine this wavelength division multiplexing (WDM) paradigm in a novel context--the differentiated detection and identification of single influenza viruses on a chip. We use a single multimode interference (MMI) waveguide to create wavelength-dependent spot patterns across the entire visible spectrum and enable multiplexed single biomolecule detection on an optofluidic chip. Each target is identified by its time-dependent fluorescence signal without the need for spectral demultiplexing upon detection. We demonstrate detection of individual fluorescently labeled virus particles of three influenza A subtypes in two implementations: labeling of each virus using three different colors and two-color combinatorial labeling. By extending combinatorial multiplexing to three or more colors, MMI-based WDM provides the multiplexing power required for differentiated clinical tests and the growing field of personalized medicine. PMID:26438840

  5. Probabilistic record linkage

    PubMed Central

    Sayers, Adrian; Ben-Shlomo, Yoav; Blom, Ashley W; Steele, Fiona

    2016-01-01

    Studies involving the use of probabilistic record linkage are becoming increasingly common. However, the methods underpinning probabilistic record linkage are not widely taught or understood, and therefore these studies can appear to be a ‘black box’ research tool. In this article, we aim to describe the process of probabilistic record linkage through a simple exemplar. We first introduce the concept of deterministic linkage and contrast this with probabilistic linkage. We illustrate each step of the process using a simple exemplar and describe the data structure required to perform a probabilistic linkage. We describe the process of calculating and interpreting matched weights and how to convert matched weights into posterior probabilities of a match using Bayes theorem. We conclude this article with a brief discussion of some of the computational demands of record linkage, how you might assess the quality of your linkage algorithm, and how epidemiologists can maximize the value of their record-linked research using robust record linkage methods. PMID:26686842

  6. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

  7. Multiplex PageRank.

    PubMed

    Halu, Arda; Mondragón, Raúl J; Panzarasa, Pietro; Bianconi, Ginestra

    2013-01-01

    Many complex systems can be described as multiplex networks in which the same nodes can interact with one another in different layers, thus forming a set of interacting and co-evolving networks. Examples of such multiplex systems are social networks where people are involved in different types of relationships and interact through various forms of communication media. The ranking of nodes in multiplex networks is one of the most pressing and challenging tasks that research on complex networks is currently facing. When pairs of nodes can be connected through multiple links and in multiple layers, the ranking of nodes should necessarily reflect the importance of nodes in one layer as well as their importance in other interdependent layers. In this paper, we draw on the idea of biased random walks to define the Multiplex PageRank centrality measure in which the effects of the interplay between networks on the centrality of nodes are directly taken into account. In particular, depending on the intensity of the interaction between layers, we define the Additive, Multiplicative, Combined, and Neutral versions of Multiplex PageRank, and show how each version reflects the extent to which the importance of a node in one layer affects the importance the node can gain in another layer. We discuss these measures and apply them to an online multiplex social network. Findings indicate that taking the multiplex nature of the network into account helps uncover the emergence of rankings of nodes that differ from the rankings obtained from one single layer. Results provide support in favor of the salience of multiplex centrality measures, like Multiplex PageRank, for assessing the prominence of nodes embedded in multiple interacting networks, and for shedding a new light on structural properties that would otherwise remain undetected if each of the interacting networks were analyzed in isolation. PMID:24205186

  8. Linkage analysis: Inadequate for detecting susceptibility loci in complex disorders?

    SciTech Connect

    Field, L.L.; Nagatomi, J.

    1994-09-01

    Insulin-dependent diabetes mellitus (IDDM) may provide valuable clues about approaches to detecting susceptibility loci in other oligogenic disorders. Numerous studies have demonstrated significant association between IDDM and a VNTR in the 5{prime} flanking region of the insulin (INS) gene. Paradoxically, all attempts to demonstrate linkage of IDDM to this VNTR have failed. Lack of linkage has been attributed to insufficient marker locus information, genetic heterogeneity, or high frequency of the IDDM-predisposing allele in the general population. Tyrosine hydroxylase (TH) is located 2.7 kb from INS on the 5` side of the VNTR and shows linkage disequilibrium with INS region loci. We typed a highly polymorphic microsatellite within TH in 176 multiplex families, and performed parametric (lod score) linkage analysis using various intermediate reduced penetrance models for IDDM (including rare and common disease allele frequencies), as well as non-parametric (affected sib pair) linkage analysis. The scores significantly reject linkage for recombination values of .05 or less, excluding the entire 19 kb region containing TH, the 5{prime} VNTR, the INS gene, and IGF2 on the 3{prime} side of INS. Non-parametric linkage analysis also provided no significant evidence for linkage (mean TH allele sharing 52.5%, P=.12). These results have important implications for efforts to locate genes predisposing to complex disorders, strongly suggesting that regions which are significantly excluded by linkage methods may nevertheless contain predisposing genes readily detectable by association methods. We advocate that investigators routinely perform association analyses in addition to linkage analyses.

  9. Multiplex gas chromatography

    NASA Technical Reports Server (NTRS)

    Valentin, Jose R.

    1990-01-01

    The principles of the multiplex gas chromatography (GC) technique, which is a possible candidate for chemical analysis of planetary atmospheres, are discussed. Particular attention is given to the chemical modulators developed by present investigators for multiplex GC, namely, the thermal-desorption, thermal-decomposition, and catalytic modulators, as well as to mechanical modulators. The basic technique of multiplex GC using chemical modulators and a mechanical modulator is demonstrated. It is shown that, with the chemical modulators, only one gas stream consisting of the carrier in combination with the components is being analyzed, resulting in a simplified instrument that requires relatively few consumables. The mechanical modulator demonstrated a direct application of multiplex GC for the analysis of gases in atmosphere of Titan at very low pressures.

  10. Apollo Multiplexer operations manual

    SciTech Connect

    Miller, M.M.

    1985-04-01

    This report describes the operation of the the Apollo Multiplexer, a microprocessor based communications device designed to process data between an Apollo computer and up to four Gandalf PACXIV data switches. Details are given on overall operation, hardware, and troubleshooting. The reader should gain sufficient knowledge from this report to understand the operation of the multiplexer and effectively analyze and correct any problems that might occur.

  11. Downlink data multiplexer

    NASA Technical Reports Server (NTRS)

    Holland, S. Douglas (Inventor); Steele, Glen F. (Inventor); Romero, Denise M. (Inventor); Koudelka, Robert David (Inventor)

    2008-01-01

    A data multiplexer that accommodates both industry standard CCSDS data packets and bits streams and standard IEEE 1394 data is described. The multiplexer provides a statistical allotment of bandwidth to the channels in turn, preferably four, but expandable in increments of four up to sixteen. A microcontroller determines bandwidth requested by the plurality of channels, as well as the bandwidth available, and meters out the available bandwidth on a statistical basis employing flow control to the input channels.

  12. Multiplexed chirp waveform synthesizer

    DOEpatents

    Dudley, Peter A.; Tise, Bert L.

    2003-09-02

    A synthesizer for generating a desired chirp signal has M parallel channels, where M is an integer greater than 1, each channel including a chirp waveform synthesizer generating at an output a portion of a digital representation of the desired chirp signal; and a multiplexer for multiplexing the M outputs to create a digital representation of the desired chirp signal. Preferably, each channel receives input information that is a function of information representing the desired chirp signal.

  13. Coevolution and Correlated Multiplexity in Multiplex Networks

    NASA Astrophysics Data System (ADS)

    Kim, Jung Yeol; Goh, K.-I.

    2013-08-01

    Distinct channels of interaction in a complex networked system define network layers, which coexist and cooperate for the system’s function. Towards understanding such multiplex systems, we propose a modeling framework based on coevolution of network layers, with a class of minimalistic growing network models as working examples. We examine how the entangled growth of coevolving layers can shape the network structure and show analytically and numerically that the coevolution can induce strong degree correlations across layers, as well as modulate degree distributions. We further show that such a coevolution-induced correlated multiplexity can alter the system’s response to the dynamical process, exemplified by the suppressed susceptibility to a social cascade process.

  14. Automated linkage analysis in psychiatric disorders

    SciTech Connect

    He, L.; Mansfield, D.C.; Brown, A.F.; Green, D.K.

    1995-06-19

    A genome-wide search for linkage of microsatellite markers to chromosomal loci containing genes responsible for the major psychoses is a laborious task which can be carried out with greater speed and economy by introducing automation to several steps in the procedure. We describe the use of the Automated Linkage Preprocessor (ALP) program for the computer analysis of the waveform generated by fluorescein-labelled markers after electrophoretic separation. (To obtain a copy send a request to A.F. Brown at the below MRC address or use Anonymous FTP to ftp.hgu.mrc.ac.uk. Software is in directory pub/ALP.) The program runs on a PC in the Microsoft Windows environment, and is used in conjunction with an automated laser fluorescence (ALF) sequencer (Pharmacia) and its Fragment Manager{trademark} software to detect and size the PCR products, filter out peaks of fluorescence due to nonallele fragments, and generate genotypes in a format suitable for direct input to standard linkage analysis programs. The method should offer the advantages of speed, accuracy, and reduced cost. Its use in linkage studies in a large family with manic-depressive illness is discussed. 14 refs., 3 figs., 1 tab.

  15. 3D multiplexed immunoplasmonics microscopy.

    PubMed

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-21

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K(+) channel subunit KV1.1) on human cancer CD44(+) EGFR(+) KV1.1(+) MDA-MB-231 cells and reference CD44(-) EGFR(-) KV1.1(+) 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third

  16. Compact spatial multiplexers for mode division multiplexing.

    PubMed

    Chen, Haoshuo; van Uden, Roy; Okonkwo, Chigo; Koonen, Ton

    2014-12-29

    Spatial multiplexer (SMUX) for mode division multiplexing (MDM) has evolved from mode-selective excitation, multiple-spot and photonic-lantern based solutions in order to minimize both mode-dependent loss (MDL) and coupler insertion loss (CIL). This paper discusses the implementation of all the three solutions by compact components in a small footprint. Moreover, the compact SMUX can be manufactured in mass production and packaged to assure high reliability. First, push-pull scheme and center launch based SMUXes are demonstrated on two mostly-popular photonic integration platforms: Silicon-on-insulator (SOI) and Indium Phosphide (InP) for selectively exciting LP01 and LP11 modes. 2-dimensional (2D) top-coupling by using vertical emitters is explored to provide a coupling interface between a few-mode fiber (FMF) and the photonic integrated SMUX. SOI-based grating couplers and InP-based 45° vertical mirrors are proposed and researched as vertical emitters in each platform. Second, a 3-spot SMUX is realized on an InP-based circuit through employing 45° vertical mirrors. Third, as a newly-emerging photonic integration platform, laser-inscribed 3D waveguide (3DW) technology is applied for a fully-packaged dual-channel 6-mode SMUX including two 6-core photonic lantern structures as mode multiplexer and demultiplexer, respectively. PMID:25607130

  17. Multiplexed Biosensors for Mycotoxins.

    PubMed

    Maragos, Chris M

    2016-07-01

    Significant progress has been made in the development of biosensors that can be used to detect low-MW toxins produced by fungi (mycotoxins). The number of formats that have been investigated is impressive and is an indication of the importance attached to finding easy-to-use, accurate, and rapid methods for detecting these toxins in commodities and foods. This review explores the details of multiplexed biosensors based on many formats, including multiplexed immunoassays, suspension arrays, membrane-based devices (flow-through and immunochromatographic), and planar microarrays. Each assay format has its own strengths and areas that need improvement. Certain formats, such as multiplexed immunochromatographic devices, are well developed and relatively easy to use, and in some cases, commercial products are being sold. Others, such as the suspension arrays and microarrays, are laboratory-based assays that, although more complicated, are also more amenable to a larger scale of multiplexing. The diversity of such efforts and the multitude of formats under investigation suggest that multiple solutions will be found to satisfy the need for multiplexed toxin detection. PMID:27455928

  18. Tunable lifetime multiplexing using luminescent nanocrystals

    NASA Astrophysics Data System (ADS)

    Lu, Yiqing; Zhao, Jiangbo; Zhang, Run; Liu, Yujia; Liu, Deming; Goldys, Ewa M.; Yang, Xusan; Xi, Peng; Sunna, Anwar; Lu, Jie; Shi, Yu; Leif, Robert C.; Huo, Yujing; Shen, Jian; Piper, James A.; Robinson, J. Paul; Jin, Dayong

    2014-01-01

    Optical multiplexing plays an important role in applications such as optical data storage, document security, molecular probes and bead assays for personalized medicine. Conventional fluorescent colour coding is limited by spectral overlap and background interference, restricting the number of distinguishable identities. Here, we show that tunable luminescent lifetimes τ in the microsecond region can be exploited to code individual upconversion nanocrystals. In a single colour band, one can generate more than ten nanocrystal populations with distinct lifetimes ranging from 25.6 µs to 662.4 µs and decode their well-separated lifetime identities, which are independent of both colour and intensity. Such `τ-dots' potentially suit multichannel bioimaging, high-throughput cytometry quantification, high-density data storage, as well as security codes to combat counterfeiting. This demonstration extends the optical multiplexing capability by adding the temporal dimension of luminescent signals, opening new opportunities in the life sciences, medicine and data security.

  19. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

  20. Multiplexed spectroscopy with holographic optical tweezers

    NASA Astrophysics Data System (ADS)

    Cibula, Matthew A.; McIntyre, David H.

    2014-09-01

    We have developed a multiplexed holographic optical tweezers system with an imaging spectrometer to manipulate multiple optically trapped nanosensors and detect multiple fluorescence spectra. The system uses a spatial light modulator (SLM) to control the positions of infrared optical traps in the sample so that multiple nanosensors can be positioned into regions of interest. Spectra of multiple nanosensors are detected simultaneously with the application of an imaging spectrometer. Nanosensors are capable of detecting changes in their environment such as pH, ion concentration, temperature, and voltage by monitoring changes in the nanosensors' emitted fluorescence spectra. We use streptavidin labeled quantum dots bound to the surface of biotin labeled polystyrene microspheres to measure temperature changes by observing a corresponding shift in the wavelength of the spectral peak. The fluorescence is excited at 532 nm with a wide field source.

  1. A multiplexed quantum memory.

    PubMed

    Lan, S-Y; Radnaev, A G; Collins, O A; Matsukevich, D N; Kennedy, T A; Kuzmich, A

    2009-08-01

    A quantum repeater is a system for long-distance quantum communication that employs quantum memory elements to mitigate optical fiber transmission losses. The multiplexed quantum memory (O. A. Collins, S. D. Jenkins, A. Kuzmich, and T. A. B. Kennedy, Phys. Rev. Lett. 98, 060502 (2007)) has been shown theoretically to reduce quantum memory time requirements. We present an initial implementation of a multiplexed quantum memory element in a cold rubidium gas. We show that it is possible to create atomic excitations in arbitrary memory element pairs and demonstrate the violation of Bell's inequality for light fields generated during the write and read processes. PMID:19654771

  2. Von Willebrand gene tracking by single-tube automated fluorescent analysis of four short tandem repeat polymorphisms.

    PubMed

    Vidal, Francisco; Julià, Antoni; Altisent, Carme; Puig, Lluís; Gallardo, Doinique

    2005-05-01

    Molecular diagnosis of von Willebrand disease (VWD) has been hampered by the large size and complex genomic characteristics of the gene involved. For this reason, indirect methods using intragenic polymorphic markers described along the von Willebrand factor (VWF) gene are valuable tools for gene monitoring and linkage analysis. Several studies have demonstrated the four commonly utilized short tandem repeats (STRs), three located in intron 40 and one in the promoter region of the VWF gene, to be highly informative for this task. Our objective was t o develop a rapid, automated method to simultaneously analyze these four STRs for VWF gene tracking. Amplification of the four loci is achieved in a single multiplex fluorescent PCR which is then analyzed in the same run by capillary electrophoresis. Data processing with GeneScan and Genotyper software has simplified management and tabulation of the resulting haplotypes. Analysis of the VWF gene in DNA from 102 individuals (204 chromosomes) revealed that the three STRs within intron 40 showed significant linkage disequilibrium against each other but not against the VWP locus. Moreover, the combination of the four markers offers a high heterozygosity rate (>99%) that improves tracing VWF gene inheritance. In conclusion, the automated fluorescent capillary electrophoresis method presented here is an extremely rapid, simple and highly informative technique for association studies between VWD and the VWF gene in addition to genetic counseling and prenatal diagnosis by precise linkage analysis in VWD-affected families. PMID:15886817

  3. Linkage results in Schizophrenia

    SciTech Connect

    Baron, M.

    1996-04-09

    In setting a model for replication studies, the collective effort by the various investigators is praiseworthy. The linkage reported is intriguing, but given the aforementioned caveats it would be premature to dub it {open_quotes}significant -- and, probably, confirmed.{close_quotes} The extent to which a real genetic effect exists on chromosome 6p24-22 remains to be seen. Compelling confirmation, which further study might proffer, would be a welcome boost to a fledgling enterprise, where other findings of promise have faltered or failed to gain unequivocal support. The caution advised in this commentary may guide the design and interpretation of other linkage studies in psychiatric disorders.

  4. Time-division SQUID multiplexers

    NASA Astrophysics Data System (ADS)

    Irwin, K. D.; Vale, L. R.; Bergren, N. E.; Deiker, S.; Grossman, E. N.; Hilton, G. C.; Nam, S. W.; Reintsema, C. D.; Rudman, D. A.; Huber, M. E.

    2002-02-01

    SQUID multiplexers make it possible to build arrays of thousands of low-temperature bolometers and microcalorimeters based on superconducting transition-edge sensors with a manageable number of readout channels. We discuss the technical tradeoffs between proposed time-division multiplexer and frequency-division multiplexer schemes and motivate our choice of time division. Our first-generation SQUID multiplexer is now in use in an astronomical instrument. We describe our second-generation SQUID multiplexer, which is based on a new architecture that significantly reduces the dissipation of power at the first stage, allowing thousands of SQUIDs to be operated at the base temperature of a cryostat. .

  5. 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

  6. Extracting information from multiplex networks.

    PubMed

    Iacovacci, Jacopo; Bianconi, Ginestra

    2016-06-01

    Multiplex networks are generalized network structures that are able to describe networks in which the same set of nodes are connected by links that have different connotations. Multiplex networks are ubiquitous since they describe social, financial, engineering, and biological networks as well. Extending our ability to analyze complex networks to multiplex network structures increases greatly the level of information that is possible to extract from big data. For these reasons, characterizing the centrality of nodes in multiplex networks and finding new ways to solve challenging inference problems defined on multiplex networks are fundamental questions of network science. In this paper, we discuss the relevance of the Multiplex PageRank algorithm for measuring the centrality of nodes in multilayer networks and we characterize the utility of the recently introduced indicator function Θ̃(S) for describing their mesoscale organization and community structure. As working examples for studying these measures, we consider three multiplex network datasets coming for social science. PMID:27368796

  7. Extracting information from multiplex networks

    NASA Astrophysics Data System (ADS)

    Iacovacci, Jacopo; Bianconi, Ginestra

    2016-06-01

    Multiplex networks are generalized network structures that are able to describe networks in which the same set of nodes are connected by links that have different connotations. Multiplex networks are ubiquitous since they describe social, financial, engineering, and biological networks as well. Extending our ability to analyze complex networks to multiplex network structures increases greatly the level of information that is possible to extract from big data. For these reasons, characterizing the centrality of nodes in multiplex networks and finding new ways to solve challenging inference problems defined on multiplex networks are fundamental questions of network science. In this paper, we discuss the relevance of the Multiplex PageRank algorithm for measuring the centrality of nodes in multilayer networks and we characterize the utility of the recently introduced indicator function Θ ˜ S for describing their mesoscale organization and community structure. As working examples for studying these measures, we consider three multiplex network datasets coming for social science.

  8. Multiplexed labeling system for high-throughput cell sorting.

    PubMed

    Shin, Seung Won; Park, Kyung Soo; Song, In Hyun; Shin, Woo Jung; Kim, Byung Woo; Kim, Dong-Ik; Um, Soong Ho

    2016-09-01

    Flow cytometry and fluorescence activated cell sorting techniques were designed to realize configurable classification and separation of target cells. A number of cell phenotypes with different functionalities have recently been revealed. Before simultaneous selective capture of cells, it is desirable to label different samples with the corresponding dyes in a multiplexing manner to allow for a single analysis. However, few methods to obtain multiple fluorescent colors for various cell types have been developed. Even when restricted laser sources are employed, a small number of color codes can be expressed simultaneously. In this study, we demonstrate the ability to manifest DNA nanostructure-based multifluorescent colors formed by a complex of dyes. Highly precise self-assembly of fluorescent dye-conjugated oligonucleotides gives anisotropic DNA nanostructures, Y- and tree-shaped DNA (Y-DNA and T-DNA, respectively), which may be used as platforms for fluorescent codes. As a proof of concept, we have demonstrated seven different fluorescent codes with only two different fluorescent dyes using T-DNA. This method provides maximum efficiency for current flow cytometry. We are confident that this system will provide highly efficient multiplexed fluorescent detection for bioanalysis compared with one-to-one fluorescent correspondence for specific marker detection. PMID:27181032

  9. The Market Linkage.

    ERIC Educational Resources Information Center

    Fuchs, Victor E.

    The Market Linkage Project (ML) for Special Education and the Basic Skills Validation and Marketing Program are two federally sponsored marketing projects developed under contract by LINC Resources, Inc., a professional marketing organization, for the U.S. Department of Education. LINC developed the marketing programs to provide the option for the…

  10. Transitions and Linkages.

    ERIC Educational Resources Information Center

    Ilfeld, Ellen M., Ed.; Hanssen, Elizabeth, Ed.

    1997-01-01

    If children are to benefit from a healthy, supportive early childhood experience, it is important to strengthen transitions between early childhood experiences in educational and care settings and the more formal educational system. This issue of Coordinator's Notebook focuses on strengthening linkages and transitions between home, preschool, and…

  11. Genetic linkage analysis using pooled DNA and infrared detection of tailed STRP primer patterns

    NASA Astrophysics Data System (ADS)

    Oetting, William S.; Wildenberg, Scott C.; King, Richard A.

    1996-04-01

    The mapping of a disease locus to a specific chromosomal region is an important step in the eventual isolation and analysis of a disease causing gene. Conventional mapping methods analyze large multiplex families and/or smaller nuclear families to find linkage between the disease and a chromosome marker that maps to a known chromosomal region. This analysis is time consuming and tedious, typically requiring the determination of 30,000 genotypes or more. For appropriate populations, we have instead utilized pooled DNA samples for gene mapping which greatly reduces the amount of time necessary for an initial chromosomal screen. This technique assumes a common founder for the disease locus of interest and searches for a region of a chromosome shared between affected individuals. Our analysis involves the PCR amplification of short tandem repeat polymorphisms (STRP) to detect these shared regions. In order to reduce the cost of genotyping, we have designed unlabeled tailed PCR primers which, when combined with a labeled universal primer, provides for an alternative to synthesizing custom labeled primers. The STRP pattern is visualized with an infrared fluorescence based automated DNA sequencer and the patterns quantitated by densitometric analysis of the allele pattern. Differences in the distribution of alleles between pools of affected and unaffected individuals, including a reduction in the number of alleles in the affected pool, indicate the sharing of a region of a chromosome. We have found this method effective for markers 10 - 15 cM away from the disease locus for a recessive genetic disease.

  12. Downlink Data Multiplexer

    NASA Technical Reports Server (NTRS)

    Holland, Douglas; Steele, Glen F.; Romero, Denise M.; Koudelka, Robert David

    2004-01-01

    A multiplexer/demultiplexer system has been developed to enable the transmission, over a single channel, of four data streams generated by a variety of sources at different (including variable) bit rates. In the original intended application, replicas of this multiplexer/demultiplexer system would be incorporated into the spacecraft-to-ground communication systems of the space shuttles. The multiplexer of each system would be installed in the spacecraft, where it would acquire and process data from such sources as commercial digital camcorders, video tape recorders, and the spacecraft telemetry system. The demultiplexer of each system would be installed in a ground station. Purely terrestrial systems of similar design could be attractive for use in situations in which there are requirements to transmit multiple streams of high-quality video data and possibly other data over single channels. The figure is a block diagram of the multiplexer as configured to process data received via three fiber-optic channels like those of the International Space Station and one electrical-cable channel that conforms to the Institute of Electrical and Electronic Engineers (IEEE) 1394 standard. (This standard consists of specifications of a high-speed serial data interface, the physical layer of which includes a cable known in the art as "FireWire." An IEEE 1394 interface can also transfer power between the components to which it is connected.) The fiber-optic channels carry packet and/or bit-stream signals that conform to the standards of the Consultative Committee for Space Data Systems (CCSDS). The IEEE 1394 interface accepts an isochronous signal like that from a digital camcorder or a video tape recorder. The processing of the four input data streams to combine them into one output stream is governed by a statistical multiplexing algorithm that features a flow-control capability and makes it possible to utilize the transmission channel with nearly 100-percent efficiency. This

  13. Two-locus linkage analysis in multiple sclerosis (MS)

    SciTech Connect

    Tienari, P.J. Univ. of Helsinki ); Terwilliger, J.D.; Ott, J. ); Palo, J. ); Peltonen, L. )

    1994-01-15

    One of the major challenges in genetic linkage analyses is the study of complex diseases. The authors demonstrate here the use of two-locus linkage analysis in multiple sclerosis (MS), a multifactorial disease with a complex mode of inheritance. In a set of Finnish multiplex families, they have previously found evidence for linkage between MS susceptibility and two independent loci, the myelin basic protein gene (MBP) on chromosome 18 and the HLA complex on chromosome 6. This set of families provides a unique opportunity to perform linkage analysis conditional on two loci contributing to the disease. In the two-trait-locus/two-marker-locus analysis, the presence of another disease locus is parametrized and the analysis more appropriately treats information from the unaffected family member than single-disease-locus analysis. As exemplified here in MS, the two-locus analysis can be a powerful method for investigating susceptibility loci in complex traits, best suited for analysis of specific candidate genes, or for situations in which preliminary evidence for linkage already exists or is suggested. 41 refs., 6 tabs.

  14. Tumor specific lung cancer diagnostics with multiplexed FRET immunoassays

    NASA Astrophysics Data System (ADS)

    Geißler, D.; Hill, D.; Löhmannsröben, H.-G.; Thomas, E.; Lavigne, A.; Darbouret, B.; Bois, E.; Charbonnière, L. J.; Ziessel, R. F.; Hildebrandt, N.

    2010-02-01

    An optical multiplexed homogeneous (liquid phase) immunoassay based on FRET from a terbium complex to eight different fluorescent dyes is presented. We achieved highly sensitive parallel detection of four different lung cancer specific tumor markers (CEA, NSE, SCC and CYFRA21-1) within a single assay and show a proof-of-principle for 5- fold multiplexing. The method is well suited for fast and low-cost miniaturized point-of-care testing as well as for highthroughput screening in a broad range of in-vitro diagnostic applications.

  15. Sub-diffraction-limit imaging using mode multiplexing

    NASA Astrophysics Data System (ADS)

    Wang, Nan; Miyazaki, Jun; He, Jinping; Seto, Keisuke; Kobayashi, Takayoshi

    2015-05-01

    Pixel-by-pixel processed fluorescence difference microscopy is experimentally demonstrated by multiplexing excitation laser beams with Gaussian and donut spot shapes and then demultiplexing the fluorescent signals using lock-in amplifiers. With this scheme, a fixed sample of fluorescent spheres and a slice of mouse brain tissue are imaged with resolutions that exceed the diffraction limit. Compared to previously reported subtraction imaging techniques, this pixel-by-pixel scan can be applied to improve the resolution of a moving sample without introducing subtraction errors. The synchronized signal detection feature makes this method extendible to various applications.

  16. Multiplex genomic walking: Integration of the wet lab and computer lab into a single prototyping environment

    SciTech Connect

    Gillevet, P.M.

    1993-12-31

    The authors are presently sequencing the entire genome of Mycoplasma capricolum, one of the smallest of free living organisms by a Multiplex Genomic Walking strategy. This technique involves the repetitive hybridization of sequencing membranes with oligonucleotide probes to acquire sequence data in discrete steps along the genome. The technique allows one to walk a genome in a directed manner eliminating the problems associated with random shotgun assembly. Furthermore, the repetitive stripping and hybridization process is relatively simple to reproduce and has the potential to be easily automated. The Genetic Data Environment (GDE), an X Windows based Graphic User Interface has allowed the seamless integration of a core multiple sequence editor with pre-existing external sequence analysis programs and internally developed programs into a single prototypic environment. This system has facilitated linkage of the 9 Harvard Genome Lab`s internal database and automated data control systems into one Graphic User Interface which can handle the archiving and analysis of both random fluorescent sequencing data and genomic walking data from the Mycoplasma project. Finally, it has facilitated the integration of the Genomic sequence data into a PROLOG database environment for the comparative analysis of Mycoplasma capricolum and other organisms.

  17. Multiplexing oscillatory biochemical signals.

    PubMed

    de Ronde, Wiet; ten Wolde, Pieter Rein

    2014-04-01

    In recent years it has been increasingly recognized that biochemical signals are not necessarily constant in time and that the temporal dynamics of a signal can be the information carrier. Moreover, it is now well established that the protein signaling network of living cells has a bow-tie structure and that components are often shared between different signaling pathways. Here we show by mathematical modeling that living cells can multiplex a constant and an oscillatory signal: they can transmit these two signals simultaneously through a common signaling pathway, and yet respond to them specifically and reliably. We find that information transmission is reduced not only by noise arising from the intrinsic stochasticity of biochemical reactions, but also by crosstalk between the different channels. Yet, under biologically relevant conditions more than 2 bits of information can be transmitted per channel, even when the two signals are transmitted simultaneously. These observations suggest that oscillatory signals are ideal for multiplexing signals. PMID:24685537

  18. Multiplex data bus simulator

    SciTech Connect

    Garbo, D.L.

    1983-01-01

    A multiplex data-bus simulator for analyzing multiprocessor designs is presented. The simulator was designed to be user-friendly, thus allowing a multiprocessor designer to enter various configuration inputs in a concise and orderly fashion through the use of menus. The designer is also provided a method of visualizing a message traffic flow through the use of graphical representation of events. 3 references.

  19. Single-Step Multiplex PCR Assay for Determining 92 Pneumococcal Serotypes.

    PubMed

    Marimón, José M; Ercibengoa, María; Santacatterina, Erica; Alonso, Marta; Pérez-Trallero, Emilio

    2016-08-01

    For pneumococcal disease surveillance, simple and cost-effective methods capable of determining all serotypes are needed. Combining a single-tube multiplex PCR with fluorescently labeled primers followed by amplicon analysis using automated fluorescent capillary electrophoresis, each serotype of 92 reference isolates and 297 recently collected clinical isolates was successfully determined. PMID:27280423

  20. Self-calibrating multiplexer circuit

    DOEpatents

    Wahl, Chris P.

    1997-01-01

    A time domain multiplexer system with automatic determination of acceptable multiplexer output limits, error determination, or correction is comprised of a time domain multiplexer, a computer, a constant current source capable of at least three distinct current levels, and two series resistances employed for calibration and testing. A two point linear calibration curve defining acceptable multiplexer voltage limits may be defined by the computer by determining the voltage output of the multiplexer to very accurately known input signals developed from predetermined current levels across the series resistances. Drift in the multiplexer may be detected by the computer when the output voltage limits, expected during normal operation, are exceeded, or the relationship defined by the calibration curve is invalidated.

  1. Self-calibrating multiplexer circuit

    SciTech Connect

    Wahl, C.P.

    1995-12-31

    A time domain multiplexer system with automatic determination of acceptable multiplexer output limits, error determination, or correction is comprised of a time domain multiplexer, a computer, a constant current source capable of at least three distinct current levels, and two series resistances employed for calibration and testing. A two point linear calibration curve defining acceptable multiplexer voltage limits may be defined by the computer by determining the voltage output of the multiplexer to very accurately known input signals developed from predetermined current levels across the series resistances. Drift in the multiplexer may be detected by the computer when the output voltage limits, expected during normal operation, are exceeded, or the relationship defined by the calibration curve is invalidated.

  2. Linkage map integration

    SciTech Connect

    Collins, A.; Teague, J.; Morton, N.E.; Keats, B.J.

    1996-08-15

    The algorithms that drive the map+ program for locus-oriented linkage mapping are presented. They depend on the enhanced location database program ldb+ to specify an initial comprehensive map that includes all loci in the summary lod file. Subsequently the map may be edited or order constrained and is automatically improved by estimating the location of each locus conditional on the remainder, beginning with the most discrepant loci. Operating characteristics permit rapid and accurate construction of linkage maps with several hundred loci. The map+ program also performs nondisjunction mapping with tests of nonstandard recombination. We have released map+ on Internet as a source program in the C language together with the location database that now includes the LODSOURCE database. 28 refs., 5 tabs.

  3. Spectrally resolved multidepth fluorescence imaging

    PubMed Central

    Luo, Yuan; Zervantonakis, Ioannis K.; Oh, Se Baek; Kamm, Roger D.; Barbastathis, George

    2011-01-01

    We present a multicolor fluorescence imaging modality to visualize in real-time tissue structures emitting multispectral fluorescent light from different focal depths. Each designated spectrum of fluorescent emission from a specific depth within a volumetric tissue is probed by a depth-spectrum selective holographic grating. The grating for each fluorescent color are multiplexed within a volume hologram, which enables simultaneously obtaining multicolored fluorescent information at different depths within a biological tissue sample. We demonstrate the imaging modality's ability to obtain laser-induced multicolored fluorescence images of a biological sample from different depths without scanning. We also experimentally demonstrate that the imaging modality can be simultaneously operated at both fluorescent and bright field modes to provide complementary information of volumetric tissue structures at different depths in real-time. PMID:21950929

  4. Spectrally resolved multidepth fluorescence imaging

    NASA Astrophysics Data System (ADS)

    Luo, Yuan; Zervantonakis, Ioannis K.; Oh, Se Baek; Kamm, Roger D.; Barbastathis, George

    2011-09-01

    We present a multicolor fluorescence imaging modality to visualize in real-time tissue structures emitting multispectral fluorescent light from different focal depths. Each designated spectrum of fluorescent emission from a specific depth within a volumetric tissue is probed by a depth-spectrum selective holographic grating. The grating for each fluorescent color are multiplexed within a volume hologram, which enables simultaneously obtaining multicolored fluorescent information at different depths within a biological tissue sample. We demonstrate the imaging modality's ability to obtain laser-induced multicolored fluorescence images of a biological sample from different depths without scanning. We also experimentally demonstrate that the imaging modality can be simultaneously operated at both fluorescent and bright field modes to provide complementary information of volumetric tissue structures at different depths in real-time.

  5. Hardware Counter Multiplexing

    Energy Science and Technology Software Center (ESTSC)

    2000-10-13

    The Hardware Counter Multiplexer works with the built-in counter registers on computer processors. These counters record various low-level events as software runs, but they can not record all possible events at the same time. This software helps work around that limitation by counting a series of different events in sequence over a period of time. This in turn allows programmers to measure interesting combinations of events, rather than single events. The software is designed tomore » work with multithreaded or single-threaded programs.« less

  6. Optofluidic wavelength division multiplexing for single-virus detection

    PubMed Central

    Ozcelik, Damla; Parks, Joshua W.; Wall, Thomas A.; Stott, Matthew A.; Cai, Hong; Parks, Joseph W.; Hawkins, Aaron R.; Schmidt, Holger

    2015-01-01

    Optical waveguides simultaneously transport light at different colors, forming the basis of fiber-optic telecommunication networks that shuttle data in dozens of spectrally separated channels. Here, we reimagine this wavelength division multiplexing (WDM) paradigm in a novel context––the differentiated detection and identification of single influenza viruses on a chip. We use a single multimode interference (MMI) waveguide to create wavelength-dependent spot patterns across the entire visible spectrum and enable multiplexed single biomolecule detection on an optofluidic chip. Each target is identified by its time-dependent fluorescence signal without the need for spectral demultiplexing upon detection. We demonstrate detection of individual fluorescently labeled virus particles of three influenza A subtypes in two implementations: labeling of each virus using three different colors and two-color combinatorial labeling. By extending combinatorial multiplexing to three or more colors, MMI-based WDM provides the multiplexing power required for differentiated clinical tests and the growing field of personalized medicine. PMID:26438840

  7. Duck (Anas platyrhynchos) linkage mapping by AFLP fingerprinting

    PubMed Central

    Huang, Chang-Wen; Cheng, Yu-Shin; Rouvier, Roger; Yang, Kuo-Tai; Wu, Chean-Ping; Huang, Hsiu-Lin; Huang, Mu-Chiou

    2009-01-01

    Amplified fragment length polymorphism (AFLP) with multicolored fluorescent molecular markers was used to analyze duck (Anas platyrhynchos) genomic DNA and to construct the first AFLP genetic linkage map. These markers were developed and genotyped in 766 F2 individuals from six families from a cross between two different selected duck lines, brown Tsaiya and Pekin. Two hundred and ninety-six polymorphic bands (64% of all bands) were detected using 18 pairs of fluorescent TaqI/EcoRI primer combinations. Each primer set produced a range of 7 to 29 fragments in the reactions, and generated on average 16.4 polymorphic bands. The AFLP linkage map included 260 co-dominant markers distributed in 32 linkage groups. Twenty-one co-dominant markers were not linked with any other marker. Each linkage group contained three to 63 molecular markers and their size ranged between 19.0 cM and 171.9 cM. This AFLP linkage map provides important information for establishing a duck chromosome map, for mapping quantitative trait loci (QTL mapping) and for breeding applications. PMID:19291328

  8. Highspeed multiplexed heterodyne interferometry.

    PubMed

    Isleif, Katharina-S; Gerberding, Oliver; Köhlenbeck, Sina; Sutton, Andrew; Sheard, Benjamin; Goßler, Stefan; Shaddock, Daniel; Heinzel, Gerhard; Danzmann, Karsten

    2014-10-01

    Digitally enhanced heterodyne interferometry is a metrology technique that uses pseudo-random noise codes for modulating the phase of the laser light. Multiple interferometric signals from the same beam path can thereby be isolated based on their propagation delay, allowing one to use advantageous optical layouts in comparison to classic laser interferometers. We present here a high speed version of this technique for measuring multiple targets spatially separated by only a few centimetres. This allows measurements of multiplexed signals using free beams, making the technique attractive for several applications requiring compact optical set-ups like for example space-based interferometers. In an experiment using a modulation and sampling rate of 1.25 GHz we are able to demonstrate multiplexing between targets only separated by 36 cm and we achieve a displacement measurement noise floor of <3 pm/√Hz at 10 Hz between them. We identify a limiting excess noise at low frequencies which is unique to this technique and is probably caused by the finite bandwidth in our measurement set-up. Utilising an active clock jitter correction scheme we are also able to reduce this noise in a null measurement configuration by one order of magnitude. PMID:25322043

  9. Genetic structure and linkage disequilibrium in a diverse, representative collection of the C4 model plant, Sorghum bicolor

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To facilitate the mapping of genes in sorghum [Sorghum bicolor (L.) Moench] underlying economically important traits, we analyzed the genetic structure and linkage disequilibrium in a sorghum mini core collection of 242 landraces with 14,739 SNPs. The SNPs were produced using a highly multiplexed g...

  10. Multiplexed aberration measurement for deep tissue imaging in vivo

    PubMed Central

    Wang, Chen; Liu, Rui; Milkie, Daniel E.; Sun, Wenzhi; Tan, Zhongchao; Kerlin, Aaron; Chen, Tsai-Wen; Kim, Douglas S.; Ji, Na

    2014-01-01

    We describe a multiplexed aberration measurement method that modulates the intensity or phase of light rays at multiple pupil segments in parallel to determine their phase gradients. Applicable to fluorescent-protein-labeled structures of arbitrary complexity, it allows us to obtain diffraction-limited resolution in various samples in vivo. For the strongly scattering mouse brain, a single aberration correction improves structural and functional imaging of fine neuronal processes over a large imaging volume. PMID:25128976

  11. Irish study of high-density Schizophrenia families: Field methods and power to detect linkage

    SciTech Connect

    Kendler, K.S.; Straub, R.E.; MacLean, C.J.

    1996-04-09

    Large samples of multiplex pedigrees will probably be needed to detect susceptibility loci for schizophrenia by linkage analysis. Standardized ascertainment of such pedigrees from culturally and ethnically homogeneous populations may improve the probability of detection and replication of linkage. The Irish Study of High-Density Schizophrenia Families (ISHDSF) was formed from standardized ascertainment of multiplex schizophrenia families in 39 psychiatric facilities covering over 90% of the population in Ireland and Northern Ireland. We here describe a phenotypic sample and a subset thereof, the linkage sample. Individuals were included in the phenotypic sample if adequate diagnostic information, based on personal interview and/or hospital record, was available. Only individuals with available DNA were included in the linkage sample. Inclusion of a pedigree into the phenotypic sample required at least two first, second, or third degree relatives with non-affective psychosis (NAP), one of whom had schizophrenia (S) or poor-outcome schizoaffective disorder (PO-SAD). Entry into the linkage sample required DNA samples on at least two individuals with NAP, of whom at least one had S or PO-SAD. Affection was defined by narrow, intermediate, and broad criteria. 75 refs., 6 tabs.

  12. Information multiplexing in ptychography.

    PubMed

    Batey, Darren J; Claus, Daniel; Rodenburg, John M

    2014-03-01

    We show for the first time that ptychography (a form of lensless diffractive imaging) can recover the spectral response of an object through simultaneous reconstruction of multiple images that represent the object's response to a particular mode present in the illumination. We solve the phase problem for each mode independently, even though the intensity arriving at every detector pixel is an incoherent superposition of several uncorrelated diffracted waves. Until recently, the addition of incoherent modes has been seen as a nuisance in diffractive imaging: here we show that not only can the difficulties they pose be removed, but that they can also be used to discover much more information about the object. If the illumination function is also mode-specific, we show that we can also solve simultaneously for a multiplicity of such illumination modes. The work opens exciting possibilities for information multiplexing in ptychography over all visible, X-ray and electron wavelengths. PMID:24413077

  13. A variable age of onset segregation model for linkage analysis, with correction for ascertainment, applied to glioma

    PubMed Central

    Sun, Xiangqing; Vengoechea, Jaime; Elston, Robert; Chen, Yanwen; Amos, Christopher I.; Armstrong, Georgina; Bernstein, Jonine L; Claus, Elizabeth; Davis, Faith; Houlston, Richard S; Il'yasova, Dora; Jenkins, Robert B; Johansen, Christoffer; Lai, Rose; Lau, Ching C; Liu, Yanhong; McCarthy, Bridget J; Olson, Sara H; Sadetzki, Siegal; Schildkraut, Joellen; Shete, Sanjay; Yu, Robert; Vick, Nicholas A; Merrell, Ryan; Wrensch, Margaret; Yang, Ping; Melin, Beatrice; Bondy, Melissa L.; Barnholtz-Sloan, Jill S.

    2012-01-01

    Background We propose a two-step model-based approach, with correction for ascertainment, to linkage analysis of a binary trait with variable age of onset and apply it to a set of multiplex pedigrees segregating for adult glioma. Methods First, we fit segregation models by formulating the likelihood for a person to have a bivariate phenotype, affection status and age of onset, along with other covariates, and from these we estimate population trait allele frequencies and penetrance parameters as a function of age (N=281 multiplex glioma pedigrees). Second, the best fitting models are used as trait models in multipoint linkage analysis (N=74 informative multiplex glioma pedigrees). To correct for ascertainment, a prevalence constraint is used in the likelihood of the segregation models for all 281 pedigrees. Then the trait allele frequencies are re-estimated for the pedigree founders of the subset of 74 pedigrees chosen for linkage analysis. Results Using the best fitting segregation models in model-based multipoint linkage analysis, we identified two separate peaks on chromosome 17; the first agreed with a region identified by Shete et al. who used model-free affected-only linkage analysis, but with a narrowed peak: and the second agreed with a second region they found but had a larger maximum log of the odds (LOD). Conclusions/Impact Our approach has the advantage of not requiring markers to be in linkage equilibrium unless the minor allele frequency is small (markers which tend to be uninformative for linkage), and of using more of the available information for LOD-based linkage analysis. PMID:22962404

  14. Multiplexer and time duration measuring circuit

    SciTech Connect

    Gray, Jr., James

    1980-01-01

    A multiplexer device is provided for multiplexing data in the form of randomly developed, variable width pulses from a plurality of pulse sources to a master storage. The device includes a first multiplexer unit which includes a plurality of input circuits each coupled to one of the pulse sources, with all input circuits being disabled when one input circuit receives an input pulse so that only one input pulse is multiplexed by the multiplexer unit at any one time.

  15. A 128 Multiplexing Factor Time-Domain SQUID Multiplexer

    NASA Astrophysics Data System (ADS)

    Prêle, D.; Voisin, F.; Piat, M.; Decourcelle, T.; Perbost, C.; Chapron, C.; Rambaud, D.; Maestre, S.; Marty, W.; Montier, L.

    2016-01-01

    A cryogenic 128:1 Time-Domain Multiplexer (TDM) has been developed for the readout of kilo-pixel Transition Edge Sensor (TES) arrays dedicated to the Q&U Bolometric Interferometer for Cosmology (QUBIC) instrument which aims to measure the B-mode polarization of the Cosmic Microwave Background. Superconducting QUantum Interference Devices (SQUIDs) are usually used to read out TESs. Moreover, SQUIDs are used to build TDM by biasing sequentially the SQUIDs connected together—one for each TES. In addition to this common technique which allows a typical 32 multiplexing factor, a cryogenic integrated circuit provides a 4:1 second multiplexing stage. This cryogenic integrated circuit is one of the original part of our TDM achieving an unprecedented 128 multiplexing factor. We present these two dimension TDM stages: topology of the SQUID multiplexer, operation of the cryogenic integrated circuit, and integration of the full system to read out a TES array dedicated to the QUBIC instrument. Flux-locked loop operation in multiplexed mode is also discussed.

  16. A 128 Multiplexing Factor Time-Domain SQUID Multiplexer

    NASA Astrophysics Data System (ADS)

    Prêle, D.; Voisin, F.; Piat, M.; Decourcelle, T.; Perbost, C.; Chapron, C.; Rambaud, D.; Maestre, S.; Marty, W.; Montier, L.

    2016-07-01

    A cryogenic 128:1 Time-Domain Multiplexer (TDM) has been developed for the readout of kilo-pixel Transition Edge Sensor (TES) arrays dedicated to the Q&U Bolometric Interferometer for Cosmology (QUBIC) instrument which aims to measure the B-mode polarization of the Cosmic Microwave Background. Superconducting QUantum Interference Devices (SQUIDs) are usually used to read out TESs. Moreover, SQUIDs are used to build TDM by biasing sequentially the SQUIDs connected together—one for each TES. In addition to this common technique which allows a typical 32 multiplexing factor, a cryogenic integrated circuit provides a 4:1 second multiplexing stage. This cryogenic integrated circuit is one of the original part of our TDM achieving an unprecedented 128 multiplexing factor. We present these two dimension TDM stages: topology of the SQUID multiplexer, operation of the cryogenic integrated circuit, and integration of the full system to read out a TES array dedicated to the QUBIC instrument. Flux-locked loop operation in multiplexed mode is also discussed.

  17. Multiplexed Microsphere Suspension Array-Based Immunoassays.

    PubMed

    Lin, Andrew; Salvador, Alexandra; Carter, J Mark

    2015-01-01

    ELISA is an extremely powerful tool to detect analytes because of its sensitivity, selectivity, reproducibility and ease of use. Here we describe sandwich immunoassays performed in suspension on spectrally unique microspheres developed by Luminex. Luminex assays offer the benefit of multiplex analysis of large numbers of analytes in a single reaction. Because the microspheres are spectrally unique, many microspheres, each attached to various antibodies, can be added to a single sample. Luminex instruments can distinguish each microsphere and detect the intensity of a reporter signal for each microsphere. Results are reported in Median Fluorescent Intensities for each analyte. Luminex assays can be used to detect up to 500 analytes in a high-throughput format. Luminex refers to this technology as xMAP(®). Here we describe a routine protocol for a Luminex immunoassay. Other Luminex assays would have to be optimized for specific conditions according to their use. PMID:26160569

  18. Linkage analysis of anorexia nervosa incorporating behavioral covariates.

    PubMed

    Devlin, Bernie; Bacanu, Silviu-Alin; Klump, Kelly L; Bulik, Cynthia M; Fichter, Manfred M; Halmi, Katherine A; Kaplan, Allan S; Strober, Michael; Treasure, Janet; Woodside, D Blake; Berrettini, Wade H; Kaye, Walter H

    2002-03-15

    Eating disorders, such as anorexia nervosa (AN) and bulimia nervosa (BN), have genetic and environmental underpinnings. To explore genetic contributions to AN, we measured psychiatric, personality and temperament phenotypes of individuals diagnosed with eating disorders from 196 multiplex families, all accessed through an AN proband, as well as genotyping a battery of 387 short tandem repeat (STR) markers distributed across the genome. On these data we performed a multipoint affected sibling pair (ASP) linkage analysis using a novel method that incorporates covariates. By exploring seven attributes thought to typify individuals with eating disorders, we identified two variables, drive-for-thinness and obsessionality, which delimit populations among the ASPs. For both of these traits, or covariates, there were a cluster of ASPs who have high and concordant values for these traits, in keeping with our expectations for individuals with AN, and other clusters of ASPs who did not meet those expectations. When we incorporated these covariates into the ASP linkage analysis, both jointly and separately, we found several regions of suggestive linkage: one close to genome-wide significance on chromosome 1 (at 210 cM, D1S1660; LOD = 3.46, P = 0.00003), another on chromosome 2 (at 114 cM, D2S1790; LOD = 2.22, P = 0.00070) and a third region on chromosome 13 (at 26 cM, D13S894; LOD = 2.50, P = 0.00035). By comparing our results to those implemented using more standard linkage methods, we find the covariates convey substantial information for the linkage analysis. PMID:11912184

  19. A protein multiplex microarray substrate with high sensitivity and specificity

    PubMed Central

    Fici, Dolores A.; McCormick, William; Brown, David W.; Herrmann, John E.; Kumar, Vikram; Awdeh, Zuheir L.

    2010-01-01

    The problems that have been associated with protein multiplex microarray immunoassay substrates and existing technology platforms include: binding, sensitivity, a low signal to noise ratio, target immobilization and the optimal simultaneous detection of diverse protein targets. Current commercial substrates for planar multiplex microarrays rely on protein attachment chemistries that range from covalent attachment to affinity ligand capture, to simple adsorption. In this pilot study, experimental performance parameters for direct monoclonal mouse IgG detection were compared for available two and three dimensional slide surface coatings with a new colloidal nitrocellulose substrate. New technology multiplex microarrays were also developed and evaluated for the detection of pathogen specific antibodies in human serum and the direct detection of enteric viral antigens. Data supports the nitrocellulose colloid as an effective reagent with the capacity to immobilize sufficient diverse protein target quantities for increased specificory signal without compromising authentic protein structure. The nitrocellulose colloid reagent is compatible with the array spotters and scanners routinely used for microarray preparation and processing. More importantly, as an alternate to fluorescence, colorimetric chemistries may be used for specific and sensitive protein target detection. The advantages of the nitrocellulose colloid platform indicate that this technology may be a valuable tool for the further development and expansion of multiplex microarray immunoassays in both the clinical and research laborat environment. PMID:20974147

  20. Multiplexed Dip Pen Nanolithography patterning by simple desktop nanolithography platform

    NASA Astrophysics Data System (ADS)

    Jang, Jae-Won; Smetana, Alexander; Stiles, Paul

    2010-02-01

    Multiplexed patterning in the micro-scale has been required in order to accomplish functional bio-materials templating on the subcellular length scale. Multiplexed bio-material patterns can be used in several fields: high sensitivity DNA/protein chip development, cell adhesion/differentiation studies, and biological sensor applications. Especially, two or more materials' patterning in subcellular length scale is highly demanding to develop a multi-functional and highintegrated chip device. The multiplexing patterning of two or more materials is a challenge because of difficulty in an alignment and a precision of patterning. In this work, we demonstrate that multiplexed dip pen nanolithography® (DPN®) patterning up to four different material inks by means of using recently developed new generation nanolithography platform (NLP 2000™, NanoInk, Inc., Skokie, IL). Ink materials were prepared by adding different colored fluorescent dyes to matrix carrier materials, such as poly(ethylene glycol) dimethacrylate (PEG-DMA) and lipid material (1,2- dioleoyl-sn-glycero-3-phosphocholine, DOPC). Finally, dot-array patterns of four different inks were obtained in 50 × 50 μm2 area. This lithography platform is capable of patterning 12 separate materials within micrometer areas by efficient use of the available MEMS accessories. This number can be scaled up further with development of new accessories.

  1. Multiplex suspension array for human anti-carbohydrate antibody profiling.

    PubMed

    Pochechueva, Tatiana; Chinarev, Alexander; Spengler, Marianne; Korchagina, Elena; Heinzelmann-Schwarz, Viola; Bovin, Nicolai; Rieben, Robert

    2011-02-01

    Glycan-binding antibodies form a significant subpopulation of both natural and acquired antibodies and play an important role in various immune processes. They are for example involved in innate immune responses, cancer, autoimmune diseases, and neurological disorders. In the present study, a microsphere-based flow-cytometric immunoassay (suspension array) was applied for multiplexed detection of glycan-binding antibodies in human serum. Several approaches for immobilization of glycoconjugates onto commercially available fluorescent microspheres were compared, and as the result, the design based on coupling of end-biotinylated glycopolymers has been selected. This method requires only minute amounts of glycans, similar to a printed glycan microarray. The resulting glyco-microspheres were used for detection of IgM and IgG antibodies directed against ABO blood group antigens. The possibility of multiplexing this assay was demonstrated with mixtures of microspheres modified with six different ABO related glycans. Multiplexed detection of anti-glycan IgM and IgG correlated well with singleplex assays (Pearson's correlation coefficient r = 0.95-0.99 for sera of different blood groups). The suspension array in singleplex format for A/B trisaccharide, H(di) and Le(x) microspheres corresponded well to the standard ELISA (r > 0.94). Therefore, the described method is promising for rapid, sensitive, and reproducible detection of anti-glycan antibodies in a multiplexed format. PMID:21107457

  2. Linkage analysis of candidate myelin genes in familial multiple sclerosis.

    PubMed

    Seboun, E; Oksenberg, J R; Rombos, A; Usuku, K; Goodkin, D E; Lincoln, R R; Wong, M; Pham-Dinh, D; Boesplug-Tanguy, O; Carsique, R; Fitoussi, R; Gartioux, C; Reyes, C; Ribierre, F; Faure, S; Fizames, C; Gyapay, G; Weissenbach, J; Dautigny, A; Rimmler, J B; Garcia, M E; Pericak-Vance, M A; Haines, J L; Hauser, S L

    1999-09-01

    Multiple sclerosis (MS) is an autoimmune demyelinating disease of the central nervous system. A complex genetic etiology is thought to underlie susceptibility to this disease. The present study was designed to analyze whether differences in genes that encode myelin proteins influence susceptibility to MS. We performed linkage analysis of MS to markers in chromosomal regions that include the genes encoding myelin basic protein (MBP), proteolipid protein (PLP), myelin-associated glycoprotein (MAG), oligodendrocyte myelin glycoprotein (OMGP), and myelin oligodendrocyte glycoprotein (MOG) in a well-characterized population of 65 multiplex MS families consisting of 399 total individuals, 169 affected with MS and 102 affected sibpairs. Physical mapping data permitted placement of MAG and PLP genes on the Genethon genetic map; all other genes were mapped on the Genethon genetic map by linkage analysis. For each gene, at least one marker within the gene and/or two tightly linked flanking markers were analyzed. Marker data analysis employed a combination of genetic trait model-dependent (parametric) and model-independent linkage methods. Results indicate that MAG, MBP, OMGP, and PLP genes do not have a significant genetic effect on susceptibility to MS in this population. As MOG resides within the MHC, a potential role of the MOG gene could not be excluded. PMID:10541588

  3. Sensitive giant magnetoresistive-based immunoassay for multiplex mycotoxin detection.

    PubMed

    Mak, Andy C; Osterfeld, Sebastian J; Yu, Heng; Wang, Shan X; Davis, Ronald W; Jejelowo, Olufisayo A; Pourmand, Nader

    2010-03-15

    Rapid and multiplexed measurement is vital in the detection of food-borne pathogens. While highly specific and sensitive, traditional immunochemical assays such as enzyme-linked immunosorbent assays (ELISAs) often require expensive read-out equipment (e.g. fluorescent labels) and lack the capability of multiplex detection. By combining the superior specificity of immunoassays with the sensitivity and simplicity of magnetic detection, we have developed a novel multiplex magnetic nanotag-based detection platform for mycotoxins that functions on a sub-picomolar concentration level. Unlike fluorescent labels, magnetic nanotags (MNTs) can be detected with inexpensive giant magnetoresistive (GMR) sensors such as spin-valve sensors. In the system presented here, each spin-valve sensor has an active area of 90 microm x 90 microm, arranged in an 8 x 8 array. Sample is added to the antibody-immobilized sensor array prior to the addition of the biotinylated detection antibody. The sensor response is recorded in real time upon the addition of streptavidin-linked MNTs on the chip. Here we demonstrate the simultaneous detection of multiple mycotoxins (aflatoxins B(1), zearalenone and HT-2) and show that a detection limit of 50 pg/mL can be achieved. PMID:20047828

  4. Efficient exploration of multiplex networks

    NASA Astrophysics Data System (ADS)

    Battiston, Federico; Nicosia, Vincenzo; Latora, Vito

    2016-04-01

    Efficient techniques to navigate networks with local information are fundamental to sample large-scale online social systems and to retrieve resources in peer-to-peer systems. Biased random walks, i.e. walks whose motion is biased on properties of neighbouring nodes, have been largely exploited to design smart local strategies to explore a network, for instance by constructing maximally mixing trajectories or by allowing an almost uniform sampling of the nodes. Here we introduce and study biased random walks on multiplex networks, graphs where the nodes are related through different types of links organised in distinct and interacting layers, and we provide analytical solutions for their long-time properties, including the stationary occupation probability distribution and the entropy rate. We focus on degree-biased random walks and distinguish between two classes of walks, namely those whose transition probability depends on a number of parameters which is extensive in the number of layers, and those whose motion depends on intrinsically multiplex properties of the neighbouring nodes. We analyse the effect of the structure of the multiplex network on the steady-state behaviour of the walkers, and we find that heterogeneous degree distributions as well as the presence of inter-layer degree correlations and edge overlap determine the extent to which a multiplex can be efficiently explored by a biased walk. Finally we show that, in real-world multiplex transportation networks, the trade-off between efficient navigation and resilience to link failure has resulted into systems whose diffusion properties are qualitatively different from those of appropriately randomised multiplex graphs. This fact suggests that multiplexity is an important ingredient to include in the modelling of real-world systems.

  5. Higher Education: Labor Market Linkage.

    ERIC Educational Resources Information Center

    Asayeghn, Desta

    1982-01-01

    Examines the methodology of three case studies investigating the linkage between higher education and the world of work in the Sudan, Zambia, and Tanzania. Summarizes 12 main findings. Suggests the studies remain traditional human resources planning efforts. (NEC)

  6. Exploring linkage disequilibrium.

    PubMed

    Baird, Stuart J E

    2015-09-01

    Linkage disequilibrium (LD, association of allelic states across loci) is poorly understood by many evolutionary biologists, but as technology for multilocus sampling improves, we ignore LD at our peril. If we sample variation at 10 loci in an organism with 20 chromosomes, we can reasonably treat them as 10 'independent witnesses' of the evolutionary process. If instead, we sample variation at 1000 loci, many are bound to be close together on a chromosome. With only one or two crossovers per meiosis, associations between close neighbours decay so slowly that even LD created far in the past will not have dissipated, so we cannot treat the 1000 loci as independent witnesses (Barton ). This means that as marker density on genomes increases classic analyses assuming independent loci become mired in the problem of overconfidence: if 1000 independent witnesses are assumed, and that number should be much lower, any conclusion will be overconfident. This is of special concern because our literature suffers from a strong publication bias towards confident answers, even when they turn out to be wrong (Knowles ). In contrast, analyses that take into account associations across loci both control for overconfidence and can inform us about LD generating events far in the past, for example human/Neanderthal admixture (Fu et al. ). With increased marker density, biologists must increase their awareness of LD and, in this issue of Molecular Ecology Resources, Kemppainen et al. () make software available that can only help in this process: LDna allows patterns of LD in a data set to be explored using tools borrowed from network analysis. This has great potential, but realizing that potential requires understanding LD. PMID:26261040

  7. Thermally multiplexed polymerase chain reaction

    PubMed Central

    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.

    2015-01-01

    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. PMID:26339317

  8. Structural measures for multiplex networks

    NASA Astrophysics Data System (ADS)

    Battiston, Federico; Nicosia, Vincenzo; Latora, Vito

    2014-03-01

    Many real-world complex systems consist of a set of elementary units connected by relationships of different kinds. All such systems are better described in terms of multiplex networks, where the links at each layer represent a different type of interaction between the same set of nodes rather than in terms of (single-layer) networks. In this paper we present a general framework to describe and study multiplex networks, whose links are either unweighted or weighted. In particular, we propose a series of measures to characterize the multiplexicity of the systems in terms of (i) basic node and link properties such as the node degree, and the edge overlap and reinforcement, (ii) local properties such as the clustering coefficient and the transitivity, and (iii) global properties related to the navigability of the multiplex across the different layers. The measures we introduce are validated on a genuinely multiplex data set of Indonesian terrorists, where information among 78 individuals are recorded with respect to mutual trust, common operations, exchanged communications, and business relationships.

  9. Structural measures for multiplex networks.

    PubMed

    Battiston, Federico; Nicosia, Vincenzo; Latora, Vito

    2014-03-01

    Many real-world complex systems consist of a set of elementary units connected by relationships of different kinds. All such systems are better described in terms of multiplex networks, where the links at each layer represent a different type of interaction between the same set of nodes rather than in terms of (single-layer) networks. In this paper we present a general framework to describe and study multiplex networks, whose links are either unweighted or weighted. In particular, we propose a series of measures to characterize the multiplexicity of the systems in terms of (i) basic node and link properties such as the node degree, and the edge overlap and reinforcement, (ii) local properties such as the clustering coefficient and the transitivity, and (iii) global properties related to the navigability of the multiplex across the different layers. The measures we introduce are validated on a genuinely multiplex data set of Indonesian terrorists, where information among 78 individuals are recorded with respect to mutual trust, common operations, exchanged communications, and business relationships. PMID:24730896

  10. Bond Percolation on Multiplex Networks

    NASA Astrophysics Data System (ADS)

    Hackett, A.; Cellai, D.; Gómez, S.; Arenas, A.; Gleeson, J. P.

    2016-04-01

    We present an analytical approach for bond percolation on multiplex networks and use it to determine the expected size of the giant connected component and the value of the critical bond occupation probability in these networks. We advocate the relevance of these tools to the modeling of multilayer robustness and contribute to the debate on whether any benefit is to be yielded from studying a full multiplex structure as opposed to its monoplex projection, especially in the seemingly irrelevant case of a bond occupation probability that does not depend on the layer. Although we find that in many cases the predictions of our theory for multiplex networks coincide with previously derived results for monoplex networks, we also uncover the remarkable result that for a certain class of multiplex networks, well described by our theory, new critical phenomena occur as multiple percolation phase transitions are present. We provide an instance of this phenomenon in a multiplex network constructed from London rail and European air transportation data sets.

  11. Linkages in thermal copolymers of lysine

    NASA Technical Reports Server (NTRS)

    Fox, S. W.; Suzuki, F.

    1975-01-01

    The thermal copolymerization of lysine with other alpha-amino acids was studied. The identity of the second amino acid influences various properties of the polymer obtained, including the proportion of alpha and epsilon linkages of lysine. A review of linkages in proteinoids indicates alpha and beta linkages for aspartic acid, alpha and gamma linkages for glutamic acid, alpha and epsilon linkages for lysine, and alpha linkages for other amino acids. Thermal proteinoids are thus more complex in types of linkage than are proteins.

  12. Linkages in thermal copolymers of lysine

    NASA Technical Reports Server (NTRS)

    Fox, S. W.; Suzuki, F.

    1976-01-01

    The thermal copolymerization of lysine with other alpha-amino acids has been studied further. The identity of the second amino acid influences various properties of the polymer obtained, including the proportion of alpha and epsilon linkages of lysine. A review of linkages in proteinoids indicates alpha and beta linkages for aspartic acid, alpha and gamma linkages for glutamic acid, alpha and epsilon linkages for lysine, and alpha linkages for other amino acids. Thermal proteinoids are thus more complex in types of linkage than are proteins

  13. Helicity multiplexed broadband metasurface holograms

    PubMed Central

    Wen, Dandan; Yue, Fuyong; Li, Guixin; Zheng, Guoxing; Chan, Kinlong; Chen, Shumei; Chen, Ming; Li, King Fai; Wong, Polis Wing Han; Cheah, Kok Wai; Yue Bun Pun, Edwin; Zhang, Shuang; Chen, Xianzhong

    2015-01-01

    Metasurfaces are engineered interfaces that contain a thin layer of plasmonic or dielectric nanostructures capable of manipulating light in a desirable manner. Advances in metasurfaces have led to various practical applications ranging from lensing to holography. Metasurface holograms that can be switched by the polarization state of incident light have been demonstrated for achieving polarization multiplexed functionalities. However, practical application of these devices has been limited by their capability for achieving high efficiency and high image quality. Here we experimentally demonstrate a helicity multiplexed metasurface hologram with high efficiency and good image fidelity over a broad range of frequencies. The metasurface hologram features the combination of two sets of hologram patterns operating with opposite incident helicities. Two symmetrically distributed off-axis images are interchangeable by controlling the helicity of the input light. The demonstrated helicity multiplexed metasurface hologram with its high performance opens avenues for future applications with functionality switchable optical devices. PMID:26354497

  14. Helicity multiplexed broadband metasurface holograms.

    PubMed

    Wen, Dandan; Yue, Fuyong; Li, Guixin; Zheng, Guoxing; Chan, Kinlong; Chen, Shumei; Chen, Ming; Li, King Fai; Wong, Polis Wing Han; Cheah, Kok Wai; Pun, Edwin Yue Bun; Zhang, Shuang; Chen, Xianzhong

    2015-01-01

    Metasurfaces are engineered interfaces that contain a thin layer of plasmonic or dielectric nanostructures capable of manipulating light in a desirable manner. Advances in metasurfaces have led to various practical applications ranging from lensing to holography. Metasurface holograms that can be switched by the polarization state of incident light have been demonstrated for achieving polarization multiplexed functionalities. However, practical application of these devices has been limited by their capability for achieving high efficiency and high image quality. Here we experimentally demonstrate a helicity multiplexed metasurface hologram with high efficiency and good image fidelity over a broad range of frequencies. The metasurface hologram features the combination of two sets of hologram patterns operating with opposite incident helicities. Two symmetrically distributed off-axis images are interchangeable by controlling the helicity of the input light. The demonstrated helicity multiplexed metasurface hologram with its high performance opens avenues for future applications with functionality switchable optical devices. PMID:26354497

  15. Laboratory Tests of Multiplex Detection of PCR Amplicons Using the Luminex 100 Flow Analyzer

    SciTech Connect

    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 PCR 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.

  16. Genome Screen to Detect Linkage to Intracranial Aneurysm Susceptibility Genes

    PubMed Central

    Foroud, Tatiana; Sauerbeck, Laura; Brown, Robert; Anderson, Craig; Woo, Daniel; Kleindorfer, Dawn; Flaherty, Matthew L.; Deka, Ranjan; Hornung, Richard; Meissner, Irene; Bailey-Wilson, Joan E.; Rouleau, Guy; Sander Connolly, E.; Lai, Dongbing; Koller, Daniel L.; Huston, John; Broderick, Joseph P.

    2008-01-01

    Background and Purpose Evidence supports a substantial genetic contribution to the risk of intracranial aneurysm (IA). The purpose of this study was to identify chromosomal regions likely to harbor genes that contribute to the risk of IA. Methods Multiplex families having at least 2 individuals with “definite” or “probable” IA were ascertained through an international consortium. First-degree relatives of individuals with IA who were at increased risk of an IA because of a history of hypertension or present smoking were offered cerebral magnetic resonance angiography. A genome screen was completed using the Illumina 6K SNP system, and the resulting data from 192 families, containing 1155 genotyped individuals, were analyzed. Narrow and broad disease definitions were used when testing for linkage using multipoint model-independent methods. Ordered subset analysis was performed to test for a gene×smoking (pack-years) interaction. Results The greatest evidence of linkage was found on chromosomes 4 (LOD=2.5; 156 cM), 7 (LOD=1.7; 183 cM), 8 (LOD=1.9; 70 cM), and 12 (LOD=1.6; 102 cM) using the broad disease definition. Using the average pack-years for the affected individuals in each family, the genes on chromosomes 4 (LOD=3.5; P=0.03), 7 (LOD=4.1; P=0.01) and 12 (LOD=3.6; P=0.02) all appear to be modulated by the degree of smoking in the affected members of the family. On chromosome 8, inclusion of smoking as a covariate did not significantly strengthen the linkage evidence, suggesting no interaction between the loci in this region and smoking. Conclusions We have detected possible evidence of linkage to 4 chromosomal regions. There is potential evidence for a gene×smoking interaction with 3 of the loci. PMID:18323491

  17. Integrated multiplexed capillary electrophoresis system

    SciTech Connect

    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.

  18. Turing patterns in multiplex networks

    NASA Astrophysics Data System (ADS)

    Asllani, Malbor; Busiello, Daniel M.; Carletti, Timoteo; Fanelli, Duccio; Planchon, Gwendoline

    2014-10-01

    The theory of patterns formation for a reaction-diffusion system defined on a multiplex is developed by means of a perturbative approach. The interlayer diffusion constants act as a small parameter in the expansion and the unperturbed state coincides with the limiting setting where the multiplex layers are decoupled. The interaction between adjacent layers can seed the instability of a homogeneous fixed point, yielding self-organized patterns which are instead impeded in the limit of decoupled layers. Patterns on individual layers can also fade away due to cross-talking between layers. Analytical results are compared to direct simulations.

  19. On-chip multiplexing conversion between wavelength division multiplexing-polarization division multiplexing and wavelength division multiplexing-mode division multiplexing.

    PubMed

    Ye, Mengyuan; Yu, Yu; Zou, Jinghui; Yang, Weili; Zhang, Xinliang

    2014-02-15

    A compact silicon-on-insulator device used for conversions between polarization division multiplexing (PDM) and mode division multiplexing (MDM) signals is proposed and experimentally demonstrated by utilizing a structure combining the improved two-dimensional grating coupler and two-mode multiplexer. The detailed design of the proposed device is presented and the results show the extinction ratio of 16 and 20 dB for X- and Y-pol input, respectively. The processing of 40  Gb/s signal is achieved within the C-band with good performance. The proposed converter is capable of handling multiple wavelengths in wavelength division multiplexing (WDM) networks, enabling the conversions between WDM-PDM and WDM-MDM, which is promising to further increase the throughput at the network interface. PMID:24562199

  20. Holographic data storage system combining shift-multiplexing with peristrophic-multiplexing

    NASA Astrophysics Data System (ADS)

    Yoshikawa, Kengo; Tsukamoto, Yu; Okubo, Kaito; Yamamoto, Manabu

    2014-02-01

    Holographic data storage (HDS) is a next-generation optical storage that uses the principles of holography. The multiplex holographic recording method is an important factor that affects the recording capacity of this storage. Various multiplex recording methods have been proposed so far. In this study, we focus on shift multiplexing with spherical waves and propose a method of shift multiplex recording that combines the peristrophic multiplexed recording. Simulation and experimental verification shows that the proposed method is effective in principle.

  1. Weak percolation on multiplex networks.

    PubMed

    Baxter, Gareth J; Dorogovtsev, Sergey N; Mendes, José F F; Cellai, Davide

    2014-04-01

    Bootstrap percolation is a simple but nontrivial model. It has applications in many areas of science and has been explored on random networks for several decades. In single-layer (simplex) networks, it has been recently observed that bootstrap percolation, which is defined as an incremental process, can be seen as the opposite of pruning percolation, where nodes are removed according to a connectivity rule. Here we propose models of both bootstrap and pruning percolation for multiplex networks. We collectively refer to these two models with the concept of "weak" percolation, to distinguish them from the somewhat classical concept of ordinary ("strong") percolation. While the two models coincide in simplex networks, we show that they decouple when considering multiplexes, giving rise to a wealth of critical phenomena. Our bootstrap model constitutes the simplest example of a contagion process on a multiplex network and has potential applications in critical infrastructure recovery and information security. Moreover, we show that our pruning percolation model may provide a way to diagnose missing layers in a multiplex network. Finally, our analytical approach allows us to calculate critical behavior and characterize critical clusters. PMID:24827287

  2. Code retrieval via undercover multiplexing

    NASA Astrophysics Data System (ADS)

    Barrera, John Fredy; Henao, Rodrigo; Tebaldi, Myrian; Torroba, Roberto; Bolognini, Nestor

    2008-02-01

    The purpose of this research is to develop an undercover multiplexing technique to give additional protection for optical information encryption. We employ the double random phase mask as our basic optical encryption system. The holographic storage medium of choice is a photorefractive crystal. To achieve the multiplexing we use the aperture size of the pupil in the optical system, as it governs the speckle size. We introduce such variation in order to produce a decorrelation between two consecutively stored speckle patterns. Each stored speckle pattern is associated to an input encrypted image, thus producing a multiplexing of the encrypted information. We implement this operation without altering the setup architecture and the random phase masks. This multiplexing is our undercover operation to encipher a true code behind a fake code. Under this approach, the user can only recover the bulk information stored in the volume hologram. However, he cannot recover the true code without the additional information on the pupil size key, even if accessed in position of the original decoding mask.

  3. Weak percolation on multiplex networks

    NASA Astrophysics Data System (ADS)

    Baxter, Gareth J.; Dorogovtsev, Sergey N.; Mendes, José F. F.; Cellai, Davide

    2014-04-01

    Bootstrap percolation is a simple but nontrivial model. It has applications in many areas of science and has been explored on random networks for several decades. In single-layer (simplex) networks, it has been recently observed that bootstrap percolation, which is defined as an incremental process, can be seen as the opposite of pruning percolation, where nodes are removed according to a connectivity rule. Here we propose models of both bootstrap and pruning percolation for multiplex networks. We collectively refer to these two models with the concept of "weak" percolation, to distinguish them from the somewhat classical concept of ordinary ("strong") percolation. While the two models coincide in simplex networks, we show that they decouple when considering multiplexes, giving rise to a wealth of critical phenomena. Our bootstrap model constitutes the simplest example of a contagion process on a multiplex network and has potential applications in critical infrastructure recovery and information security. Moreover, we show that our pruning percolation model may provide a way to diagnose missing layers in a multiplex network. Finally, our analytical approach allows us to calculate critical behavior and characterize critical clusters.

  4. Quantitative linkage analysis to the autism endophenotype social responsiveness identifies genome-wide significant linkage to two regions on chromosome 8

    PubMed Central

    Lowe, Jennifer K.; Werling, Donna M.; Constantino, John N.; Cantor, Rita M.; Geschwind, Daniel H.

    2015-01-01

    Objective Autism Spectrum Disorder (ASD) is characterized by deficits in social function and the presence of repetitive and restrictive behaviors. Following a previous test of principle, we adopted a quantitative approach to discovering genes contributing to the broader autism phenotype by using social responsiveness as an endophenotype for ASD. Method Linkage analyses using scores from the Social Responsiveness Scale (SRS) were performed in 590 families from AGRE, a largely multiplex ASD cohort. Regional and genome-wide association analyses were performed to search for common variants contributing to social responsiveness. Results SRS is unimodally distributed in male offspring from multiplex autism families, in contrast with a bimodal distribution observed in females. In correlated analyses differing by SRS respondent, genome-wide significant linkage for social responsiveness was identified at chr8p21.3 (multi-point LOD=4.11; teacher/parent scores) and chr8q24.22 (multi-point LOD=4.54; parent-only scores), respectively. Genome-wide or linkage-directed association analyses did not detect common variants contributing to social responsiveness. Conclusions The sex-differential distributions of SRS in multiplex autism families likely reflect mechanisms contributing to the sex ratio for autism observed in the general population and form a quantitative signature of reduced penetrance of inherited liability to ASD among females. The identification of two strong loci for social responsiveness validates the endophenotype approach for the identification of genetic variants contributing to complex traits such as ASD. While causal mutations have yet to be identified, these findings are consistent with segregation of rare genetic variants influencing social responsiveness and underscore the increasingly recognized role of rare inherited variants in the genetic architecture of ASD. PMID:25727539

  5. High-throughput SNP scoring with GAMMArrays: genomic analysis using multiplexed microsphere arrays

    NASA Astrophysics Data System (ADS)

    Green, Lance D.; Cai, Hong; Torney, David C.; Wood, Diane J.; Uribe-Romeo, Francisco J.; Kaderali, Lars; Nolan, John P.; White, P. S.

    2002-06-01

    We have developed a SNP scoring platform, yielding high throughput, inexpensive assays. The basic platform uses fluorescently labeled DNA fragments bound to microspheres, which are analyzed using flow cytometry. SNP scoring is performed using minisequencing primers and fluorescently labeled dideoxynucleotides. Furthermore, multiplexed microspheres make it possible to score hundreds of SNPs simultaneously. Multiplexing, coupled with high throughput rates allow inexpensive scoring of several million SNPs/day. GAMMArrays use universal tags that consist of computer designed, unique DNA tails. These are incorporated into each primer, and the reverse-component is attached to a discrete population of microspheres in a multiplexed set. This enables simultaneous minisequencing of many SNPs in solution, followed by capture onto the appropriate microsphere for multiplexed analysis by flow cytometry. We present results from multiplexed SNP analyses of bacterial pathogens, and human mtDNA variation. Analytes are performed on PCR amplicons, each containing numerous SNPs scored simultaneously. In addition, these assays easily integrate into conventional liquid handling automation, and require no unique instrumentation for setup and analysis. Very high signal-to-noise ratios, ease of setup, flexibility in format and scale, and low cost make these assays extremely versatile and valuable tools for a wide variety of SNP scoring applications.

  6. Capillaries for use in a multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, E.S.; Chang, H.T.; Fung, E.N.

    1997-12-09

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification (``base calling``) is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations. 19 figs.

  7. Capillaries for use in a multiplexed capillary electrophoresis system

    SciTech Connect

    Yeung, Edward S.; Chang, Huan-Tsang; Fung, Eliza N.

    1997-12-09

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification ("base calling") is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations.

  8. Validation of a Short Tandem Repeat Multiplex Typing System for Genetic Individualization of Domestic Cat Samples

    PubMed Central

    Coomber, Nikia; David, Victor A.; O’Brien, Stephen J.; Menotti-Raymond, Marilyn

    2007-01-01

    Aim To conduct developmental validation studies on a polymerase chain reaction (PCR) based short tandem repeat (STR) multiplex typing system, developed for the purpose of genetic individualization and parentage testing in domestic cat samples. Methods To evaluate reproducibility of the typing system, the multiplex was amplified using DNA extracted from hair, blood, and buccal samples obtained from the same individual (n = 13). Additional studies were performed to evaluate the system’s species’ specificity, using 26 North American mammalian species and two prokaryotes Sacchromyces and Escherichia coli, sensitivity, and ability to identify DNA mixtures. Patterns of Mendelian inheritance and mutation rates for the 11 loci were directly examined in a large multi-generation domestic cat pedigree (n = 263). Results Our studies confirm that the multiplex system was species-specific for feline DNA and amplified robustly with as little as 125 picograms of genomic template DNA, demonstrating good product balance. The multiplex generated all components of a two DNA mixture when the minor component was one tenth of the major component at a threshold of 50 relative fluorescence units. The multiplex was reproducible in multiple tissue types of the same individual. Mutation rates for the 11 STR were within the range of sex averaged rates observed for Combined DNA Index System (CODIS) loci. Conclusion The cat STR multiplex typing system is a robust and reliable tool for the use of forensic DNA analysis of domestic cat samples. PMID:17696310

  9. Task Structure Design: Beyond Linkage.

    ERIC Educational Resources Information Center

    Baker, Eva L.; Herman, Joan L.

    1983-01-01

    This analysis of the role of testing in educational programs and services maintains that the connection between tests and instruction is best made integrally through an understanding of the design of learning tasks rather than through linkage. The context for, use of, and limitations of task structures are described. (Author/CM)

  10. Catch and Release: Integrated system for multiplexed detection of bacteria

    PubMed Central

    Verbarg, Jasenka; Plath, William D.; Shriver-Lake, Lisa C.; Howell, Peter B.; Erickson, Jeffrey S.; Golden, Joel P.; Ligler, Frances S.

    2013-01-01

    An integrated system with automated immunomagnetic separation and processing of fluidic samples was demonstrated for multiplexed optical detection of bacterial targets. Mixtures of target-specific magnetic bead sets were processed in the NRL MagTrap with the aid of rotating magnet arrays that entrapped and moved the beads within the channel during reagent processing. Processing was performed in buffer and human serum matrices with 10-fold dilutions in the range of 102 – 106 cells/mL of target bacteria. Reversal of magnets’ rotation post processing released the beads back into the flow and moved them into the Microflow Cytometer for optical interrogation. Identification of the beads and the detection of PE fluorescence were performed simultaneously for multiplexed detection. Multiplexing was performed with specifically targeted bead sets to detect E. coli 0157.H7, Salmonella Common Structural Antigen, Listeria sp. and Shigella sp. Dose-response curves were obtained, and limits of detection were calculated for each target in the buffer and clinical matrix. Additional tests demonstrated the potential for using the MagTrap to concentrate target from larger volumes of sample prior to the addition of assay reagents. PMID:23631439

  11. Multiplexed miRNA northern blots via hybridization chain reaction.

    PubMed

    Schwarzkopf, Maayan; Pierce, Niles A

    2016-09-01

    Northern blots enable detection of a target RNA of interest in a biological sample using standard benchtop equipment. miRNAs are the most challenging targets as they must be detected with a single short nucleic acid probe. With existing approaches, it is cumbersome to perform multiplexed blots in which several RNAs are detected simultaneously, impeding the study of interacting regulatory elements. Here, we address this shortcoming by demonstrating multiplexed northern blotting based on the mechanism of hybridization chain reaction (HCR). With this approach, nucleic acid probes complementary to RNA targets trigger chain reactions in which fluorophore-labeled DNA hairpins self-assemble into tethered fluorescent amplification polymers. The programmability of HCR allows multiple amplifiers to operate simultaneously and independently within a blot, enabling straightforward multiplexing. We demonstrate simultaneous detection of three endogenous miRNAs in total RNA extracted from 293T and HeLa cells. For a given target, HCR signal scales linearly with target abundance, enabling relative and absolute quantitation. Using non-radioactive HCR, sensitive and selective miRNA detection is achieved using 2'OMe-RNA probes. The HCR northern blot protocol takes ∼1.5 days independent of the number of target RNAs. PMID:27270083

  12. Multiplexed miRNA northern blots via hybridization chain reaction

    PubMed Central

    Schwarzkopf, Maayan; Pierce, Niles A.

    2016-01-01

    Northern blots enable detection of a target RNA of interest in a biological sample using standard benchtop equipment. miRNAs are the most challenging targets as they must be detected with a single short nucleic acid probe. With existing approaches, it is cumbersome to perform multiplexed blots in which several RNAs are detected simultaneously, impeding the study of interacting regulatory elements. Here, we address this shortcoming by demonstrating multiplexed northern blotting based on the mechanism of hybridization chain reaction (HCR). With this approach, nucleic acid probes complementary to RNA targets trigger chain reactions in which fluorophore-labeled DNA hairpins self-assemble into tethered fluorescent amplification polymers. The programmability of HCR allows multiple amplifiers to operate simultaneously and independently within a blot, enabling straightforward multiplexing. We demonstrate simultaneous detection of three endogenous miRNAs in total RNA extracted from 293T and HeLa cells. For a given target, HCR signal scales linearly with target abundance, enabling relative and absolute quantitation. Using non-radioactive HCR, sensitive and selective miRNA detection is achieved using 2′OMe-RNA probes. The HCR northern blot protocol takes ∼1.5 days independent of the number of target RNAs. PMID:27270083

  13. Catch and release: integrated system for multiplexed detection of bacteria.

    PubMed

    Verbarg, Jasenka; Plath, William D; Shriver-Lake, Lisa C; Howell, Peter B; Erickson, Jeffrey S; Golden, Joel P; Ligler, Frances S

    2013-05-21

    An integrated system with automated immunomagnetic separation and processing of fluidic samples was demonstrated for multiplexed optical detection of bacterial targets. Mixtures of target-specific magnetic bead sets were processed in the NRL MagTrap with the aid of rotating magnet arrays that entrapped and moved the beads within the channel during reagent processing. Processing was performed in buffer and human serum matrixes with 10-fold dilutions in the range of 10(2)-10(6) cells/mL of target bacteria. Reversal of magnets' rotation post-processing released the beads back into the flow and moved them into the microflow cytometer for optical interrogation. Identification of the beads and the detection of PE fluorescence were performed simultaneously for multiplexed detection. Multiplexing was performed with specifically targeted bead sets to detect E. coli 0157.H7, Salmonella Common Structural Antigen, Listeria sp., and Shigella sp., dose-response curves were obtained, and limits of detection were calculated for each target in the buffer and clinical matrix. Additional tests demonstrated the potential for using the MagTrap to concentrate target from larger volumes of sample prior to the addition of assay reagents. PMID:23631439

  14. Parallel multiplex laser feedback interferometry

    SciTech Connect

    Zhang, Song; Tan, Yidong; Zhang, Shulian

    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, experimental results show a resolution of 1.6 nm and accuracy of 7.8 nm within the range of 100 μm.

  15. Pattern formation in multiplex networks

    PubMed Central

    Kouvaris, Nikos E.; Hata, Shigefumi; Guilera, Albert Díaz-

    2015-01-01

    The advances in understanding complex networks have generated increasing interest in dynamical processes occurring on them. Pattern formation in activator-inhibitor systems has been studied in networks, revealing differences from the classical continuous media. Here we study pattern formation in a new framework, namely multiplex networks. These are systems where activator and inhibitor species occupy separate nodes in different layers. Species react across layers but diffuse only within their own layer of distinct network topology. This multiplicity generates heterogeneous patterns with significant differences from those observed in single-layer networks. Remarkably, diffusion-induced instability can occur even if the two species have the same mobility rates; condition which can never destabilize single-layer networks. The instability condition is revealed using perturbation theory and expressed by a combination of degrees in the different layers. Our theory demonstrates that the existence of such topology-driven instabilities is generic in multiplex networks, providing a new mechanism of pattern formation. PMID:26042606

  16. (Multiplex mapping of human cDNAs)

    SciTech Connect

    Nierman, W.C.

    1991-01-01

    J. Craig Venter, National Institute of Neurological Disorders and Stroke, has begun to identify genes expressed in the human brain by partially sequences cDNA clones. We are collaborating with the Venter group and using their sequence data to develop methods for rapid localization of newly identified cDNAs to human chromosomes. We are applying the ABI automated DNA sequencer to the analysis of fluorescently-tagged PCR products for assigning sequences to individual human chromosomes. The steps in our mapping protocol are (1) to design PCR primers from the Venter laboratory-generated sequence data, (2) to test the primers for specific amplification from human genomic DNA, (3) to use the primers for PCR amplification from a somatic cell hybrid cell mapping panel, (4) to determine the presence or absence of the specific amplification products from each cell line DNA by electrophoretic analysis using the ABI sequencer, and (5) to analyze the pattern of amplification results from the hybrid panel to identify the chromosomal origin of the cDNA sequence. We have demonstrated the principle by mapping 12 sequences or Expressed Sequence Tags'' (ESTs), providing primer sequence data for subsequent subchromosomal localizations. We will now concentrate on developing methodology to allow multiplexing the amplification reactions and analysis of the reaction products, to achieve a high throughput with a minimum allocation of resources. This project will generate a data set from which to evaluate strategies to identify functional primer sequences from cDNA sequence data.

  17. (Multiplex mapping of human cDNAs)

    SciTech Connect

    Nierman, W.C.

    1992-01-01

    We have tested and implemented several protocols to increase productivity for mapping expressed sequence tags EST sequences to human chromosomes. These protocols include adopting PRIMER which permits utilization of batch files, as the standard software for PCR primer design; adding a human 21-only cell line to the NIGMS panel No. 1 to improve discrimination in discordancy analyses involving chromosome 21, adding a monochromosomal hybrid panel to facilitate chromosome assignment of sequences that are amplified from more than 1 chromosome; combining the products of multiple PCR reactions for electrophoretic analysis (pseudoplexing); routinely multiplexing PCR reactions; and automating data entry and analysis as much as possible. We have applied these protocols to assign an overall total of 132 human brain CDNA sequences to individual human chromosomes. PCR primers were designed from ESTS and tested for specific amplification from human genomic DNA. DNA was then amplified using DNA from somatic cell hybrid mapping panels as templates. The amplification products were identified using an automated fluorescence detection system. Chromosomal assignments were made by discordancy analysis. The localized cDNAs include 2 for known human genes, 2 that map to 2 different human chromosomes, and 25 for cDNAs matching existing database records.

  18. Nanoscale Test Strips for Multiplexed Blood Analysis

    NASA Technical Reports Server (NTRS)

    Chan, Eugene

    2015-01-01

    A critical component of the DNA Medicine Institute's Reusable Handheld Electrolyte and Lab Technology for Humans (rHEALTH) sensor are nanoscale test strips, or nanostrips, that enable multiplexed blood analysis. Nanostrips are conceptually similar to the standard urinalysis test strip, but the strips are shrunk down a billionfold to the microscale. Each nanostrip can have several sensor pads that fluoresce in response to different targets in a sample. The strips carry identification tags that permit differentiation of a specific panel from hundreds of other nanostrip panels during a single measurement session. In Phase I of the project, the company fabricated, tested, and demonstrated functional parathyroid hormone and vitamin D nanostrips for bone metabolism, and thrombin aptamer and immunoglobulin G antibody nanostrips. In Phase II, numerous nanostrips were developed to address key space flight-based medical needs: assessment of bone metabolism, immune response, cardiac status, liver metabolism, and lipid profiles. This unique approach holds genuine promise for space-based portable biodiagnostics and for point-of-care (POC) health monitoring and diagnostics here on Earth.

  19. 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.

  20. 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.

  1. Efficient Record Linkage Algorithms Using Complete Linkage Clustering

    PubMed Central

    Mamun, Abdullah-Al; Aseltine, Robert; Rajasekaran, Sanguthevar

    2016-01-01

    Data from different agencies share data of the same individuals. Linking these datasets to identify all the records belonging to the same individuals is a crucial and challenging problem, especially given the large volumes of data. A large number of available algorithms for record linkage are prone to either time inefficiency or low-accuracy in finding matches and non-matches among the records. In this paper we propose efficient as well as reliable sequential and parallel algorithms for the record linkage problem employing hierarchical clustering methods. We employ complete linkage hierarchical clustering algorithms to address this problem. In addition to hierarchical clustering, we also use two other techniques: elimination of duplicate records and blocking. Our algorithms use sorting as a sub-routine to identify identical copies of records. We have tested our algorithms on datasets with millions of synthetic records. Experimental results show that our algorithms achieve nearly 100% accuracy. Parallel implementations achieve almost linear speedups. Time complexities of these algorithms do not exceed those of previous best-known algorithms. Our proposed algorithms outperform previous best-known algorithms in terms of accuracy consuming reasonable run times. PMID:27124604

  2. Rotation spacing and multiplexing number in angle-peristrophic multiplexing holographic memory

    NASA Astrophysics Data System (ADS)

    Sawada, Masamitsu; Kinoshita, Nobuhiro; Muroi, Tetsuhiko; Motohashi, Mitsuya; Saito, Nobuo

    2015-09-01

    Holographic memory is expected to be the next-generation optical memory with several advantages including high data transfer rate and high recording density. Holographic memory enables the storage of holograms in the same location in a holographic medium typically using the angle multiplexing method. The multiplexing number is an important factor that determines the recording density when using this method. To increase the multiplexing number, it is known as an effective method to combine peristrophic (or rotation) multiplexing with angle multiplexing. We use the k-sphere to describe that the rotation spacing for peristrophic multiplexing depends on both the numerical aperture in the signal beam path and the angle between the reference and signal beams. We then formulate the rotation spacing and compare the results obtained using the theoretical formula with the measured results. Finally, we estimate the maximum multiplexing number for our experimental system using the angle-peristrophic multiplexing method on the basis of the measured results.

  3. Record linkage for drug monitoring.

    PubMed Central

    Skegg, D C; Doll, R

    1981-01-01

    A study was carried out to assess the feasibility of using record linkage for drug monitoring. For two years, three types of records were collected for a total of 43 117 people: (1) details of basic attributes, such as sex and age; (2) details of prescriptions dispensed; and (3) records of hospital admissions, obstetric deliveries, and deaths. The records about each person were linked together, and analyses were performed to reveal associations between drugs and diagnoses. The study suggested that record linkage would be useful both for generating and for testing hypotheses about the adverse effects of drugs. The method would be especially valuable for detection of delayed effects (such as the induction of cancer), sudden deaths outside hospital, and effects of the fetus-all of which are difficult to study by other means. A full-scale project would need to cover a large population, and some of the practical issues that would arise are discussed. PMID:7264530

  4. Multiplexing of encrypted data using fractal masks.

    PubMed

    Barrera, John F; Tebaldi, Myrian; Amaya, Dafne; Furlan, Walter D; Monsoriu, Juan A; Bolognini, Néstor; Torroba, Roberto

    2012-07-15

    In this Letter, we present to the best of our knowledge a new all-optical technique for multiple-image encryption and multiplexing, based on fractal encrypting masks. The optical architecture is a joint transform correlator. The multiplexed encrypted data are stored in a photorefractive crystal. The fractal parameters of the key can be easily tuned to lead to a multiplexing operation without cross talk effects. Experimental results that support the potential of the method are presented. PMID:22825170

  5. Multiplex Holograms And Their Applications In Medicine

    NASA Astrophysics Data System (ADS)

    Tsujiuchi, Jumpei

    1988-01-01

    Fundamental properties of reconstructed images from a multiplex hologram are studied, and conditions for compensating distortions and for designing a reconstructing source are proposed. Applications of multiplex hologram to medical objects are reviewed, and a computer-aided hologram synthesizing system is proposed for obtaining better images and wider applications. An example of multiplex holograms synthesized from a series of CT images is also presented.

  6. Linkage isomerism in coordination polymers.

    PubMed

    Benmansour, Samia; Setifi, Fatima; Triki, Smail; Gómez-García, Carlos J

    2012-02-20

    The use of the recently prepared polynitrile ligand tcnopr3OH(-) ([(NC)(2)CC(OCH(2)CH(2)CH(2)OH)C(CN)(2)](-)) with different salts of Fe(II), Co(II), and Ni(II) has led to a very rare example of linkage isomerism in a coordination chain. These pairs of linkage isomers can be formulated as [M(tcnopr3OH-κN,κO)(2)(H(2)O)(2)]; M = Fe (1), Co (3), and Ni(5) and [M(tcnopr3OH-κN,κN')(2)(H(2)O)(2)]; M = Fe (2), Co (4), and Ni (6). Compounds 1-2, 3-4, and 5-6 are three pairs of linkage isomers since they present the same formula and chain structure and they only differ in the connectivity of the polynitrile ligand bridging the metal ions in the chain: through a N and an O atom (1κN:2κO-isomer) or through two N atoms (1κN:2κN'-isomer). The magnetic properties show, as expected, very similar behaviors for both isomers. PMID:22296602

  7. Multiplex pathogen detection based on spatially addressable microarrays of barcoded resins.

    PubMed

    Blais, David R; Alvarez-Puebla, Ramon A; Bravo-Vasquez, Juan P; Fenniri, Hicham; Pezacki, John Paul

    2008-07-01

    Suspension microsphere immunoassays are rapidly gaining recognition in antigen identification and infectious disease biodetection due to their simplicity, versatility and high-throughput multiplex screening. We demonstrate a multiplex assay based on antibody-functionalized barcoded resins (BCRs) to identify pathogen antigens in complex biological fluids. The binding event of a particular antibody on given bead (fluorescence) and the identification of the specific pathogen agent (vibrational fingerprint of the bead) can be achieved in a dispersive Raman system by exciting the sample with two different laser lines. Anthrax protective antigen, Franciscella tularensis lipopolysaccharide and CD14 antigens were accurately identified and quantified in tetraplex assays with a detection limit of 1 ng/mL. The rapid, versatile and simple analysis enabled by the BCRs demonstrates their potential for multiplex antigen detection and identification in a reconfigurable microarray format. PMID:18566958

  8. Measuring and modeling correlations in multiplex networks.

    PubMed

    Nicosia, Vincenzo; Latora, Vito

    2015-09-01

    The interactions among the elementary components of many complex systems can be qualitatively different. Such systems are therefore naturally described in terms of multiplex or multilayer networks, i.e., networks where each layer stands for a different type of interaction between the same set of nodes. There is today a growing interest in understanding when and why a description in terms of a multiplex network is necessary and more informative than a single-layer projection. Here we contribute to this debate by presenting a comprehensive study of correlations in multiplex networks. Correlations in node properties, especially degree-degree correlations, have been thoroughly studied in single-layer networks. Here we extend this idea to investigate and characterize correlations between the different layers of a multiplex network. Such correlations are intrinsically multiplex, and we first study them empirically by constructing and analyzing several multiplex networks from the real world. In particular, we introduce various measures to characterize correlations in the activity of the nodes and in their degree at the different layers and between activities and degrees. We show that real-world networks exhibit indeed nontrivial multiplex correlations. For instance, we find cases where two layers of the same multiplex network are positively correlated in terms of node degrees, while other two layers are negatively correlated. We then focus on constructing synthetic multiplex networks, proposing a series of models to reproduce the correlations observed empirically and/or to assess their relevance. PMID:26465526

  9. Measuring and modeling correlations in multiplex networks

    NASA Astrophysics Data System (ADS)

    Nicosia, Vincenzo; Latora, Vito

    2015-09-01

    The interactions among the elementary components of many complex systems can be qualitatively different. Such systems are therefore naturally described in terms of multiplex or multilayer networks, i.e., networks where each layer stands for a different type of interaction between the same set of nodes. There is today a growing interest in understanding when and why a description in terms of a multiplex network is necessary and more informative than a single-layer projection. Here we contribute to this debate by presenting a comprehensive study of correlations in multiplex networks. Correlations in node properties, especially degree-degree correlations, have been thoroughly studied in single-layer networks. Here we extend this idea to investigate and characterize correlations between the different layers of a multiplex network. Such correlations are intrinsically multiplex, and we first study them empirically by constructing and analyzing several multiplex networks from the real world. In particular, we introduce various measures to characterize correlations in the activity of the nodes and in their degree at the different layers and between activities and degrees. We show that real-world networks exhibit indeed nontrivial multiplex correlations. For instance, we find cases where two layers of the same multiplex network are positively correlated in terms of node degrees, while other two layers are negatively correlated. We then focus on constructing synthetic multiplex networks, proposing a series of models to reproduce the correlations observed empirically and/or to assess their relevance.

  10. 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

    2015-07-01

    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. PMID:26016439

  11. Privacy preserving interactive record linkage (PPIRL)

    PubMed Central

    Kum, Hye-Chung; Krishnamurthy, Ashok; Machanavajjhala, Ashwin; Reiter, Michael K; Ahalt, Stanley

    2014-01-01

    Objective Record linkage to integrate uncoordinated databases is critical in biomedical research using Big Data. Balancing privacy protection against the need for high quality record linkage requires a human–machine hybrid system to safely manage uncertainty in the ever changing streams of chaotic Big Data. Methods In the computer science literature, private record linkage is the most published area. It investigates how to apply a known linkage function safely when linking two tables. However, in practice, the linkage function is rarely known. Thus, there are many data linkage centers whose main role is to be the trusted third party to determine the linkage function manually and link data for research via a master population list for a designated region. Recently, a more flexible computerized third-party linkage platform, Secure Decoupled Linkage (SDLink), has been proposed based on: (1) decoupling data via encryption, (2) obfuscation via chaffing (adding fake data) and universe manipulation; and (3) minimum information disclosure via recoding. Results We synthesize this literature to formalize a new framework for privacy preserving interactive record linkage (PPIRL) with tractable privacy and utility properties and then analyze the literature using this framework. Conclusions Human-based third-party linkage centers for privacy preserving record linkage are the accepted norm internationally. We find that a computer-based third-party platform that can precisely control the information disclosed at the micro level and allow frequent human interaction during the linkage process, is an effective human–machine hybrid system that significantly improves on the linkage center model both in terms of privacy and utility. PMID:24201028

  12. Homo-FRET Based Biosensors and Their Application to Multiplexed Imaging of Signalling Events in Live Cells

    PubMed Central

    Warren, Sean C.; Margineanu, Anca; Katan, Matilda; Dunsby, Chris; French, Paul M. W.

    2015-01-01

    Multiplexed imaging of Förster Resonance Energy Transfer (FRET)-based biosensors potentially presents a powerful approach to monitoring the spatio-temporal correlation of signalling pathways within a single live cell. Here, we discuss the potential of homo-FRET based biosensors to facilitate multiplexed imaging. We demonstrate that the homo-FRET between pleckstrin homology domains of Akt (Akt-PH) labelled with mCherry may be used to monitor 3′-phosphoinositide accumulation in live cells and show how global analysis of time resolved fluorescence anisotropy measurements can be used to quantify this accumulation. We further present multiplexed imaging readouts of calcium concentration, using fluorescence lifetime measurements of TN-L15-a CFP/YFP based hetero-FRET calcium biosensor-with 3′-phosphoinositide accumulation. PMID:26133241

  13. Multiplex detection of respiratory pathogens

    DOEpatents

    McBride, Mary; Slezak, Thomas; Birch, James M.

    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.

  14. Assignment of Rainbow Trout Linkage Groups to Specific Chromosomes

    PubMed Central

    Phillips, Ruth B.; Nichols, Krista M.; DeKoning, Jenefer J.; Morasch, Matthew R.; Keatley, Kimberly A.; Rexroad, Caird; Gahr, Scott A.; Danzmann, Roy G.; Drew, Robert E.; Thorgaard, Gary H.

    2006-01-01

    The rainbow trout genetic linkage groups have been assigned to specific chromosomes in the OSU (2N = 60) strain using fluorescence in situ hybridization (FISH) with BAC probes containing genes mapped to each linkage group. There was a rough correlation between chromosome size and size of the genetic linkage map in centimorgans for the genetic maps based on recombination from the female parent. Chromosome size and structure have a major impact on the female:male recombination ratio, which is much higher (up to 10:1 near the centromeres) on the larger metacentric chromosomes compared to smaller acrocentric chromosomes. Eighty percent of the BAC clones containing duplicate genes mapped to a single chromosomal location, suggesting that diploidization resulted in substantial divergence of intergenic regions. The BAC clones that hybridized to both duplicate loci were usually located in the distal portion of the chromosome. Duplicate genes were almost always found at a similar location on the chromosome arm of two different chromosome pairs, suggesting that most of the chromosome rearrangements following tetraploidization were centric fusions and did not involve homeologous chromosomes. The set of BACs compiled for this research will be especially useful in construction of genome maps and identification of QTL for important traits in other salmonid fishes. PMID:16951085

  15. System for Multiplexing Acoustic Emission (AE) Instrumentation

    NASA Technical Reports Server (NTRS)

    Prosser, William H. (Inventor); Perey, Daniel F. (Inventor); Gorman, Michael R. (Inventor); Scales, Edgar F. (Inventor)

    2003-01-01

    An acoustic monitoring device has at least two acoustic sensors with a triggering mechanism and a multiplexing circuit. After the occurrence of a triggering event at a sensor, the multiplexing circuit allows a recording component to record acoustic emissions at adjacent sensors. The acoustic monitoring device is attached to a solid medium to detect the occurrence of damage.

  16. Significant linkage on chromosome 10p in families with bulimia nervosa.

    PubMed

    Bulik, Cynthia M; Devlin, B; Bacanu, Silviu-Alin; Thornton, Laura; Klump, Kelly L; Fichter, Manfred M; Halmi, Katherine A; Kaplan, Allan S; Strober, Michael; Woodside, D Blake; Bergen, Andrew W; Ganjei, J Kelly; Crow, Scott; Mitchell, James; Rotondo, Alessandro; Mauri, Mauro; Cassano, Giovanni; Keel, Pamela; Berrettini, Wade H; Kaye, Walter H

    2003-01-01

    Bulimia nervosa (BN) is strongly familial, and additive genetic effects appear to contribute substantially to the observed familiality. In turn, behavioral components of BN, such as self-induced vomiting, are reliably measured and heritable. To identify regions of the genome harboring genetic variants conferring susceptibility to BN, we conducted a linkage analysis of multiplex families with eating disorders that were identified through a proband with BN. Linkage analysis of the entire sample of 308 families yielded a double peak, with the highest nonparametric multipoint maximum LOD score (MLS), of 2.92, on chromosome 10. Given the high heritability of self-induced vomiting and the reliability with which it can be measured, we performed linkage analysis in a subset (n=133) of families in which at least two affected relatives reported a symptom pattern that included self-induced vomiting. The highest MLS (3.39) observed was on chromosome 10, between markers D10S1430 and D10S1423. These results provide evidence of the presence of a susceptibility locus for BN on chromosome 10p. Using simulations, we demonstrate that both of these scores, 2.92 and 3.39, meet the widely accepted criterion for genomewide significance. Another region on 14q meets the criterion for genomewide suggestive linkage, with MLSs of 1.97 (full sample) and 1.75 (subset) at 62 centimorgans from p-ter. PMID:12476400

  17. SQUID Multiplexers for Cryogenic Detector Arrays

    NASA Technical Reports Server (NTRS)

    Irwin, Kent; Beall, James; Deiker, Steve; Doriese, Randy; Duncan, William; Hilton, Gene; Moseley, S. Harvey; Reintsema, Carl; Stahle, Caroline; Ullom, Joel; Vale, Leila

    2004-01-01

    SQUID multiplexers make it possible to build arrays of thousands of cryogenic detectors with a manageable number of readout channels. We are developing time-division SQUID multiplexers based on Nb trilayer SQUIDs to read arrays of superconducting transition-edge sensors. Our first-generation, 8-channel SQUID multiplexer was used in FIBRE, a one-dimensional TES array for submillimeter astronomy. Our second-generation 32-pixel multiplexer, based on an improved architecture, has been developed for instruments including Constellation-X, SCUBA-2, and solar x-ray astronomy missions. SCUBA-2, which is being developed for the James Clerk Maxwell Telescope, will have more than 10,000 pixels. We are now developing a third-generation architecture based on superconducting hot-electron switches. The use of SQUID multiplexers in instruments operating at above 2 K will also be discussed.

  18. Information transport in multiplex networks

    NASA Astrophysics Data System (ADS)

    Pu, Cunlai; Li, Siyuan; Yang, Xianxia; Yang, Jian; Wang, Kai

    2016-04-01

    In this paper, we study information transport in multiplex networks comprised of two coupled subnetworks. The upper subnetwork, called the logical layer, employs the shortest paths protocol to determine the logical paths for packets transmission, while the lower subnetwork acts as the physical layer, in which packets are delivered by the biased random walk mechanism characterized with a parameter α. Through simulation, we obtain the optimal α corresponding to the maximum network lifetime and the maximum number of the arrival packets. Assortative coupling is better than random coupling and disassortative coupling, since it achieves better transmission performance. Generally, the more homogeneous the lower subnetwork is, the better the transmission performance, which is the opposite for the upper subnetwork. Finally, we propose an attack centrality for nodes based on the topological information of both subnetworks, and investigate the transmission performance under targeted attacks. Our work aids in understanding the spread and robustness issues of multiplex networks and provides some clues about the design of more efficient and robust routing architectures in communication systems.

  19. Linkage map construction involving a reciprocal translocation.

    PubMed

    Farré, A; Benito, I Lacasa; Cistué, L; de Jong, J H; Romagosa, I; Jansen, J

    2011-03-01

    This paper is concerned with a novel statistical-genetic approach for the construction of linkage maps in populations obtained from reciprocal translocation heterozygotes of barley (Hordeum vulgare L.). Using standard linkage analysis, translocations usually lead to 'pseudo-linkage': the mixing up of markers from the chromosomes involved in the translocation into a single linkage group. Close to the translocation breakpoints recombination is severely suppressed and, as a consequence, ordering markers in those regions is not feasible. The novel strategy presented in this paper is based on (1) disentangling the "pseudo-linkage" using principal coordinate analysis, (2) separating individuals into translocated types and normal types and (3) separating markers into those close to and those more distant from the translocation breakpoints. The methods make use of a consensus map of the species involved. The final product consists of integrated linkage maps of the distal parts of the chromosomes involved in the translocation. PMID:21153624

  20. Gripper deploying and inverting linkage

    DOEpatents

    Minichan, Richard L.; Killian, Mark A.

    1993-01-01

    An end effector deploying and inverting linkage. The linkage comprises an air cylinder mounted in a frame or tube, a sliding bracket next to the air cylinder, a stopping bracket depending from the frame and three, pivotally-attached links that are attached to the end effector and to each other in such a way as to be capable of inverting the end effector and translating it laterally. The first of the three links is a straight element that is moved up and down by the shaft of the air cylinder. The second link is attached at one end to the stopping bracket and to the side of the end effector at the other end. The first link is attached near the middle of the second, sharply angled link so that, as the shaft of the air cylinder moves up and down, the second link rotates about an axis perpendicular to the frame and inverts and translates the end effector. The rotation of the second link is stopped at both ends when the link engages stops on the stopping bracket. The third link, slightly angled, is attached to the sliding bracket at one end and to the end of the end effector at the other. The third helps to control the end effector in its motion.

  1. Gripper deploying and inverting linkage

    DOEpatents

    Minichan, R.L.; Killian, M.A.

    1993-03-02

    An end effector deploying and inverting linkage. The linkage comprises an air cylinder mounted in a frame or tube, a sliding bracket next to the air cylinder, a stopping bracket depending from the frame and three, pivotally-attached links that are attached to the end effector and to each other in such a way as to be capable of inverting the end effector and translating it laterally. The first of the three links is a straight element that is moved up and down by the shaft of the air cylinder. The second link is attached at one end to the stopping bracket and to the side of the end effector at the other end. The first link is attached near the middle of the second, sharply angled link so that, as the shaft of the air cylinder moves up and down, the second link rotates about an axis perpendicular to the frame and inverts and translates the end effector. The rotation of the second link is stopped at both ends when the link engages stops on the stopping bracket. The third link, slightly angled, is attached to the sliding bracket at one end and to the end of the end effector at the other. The third helps to control the end effector in its motion.

  2. An introduction to recombination and linkage analysis

    SciTech Connect

    Mcpeek, M.S.

    1996-12-31

    With a garden as his laboratory, Mendel was able to discern basic probabilistic laws of heredity. Although it first appeared as a baffling exception to one of Mendel`s principles, the phenomenon of variable linkage between characters was soon recognized to be a powerful tool in the process of chromosome mapping and location of genes of interest. In this introduction, we first describe Mendel`s work and the subsequent discovery of linkage. Next we describe the apparent cause of variable linkage, namely recombination, and we introduce linkage analysis. 33 refs., 1 fig., 2 tabs.

  3. Functionalization of optical nanotip arrays with an electrochemical microcantilever for multiplexed DNA detection.

    PubMed

    Descamps, Emeline; Duroure, Nathalie; Deiss, Frédérique; Leichlé, Thierry; Adam, Catherine; Mailley, Pascal; Aït-Ikhlef, Ali; Livache, Thierry; Nicu, Liviu; Sojic, Neso

    2013-08-01

    Optical nanotip arrays fabricated on etched fiber bundles were functionalized with DNA spots. Such unconventional substrates (3D and non-planar) are difficult to pattern with standard microfabrication techniques but, using an electrochemical cantilever, up to 400 spots were electrodeposited on the nanostructured optical surface in 5 min. This approach allows each spot to be addressed individually and multiplexed fluorescence detection is demonstrated. Finally, remote fluorescence detection was performed by imaging through the optical fiber bundle itself after hybridisation with the complementary sequence. PMID:23695411

  4. Structure of triadic relations in multiplex networks

    NASA Astrophysics Data System (ADS)

    Cozzo, Emanuele; Kivelä, Mikko; De Domenico, Manlio; Solé-Ribalta, Albert; Arenas, Alex; Gómez, Sergio; Porter, Mason A.; Moreno, Yamir

    2015-07-01

    Recent advances in the study of networked systems have highlighted that our interconnected world is composed of networks that are coupled to each other through different ‘layers’ that each represent one of many possible subsystems or types of interactions. Nevertheless, it is traditional to aggregate multilayer networks into a single weighted network in order to take advantage of existing tools. This is admittedly convenient, but it is also extremely problematic, as important information can be lost as a result. It is therefore important to develop multilayer generalizations of network concepts. In this paper, we analyze triadic relations and generalize the idea of transitivity to multiplex networks. By focusing on triadic relations, which yield the simplest type of transitivity, we generalize the concept and computation of clustering coefficients to multiplex networks. We show how the layered structure of such networks introduces a new degree of freedom that has a fundamental effect on transitivity. We compute multiplex clustering coefficients for several real multiplex networks and illustrate why one must take great care when generalizing standard network concepts to multiplex networks. We also derive analytical expressions for our clustering coefficients for ensemble averages of networks in a family of random multiplex networks. Our analysis illustrates that social networks have a strong tendency to promote redundancy by closing triads at every layer and that they thereby have a different type of multiplex transitivity from transportation networks, which do not exhibit such a tendency. These insights are invisible if one only studies aggregated networks.

  5. Multiwavelength metasurfaces through spatial multiplexing

    PubMed Central

    Arbabi, Ehsan; Arbabi, Amir; Kamali, Seyedeh Mahsa; Horie, Yu; Faraon, Andrei

    2016-01-01

    Metasurfaces are two-dimensional arrangements of optical scatterers rationally arranged to control optical wavefronts. Despite the significant advances made in wavefront engineering through metasurfaces, most of these devices are designed for and operate at a single wavelength. Here we show that spatial multiplexing schemes can be applied to increase the number of operation wavelengths. We use a high contrast dielectric transmittarray platform with amorphous silicon nano-posts to demonstrate polarization insensitive metasurface lenses with a numerical aperture of 0.46, that focus light at 915 and 1550 nm to the same focal distance. We investigate two different methods, one based on large scale segmentation and one on meta-atom interleaving, and compare their performances. An important feature of this method is its simple generalization to adding more wavelengths or new functionalities to a device. Therefore, it provides a relatively straightforward method for achieving multi-functional and multiwavelength metasurface devices. PMID:27597568

  6. Code-multiplexed optical scanner

    NASA Astrophysics Data System (ADS)

    Riza, Nabeel A.; Arain, Muzammil A.

    2003-03-01

    A three-dimensional (3-D) optical-scanning technique is proposed based on spatial optical phase code activation on an input beam. This code-multiplexed optical scanner (C-MOS) relies on holographically stored 3-D beam-forming information. Proof-of-concept C-MOS experimental results by use of a photorefractive crystal as a holographic medium generates eight beams representing a basic 3-D voxel element generated via a binary-code matrix of the Hadamard type. The experiment demonstrates the C-MOS features of no moving parts, beam-forming flexibility, and large centimeter-size apertures. A novel application of the C-MOS as an optical security lock is highlighted.

  7. Cooperative epidemics on multiplex networks

    NASA Astrophysics Data System (ADS)

    Azimi-Tafreshi, N.

    2016-04-01

    The spread of one disease, in some cases, can stimulate the spreading of another infectious disease. Here, we treat analytically a symmetric coinfection model for spreading of two diseases on a two-layer multiplex network. We allow layer overlapping, but we assume that each layer is random and locally loopless. Infection with one of the diseases increases the probability of getting infected with the other. Using the generating function method, we calculate exactly the fraction of individuals infected with both diseases (so-called coinfected clusters) in the stationary state, as well as the epidemic spreading thresholds and the phase diagram of the model. With increasing cooperation, we observe a tricritical point and the type of transition changes from continuous to hybrid. Finally, we compare the coinfected clusters in the case of cooperating diseases with the so-called "viable" clusters in networks with dependencies.

  8. Multiplexed Primer Prediction for PCR

    Energy Science and Technology Software Center (ESTSC)

    2007-07-23

    MPP predicts sets of multiplex-compatible primers for Polymerase Chain Reaction (PCR), finding a near minimal set of primers such that at least one amplicon will be generated from every target sequence in the input file. The code finds highly conserved oligos that are suitable as primers, according to user-specified desired primer characteristics such as length, melting temperature, and amplicon length. The primers are predicted not to form unwanted dimer or hairpin structures. The target sequencesmore » used as input can be diverse, since no multiple sequence alighment is required. The code is scalable, taking up to tens of thousands of sequences as input, and works, for example, to find a "universal primer set" for all viral genomes provided as a single input file. The code generates a periodic check-point file, thus in the event of premature execution termination, the application can be restarted from the last check-point file.« less

  9. 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.

  10. Multiwavelength metasurfaces through spatial multiplexing.

    PubMed

    Arbabi, Ehsan; Arbabi, Amir; Kamali, Seyedeh Mahsa; Horie, Yu; Faraon, Andrei

    2016-01-01

    Metasurfaces are two-dimensional arrangements of optical scatterers rationally arranged to control optical wavefronts. Despite the significant advances made in wavefront engineering through metasurfaces, most of these devices are designed for and operate at a single wavelength. Here we show that spatial multiplexing schemes can be applied to increase the number of operation wavelengths. We use a high contrast dielectric transmittarray platform with amorphous silicon nano-posts to demonstrate polarization insensitive metasurface lenses with a numerical aperture of 0.46, that focus light at 915 and 1550 nm to the same focal distance. We investigate two different methods, one based on large scale segmentation and one on meta-atom interleaving, and compare their performances. An important feature of this method is its simple generalization to adding more wavelengths or new functionalities to a device. Therefore, it provides a relatively straightforward method for achieving multi-functional and multiwavelength metasurface devices. PMID:27597568

  11. Focus issue introduction: space-division multiplexing.

    PubMed

    Li, Guifang; Karlsson, Magnus; Liu, Xiang; Quiquempois, Yves

    2014-12-29

    Since the publication of the first focus issue [Opt. Express 19(11), 2011], single-fiber transmission capacity has eclipsed the 1 Pb/s mark. All aspects related to space-division multiplexing including fiber, passive components [(de)multiplexer, couplers], active components (EDFA and Raman amplifiers), switching and routing elements (ROADM and WSS), as well as transmission and networking have progressed rapidly. This focus issue is intended to bring together the most up-to-date research in space-division multiplexing, including fibers, passive and active components, transmission systems and networking. PMID:25607215

  12. Low-cost, multiplexed biosensor for disease diagnosis

    NASA Astrophysics Data System (ADS)

    Myatt, Christopher J.; Delaney, Marie; Todorof, Kathryn; Heil, James; Givens, Monique; Schooley, Robert T.; Lochhead, Michael J.

    2009-02-01

    Cost-effective disease diagnosis in resource-limited settings remains a critical global health challenge. Qualitative rapid tests based on lateral flow technology provide valuable screening information, but require relatively expensive confirmatory tests and generally lack quantitation. We report on a fluorescence technology that combines low cost instrumented readout with passive pumping in a disposable cartridge. The detection system utilizes a novel waveguide illumination approach in conjunction with commercial CMOS imagers. Total instrument cost in production are projected to be around $100 This cost structure and instrument ease of use will enable use in point-of-care settings, outside of centralized laboratories. The system has been used for detection and analysis of proteins, antibodies, nucleic acids, and cells. Here we will report first on our development of a multiplexed, array-based serology assay for HIV and common AIDS co-infections. Data will be presented for HIV/HCV antibody testing in human serum samples. In addition, we will present data on the use of the system for sensitive detection of bacterial RNA. Current detection limit for the model multiplexed RNA sandwich assay is 1 femtomolar target RNA. Finally, a high magnification version of the system is used to image immunostained human T cells.

  13. Multiplexed Dosing Assays by Digitally Definable Hydrogel Volumes.

    PubMed

    Faralli, Adele; Melander, Fredrik; Larsen, Esben Kjaer Unmack; Chernyy, Sergey; Andresen, Thomas L; Larsen, Niels B

    2016-01-21

    Stable and low-cost multiplexed drug sensitivity assays using small volumes of cells or tissue are in demand for personalized medicine, including patient-specific combination chemotherapy. Spatially defined projected light photopolymerization of hydrogels with embedded active compounds is introduced as a flexible and cost-efficient method for producing multiplexed dosing assays. The high spatial resolution of light projector technology defines multiple compound doses by the volume of individual compound-embedded hydrogel segments. Quantitative dosing of multiple proteins with a dynamic range of 1-2 orders of magnitude is demonstrated using fluorescently labeled albumins. The hydrogel matrix results from photopolymerization of low-cost poly(ethylene glycol) diacrylates (PEGDA), and tuning of the PEGDA composition enables fast complete dosing of all tested species. Dosing of hydrophilic and hydrophobic compounds is demonstrated using two first-line chemotherapy regimens combining oxaliplatin, SN-38, 5-fluorouracil, and folinic acid, with each compound being dosed from a separate light-defined hydrogel segment. Cytotoxicity studies using a colorectal cancer cell line show equivalent effects of dissolved and released compounds. Further control of the dosing process is demonstrated by liposomal encapsulation of oxaliplatin, stable embedding of the liposomes in hydrogels for more than 3 months, and heat-triggered complete release of the loaded oxaliplatin. PMID:26619161

  14. Single-channel multiplexing without melting curve analysis in real-time PCR.

    PubMed

    Lee, Young-Jo; Kim, Daeyoung; Lee, Kihoon; Chun, Jong-Yoon

    2014-01-01

    Multiplex real-time PCR with quantification of targets in a single fluorescence channel has been the demand in biotechnology industry. Here, we develop a novel analytical real-time PCR technique to detect multiple targets in a single fluorescence channel without melting curve analysis. In this technique, we show the intensity of the fluorescence signals of two discrete Tm targets is different at certain temperatures called detection temperatures, by which a high Tm target can be detected regardless of a low Tm target. We then identify the low Tm target by utilizing a change of the fluorescence signals between two different detection temperatures. Furthermore, it enables us to determine quantification of each target in a single channel, possibly facilitating convenient patient care for drug treatment in clinics. PMID:25501038

  15. Single-channel multiplexing without melting curve analysis in real-time PCR

    PubMed Central

    Lee, Young-Jo; Kim, Daeyoung; Lee, Kihoon; Chun, Jong-Yoon

    2014-01-01

    Multiplex real-time PCR with quantification of targets in a single fluorescence channel has been the demand in biotechnology industry. Here, we develop a novel analytical real-time PCR technique to detect multiple targets in a single fluorescence channel without melting curve analysis. In this technique, we show the intensity of the fluorescence signals of two discrete Tm targets is different at certain temperatures called detection temperatures, by which a high Tm target can be detected regardless of a low Tm target. We then identify the low Tm target by utilizing a change of the fluorescence signals between two different detection temperatures. Furthermore, it enables us to determine quantification of each target in a single channel, possibly facilitating convenient patient care for drug treatment in clinics. PMID:25501038

  16. Bovine embryo sex determination by multiplex loop-mediated isothermal amplification.

    PubMed

    Khamlor, Trisadee; Pongpiachan, Petai; Parnpai, Rangsun; Punyawai, Kanchana; Sangsritavong, Siwat; Chokesajjawatee, Nipa

    2015-03-15

    In cattle, the ability to determine the sex of embryos before embryo transfer is beneficial for increasing the number of animals with the desired sex. This study therefore developed a new modification of loop-mediated isothermal amplification in a multiplex format (multiplex LAMP) for highly efficient bovine embryo sexing. Two chromosomal regions, one specific for males (Y chromosome, S4 region) and the other common to both males and females (1.715 satellite DNA), were amplified in the same reaction tube. Each target was amplified by specifically designed inner primers, outer primers, and loop primers, where one of the S4 loop primers was labeled with the fluorescent dye 6-carboxyl-X-rhodamine (emitting a red color), whereas both satellite loop primers were labeled with the fluorescent dye fluorescein isothiocyanate (emitting a green color). After amplification at 63 °C for 1 hour, the amplified products were precipitated by a small volume of cationic polymer predispensed inside the reaction tube cap. Green precipitate indicated the presence of only control DNA without the Y chromosome, whereas orange precipitate indicated the presence of both target DNAs, enabling interpretation as female and male, respectively. Accuracy of the multiplex LAMP assay was evaluated using 46 bovine embryos with known sex (25 male and 21 female) generated by somatic cell nuclear transfer and confirmed by multiplex polymerase chain reaction. The multiplex LAMP showed 100% accuracy in identifying the actual sex of the embryos and provides a fast, simple, and cost-effective tool for bovine embryo sexing. PMID:25542460

  17. Examining the Linkage Between FRAMES and GMS

    SciTech Connect

    Whelan, Gene; Castleton, Karl J.

    2006-02-13

    Because GMS provides so many features, of which some are also addressed by FRAMES, it could represent a platform to link to FRAMES, or FRAMES could represent a platform to link to GMS. The focus of this summary is to examine the strengths and weaknesses of the potential linkage direction and provide recommendations for the linkage between FRAMES and GMS.

  18. Linkage Disequilibrium Mapping of Meat Quality QTL

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous studies based on linkage analysis have identified broad areas in the bovine genome associated with meat quality. Linkage disequilibrium (LD) analyses have the potential to identify narrower regions and point towards candidate genes. Tenderness and marbling were chosen to be evaluated in a ...

  19. Compensating linkage for main rotor control

    NASA Technical Reports Server (NTRS)

    Jeffery, P. A. E.; Huber, R. F. (Inventor)

    1981-01-01

    A compensating linkage for the rotor control system on rotary wing aircraft is described. The main rotor and transmission are isolated from the airframe structure by clastic suspension. The compensating linkage prevents unwanted signal inputs to the rotor control system caused by relative motion of the airframe structure and the main rotor and transmission.

  20. Spatially resolved, highly multiplexed RNA profiling in single cells

    PubMed Central

    Chen, Kok Hao; Boettiger, Alistair N.; Moffitt, Jeffrey R.; Wang, Siyuan; Zhuang, Xiaowei

    2015-01-01

    Knowledge of the expression profile and spatial landscape of the transcriptome in individual cells is essential for understanding the rich repertoire of cellular behaviors. Here we report multiplexed error-robust fluorescence in situ hybridization (MERFISH), a single-molecule imaging approach that allows the copy numbers and spatial localizations of thousands of RNA species to be determined in single cells. Using error-robust encoding schemes to combat single-molecule labeling and detection errors, we demonstrated the imaging of 100 – 1000 unique RNA species in hundreds of individual cells. Correlation analysis of the ~104 – 106 pairs of genes allowed us to constrain gene regulatory networks, predict novel functions for many unannotated genes, and identify distinct spatial distribution patterns of RNAs that correlate with properties of the encoded proteins. PMID:25858977

  1. A model for linkage analysis with apomixis.

    PubMed

    Hou, Wei; Lin, Shen; Li, Yao; Pang, Xiaoming; Zeng, Yanru; Wu, Rongling

    2011-09-01

    Apomixis, or asexual reproduction through seeds, occurs in over 400 species of angiosperms. Although apomixis can favorably perpetuate desired genotypes through successive seed generation, it may also bring about some difficulty for linkage analysis and quantitative trait locus mapping. In this article, we explore the issue of how apomixis affects the precision and power of linkage analysis with molecular markers. We derive a statistical model for estimating the linkage between different markers when some progeny are derived from apomixis. The model was constructed within the maximum likelihood framework and implemented with the EM algorithm. A series of procedures are formulated to test the linkage of markers, the rate of apomixis, and the degree of genetic interference during meiosis. The model was examined and validated through simulation studies. The model will provide a tool for linkage mapping and evolutionary studies for plant species that undergo apomixis. PMID:21625991

  2. Equivalence of time-multiplexed and frequency-multiplexed signals in digital communications.

    NASA Technical Reports Server (NTRS)

    Timor, U.

    1972-01-01

    In comparing different techniques for multiplexing N binary data signals into a single channel, time-division multiplexing (TDM) is known to have a theoretic efficiency of 100 percent (neglecting sync power) and thus seems to outperform frequency-division multiplexing systems (FDM). By considering more general FDM systems, we will show that both TDM and FDM are equivalent and have an efficiency of 100 percent. The difference between the systems is in the multiplexing and demultiplexing subsystems, but not in the performance or in the generated waveforms.

  3. Fluorescent taggants with temporally coded signatures.

    PubMed

    Wang, Siyang; Vyas, Raul; Dwyer, Chris

    2016-07-11

    In this paper, resonance energy transfer (RET) networks between chromophores are used to implement fluorescent taggants with temporally coded signatures. Because the temporal signature of such a fluorescent taggant is a phase-type distribution defined by the geometry of its RET network, the taggant design is not constrained by resolvable dyes and has a significantly larger coding capacity than spectrally or lifetime coded fluorescent taggants. Meanwhile, the detection process becomes highly efficient when the signatures are coded in the time domain. The taggant identification method is based on the multinomial distribution of detected photons and Maximum Likelihood Estimation, which guarantees high accuracy even with only a few hundred photons and also applies to a mixture of taggants in multiplex detection. Therefore, these temporally coded fluorescent taggants have great potential for both in situ and Lidar applications. PMID:27410827

  4. Genome-Wide Linkage Scan for Primary Open Angle Glaucoma: Influences of Ancestry and Age at Diagnosis

    PubMed Central

    Qin, Xuejun; Liu, Yutao; Gibson, Jason R.; Santiago-Turla, Cecilia; Larocque-Abramson, Karen R.; Del Bono, Elizabeth; Challa, Pratap; Herndon, Leon W.; Akafo, Stephen; Wiggs, Janey L.; Schmidt, Silke; Hauser, Michael A.

    2011-01-01

    Primary open-angle glaucoma (POAG) is the most common form of glaucoma and one of the leading causes of vision loss worldwide. The genetic etiology of POAG is complex and poorly understood. The purpose of this work is to identify genomic regions of interest linked to POAG. This study is the largest genetic linkage study of POAG performed to date: genomic DNA samples from 786 subjects (538 Caucasian ancestry, 248 African ancestry) were genotyped using either the Illumina GoldenGate Linkage 4 Panel or the Illumina Infinium Human Linkage-12 Panel. A total of 5233 SNPs was analyzed in 134 multiplex POAG families (89 Caucasian ancestry, 45 African ancestry). Parametric and non-parametric linkage analyses were performed on the overall dataset and within race-specific datasets (Caucasian ancestry and African ancestry). Ordered subset analysis was used to stratify the data on the basis of age of glaucoma diagnosis. Novel linkage regions were identified on chromosomes 1 and 20, and two previously described loci—GLC1D on chromosome 8 and GLC1I on chromosome 15—were replicated. These data will prove valuable in the context of interpreting results from genome-wide association studies for POAG. PMID:21765929

  5. Recent developments in multiplexing techniques for immunohistochemistry

    PubMed Central

    Dixon, Angela R; Bathany, Cédric; Tsuei, Michael; White, Joshua; Barald, Kate F; Takayama, Shuichi

    2016-01-01

    Methods to detect immuno-labelled molecules at increasingly higher resolution, even when present at low levels, are revolutionizing immunohistochemistry (IHC). These technologies can be valuable for management and examination of rare patient tissue specimens, and for improved accuracy of early disease detection. The purpose of this mini-review is to highlight recent multiplexing methods that are candidates for more prevalent use in clinical research and potential translation to the clinic. Multiplex IHC methods, which permit identification of at least 3 and up to 30 discrete antigens, have been divided into whole section staining and spatially-patterned staining categories. Associated signal enhancement technologies that can enhance performance and throughput of multiplex IHC assays are also discussed. Each multiplex IHC technique, detailed herein, is associated with several advantages as well as tradeoffs that must be taken into consideration for proper evaluation and use of the methods. PMID:26289603

  6. A design for a 32-channel multiplexer

    NASA Astrophysics Data System (ADS)

    Martinson, P. F.

    1981-01-01

    A time scan analog system multiplexer used for recording data during flight trials of unmanned aircraft navigation sensors is described. The 32 inputs are buffered, then multiplexed in groups of 8 onto 4 lines. These four are multiplexed onto one line and the signal passes through the output buffer to the recorder. Aircraft attitude, heading and height are recorded. Signals from a camera and a kinetheodolite tracking system are synchronized. Operating conditions were simulated using a helicopter. Noise and drift are due to the recorder. The multiplexer copes well with signals of several kHz bandwidth (raw data) and signals of a few Hz bandwidth (processed data, test signals). It can be used with any multitrack tape recorder having an FM recording format on at least two tracks. It can be converted for use in a digital telemetry system.

  7. Correlated edge overlaps in multiplex networks.

    PubMed

    Baxter, Gareth J; Bianconi, Ginestra; da Costa, Rui A; Dorogovtsev, Sergey N; Mendes, José F F

    2016-07-01

    We develop the theory of sparse multiplex networks with partially overlapping links based on their local treelikeness. This theory enables us to find the giant mutually connected component in a two-layer multiplex network with arbitrary correlations between connections of different types. We find that correlations between the overlapping and nonoverlapping links markedly change the phase diagram of the system, leading to multiple hybrid phase transitions. For assortative correlations we observe recurrent hybrid phase transitions. PMID:27575144

  8. Switchable holograms and approaches to storage multiplexing

    NASA Astrophysics Data System (ADS)

    Domash, Lawrence H.; Chen, Yong-Ming; Snowbell, Michael; Gozewski, Conrad M.

    1994-09-01

    Holographic data storage requires reference beam encoding for multiplexing and demultiplexing. Electrically switchable holographic composites (ESHC) based on a Polaroid photopolymer films are being investigated as a basis for several types of reference beam encoding devices. A laboratory demonstration reported here recorded four holograms in a photoresponsive storage medium. Both random phase encoding and angle multiplexing approaches were tested. ESHC encoding devices have much higher diffraction efficiency than spatial light modulators used in many other encoding schemes.

  9. Correlated edge overlaps in multiplex networks

    NASA Astrophysics Data System (ADS)

    Baxter, Gareth J.; Bianconi, Ginestra; da Costa, Rui A.; Dorogovtsev, Sergey N.; Mendes, José F. F.

    2016-07-01

    We develop the theory of sparse multiplex networks with partially overlapping links based on their local treelikeness. This theory enables us to find the giant mutually connected component in a two-layer multiplex network with arbitrary correlations between connections of different types. We find that correlations between the overlapping and nonoverlapping links markedly change the phase diagram of the system, leading to multiple hybrid phase transitions. For assortative correlations we observe recurrent hybrid phase transitions.

  10. Resource linkages and sustainable development

    NASA Astrophysics Data System (ADS)

    Anouti, Yahya

    Historically, fossil fuel consumers in most developing hydrocarbon-rich countries have enjoyed retail prices at a discount from international benchmarks. Governments of these countries consider the subsidy transfer to be a means for sharing the wealth from their resource endowment. These subsidies create negative economic, environmental, and social distortions, which can only increase over time with a fast growing, young, and rich population. The pressure to phase out these subsidies has been mounting over the last years. At the same time, policy makers in resource-rich developing countries are keen to obtain the greatest benefits for their economies from the extraction of their exhaustible resources. To this end, they are deploying local content policies with the aim of increasing the economic linkages from extracting their resources. Against this background, this dissertation's three essays evaluate (1) the global impact of rationalizing transport fuel prices, (2) how resource-rich countries can achieve the objectives behind fuel subsidies more efficiently through direct cash transfers, and (3) the economic tradeoffs from deploying local content policies and the presence of an optimal path. We begin by reviewing the literature and building the case for rationalizing transport fuel prices to reflect their direct costs (production), indirect costs (road maintenance) and negative externalities (climate change, local pollutants, traffic accidents and congestion). To do so, we increase the scope of the economic literature by presenting an algorithm to evaluate the rationalized prices in different countries. Then, we apply this algorithm to quantify the rationalized prices across 123 countries in a partial equilibrium setting. Finally, we present the first comprehensive measure of the impact of rationalizing fuel prices on the global demand for gasoline and diesel, environmental emissions, government revenues, and consumers' welfare. By rationalizing transport fuel

  11. Multiplexing of fiber optic Bragg grating sensors

    NASA Astrophysics Data System (ADS)

    Chan, Kok Cheung Peter

    2000-11-01

    The main objective of this project was to develop a novel technique for multiplexing fiber Bragg grating sensors for strain measurements. Multiplexing is a very important issue for fiber Bragg grating sensors, as it allows them to be used for distributed sensing where their greatest impact is anticipated. Three types of multiplexed fiber Bragg grating sensor system prototypes were developed in this work. Most effort was devoted to a frequency-modulated continuous wave technique for multiplexing fiber Bragg grating sensors. A detailed mathematical analysis of the frequency-modulated continuous wave multiplexing technique was performed. It was identified that the technique can be used to multiplex up to 32 fiber Bragg grating sensors of the same nominal Bragg wavelength with a theoretical crosstalk performance of below -48 dB. This level of crosstalk corresponds to a wavelength detected error of well below 1 pm if fiber Bragg gratings having a bandwidth of around 0.2 nm are used. A few hundreds of sensors could be multiplexed by combining the frequency-modulated continuous wave technique with the well known wavelength-division-multiplexing technique. The practical factors which limit the performance, including the effect of biasing from the optimal working condition and the effect of non-ideal frequency sweeping intensity modulation, were investigated. The system performance, in terms of power budget and inter-sensor crosstalk for a serial and parallel architecture was also determined. A series of experiments were carried out to verify the principle of operation and to study the effects arising from the various practical performance limiting factors and from different network architectures. A three sensor system was experimentally demonstrated with -30 dB crosstalk level and with 2 μɛ resolution in terms of root-mean-square strain value. The system performance was found to be limited by the residual amplitude modulation due to the non-ideal frequency response of

  12. Hyperspectral fluorescence imaging with multi wavelength LED excitation

    NASA Astrophysics Data System (ADS)

    Luthman, A. Siri; Dumitru, Sebastian; Quirós-Gonzalez, Isabel; Bohndiek, Sarah E.

    2016-04-01

    Hyperspectral imaging (HSI) can combine morphological and molecular information, yielding potential for real-time and high throughput multiplexed fluorescent contrast agent imaging. Multiplexed readout from targets, such as cell surface receptors overexpressed in cancer cells, could improve both sensitivity and specificity of tumor identification. There remains, however, a need for compact and cost effective implementations of the technology. We have implemented a low-cost wide-field multiplexed fluorescence imaging system, which combines LED excitation at 590, 655 and 740 nm with a compact commercial solid state HSI system operating in the range 600 - 1000 nm. A key challenge for using reflectance-based HSI is the separation of contrast agent fluorescence from the reflectance of the excitation light. Here, we illustrate how it is possible to address this challenge in software, using two offline reflectance removal methods, prior to least-squares spectral unmixing. We made a quantitative comparison of the methods using data acquired from dilutions of contrast agents prepared in well-plates. We then established the capability of our HSI system for non-invasive in vivo fluorescence imaging in small animals using the optimal reflectance removal method. The HSI presented here enables quantitative unmixing of at least four fluorescent contrast agents (Alexa Fluor 610, 647, 700 and 750) simultaneously in living mice. A successful unmixing of the four fluorescent contrast agents was possible both using the pure contrast agents and with mixtures. The system could in principle also be applied to imaging of ex vivo tissue or intraoperative imaging in a clinical setting. These data suggest a promising approach for developing clinical applications of HSI based on multiplexed fluorescence contrast agent imaging.

  13. Simplified development of multiplex real-time PCR through master mix augmented by universal fluorogenic reporters.

    PubMed

    Wadle, Simon; Lehnert, Michael; Schuler, Friedrich; Köppel, René; Serr, Annerose; Zengerle, Roland; von Stetten, Felix

    2016-01-01

    Mediator probe (MP) PCR is a real-time PCR approach that uses standardized universal fluorogenic reporter oligonucleotides (UR) in conjunction with label-free sequence-specific probes. To enable multiplex real-time MP PCR, we designed a set of five optimized URs with different fluorescent labels. Performance of the optimized URs was verified in multiplex real-time MP PCR for the detection of a pentaplex food panel and a quadruplex methicillin-resistant Staphylococcus aureus (MRSA) panel. Results were comparable to corresponding multiplex hydrolysis probe (HP) PCR, also designated as TaqMan PCR. Analyses of MRSA DNA standards and DNA extracted from patient swab samples showed improved lower limits of detection (LoDs) by a factor of 2-5 when using quadruplex real-time MP PCR instead of HP PCR. The novel set of standardized URs we present here simplifies development of multiplex real-time PCR assays by requiring only the design of label-free probes. In the future, real-time PCR master mixes could be augmented with up to five standardized fluorogenic URs, each emitting light at a different wavelength. PMID:27625206

  14. Serodiagnosis of Lyme borreliosis with bead based immunoassays using multiplex technology.

    PubMed

    Gerritzen, Andreas; Brandt, Sabine

    2012-04-01

    The serological diagnosis of Lyme borreliosis is accomplished by the detection of IgG and IgM antibodies specific for relevant antigens of the spirochetal pathogen Borrelia burgdorferi. Instead of the usual enzyme immune assay for screening and the Western blot technique for confirmation, bead based multiplex assays with multiple simultaneously performed distinct reactions can provide quick, automatically derived and reliable results in a single run by flow cytometer technology. The broad analytical dynamic range of assay signals and the high sensitivity and specificity of the multiplex formats allow even for a reliable use in CSF based analyses for antibody specificity index in supposed neuroborreliosis. Fluorescence intensity of the bead based reactions can be transformed into quantified values as U/ml, either for each single antigen or summed up for a group of relevant key antigens. Additionally or alternatively distinct reactions of single bead populations can be transformed to Western blot band equivalents. Internal and external quality controls with the multiplex systems show characteristic data equivalent to the conventional assay formats, so that the advantages of the multiplex assays are ready for use in the routine diagnostic laboratory. PMID:22406491

  15. Multi-Channel Hyperspectral Fluorescence Detection Excited by Coupled Plasmon-Waveguide Resonance

    PubMed Central

    Du, Chan; Liu, Le; Zhang, Lin; Guo, Jun; Guo, Jihua; Ma, Hui; He, Yonghong

    2013-01-01

    We propose in this paper a biosensor scheme based on coupled plasmon-waveguide resonance (CPWR) excited fluorescence spectroscopy. A symmetrical structure that offers higher surface electric field strengths, longer surface propagation lengths and depths is developed to support guided waveguide modes for the efficient excitation of fluorescence. The optimal parameters for the sensor films are theoretically and experimentally investigated, leading to a detection limit of 0.1 nM (for a Cy5 solution). Multiplex analysis possible with the fluorescence detection is further advanced by employing the hyperspectral fluorescence technique to record the full spectra for every pixel on the sample plane. We demonstrate experimentally that highly overlapping fluorescence (Cy5 and Dylight680) can be distinguished and ratios of different emission sources can be determined accurately. This biosensor shows great potential for multiplex detections of fluorescence analytes. PMID:24129023

  16. The REBUS-MCNP linkage.

    SciTech Connect

    Stevens, J. G.; Nuclear Engineering Division

    2009-04-24

    The Reduced Enrichment Research and Test Reactor (RERTR) Program uses the REBUS-PC computer code to provide reactor physics and core design information such as neutron flux distributions in space, energy, and time, and to track isotopic changes in fuel and neutron absorbers with burnup. REBUS-PC models the complete fuel cycle including shuffling capability. REBUS-PC evolved using the neutronic capabilities of multi-group diffusion theory code DIF3D 9.0, but was extended to apply the continuous energy Monte Carlo code MCNP for one-group fluxes and cross-sections. The linkage between REBUS-PC and MCNP has recently been modernized and extended, as described in this manual. REBUS-PC now calls MCNP via a system call so that the user can apply any valid MCNP executable. The interface between REBUS-PC and MCNP requires minimal changes to an existing MCNP model, and little additional input. The REBUS-MCNP interface can also be used in conjunction with DIF3D neutronics to update an MCNP model with fuel compositions predicted using a DIF3D based depletion.

  17. Multiplexed modulation of behavioral choice

    PubMed Central

    Palmer, Chris R.; Barnett, Megan N.; Copado, Saul; Gardezy, Fred; Kristan, William B.

    2014-01-01

    Stimuli in the environment, as well as internal states, influence behavioral choice. Of course, animals are often exposed to multiple external and internal factors simultaneously, which makes the ultimate determinants of behavior quite complex. We observed the behavioral responses of European leeches, Hirudo verbana, as we varied one external factor (surrounding water depth) with either another external factor (location of tactile stimulation along the body) or an internal factor (body distention following feeding). Stimulus location proved to be the primary indicator of behavioral response. In general, anterior stimulation produced shortening behavior, midbody stimulation produced local bending, and posterior stimulation usually produced either swimming or crawling but sometimes a hybrid of the two. By producing a systematically measured map of behavioral responses to body stimulation, we found wide areas of overlap between behaviors. When we varied the surrounding water depth, this map changed significantly, and a new feature – rotation of the body along its long axis prior to swimming – appeared. We found additional interactions between water depth and time since last feeding. A large blood meal initially made the animals crawl more and swim less, an effect that was attenuated as water depth increased. The behavioral map returned to its pre-feeding form after approximately 3 weeks as the leeches digested their blood meal. In summary, we found multiplexed impacts on behavioral choice, with the map of responses to tactile stimulation modified by water depth, which itself modulated the impact that feeding had on the decision to swim or crawl. PMID:24902753

  18. Graphene-based aptamer logic gates and their application to multiplex detection.

    PubMed

    Wang, Li; Zhu, Jinbo; Han, Lei; Jin, Lihua; Zhu, Chengzhou; Wang, Erkang; Dong, Shaojun

    2012-08-28

    In this work, a GO/aptamer system was constructed to create multiplex logic operations and enable sensing of multiplex targets. 6-Carboxyfluorescein (FAM)-labeled adenosine triphosphate binding aptamer (ABA) and FAM-labeled thrombin binding aptamer (TBA) were first adsorbed onto graphene oxide (GO) to form a GO/aptamer complex, leading to the quenching of the fluorescence of FAM. We demonstrated that the unique GO/aptamer interaction and the specific aptamer-target recognition in the target/GO/aptamer system were programmable and could be utilized to regulate the fluorescence of FAM via OR and INHIBIT logic gates. The fluorescence changed according to different input combinations, and the integration of OR and INHIBIT logic gates provided an interesting approach for logic sensing applications where multiple target molecules were present. High-throughput fluorescence imagings that enabled the simultaneous processing of many samples by using the combinatorial logic gates were realized. The developed logic gates may find applications in further development of DNA circuits and advanced sensors for the identification of multiple targets in complex chemical environments. PMID:22823159

  19. In-solution multiplex miRNA detection using DNA-templated silver nanocluster probes.

    PubMed

    Shah, Pratik; Thulstrup, Peter Waaben; Cho, Seok Keun; Bhang, Yong-Joo; Ahn, Jong Cheol; Choi, Suk Won; Bjerrum, Morten Jannik; Yang, Seong Wook

    2014-05-01

    MicroRNAs (miRNAs) are small regulatory RNAs (size ∼21nt to ∼25nt) that can be used as biomarkers of disease diagnosis, and efforts have been directed towards the invention of a rapid, simple and sequence-selective detection method for miRNAs. We recently developed a DNA/silver nanoclusters (AgNCs)-based turn-off fluorescence method in the presence of target miRNA. To further advance our method toward multiplex miRNA detection in solution, the design of various fluorescent DNA/AgNCs probes was essential. Therefore, tethering of DNA-12nt scaffolds with 9 different AgNCs emitters to target-sensing DNA sequences was investigated. Interestingly, for the creation of spectrally different DNA/AgNCs probes, not only were the emitters encapsulated in 9 different DNA-12nt scaffolds necessary but the tethered target-sensing DNA sequences are also crucial to tune the fluorescence across the visible to infra-red region. In this study, we obtained three spectrally distinctive emitters of each DNA/AgNCs probes such as green, red, and near-infrared (NIR) fluorescence. Using these DNA/AgNCs probes, we here show a proof of concept for a rapid, one-step, in-solution multiplex miRNA detection method. PMID:24616905

  20. A GENOME-WIDE LINKAGE AND ASSOCIATION SCAN REVEALS NOVEL LOCI FOR AUTISM

    PubMed Central

    Weiss, Lauren A.; Arking, Dan E.

    2009-01-01

    Summary Although autism is a highly heritable neurodevelopmental disorder, attempts to identify specific susceptibility genes have thus far met with limited success 1. Genome-wide association studies (GWAS) using half a million or more markers, particularly those with very large sample sizes achieved through meta-analysis, have shown great success in mapping genes for other complex genetic traits (http://www.genome.gov/26525384). Consequently, we initiated a linkage and association mapping study using half a million genome-wide SNPs in a common set of 1,031 multiplex autism families (1,553 affected offspring). We identified regions of suggestive and significant linkage on chromosomes 6q27 and 20p13, respectively. Initial analysis did not yield genome-wide significant associations; however, genotyping of top hits in additional families revealed a SNP on chromosome 5p15 (between SEMA5A and TAS2R1) that was significantly associated with autism (P = 2 × 10−7). We also demonstrated that expression of SEMA5A is reduced in brains from autistic patients, further implicating SEMA5A as an autism susceptibility gene. The linkage regions reported here provide targets for rare variation screening while the discovery of a single novel association demonstrates the action of common variants. PMID:19812673

  1. Intracavity absorption multiplexed sensor network based on dense wavelength division multiplexing filter.

    PubMed

    Zhang, Haiwei; Lu, Ying; Duan, Liangcheng; Zhao, Zhiqiang; Shi, Wei; Yao, Jianquan

    2014-10-01

    We report the system design and experimental verification of an intracavity absorption multiplexed sensor network with hollow core photonic crystal fiber (HCPCF) sensors and dense wavelength division multiplexing (DWDM) filters. Compared with fiber Bragg grating (FBG), it is easier for the DWDM to accomplish a stable output. We realize the concentration detection of three gas cells filled with acetylene. The sensitivity is up to 100 ppmV at 1536.71 nm. Voltage gradient is firstly used to optimize the intracavity sensor network enhancing the detection efficiency up to 6.5 times. To the best of our knowledge, DWDM is firstly used as a wavelength division multiplexing device to realize intracavity absorption multiplexed sensor network. It make it possible to realize high capacity intracavity sensor network via multiplexed technique. PMID:25322029

  2. 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. PMID:26245682

  3. Dual-color encoded DNAzyme nanostructures for multiplexed detection of intracellular metal ions in living cells.

    PubMed

    Zhou, Wenjiao; Liang, Wenbing; Li, Daxiu; Yuan, Ruo; Xiang, Yun

    2016-11-15

    The detection of intracellular metal ions is of great importance in understanding metal homeostasis in cells and related diseases, and yet it remains a significant challenge to achieve this goal. Based on a new self-assembled and dual-color encoded DNAzyme nanostructure, we describe here an approach for multiplexed sensing of UO2(2+) and Pb(2+) in living cells. The fluorescently quenched nanoprobes can be prepared by simple thermal annealing of four ssDNAs containing the metal ion-dependent enzymatic and substrate sequences. The self-assembly formation of the nanostructures are verified by native polyacrylamide gel electrophoresis. The target metal ions can cleave the substrate sequences in the DNAzyme nanostructures to recover fluorescent emissions at different wavelengths for sensitive and selective in vitro multiplexed detection of UO2(2+) and Pb(2+) with the detection limits of 0.6nM and 3.9nM, respectively. Importantly, we demonstrate that these nanoprobes are stable in cell lysates and can enter cells without the aid of any transfection agents for simultaneous imaging intracellular UO2(2+) and Pb(2+). Moreover, the nanoprobes offer excellent biocompatibility and non-cytotoxicity. With these unique features, the dual-color encoded nanostructures presented here can thus offer new opportunities for multiplexed detection of specific intracellular species. PMID:27236722

  4. Linkage studies in primary open angle glaucoma

    SciTech Connect

    Avramopoulos, D.; Grigoriadu, M.; Kitsos, G.

    1994-09-01

    Glaucoma is a leading cause of blindness worldwide. The majority of glaucoma is associated with an open, normal appearing anterior chamber angle and is termed primary open angle glaucoma (POAG, MIM 137760). It is characterized by elevated intraocular pressure and onset in middle age or later. A subset of POAG with juvenile onset has recently been linked to chromosome 1q in two families with autosomal dominant inheritance. Eleven pedigrees with autosomal dominant POG (non-juvenile-onset) have been identified in Epirus, Greece. In the present study DNA samples have been collected from 50 individuals from one large pedigree, including 12 affected individuals. Preliminary results of linkage analysis with chromosome 1 microsatellites using the computer program package LINKAGE Version 5.1 showed no linkage with the markers previously linked to juvenile-onset POAG. Further linkage analysis is being pursued, and the results will be presented.

  5. Linkage: from particulate to interactive genetics.

    PubMed

    Falk, Raphael

    2003-01-01

    Genetics was established on a strict particulate conception of heredity. Genetic linkage, the deviation from independent segregation of Mendelian factors, was conceived as a function of the material allocation of the factors to the chromosomes, rather than to the multiple effects (pleiotropy) of discrete factors. Although linkage maps were abstractions they provided strong support for the chromosomal theory of inheritance. Direct Cytogenetic evidence was scarce until X-ray induced major chromosomal rearrangements allowed direct correlation of genetic and cytological rearrangements. Only with the discovery of the polytenic giant chromosomes in Drosophila larvae in the 1930s were the virtual maps backed up by physical maps of the genetic loci. Genetic linkage became a pivotal experimental tool for the examination of the integration of genetic functions in development and in evolution. Genetic mapping has remained a hallmark of genetic analysis. The location of genes in DNA is a modern extension of the notion of genetic linkage. PMID:12778899

  6. Resource linkages and sustainable development

    NASA Astrophysics Data System (ADS)

    Anouti, Yahya

    Historically, fossil fuel consumers in most developing hydrocarbon-rich countries have enjoyed retail prices at a discount from international benchmarks. Governments of these countries consider the subsidy transfer to be a means for sharing the wealth from their resource endowment. These subsidies create negative economic, environmental, and social distortions, which can only increase over time with a fast growing, young, and rich population. The pressure to phase out these subsidies has been mounting over the last years. At the same time, policy makers in resource-rich developing countries are keen to obtain the greatest benefits for their economies from the extraction of their exhaustible resources. To this end, they are deploying local content policies with the aim of increasing the economic linkages from extracting their resources. Against this background, this dissertation's three essays evaluate (1) the global impact of rationalizing transport fuel prices, (2) how resource-rich countries can achieve the objectives behind fuel subsidies more efficiently through direct cash transfers, and (3) the economic tradeoffs from deploying local content policies and the presence of an optimal path. We begin by reviewing the literature and building the case for rationalizing transport fuel prices to reflect their direct costs (production), indirect costs (road maintenance) and negative externalities (climate change, local pollutants, traffic accidents and congestion). To do so, we increase the scope of the economic literature by presenting an algorithm to evaluate the rationalized prices in different countries. Then, we apply this algorithm to quantify the rationalized prices across 123 countries in a partial equilibrium setting. Finally, we present the first comprehensive measure of the impact of rationalizing fuel prices on the global demand for gasoline and diesel, environmental emissions, government revenues, and consumers' welfare. By rationalizing transport fuel

  7. Linkage of the VNTR/insulin-gene and type I diabetes mellitus: Increased gene sharing in affected sibling pairs

    SciTech Connect

    Owerbach, D.; Gabbay, K.H. )

    1994-05-01

    Ninety-six multiplex type I diabetic families were typed at the 5' flanking region of the insulin gene by using a PCR assay that better resolves the VNTR into multiple alleles. Affected sibling pairs shared 2, 1, and 0 VNTR alleles - identical by descent - at a frequency of .47, .45, and .08, respectively, a ratio that deviated from the expected 1:2:1 ratio (P<.001). These results confirm linkage of the chromosome 11p15.5 region with type I diabetes mellitus susceptibility. 20 refs., 2 tabs.

  8. Method and apparatus for multiplexing switch signals

    NASA Technical Reports Server (NTRS)

    Hannaford, Blake (Inventor)

    1989-01-01

    Apparatus for multiplexing switch state signals comprises a plurality of switches and parallel weighted resistors connected in series between circuit ground and a node at a utilization device. The resistors are weighted as a function of a power of the same base, such as the power of the base 2, for coding the multiplexed switch state signals. A constant current source connected between the node and circuit ground drives current over a single cable conductor through the resistor. Each switch may be independently closed to change the switch state voltage signals multiplexed to the node. An analog-to-digital converter connected between the node and circuit ground demultiplexes the switch state signals received at the node and provides a switch state signal at each analog-to-digital output corresponding to the state of the switches at the moment. A potentiometer may replace a resistor and bypass switch combination in a position where the potentiometer has a maximum value of the lowest power of the base in order to multiplex a true analog voltage signal while switch state signals are unambiguously coded and multiplexed. The potentiometer in the least significant position permits the analog value to be in the range from 0 to a maximum corresponding to the least significant position of the switch state encoding. The invention may be used in redundancy systems by duplicating the invention with corresponding switches in each duplication ganged to open and close simultaneously upon operation of a pushbutton switch.

  9. Giant components in directed multiplex networks.

    PubMed

    Azimi-Tafreshi, N; Dorogovtsev, S N; Mendes, J F F

    2014-11-01

    We describe the complex global structure of giant components in directed multiplex networks that generalizes the well-known bow-tie structure, generic for ordinary directed networks. By definition, a directed multiplex network contains vertices of one type and directed edges of m different types. In directed multiplex networks, we distinguish a set of different giant components based on the existence of directed paths of different types between their vertices such that for each type of edges, the paths run entirely through only edges of that type. If, in particular, m=2, we define a strongly viable component as a set of vertices in which for each type of edges each two vertices are interconnected by at least two directed paths in both directions, running through the edges of only this type. We show that in this case, a directed multiplex network contains in total nine different giant components including the strongly viable component. In general, the total number of giant components is 3^{m}. For uncorrelated directed multiplex networks, we obtain exactly the size and the emergence point of the strongly viable component and estimate the sizes of other giant components. PMID:25493836

  10. Optical encryption system using quadrature multiplexing

    NASA Astrophysics Data System (ADS)

    Islam, Mohammed Nazrul; Alam, Mohammad S.

    2006-08-01

    Optical security systems have attracted much research interest recently for information security and fraud deterrent applications. A number of encryption techniques have been proposed in the literature, which includes double random-phase encryption, polarization encoding, encryption and verification using a multiplexed minimum average correlation energy phase-encrypted filter. Most of these reports employ a pseudo-random code for each information to be encrypted, where it requires individual storage capacity or transmission channel for further processing of each information. The objective of this paper is to develop an optical encryption system employing quadrature multiplexing to enhance the storage/transmission capacity of the system. Two information signals are encrypted using the same code but employing two orthogonal functions and then they are multiplexed together in the same domain. As the orthogonal functions have zero cross-correlation between them, so the encrypted information are expected to be unaffected by each other. Each encryption and multiplexing process can accommodate two information signals for a single code and a single storage cell or transmission channel. The same process can be performed in multiple steps to increase the multiplexing capability of the system. For decryption purpose, the composite encoded signal is correlated using the appropriate code and the appropriate function. The proposed technique has been found to work excellent in computer simulation with binary as well as gray level images. It has also been verified that the encrypted images remain secure, because no unwanted reproduction is possible without having the appropriate code and function.

  11. Chemically modified primers for improved multiplex PCR

    PubMed Central

    Shum, Jonathan; Paul, Natasha

    2009-01-01

    Multiplexed PCR, the amplification of multiple targets in a single reaction, presents a new set of challenges that further complicate more traditional PCR set-ups. These complications include a greater probability for non-specific amplicon formation and for imbalanced amplification of different targets, each of which can compromise quantification and detection of multiple targets. Despite these difficulties, multiplex PCR is frequently used in such applications as pathogen detection, RNA quantification, mutation analysis and now, next generation DNA sequencing. Herein, we investigate the utility of primers with one or two thermolabile 4-oxo-1-pentyl phosphotriester modifications in improving multiplex PCR performance. Initial endpoint and real-time analyses reveal a decrease in off-target amplification and subsequent increase in amplicon yield. Furthermore, the use of modified primers in multiplex set-ups revealed a greater limit of detection and more uniform amplification of each target as compared to unmodified primers. Overall, the thermolabile modified primers present a novel and exciting avenue in improving multiplex PCR performance. PMID:19258004

  12. Giant components in directed multiplex networks

    NASA Astrophysics Data System (ADS)

    Azimi-Tafreshi, N.; Dorogovtsev, S. N.; Mendes, J. F. F.

    2014-11-01

    We describe the complex global structure of giant components in directed multiplex networks that generalizes the well-known bow-tie structure, generic for ordinary directed networks. By definition, a directed multiplex network contains vertices of one type and directed edges of m different types. In directed multiplex networks, we distinguish a set of different giant components based on the existence of directed paths of different types between their vertices such that for each type of edges, the paths run entirely through only edges of that type. If, in particular, m =2 , we define a strongly viable component as a set of vertices in which for each type of edges each two vertices are interconnected by at least two directed paths in both directions, running through the edges of only this type. We show that in this case, a directed multiplex network contains in total nine different giant components including the strongly viable component. In general, the total number of giant components is 3m. For uncorrelated directed multiplex networks, we obtain exactly the size and the emergence point of the strongly viable component and estimate the sizes of other giant components.

  13. Fluorescent refrigeration

    DOEpatents

    Epstein, Richard I.; Edwards, Bradley C.; Buchwald, Melvin I.; Gosnell, Timothy R.

    1995-01-01

    Fluorescent refrigeration is based on selective radiative pumping, using substantially monochromatic radiation, of quantum excitations which are then endothermically redistributed to higher energies. Ultimately, the populated energy levels radiatively deexcite emitting, on the average, more radiant energy than was initially absorbed. The material utilized to accomplish the cooling must have dimensions such that the exciting radiation is strongly absorbed, but the fluorescence may exit the material through a significantly smaller optical pathlength. Optical fibers and mirrored glasses and crystals provide this requirement.

  14. Single Quantum Dot Analysis Enables Multiplexed Point Mutation Detection by Gap Ligase Chain Reaction

    PubMed Central

    Song, Yunke; Zhang, Yi; Wang, Tza-Huei

    2014-01-01

    Gene point mutations present important biomarkers for genetic diseases. However, existing point mutation detection methods suffer from low sensitivity, specificity, and tedious assay processes. In this report, we propose an assay technology which combines the outstanding specificity of gap ligase chain reaction (Gap-LCR), the high sensitivity of single molecule coincidence detection and superior optical properties of quantum dots (QDs) for multiplexed detection of point mutations in genomic DNA. Mutant-specific ligation products are generated by Gap-LCR and subsequently captured by QDs to form DNA-QD nanocomplexes that are detected by single molecule spectroscopy (SMS) through multi-color fluorescence burst coincidence analysis, allowing for multiplexed mutation detection in a separation-free format. The proposed assay is capable of detecting zeptomoles of KRAS codon 12 mutation variants with near 100% specificity. Its high sensitivity allows direct detection of KRAS mutation in crude genomic DNA without PCR pre-amplification. PMID:23239594

  15. Genomic convergence: identifying candidate genes for Parkinson's disease by combining serial analysis of gene expression and genetic linkage.

    PubMed

    Hauser, Michael A; Li, Yi-Ju; Takeuchi, Satoshi; Walters, Robert; Noureddine, Maher; Maready, Melinda; Darden, Tiffany; Hulette, Christine; Martin, Eden; Hauser, Elizabeth; Xu, Hong; Schmechel, Don; Stenger, Judith E; Dietrich, Fred; Vance, Jeffery

    2003-03-15

    We present a multifactorial, multistep approach called genomic convergence that combines gene expression with genomic linkage analysis to identify and prioritize candidate susceptibility genes for Parkinson's disease (PD). To initiate this process, we used serial analysis of gene expression (SAGE) to identify genes expressed in two normal substantia nigras (SN) and adjacent midbrain tissue. This identified over 3700 transcripts, including the three most abundant SAGE tags, which did not correspond to any known genes or ESTs. We developed high-throughput bioinformatics methods to map the genes corresponding to these tags and identified 402 SN genes that lay within five large genomic linkage regions, previously identified in 174 multiplex PD families. These genes represent excellent candidates for PD susceptibility alleles and further genomic convergence and analyses. PMID:12620972

  16. Ag@poly(m-phenylenediamine) core-shell nanoparticles for highly selective, multiplex nucleic acid detection.

    PubMed

    Zhang, Yingwei; Wang, Lei; Tian, Jingqi; Li, Hailong; Luo, Yonglan; Sun, Xuping

    2011-03-15

    In this letter, we report on the one-step synthesis of Ag@poly(m-phenylenediamine) core-shell nanoparticles (APCSNPs), carried out by direct mixing of aqueous silver nitrate and m-phenylenediamine solutions at room temperature. We further demonstrate the use of APCSNP as a novel fluorescent sensing platform for nucleic acid detection. In this regard, the detection of DNA is accomplished in two steps. First, APCSNP absorbs and quenches the fluorescence of dye-labeled single-stranded DNA (ssDNA) as a probe. Second, hybridizing of the probe with its target produces a double-stranded DNA (dsDNA) that detaches from APCSNP, resulting in the recovery of dye fluorescence. It suggests that this sensing system has a high selectivity down to single-base mismatch, and the results exhibit good reproducibility. Furthermore, we also demonstrate its application for the multiplex detection of nucleic acid sequences. PMID:21302954

  17. Multiplex quantification of 12 European Union authorized genetically modified maize lines with droplet digital polymerase chain reaction.

    PubMed

    Dobnik, David; Spilsberg, Bjørn; Bogožalec Košir, Alexandra; Holst-Jensen, Arne; Žel, Jana

    2015-08-18

    Presence of genetically modified organisms (GMO) in food and feed products is regulated in many countries. The European Union (EU) has implemented a threshold for labeling of products containing more than 0.9% of authorized GMOs per ingredient. As the number of GMOs has increased over time, standard-curve based simplex quantitative polymerase chain reaction (qPCR) analyses are no longer sufficiently cost-effective, despite widespread use of initial PCR based screenings. Newly developed GMO detection methods, also multiplex methods, are mostly focused on screening and detection but not quantification. On the basis of droplet digital PCR (ddPCR) technology, multiplex assays for quantification of all 12 EU authorized GM maize lines (per April first 2015) were developed. Because of high sequence similarity of some of the 12 GM targets, two separate multiplex assays were needed. In both assays (4-plex and 10-plex), the transgenes were labeled with one fluorescence reporter and the endogene with another (GMO concentration = transgene/endogene ratio). It was shown that both multiplex assays produce specific results and that performance parameters such as limit of quantification, repeatability, and trueness comply with international recommendations for GMO quantification methods. Moreover, for samples containing GMOs, the throughput and cost-effectiveness is significantly improved compared to qPCR. Thus, it was concluded that the multiplex ddPCR assays could be applied for routine quantification of 12 EU authorized GM maize lines. In case of new authorizations, the events can easily be added to the existing multiplex assays. The presented principle of quantitative multiplexing can be applied to any other domain. PMID:26169291

  18. Sequential strategy to identify a susceptibility gene for schizophrenia: Report of potential linkage on chromosome 22q12-q13.1: Part 1

    SciTech Connect

    Pulver, A.E.; Wolyniec, P.S.; Lasseter, V.K.

    1994-03-15

    To identify genes responsible for the susceptibility for schizophrenia, and to test the hypothesis that schizophrenia is etiologically heterogeneous, we have studied 39 multiplex families from a systematic sample of schizophrenic patients. Using a complex autosomal dominant model, which considers only those with a diagnosis of schizophrenia or schizoaffective disorder as affected, a random search of the genome for detection of linkage was undertaken. Pairwise linkage analyses suggest a potential linkage (LRH = 34.7 or maximum lod score = 1.54) for one region (22q12-q13.1). Reanalyses, varying parameters in the dominant model, maximized the LRH at 660.7 (maximum lod score 2.82). This finding is of sufficient interest to warrant further investigation through collaborative studies. 72 refs., 5 tabs.

  19. Development of the 19 X-STR loci multiplex system and genetic analysis of a Zhejiang Han population in China.

    PubMed

    Yang, XingYi; Wu, WeiWei; Chen, LinLi; Liu, ChangHui; Zhang, XiaoFang; Chen, Ling; Feng, XingLin; Wang, HuiJun; Liu, Chao

    2016-08-01

    The 19 X-STRs multiplex system is a PCR-based amplification kit that facilitates simultaneous amplification of 19 X-chromosomal STR loci (i.e. DXS7423, DXS10148, DXS10159, DXS6809, DXS7424, DXS8378, DXS10164, DXS10162, DXS7132, DXS10079, DXS6789, DXS101, DXS10103,DXS10101, HPTRB, DXS10075, DXS10074, DXS10135, and DXS10134). Eleven loci were extensively used in an Investigator Qiagen Argus X-12 (DXS7423, DXS10148, DXS8378, DXS10162, DXS7132, DXS10079, DXS10103, DXS10101, HPTRB, DXS10074, and DXS10135). In this research, the multiplex system was tested for detection sensitivity, DNA mixtures, inhibitor tolerance and species specificity; SWGDAM Validation Guidelines - Approved December 2012 were followed for the human fluorescent STR multiplex PCR reagent. Samples from 181 unrelated Zhejiang Han individuals (121 males and 60 females) were typed using this multiplex system. The results show that this 19X-STRs multiplex system is a robust and reliable amplification means to facilitate forensic and human identification testing. PMID:27184937

  20. Multiplexed image storage by electromagnetically induced transparency in a solid

    NASA Astrophysics Data System (ADS)

    Heinze, G.; Rentzsch, N.; Halfmann, T.

    2012-11-01

    We report on frequency- and angle-multiplexed image storage by electromagnetically induced transparency (EIT) in a Pr3+:Y2SiO5 crystal. Frequency multiplexing by EIT relies on simultaneous storage of light pulses in atomic coherences, driven in different frequency ensembles of the inhomogeneously broadened solid medium. Angular multiplexing by EIT relies on phase matching of the driving laser beams, which permits simultaneous storage of light pulses propagating under different angles into the crystal. We apply the multiplexing techniques to increase the storage capacity of the EIT-driven optical memory, in particular to implement multiplexed storage of larger two-dimensional amounts of data (images). We demonstrate selective storage and readout of images by frequency-multiplexed EIT and angular-multiplexed EIT, as well as the potential to combine both multiplexing approaches towards further enhanced storage capacities.

  1. An X-band SQUID Multiplexer

    NASA Astrophysics Data System (ADS)

    Hahn, I.; Bumble, B.; LeDuc, H. G.; Weilert, M.; Day, P.

    2006-09-01

    We are developing a microwave readout multiplexer for arrays of superconducting quantum interference devices (SQUIDs). A series of microwave resonators with frequencies ˜10 GHz are each loaded by a dc SQUID to a degree that depends on the flux state of the SQUID. By using resonators with high quality factors and slightly different resonance frequencies, many of these resonator-coupled SQUIDs may be read out with a single excitation line and cryogenic amplifier. Our multiplexer is similar to the one demonstrated by Irwin and Lehnert except for the use of higher-frequency, fully-lithographed transmission line resonators. We discuss a technique for modulating the SQUID array in series that alleviates the need to individually flux-bias the SQUIDs. The multiplexer has applications to the readout of detector arrays for astronomy as well as medical magnetic imaging.

  2. 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.

  3. Metric projection for dynamic multiplex networks.

    PubMed

    Jurman, Giuseppe

    2016-08-01

    Evolving multiplex networks are a powerful model for representing the dynamics along time of different phenomena, such as social networks, power grids, biological pathways. However, exploring the structure of the multiplex network time series is still an open problem. Here we propose a two-step strategy to tackle this problem based on the concept of distance (metric) between networks. Given a multiplex graph, first a network of networks is built for each time step, and then a real valued time series is obtained by the sequence of (simple) networks by evaluating the distance from the first element of the series. The effectiveness of this approach in detecting the occurring changes along the original time series is shown on a synthetic example first, and then on the Gulf dataset of political events. PMID:27626089

  4. Positional Cloning by Linkage Disequilibrium

    PubMed Central

    Maniatis, Nikolas; Collins, Andrew; Gibson, Jane; Zhang, Weihua; Tapper, William; Morton, Newton E.

    2004-01-01

    Recently, metric linkage disequilibrium (LD) maps that assign an LD unit (LDU) location for each marker have been developed (Maniatis et al. 2002). Here we present a multiple pairwise method for positional cloning by LD within a composite likelihood framework and investigate the operating characteristics of maps in physical units (kb) and LDU for two bodies of data (Daly et al. 2001; Jeffreys et al. 2001) on which current ideas of blocks are based. False-negative indications of a disease locus (type II error) were examined by selecting one single-nucleotide polymorphism (SNP) at a time as causal and taking its allelic count (0, 1, or 2, for the three genotypes) as a pseudophenotype, Y. By use of regression and correlation, association between every pseudophenotype and the allelic count of each SNP locus (X) was based on an adaptation of the Malecot model, which includes a parameter for location of the putative gene. By expressing locations in kb or LDU, greater power for localization was observed when the LDU map was fitted. The efficiency of the kb map, relative to the LDU map, to describe LD varied from a maximum of 0.87 to a minimum of 0.36, with a mean of 0.62. False-positive indications of a disease locus (type I error) were examined by simulating an unlinked causal SNP and the allele count was used as a pseudophenotype. The type I error was in good agreement with Wald’s likelihood theorem for both metrics and all models that were tested. Unlike tests that select only the most significant marker, haplotype, or haploset, these methods are robust to large numbers of markers in a candidate region. Contrary to predictions from tagging SNPs that retain haplotype diversity, the sample with smaller size but greater SNP density gave less error. The locations of causal SNPs were estimated with the same precision in blocks and steps, suggesting that block definition may be less useful than anticipated for mapping a causal SNP. These results provide a guide to

  5. Mass cytometry: a highly multiplexed single-cell technology for advancing drug development.

    PubMed

    Atkuri, Kondala R; Stevens, Jeffrey C; Neubert, Hendrik

    2015-02-01

    Advanced single-cell analysis technologies (e.g., mass cytometry) that help in multiplexing cellular measurements in limited-volume primary samples are critical in bridging discovery efforts to successful drug approval. Mass cytometry is the state-of-the-art technology in multiparametric single-cell analysis. Mass cytometers (also known as cytometry by time-of-flight or CyTOF) combine the cellular analysis principles of traditional fluorescence-based flow cytometry with the selectivity and quantitative power of inductively coupled plasma-mass spectrometry. Standard flow cytometry is limited in the number of parameters that can be measured owing to the overlap in signal when detecting fluorescently labeled antibodies. Mass cytometry uses antibodies tagged to stable isotopes of rare earth metals, which requires minimal signal compensation between the different metal tags. This unique feature enables researchers to seamlessly multiplex up to 40 independent measurements on single cells. In this overview we first present an overview of mass cytometry and compare it with traditional flow cytometry. We then discuss the emerging and potential applications of CyTOF technology in the pharmaceutical industry, including quantitative and qualitative deep profiling of immune cells and their applications in assessing drug immunogenicity, extensive mapping of signaling networks in single cells, cell surface receptor quantification and multiplexed internalization kinetics, multiplexing sample analysis by barcoding, and establishing cell ontologies on the basis of phenotype and/or function. We end with a discussion of the anticipated impact of this technology on drug development lifecycle with special emphasis on the utility of mass cytometry in deciphering a drug's pharmacokinetics and pharmacodynamics relationship. PMID:25349123

  6. Automated Methods for Multiplexed Pathogen Detection

    SciTech Connect

    Straub, Tim M.; Dockendorff, Brian P.; Quinonez-Diaz, Maria D.; Valdez, Catherine O.; Shutthanandan, Janani I.; Tarasevich, Barbara J.; Grate, Jay W.; Bruckner-Lea, Cindy 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

  7. Eigenvector centrality of nodes in multiplex networks.

    PubMed

    Solá, Luis; Romance, Miguel; Criado, Regino; Flores, Julio; García del Amo, Alejandro; Boccaletti, Stefano

    2013-09-01

    We extend the concept of eigenvector centrality to multiplex networks, and introduce several alternative parameters that quantify the importance of nodes in a multi-layered networked system, including the definition of vectorial-type centralities. In addition, we rigorously show that, under reasonable conditions, such centrality measures exist and are unique. Computer experiments and simulations demonstrate that the proposed measures provide substantially different results when applied to the same multiplex structure, and highlight the non-trivial relationships between the different measures of centrality introduced. PMID:24089967

  8. Line graphs for a multiplex network.

    PubMed

    Criado, Regino; Flores, Julio; García Del Amo, Alejandro; Romance, Miguel; Barrena, Eva; Mesa, Juan A

    2016-06-01

    It is well known that line graphs offer a good summary of the graphs properties, which make them easier to analyze and highlight the desired properties. We extend the concept of line graph to multiplex networks in order to analyze multi-plexed and multi-layered networked systems. As these structures are very rich, different approaches to this notion are required to capture a variety of situations. Some relationships between these approaches are established. Finally, by means of some simulations, the potential utility of this concept is illustrated. PMID:27368798

  9. Cooperative spreading processes in multiplex networks

    NASA Astrophysics Data System (ADS)

    Wei, Xiang; Chen, Shihua; Wu, Xiaoqun; Ning, Di; Lu, Jun-an

    2016-06-01

    This study is concerned with the dynamic behaviors of epidemic spreading in multiplex networks. A model composed of two interacting complex networks is proposed to describe cooperative spreading processes, wherein the virus spreading in one layer can penetrate into the other to promote the spreading process. The global epidemic threshold of the model is smaller than the epidemic thresholds of the corresponding isolated networks. Thus, global epidemic onset arises in the interacting networks even though an epidemic onset does not arise in each isolated network. Simulations verify the analysis results and indicate that cooperative spreading processes in multiplex networks enhance the final infection fraction.

  10. Multiplexed imaging of intracellular protein networks.

    PubMed

    Grecco, Hernán E; Imtiaz, Sarah; Zamir, Eli

    2016-08-01

    Cellular functions emerge from the collective action of a large number of different proteins. Understanding how these protein networks operate requires monitoring their components in intact cells. Due to intercellular and intracellular molecular variability, it is important to monitor simultaneously multiple components at high spatiotemporal resolution. However, inherent trade-offs narrow the boundaries of achievable multiplexed imaging. Pushing these boundaries is essential for a better understanding of cellular processes. Here the motivations, challenges and approaches for multiplexed imaging of intracellular protein networks are discussed. © 2016 International Society for Advancement of Cytometry. PMID:27183498

  11. Nanowire sensors for multiplexed detection of biomolecules

    PubMed Central

    He, Bo; Morrow, Thomas J; Keating, Christine D

    2009-01-01

    Nanowire-based detection strategies provide promising new routes to bioanalysis that could one day revolutionize the healthcare industry. This review covers recent developments in nanowire sensors for multiplexed detection of biomolecules such as nucleic acids and proteins. We focus on encoded nanowire suspension arrays and semiconductor nanowire-based field-effect transistors. Nanowire assembly and integration with microchip technology is emphasized as a key step toward the ultimate goal of multiplexed detection at the point of care using portable, low power, electronic biosensor chips. PMID:18804551

  12. 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.

  13. Line graphs for a multiplex network

    NASA Astrophysics Data System (ADS)

    Criado, Regino; Flores, Julio; García del Amo, Alejandro; Romance, Miguel; Barrena, Eva; Mesa, Juan A.

    2016-06-01

    It is well known that line graphs offer a good summary of the graphs properties, which make them easier to analyze and highlight the desired properties. We extend the concept of line graph to multiplex networks in order to analyze multi-plexed and multi-layered networked systems. As these structures are very rich, different approaches to this notion are required to capture a variety of situations. Some relationships between these approaches are established. Finally, by means of some simulations, the potential utility of this concept is illustrated.

  14. Polarization-multiplexed encoding at nanometer scales.

    PubMed

    Macias-Romero, C; Munro, P R T; Török, P

    2014-10-20

    Optical data storage was developed using binary encoding primarily due to signal to noise ratio considerations. We report on a multiplexing method that allows a seven fold storage increase, per storage layer, per side, and propose one that can yield theoretically a 20+ fold increase. Multiplexing is achieved by encoding information in polarization via appropriately oriented nanostructures that emit strongly polarized light when excited by unpolarized light. The storage increase is possible due to the significantly reduced crosstalk that results form using unpolarized light. PMID:25401656

  15. A Genomewide Screen for Autism: Strong Evidence for Linkage to Chromosomes 2q, 7q, and 16p

    PubMed Central

    2001-01-01

    Autism is characterized by impairments in reciprocal communication and social interaction and by repetitive and stereotyped patterns of activities and interests. Evidence for a strong underlying genetic predisposition comes from twin and family studies, although susceptibility genes have not yet been identified. A whole-genome screen for linkage, using 83 sib pairs with autism, has been completed, and 119 markers have been genotyped in 13 candidate regions in a further 69 sib pairs. The addition of new families and markers provides further support for previous reports of linkages on chromosomes 7q and 16p. Two new regions of linkage have also been identified on chromosomes 2q and 17q. The most significant finding was a multipoint maximum LOD score (MLS) of 3.74 at marker D2S2188 on chromosome 2; this MLS increased to 4.80 when only sib pairs fulfilling strict diagnostic criteria were included. The susceptibility region on chromosome 7 was the next most significant, generating a multipoint MLS of 3.20 at marker D7S477. Chromosome 16 generated a multipoint MLS of 2.93 at D16S3102, whereas chromosome 17 generated a multipoint MLS of 2.34 at HTTINT2. With the addition of new families, there was no increased allele sharing at a number of other loci originally showing some evidence of linkage. These results support the continuing collection of multiplex sib-pair families to identify autism-susceptibility genes. PMID:11481586

  16. Microsatellite marker based genetic linkage maps of Oreochromis aureus and O. niloticus (Cichlidae): extensive linkage group segment homologies revealed.

    PubMed

    McConnell, S K; Beynon, C; Leamon, J; Skibinski, D O

    2000-06-01

    Partial genetic linkage maps, based on microsatellite markers, were constructed for two tilapia species, Oreochromis aureus and Oreochromis niloticus using an interspecific backcross population. The linkage map for O. aureus comprised 28 markers on 10 linkage groups and covered 212.8 CM. Nine markers were mapped to four linkage groups on an O. niloticus female linkage map covering 40.6 CM. Results revealed a high degree of conservation of synteny between the linkage groups defined in O. aureus and the previously published genetic linkage map of O. niloticus. PMID:10895314

  17. AUTOGSCAN: powerful tools for automated genome-wide linkage and linkage disequilibrium analysis.

    PubMed

    Hiekkalinna, Tero; Terwilliger, Joseph D; Sammalisto, Sampo; Peltonen, Leena; Perola, Markus

    2005-02-01

    Genome-wide linkage analysis using multiple traits and statistical software packages is a tedious process which requires a significant amount of manual file manipulation. Different linkage analysis programs require different input file formats, making the task of analyzing data with multiple methods even more time-consuming. We have developed a software tool, AUTOGSCAN, that automates file formatting, the running of statistical analyses, and the summarizing of resulting statistics for whole genome scans with a push of a button, using several independent, and often idiosyncratic, statistical software packages such as MERLIN, SOLAR and GENEHUNTER. We also describe a program, ANALYZE, designed to run qualitative linkage analysis with several different statistical strategies and programs to efficiently screen for linkage and linkage disequilibrium for a given discrete trait. The ANALYZE program can also be used by AUTOGSCAN in a genome-wide sense. PMID:15836805

  18. Antibody-protein A conjugated quantum dots for multiplexed imaging of surface receptors in living cells.

    PubMed

    Jin, Takashi; Tiwari, Dhermendra K; Tanaka, Shin-Ichi; Inouye, Yasushi; Yoshizawa, Keiko; Watanabe, Tomonobu M

    2010-11-01

    To use quantum dots (QDs) as fluorescent probes for receptor imaging, QD surface should be modified with biomolecules such as antibodies, peptides, carbohydrates, and small-molecule ligands for receptors. Among these QDs, antibody conjugated QDs are the most promising fluorescent probes. There are many kinds of coupling reactions that can be used for preparing antibody conjugated QDs. Most of the antibody coupling reactions, however, are non-selective and time-consuming. In this paper, we report a facile method for preparing antibody conjugated QDs for surface receptor imaging. We used ProteinA as an adaptor protein for binding of antibody to QDs. By using ProteinA conjugated QDs, various types of antibodies are easily attached to the surface of the QDs via non-covalent binding between the F(c) (fragment crystallization) region of antibody and ProteinA. To show the utility of ProteinA conjugated QDs, HER2 (anti-human epidermal growth factor receptor 2) in KPL-4 human breast cancer cells were stained by using anti-HER2 antibody conjugated ProteinA-QDs. In addition, multiplexed imaging of HER2 and CXCR4 (chemokine receptor) in the KPL-4 cells was performed. The result showed that CXCR4 receptors coexist with HER2 receptors in the membrane surface of KPL-4 cells. ProteinA mediated antibody conjugation to QDs is very useful to prepare fluorescent probes for multiplexed imaging of surface receptors in living cells. PMID:20835432

  19. A Bead-Based Method for Multiplexed Identification and Quantitation of DNA Sequences Using Flow Cytometry

    PubMed Central

    Spiro, Alexander; Lowe, Mary; Brown, Drew

    2000-01-01

    A new multiplexed, bead-based method which utilizes nucleic acid hybridizations on the surface of microscopic polystyrene spheres to identify specific sequences in heterogeneous mixtures of DNA sequences is described. The method consists of three elements: beads (5.6-μm diameter) with oligomer capture probes attached to the surface, three fluorophores for multiplexed detection, and flow cytometry instrumentation. Two fluorophores are impregnated within each bead in varying amounts to create different bead types, each associated with a unique probe. The third fluorophore is a reporter. Following capture of fluorescent cDNA sequences from environmental samples, the beads are analyzed by flow cytometric techniques which yield a signal intensity for each capture probe proportional to the amount of target sequences in the analyte. In this study, a direct hybrid capture assay was developed and evaluated with regard to sequence discrimination and quantitation of abundances. The target sequences (628 to 728 bp in length) were obtained from the 16S/23S intergenic spacer region of microorganisms collected from polluted groundwater at the nuclear waste site in Hanford, Wash. A fluorescence standard consisting of beads with a known number of fluorescent DNA molecules on the surface was developed, and the resolution, sensitivity, and lower detection limit for measuring abundances were determined. The results were compared with those of a DNA microarray using the same sequences. The bead method exhibited far superior sequence discrimination and possesses features which facilitate accurate quantitation. PMID:11010868

  20. 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. PMID:26971274

  1. Surface-Enhanced Raman Scattering Based Nonfluorescent Probe for Multiplex DNA Detection

    PubMed Central

    Sun, Lan; Yu, Chenxu; Irudayaraj, Joseph

    2008-01-01

    To provide rapid and accurate detection of DNA markers in a straightforward, inexpensive and multiplex format, an alternative surface enhanced Raman scattering (SERS) based probe was designed and fabricated to covalently attach both DNA probing sequence and non-fluorescent Raman tags to the surface of gold nanoparticles (DNA-AuP-RTag). The intensity of Raman signal of the probes could be controlled through the surface coverage of the non-fluorescent Raman tags (RTags). Detection sensitivity of these probes could be optimized by fine-tuning the amount of DNA molecules and RTags on the probes. Long-term stability of the DNA-AuP-RTag probes was found to be good (over 3 months). Excellent multiplexing capability of the DNA-AuP-RTag scheme was demonstrated by simultaneous identification of up to eight probes in a mixture. Detection of hybridization of single-stranded DNA (ssDNA) to its complementary targets was successfully accomplished with a long-term goal to use non-fluorescent RTags in a Raman-based DNA microarray platform. PMID:17465531

  2. Rapid point-of-care multiplex immunodetection using two-dimensional microarray technology

    NASA Astrophysics Data System (ADS)

    Chuang, Frank Y. S.; Gutierrez, Dora M.; Nguyen, Christine P.; Johnson, David C.; Palmer, Richard A.; Richards, James B.; Chang, John T.; Visuri, Steven R.; Colston, Bill W., Jr.

    2003-07-01

    In response to a broad-based need for point-of-care multiplex diagnostic capability, we have developed a novel hybrid platform to analyze optically encoded microspheres arranged on a 2-dimensional planar array. The microspheres which we have initially selected are developed by Luminex Inc. as substrates for sandwich-type fluorescent immunoassays and are typically used in conjunction with a customized flow analyzer. CCD-based optics are the essential feature which enables the development of a rugged diagnostic instrument which can be scaled for point-of-care applications. We have characterized the Multiplex Immunoassay Diagnostic System (MIDS) using a benchtop prototype built around a conventional 12-bit CCD. This system is capable of resolving up to 6 discrete classes of fluorescent microbeads, and measuring their corresponding reporter signal. The MIDS sensitivity to the phycoerythrin (PE) reporter compared favorably to that of the reference Luminex flow system, and is capable of identifying viral, bacterial, and protein simulants in laboratory samples, at concentrations less than 1μg/ml. The ability to resolve small differences in the average PE fluorescence is a direct function of CCD performance, and may be a necessary trade-off for developing a portable and economical detection system. However, we are confident that the MIDS platform can easily be scaled to meet the nominal requirements of any given point-of-care or screening application, and furthermore provide much-needed diagnostic functionality in this particular environment.

  3. Fluorescent refrigeration

    DOEpatents

    Epstein, R.I.; Edwards, B.C.; Buchwald, M.I.; Gosnell, T.R.

    1995-09-05

    Fluorescent refrigeration is based on selective radiative pumping, using substantially monochromatic radiation, of quantum excitations which are then endothermically redistributed to higher energies. Ultimately, the populated energy levels radiatively deexcite emitting, on the average, more radiant energy than was initially absorbed. The material utilized to accomplish the cooling must have dimensions such that the exciting radiation is strongly absorbed, but the fluorescence may exit the material through a significantly smaller optical pathlength. Optical fibers and mirrored glasses and crystals provide this requirement. 6 figs.

  4. Fluorescence Microscopy

    PubMed Central

    Sanderson, Michael J.; Smith, Ian; Parker, Ian; Bootman, Martin D.

    2016-01-01

    Fluorescence microscopy is a major tool with which to monitor cell physiology. Although the concepts of fluorescence and its optical separation using filters remain similar, microscope design varies with the aim of increasing image contrast and spatial resolution. The basics of wide-field microscopy are outlined to emphasize the selection, advantages, and correct use of laser scanning confocal microscopy, two-photon microscopy, scanning disk confocal microscopy, total internal reflection, and super-resolution microscopy. In addition, the principles of how these microscopes form images are reviewed to appreciate their capabilities, limitations, and constraints for operation. PMID:25275114

  5. Exclusion of close linkage between the synaptic vesicular monoamine transporter locus and schizophrenia spectrum disorders

    SciTech Connect

    Persico, A.M.; Uhl, G.R.; Wang, Zhe Wu

    1995-12-18

    The principal brain synaptic vesicular monoamine transporter (VMAT2) is responsible for the reuptake of serotonin, dopamine, norepinephrine, epinephrine, and histamine from the cytoplasm into synaptic vesicles, thus contributing to determination of the size of releasable neurotransmitter vesicular pools. Potential involvement of VMAT2 gene variants in the etiology of schizophrenia and related disorders was tested using polymorphic VMAT2 gene markers in 156 subjects from 16 multiplex pedigrees with schizophrenia, schizophreniform, schizoaffective, and schizotypal disorders and mood incongruent psychotic depression. Assuming genetic homogeneity, complete ({theta} = 0.0) linkage to the schizophrenia spectrum was excluded under both dominant and recessive models. Allelic variants at the VMAT2 locus do not appear to provide major genetic contributions to the etiology of schizophrenia spectrum disorders in these pedigrees. 16 refs.

  6. Microwave multiplex readout for superconducting sensors

    NASA Astrophysics Data System (ADS)

    Ferri, E.; Becker, D.; Bennett, D.; Faverzani, M.; Fowler, J.; Gard, J.; Giachero, A.; Hays-Wehle, J.; Hilton, G.; Maino, M.; Mates, J.; Puiu, A.; Nucciotti, A.; Reintsema, C.; Schmidt, D.; Swetz, D.; Ullom, J.; Vale, L.

    2016-07-01

    The absolute neutrino mass scale is still an outstanding challenge in both particle physics and cosmology. The calorimetric measurement of the energy released in a nuclear beta decay is a powerful tool to determine the effective electron-neutrino mass. In the last years, the progress on low temperature detector technologies has allowed to design large scale experiments aiming at pushing down the sensitivity on the neutrino mass below 1 eV. Even with outstanding performances in both energy (~ eV on keV) and time resolution (~ 1 μs) on the single channel, a large number of detectors working in parallel is required to reach a sub-eV sensitivity. Microwave frequency domain readout is the best available technique to readout large array of low temperature detectors, such as Transition Edge Sensors (TESs) or Microwave Kinetic Inductance Detectors (MKIDs). In this way a multiplex factor of the order of thousands can be reached, limited only by the bandwidth of the available commercial fast digitizers. This microwave multiplexing system will be used to readout the HOLMES detectors, an array of 1000 microcalorimeters based on TES sensors in which the 163Ho will be implanted. HOLMES is a new experiment for measuring the electron neutrino mass by means of the electron capture (EC) decay of 163Ho. We present here the microwave frequency multiplex which will be used in the HOLMES experiment and the microwave frequency multiplex used to readout the MKID detectors developed in Milan as well.

  7. Highly multiplexed DNA sequencing by capillary electrophoresis

    SciTech Connect

    Yeung, E.S.; Ueno, K.; Chang, H.T.

    1994-12-31

    It is obvious that irrespective of whichever basic technology is eventually selected to sequence the entire human genome there are substantial gains to be made if a high degree of multiplexing of parallel runs can be implemented. Such multiplexing should not involve expensive instrumentation and should not require additional personnel, or else the main objective of cost reduction will not be satisfied even though the total time for sequencing is reduced. In the last two years, several research groups have shown that capillary electrophoresis (CE) is an attractive alternative for DNA sequencing. Part of the improvement in sequencing speed in CE is counteracted by the inherent ability of slab gels for accommodating multiple lanes in a single run. Recently, the authors have developed several excitation schemes for highly multiplexed capillary electrophoresis. Detection at the pM level was demonstrated. The authors report here the use of a novel excitation geometry to simultaneously monitor 100 capillary tubes during electrophoresis. This represents a truly parallel multiplexing scheme for high-speed DNA sequencing.

  8. Moving through a multiplex holographic scene

    NASA Astrophysics Data System (ADS)

    Mrongovius, Martina

    2013-02-01

    This paper explores how movement can be used as a compositional element in installations of multiplex holograms. My holographic images are created from montages of hand-held video and photo-sequences. These spatially dynamic compositions are visually complex but anchored to landmarks and hints of the capturing process - such as the appearance of the photographer's shadow - to establish a sense of connection to the holographic scene. Moving around in front of the hologram, the viewer animates the holographic scene. A perception of motion then results from the viewer's bodily awareness of physical motion and the visual reading of dynamics within the scene or movement of perspective through a virtual suggestion of space. By linking and transforming the physical motion of the viewer with the visual animation, the viewer's bodily awareness - including proprioception, balance and orientation - play into the holographic composition. How multiplex holography can be a tool for exploring coupled, cross-referenced and transformed perceptions of movement is demonstrated with a number of holographic image installations. Through this process I expanded my creative composition practice to consider how dynamic and spatial scenes can be conveyed through the fragmented view of a multiplex hologram. This body of work was developed through an installation art practice and was the basis of my recently completed doctoral thesis: 'The Emergent Holographic Scene — compositions of movement and affect using multiplex holographic images'.

  9. Immunity of multiplex networks via acquaintance vaccination

    NASA Astrophysics Data System (ADS)

    Wang, Zhen; Zhao, Da-Wei; Wang, Lin; Sun, Gui-Quan; Jin, Zhen

    2015-11-01

    How to find the effective approach of immunizing a population is one open question in the research of complex systems. Up to now, there have been a great number of works focusing on the efficiency of various immunization strategies. However, the majority of these existing achievements are limited to isolated networks, how immunization affects disease spreading in multiplex networks seems to need further exploration. In this letter, we explore the impact of the acquaintance immunization in multiplex networks, where two kinds of immunization strategies, multiplex node-based acquaintance immunization and layer node-based acquaintance immunization, are proposed. With the generating function method, our theoretical framework is able to accurately calculate the critical immunization threshold which is one of the most important indexes to predict the epidemic regime. Moreover, we further uncover that, with the increment of degree correlation between network layers, the immunization threshold declines for multiplex node-based acquaintance immunization, but slowly increases for layer node-based acquaintance immunization.

  10. Multiplexing schemes for quantum repeater networks

    NASA Astrophysics Data System (ADS)

    Aparicio, Luciano; Van Meter, Rodney

    2011-08-01

    When built, quantum repeaters will allow the distribution of entangled quantum states across large distances, playing a vital part in many proposed quantum technologies. Enabling multiple users to connect through the same network will be key to their real-world deployment. Previous work on repeater technologies has focussed only on simple entanglment production, without considering the issues of resource scarcity and competition that necessarily arise in a network setting. In this paper we simulated a thirteen-node network with up to five flows sharing different parts of the network, measuring the total throughput and fairness for each case. Our results suggest that the Internet-like approach of statistical multiplexing use of a congested link gives the highest aggregate throughput. Time division multiplexing and buffer space multiplexing were slightly less effective, but all three schemes allow the sum of multiple flows to substantially exceed that of any one flow, improving over circuit switching by taking advantage of resources that are forced to remain idle in circuit switching. All three schemes proved to have excellent fairness. The high performance, fairness and simplicity of implementation support a recommendation of statistical multiplexing for shared quantum repeater networks.

  11. Fiber optics wavelength division multiplexing(components)

    NASA Technical Reports Server (NTRS)

    Hendricks, Herbert D.

    1985-01-01

    The long term objectives are to develop optical multiplexers/demultiplexers, different wavelength and modulation stable semiconductor lasers and high data rate transceivers, as well as to test and evaluate fiber optic networks applicable to the Space Station. Progress in each of the above areas is briefly discussed.

  12. Private Medical Record Linkage with Approximate Matching

    PubMed Central

    Durham, Elizabeth; Xue, Yuan; Kantarcioglu, Murat; Malin, Bradley

    2010-01-01

    Federal regulations require patient data to be shared for reuse in a de-identified manner. However, disparate providers often share data on overlapping populations, such that a patient’s record may be duplicated or fragmented in the de-identified repository. To perform unbiased statistical analysis in a de-identified setting, it is crucial to integrate records that correspond to the same patient. Private record linkage techniques have been developed, but most methods are based on encryption and preclude the ability to determine similarity, decreasing the accuracy of record linkage. The goal of this research is to integrate a private string comparison method that uses Bloom filters to provide an approximate match, with a medical record linkage algorithm. We evaluate the approach with 100,000 patients’ identifiers and demographics from the Vanderbilt University Medical Center. We demonstrate that the private approximation method achieves sensitivity that is, on average, 3% higher than previous methods. PMID:21346965

  13. A Genetic Linkage Map for Cattle

    PubMed Central

    Bishop, M. D.; Kappes, S. M.; Keele, J. W.; Stone, R. T.; Sunden, SLF.; Hawkins, G. A.; Toldo, S. S.; Fries, R.; Grosz, M. D.; Yoo, J.; Beattie, C. W.

    1994-01-01

    We report the most extensive physically anchored linkage map for cattle produced to date. Three-hundred thirteen genetic markers ordered in 30 linkage groups, anchored to 24 autosomal chromosomes (n = 29), the X and Y chromosomes, four unanchored syntenic groups and two unassigned linkage groups spanning 2464 cM of the bovine genome are summarized. The map also assigns 19 type I loci to specific chromosomes and/or syntenic groups and four cosmid clones containing informative microsatellites to chromosomes 13, 25 and 29 anchoring syntenic groups U11, U7 and U8, respectively. This map provides the skeletal framework prerequisite to development of a comprehensive genetic map for cattle and analysis of economic trait loci (ETL). PMID:7908653

  14. Intragroup Emotions: Physiological Linkage and Social Presence.

    PubMed

    Järvelä, Simo; Kätsyri, Jari; Ravaja, Niklas; Chanel, Guillaume; Henttonen, Pentti

    2016-01-01

    We investigated how technologically mediating two different components of emotion-communicative expression and physiological state-to group members affects physiological linkage and self-reported feelings in a small group during video viewing. In different conditions the availability of second screen text chat (communicative expression) and visualization of group level physiological heart rates and their dyadic linkage (physiology) was varied. Within this four person group two participants formed a physically co-located dyad and the other two were individually situated in two separate rooms. We found that text chat always increased heart rate synchrony but HR visualization only with non-co-located dyads. We also found that physiological linkage was strongly connected to self-reported social presence. The results encourage further exploration of the possibilities of sharing group member's physiological components of emotion by technological means to enhance mediated communication and strengthen social presence. PMID:26903913

  15. Intragroup Emotions: Physiological Linkage and Social Presence

    PubMed Central

    Järvelä, Simo; Kätsyri, Jari; Ravaja, Niklas; Chanel, Guillaume; Henttonen, Pentti

    2016-01-01

    We investigated how technologically mediating two different components of emotion—communicative expression and physiological state—to group members affects physiological linkage and self-reported feelings in a small group during video viewing. In different conditions the availability of second screen text chat (communicative expression) and visualization of group level physiological heart rates and their dyadic linkage (physiology) was varied. Within this four person group two participants formed a physically co-located dyad and the other two were individually situated in two separate rooms. We found that text chat always increased heart rate synchrony but HR visualization only with non-co-located dyads. We also found that physiological linkage was strongly connected to self-reported social presence. The results encourage further exploration of the possibilities of sharing group member's physiological components of emotion by technological means to enhance mediated communication and strengthen social presence. PMID:26903913

  16. Analysis of data obtained from a frequency-multiplexed phase-modulation fluorometer using an autoregressive model.

    PubMed

    Iwata, Tetsuo; Muneshige, Akitaka; Araki, Tsutomu

    2007-09-01

    In order to derive plural values of fluorescence lifetimes simultaneously from a multi-component sample, we formulate a mathematical method for analyzing data obtained from a frequency-multiplexed phase-modulation fluorometer (FM-PMF) using an autoregressive (AR) model. Various parameter settings necessary for performing accurate data analysis based on the AR model are studied through numerical simulations. Measurement results of fluorescence lifetimes of real samples, 10 ppm quinine sulfate in 0.1 N H(2)SO(4), 10 ppm rhodamine 6G in ethanol, and their mixture with a volume ratio of 1:1, demonstrate that the proposed method works quite well. PMID:17910791

  17. Anosov Geodesic Flows, Billiards and Linkages

    NASA Astrophysics Data System (ADS)

    Kourganoff, Mickaël

    2016-06-01

    Any smooth surface in {{mathbb R}3} may be flattened along the z-axis, and the flattened surface becomes close to a billiard table in {{mathbb R}2}. We show that, under some hypotheses, the geodesic flow of this surface converges locally uniformly to the billiard flow. Moreover, if the billiard is dispersive and has finite horizon, then the geodesic flow of the corresponding surface is Anosov. We apply this result to the theory of mechanical linkages and their dynamics: we provide a new example of a simple linkage whose physical behavior is Anosov. For the first time, the edge lengths of the mechanism are given explicitly.

  18. Some methods for blindfolded record linkage

    PubMed Central

    Churches, Tim; Christen, Peter

    2004-01-01

    Background The linkage of records which refer to the same entity in separate data collections is a common requirement in public health and biomedical research. Traditionally, record linkage techniques have required that all the identifying data in which links are sought be revealed to at least one party, often a third party. This necessarily invades personal privacy and requires complete trust in the intentions of that party and their ability to maintain security and confidentiality. Dusserre, Quantin, Bouzelat and colleagues have demonstrated that it is possible to use secure one-way hash transformations to carry out follow-up epidemiological studies without any party having to reveal identifying information about any of the subjects – a technique which we refer to as "blindfolded record linkage". A limitation of their method is that only exact comparisons of values are possible, although phonetic encoding of names and other strings can be used to allow for some types of typographical variation and data errors. Methods A method is described which permits the calculation of a general similarity measure, the n-gram score, without having to reveal the data being compared, albeit at some cost in computation and data communication. This method can be combined with public key cryptography and automatic estimation of linkage model parameters to create an overall system for blindfolded record linkage. Results The system described offers good protection against misdeeds or security failures by any one party, but remains vulnerable to collusion between or simultaneous compromise of two or more parties involved in the linkage operation. In order to reduce the likelihood of this, the use of last-minute allocation of tasks to substitutable servers is proposed. Proof-of-concept computer programmes written in the Python programming language are provided to illustrate the similarity comparison protocol. Conclusion Although the protocols described in this paper are not

  19. Metal Stable Isotope Tagging: Renaissance of Radioimmunoassay for Multiplex and Absolute Quantification of Biomolecules.

    PubMed

    Liu, Rui; Zhang, Shixi; Wei, Chao; Xing, Zhi; Zhang, Sichun; Zhang, Xinrong

    2016-05-17

    The unambiguous quantification of biomolecules is of great significance in fundamental biological research as well as practical clinical diagnosis. Due to the lack of a detectable moiety, the direct and highly sensitive quantification of biomolecules is often a "mission impossible". Consequently, tagging strategies to introduce detectable moieties for labeling target biomolecules were invented, which had a long and significant impact on studies of biomolecules in the past decades. For instance, immunoassays have been developed with radioisotope tagging by Yalow and Berson in the late 1950s. The later languishment of this technology can be almost exclusively ascribed to the use of radioactive isotopes, which led to the development of nonradioactive tagging strategy-based assays such as enzyme-linked immunosorbent assay, fluorescent immunoassay, and chemiluminescent and electrochemiluminescent immunoassay. Despite great success, these strategies suffered from drawbacks such as limited spectral window capacity for multiplex detection and inability to provide absolute quantification of biomolecules. After recalling the sequences of tagging strategies, an apparent question is why not use stable isotopes from the start? A reasonable explanation is the lack of reliable means for accurate and precise quantification of stable isotopes at that time. The situation has changed greatly at present, since several atomic mass spectrometric measures for metal stable isotopes have been developed. Among the newly developed techniques, inductively coupled plasma mass spectrometry is an ideal technique to determine metal stable isotope-tagged biomolecules, for its high sensitivity, wide dynamic linear range, and more importantly multiplex and absolute quantification ability. Since the first published report by our group, metal stable isotope tagging has become a revolutionary technique and gained great success in biomolecule quantification. An exciting research highlight in this area

  20. Antibody-Based Protein Multiplex Platforms: Technical and Operational Challenges

    PubMed Central

    Ellington, Allison A.; Kullo, Iftikhar J.; Bailey, Kent R.; Klee, George G.

    2010-01-01

    BACKGROUND The measurement of multiple protein biomarkers may refine risk stratification in clinical settings. This concept has stimulated development of multiplexed immunoassay platforms that provide multiple, parallel protein measurements on the same specimen. CONTENT We provide an overview of antibody-based multiplexed immunoassay platforms and discuss technical and operational challenges. Multiplexed immunoassays use traditional immunoassay principles in which high-affinity capture ligands are immobilized in parallel arrays in either planar format or on microspheres in suspension. Development of multiplexed immunoassays requires rigorous validation of assay configuration and analytical performance to minimize assay imprecision and inaccuracy. Challenges associated with multiplex configuration include selection and immobilization of capture ligands, calibration, interference between antibodies and proteins and assay diluents, and compatibility of assay limits of quantification. We discuss potential solutions to these challenges. Criteria for assessing analytical multiplex assay performance include the range of linearity, analytical specificity, recovery, and comparison to a quality reference method. Quality control materials are not well developed for multiplexed protein immunoassays, and algorithms for interpreting multiplex quality control data are needed. SUMMARY Technical and operational challenges have hindered implementation of multiplexed assays in clinical settings. Formal procedures that guide multiplex assay configuration, analytical validation, and quality control are needed before broad application of multiplexed arrays can occur in the in vitro diagnostic market. PMID:19959625

  1. TES Detector Noise Limited Readout Using SQUID Multiplexers

    NASA Technical Reports Server (NTRS)

    Staguhn, J. G.; Benford, D. J.; Chervenak, J. A.; Khan, S. A.; Moseley, S. H.; Shafer, R. A.; Deiker, S.; Grossman, E. N.; Hilton, G. C.; Irwin, K. D.

    2004-01-01

    The availability of superconducting Transition Edge Sensors (TES) with large numbers of individual detector pixels requires multiplexers for efficient readout. The use of multiplexers reduces the number of wires needed between the cryogenic electronics and the room temperature electronics and cuts the number of required cryogenic amplifiers. We are using an 8 channel SQUID multiplexer to read out one-dimensional TES arrays which are used for submillimeter astronomical observations. We present results from test measurements which show that the low noise level of the SQUID multiplexers allows accurate measurements of the TES Johnson noise, and that in operation, the readout noise is dominated by the detector noise. Multiplexers for large number of channels require a large bandwidth for the multiplexed readout signal. We discuss the resulting implications for the noise performance of these multiplexers which will be used for the readout of two dimensional TES arrays in next generation instruments.

  2. Capacity limits of spatially multiplexed free-space communication

    NASA Astrophysics Data System (ADS)

    Zhao, Ningbo; Li, Xiaoying; Li, Guifang; Kahn, Joseph M.

    2015-12-01

    Increasing the information capacity per unit bandwidth has been a perennial goal of scientists and engineers. Multiplexing of independent degrees of freedom, such as wavelength, polarization and more recently space, has been a preferred method to increase capacity in both radiofrequency and optical communication. Orbital angular momentum, a physical property of electromagnetic waves discovered recently, has been proposed as a new degree of freedom for multiplexing to achieve capacity beyond conventional multiplexing techniques, and has generated widespread and significant interest in the scientific community. However, the capacity of orbital angular momentum multiplexing has not been established or compared to other multiplexing techniques. Here, we show that orbital angular momentum multiplexing is not an optimal technique for realizing the capacity limits of a free-space communication channel and is outperformed by both conventional line-of-sight multi-input multi-output transmission and spatial-mode multiplexing.

  3. A Protocol for a High-Throughput Multiplex Cell Viability Assay.

    PubMed

    Gilbert, Daniel F; Boutros, Michael

    2016-01-01

    High-throughput cell viability assays are broadly used in RNAi and small molecule screening experiments to identify compounds that selectively kill cancer cells or as counter screens to exclude the compounds that have a generic effect on cell growth. While there are several assaying techniques available, cellular fitness is often assessed on the basis of one single and often rather indirect physiological indicator. This can lead to inconsistencies and poor correspondence between cell viability screening experiments, conducted under comparable conditions but with different viability indicators. Multiplexing, i.e., the combination of different individual assaying techniques in one experiment and subsequent comparative analysis of multiparametric data can decrease inter-assay variability and increase dataset concordance. Here, we describe a protocol for a multiplexing approach for high-throughput cell viability screening to address the issues encountered in the classical strategy using a single fitness indicator described above. The method combines a biochemical, luminescence-based approach and two fluorescence-based assay types. The biochemical method assesses cellular fitness by quantifying intracellular ATP concentration. Calcein labeling reflects cell fitness through membrane integrity and indirect measurement of ATP-dependent enzymatic esterase activity. Hoechst DNA stain correlates cell fitness with cellular DNA content. The presented multiplexing approach is suitable for low, medium and high-throughput screening and has the potential to decrease inter-assay variability and increase dataset concordance as well as reproducibility of experimental results. PMID:27581285

  4. Multiplexed molecular profiling of prostate cancer specimens using semiconductor quantum dot bioconjugates

    NASA Astrophysics Data System (ADS)

    Xing, Yun; Numora, Takeo; Chung, Leland; Zhau, Haiyen; Nie, Shuming

    2007-02-01

    Quantum dots (QDs) are light emitting semi-conductor nanocrystals with novel optical properties including superior photostability, narrow emission spectra with continuous excitation spectra. These properties make QDs especially suitable for multiplexed fluorescent labeling, live cell imaging, and in vivo animal imaging. The multiplexing potential has been recognized but real applications of biological/clinical significance are few. In this study, we used quantum dots to study epithelial mesenchymal transition (EMT), an important process involved in the bone metastasis of prostate cancer. Two prostate cancer cells lines with distinct molecular profiles, representing the two ends of the EMT process, were selected for this study. Four EMT-related biomarkers including E-cadherin, N-cadherin, Vimentin, and RANKL were stained with QD-antibody conjugates with elongation factor 1alpha as the internal control. Morphological information of the QD-stained cells was obtained by digital-color imaging and quantitative information obtained by spectra analysis using a spectrometer. Two types of analysis were performed: abundance of each biomarker in the same cell line relative to the internal control; and the relative abundance of these markers between the two cell lines. Our results demonstrate the feasibility of QDs for multiplexed profiling of FFPE cells/tissue of clinical significance; however, the standardization and quantification still awaits optimization.

  5. Linkage Drag: Implication for Plant Breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Linkage drag is commonly observed in plant breeding, yet the molecular mechanisms controlling this is unclear. The Pi-ta gene, a single copy gene near the centromere region of chromosome 12, confers resistance to races of Magnaporthe oryzae that contain AVR-Pita. The Pi-ta gene in Tetep has been su...

  6. Dialogic Linkage and Resonance in Autism

    ERIC Educational Resources Information Center

    Hobson, R. Peter; Hobson, Jessica A.; Garcia-Perez, Rosa; Du Bois, John

    2012-01-01

    We evaluated how children with autism make linguistic adjustments when talking with someone else. We devised two novel measures to assess (a) overall conversational linkage and (b) utterance-by-utterance resonance within dialogue between an adult and matched participants with and without autism (n = 12 per group). Participants with autism were…

  7. Permethylation Linkage Analysis Techniques for Residual Carbohydrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Permethylation analysis is the classic approach to establishing the position of glycosidic linkages between sugar residues. Typically, the carbohydrate is derivatized to form acid-stable methyl ethers, hydrolyzed, peracetylated, and analyzed by gas chromatography-mass spectrometry (GC-MS). The pos...

  8. Past CETA Linkages: Models for the Future.

    ERIC Educational Resources Information Center

    Lapin, Joel D.

    1982-01-01

    Examines lessons learned from successful linkages between community colleges and Comprehensive Employment and Training Act (CETA) sponsors as the basis for future occupational training and employment programs. Reviews research examining CETA funding patterns in California and exemplary arrangements between community colleges and CETA nationwide.…

  9. Regional Workshops on CETA/Educational Linkages.

    ERIC Educational Resources Information Center

    McGough, Robert; And Others

    This document presents a summary of the proceedings of five regional workshops in Virginia which focused on planning for future involvement and linkages, as well as giving an orientation to the capabilities and operational philosophies of both Comprehensive Employment and Training Act (CETA) programs and educational organizations. Following…

  10. Rotating sample holder without mechanical linkages.

    PubMed

    Azevedo, L J

    1979-02-01

    A sample rotator which operates in applied magnetic fields is described. The design eliminates mechanical linkages by magnetically orienting a gimbal ring. Three mutually orthogonal coils mounted on the gimbal provide a magnetic moment which is aligned along the field direction. The rotator is useful from room temperature down to the liquid helium range. Rotations about any desired axis are possible. PMID:18699475

  11. Job Linkages Review: Promise and Challenge.

    ERIC Educational Resources Information Center

    Welch, Nancy

    In 1996, the City of Phoenix Enterprise Community Job Linkages Initiative sought to increase employment by matching local people with local jobs. Evaluation of the second project at Friendly House found that Friendly House, during the 18 months of the grant, increased residents' employability skills and linked them with Enterprise Community…

  12. Whole genome linkage disequilibrium maps in cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and also provides bac...

  13. Linkage disequilibrium in Theobroma cacao L. populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although the potential of Linkage Disequilibrium (LD) mapping to associate markers to agronomic and horticultural traits has been already recognized in cacao, its real efficiency depends on the nature and structure of the LD in the genome of the populations under study. LD is dependent on several fa...

  14. ARE COASTAL WETLAND-LAKE LINKAGES IMPORTANT?

    EPA Science Inventory

    Because coastal werlands typically comprise only a small percentage of the overall surface area in large lakes, an assumption has often been made that functional links between wetlands and the lake proper are of little significance. Recent investigations of functional linkages be...

  15. Composite Bloom Filters for Secure Record Linkage

    PubMed Central

    Durham, Elizabeth Ashley; Kantarcioglu, Murat; Xue, Yuan; Toth, Csaba; Kuzu, Mehmet; Malin, Bradley

    2014-01-01

    The process of record linkage seeks to integrate instances that correspond to the same entity. Record linkage has traditionally been performed through the comparison of identifying field values (e.g., Surname), however, when databases are maintained by disparate organizations, the disclosure of such information can breach the privacy of the corresponding individuals. Various private record linkage (PRL) methods have been developed to obscure such identifiers, but they vary widely in their ability to balance competing goals of accuracy, efficiency and security. The tokenization and hashing of field values into Bloom filters (BF) enables greater linkage accuracy and efficiency than other PRL methods, but the encodings may be compromised through frequency-based cryptanalysis. Our objective is to adapt a BF encoding technique to mitigate such attacks with minimal sacrifices in accuracy and efficiency. To accomplish these goals, we introduce a statistically-informed method to generate BF encodings that integrate bits from multiple fields, the frequencies of which are provably associated with a minimum number of fields. Our method enables a user-specified tradeoff between security and accuracy. We compare our encoding method with other techniques using a public dataset of voter registration records and demonstrate that the increases in security come with only minor losses to accuracy. PMID:25530689

  16. Evaluation of a 13-loci STR multiplex system for Cannabis sativa genetic identification.

    PubMed

    Houston, Rachel; Birck, Matthew; Hughes-Stamm, Sheree; Gangitano, David

    2016-05-01

    Marijuana (Cannabis sativa) is the most commonly used illicit substance in the USA. The development of a validated method using Cannabis short tandem repeats (STRs) could aid in the individualization of samples as well as serve as an intelligence tool to link multiple cases. For this purpose, a modified 13-loci STR multiplex method was optimized and evaluated according to ISFG and SWGDAM guidelines. A real-time PCR quantification method for C. sativa was developed and validated, and a sequenced allelic ladder was also designed to accurately genotype 199 C. sativa samples from 11 U.S. Customs and Border Protection seizures. Distinguishable DNA profiles were generated from 127 samples that yielded full STR profiles. Four duplicate genotypes within seizures were found. The combined power of discrimination of this multilocus system is 1 in 70 million. The sensitivity of the multiplex STR system is 0.25 ng of template DNA. None of the 13 STR markers cross-reacted with any of the studied species, except for Humulus lupulus (hops) which generated unspecific peaks. Phylogenetic analysis and case-to-case pairwise comparison of 11 cases using F st as genetic distance revealed the genetic association of four groups of cases. Moreover, due to their genetic similarity, a subset of samples (N = 97) was found to form a homogeneous population in Hardy-Weinberg and linkage equilibrium. The results of this research demonstrate the applicability of this 13-loci STR system in associating Cannabis cases for intelligence purposes. PMID:26661945

  17. Multiplexed, Proteome-Wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains

    PubMed Central

    Isasa, Marta; Rose, Christopher M.; Elsasser, Suzanne; Navarrete-Perea, José; Paulo, Joao A.; Finley, Daniel J.; Gygi, Steven P.

    2016-01-01

    Characterizing a protein’s function often requires a description of the cellular state in its absence. Multiplexing in mass spectrometry-based proteomics has now achieved the ability to globally measure protein expression levels in yeast from 10 cell states simultaneously. We applied this approach to quantify expression differences in wild type and nine deubiquitylating enzyme (DUB) knockout strains with the goal of creating “information networks” that might provide deeper, mechanistic insights into a protein’s biological role. In total, more than 3700 proteins were quantified with high reproducibility across three biological replicates (30 samples in all). DUB mutants demonstrated different proteomics profiles, consistent with distinct roles for each family member. These included differences in total ubiquitin levels and specific chain linkages. Moreover, specific expression changes suggested novel functions for several DUB family members. For instance, the ubp3Δ mutant showed large expression changes for members of the cytochrome C oxidase complex, consistent with a role for Ubp3 in mitochondrial regulation. Several DUBs also showed broad expression changes for phosphate transporters as well as other components of the inorganic phosphate signaling pathway, suggesting a role for these DUBs in regulating phosphate metabolism. These data highlight the potential of multiplexed proteome-wide analyses for biological investigation and provide a framework for further study of the DUB family. Our methods are readily applicable to the entire collection of yeast deletion mutants and may help facilitate systematic analysis of yeast and other organisms. PMID:26503604

  18. Three Degree of Freedom Parallel Mechanical Linkage

    NASA Technical Reports Server (NTRS)

    Adelstein, Bernard D. (Inventor)

    1998-01-01

    A three degree of freedom parallel mechanism or linkage that couples three degree of freedom translational displacements at an endpoint, such as a handle, a hand grip, or a robot tool, to link rotations about three axes that are fixed with respect to a common base or ground link. The mechanism includes a three degree of freedom spherical linkage formed of two closed loops, and a planar linkage connected to the endpoint. The closed loops are rotatably interconnected, and made of eight rigid links connected by a plurality of single degree of freedom revolute joints. Three of these revolute joints are base joints and are connected to a common ground. such that the axis lines passing through the revolute joints intersect at a common fixed center point K forming the center of a spherical work volume in which the endpoint is capable of moving. 'Me three degrees of freedom correspond to the spatial displacement of the endpoint, for instance. The mechanism provides a new overall spatial kinematic linkage composed of a minimal number of rigid links and rotary joints. The mechanism has improved mechanical stiffness, and conveys mechanical power bidirectionally between the human operator and the electromechanical actuators. It does not require gears, belts. cable, screw or other types of transmission elements, and is useful in applications requiring full backdrivability. Thus, this invention can serve as the mechanical linkage for actively powered devices such as compliant robotic manipulators and force-reflecting hand controllers, and passive devices such as manual input devices for computers and other systems.

  19. Model-free linkage analysis using likelihoods

    SciTech Connect

    Curtis, D.; Sham, P.C.

    1995-09-01

    Misspecification of transmission model parameters can produce artifactually lod scores at small recombination fractions and in multipoint analysis. To avoid this problem, we have tried to devise a test that aims to detect a genetic effect at a particular locus, rather than attempting to estimate the map position of a locus with specified effect. Maximizing likelihoods over transmission model parameters, as well as linkage parameters, can produce seriously biased parameter estimates and so yield tests that lack power for the detection of linkage. However, constraining the transmission model parameters to produce the correct population prevalence largely avoids this problem. For computational convenience, we recommend that the likelihoods under linkage and nonlinkage are independently maximized over a limited set of transmission models, ranging from Mendelian dominant to null effect and from null effect to Mendelian recessive. In order to test for a genetic effect at a given map position, the likelihood under linkage is maximized over admixture, the proportion of families linked. Application to simulated data for a wide range of transmission models in both affected sib pairs and pedigrees demonstrates that the new method is well behaved under the null hypothesis and provides a powerful test for linkage when it is present. This test requires no specification of transmission model parameters, apart from an approximate estimate of the population prevalence. It can be applied equally to sib pairs and pedigrees, and, since it does not diminish the lod score at test positions very close to a marker, it is suitable for application to multipoint data. 24 refs., 1 fig., 4 tabs.

  20. Graphdiyne oxide as a platform for fluorescence sensing.

    PubMed

    Wang, Chunxia; Yu, Ping; Guo, Shuyue; Mao, Lanqun; Liu, Huibiao; Li, Yuliang

    2016-04-12

    Graphdiyne (GD), a new kind of two-dimensional carbon allotrope consisting of a hexagonal ring and a diacetylenic linkage unit, is observed to exhibit a high fluorescence quenching ability and can be used as a new platform for fluorescence sensing, where GD oxide, the oxidized form of GD, is found to exhibit higher quenching ability than GD. As a proof-of-concept demonstration, GD oxide is used to establish a new platform for effective fluorescence sensing of DNA and thrombin with a high sensitivity and selectivity. PMID:27032989

  1. Evidence for Linkage and Association of GABRB3 and GABRA5 to Panic Disorder

    PubMed Central

    Hodges, Laura M; Fyer, Abby J; Weissman, Myrna M; Logue, Mark W; Haghighi, Fatemeh; Evgrafov, Oleg; Rotondo, Allessandro; Knowles, James A; Hamilton, Steven P

    2014-01-01

    Panic disorder (PD) is a debilitating anxiety disorder characterized by episodes of intense fear with autonomic and psychological symptoms that lead to behavioral impairment. A convergence of genetic and biological evidence implicates gamma-aminobutyric acid type A receptor subunits on chromosome 15q12 as candidate genes for PD. This study investigated 120 Caucasian, multiplex PD pedigrees using regional microsatellites (chr15q11–13) and found support for linkage (logarithm of odds (LOD) ⩾2), with a prominent parent-of-origin effect. Genotyping with 10 single-nucleotide polymorphisms (SNPs) showed linkage to GABRB3 (rs11631421, LOD=4.6) and GABRA5 (rs2075716, LOD=2.2), and allelic association to GABRB3 (rs8024564, p=0.005; rs8025575, p=0.02) and GABRA5 (rs35399885, p=0.05). Genotyping of an independent Sardinian PD trio sample also supported association in the region, again with a parent-of-origin effect. These findings provide genetic evidence for the involvement of the genes GABRB3 and GABRA5 in the susceptibility to PD. PMID:24755890

  2. External linkage tie permits reduction in ducting system flange thickness

    NASA Technical Reports Server (NTRS)

    Pfleger, R. O.

    1966-01-01

    External linkage tie reduces flange thickness and increases seal efficiency in high pressure ducting and piping systems. The linkage transmits the pressure separating load to the tube wall behind the flange allowing the flange to support only the seal.

  3. Genetic analysis of diabetic nephropathy on chromosome 18 in African Americans: linkage analysis and dense SNP mapping.

    PubMed

    McDonough, Caitrin W; Bostrom, Meredith A; Lu, Lingyi; Hicks, Pamela J; Langefeld, Carl D; Divers, Jasmin; Mychaleckyj, Josyf C; Freedman, Barry I; Bowden, Donald W

    2009-12-01

    Genetic studies in Turkish, Native American, European American, and African American (AA) families have linked chromosome 18q21.1-23 to susceptibility for diabetes-associated nephropathy. In this study, we have carried out fine linkage mapping in the 18q region previously linked to diabetic nephropathy in AAs by genotyping both microsatellite and single nucleotide polymorphisms (SNPs) for linkage analysis in an expanded set of 223 AA families multiplexed for type 2 diabetes associated ESRD (T2DM-ESRD). Several approaches were used to evaluate evidence of linkage with the strongest evidence for linkage in ordered subset analysis with an earlier age of T2DM diagnosis compared to the remaining pedigrees (LOD 3.9 at 90.1 cM, ΔP = 0.0161, NPL P value = 0.00002). Overall, the maximum LODs and LOD-1 intervals vary in magnitude and location depending upon analysis. The linkage mapping was followed up by performing a dense SNP map, genotyping 2,814 SNPs in the refined LOD-1 region in 1,029 AA T2DM-ESRD cases and 1,027 AA controls. Of the top 25 most associated SNPs, 10 resided within genic regions. Two candidate genes stood out: NEDD4L and SERPINB7. SNP rs512099, located in intron 1 of NEDD4L, was associated under a dominant model of inheritance [P value = 0.0006; Odds ratio (95% Confidence Interval) OR (95% CI) = 0.70 (0.57-0.86)]. SNP rs1720843, located in intron 2 of SERPINB7, was associated under a recessive model of inheritance [P value = 0.0017; OR (95% CI) = 0.65 (0.50-0.85)]. Collectively, these results suggest that multiple genes in this region may influence diabetic nephropathy susceptibility in AAs. PMID:19690890

  4. Exclusion of linkage between cleft lip with or without cleft palate and markers on chromosomes 4 and 6

    SciTech Connect

    Blanton, S.H.; Malcolm, S.; Winter, R.

    1996-01-01

    Nonsyndromic cleft lip with or without associate cleft palate (CLP) is a common craniofacial defect, occurring in {approximately}1/1,000 live births. While the defect generally occurs sporadically, multiplex families have been reported. Segregation analyses have demonstrated that, in some families, CLP is inherited as an autosomal dominant/codominant disorder with low penetrance. Several clefting loci have been proposed on multiple chromosomes, including 6p24, 4q, and 19q13.1. Association studies and linkage studies suggested a locus that mapped to 6p24. We were unable to confirm this in a linkage study of 12 multigenerational families. A subsequent linkage study by Carinci et al., however, found evidence for linkage to this region in 14 of 21 clefting families. Additionally, Davies et al. studied the chromosomes of three individuals with cleft lip and palate, all of whom had a rearrangement involving 6p24. Their investigation supported a locus at 6p24. Carinci et al. reported that the most likely position for a clefting locus was at D6S89, which is centromeric to EDN1. This is in contrast to the findings of Davies et al., who suggested a placement telomeric to EDN1. F13A, which had been implicated in the initial association studies, is telomeric to EDN1. Thus, the region between F13A and D6S89 encompasses the regions proposed by both Davies et al. and Carinci et al. A second clefting locus, at 4q, was proposed by Beiraghi et al., who studied a single multigenerational family by linkage analysis. Their data suggested a locus near D4S175 and D4S192. 10 refs., 1 tab.

  5. Integrated mode converter for mode division multiplexing

    NASA Astrophysics Data System (ADS)

    Perez-Galacho, Diego; Alonso-Ramos, Carlos Alberto; Marris-Morini, Delphine; Vakarin, Vladyslav; Le Roux, Xavier; Ortega-Moñux, Alejandro; Wangüemert-Perez, Juan Gonzalo; Vivien, Laurent

    2016-05-01

    The ever growing demands of bandwidth in optical communication systems are making traditional Wavelength Division Multiplexing (WDM) based systems to reach its limit. In order to cope with future bandwidth demand is necessary to use new levels of orthogonality, such as the waveguide mode or the polarization state. Mode Division Multiplexing (MDM) has recently attracted attention as a possible solution to increase aggregate bandwidth. In this work we discuss the proposition a of mode converter that can cover the whole C-Band of optical communications. The Mode Converter is based on two Multimode Interference (MMI) couplers and a phase shifter. Insertion loss (IL) below 0.2 dB and Extinction ratio (ER) higher than 20 dB in a broad bandwidth range of 1.5 μm to 1.6 μm have been estimated. The total length of the device is less than 30 μm.

  6. Spin and wavelength multiplexed nonlinear metasurface holography

    PubMed Central

    Ye, Weimin; Zeuner, Franziska; Li, Xin; Reineke, Bernhard; He, Shan; Qiu, Cheng-Wei; Liu, Juan; Wang, Yongtian; Zhang, Shuang; Zentgraf, Thomas

    2016-01-01

    Metasurfaces, as the ultrathin version of metamaterials, have caught growing attention due to their superior capability in controlling the phase, amplitude and polarization states of light. Among various types of metasurfaces, geometric metasurface that encodes a geometric or Pancharatnam–Berry phase into the orientation angle of the constituent meta-atoms has shown great potential in controlling light in both linear and nonlinear optical regimes. The robust and dispersionless nature of the geometric phase simplifies the wave manipulation tremendously. Benefitting from the continuous phase control, metasurface holography has exhibited advantages over conventional depth controlled holography with discretized phase levels. Here we report on spin and wavelength multiplexed nonlinear metasurface holography, which allows construction of multiple target holographic images carried independently by the fundamental and harmonic generation waves of different spins. The nonlinear holograms provide independent, nondispersive and crosstalk-free post-selective channels for holographic multiplexing and multidimensional optical data storages, anti-counterfeiting, and optical encryption. PMID:27306147

  7. Multiplexed Energy Coupler for Rotating Equipment

    NASA Technical Reports Server (NTRS)

    Zhao, Xiaoliang

    2011-01-01

    A multiplexing antenna assembly can efficiently couple AC signal/energy into, or out of, rotating equipment. The unit only passes AC energy while blocking DC energy. Concentric tubes that are sliced into multiple pieces are assembled together so that, when a piece from an outer tube aligns well with an inner tube piece, efficient energy coupling is achieved through a capacitive scheme. With N outer pieces and M inner pieces, an effective N x M combination can be achieved in a multiplexed manner. The energy coupler is non-contact, which is useful if isolation from rotating and stationary parts is required. Additionally, the innovation can operate in high temperatures. Applications include rotating structure sensing, non-contact energy transmission, etc.

  8. Dual phase multiplex polymerase chain reaction

    DOEpatents

    Pemov, Alexander; Bavykin, Sergei

    2008-10-07

    Highly specific and sensitive methods were developed for multiplex amplification of nucleic acids on supports such as microarrays. Based on a specific primer design, methods include five types of amplification that proceed in a reaction chamber simultaneously. These relate to four types of multiplex amplification of a target DNA on a solid support, directed by forward and reverse complex primers immobilized to the support and a fifth type--pseudo-monoplex polymerase chain reaction (PCR) of multiple targets in solution, directed by a single pair of unbound universal primers. The addition of the universal primers in the reaction mixture increases the yield over the traditional "bridge" amplification on a solid support by approximately ten times. Methods that provide multitarget amplification and detection of as little as 0.45-4.5.times.10.sup.-12 g (equivalent to 10.sup.2-10.sup.3 genomes) of a bacterial genomic DNA are disclosed.

  9. Spin and wavelength multiplexed nonlinear metasurface holography

    NASA Astrophysics Data System (ADS)

    Ye, Weimin; Zeuner, Franziska; Li, Xin; Reineke, Bernhard; He, Shan; Qiu, Cheng-Wei; Liu, Juan; Wang, Yongtian; Zhang, Shuang; Zentgraf, Thomas

    2016-06-01

    Metasurfaces, as the ultrathin version of metamaterials, have caught growing attention due to their superior capability in controlling the phase, amplitude and polarization states of light. Among various types of metasurfaces, geometric metasurface that encodes a geometric or Pancharatnam-Berry phase into the orientation angle of the constituent meta-atoms has shown great potential in controlling light in both linear and nonlinear optical regimes. The robust and dispersionless nature of the geometric phase simplifies the wave manipulation tremendously. Benefitting from the continuous phase control, metasurface holography has exhibited advantages over conventional depth controlled holography with discretized phase levels. Here we report on spin and wavelength multiplexed nonlinear metasurface holography, which allows construction of multiple target holographic images carried independently by the fundamental and harmonic generation waves of different spins. The nonlinear holograms provide independent, nondispersive and crosstalk-free post-selective channels for holographic multiplexing and multidimensional optical data storages, anti-counterfeiting, and optical encryption.

  10. Spin and wavelength multiplexed nonlinear metasurface holography.

    PubMed

    Ye, Weimin; Zeuner, Franziska; Li, Xin; Reineke, Bernhard; He, Shan; Qiu, Cheng-Wei; Liu, Juan; Wang, Yongtian; Zhang, Shuang; Zentgraf, Thomas

    2016-01-01

    Metasurfaces, as the ultrathin version of metamaterials, have caught growing attention due to their superior capability in controlling the phase, amplitude and polarization states of light. Among various types of metasurfaces, geometric metasurface that encodes a geometric or Pancharatnam-Berry phase into the orientation angle of the constituent meta-atoms has shown great potential in controlling light in both linear and nonlinear optical regimes. The robust and dispersionless nature of the geometric phase simplifies the wave manipulation tremendously. Benefitting from the continuous phase control, metasurface holography has exhibited advantages over conventional depth controlled holography with discretized phase levels. Here we report on spin and wavelength multiplexed nonlinear metasurface holography, which allows construction of multiple target holographic images carried independently by the fundamental and harmonic generation waves of different spins. The nonlinear holograms provide independent, nondispersive and crosstalk-free post-selective channels for holographic multiplexing and multidimensional optical data storages, anti-counterfeiting, and optical encryption. PMID:27306147

  11. Multiplexing Short Primers for Viral Family PCR

    SciTech Connect

    Gardner, S N; Hiddessen, A L; Hara, C A; Williams, P L; Wagner, M; Colston, B W

    2008-06-26

    We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets for large, diverse, and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers ({approx}3700 18-mers or {approx}2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus, hemagglutinin and neuraminidase segments of influenza A virus, Norwalk virus, and HIV-1.

  12. Spectrally multiplexed chromatic confocal multipoint sensing.

    PubMed

    Hillenbrand, Matthias; Lorenz, Lucia; Kleindienst, Roman; Grewe, Adrian; Sinzinger, Stefan

    2013-11-15

    We present a concept for chromatic confocal distance sensing that employs two levels of spectral multiplexing for the parallelized evaluation of multiple lateral measurement points; at the first level, the chromatic confocal principle is used to encode distance information within the spectral distribution of the sensor signal. For lateral multiplexing, the total spectral bandwidth of the sensor is split into bands. Each band is assigned to a different lateral measurement point by a segmented diffractive element. Based on this concept, we experimentally demonstrate a chromatic confocal three-point sensor that is suitable for harsh production environments, since it works with a single-point spectrometer and does not require scanning functionality. The experimental system has a working distance of more than 50 mm, a measurement range of 9 mm, and an axial resolution of 50 μm. PMID:24322108

  13. [Multiplex mapping of human cDNAs]. Technical progress report

    SciTech Connect

    Nierman, W.C.

    1991-12-31

    J. Craig Venter, National Institute of Neurological Disorders and Stroke, has begun to identify genes expressed in the human brain by partially sequences cDNA clones. We are collaborating with the Venter group and using their sequence data to develop methods for rapid localization of newly identified cDNAs to human chromosomes. We are applying the ABI automated DNA sequencer to the analysis of fluorescently-tagged PCR products for assigning sequences to individual human chromosomes. The steps in our mapping protocol are (1) to design PCR primers from the Venter laboratory-generated sequence data, (2) to test the primers for specific amplification from human genomic DNA, (3) to use the primers for PCR amplification from a somatic cell hybrid cell mapping panel, (4) to determine the presence or absence of the specific amplification products from each cell line DNA by electrophoretic analysis using the ABI sequencer, and (5) to analyze the pattern of amplification results from the hybrid panel to identify the chromosomal origin of the cDNA sequence. We have demonstrated the principle by mapping 12 sequences or ``Expressed Sequence Tags`` (ESTs), providing primer sequence data for subsequent subchromosomal localizations. We will now concentrate on developing methodology to allow multiplexing the amplification reactions and analysis of the reaction products, to achieve a high throughput with a minimum allocation of resources. This project will generate a data set from which to evaluate strategies to identify functional primer sequences from cDNA sequence data.

  14. [Multiplex mapping of human cDNAs]. Technical progress report

    SciTech Connect

    Nierman, W.C.

    1992-11-01

    We have tested and implemented several protocols to increase productivity for mapping expressed sequence tags EST sequences to human chromosomes. These protocols include adopting PRIMER which permits utilization of batch files, as the standard software for PCR primer design; adding a human 21-only cell line to the NIGMS panel No. 1 to improve discrimination in discordancy analyses involving chromosome 21, adding a monochromosomal hybrid panel to facilitate chromosome assignment of sequences that are amplified from more than 1 chromosome; combining the products of multiple PCR reactions for electrophoretic analysis (pseudoplexing); routinely multiplexing PCR reactions; and automating data entry and analysis as much as possible. We have applied these protocols to assign an overall total of 132 human brain CDNA sequences to individual human chromosomes. PCR primers were designed from ESTS and tested for specific amplification from human genomic DNA. DNA was then amplified using DNA from somatic cell hybrid mapping panels as templates. The amplification products were identified using an automated fluorescence detection system. Chromosomal assignments were made by discordancy analysis. The localized cDNAs include 2 for known human genes, 2 that map to 2 different human chromosomes, and 25 for cDNAs matching existing database records.

  15. Multiplex Detection of Plant Pathogens Using a Microsphere Immunoassay Technology

    PubMed Central

    Charlermroj, Ratthaphol; Himananto, Orawan; Seepiban, Channarong; Kumpoosiri, Mallika; Warin, Nuchnard; Oplatowska, Michalina; Gajanandana, Oraprapai; Grant, Irene R.; Karoonuthaisiri, Nitsara; Elliott, Christopher T.

    2013-01-01

    Plant pathogens are a serious problem for seed export, plant disease control and plant quarantine. Rapid and accurate screening tests are urgently required to protect and prevent plant diseases spreading worldwide. A novel multiplex detection method was developed based on microsphere immunoassays to simultaneously detect four important plant pathogens: a fruit blotch bacterium Acidovorax avenae subsp. citrulli (Aac), chilli vein-banding mottle virus (CVbMV, potyvirus), watermelon silver mottle virus (WSMoV, tospovirus serogroup IV) and melon yellow spot virus (MYSV, tospovirus). An antibody for each plant pathogen was linked on a fluorescence-coded magnetic microsphere set which was used to capture corresponding pathogen. The presence of pathogens was detected by R-phycoerythrin (RPE)-labeled antibodies specific to the pathogens. The assay conditions were optimized by identifying appropriate antibody pairs, blocking buffer, concentration of RPE-labeled antibodies and assay time. Once conditions were optimized, the assay was able to detect all four plant pathogens precisely and accurately with substantially higher sensitivity than enzyme-linked immunosorbent assay (ELISA) when spiked in buffer and in healthy watermelon leaf extract. The assay time of the microsphere immunoassay (1 hour) was much shorter than that of ELISA (4 hours). This system was also shown to be capable of detecting the pathogens in naturally infected plant samples and is a major advancement in plant pathogen detection. PMID:23638044

  16. Molecularly Imprinted Polymer Coated Quantum Dots for Multiplexed Cell Targeting and Imaging.

    PubMed

    Panagiotopoulou, Maria; Salinas, Yolanda; Beyazit, Selim; Kunath, Stephanie; Duma, Luminita; Prost, Elise; Mayes, Andrew G; Resmini, Marina; Tse Sum Bui, Bernadette; Haupt, Karsten

    2016-07-11

    Advanced tools for cell imaging are of great interest for the detection, localization, and quantification of molecular biomarkers of cancer or infection. We describe a novel photopolymerization method to coat quantum dots (QDs) with polymer shells, in particular, molecularly imprinted polymers (MIPs), by using the visible light emitted from QDs excited by UV light. Fluorescent core-shell particles specifically recognizing glucuronic acid (GlcA) or N-acetylneuraminic acid (NANA) were prepared. Simultaneous multiplexed labeling of human keratinocytes with green QDs conjugated with MIP-GlcA and red QDs conjugated with MIP-NANA was demonstrated by fluorescence imaging. The specificity of binding was verified with a non-imprinted control polymer and by enzymatic cleavage of the terminal GlcA and NANA moieties. The coating strategy is potentially a generic method for the functionalization of QDs to address a much wider range of biocompatibility and biorecognition issues. PMID:27238424

  17. High Throughput Flow Cytometry Bead-based Multiplex Assay for Identification of Rho GTPase Inhibitors

    PubMed Central

    Surviladze, Zurab; Young, Susan M; Sklar, Larry A

    2015-01-01

    Summary Rho family GTPases and their effector proteins regulate a wide range of cell signaling pathways. In normal physiological conditions their activity is tightly controlled and it is not surprising that their aberrant activation contributes to tumorigenesis or other diseases. For this reason, the identification of small, cell permeable molecules capable of inhibition of Rho GTPases can be extraordinarily useful, particularly if they are specific and act reversibly. Herein we describe a flow cytometric assay, which allows us to measure the activity of six small GTPases simultaneously. GST-tagged small GTPases are bound to six glutathione bead sets each set having a different intensity of red fluorescence at a fixed wavelength. The coated bead sets were washed, combined, and dispensed into 384-well plates with test compounds, and fluorescent-GTP binding was used as the read-out. This multiplex bead-based assay was successfully used for to identify both general and selective inhibitors of Rho family GTPases. PMID:22144280

  18. A novel multiplex bead-based platform highlights the diversity of extracellular vesicles

    PubMed Central

    Koliha, Nina; Wiencek, Yvonne; Heider, Ute; Jüngst, Christian; Kladt, Nikolay; Krauthäuser, Susanne; Johnston, Ian C. D.; Bosio, Andreas; Schauss, Astrid; Wild, Stefan

    2016-01-01

    The surface protein composition of extracellular vesicles (EVs) is related to the originating cell and may play a role in vesicle function. Knowledge of the protein content of individual EVs is still limited because of the technical challenges to analyse small vesicles. Here, we introduce a novel multiplex bead-based platform to investigate up to 39 different surface markers in one sample. The combination of capture antibody beads with fluorescently labelled detection antibodies allows the analysis of EVs that carry surface markers recognized by both antibodies. This new method enables an easy screening of surface markers on populations of EVs. By combining different capture and detection antibodies, additional information on relative expression levels and potential vesicle subpopulations is gained. We also established a protocol to visualize individual EVs by stimulated emission depletion (STED) microscopy. Thereby, markers on single EVs can be detected by fluorophore-conjugated antibodies. We used the multiplex platform and STED microscopy to show for the first time that NK cell–derived EVs and platelet-derived EVs are devoid of CD9 or CD81, respectively, and that EVs isolated from activated B cells comprise different EV subpopulations. We speculate that, according to our STED data, tetraspanins might not be homogenously distributed but may mostly appear as clusters on EV subpopulations. Finally, we demonstrate that EV mixtures can be separated by magnetic beads and analysed subsequently with the multiplex platform. Both the multiplex bead-based platform and STED microscopy revealed subpopulations of EVs that have been indistinguishable by most analysis tools used so far. We expect that an in-depth view on EV heterogeneity will contribute to our understanding of different EVs and functions. PMID:26901056

  19. A novel multiplex bead-based platform highlights the diversity of extracellular vesicles.

    PubMed

    Koliha, Nina; Wiencek, Yvonne; Heider, Ute; Jüngst, Christian; Kladt, Nikolay; Krauthäuser, Susanne; Johnston, Ian C D; Bosio, Andreas; Schauss, Astrid; Wild, Stefan

    2016-01-01

    The surface protein composition of extracellular vesicles (EVs) is related to the originating cell and may play a role in vesicle function. Knowledge of the protein content of individual EVs is still limited because of the technical challenges to analyse small vesicles. Here, we introduce a novel multiplex bead-based platform to investigate up to 39 different surface markers in one sample. The combination of capture antibody beads with fluorescently labelled detection antibodies allows the analysis of EVs that carry surface markers recognized by both antibodies. This new method enables an easy screening of surface markers on populations of EVs. By combining different capture and detection antibodies, additional information on relative expression levels and potential vesicle subpopulations is gained. We also established a protocol to visualize individual EVs by stimulated emission depletion (STED) microscopy. Thereby, markers on single EVs can be detected by fluorophore-conjugated antibodies. We used the multiplex platform and STED microscopy to show for the first time that NK cell-derived EVs and platelet-derived EVs are devoid of CD9 or CD81, respectively, and that EVs isolated from activated B cells comprise different EV subpopulations. We speculate that, according to our STED data, tetraspanins might not be homogenously distributed but may mostly appear as clusters on EV subpopulations. Finally, we demonstrate that EV mixtures can be separated by magnetic beads and analysed subsequently with the multiplex platform. Both the multiplex bead-based platform and STED microscopy revealed subpopulations of EVs that have been indistinguishable by most analysis tools used so far. We expect that an in-depth view on EV heterogeneity will contribute to our understanding of different EVs and functions. PMID:26901056

  20. Optimal distributions for multiplex logistic networks.

    PubMed

    Solá Conde, Luis E; Used, Javier; Romance, Miguel

    2016-06-01

    This paper presents some mathematical models for distribution of goods in logistic networks based on spectral analysis of complex networks. Given a steady distribution of a finished product, some numerical algorithms are presented for computing the weights in a multiplex logistic network that reach the equilibrium dynamics with high convergence rate. As an application, the logistic networks of Germany and Spain are analyzed in terms of their convergence rates. PMID:27368801

  1. Physicians' Attitudes About Multiplex Tumor Genomic Testing

    PubMed Central

    Gray, Stacy W.; Hicks-Courant, Katherine; Cronin, Angel; Rollins, Barrett J.; Weeks, Jane C.

    2014-01-01

    Purpose Although predictive multiplex somatic genomic tests hold the potential to transform care by identifying targetable alterations in multiple cancer genes, little is known about how physicians will use such tests in practice. Participants and Methods Before the initiation of enterprise-wide multiplex testing at a major cancer center, we surveyed all clinically active adult cancer physicians to assess their current use of somatic testing, their attitudes about multiplex testing, and their genomic confidence. Results A total of 160 physicians participated (response rate, 61%): 57% were medical oncologists; 29%, surgeons; 14% radiation oncologists; 37%, women; and 83%, research principal investigators. Twenty-two percent of physicians reported low confidence in their genomic knowledge. Eighteen percent of physicians anticipated testing patients infrequently (≤ 10%), whereas 25% anticipate testing most patients (≥ 90%). Higher genomic confidence was associated with wanting to test a majority of patients (adjusted odds ratio [OR], 6.09; 95% CI, 2.1 to 17.5) and anticipating using actionable (adjusted OR, 2.46; 95% CI, 1.2 to 5.2) or potentially actionable (adjusted OR, 2.89; 95% CI, 1.1 to 7.9) test results to inform treatment recommendations. Forty-two percent of physicians endorsed disclosure of uncertain genomic findings to patients. Conclusion Physicians at a tertiary-care National Cancer Institute–designated comprehensive cancer center varied considerably in how they planned to incorporate predictive multiplex somatic genomic tests into practice and in their attitudes about the disclosure of genomic information of uncertain significance. Given that many physicians reported low genomic confidence, evidence-based guidelines and enhanced physician genomic education efforts may be needed to ensure that genomically guided cancer care is adequately delivered. PMID:24663044

  2. Space division multiplexing in access networks

    NASA Astrophysics Data System (ADS)

    Effenberger, Frank J.

    2015-01-01

    Space division multiplexing (SDM) has received a lot of attention in the past years, as it is seen as the final frontier of fiber optic capacity improvement for long haul transmission. Its use in access networks is even more interesting, due to the different design optimization goals in access versus transport. This paper explores some of the applications of SDM in access that have the potential for early adoption.

  3. Selecting optimal oligonucleotide primers for multiplex PCR.

    PubMed

    Nicodème, P; Steyaert, J M

    1997-01-01

    We investigate the problem of designing efficient multiplex PCR for medical applications. We show that the problem is NP-complete by transformation to the Multiple Choice Matching problem and give an efficient approximation algorithm. We developed this algorithm in a computer program that predicts which genomic regions may be simultaneously amplified by PCR. Practical use of the software shows that the method can treat 250 non-polymorphic loci with less than 5 simultaneous experiments. PMID:9322038

  4. Broadband Hybrid Holographic Multiplexing with Geometric Metasurfaces.

    PubMed

    Huang, Lingling; Mühlenbernd, Holger; Li, Xiaowei; Song, Xu; Bai, Benfeng; Wang, Yongtian; Zentgraf, Thomas

    2015-11-01

    An effective way for broadband holographic multiplexing based on geometric metasurfaces is demonstrated by the integration of several recording channels into a single device. Each image can be individually addressed with a unique set of parameters, such as circular polarization, position, and angle. Such a technique paves the way for a wide range of applications related to optical patterning, encryption, and information processing. PMID:26398589

  5. Wireless Multiplexed Surface Acoustic Wave Sensors Project

    NASA Technical Reports Server (NTRS)

    Youngquist, Robert C.

    2014-01-01

    Wireless Surface Acoustic Wave (SAW) Sensor is a new technology for obtaining multiple, real-time measurements under extreme environmental conditions. This project plans to develop a wireless multiplexed sensor system that uses SAW sensors, with no batteries or semiconductors, that are passive and rugged, can operate down to cryogenic temperatures and up to hundreds of degrees C, and can be used to sense a wide variety of parameters over reasonable distances (meters).

  6. Optimal distributions for multiplex logistic networks

    NASA Astrophysics Data System (ADS)

    Solá Conde, Luis E.; Used, Javier; Romance, Miguel

    2016-06-01

    This paper presents some mathematical models for distribution of goods in logistic networks based on spectral analysis of complex networks. Given a steady distribution of a finished product, some numerical algorithms are presented for computing the weights in a multiplex logistic network that reach the equilibrium dynamics with high convergence rate. As an application, the logistic networks of Germany and Spain are analyzed in terms of their convergence rates.

  7. Anorganic fluorescence reference materials for decay time of fluorescence emission

    NASA Astrophysics Data System (ADS)

    Engel, A.; Ottermann, C.; Klahn, J.; Korb, T.; Resch-Genger, U.; Hoffmann, K.; Kynast, U.; Rupertus, V.

    2008-02-01

    Fluorescence techniques are known for their high sensitivity and are widely used as analytical tools, detection methods and imaging applications for product and process control, material sciences, environmental and bio-technical analysis, molecular genetics, cell biology, medical diagnostics, and drug screening. According to DIN/ISO 17025 certified standards are used for steady state fluorescence diagnostics, a method having the drawback of giving relative values for fluorescence intensities only. Therefore reference materials for a quantitative characterization have to be related directly to the materials under investigation. In order to evaluate these figures it is necessary to calculate absolute numbers such as absorption/excitation cross sections and quantum yield. This has been done for different types of dopands in different materials such as glass, glass ceramics, crystals or nano crystalline material embedded in polymer matrices. Samples doped with several fluophores of different emission wavelengths and decay times are required for fluorescent multiplexing applications. Decay times shorter than 100 ns are of special interest. In addition, a proper knowledge is necessary of quantum efficiency in highly scattering media. Recently, quantum efficiency in YAG:Ce glass ceramics has been successfully investigated. Glass and glass ceramics doped with threefold charged rare earth elements are available. However, these samples have the disadvantage of emission decay times much longer than 1 microsecond, due to the excitation and emission of their optical forbidden electronic transitions. Therefore first attempts have been made to produce decay-time standards based on organic and inorganic fluophores. Stable LUMOGEN RED pigments and YAG:Ce phosphors are diluted simultaneously in silicone matrices using a wide range of concentrations between 0.0001 and 2 wt%. Organic LUMOGEN RED has decay times in the lower nanosecond range with a slight dependency on concentration

  8. Genome-wide linkage using the Social Responsiveness Scale in Utah autism pedigrees

    PubMed Central

    2010-01-01

    Background Autism Spectrum Disorders (ASD) are phenotypically heterogeneous, characterized by impairments in the development of communication and social behaviour and the presence of repetitive behaviour and restricted interests. Dissecting the genetic complexity of ASD may require phenotypic data reflecting more detail than is offered by a categorical clinical diagnosis. Such data are available from the Social Responsiveness Scale (SRS) which is a continuous, quantitative measure of social ability giving scores that range from significant impairment to above average ability. Methods We present genome-wide results for 64 multiplex and extended families ranging from two to nine generations. SRS scores were available from 518 genotyped pedigree subjects, including affected and unaffected relatives. Genotypes from the Illumina 6 k single nucleotide polymorphism panel were provided by the Center for Inherited Disease Research. Quantitative and qualitative analyses were done using MCLINK, a software package that uses Markov chain Monte Carlo (MCMC) methods to perform multilocus linkage analysis on large extended pedigrees. Results When analysed as a qualitative trait, linkage occurred in the same locations as in our previous affected-only genome scan of these families, with findings on chromosomes 7q31.1-q32.3 [heterogeneity logarithm of the odds (HLOD) = 2.91], 15q13.3 (HLOD = 3.64), and 13q12.3 (HLOD = 2.23). Additional positive qualitative results were seen on chromosomes 6 and 10 in regions that may be of interest for other neuropsychiatric disorders. When analysed as a quantitative trait, results replicated a peak found in an independent sample using quantitative SRS scores on chromosome 11p15.1-p15.4 (HLOD = 2.77). Additional positive quantitative results were seen on chromosomes 7, 9, and 19. Conclusions The SRS linkage peaks reported here substantially overlap with peaks found in our previous affected-only genome scan of clinical diagnosis. In addition, we

  9. Emergence of Multiplex Communities in Collaboration Networks

    PubMed Central

    Nicosia, Vincenzo; Bianconi, Ginestra; Latora, Vito

    2016-01-01

    Community structures in collaboration networks reflect the natural tendency of individuals to organize their work in groups in order to better achieve common goals. In most of the cases, individuals exploit their connections to introduce themselves to new areas of interests, giving rise to multifaceted collaborations which span different fields. In this paper, we analyse collaborations in science and among movie actors as multiplex networks, where the layers represent respectively research topics and movie genres, and we show that communities indeed coexist and overlap at the different layers of such systems. We then propose a model to grow multiplex networks based on two mechanisms of intra and inter-layer triadic closure which mimic the real processes by which collaborations evolve. We show that our model is able to explain the multiplex community structure observed empirically, and we infer the strength of the two underlying social mechanisms from real-world systems. Being also able to correctly reproduce the values of intra-layer and inter-layer assortativity correlations, the model contributes to a better understanding of the principles driving the evolution of social networks. PMID:26815700

  10. Emergence of Multiplex Communities in Collaboration Networks.

    PubMed

    Battiston, Federico; Iacovacci, Jacopo; Nicosia, Vincenzo; Bianconi, Ginestra; Latora, Vito

    2016-01-01

    Community structures in collaboration networks reflect the natural tendency of individuals to organize their work in groups in order to better achieve common goals. In most of the cases, individuals exploit their connections to introduce themselves to new areas of interests, giving rise to multifaceted collaborations which span different fields. In this paper, we analyse collaborations in science and among movie actors as multiplex networks, where the layers represent respectively research topics and movie genres, and we show that communities indeed coexist and overlap at the different layers of such systems. We then propose a model to grow multiplex networks based on two mechanisms of intra and inter-layer triadic closure which mimic the real processes by which collaborations evolve. We show that our model is able to explain the multiplex community structure observed empirically, and we infer the strength of the two underlying social mechanisms from real-world systems. Being also able to correctly reproduce the values of intra-layer and inter-layer assortativity correlations, the model contributes to a better understanding of the principles driving the evolution of social networks. PMID:26815700

  11. Multiplex congruence network of natural numbers

    NASA Astrophysics Data System (ADS)

    Yan, Xiao-Yong; Wang, Wen-Xu; Chen, Guan-Rong; Shi, Ding-Hua

    2016-03-01

    Congruence theory has many applications in physical, social, biological and technological systems. Congruence arithmetic has been a fundamental tool for data security and computer algebra. However, much less attention was devoted to the topological features of congruence relations among natural numbers. Here, we explore the congruence relations in the setting of a multiplex network and unveil some unique and outstanding properties of the multiplex congruence network. Analytical results show that every layer therein is a sparse and heterogeneous subnetwork with a scale-free topology. Counterintuitively, every layer has an extremely strong controllability in spite of its scale-free structure that is usually difficult to control. Another amazing feature is that the controllability is robust against targeted attacks to critical nodes but vulnerable to random failures, which also differs from ordinary scale-free networks. The multi-chain structure with a small number of chain roots arising from each layer accounts for the strong controllability and the abnormal feature. The multiplex congruence network offers a graphical solution to the simultaneous congruences problem, which may have implication in cryptography based on simultaneous congruences. Our work also gains insight into the design of networks integrating advantages of both heterogeneous and homogeneous networks without inheriting their limitations.

  12. Multiplexed Holographic Data Storage in Bacteriorhodopsin

    NASA Technical Reports Server (NTRS)

    Mehrl, David J.; Krile, Thomas F.

    1997-01-01

    High density optical data storage, driven by the information revolution, remains at the forefront of current research areas. Much of the current research has focused on photorefractive materials (SBN and LiNbO3) and polymers, despite various problems with expense, durability, response time and retention periods. Photon echo techniques, though promising, are questionable due to the need for cryogenic conditions. Bacteriorhodopsin (BR) films are an attractive alternative recording medium. Great strides have been made in refining BR, and materials with storage lifetimes as long as 100 days have recently become available. The ability to deposit this robust polycrystalline material as high quality optical films suggests the use of BR as a recording medium for commercial optical disks. Our own recent research has demonstrated the suitability of BR films for real time spatial filtering and holography. We propose to fully investigate the feasibility of performing holographic mass data storage in BR. Important aspects of the problem to be investigated include various data multiplexing techniques (e.g. angle- amplitude- and phase-encoded multiplexing, and in particular shift-multiplexing), multilayer recording techniques, SLM selection and data readout using crossed polarizers for noise rejection. Systems evaluations of storage parameters, including access times, memory refresh constraints, erasure, signal-to-noise ratios and bit error rates, will be included in our investigations.

  13. Emergence of Chimera in Multiplex Network

    NASA Astrophysics Data System (ADS)

    Ghosh, Saptarshi; Jalan, Sarika

    2016-06-01

    Chimera is a relatively new emerging phenomenon where coexistence of synchronous and asynchronous states is observed in symmetrically coupled dynamical units. We report the observation of the chimera state in multiplex networks where individual layer is represented by 1-d lattice with nonlocal interactions. While, multiplexing does not change the type of the chimera state and retains the multi-chimera state displayed by the isolated networks, it changes the regions of the incoherence. We investigate the emergence of coherent-incoherent bifurcation upon varying the control parameters, namely, the coupling strength and the network size. Additionally, we investigate the effect of initial condition on the dynamics of the chimera state. Using a measure based on the differences between the neighboring nodes which distinguishes smooth and nonsmooth spatial profiles, we find the critical coupling strength for the transition to the chimera state. Observing chimera in a multiplex network with one-to-one inter layer coupling is important to gain insight to many real world complex systems which inherently posses multilayer architecture.

  14. Multiplex congruence network of natural numbers.

    PubMed

    Yan, Xiao-Yong; Wang, Wen-Xu; Chen, Guan-Rong; Shi, Ding-Hua

    2016-01-01

    Congruence theory has many applications in physical, social, biological and technological systems. Congruence arithmetic has been a fundamental tool for data security and computer algebra. However, much less attention was devoted to the topological features of congruence relations among natural numbers. Here, we explore the congruence relations in the setting of a multiplex network and unveil some unique and outstanding properties of the multiplex congruence network. Analytical results show that every layer therein is a sparse and heterogeneous subnetwork with a scale-free topology. Counterintuitively, every layer has an extremely strong controllability in spite of its scale-free structure that is usually difficult to control. Another amazing feature is that the controllability is robust against targeted attacks to critical nodes but vulnerable to random failures, which also differs from ordinary scale-free networks. The multi-chain structure with a small number of chain roots arising from each layer accounts for the strong controllability and the abnormal feature. The multiplex congruence network offers a graphical solution to the simultaneous congruences problem, which may have implication in cryptography based on simultaneous congruences. Our work also gains insight into the design of networks integrating advantages of both heterogeneous and homogeneous networks without inheriting their limitations. PMID:27029650

  15. Multiplex congruence network of natural numbers

    PubMed Central

    Yan, Xiao-Yong; Wang, Wen-Xu; Chen, Guan-Rong; Shi, Ding-Hua

    2016-01-01

    Congruence theory has many applications in physical, social, biological and technological systems. Congruence arithmetic has been a fundamental tool for data security and computer algebra. However, much less attention was devoted to the topological features of congruence relations among natural numbers. Here, we explore the congruence relations in the setting of a multiplex network and unveil some unique and outstanding properties of the multiplex congruence network. Analytical results show that every layer therein is a sparse and heterogeneous subnetwork with a scale-free topology. Counterintuitively, every layer has an extremely strong controllability in spite of its scale-free structure that is usually difficult to control. Another amazing feature is that the controllability is robust against targeted attacks to critical nodes but vulnerable to random failures, which also differs from ordinary scale-free networks. The multi-chain structure with a small number of chain roots arising from each layer accounts for the strong controllability and the abnormal feature. The multiplex congruence network offers a graphical solution to the simultaneous congruences problem, which may have implication in cryptography based on simultaneous congruences. Our work also gains insight into the design of networks integrating advantages of both heterogeneous and homogeneous networks without inheriting their limitations. PMID:27029650

  16. Standard nomenclature for common bean chromosomes and linkage groups

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several DNA-based linkage maps have been developed for common bean including the core common bean linkage map using the BAT93 x Jalo EEP558 recombinant inbred line (RIL) population. Correlation of common bean chromosomes to the genetic linkage groups was completed using RFLP markers to assign each l...

  17. Linkage Analysis in Autoimmune Addison’s Disease: NFATC1 as a Potential Novel Susceptibility Locus

    PubMed Central

    Mitchell, Anna L.; Bøe Wolff, Anette; MacArthur, Katie; Weaver, Jolanta U.; Vaidya, Bijay; Erichsen, Martina M.; Darlay, Rebecca; Husebye, Eystein S.; Cordell, Heather J.; Pearce, Simon H. S.

    2015-01-01

    Background Autoimmune Addison’s disease (AAD) is a rare, highly heritable autoimmune endocrinopathy. It is possible that there may be some highly penetrant variants which confer disease susceptibility that have yet to be discovered. Methods DNA samples from 23 multiplex AAD pedigrees from the UK and Norway (50 cases, 67 controls) were genotyped on the Affymetrix SNP 6.0 array. Linkage analysis was performed using Merlin. EMMAX was used to carry out a genome-wide association analysis comparing the familial AAD cases to 2706 UK WTCCC controls. To explore some of the linkage findings further, a replication study was performed by genotyping 64 SNPs in two of the four linked regions (chromosomes 7 and 18), on the Sequenom iPlex platform in three European AAD case-control cohorts (1097 cases, 1117 controls). The data were analysed using a meta-analysis approach. Results In a parametric analysis, applying a rare dominant model, loci on chromosomes 7, 9 and 18 had LOD scores >2.8. In a non-parametric analysis, a locus corresponding to the HLA region on chromosome 6, known to be associated with AAD, had a LOD score >3.0. In the genome-wide association analysis, a SNP cluster on chromosome 2 and a pair of SNPs on chromosome 6 were associated with AAD (P <5x10-7). A meta-analysis of the replication study data demonstrated that three chromosome 18 SNPs were associated with AAD, including a non-synonymous variant in the NFATC1 gene. Conclusion This linkage study has implicated a number of novel chromosomal regions in the pathogenesis of AAD in multiplex AAD families and adds further support to the role of HLA in AAD. The genome-wide association analysis has also identified a region of interest on chromosome 2. A replication study has demonstrated that the NFATC1 gene is worthy of future investigation, however each of the regions identified require further, systematic analysis. PMID:26042420

  18. Simple, Sensitive and Accurate Multiplex Detection of Clinically Important Melanoma DNA Mutations in Circulating Tumour DNA with SERS Nanotags

    PubMed Central

    Wee, Eugene J.H.; Wang, Yuling; Tsao, Simon Chang-Hao; Trau, Matt

    2016-01-01

    Sensitive and accurate identification of specific DNA mutations can influence clinical decisions. However accurate diagnosis from limiting samples such as circulating tumour DNA (ctDNA) is challenging. Current approaches based on fluorescence such as quantitative PCR (qPCR) and more recently, droplet digital PCR (ddPCR) have limitations in multiplex detection, sensitivity and the need for expensive specialized equipment. Herein we describe an assay capitalizing on the multiplexing and sensitivity benefits of surface-enhanced Raman spectroscopy (SERS) with the simplicity of standard PCR to address the limitations of current approaches. This proof-of-concept method could reproducibly detect as few as 0.1% (10 copies, CV < 9%) of target sequences thus demonstrating the high sensitivity of the method. The method was then applied to specifically detect three important melanoma mutations in multiplex. Finally, the PCR/SERS assay was used to genotype cell lines and ctDNA from serum samples where results subsequently validated with ddPCR. With ddPCR-like sensitivity and accuracy yet at the convenience of standard PCR, we believe this multiplex PCR/SERS method could find wide applications in both diagnostics and research. PMID:27446486

  19. Time division multiplexed orbital angular momentum access system

    NASA Astrophysics Data System (ADS)

    Shi, Jianyang; Fang, Yuan; Chi, Nan

    2016-03-01

    We propose and experimentally demonstrate time division multiplexed orbital angular momentum (OAM) access system to increase transmission capacity and spectral efficiency. In this system, data carried on different time tributaries share the same OAM mode. Multiple time division multiplexed OAM modes are multiplexed to realize two-dimensional (time dimension and OAM dimension) multiplexing. Therefore, the capacity and spectral efficiency of the access system will increase. The orthogonality between optical time division multiplexing (OTDM) and OAM techniques is also verified in our experiment. In a proof-of-concept experiment, 2×5-Gbps return-to-zero signal over OAM mode +4 is transmitted and investigated. The bit error ratio performance after transmission in this system can be smaller than 1×10-9. Results show that the proposed time division multiplexed OAM access system is suitable for future broadband access network.

  20. Multiplex PCR for rapid diagnosis of tuberculous meningitis.

    PubMed

    Kusum, Sharma; Aman, Sharma; Pallab, Ray; Kumar, Sharma Shiv; Manish, Modi; Sudesh, Prabhakar; Subhash, Varma; Meera, Sharma

    2011-10-01

    Rapid and specific diagnosis of tubercular meningitis is of paramount importance to decrease morbidity and mortality. The aim of the study was to evaluate multiplex PCR using protein b, MPB 64, and IS6110 primers directed against M. tuberculosis complex for the diagnosis of tuberculous meningitis (TBM). Multiplex PCR was performed on 18 TBM confirmed cases (culture was positive), 92 clinically suspected TBM cases and 100 non-TBM (control group) patients. Multiplex PCR had a sensitivity of 94.4% for confirmed cases and specificity of 100% for confirmed TBM cases. In 92 clinically diagnosed but unconfirmed TBM cases, multiplex PCR was positive in 84.78% cases. The overall sensitivity of microscopy, culture and multiplex cases were 1.81, 16.73, and 86.63% and specificity was 100, 100, and 100% respectively. Multiplex PCR using protein b, MPB 64, and IS6110 primers has a high sensitivity and specificity in diagnosis of tubercular meningitis. PMID:21455603

  1. Demonstration of hybrid orbital angular momentum multiplexing and time-division multiplexing passive optical network.

    PubMed

    Wang, Andong; Zhu, Long; Liu, Jun; Du, Cheng; Mo, Qi; Wang, Jian

    2015-11-16

    Mode-division multiplexing passive optical network (MDM-PON) is a promising scheme for next-generation access networks to further increase fiber transmission capacity. In this paper, we demonstrate the proof-of-concept experiment of hybrid mode-division multiplexing (MDM) and time-division multiplexing (TDM) PON architecture by exploiting orbital angular momentum (OAM) modes. Bidirectional transmissions with 2.5-Gbaud 4-level pulse amplitude modulation (PAM-4) downstream and 2-Gbaud on-off keying (OOK) upstream are demonstrated in the experiment. The observed optical signal-to-noise ratio (OSNR) penalties for downstream and upstream transmissions at a bit-error rate (BER) of 2 × 10(-3) are less than 2.0 dB and 3.0 dB, respectively. PMID:26698429

  2. Monochrome Multiplexing in Polymerase Chain Reaction by Photobleaching of Fluorogenic Hydrolysis Probes.

    PubMed

    Schuler, Friedrich; Trotter, Martin; Zengerle, Roland; von Stetten, Felix

    2016-03-01

    Multiplexing in polymerase chain reaction (PCR) is a technique widely used to save cost and sample material and to increase sensitivity compared to distributing a sample to several singleplex reactions. One of the most common methods to detect the different amplification products is the use of fluorogenic probes that emit at different wavelengths (colors). To reduce the number of detection channels, several methods for monochrome multiplexing have been suggested. However, they pose restrictions to the amplifiable target length, the sequence, or the melting temperature. To circumvent these limitations, we suggest a novel approach that uses different fluorophores with the same emission maximum. Discrimination is achieved by their different fluorescence stability during photobleaching. Atto488 (emitting at the same wavelength as 6-carboxyfluorescein, FAM) and Atto467N (emitting at the same wavelength as cyanine 5, Cy5) were found to bleach significantly less than FAM and Cy5; i.e., the final fluorescence of Atto dyes was more than tripled compared to FAM and Cy5. We successfully applied this method by performing a 4-plex PCR targeting antibiotic resistance genes in S. aureus using only 2 color channels. Confidence of discrimination between the targets was >99.9% at high copy initial copy numbers of 100 000 copies. Cases where both targets were present could be discriminated with equal confidence for Cy5 channel and reduced levels of confidence (>68%) for FAM channel. Moreover, a 2-plex digital PCR reaction in 1 color channel was shown. In the future, the degree of multiplexing may be increased by adding fluorogenic probe pairs with other emission wavelengths. The method may also be applied to other probe and assay formats, such as Förster resonance energy transfer (FRET) probes and immunoassays. PMID:26840905

  3. Toward photostable multiplex analyte detection on a single mode planar optical waveguide

    SciTech Connect

    Mukundan, Harshini; Xei, Hongshi; Anderson, Aaron S; Grace, Wynne K; Martinez, Jennifer S; Swanson, Basil

    2009-01-01

    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.

  4. 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.

  5. A novel multiplex isothermal amplification method for rapid detection and identification of viruses

    PubMed Central

    Nyan, Dougbeh-Chris; Swinson, Kevin L.

    2015-01-01

    A rapid multiplex isothermal amplification assay has been developed for detection and identification of multiple blood-borne viruses that infect millions of people world-wide. These infections may lead to chronic diseases or death if not diagnosed and treated in a timely manner. Sets of virus-specific oligonucleotides and oligofluorophores were designed and used in a reverse-transcription loop-mediated multiplexed isothermal amplification reaction for detection and gel electrophoretic identification of human Immunodeficiency virus (HIV), hepatitis-B virus (HBV), hepatitis-C virus (HCV), hepatitis-E virus (HEV), dengue virus (DENV), and West Nile (WNV) virus infection in blood plasma. Amplification was catalyzed with two thermostable enzymes for 30–60 minutes under isothermal condition, utilizing a simple digital heat source. Electrophoretic analysis of amplified products demonstrated simultaneous detection of 6 viruses that were distinctly identified by unique ladder-like banding patterns. Naked-eye fluorescent visualization of amplicons revealed intensely fluorescing products that indicated positive detection. The test demonstrated a 97% sensitivity and a 100% specificity, with no cross-reaction with other viruses observed. This portable detection tool may have clinical and field utility in the developing and developed world settings. This may enable rapid diagnosis and identification of viruses for targeted therapeutic intervention and prevention of disease transmission. PMID:26643761

  6. Multiplexed protein detection using antibody-conjugated microbead arrays in a microfabricated electrophoretic device

    PubMed Central

    Barbee, Kristopher D.; Hsiao, Alexander P.; Roller, Eric E.; Huang, Xiaohua

    2011-01-01

    We report the development of a microfabricated electrophoretic device for assembling high-density arrays of antibody-conjugated microbeads for chip-based protein detection. The device consists of a flow cell formed between a gold-coated silicon chip with an array of microwells etched in a silicon dioxide film and a glass coverslip with a series of thin gold counter electrode lines. We have demonstrated that 0.4 and 1 μm beads conjugated with antibodies can be rapidly assembled into the microwells by applying a pulsed electric field across the chamber. By assembling step-wise a mixture of fluorescently labeled antibody-conjugated microbeads, we incorporated both spatial and fluorescence encoding strategies to demonstrate significant multiplexing capabilities. We have shown that these antibody-conjugated microbead arrays can be used to perform on-chip sandwich immunoassays to detect test antigens at concentrations as low as 40 pM (6 ng/mL). A finite element model was also developed to examine the electric field distribution within the device for different counter electrode configurations over a range of line pitches and chamber heights. This device will be useful for assembling high-density, encoded antibody arrays for multiplexed detection of proteins and other types of protein-conjugated microbeads for applications such as the analysis of protein-protein interactions. PMID:20820631

  7. Multiplexed aptasensors and amplified DNA sensors using functionalized graphene oxide: application for logic gate operations.

    PubMed

    Liu, Xiaoqing; Aizen, Ruth; Freeman, Ronit; Yehezkeli, Omer; Willner, Itamar

    2012-04-24

    Graphene oxide (GO) is implemented as a functional matrix for developing fluorescent sensors for the amplified multiplexed detection of DNA, aptamer-substrate complexes, and for the integration of predesigned DNA constructs that activate logic gate operations. Fluorophore-labeled DNA strands acting as probes for two different DNA targets are adsorbed onto GO, leading to the quenching of the luminescence of the fluorophores. Desorption of the probes from the GO, through hybridization with the target DNAs, leads to the fluorescence of the respective label. By coupling exonuclease III, Exo III, to the system, the recycling of the target DNAs is demonstrated, and this leads to the amplified detection of the DNA targets (detection limit 5 × 10(-12) M). Similarly, adsorption of fluorophore-functionalized aptamers against thrombin or ATP onto the GO leads to the desorption of the aptamer-substrate complexes from GO and to the triggering of the luminescence corresponding to the respective fluorophore, thus, allowing the multiplexed analysis of the aptamer-substrate complexes. By designing functional fluorophore-labeled DNA constructs and their interaction with GO, in the presence (or absence) of nucleic acids, or two different substrates for aptamers, as inputs, the activation of the "OR" and "AND" logic gates is demonstrated. PMID:22404375

  8. Technical challenges of providing record linkage services for research

    PubMed Central

    2014-01-01

    Background Record linkage techniques are widely used to enable health researchers to gain event based longitudinal information for entire populations. The task of record linkage is increasingly being undertaken by specialised linkage units (SLUs). In addition to the complexity of undertaking probabilistic record linkage, these units face additional technical challenges in providing record linkage ‘as a service’ for research. The extent of this functionality, and approaches to solving these issues, has had little focus in the record linkage literature. Few, if any, of the record linkage packages or systems currently used by SLUs include the full range of functions required. Methods This paper identifies and discusses some of the functions that are required or undertaken by SLUs in the provision of record linkage services. These include managing routine, on-going linkage; storing and handling changing data; handling different linkage scenarios; accommodating ever increasing datasets. Automated linkage processes are one way of ensuring consistency of results and scalability of service. Results Alternative solutions to some of these challenges are presented. By maintaining a full history of links, and storing pairwise information, many of the challenges around handling ‘open’ records, and providing automated managed extractions are solved. A number of these solutions were implemented as part of the development of the National Linkage System (NLS) by the Centre for Data Linkage (part of the Population Health Research Network) in Australia. Conclusions The demand for, and complexity of, linkage services is growing. This presents as a challenge to SLUs as they seek to service the varying needs of dozens of research projects annually. Linkage units need to be both flexible and scalable to meet this demand. It is hoped the solutions presented here can help mitigate these difficulties. PMID:24678656

  9. Linkages among global and regional air issues

    SciTech Connect

    Maarouf, A.R.

    1997-11-01

    Six air issues are currently on science and policy agendas in Canada and elsewhere. These are climate change, stratospheric ozone depletion, acidic deposition, SMOG, suspended particulate matter, and hazardous air pollutants. It is now recognized that these issues are interrelated, and they may interact to cause negative as well as some beneficial effects. The linkages among these issues must therefore be better understood in order to develop effective policies to deal with this ensemble of related issues. This paper illustrates through several examples the linkages among the air issues. It also points to potentially conflicting policies arising from the single-issue approach, and it emphasizes the need for better integration of air issues. 14 refs., 1 tab.

  10. Adjustable throttle linkage for outboard motors

    SciTech Connect

    Dunham, W.D.; Miller, G.L.

    1986-02-17

    An adjustable throttle linkage is described for use in controlling operation of an internal combustion engine having a carburetor including a pivotable throttle valve, a throttle valve position control member operably connected to the throttle valve and movable so as to control the position of the throttle valve, and a throttle lever for controlling the position of the throttle valve. The adjustable throttle linkage comprises a connecting link having one end connected to one of the throttle lever and the control member, and having a threaded portion, means for adjustably connecting the threaded portion to the other of the throttle lever and the control member. The adjustable connecting means includes a slot in the other of the throttle lever and the control member, and a rotatable member threaded onto the threaded portion and receive in the slot such that rotation of the rotatable member causes relative movement between the link and the other of the throttle lever and the control member.

  11. Anxiety and Depression: Linkages with Viral Diseases

    PubMed Central

    Coughlin, Steven S.

    2012-01-01

    Anxiety and mood disorders are common in the general population in countries around the world. This article provides a review of the recent literature on anxiety and depressive disorders with a focus on linkages with several important viral diseases. Although the majority of studies have been conducted in developed countries such as the United States and Great Britain, some studies have been carried out in less developed nations where only a small percentage of persons with mental illness receive treatment for their condition. The studies summarized in this review indicate that there are important linkages between anxiety and depression and viral diseases such as influenza A (H1N1) and other influenza viruses, varicella-zoster virus, herpes simplex virus, human immunodeficiency virus/acquired immune deficiency syndrome, and hepatitis C. Additional studies are needed to further clarify the mechanisms for interactions between mental health and communicable diseases, in order to assist patients and further prevention and control efforts. PMID:25264396

  12. Linkage of typical pseudoachondroplasia to chromosome 19

    SciTech Connect

    Hecht, J.T.; Deere, M.; Conner, B.; Horton, W.A. ); Francomano, C.A. ); Briggs, M.D.; Cohn, D.H. ); Warman, M. ); Blanton, S.H. )

    1993-12-01

    Pseudoachondroplasia (PSACH) is an autosomal dominant dwarfing condition associated with disproportionate short stature, marked joint deformities, and early onset osteoarthritis. Previous linkage studies have excluded linkage to cartilage and noncartilagenous extracellular matrix candidate genes. Here, the authors report mapping the pseudoachondroplasia gene to chromosome 19. Maximum lod scores of 4.70, 4.15, and 4.86 at [theta] = 0.00 were found for D19S212, D19S215, and D19S49, respectively. Multipoint analysis suggests the following order: D19S253-D19S199-(D19S212/PSACH/D19S215)-D19S222-D19S49. 24 refs., 4 figs., 1 tab.

  13. A nucleic acid strand displacement system for the multiplexed detection of tuberculosis-specific mRNA using quantum dots

    NASA Astrophysics Data System (ADS)

    Gliddon, H. D.; Howes, P. D.; Kaforou, M.; Levin, M.; Stevens, M. M.

    2016-05-01

    The development of rapid, robust and high performance point-of-care diagnostics relies on the advancement and combination of various areas of research. We have developed an assay for the detection of multiple mRNA molecules that combines DNA nanotechnology with fluorescent nanomaterials. The core switching mechanism is toehold-mediated strand displacement. We have used fluorescent quantum dots (QDs) as signal transducers in this assay, as they bring many benefits including bright fluorescence and multiplexing abilities. The resulting assay is capable of multiplexed detection of long RNA targets against a high concentration of background non-target RNA, with high sensitivity and specificity and limits of detection in the nanomolar range using only a standard laboratory plate reader. We demonstrate the utility of our QD-based system for the detection of two genes selected from a microarray-derived tuberculosis-specific gene expression signature. Levels of up- and downregulated gene transcripts comprising this signature can be combined to give a disease risk score, making the signature more amenable for use as a diagnostic marker. Our QD-based approach to detect these transcripts could pave the way for novel diagnostic assays for tuberculosis.The development of rapid, robust and high performance point-of-care diagnostics relies on the advancement and combination of various areas of research. We have developed an assay for the detection of multiple mRNA molecules that combines DNA nanotechnology with fluorescent nanomaterials. The core switching mechanism is toehold-mediated strand displacement. We have used fluorescent quantum dots (QDs) as signal transducers in this assay, as they bring many benefits including bright fluorescence and multiplexing abilities. The resulting assay is capable of multiplexed detection of long RNA targets against a high concentration of background non-target RNA, with high sensitivity and specificity and limits of detection in the nanomolar

  14. Liquid Chromatography-Selected Reaction Monitoring (LC-SRM) Approach for the Separation and Quantitation of Sialylated N-Glycans Linkage Isomers

    PubMed Central

    2015-01-01

    The study of N-linked glycans is among the most challenging bioanalytical tasks because of their complexity and variety. The presence of glycoform families that differ only in branching and/or linkage position makes the identification and quantitation of individual glycans exceedingly difficult. Quantitation of these individual glycans is important because changes in the abundance of these isomers are often associated with significant biomedical events. For instance, previous studies have shown that the ratio of α2-3 to α2-6 linked sialic acid (SA) plays an important role in cancer biology. Consequently, quantitative methods to detect alterations in the ratios of glycans based on their SA linkages could serve as a diagnostic tool in oncology, yet traditional glycomic profiling cannot readily differentiate between these linkage isomers. Here, we present a liquid chromatography-selected reaction monitoring (LC-SRM) approach that we demonstrate is capable of quantitating the individual SA linkage isomers. The LC method is capable of separating sialylated N-glycan isomers differing in α2-3 and α2-6 linkages using a novel superficially porous particle (Fused-Core) Penta-HILIC (hydrophilic interaction liquid chromatography) column. SRM detection provides the relative quantitation of each SA linkage isomer, and minimizes interferences from coeluting glycans that are problematic for UV/Fluorescence based quantitation. With our approach, the relative quantitation of each SA linkage isomer is obtained from a straightforward liquid chromatography-mass spectrometry (LC-MS) experiment. PMID:25299151

  15. Liquid chromatography-selected reaction monitoring (LC-SRM) approach for the separation and quantitation of sialylated N-glycans linkage isomers.

    PubMed

    Tao, Shujuan; Huang, Yining; Boyes, Barry E; Orlando, Ron

    2014-11-01

    The study of N-linked glycans is among the most challenging bioanalytical tasks because of their complexity and variety. The presence of glycoform families that differ only in branching and/or linkage position makes the identification and quantitation of individual glycans exceedingly difficult. Quantitation of these individual glycans is important because changes in the abundance of these isomers are often associated with significant biomedical events. For instance, previous studies have shown that the ratio of α2-3 to α2-6 linked sialic acid (SA) plays an important role in cancer biology. Consequently, quantitative methods to detect alterations in the ratios of glycans based on their SA linkages could serve as a diagnostic tool in oncology, yet traditional glycomic profiling cannot readily differentiate between these linkage isomers. Here, we present a liquid chromatography-selected reaction monitoring (LC-SRM) approach that we demonstrate is capable of quantitating the individual SA linkage isomers. The LC method is capable of separating sialylated N-glycan isomers differing in α2-3 and α2-6 linkages using a novel superficially porous particle (Fused-Core) Penta-HILIC (hydrophilic interaction liquid chromatography) column. SRM detection provides the relative quantitation of each SA linkage isomer, and minimizes interferences from coeluting glycans that are problematic for UV/Fluorescence based quantitation. With our approach, the relative quantitation of each SA linkage isomer is obtained from a straightforward liquid chromatography-mass spectrometry (LC-MS) experiment. PMID:25299151

  16. Hidden linkages between urbanization and food systems.

    PubMed

    Seto, Karen C; Ramankutty, Navin

    2016-05-20

    Global societies are becoming increasingly urban. This shift toward urban living is changing our relationship with food, including how we shop and what we buy, as well as ideas about sanitation and freshness. Achieving food security in an era of rapid urbanization will require considerably more understanding about how urban and food systems are intertwined. Here we discuss some potential understudied linkages that are ripe for further examination. PMID:27199419

  17. Communicability reveals a transition to coordinated behavior in multiplex networks

    NASA Astrophysics Data System (ADS)

    Estrada, Ernesto; Gómez-Gardeñes, Jesús

    2014-04-01

    We analyze the flow of information in multiplex networks by means of the communicability function. First, we generalize this measure from its definition from simple graphs to multiplex networks. Then, we study its relevance for the analysis of real-world systems by studying a social multiplex where information flows using formal-informal channels and an air transportation system where the layers represent different air companies. Accordingly, the communicability, which is essential for the good performance of these complex systems, emerges at a systemic operation point in the multiplex where the performance of the layers operates in a coordinated way very differently from the state represented by a collection of unconnected networks.

  18. Diffraction model of peristrophic multiplexing with spherical reference wave.

    PubMed

    Yoshida, Shuhei; Takahata, Yosuke; Horiuchi, Shuma; Yamamoto, Manabu

    2015-02-01

    Multiplexing recording is a primary contributor to determining the recording density in holographic data storage. Therefore, many different kinds of recording methods have been proposed. Among them, the method that utilizes spherical waves as reference waves is characterized by the ability to enable multiplexing recording only by moving (shifting or rotating) the recording medium. In our research, we propose a theoretical diffraction model of peristrophic multiplexing with a spherical reference wave and evaluate the diffraction efficiency; this multiplexing recording method has incorporated spherical reference waves in rotation of the media. Additionally, we verify the effectiveness of the model by comparing it with experimental results. PMID:26366593

  19. Shift-peristrophic multiplexing for holographic data storage

    NASA Astrophysics Data System (ADS)

    Kurata, Hiroyuki; Mori, Jun; Tsukamoto, Yu; Yamamoto, Keiko; Yoshida, Shuhei; Yamamoto, Manabu

    2014-09-01

    Holographic data storage (HDS) is a promising technology that has huge capacity. A multiplexing method plays a significant role in increasing the data capacity. Various multiplexing methods have been researched so far. In this paper, we proposed shift-peristrophic multiplexing using spherical reference wave and experimentally verified that this method is efficiently increase the data capacity. A series of holograms was recorded with shift multiplexing and rotating recording material with the axis of rotation being perpendicular to the material's surface. This method can realize more than 1 Tbits/inch2 data density recording. Furthermore if we maximize the performance of a recording medium, several TB per disk capacity would be available.

  20. Multiplex PCR Tests for Detection of Pathogens Associated with Gastroenteritis

    PubMed Central

    Zhang, Hongwei; Morrison, Scott; Tang, Yi-Wei

    2016-01-01

    Synopsis A wide range of enteric pathogens can cause infectious gastroenteritis. Conventional diagnostic algorithms including culture, biochemical identification, immunoassay and microscopic examination are time consuming and often lack sensitivity and specificity. Advances in molecular technology have as allowed its use as clinical diagnostic tools. Multiplex PCR based testing has made its way to gastroenterology diagnostic arena in recent years. In this article we present a review of recent laboratory developed multiplex PCR tests and current commercial multiplex gastrointestinal pathogen tests. We will focus on two FDA cleared commercial syndromic multiplex tests: Luminex xTAG GPP and Biofire FimArray GI test. These multiplex tests can detect and identify multiple enteric pathogens in one test and provide results within hours. Multiplex PCR tests have shown superior sensitivity to conventional methods for detection of most pathogens. The high negative predictive value of these multiplex tests has led to the suggestion that they be used as screening tools especially in outbreaks. Although the clinical utility and benefit of multiplex PCR test are to be further investigated, implementing these multiplex PCR tests in gastroenterology diagnostic algorithm has the potential to improve diagnosis of infectious gastroenteritis. PMID:26004652

  1. A genetic linkage map of the model legume Lotus japonicus and strategies for fast mapping of new loci.

    PubMed Central

    Sandal, Niels; Krusell, Lene; Radutoiu, Simona; Olbryt, Magdalena; Pedrosa, Andrea; Stracke, Silke; Sato, Shusei; Kato, Tomohiko; Tabata, Satoshi; Parniske, Martin; Bachmair, Andreas; Ketelsen, Tina; Stougaard, Jens

    2002-01-01

    A genetic map for the model legume Lotus japonicus has been developed. The F(2) mapping population was established from an interspecific cross between L. japonicus and L. filicaulis. A high level of DNA polymorphism between these parents was the source of markers for linkage analysis and the map is based on a framework of amplified fragment length polymorphism (AFLP) markers. Additional markers were generated by restriction fragment length polymorphism (RFLP) and sequence-specific PCR. A total of 524 AFLP markers, 3 RAPD markers, 39 gene-specific markers, 33 microsatellite markers, and six recessive symbiotic mutant loci were mapped. This genetic map consists of six linkage groups corresponding to the six chromosomes in L. japonicus. Fluorescent in situ hybridization (FISH) with selected markers aligned the linkage groups to chromosomes as described in the accompanying article by Pedrosa et al. 2002(this issue). The length of the linkage map is 367 cM and the average marker distance is 0.6 cM. Distorted segregation of markers was found in certain sections of the map and linkage group I could be assembled only by combining colormapping and cytogenetics (FISH). A fast method to position genetic loci employing three AFLP primer combinations yielding 89 markers was developed and evaluated by mapping three symbiotic loci, Ljsym1, Ljsym5, and Ljhar1-3. PMID:12196410

  2. Methods for genetic linkage analysis using trisomies

    SciTech Connect

    Feingold, E.; Lamb, N.E.; Sherman, S.L.

    1995-02-01

    Certain genetic disorders are rare in the general population, but more common in individuals with specific trisomies. Examples of this include leukemia and duodenal atresia in trisomy 21. This paper presents a linkage analysis method for using trisomic individuals to map genes for such traits. It is based on a very general gene-specific dosage model that posits that the trait is caused by specific effects of different alleles at one or a few loci and that duplicate copies of {open_quotes}susceptibility{close_quotes} alleles inherited from the nondisjoining parent give increased likelihood of having the trait. Our mapping method is similar to identity-by-descent-based mapping methods using affected relative pairs and also to methods for mapping recessive traits using inbred individuals by looking for markers with greater than expected homozygosity by descent. In the trisomy case, one would take trisomic individuals and look for markers with greater than expected homozygosity in the chromosomes inherited from the nondisjoining parent. We present statistical methods for performing such a linkage analysis, including a test for linkage to a marker, a method for estimating the distance from the marker to the trait gene, a confidence interval for that distance, and methods for computing power and sample sizes. We also resolve some practical issues involved in implementing the methods, including how to use partially informative markers and how to test candidate genes. 20 refs., 5 figs., 1 tab.

  3. Genetic linkage for Darier disease (keratosis follicularis)

    SciTech Connect

    Kennedy, J.L.; King, N.; Perkins, M.

    1995-01-30

    Darier disease is an autosomal dominant skin disorder characterized by abnormal keratinocyte adhesion. Recent data have provided evidence for linkage of the Darier disease locus to 12q23-24.1 in British families. We have carried out linkage analysis using the 12q markers D12S58, D12S84, D12S79, D12S86, PLA2, and D12S63 in 6 Canadian families. Pairwise linkage analysis generated positive lod scores at all 6 markers at various recombination fractions, and each family showed positive lod scores with more than one marker. The peak lod score in the multipoint analysis (Z{sub max}) was 5.5 in the interval between markers D12S58 and D12S84. These positive lod scores in North American families of varied European ancestry confirm the location of the Darier disease gene, and suggest genetic homogeneity. The future identification and sequencing of the gene responsible for Darier disease should lead to improved understanding of the disease and of keratinocyte adhesion in general. 22 refs., 2 figs., 2 tabs.

  4. A Novel Method for Estimating Linkage Maps

    PubMed Central

    Tan, Yuan-De; Fu, Yun-Xin

    2006-01-01

    The goal of linkage mapping is to find the true order of loci from a chromosome. Since the number of possible orders is large even for a modest number of loci, the problem of finding the optimal solution is known as a NP-hard problem or traveling salesman problem (TSP). Although a number of algorithms are available, many either are low in the accuracy of recovering the true order of loci or require tremendous amounts of computational resources, thus making them difficult to use for reconstructing a large-scale map. We developed in this article a novel method called unidirectional growth (UG) to help solve this problem. The UG algorithm sequentially constructs the linkage map on the basis of novel results about additive distance. It not only is fast but also has a very high accuracy in recovering the true order of loci according to our simulation studies. Since the UG method requires n − 1 cycles to estimate the ordering of n loci, it is particularly useful for estimating linkage maps consisting of hundreds or even thousands of linked codominant loci on a chromosome. PMID:16783016

  5. 'Linkage' pharmaceutical evergreening in Canada and Australia.

    PubMed

    Faunce, Thomas A; Lexchin, Joel

    2007-01-01

    'Evergreening' is not a formal concept of patent law. It is best understood as a social idea used to refer to the myriad ways in which pharmaceutical patent owners utilise the law and related regulatory processes to extend their high rent-earning intellectual monopoly privileges, particularly over highly profitable (either in total sales volume or price per unit) 'blockbuster' drugs. Thus, while the courts are an instrument frequently used by pharmaceutical brand name manufacturers to prolong their patent royalties, 'evergreening' is rarely mentioned explicitly by judges in patent protection cases. The term usually refers to threats made to competitors about a brand-name manufacturer's tactical use of pharmaceutical patents (including over uses, delivery systems and even packaging), not to extension of any particular patent over an active product ingredient. This article focuses in particular on the 'evergreening' potential of so-called 'linkage' provisions, imposed on the regulatory (safety, quality and efficacy) approval systems for generic pharmaceuticals of Canada and Australia, by specific articles in trade agreements with the US. These 'linkage' provisions have also recently appeared in the Korea-US Free Trade Agreement (KORUSFTA). They require such drug regulators to facilitate notification of, or even prevent, any potential patent infringement by a generic pharmaceutical manufacturer. This article explores the regulatory lessons to be learnt from Canada's and Australia's shared experience in terms of minimizing potential adverse impacts of such 'linkage evergreening' provisions on drug costs and thereby potentially on citizen's access to affordable, essential medicines. PMID:17543113

  6. Highly sensitive and multiplexed platforms for allergy diagnostics

    NASA Astrophysics Data System (ADS)

    Monroe, Margo R.

    Allergy is a disorder of the immune system caused by an immune response to otherwise harmless environmental allergens. Currently 20% of the US population is allergic and 90% of pediatric patients and 60% of adult patients with asthma have allergies. These percentages have increased by 18.5% in the past decade, with predicted similar trends for the future. Here we design sensitive, multiplexed platforms to detect allergen-specific IgE using the Interferometric Reflectance Imaging Sensor (IRIS) for various clinical settings. A microarray platform for allergy diagnosis allows for testing of specific IgE sensitivity to a multitude of allergens, while requiring only small volumes of patient blood sample. However, conventional fluorescent microarray technology is limited by i) the variation of probe immobilization, which hinders the ability to make quantitative, assertive, and statistically relevant conclusions necessary in immunodiagnostics and ii) the use of fluorophore labels, which is not suitable for some clinical applications due to the tendency of fluorophores to stick to blood particulates and require daily calibration methods. This calibrated fluorescence enhancement (CaFE) method integrates the low magnification modality of IRIS with enhanced fluorescence sensing in order to directly correlate immobilized probe (major allergens) density to allergen-specific IgE in patient serum. However, this platform only operates in processed serum samples, which is not ideal for point of care testing. Thus, a high magnification modality of IRIS was adapted as an alternative allergy diagnostic platform to automatically discriminate and size single nanoparticles bound to specific IgE in unprocessed, characterized human blood and serum samples. These features make IRIS an ideal candidate for clinical and diagnostic applications, such a POC testing. The high magnification (nanoparticle counting) modality in conjunction with low magnification of IRIS in a combined instrument

  7. Genome-wide linkage analyses of two repetitive behavior phenotypes in Utah pedigrees with autism spectrum disorders

    PubMed Central

    2010-01-01

    Background It has been suggested that efforts to identify genetic risk markers of autism spectrum disorder (ASD) would benefit from the analysis of more narrowly defined ASD phenotypes. Previous research indicates that 'insistence on sameness' (IS) and 'repetitive sensory-motor actions' (RSMA) are two factors within the ASD 'repetitive and stereotyped behavior' domain. The primary aim of this study was to identify genetic risk markers of both factors to allow comparison of those markers with one another and with markers found in the same set of pedigrees using ASD diagnosis as the phenotype. Thus, we empirically addresses the possibilities that more narrowly defined phenotypes improve linkage analysis signals and that different narrowly defined phenotypes are associated with different loci. Secondary aims were to examine the correlates of IS and RSMA and to assess the heritability of both scales. Methods A genome-wide linkage analysis was conducted with a sample of 70 multiplex ASD pedigrees using IS and RSMA as phenotypes. Genotyping services were provided by the Center for Inherited Disease Research using the 6 K single nucleotide polymorphism linkage panel. Analysis was done using the multipoint linkage software program MCLINK, a Markov chain Monte Carlo (MCMC) method that allows for multilocus linkage analysis on large extended pedigrees. Results Genome-wide significance was observed for IS at 2q37.1-q37.3 (dominant model heterogeneity lod score (hlod) 3.42) and for RSMA at 15q13.1-q14 (recessive model hlod 3.93). We found some linkage signals that overlapped and others that were not observed in our previous linkage analysis of the ASD phenotype in the same pedigrees, and regions varied in the range of phenotypes with which they were linked. A new finding with respect to IS was that it is positively associated with IQ if the IS-RSMA correlation is statistically controlled. Conclusions The finding that IS and RSMA are linked to different regions that only

  8. Multiplex Flow Cytometry Barcoding and Antibody Arrays Identify Surface Antigen Profiles of Primary and Metastatic Colon Cancer Cell Lines

    PubMed Central

    Sukhdeo, Kumar; Paramban, Rosanto I.; Vidal, Jason G.; Elia, Jeanne; Martin, Jody; Rivera, Maricruz; Carrasco, Daniel R.; Jarrar, Awad; Kalady, Matthew F.; Carson, Christian T.; Balderas, Robert; Hjelmeland, Anita B.; Lathia, Justin D.; Rich, Jeremy N.

    2013-01-01

    Colon cancer is a deadly disease affecting millions of people worldwide. Current treatment challenges include management of disease burden as well as improvements in detection and targeting of tumor cells. To identify disease state-specific surface antigen signatures, we combined fluorescent cell barcoding with high-throughput flow cytometric profiling of primary and metastatic colon cancer lines (SW480, SW620, and HCT116). Our multiplexed technique offers improvements over conventional methods by permitting the simultaneous and rapid screening of cancer cells with reduced effort and cost. The method uses a protein-level analysis with commercially available antibodies on live cells with intact epitopes to detect potential tumor-specific targets that can be further investigated for their clinical utility. Multiplexed antibody arrays can easily be applied to other tumor types or pathologies for discovery-based approaches to target identification. PMID:23308131

  9. Linkage and Linkage Disequilibrium Scan for Autism Loci in an Extended Pedigree from Finland

    PubMed Central

    Kilpinen, Helena; Ylisaukko-oja, Tero; Rehnström, Karola; Gaál, Emilia; Turunen, Joni A.; Kempas, Elli; von Wendt, Lennart; Varilo, Teppo; Peltonen, Leena

    2009-01-01

    Population isolates, such as Finland, have proved beneficial in mapping rare causative genetic variants due to a limited number of founders resulting in reduced genetic heterogeneity and extensive linkage disequilibrium. We have here used this special opportunity to identify rare alleles in autism by genealogically tracing 20 autism families into one extended pedigree with verified genealogical links reaching back to the 17th century. In this unique pedigree we performed a dense microsatellite marker genome-wide scan of linkage and linkage disequilibrium, and followed initial findings with extensive fine-mapping. We identified a putative autism susceptibility locus at 19p13.3, and obtained further evidence for previously identified loci at 1q23 and 15q11-13. Most promising candidate genes were TLE2 and TLE6 genes clustered at 19p13 and ATP1A2 at 1q23. PMID:19454485

  10. Miniaturized, multiplexed readout of droplet-based microfluidic assays using time-domain modulation†

    PubMed Central

    Muluneh, Melaku; Kim, Bawul; Buchsbaum, Gershon

    2015-01-01

    Recent advances in microfluidics to generate and control picoliter emulsions of water in oil have enabled ultra-sensitive assays for small molecules, proteins, nucleic acids, and cells. Unfortunately, the conventional fluorescence detection used to measure the outcome of these droplet-based assays has not proven suited to match the time and space multiplexing capabilities of microfluidic systems. To address this challenge, we developed an in-flow fluorescence detection platform that enables multiple streams of droplets to be monitored using only a single photodetector and no lenses. The key innovation of our technology is the amplitude modulation of the signal from fluorescent droplets using distinct micro-patterned masks for each channel. By taking advantage of the high bandwidth of electronics, our technique enables the velocity-independent recovery of weak fluorescent signals (SNR ≪ 1) using only simple hardware, obviating the need for lasers, bulky detectors, and complex fluid control. We demonstrated a handheld-sized device that simultaneously monitors four independent channels with the capability to be scaled-up to more than sixteen, limited primarily by the droplet density. PMID:25311204

  11. High thickness acrylamide photopolymer for peristrophic multiplexing

    NASA Astrophysics Data System (ADS)

    Ortuño, M.; Fernández, E.; Márquez, A.; Gallego, S.; Neipp, C.; Pascual, I.

    2006-05-01

    The acrylamide photolymers are considered interesting materials for holographic media. They have high diffraction efficiency (ratio of the intensities of the diffracted and the incident beams), an intermediate energetic sensitivity among other materials and post-processing steps are not necessary, therefore the media is not altered. The layers of these materials, about 1 mm thick, are a suitable media for recording many diffraction gratings in the same volume of photopolymer using peristrophic multiplexing technique, with great practical importance in the field of holographic memories type WORM (write once read many). In this work we study the recording of diffraction gratings by peristrophic multiplexing with axis of rotation perpendicular to the recording media. The photopolymer is composed of acrylamide as the polymerizable monomer, triethanolamine as radical generator, yellowish eosin as sensitizer and a binder of polyvinyl alcohol. We analyze the holographic behaviour of the material during recording and reconstruction of diffraction gratings using a continuous Nd:YAG laser (532 nm) at an intensity of 5 mW/cm2 as recording laser. The response of the material is monitored after recording with an He-Ne laser. We study the recording process of unslanted diffraction gratings of 1125 lines/mm. The diffraction efficiency of each hologram is seen to decrease as the number of holograms recorded increases, due to consumption of the available dynamic range, in a constant exposure scheduling. It can be seen that the photopolymer works well with high energy levels, without excessive dispersion of light by noise gratings. In order to homogenize the diffraction efficiency of each hologram we use the method proposed by Pu. This method is designed to share all or part of the avaliable dynamic range of the recording material among the holograms to be multiplexed. Using exposure schedules derived from this method we have used 3 scheduling recordings from the algorithm used

  12. Multiplexed Western Blotting Using Microchip Electrophoresis.

    PubMed

    Jin, Shi; Furtaw, Michael D; Chen, Huaxian; Lamb, Don T; Ferguson, Stephen A; Arvin, Natalie E; Dawod, Mohamed; Kennedy, Robert T

    2016-07-01

    Western blotting is a commonly used protein assay that combines the selectivity of electrophoretic separation and immunoassay. The technique is limited by long time, manual operation with mediocre reproducibility, and large sample consumption, typically 10-20 μg per assay. Western blots are also usually used to measure only one protein per assay with an additional housekeeping protein for normalization. Measurement of multiple proteins is possible; however, it requires stripping membranes of antibody and then reprobing with a second antibody. Miniaturized alternatives to Western blot based on microfluidic or capillary electrophoresis have been developed that enable higher-throughput, automation, and greater mass sensitivity. In one approach, proteins are separated by electrophoresis on a microchip that is dragged along a polyvinylidene fluoride membrane so that as proteins exit the chip they are captured on the membrane for immunoassay. In this work, we improve this method to allow multiplexed protein detection. Multiple injections made from the same sample can be deposited in separate tracks so that each is probed with a different antibody. To further enhance multiplexing capability, the electrophoresis channel dimensions were optimized for resolution while keeping separation and blotting times to less than 8 min. Using a 15 μm deep × 50 μm wide × 8.6 cm long channel, it is possible to achieve baseline resolution of proteins that differ by 5% in molecular weight, e.g., ERK1 (44 kDa) from ERK2 (42 kDa). This resolution allows similar proteins detected by cross-reactive antibodies in a single track. We demonstrate detection of 11 proteins from 9 injections from a single Jurkat cell lysate sample consisting of 400 ng of total protein using this procedure. Thus, multiplexed Western blots are possible without cumbersome stripping and reprobing steps. PMID:27270033

  13. Hardware Counter Multiplexing V1.2

    Energy Science and Technology Software Center (ESTSC)

    2000-10-13

    The Hardware Counter Multiplexer works with the built-in counter registers on computer processors. These counters record varius low-level events as software runs, but they can cannot record all possible events at the same time. This software helps work around that limitation by counting a series of different events in sequence over a period of time. This in turn allows programmers to measure interesting combinations of events, rather than single events. The software is designed tomore » work with multithreaded or single-threaded programs.« less

  14. Multiplexed microsatellite markers for seven Metarhizium species.

    PubMed

    Mayerhofer, Johanna; Lutz, Andy; Widmer, Franco; Rehner, Stephen A; Leuchtmann, Adrian; Enkerli, Jürg

    2015-11-01

    Cross-species transferability of 41 previously published simple sequence repeat (SSR) markers was assessed for 11 species of the entomopathogenic fungus Metarhizium. A collection of 65 Metarhizium strains including all 54 used in a recent phylogenetic revision of the genus were characterized. Between 15 and 34 polymorphic SSR markers produced scorable PCR amplicons in seven species, including M. anisopliae, M. brunneum, M. guizhouense, M. lepidiotae, M. majus, M. pingshaense, and M. robertsii. To provide genotyping tools for concurrent analysis of these seven species fifteen markers grouped in five multiplex pools were selected based on high allelic diversity and easy scorability of SSR chromatograms. PMID:26407949

  15. Two wavelength division multiplexing WAN trials

    SciTech Connect

    Lennon, W.J.; Thombley, R.L.

    1995-01-20

    Lawrence Livermore National Laboratory, as a super-user, supercomputer, and super-application site, is anticipating the future bandwidth and protocol requirements necessary to connect to other such sites as well as to connect to remote-sited control centers and experiments. In this paper the authors discuss their vision of the future of Wide Area Networking, describe the plans for a wavelength division multiplexed link connecting Livermore with the University of California at Berkeley and describe plans for a transparent, {approx} 10 Gb/s ring around San Francisco Bay.

  16. Replicator dynamics with diffusion on multiplex networks

    NASA Astrophysics Data System (ADS)

    Requejo, R. J.; Díaz-Guilera, A.

    2016-08-01

    In this study we present an extension of the dynamics of diffusion in multiplex graphs, which makes the equations compatible with the replicator equation with mutations. We derive an exact formula for the diffusion term, which shows that, while diffusion is linear for numbers of agents, it is necessary to account for nonlinear terms when working with fractions of individuals. We also derive the transition probabilities that give rise to such macroscopic behavior, completing the bottom-up description. Finally, it is shown that the usual assumption of constant population sizes induces a hidden selective pressure due to the diffusive dynamics, which favors the increase of fast diffusing strategies.

  17. A Whole-Genome Scan and Fine-Mapping Linkage Study of Auditory-Visual Synesthesia Reveals Evidence of Linkage to Chromosomes 2q24, 5q33, 6p12, and 12p12

    PubMed Central

    Asher, Julian E.; Lamb, Janine A.; Brocklebank, Denise; Cazier, Jean-Baptiste; Maestrini, Elena; Addis, Laura; Sen, Mallika; Baron-Cohen, Simon; Monaco, Anthony P.

    2009-01-01

    Synesthesia, a neurological condition affecting between 0.05%–1% of the population, is characterized by anomalous sensory perception and associated alterations in cognitive function due to interference from synesthetic percepts. A stimulus in one sensory modality triggers an automatic, consistent response in either another modality or a different aspect of the same modality. Familiality studies show evidence of a strong genetic predisposition; whereas initial pedigree analyses supported a single-gene X-linked dominant mode of inheritance with a skewed F:M ratio and a notable absence of male-to-male transmission, subsequent analyses in larger samples indicated that the mode of inheritance was likely to be more complex. Here, we report the results of a whole-genome linkage scan for auditory-visual synesthesia with 410 microsatellite markers at 9.05 cM density in 43 multiplex families (n = 196) with potential candidate regions fine-mapped at 5 cM density. Using NPL and HLOD analysis, we identified four candidate regions. Significant linkage at the genome-wide level was detected to chromosome 2q24 (HLOD = 3.025, empirical genome-wide p = 0.047). Suggestive linkage was found to chromosomes 5q33, 6p12, and 12p12. No support was found for linkage to the X chromosome; furthermore, we have identified two confirmed cases of male-to-male transmission of synesthesia. Our results demonstrate that auditory-visual synesthesia is likely to be an oligogenic disorder subject to multiple modes of inheritance and locus heterogeneity. This study comprises a significant step toward identifying the genetic substrates underlying synesthesia, with important implications for our understanding of the role of genes in human cognition and perception. PMID:19200526

  18. DNA sequencing using fluorescence background electroblotting membrane

    DOEpatents

    Caldwell, K.D.; Chu, T.J.; Pitt, W.G.

    1992-05-12

    A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through amino groups contained on the surface. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to the target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membranes may be reprobed numerous times. No Drawings

  19. DNA sequencing using fluorescence background electroblotting membrane

    DOEpatents

    Caldwell, Karin D.; Chu, Tun-Jen; Pitt, William G.

    1992-01-01

    A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through said smino groups contained on the surface thereof. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to said target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membrances may be reprobed numerous times.

  20. Preliminary study of visual effect of multiplex hologram

    NASA Astrophysics Data System (ADS)

    Fu, Huaiping; Xiong, Bingheng; Yang, Hong; Zhang, Xueguo

    2004-06-01

    The process of any movement of real object can be recorded and displayed by a multiplex holographic stereogram. An embossing multiplex holographic stereogram and a multiplex rainbow holographic stereogram have been made by us, the multiplex rainbow holographic stereogram reconstructs the dynamic 2D line drawing of speech organs, the embossing multiplex holographic stereogram reconstructs the process of an old man drinking water. In this paper, we studied the visual result of an embossing multiplex holographic stereogram made with 80 films of 2-D pictures. Forty-eight persons of aged from 13 to 67 were asked to see the hologram and then to answer some questions about the feeling of viewing. The results indicate that this kind of holograms could be accepted by human visual sense organ without any problem. This paper also discusses visual effect of the multiplex holography stereograms base on visual perceptual psychology. It is open out that the planar multiplex holograms can be recorded and present the movement of real animal and object. Not only have the human visual perceptual constancy for shape, just as that size, color, etc... but also have visual perceptual constancy for binocular parallax.

  1. 47 CFR 73.319 - FM multiplex subcarrier technical standards.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false FM multiplex subcarrier technical standards. 73.319 Section 73.319 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES FM Broadcast Stations § 73.319 FM multiplex subcarrier technical standards. (a) The technical specifications in...

  2. 47 CFR 73.319 - FM multiplex subcarrier technical standards.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false FM multiplex subcarrier technical standards. 73.319 Section 73.319 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES FM Broadcast Stations § 73.319 FM multiplex subcarrier technical standards. (a) The technical specifications in...

  3. A Microsatellite Genetic Linkage Map for Xiphophorus

    PubMed Central

    Walter, R. B.; Rains, J. D.; Russell, J. E.; Guerra, T. M.; Daniels, C.; Johnston, Dennis A.; Kumar, Jay; Wheeler, A.; Kelnar, K.; Khanolkar, V. A.; Williams, E. L.; Hornecker, J. L.; Hollek, L.; Mamerow, M. M.; Pedroza, A.; Kazianis, S.

    2004-01-01

    Interspecies hybrids between distinct species of the genus Xiphophorus are often used in varied research investigations to identify genomic regions associated with the inheritance of complex traits. There are 24 described Xiphophorus species and a greater number of pedigreed strains; thus, the number of potential interspecies hybrid cross combinations is quite large. Previously, select Xiphophorus experimental crosses have been shown to exhibit differing characteristics between parental species and among the hybrid fishes derived from crossing them, such as widely differing susceptibilities to chemical or physical agents. For instance, genomic regions harboring tumor suppressor and oncogenes have been identified via linkage association of these loci with a small set of established genetic markers. The power of this experimental strategy is related to the number of genetic markers available in the Xiphophorus interspecies cross of interest. Thus, we have undertaken the task of expanding the suite of easily scored markers by characterization of Xiphophorus microsatellite sequences. Using a cross between Xiphophorus maculatus and X. andersi, we report a linkage map predominantly composed of microsatellite markers. All 24 acrocentric chromosome sets of Xiphophorus are represented in the assembled linkage map with an average intergenomic distance of 7.5 cM. Since both male and female F1 hybrids were used to produce backcross progeny, these recombination rates were compared between “male” and “female” maps. Although several genomic regions exhibit differences in map length, male- and female-derived maps are similar. Thus Xiphophorus, in contrast to zebrafish, Danio rerio, and several other vertebrate species, does not show sex-specific differences in recombination. The microsatellite markers we report can be easily adapted to any Xiphophorus interspecies and some intraspecies crosses, and thus provide a means to directly compare results derived from independent

  4. Flexible wavelength de-multiplexer for elastic optical networking.

    PubMed

    Zhou, Rui; Gutierrez Pascual, M Deseada; Anandarajah, Prince M; Shao, Tong; Smyth, Frank; Barry, Liam P

    2016-05-15

    We report an injection locked flexible wavelength de-multiplexer (de-mux) that shows 24-h frequency stability of 1 kHz for optical comb-based elastic optical networking applications. We demonstrate 50 GHz, 87.5 GHz equal spacing and 6.25G-25G-50 GHz, 75G-50G-100 GHz unequal spacing for the de-multiplexer outputs. We also implement an unequally spaced (75G-50G-100 GHz), mixed symbol rate (12.5 GBaud and 40 GBaud) and modulation format (polarization division multiplexed quadrature phase shift keying and on-off keying) wavelength division multiplexed transmission system using the de-multiplexer outputs. The results show 0.6 dB receiver sensitivity penalty, at 7% hard decision forward error correction coding limit, of the 100 km transmitted de-mux outputs when compared to comb source seeding laser back-to-back. PMID:27176972

  5. Cascading processes on multiplex networks: Impact of weak layers

    NASA Astrophysics Data System (ADS)

    Lee, Kyu-Min; Goh, Kwang-Il

    Many real-world complex systems such as biological and socio-technological systems consist of manifold layers in multiplex networks. The multiple network layers give rise to the nonlinear effect for the emergent dynamics of systems. Especially, the weak layers plays the significant role in nonlinearity of multiplex networks, which can be neglected in single-layer network framework overlaying all layers. Here we present a simple model of cascades on multiplex networks of heterogeneous layers. The model is simulated on the multiplex network of international trades. We found that the multiplex model produces more catastrophic cascading failures which were the result of collective behaviors from coupling layers rather than the simple summation effect. Therefore risks can be systematically underestimated in simply overlaid network system because the impact of weak layers is overlooked. Our simple theoretical model would have some implications to investigate and design optimal real-world complex systems.

  6. Wavelength division multiplexing WDM, CWDM and DWDM applications

    NASA Astrophysics Data System (ADS)

    Vasile, Irina Bristena; Vasile, Alexandru; Luciana, Stan; Tache, Mihaela

    2007-05-01

    The fiber optics has become the most preferred media for this very large data traffic. TDM (Time Division Multiplexing) has been the most practical method to divide the significant capacity of a single fiber optics into several communication channels. This technology is still limited by the large complexity of high-flow modulation and multiplexing equipment. Presently, a complementary approach proves its potential: Wavelength-Division Multiplexing (WDM). The evolution of WDM allows now a very small spacing between channels wavelength, in nm, generating DWDM (Dense Wavelength Division Multiplexing). The networks with individual fibers including more than 100 independent optic channels, as well as those with bidirectional flow are already available on the market. CWDM (Coarse Wavelength Division Multiplexing) represents an economical application of a mature technology which may provide options where the capacity of fibers is limited.

  7. Fluorescence of dental porcelain.

    PubMed

    Monsénégo, G; Burdairon, G; Clerjaud, B

    1993-01-01

    This study of the fluorescence of natural enamel and of dental ceramics shows the fluorescence of ceramics not containing rare earths decreases when the color saturation increases; the fluorescence of samples of the same shade guide are not homogenous; some guides show a strong green fluorescence; and two shade guides of the same origin can present completely different fluorescence. The cementing medium can affect the fluorescence of a ceramic prosthesis. PMID:8455155

  8. Carburetion system including an adjustable throttle linkage

    SciTech Connect

    Du Bois, C.G.; Falig, J.D.

    1986-03-25

    A throttle linkage assembly is described comprising a throttle shaft rotatable about a throttle shaft axis between an idle position and a wide open throttle position, a throttle plate fixed on the throttle shaft, a driven lever pivotable about the throttle shaft axis between various angles relative to the throttle plate, and means for fixing the driven lever at a selected angle relative to the throttle plate an adjustment lever fixedly connected to the throttle adjacent the driven lever, and means for releasably securing the driven lever to the adjustment lever.

  9. Linkage mapping bovine EST-based SNP

    PubMed Central

    Snelling, Warren M; Casas, Eduardo; Stone, Roger T; Keele, John W; Harhay, Gregory P; Bennett, Gary L; Smith, Timothy PL

    2005-01-01

    Background Existing linkage maps of the bovine genome primarily contain anonymous microsatellite markers. These maps have proved valuable for mapping quantitative trait loci (QTL) to broad regions of the genome, but more closely spaced markers are needed to fine-map QTL, and markers associated with genes and annotated sequence are needed to identify genes and sequence variation that may explain QTL. Results Bovine expressed sequence tag (EST) and bacterial artificial chromosome (BAC)sequence data were used to develop 918 single nucleotide polymorphism (SNP) markers to map genes on the bovine linkage map. DNA of sires from the MARC reference population was used to detect SNPs, and progeny and mates of heterozygous sires were genotyped. Chromosome assignments for 861 SNPs were determined by twopoint analysis, and positions for 735 SNPs were established by multipoint analyses. Linkage maps of bovine autosomes with these SNPs represent 4585 markers in 2475 positions spanning 3058 cM . Markers include 3612 microsatellites, 913 SNPs and 60 other markers. Mean separation between marker positions is 1.2 cM. New SNP markers appear in 511 positions, with mean separation of 4.7 cM. Multi-allelic markers, mostly microsatellites, had a mean (maximum) of 216 (366) informative meioses, and a mean 3-lod confidence interval of 3.6 cM Bi-allelic markers, including SNP and other marker types, had a mean (maximum) of 55 (191) informative meioses, and were placed within a mean 8.5 cM 3-lod confidence interval. Homologous human sequences were identified for 1159 markers, including 582 newly developed and mapped SNP. Conclusion Addition of these EST- and BAC-based SNPs to the bovine linkage map not only increases marker density, but provides connections to gene-rich physical maps, including annotated human sequence. The map provides a resource for fine-mapping quantitative trait loci and identification of positional candidate genes, and can be integrated with other data to guide and

  10. Multiplexed Colorimetric Solid-Phase Extraction

    NASA Technical Reports Server (NTRS)

    Gazda, Daniel B.; Fritz, James S.; Porter, Marc D.

    2009-01-01

    Multiplexed colorimetric solid-phase extraction (MC-SPE) is an extension of colorimetric solid-phase extraction (C-SPE) an analytical platform that combines colorimetric reagents, solid phase extraction, and diffuse reflectance spectroscopy to quantify trace analytes in water. In CSPE, analytes are extracted and complexed on the surface of an extraction membrane impregnated with a colorimetric reagent. The analytes are then quantified directly on the membrane surface using a handheld diffuse reflectance spectrophotometer. Importantly, the use of solid-phase extraction membranes as the matrix for impregnation of the colorimetric reagents creates a concentration factor that enables the detection of low concentrations of analytes in small sample volumes. In extending C-SPE to a multiplexed format, a filter holder that incorporates discrete analysis channels and a jig that facilitates the concurrent operation of multiple sample syringes have been designed, enabling the simultaneous determination of multiple analytes. Separate, single analyte membranes, placed in a readout cartridge create unique, analyte-specific addresses at the exit of each channel. Following sample exposure, the diffuse reflectance spectrum of each address is collected serially and the Kubelka-Munk function is used to quantify each water quality parameter via calibration curves. In a demonstration, MC-SPE was used to measure the pH of a sample and quantitate Ag(I) and Ni(II).

  11. Multiplexed quantification for data-independent acquisition.

    PubMed

    Minogue, Catherine E; Hebert, Alexander S; Rensvold, Jarred W; Westphall, Michael S; Pagliarini, David J; Coon, Joshua J

    2015-03-01

    Data-independent acquisition (DIA) strategies provide a sensitive and reproducible alternative to data-dependent acquisition (DDA) methods for large-scale quantitative proteomic analyses. Unfortunately, DIA methods suffer from incompatibility with common multiplexed quantification methods, specifically stable isotope labeling approaches such as isobaric tags and stable isotope labeling of amino acids in cell culture (SILAC). Here we expand the use of neutron-encoded (NeuCode) SILAC to DIA applications (NeuCoDIA), producing a strategy that enables multiplexing within DIA scans without further convoluting the already complex MS(2) spectra. We demonstrate duplex NeuCoDIA analysis of both mixed-ratio (1:1 and 10:1) yeast and mouse embryo myogenesis proteomes. Analysis of the mixed-ratio yeast samples revealed the strong accuracy and precision of our NeuCoDIA method, both of which were comparable to our established MS(1)-based quantification approach. NeuCoDIA also uncovered the dynamic protein changes that occur during myogenic differentiation, demonstrating the feasibility of this methodology for biological applications. We consequently establish DIA quantification of NeuCode SILAC as a useful and practical alternative to DDA-based approaches. PMID:25621425

  12. Multiplexed protein profiling by sequential affinity capture.

    PubMed

    Ayoglu, Burcu; Birgersson, Elin; Mezger, Anja; Nilsson, Mats; Uhlén, Mathias; Nilsson, Peter; Schwenk, Jochen M

    2016-04-01

    Antibody microarrays enable parallelized and miniaturized analysis of clinical samples, and have proven to provide novel insights for the analysis of different proteomes. However, there are concerns that the performance of such direct labeling and single antibody assays are prone to off-target binding due to the sample context. To improve selectivity and sensitivity while maintaining the possibility to conduct multiplexed protein profiling, we developed a multiplexed and semi-automated sequential capture assay. This novel bead-based procedure encompasses a first antigen capture, labeling of captured protein targets on magnetic particles, combinatorial target elution and a read-out by a secondary capture bead array. We demonstrate in a proof-of-concept setting that target detection via two sequential affinity interactions reduced off-target contribution, while lowered background and noise levels, improved correlation to clinical values compared to single binder assays. We also compared sensitivity levels with single binder and classical sandwich assays, explored the possibility for DNA-based signal amplification, and demonstrate the applicability of the dual capture bead-based antibody microarray for biomarker analysis. Hence, the described concept enhances the possibilities for antibody array assays to be utilized for protein profiling in body fluids and beyond. PMID:26935855

  13. Multiplexing holograms in an acrylamide photopolymer

    NASA Astrophysics Data System (ADS)

    Fernández, Elena; Ortuño, Manuel; Márquez, Andrés; Gallego, Sergi; Pascual, Inmaculada

    2006-04-01

    A peristrophic multiplexing method is used to store various diffraction gratings at the same spot in the material. This material is formed of acrylamide photopolymers which are considered interesting materials for recording holographic memories. They have high diffraction efficiency (ratio between diffracted and incident beams), high energetic sensitivity and optical quality, and developing processes are not necessary. In this work, the photopolymer is composed of acrylamide (AA) as the polymerizable monomer, triethanolamine (TEA) as radical generator, N,N'methylene-bis-acrylamide (BMA) as crosslinker, yellowish eosin (YE) as sensitizer and a binder of polyvinyl alcohol (PVA). The layers of material obtained are approximately 1 mm thick. Using holographic recording schedules, the exposure energy each hologram should receive in order to achieve uniform diffraction efficiency is optimized. The purpose of these recording schedules is to enable full advantage to be taken of the whole dynamic range of the material and to share it between the individual holograms. The Scheduled Exposure Method (SEM) and the Incremental Exposure Method (IEM) are the two multiplexing schedules used to determine the recording times. Having determined these times, the results obtained with both methods are compared to ascertain which method enables the greatest number of holograms to be recorded with the highest, most uniform diffraction efficiencies.

  14. Mesoscopic quantum multiplex for channeling bunches

    NASA Astrophysics Data System (ADS)

    Shen, Jing

    1998-09-01

    (1) Bogacz-Cline channeling is an interesting idea that can transform a bunch of low particle intensity to a collider of high luminosity but it was maintained as impossible to carry out because of three technical problems. (2) The first of which is discussed in this paper, and it is how to get billions particles from each bunch to enter into and channel through a single crystal channel. (3) Two basic difficulties of entrance are discussed in this paper. The first is due to the Heisenberg's uncertainty, and the second is the dimension reduction of a beam bunch in crystal from 3D to 1D. (4) To overcome these difficulties, a hybrid device named Mesoscopic Quantum Multiplex (MQM) is designed to achieve entrance and channeling. It is a quantum generalization of classical multiplex in detector readout electronics for the classical-quantum interface. It is made by nano-crystalline technology. (5) The MQM can channel the Richter-Kimura-Takada flat e± beams of NLC-JLC, and low emittance p or heavy ion beams as well as the Bogacz-Cline μ± beams, and the Nagamine-Chu cool μ± beams.

  15. Pneumatic Valve Operated by Multiplex Pneumatic Transmission

    NASA Astrophysics Data System (ADS)

    Nishioka, Yasutaka; Suzumori, Koichi; Kanda, Takefumi; Wakimoto, Shuichi

    A pneumatic system has several advantages, which are cheapness, lightweight, and reliability to human and environment. These advantages are adapted to some research areas, such as industrial lines, medical and nursing cares, and rehabilitation tools. However, the pneumatic system needs several devices; compressor, air tube, and control valve. This research aim to downsize pneumatic system. In this paper, a new method of multiplex pneumatic transmission for multi-pneumatic servo system is proposed. The valve for this system consists of two vibrators supported by springs, which was designed with simple and cheap structure. The working principle of the valve is vibrators resonance from multiplex pneumatic transmission and it is possible to work as ON/OFF valves without electric wire. Dynamic simulation was used to confirm the working principle of the resonance driving system. A prototype device confirming the principle was designed and developed based on the simulation. The experiments show that this new control system works very well to control two separated valves through single pneumatic tube.

  16. Multiplexed microsatellite recovery using massively parallel sequencing

    USGS Publications Warehouse

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  17. Controllability of asynchronous Boolean multiplex control networks

    NASA Astrophysics Data System (ADS)

    Luo, Chao; Wang, Xingyuan; Liu, Hong

    2014-09-01

    In this article, the controllability of asynchronous Boolean multiplex control networks (ABMCNs) is studied. First, the model of Boolean multiplex control networks under Harvey' asynchronous update is presented. By means of semi-tensor product approach, the logical dynamics is converted into linear representation, and a generalized formula of control-depending network transition matrices is achieved. Second, a necessary and sufficient condition is proposed to verify that only control-depending fixed points of ABMCNs can be controlled with probability one. Third, using two types of controls, the controllability of system is studied and formulae are given to show: (a) when an initial state is given, the reachable set at time s under a group of specified controls; (b) the reachable set at time s under arbitrary controls; (c) the specific probability values from a given initial state to destination states. Based on the above formulae, an algorithm to calculate overall reachable states from a specified initial state is presented. Moreover, we also discuss an approach to find the particular control sequence which steers the system between two states with maximum probability. Examples are shown to illustrate the feasibility of the proposed scheme.

  18. Multiplexed Quantification for Data-Independent Acquisition

    PubMed Central

    Minogue, Catherine E.; Hebert, Alexander S.; Rensvold, Jarred W.; Westphall, Michael S.; Pagliarini, David J.; Coon, Joshua J.

    2015-01-01

    Data-independent acquisition (DIA) strategies provide a sensitive and reproducible alternative to data-dependent acquisition (DDA) methods for large-scale quantitative proteomic analyses. Unfortunately, DIA methods suffer from incompatibility with common multiplexed quantification methods, specifically stable isotope labeling approaches such as isobaric tags and stable isotope labeling of amino acids in cell culture (SILAC). Here we expand the use of neutron-encoded (NeuCode) SILAC to DIA applications (NeuCoDIA), producing a strategy that enables multiplexing within DIA scans without further convoluting the already complex MS2 spectra. We demonstrate duplex NeuCoDIA analysis of both mixed-ratio (1:1 and 10:1) yeast and mouse embryo myogenesis proteomes. Analysis of the mixed-ratio yeast samples revealed the strong accuracy and precision of our NeuCoDIA method, both of which were comparable to our established MS1-based quantification approach. NeuCoDIA also uncovered the dynamic protein changes that occur during myogenic differentiation, demonstrating the feasibility of this methodology for biological applications. We consequently establish DIA quantification of NeuCode SILAC as a useful and practical alternative to DDA-based approaches. PMID:25621425

  19. Dispersion-reduction technique using subcarrier multiplexing

    SciTech Connect

    Sargis, P.D.; Haigh, R.E.; McCammon, K.G.

    1995-10-18

    We have developed a novel dispersion-reduction technique using subcarrier multiplexing (SCM) which permits the transmission of multiple 2.5 Gbit/s data channels over hundreds of kilometers of conventional fiber-optic cable with negligible dispersion. Using a lithium niobate external modulator having a modulation bandwidth of 20 GHz, we are able to multiplex several high-speed data channels at a single wavelength. At the receiving end, we demultiplex the data and detect each channel using a 2-GHz bandwidth optical detector. All of the hardware in our system consists of off-the-shelf components and can be integrated to reduce the overall cost. We demonstrated our dispersion-reduction technique in a recent field trial by transmitting two 2.5 Gbit/s data channels over 90 km of commercially-installed single-mode fiber, followed by 210 km of spooled fiber. For comparison, we substituted the 300 km of fiber with equivalent optical attenuation. We also ran computer simulations to evaluate link behavior. Technical details and field trial results will be presented.

  20. Directing fluorescence with plasmonic and photonic structures.

    PubMed

    Dutta Choudhury, Sharmistha; Badugu, Ramachandram; Lakowicz, Joseph R

    2015-08-18

    potential in controlling and steering fluorescence beams. Some representative studies by other research groups with various nanoantenna structures are described. While there are complexities to near-field interactions of fluorescence with plasmonic and photonic structures, there are also many exciting possibilities. The routing of each emission wavelength along a specific direction with a given angular width and polarization will allow spatial and spectral multiplexing. Directional emission close to surface normal will be particularly useful for microscopy and array-based studies. Application-specific angular emission patterns can be obtained by varying the design parameters of the plasmonic/photonic substrates in a flexible manner. We anticipate that the ability to control the flow of emitted light in the nanoscale will lead to the development of a new generation of fluorescence-based assays, instrumentation, portable diagnostics, and emissive devices. PMID:26168343

  1. Constructing a linkage-linkage disequilibrium map using dominant-segregating markers.

    PubMed

    Zhu, Xuli; Dong, Leiming; Jiang, Libo; Li, Huan; Sun, Lidan; Zhang, Hui; Yu, Weiwu; Liu, Haokai; Dai, Wensheng; Zeng, Yanru; Wu, Rongling

    2016-02-01

    The relationship between linkage disequilibrium (LD) and recombination fraction can be used to infer the pattern of genetic variation and evolutionary process in humans and other systems. We described a computational framework to construct a linkage-LD map from commonly used biallelic, single-nucleotide polymorphism (SNP) markers for outcrossing plants by which the decline of LD is visualized with genetic distance. The framework was derived from an open-pollinated (OP) design composed of plants randomly sampled from a natural population and seeds from each sampled plant, enabling simultaneous estimation of the LD in the natural population and recombination fraction due to allelic co-segregation during meiosis. We modified the framework to infer evolutionary pasts of natural populations using those marker types that are segregating in a dominant manner, given their role in creating and maintaining population genetic diversity. A sophisticated two-level EM algorithm was implemented to estimate and retrieve the missing information of segregation characterized by dominant-segregating markers such as single methylation polymorphisms. The model was applied to study the relationship between linkage and LD for a non-model outcrossing species, a gymnosperm species, Torreya grandis, naturally distributed in mountains of the southeastern China. The linkage-LD map constructed from various types of molecular markers opens a powerful gateway for studying the history of plant evolution. PMID:26622063

  2. High Density Brassica Oleracea Linkage Map: Identification of Useful New Linkages

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We constructed a 1257-marker, high-density genetic map of Brassica oleracea spanning 703cM in nine linkage groups, named LG1-LG9. It was developed in a F2 segregating population of 143 individuals obtained by crossing two double-haploid plants of broccoli Early-Big and cauliflower An-Nan Early. The...

  3. Mode- and wavelength-division multiplexed transmission using all-fiber mode multiplexer based on mode selective couplers.

    PubMed

    Chang, Sun Hyok; Chung, Hwan Seok; Ryf, Roland; Fontaine, Nicolas K; Han, Changyo; Park, Kyung Jun; Kim, Kwangjoon; Lee, Jyung Chan; Lee, Jong Hyun; Kim, Byoung Yoon; Kim, Young Kie

    2015-03-23

    We propose all-fiber mode multiplexer composed of two consecutive LP₁₁ mode selective couplers that allows for the multiplexing of LP₀₁ mode and two-fold degenerate LP₁₁ modes. We demonstrate WDM transmission of 32 wavelength channels with 100 GHz spacing, each carrying 3 modes of 120 Gb/s polarization division multiplexed quadrature phase shifted keying (PDM-QPSK) signal, over 560 km of few-mode fiber (FMF). Long distance transmission is achieved by 6×6 multiple-input multiple-output digital signal processing and modal differential group delay compensated link of FMF. The all-fiber mode multiplexer has considerable potential to be used in mode- and wavelength-division multiplexed transmission. PMID:25837061

  4. A nucleic acid strand displacement system for the multiplexed detection of tuberculosis-specific mRNA using quantum dots.

    PubMed

    Gliddon, H D; Howes, P D; Kaforou, M; Levin, M; Stevens, M M

    2016-05-21

    The development of rapid, robust and high performance point-of-care diagnostics relies on the advancement and combination of various areas of research. We have developed an assay for the detection of multiple mRNA molecules that combines DNA nanotechnology with fluorescent nanomaterials. The core switching mechanism is toehold-mediated strand displacement. We have used fluorescent quantum dots (QDs) as signal transducers in this assay, as they bring many benefits including bright fluorescence and multiplexing abilities. The resulting assay is capable of multiplexed detection of long RNA targets against a high concentration of background non-target RNA, with high sensitivity and specificity and limits of detection in the nanomolar range using only a standard laboratory plate reader. We demonstrate the utility of our QD-based system for the detection of two genes selected from a microarray-derived tuberculosis-specific gene expression signature. Levels of up- and downregulated gene transcripts comprising this signature can be combined to give a disease risk score, making the signature more amenable for use as a diagnostic marker. Our QD-based approach to detect these transcripts could pave the way for novel diagnostic assays for tuberculosis. PMID:27088427

  5. A linkage study of bipolar disorder

    SciTech Connect

    Kelsoe, J.R.; Sadovnick, A.D.; Remick, R.A.

    1994-09-01

    We are currently surveying the genome with polymorphic DNA markers in search of loci linked to bipolar disorder (manic-depressive illness) in three populations: 20 families (175 subjects) from the general North American population from San Diego (UCSD) and Vancouver (UBC); 3 Icelandic families (55 subjects); and an Old Order Amish pedigree 110 (118 subjects). Over 50 markers on chromosomes 1, 2, 5, 11, 17, 18, 20 and 21 have been examined. All markers have been tested in the Amish and Icelandic families, and a portion of them in the UCSD/UBC families, which we have only recently begun genotyping. The following candidate genes have been examined: {beta}-TSH, dopamine transporter (HDAT), {beta}2 adrenergic receptor (ADRB2), glucocorticoid type II receptor (GRL), D2 dopamine receptor, serotonin transporter (HSERT), and G{alpha}s G protein subunit (GNAS1). Linkage analysis was conducted using an autosomal dominant model with age-dependent reduced penetrance. Subjects with bipolar, schizoaffective, or recurrent major depressive disorders were considered affected. No significant evidence for linkage was obtained. Mildly positive lods ranging between 1.1 and 1.6 were obtained for three loci: D11S29, HDAT, and GRL.

  6. Constructing Linkage Disequilibrium Map with Iterative Approach

    NASA Astrophysics Data System (ADS)

    Ao, S. I.

    2008-05-01

    With recent advance of the genotyping single nucleotide polymorphisms (SNPs) in mass scale of high density in a candidate region of the human genome, the linkage disequilibrium analysis can offer a much higher resolution of the biological samples than the traditional linkage maps. We have formulated this LD mapping problem as a constrained unidimensional scaling problem. Our method, which is directly based on the measurement of LD among SNPs, is non-parametric. Therefore it is different from LD maps derived from the given Malecot model. We have formulated with the quadratic programming approach for solving this constrained unidimensional scaling problem. Different from the classical metric unidimensional scaling problem, the constrained problem is not an NP-hard combinatorial problem. The optimal solution is determined by using the quadratic programming solver. Nevertheless, because of the large requirement for memory during the running time that may cause the out of memory problems, and the high computational time of the quadratic programming algorithm, the iterative algorithm has been developed for solving this LD constrained unidimensional scaling problem.

  7. [Linkage analysis of serial sex crimes].

    PubMed

    Yokota, Kaeko; Watanabe, Kazumi; Wachi, Taeko; Otsuka, Yusuke; Kuraishi, Hiroki; Fujita, Goro

    2015-08-01

    The purpose of this study was twofold: first, to create an index for a behavioral linkage analysis of serial sex crimes, and second, to construct a predictive model for the analysis. Data on 720 sex crimes (rape, indecent assault) committed by 360 offenders arrested between 1993 and 2005 throughout Japan were collected. The following seven behaviors were examined during a series of analyses aimed at illustrating the effectiveness of crime linkage in serial sex crimes: victim age group, area type, publicness of offense site, weapon, time, contact method, and day of the week. The results indicated that six of the seven behaviors (excluding "day of the week") significantly distinguished between linked and unlinked crime pairs. Under a logistic regression of these six variables, which were dichotomously coded in terms of the concordance or discordance between each pair of incidents, the area under the receiver operating characteristic (ROC) curve was 0.85 (95% CI = 0.82-0.87), indicating a high level of discriminative accuracy in identifying disparate sex crimes committed by the same person. PMID:26402952

  8. Methods for genetic linkage analysis using trisomies

    SciTech Connect

    Feingold, E.; Lamb, N.E.; Sherman, S.L.

    1994-09-01

    Certain genetic disorders (e.g. congenital cataracts, duodenal atresia) are rare in the general population, but more common in people with Down`s syndrome. We present a method for using individuals with trisomy 21 to map genes for such traits. Our methods are analogous to methods for mapping autosomal dominant traits using affected relative pairs by looking for markers with greater than expected identity-by-descent. In the trisomy case, one would take trisomic individuals and look for markers with greater than expected reduction to homozygosity in the chromosomes inherited form the non-disjoining parent. We present statistical methods for performing such a linkage analysis, including a test for linkage to a marker, a method for estimating the distance from the marker to the gene, a confidence interval for that distance, and methods for computing power and sample sizes. The methods are described in the context of gene-dosage model for the etiology of the disorder, but can be extended to other models. We also resolve some practical issues involved in implementing the methods, including how to use partially informative markers, how to test candidate genes, and how to handle the effect of reduced recombination associated with maternal meiosis I non-disjunction.

  9. Ionic Covalent Organic Frameworks with Spiroborate Linkage.

    PubMed

    Du, Ya; Yang, Haishen; Whiteley, Justin Michael; Wan, Shun; Jin, Yinghua; Lee, Se-Hee; Zhang, Wei

    2016-01-26

    A novel type of ionic covalent organic framework (ICOF), which contains sp(3)  hybridized boron anionic centers and tunable countercations, was constructed by formation of spiroborate linkages. These ICOFs exhibit high BET surface areas up to 1259 m(2)  g(-1) and adsorb a significant amount of H2 (up to 3.11 wt %, 77 K, 1 bar) and CH4 (up to 4.62 wt %, 273 K, 1 bar). Importantly, the materials show good thermal stabilities and excellent resistance to hydrolysis, remaining nearly intact when immersed in water or basic solution for two days. The presence of permanently immobilized ion centers in ICOFs enables the transportation of lithium ions with room-temperature lithium-ion conductivity of 3.05×10(-5)  S cm(-1) and an average Li(+) transference number value of 0.80±0.02. Our approach thus provides a convenient route to highly stable COFs with ionic linkages, which can potentially serve as absorbents for alternative energy sources such as H2, CH4, and also as solid lithium electrolytes/separators for the next-generation lithium batteries. PMID:26696304

  10. An Integrated Linkage, Chromosome, and Genome Map for the Yellow Fever Mosquito Aedes aegypti

    PubMed Central

    Timoshevskiy, Vladimir A.; Severson, David W.; deBruyn, Becky S.; Black, William C.; Sharakhov, Igor V.; Sharakhova, Maria V.

    2013-01-01

    Background Aedes aegypti, the yellow fever mosquito, is an efficient vector of arboviruses and a convenient model system for laboratory research. Extensive linkage mapping of morphological and molecular markers localized a number of quantitative trait loci (QTLs) related to the mosquito's ability to transmit various pathogens. However, linking the QTLs to Ae. aegypti chromosomes and genomic sequences has been challenging because of the poor quality of polytene chromosomes and the highly fragmented genome assembly for this species. Methodology/Principal Findings Based on the approach developed in our previous study, we constructed idiograms for mitotic chromosomes of Ae. aegypti based on their banding patterns at early metaphase. These idiograms represent the first cytogenetic map developed for mitotic chromosomes of Ae. aegypti. One hundred bacterial artificial chromosome clones carrying major genetic markers were hybridized to the chromosomes using fluorescent in situ hybridization. As a result, QTLs related to the transmission of the filarioid nematode Brugia malayi, the avian malaria parasite Plasmodium gallinaceum, and the dengue virus, as well as sex determination locus and 183 Mbp of genomic sequences were anchored to the exact positions on Ae. aegypti chromosomes. A linear regression analysis demonstrated a good correlation between positions of the markers on the physical and linkage maps. As a result of the recombination rate variation along the chromosomes, 12 QTLs on the linkage map were combined into five major clusters of QTLs on the chromosome map. Conclusion This study developed an integrated linkage, chromosome, and genome map—iMap—for the yellow fever mosquito. Our discovery of the localization of multiple QTLs in a few major chromosome clusters suggests a possibility that the transmission of various pathogens is controlled by the same genomic loci. Thus, the iMap will facilitate the identification of genomic determinants of traits responsible

  11. LINKAGE BETWEEN PRODUCTION AND RESPIRATION ON THE LOUISIANA CONTINENTAL SHELF.

    EPA Science Inventory

    Abstract for presentation. Original title, "PRIMARY PRODUCTION, BACTERIOPLANKTON PRODUCTION, AND COMMUNITY RESPIRATION IN STRATIFIED WATERS OF THE NORTHERN GULF OF MEXICO CONTINENTAL SHELF: LINKAGE TO HYPOXIA."

  12. Bessel beam fluorescence lifetime tomography of live embryos (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Xu, Dongli; Peng, Leilei

    2016-03-01

    Optical tomography allows isotropic 3D imaging of embryos. Scanning-laser optical tomography (SLOT) has superior light collecting efficiency than wide-field optical tomography, making it ideal for fluorescence imaging of live embryos. We previously reported an imaging system that combines SLOT with a novel Fourier-multiplexed fluorescence lifetime imaging (FmFLIM) technique named FmFLIM-SLOT. FmFLIM-SLOT performs multiplexed FLIM-FRET readout of multiple FRET sensors in live embryos. Here we report a recent effort on improving the spatial resolution of the FmFLIM-SLOT system in order to image complex biochemical processes in live embryos at the cellular level. Optical tomography has to compromise between resolution and the depth of view. In SLOT, the commonly-used focused Gaussian beam diverges quickly from the focal plane, making it impossible to achieve high resolution imaging in a large volume specimen. We thus introduce Bessel beam laser-scanning tomography, which illuminates the sample with a spatial-light-modulator-generated Bessel beam that has an extended focal depth. The Bessel beam is scanned across the whole specimen. Fluorescence projection images are acquired at equal angular intervals as the sample rotates. Reconstruction artifacts due to annular-rings of the Bessel beam are removed by a modified 3D filtered back projection algorithm. Furthermore, in combination of Fourier-multiplexing fluorescence lifetime imaging (FmFLIM) method, the Bessel FmFLIM-SLOT system is capable of perform 3D lifetime imaging of live embryos at cellular resolution. The system is applied to in-vivo imaging of transgenic Zebrafish embryos. Results prove that Bessel FmFLIM-SLOT is a promising imaging method in development biology research.

  13. Novel Subcarrier Multiplexing Technologies for Optical Communication

    NASA Astrophysics Data System (ADS)

    Wang, Xiaolu

    Microwave subcarrier multiplexing (SCM) has recently emerged as a potentially important multiplexing technique for wideband lightwave systems. By using a double beam modulation technique (DBM), in which the information is modulated onto an optical coherent pair instead of a single optical beam, a novel SCM system is proposed. The system, with multi-division and multi-channel capability (encompassing the multiplexing of both multi-channel analog and/or digital signals), potentially has an information bandwidth (IBW) of tens of GHz and is particularly suitable for optical fiber and free-space communications. The principle of the proposed system was first demonstrated by using a standing-wave surface-acoustic -wave optical modulator (SWSAW). The modulator was fabricated on the top of a Ti - LiNbO_3 waveguide. The highest acoustic modulation frequency achieved was 300 MHz, which corresponds to a 600 MHz subcarrier. The laser output, which had been directly modulated by VHF TV signals, passed through the SWSAW modulator and was upconverted to the UHF band. The carrier-to-noise ratio of the upconverted TV signal was measured to be 30 dB. The more advanced way of implementing the proposed SCM is utilizing a frequency-locked-laser (FLL) pair, which has virtually no upper frequency limitation and is readily FM modulated. We have demonstrated, to our knowledge, the first FM modulated FLL pair for optical communication. The subcarrier (locked) frequency of 15 GHz is also believed to be the highest reported today. The multi-channel video signals and high frequency sinusoidal modulations up to 1 GHz, after being FM modulated onto and demodulated from a 15 GHz subcarrier, are displayed directly on standard TV receivers and oscilloscopes. Another novel SCM, with ultra high millimeter -wave frequency subcarriers of up to one hundred GHz, based upon the self-sustained-pulsation (SSP) of the laser diode, was also proposed. A preliminary optical link test with multi

  14. Multiplex detection of protein-protein interactions using a next generation luciferase reporter.

    PubMed

    Verhoef, Lisette G G C; Mattioli, Michela; Ricci, Fernanda; Li, Yao-Cheng; Wade, Mark

    2016-02-01

    Cell-based assays of protein-protein interactions (PPIs) using split reporter proteins can be used to identify PPI agonists and antagonists. Generally, such assays measure one PPI at a time, and thus counterscreens for on-target activity must be run in parallel or at a subsequent stage; this increases both the cost and time during screening. Split luciferase systems offer advantages over those that use split fluorescent proteins (FPs). This is since split luciferase offers a greater signal:noise ratio and, unlike split FPs, the PPI can be reversed upon small molecule treatment. While multiplexed PPI assays using luciferase have been reported, they suffer from low signal:noise and require fairly complex spectral deconvolution during analysis. Furthermore, the luciferase enzymes used are large, which limits the range of PPIs that can be interrogated due to steric hindrance from the split luciferase fragments. Here, we report a multiplexed PPI assay based on split luciferases from Photinus pyralis (firefly luciferase, FLUC) and the deep-sea shrimp, Oplophorus gracilirostris (NanoLuc, NLUC). Specifically, we show that the binding of the p53 tumor suppressor to its two major negative regulators, MDM2 and MDM4, can be simultaneously measured within the same sample, without the requirement for complex filters or deconvolution. We provide chemical and genetic validation of this system using MDM2-targeted small molecules and mutagenesis, respectively. Combined with the superior signal:noise and smaller size of split NanoLuc, this multiplexed PPI assay format can be exploited to study the induction or disruption of pairwise interactions that are prominent in many cell signaling pathways. PMID:26646257

  15. Cost-Effectiveness of Multiplexed Predictive Biomarker Screening in Non-Small Cell Lung Cancer

    PubMed Central

    Romanus, Dorothy; Cardarella, Stephanie; Cutler, David; Landrum, Mary Beth; Lindeman, Neal I.; Gazelle, G. Scott

    2015-01-01

    Introduction Population-wide screening for epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) gene rearrangements to inform cancer therapy in non-small cell lung cancer (NSCLC) is recommended by guidelines. We estimated cost-effectiveness of multiplexed predictive biomarker screening in metastatic NSCLC from a societal perspective in the US. Methods We constructed a micro simulation model to compare the life expectancy and costs of multiplexed testing and molecularly guided therapy vs treatment with cisplatin-pemetrexed (CisPem). All testing interventions included a two-step algorithm of concurrent EGFR mutation and ALK overexpression testing with immunohistochemistry (IHC) followed by ALK rearrangement confirmation with a fluorescence in situ hybridization (FISH) assay for IHC positive results. Three test strategies were included: ‘Test-treat’ approach, where molecularly guided therapy was initiated after obtainment of test results; ‘Empiric switch therapy’, with concurrent initiation of CisPem and testing and immediate switch to test-result conditional treatment after one cycle of CisPem; and ‘Empiric therapy’ approach in which CisPem was continued for four cycles before start of a tyrosine kinase inhibitor (TKI). Results The incremental cost-effectiveness ratio (ICER) for ‘Test-treat’ compared to treatment with CisPem was $136,000 per quality-adjusted life year (QALY) gained. Both empiric treatment approaches had less favorable ICERs.‘Test-treat’ and ‘Empiric switch therapy’ yielded higher expected outcomes in terms of QALYs and life-years (LYs) than ‘Empiric therapy’.These results were robust across plausible ranges of model inputs. Conclusion From a societal perspective, our cost-effectiveness results support the value of multiplexed genetic screening and molecularly guided therapy in metastatic NSCLC. PMID:25590606

  16. Transmission of multiplexed video signals in multimode optical fiber systems

    NASA Technical Reports Server (NTRS)

    White, Preston, III

    1988-01-01

    Kennedy Space Center has the need for economical transmission of two multiplexed video signals along multimode fiberoptic systems. These systems must span unusual distances and must meet RS-250B short-haul standards after reception. Bandwidth is a major problem and studies of the installed fibers, available LEDs and PINFETs led to the choice of 100 MHz as the upper limit for the system bandwidth. Optical multiplexing and digital transmission were deemed inappropriate. Three electrical multiplexing schemes were chosen for further study. Each of the multiplexing schemes included an FM stage to help meet the stringent S/N specification. Both FM and AM frequency division multiplexing methods were investigated theoretically and these results were validated with laboratory tests. The novel application of quadrature amplitude multiplexing was also considered. Frequency division multiplexing of two wideband FM video signal appears the most promising scheme although this application requires high power highly linear LED transmitters. Futher studies are necessary to determine if LEDs of appropriate quality exist and to better quantify performance of QAM in this application.

  17. Multiplexing Strategies for Monolithic Crystal PET Detector Modules

    PubMed Central

    Pierce, L A; Hunter, W C J; Haynor, D R; MacDonald, L R; Kinahan, P E; Miyaoka, R S

    2014-01-01

    To reduce the number of output channels and associated cost in PET detectors, strategies to multiplex the signal channels have been investigated by several researchers. This work aims to find an optimal multiplexing strategy for detector modules consisting of a monolithic LYSO scintillator coupled to a 64-channel PMT. Methods We apply simulated multiplexing strategies to measured data from two continuous miniature crystal element (cMiCE) detector modules. The strategies tested include standard methods such as row-column summation and its variants, as well as new data-driven methods involving the principal components of measured data and variants of those components. The detector positioning resolution and bias is measured for each multiplexing strategy and the results are compared. Results The mean FWHM over the entire detector was 1.23 mm for no multiplexing (64 channels). Using 16 principal component channels yielded a mean FWHM resolution of 1.21 mm, while traditional row/column summation (16 channels) yielded 1.28 mm. Using 8 principal component output channels resulted in a resolution of 1.30 mm. Conclusion Using the principal components of the calibration data to guide the multiplexing scheme appears to be a viable method for reducing the number of output data channels. Further study is needed to determine if the depth-of-interaction resolution can be preserved with this multiplexing scheme. PMID:25146849

  18. Multiplexity versus correlation: the role of local constraints in real multiplexes.

    PubMed

    Gemmetto, V; Garlaschelli, D

    2015-01-01

    Several systems can be represented as multiplex networks, i.e. in terms of a superposition of various graphs, each related to a different mode of connection between nodes. Hence, the definition of proper mathematical quantities aiming at capturing the added level of complexity of those systems is required. Various steps in this direction have been made. In the simplest case, dependencies between layers are measured via correlation-based metrics, a procedure that we show to be equivalent to the use of completely homogeneous benchmarks specifying only global constraints. However, this approach does not take into account the heterogeneity in the degree and strength distributions, which is instead a fundamental feature of real-world multiplexes. In this work, we compare the observed dependencies between layers with the expected values obtained from maximum-entropy reference models that appropriately control for the observed heterogeneity in the degree and strength distributions. This information-theoretic approach results in the introduction of novel and improved multiplexity measures that we test on different datasets, i.e. the International Trade Network and the European Airport Network. Our findings confirm that the use of homogeneous benchmarks can lead to misleading results, and highlight the important role played by the distribution of hubs across layers. PMID:25767040

  19. Multiplexity versus correlation: the role of local constraints in real multiplexes

    NASA Astrophysics Data System (ADS)

    Gemmetto, V.; Garlaschelli, D.

    2015-03-01

    Several systems can be represented as multiplex networks, i.e. in terms of a superposition of various graphs, each related to a different mode of connection between nodes. Hence, the definition of proper mathematical quantities aiming at capturing the added level of complexity of those systems is required. Various steps in this direction have been made. In the simplest case, dependencies between layers are measured via correlation-based metrics, a procedure that we show to be equivalent to the use of completely homogeneous benchmarks specifying only global constraints. However, this approach does not take into account the heterogeneity in the degree and strength distributions, which is instead a fundamental feature of real-world multiplexes. In this work, we compare the observed dependencies between layers with the expected values obtained from maximum-entropy reference models that appropriately control for the observed heterogeneity in the degree and strength distributions. This information-theoretic approach results in the introduction of novel and improved multiplexity measures that we test on different datasets, i.e. the International Trade Network and the European Airport Network. Our findings confirm that the use of homogeneous benchmarks can lead to misleading results, and highlight the important role played by the distribution of hubs across layers.

  20. Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA

    NASA Astrophysics Data System (ADS)

    Lin, Chenxiang; Jungmann, Ralf; Leifer, Andrew M.; Li, Chao; Levner, Daniel; Church, George M.; Shih, William M.; Yin, Peng

    2012-10-01

    The identification and differentiation of a large number of distinct molecular species with high temporal and spatial resolution is a major challenge in biomedical science. Fluorescence microscopy is a powerful tool, but its multiplexing ability is limited by the number of spectrally distinguishable fluorophores. Here, we used (deoxy)ribonucleic acid (DNA)-origami technology to construct submicrometre nanorods that act as fluorescent barcodes. We demonstrate that spatial control over the positioning of fluorophores on the surface of a stiff DNA nanorod can produce 216 distinct barcodes that can be decoded unambiguously using epifluorescence or total internal reflection fluorescence microscopy. Barcodes with higher spatial information density were demonstrated via the construction of super-resolution barcodes with features spaced by ˜40 nm. One species of the barcodes was used to tag yeast surface receptors, which suggests their potential applications as in situ imaging probes for diverse biomolecular and cellular entities in their native environments.

  1. Emergence of network features from multiplexity.

    PubMed

    Cardillo, Alessio; Gómez-Gardeñes, Jesús; Zanin, Massimiliano; Romance, Miguel; Papo, David; del Pozo, Francisco; Boccaletti, Stefano

    2013-01-01

    Many biological and man-made networked systems are characterized by the simultaneous presence of different sub-networks organized in separate layers, with links and nodes of qualitatively different types. While during the past few years theoretical studies have examined a variety of structural features of complex networks, the outstanding question is whether such features are characterizing all single layers, or rather emerge as a result of coarse-graining, i.e. when going from the multilayered to the aggregate network representation. Here we address this issue with the help of real data. We analyze the structural properties of an intrinsically multilayered real network, the European Air Transportation Multiplex Network in which each commercial airline defines a network layer. We examine how several structural measures evolve as layers are progressively merged together. In particular, we discuss how the topology of each layer affects the emergence of structural properties in the aggregate network. PMID:23446838

  2. Prototype data terminal: Multiplexer/demultiplexer

    NASA Technical Reports Server (NTRS)

    Leck, D. E.; Goodwin, J. E.

    1972-01-01

    The design and operation of a quad redundant data terminal and a multiplexer/demultiplexer (MDU) design are described. The most unique feature is the design of the quad redundant data terminal. This is one of the few designs where the unit is fail/op, fail/op, fail/safe. Laboratory tests confirm that the unit will operate satisfactorily with the failure of three out of four channels. Although the design utilizes state-of-the-art technology. The waveform error checks, the voting techniques, and the parity bit checks are believed to be used in unique configurations. Correct word selection routines are also novel, if not unique. The MDU design, while not redundant, utilizes, the latest state-of-the-art advantages of light couplers and integrated circuit amplifiers.

  3. Multiview multiperspective time multiplexed autostereoscopic display

    NASA Astrophysics Data System (ADS)

    Kupiec, Stephen A.; Markov, Vladimir B.; Hopper, Darrel G.; Saini, Gurdial

    2008-02-01

    The implementation of a time multiplexed display capable of eight simultaneously visible viewing zones will be described. The system employs a high speed digital micromirror device (DMD) to allow for the high framerate essential for flicker free display of multiple viewing zones. A combination of custom graphical processor unit (GPU) programming and a correspondingly optimized field programmable gate array (FPGA) DMD driver allows for real time interactive rendering of scenes. The rendering engine is entirely based on off the shelf with the use of a standard DVI-D interface for data transfer to the DMD interface. A rapidly switched LED light engine is employed to overcome the speed limitations of color wheel light sources, as well as providing a highly saturated color gamut. Selection of viewing zones is achieved by the use of a high-speed shutter interfaced directly to the DMD driver for precise synchronization.

  4. Realization of a spin-wave multiplexer.

    PubMed

    Vogt, K; Fradin, F Y; Pearson, J E; Sebastian, T; Bader, S D; Hillebrands, B; Hoffmann, A; Schultheiss, H

    2014-01-01

    Recent developments in the field of spin dynamics--like the interaction of charge and heat currents with magnons, the quasi-particles of spin waves--opens the perspective for novel information processing concepts and potential applications purely based on magnons without the need of charge transport. The challenges related to the realization of advanced concepts are the spin-wave transport in two-dimensional structures and the transfer of existing demonstrators to the micro- or even nanoscale. Here we present the experimental realization of a microstructured spin-wave multiplexer as a fundamental building block of a magnon-based logic. Our concept relies on the generation of local Oersted fields to control the magnetization configuration as well as the spin-wave dispersion relation to steer the spin-wave propagation in a Y-shaped structure. Thus, the present work illustrates unique features of magnonic transport as well as their possible utilization for potential technical applications. PMID:24759754

  5. Multiplex coherent raman spectroscopy detector and method

    NASA Technical Reports Server (NTRS)

    Chen, Peter (Inventor); Joyner, Candace C. (Inventor); Patrick, Sheena T. (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.

  6. MULTIPLEXING IN THE PRIMATE MOTION PATHWAY

    PubMed Central

    Huk, Alexander C.

    2012-01-01

    This article begins by reviewing recent work on 3D motion processing in the primate visual system. Some of these results suggest that 3D motion signals may be processed in the same circuitry already known to compute 2D motion signals. Such “multiplexing” has implications for the study of visual cortical circuits and neural signals. A more explicit appreciation of multiplexing— and the computations required for demultiplexing— may enrich the study of the visual system by emphasizing the importance of a structured and balanced “encoding / decoding” framework. In addition to providing a fresh perspective on how successive stages of visual processing might be approached, multiplexing also raises caveats about the value of “neural correlates” for understanding neural computation. PMID:22811986

  7. Emergence of network features from multiplexity

    PubMed Central

    Cardillo, Alessio; Gómez-Gardeñes, Jesús; Zanin, Massimiliano; Romance, Miguel; Papo, David; Pozo, Francisco del; Boccaletti, Stefano

    2013-01-01

    Many biological and man-made networked systems are characterized by the simultaneous presence of different sub-networks organized in separate layers, with links and nodes of qualitatively different types. While during the past few years theoretical studies have examined a variety of structural features of complex networks, the outstanding question is whether such features are characterizing all single layers, or rather emerge as a result of coarse-graining, i.e. when going from the multilayered to the aggregate network representation. Here we address this issue with the help of real data. We analyze the structural properties of an intrinsically multilayered real network, the European Air Transportation Multiplex Network in which each commercial airline defines a network layer. We examine how several structural measures evolve as layers are progressively merged together. In particular, we discuss how the topology of each layer affects the emergence of structural properties in the aggregate network. PMID:23446838

  8. 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.

  9. Weighted multiplex network of air transportation

    NASA Astrophysics Data System (ADS)

    Varga, Imre

    2016-06-01

    In several real networks large heterogeneity of links is present either in intensity or in the nature of relationships. Therefore, recent studies in network science indicate that more detailed topological information are available if weighted or multi-layer aspect is applied. In the age of globalization air transportation is a representative example of huge complex infrastructure systems, which has been analyzed from different points of view. In this paper a novel approach is applied to study the airport network as a weighted multiplex taking into account the fact that the rules and fashion of domestic and international flights differ. Restricting study to only topological features and their correlations in the system (disregarding traffic) one can see reasons why simple network approximation is not adequate.

  10. Pneumosinus dilatans multiplex associated with hormonal imbalance.

    PubMed

    Ushas, P; Ravi, V; Painatt, Jaeson Mohanan; Nair, Preeti P

    2013-01-01

    Pneumosinus dilatans describes an abnormal dilation of one or more paranasal sinuses without radiological evidence of localised bone destruction, hyperostosis or mucous membrane thickening. Dilation of mastoid air cells also occurs rarely along with involvement of paranasal sinuses. This rare combination of unknown aetiology was reported in two cases in the literature and termed 'Pneumosinus Dilatans Multiplex' (PSDM). It is usually asymptomatic, and is detected incidentally on plain radiography, CT or MRI. If left untreated, it can further erode the bone leading to complications such as facial asymmetry, neurological disorders and pathological fractures. The aetiology of the condition remains obscure. Various hypotheses proposed are the presence of gas-forming microorganisms, spontaneous drainage of a mucocele, the presence of a one-way valve, dysregulation of hormonal levels leading to a disturbance of osteoblastic and osteoclastic activity. This paper describes a case of PSDM possibly secondary to hormonal disturbance. PMID:23978497

  11. Adiabatically-tapered fiber mode multiplexers.

    PubMed

    Yerolatsitis, S; Gris-Sánchez, I; Birks, T A

    2014-01-13

    Simple all-fiber three-mode multiplexers were made by adiabatically merging three dissimilar single-mode cores into one multimode core. This was achieved by collapsing air holes in a photonic crystal fiber and (in a separate device) by fusing and tapering separate telecom fibers in a fluorine-doped silica capillary. In each case the LP01 mode and both LP11 modes were individually excited from three separate input cores, with losses below 0.3 and 0.7 dB respectively and mode purities exceeding 10 dB. Scaling to more modes is challenging, but would be assisted by using single-mode fibers with a smaller ratio of cladding to core diameter. PMID:24515021

  12. Laser-induced fluorescence imaging of subsurface tissue structures with a volume holographic spatial-spectral imaging system.

    PubMed

    Luo, Yuan; Gelsinger-Austin, Paul J; Watson, Jonathan M; Barbastathis, George; Barton, Jennifer K; Kostuk, Raymond K

    2008-09-15

    A three-dimensional imaging system incorporating multiplexed holographic gratings to visualize fluorescence tissue structures is presented. Holographic gratings formed in volume recording materials such as a phenanthrenquinone poly(methyl methacrylate) photopolymer have narrowband angular and spectral transmittance filtering properties that enable obtaining spatial-spectral information within an object. We demonstrate this imaging system's ability to obtain multiple depth-resolved fluorescence images simultaneously. PMID:18794943

  13. Particle swarm optimization with recombination and dynamic linkage discovery.

    PubMed

    Chen, Ying-Ping; Peng, Wen-Chih; Jian, Ming-Chung

    2007-12-01

    In this paper, we try to improve the performance of the particle swarm optimizer by incorporating the linkage concept, which is an essential mechanism in genetic algorithms, and design a new linkage identification technique called dynamic linkage discovery to address the linkage problem in real-parameter optimization problems. Dynamic linkage discovery is a costless and effective linkage recognition technique that adapts the linkage configuration by employing only the selection operator without extra judging criteria irrelevant to the objective function. Moreover, a recombination operator that utilizes the discovered linkage configuration to promote the cooperation of particle swarm optimizer and dynamic linkage discovery is accordingly developed. By integrating the particle swarm optimizer, dynamic linkage discovery, and recombination operator, we propose a new hybridization of optimization methodologies called particle swarm optimization with recombination and dynamic linkage discovery (PSO-RDL). In order to study the capability of PSO-RDL, numerical experiments were conducted on a set of benchmark functions as well as on an important real-world application. The benchmark functions used in this paper were proposed in the 2005 Institute of Electrical and Electronics Engineers Congress on Evolutionary Computation. The experimental results on the benchmark functions indicate that PSO-RDL can provide a level of performance comparable to that given by other advanced optimization techniques. In addition to the benchmark, PSO-RDL was also used to solve the economic dispatch (ED) problem for power systems, which is a real-world problem and highly constrained. The results indicate that PSO-RDL can successfully solve the ED problem for the three-unit power system and obtain the currently known best solution for the 40-unit system. PMID:18179066

  14. Multiplex detection of food allergens and gluten.

    PubMed

    Cho, Chung Y; Nowatzke, William; Oliver, Kerry; Garber, Eric A E

    2015-05-01

    To help safeguard the food supply and detect the presence of undeclared food allergens and gluten, most producers and regulatory agencies rely on commercial test kits. Most of these are ELISAs with a few being PCR-based. These methods are very sensitive and analyte specific, requiring different assays to detect each of the different food allergens. Mass spectrometry offers an alternative approach whereby multiple allergens may be detected simultaneously. However, mass spectrometry requires expensive equipment, highly trained analysts, and several years before a quantitative approach can be achieved. Using multianalyte profiling (xMAP®) technology, a commercial multiplex test kit based on the use of established antibodies was developed for the simultaneous detection of up to 14 different food allergens plus gluten. The assay simultaneously detects crustacean seafood, egg, gluten, milk, peanut, soy, and nine tree nuts (almond, Brazil nut, cashew, coconut, hazelnut, macadamia, pine nut, pistachio, and walnut). By simultaneously performing multiple tests (typically two) for each analyte, this magnetic bead-based assay offers built-in confirmatory analyses without the need for additional resources. Twenty-five of the assays were performed on buffer extracted samples, while five were conducted on samples extracted using reduced-denatured conditions. Thus, complete analysis for all 14 allergens and gluten requires only two wells of a 96-well microtiter plate. This makes it possible to include in a single analytical run up to 48 samples. All 30 bead sets in this multiplex assay detected 5 ng/mL of food allergen and gluten with responses greater than background. In addition, 26 of the bead sets displayed signal/noise ratios of five or greater. The bead-based design makes this 30-plex assay expandable to incorporate new antibodies and capture/detector methodologies by ascribing these new detectors to any of the unassigned bead sets that are commercially available. PMID

  15. Genome-wide Linkage Analyses of Quantitative and Categorical Autism Subphenotypes

    PubMed Central

    Liu, Xiao-Qing; Paterson, Andrew D.; Szatmari, Peter

    2008-01-01

    Background The search for susceptibility genes in autism and autism spectrum disorders (ASD) has been hindered by the possible small effects of individual genes and by genetic (locus) heterogeneity. To overcome these obstacles, one method is to use autism-related subphenotypes instead of the categorical diagnosis of autism since they may be more directly related to the underlying susceptibility loci. Another strategy is to analyze subsets of families that meet certain clinical criteria to reduce genetic heterogeneity. Methods In this study, using 976 multiplex families from the Autism Genome Project consortium, we performed genome-wide linkage analyses on two quantitative subphenotypes, the total scores of the reciprocal social interaction domain and the restricted, repetitive, and stereotyped patterns of behavior domain from the Autism Diagnostic Interview-Revised. We also selected subsets of ASD families based on four binary subphenotypes, delayed onset of first words, delayed onset of first phrases, verbal status, and IQ ≥ 70. Results When the ASD families with IQ ≥ 70 were used, a logarithm of odds (LOD) score of 4.01 was obtained on chromosome 15q13.3-q14, which was previously linked to schizophrenia. We also obtained a LOD score of 3.40 on chromosome 11p15.4-p15.3 using the ASD families with delayed onset of first phrases. No significant evidence for linkage was obtained for the two quantitative traits. Conclusions This study demonstrates that selection of informative subphenotypes to define a homogeneous set of ASD families could be very important in detecting the susceptibility loci in autism. PMID:18632090

  16. Linkage analyses of stimulant dependence, craving, and heavy use in American Indians.

    PubMed

    Ehlers, Cindy L; Gizer, Ian R; Gilder, David A; Wilhelmsen, Kirk C

    2011-12-01

    Amphetamine-type substances are the second most widely used illicit drugs in the United States. There is evidence to suggest that stimulant use (cocaine and methamphetamine) has a heritable component, yet the areas of the genome underlying these use disorders are yet to be identified. This study's aims were to map loci linked to stimulant dependence, heavy use, and craving in an American Indian community at high risk for substance dependence. DSM diagnosis of stimulant dependence, as well as indices of stimulant "craving," and "heavy use," were obtained using the Semi-Structured Assessment for the Genetics of Alcoholism (SSAGA). Genotypes were determined for a panel of 791 microsatellite polymorphisms in 381 members of multiplex families using SOLAR. Stimulant dependence, stimulant "craving," and "heavy stimulant use," were all found to be heritable. Analyses of multipoint variance component LOD scores, failed to yield evidence of linkage for stimulant dependence. For the stimulant "craving" phenotype, linkage analysis revealed a locus that had a LOD score of 3.02 on chromosome 15q25.3-26.1 near the nicotinic receptor gene cluster. A LOD score of 2.05 was found at this same site for "heavy stimulant use." Additional loci with LOD scores above 2.00 were found for stimulant "craving" on chromosomes 12p13.33-13.32 and 18q22.3. These results corroborate the importance of "craving" as an important phenotype that is associated with regions on chromosome 12, 15, and 18, that have been highlighted in prior segregation studies in this and other populations for substance dependence-related phenotypes. PMID:21812097

  17. Evidence of linkage and association on 18p11.2 for psychosis.

    PubMed

    Mukherjee, O; Meera, P; Ghosh, S; Kubendran, S; Kiran, K; Manjunath, K R; Subhash, M N; Benegal, V; Brahmachari, S K; Majumder, P P; Jain, S

    2006-12-01

    The genetic basis of bipolar disorder (BPD) and schizophrenia (SCZ) has been established through numerous clinical and molecular studies. Although often considered separate nosological entities, evidence now suggests that the two syndromes may share some genetic liability. Recent studies have used a composite phenotype (psychosis) that includes BPD, SCZ, psychosis not otherwise specified, and schizoaffective disorder, to identify shared susceptibility loci. Several chromosomal regions are reported to be shared between these syndromes (18p, 6q, 10p, 13q, 22q). As a part of our endeavor to scan these regions, we report a positive linkage and association finding at 18p11.2 for psychosis. Two-point linkage analysis performed on a series of 52 multiplex pedigrees with 23 polymorphic markers yielded a LOD score of 2.02 at D18S37. An independent set of 159 parent offspring trios was used to confirm this suggestive finding. The TDT analysis yielded support for association between the marker D18S453 and the disease allele (chi2 = 4.829, P < 0.028). This region has been implicated by several studies on BPD [Sjoholt et al. (2004); Mol Psychiatry 9(6):621-629; Washizuka et al. (2004); Biol Psychiatry 56(7):483-489; Pickard et al. (2005); Psychiatr Genet 15(1):37-44], SCZ [Kikuchi et al. (2003); J Med Dent Sci 50(3):225-229; Babovic-Vuksanovic et al. (2004); Am J Med Genet 124(3):318-322] and also as a shared region between the two diseases [Ishiguro et al. (2001); J Neural Transm 108(7):849-854; Reyes et al. (2002); Mol Psychiatry 7(4):337-339; Craddock et al. (2005); J Med Genet 42(3):193-204]. Our findings provide an independent validation of the above reports, and suggest the presence of susceptibility loci for psychoses in this region. PMID:16941653

  18. Inter-layer synchronization in multiplex networks of identical layers.

    PubMed

    Sevilla-Escoboza, R; Sendiña-Nadal, I; Leyva, I; Gutiérrez, R; Buldú, J M; Boccaletti, S

    2016-06-01

    Inter-layer synchronization is a distinctive process of multiplex networks whereby each node in a given layer evolves synchronously with all its replicas in other layers, irrespective of whether or not it is synchronized with the other units of the same layer. We analytically derive the necessary conditions for the existence and stability of such a state, and verify numerically the analytical predictions in several cases where such a state emerges. We further inspect its robustness against a progressive de-multiplexing of the network, and provide experimental evidence by means of multiplexes of nonlinear electronic circuits affected by intrinsic noise and parameter mismatch. PMID:27368794

  19. Shift-multiplexed self-referential holographic data storage.

    PubMed

    Takabayashi, Masanori; Okamoto, Atsushi; Eto, Taisuke; Okamoto, Takashi

    2014-07-10

    The feasibility and the properties of shift-multiplexed self-referential holographic data storage (SR-HDS) were investigated. Although SR-HDS has attractive features as typified by referenceless holographic recording, its multiplexing properties, which are consummately important for holographic data storage, have not been clarified until now. The results of numerical and experimental evaluations of medium shift dependence in SR-HDS clarified that the shift selectivity is almost the same as in collinear holography. Furthermore, 25 datapages were successfully shift-multiplexed with the shift pitch of 8.3 μm by the numerical simulation. PMID:25090055

  20. Control of Angular Intervals for Angle-Multiplexed Holographic Memory

    NASA Astrophysics Data System (ADS)

    Kinoshita, Nobuhiro; Muroi, Tetsuhiko; Ishii, Norihiko; Kamijo, Koji; Shimidzu, Naoki

    2009-03-01

    In angle-multiplexed holographic memory, the full width at half maximum of the Bragg selectivity curves is dependent on the angle formed between the medium and incident laser beams. This indicates the possibility of high density and high multiplexing number by varying the angular intervals between adjacent holograms. We propose an angular interval scheduling for closely stacking holograms into medium even when the angle range is limited. We obtained bit error rates of the order of 10-4 under the following conditions: medium thickness of 1 mm, laser beam wavelength of 532 nm, and angular multiplexing number of 300.

  1. Multiplexing of discrete chaotic signals in presence of noise

    NASA Astrophysics Data System (ADS)

    Nagaraj, Nithin; Vaidya, Prabhakar G.

    2009-09-01

    Multiplexing of discrete chaotic signals in presence of noise is investigated. The existing methods are based on chaotic synchronization, which is susceptible to noise, precision limitations, and requires more iterates. Furthermore, most of these methods fail for multiplexing more than two discrete chaotic signals. We propose novel methods to multiplex multiple discrete chaotic signals based on the principle of symbolic sequence invariance in presence of noise and finite precision implementation of finding the initial condition of an arbitrarily long symbolic sequence of a chaotic map. Our methods work for single precision and as less as 35 iterates. For two signals, our method is robust up to 50% noise level.

  2. Multiplexed multi-longitudinal mode fiber laser sensor.

    PubMed

    Huang, Long; Wang, Peng; Gao, Liang; Zhang, Tingting; Chen, Xiangfei

    2014-10-20

    A multiplexed multi-longitudinal mode fiber laser sensor system is proposed and demonstrated. By incorporating two matched wavelength division multiplexers (WDMs) and a semiconductor optical amplifier (SOA) into a fiber laser cavity, multiwavelength oscillation is established. Each wavelength corresponding to one channel of WDMs contains multi-longitudinal modes. The multiwavelength output of the laser is directed to another WDM which functions as a demultiplexer. By monitoring the longitudinal mode beat frequency generated at photodetectors following the WDM, the sensing information can be demodulated. Preliminary results for multiplexing two sensors measuring strain and temperature are presented to verify the principle of the system. PMID:25401605

  3. Image decoding of photonic crystal beads array in the microfluidic chip for multiplex assays.

    PubMed

    Yuan, Junjie; Zhao, Xiangwei; Wang, Xiaoxia; Gu, Zhongze

    2014-01-01

    Along with the miniaturization and intellectualization of biomedical instruments, the increasing demand of health monitoring at anywhere and anytime elevates the need for the development of point of care testing (POCT). Photonic crystal beads (PCBs) as one kind of good encoded microcarriers can be integrated with microfluidic chips in order to realize cost-effective and high sensitive multiplex bioassays. However, there are difficulties in analyzing them towards automated analysis due to the characters of the PCBs and the unique detection manner. In this paper, we propose a strategy to take advantage of automated image processing for the color decoding of the PCBs array in the microfluidic chip for multiplex assays. By processing and alignment of two modal images of epi-fluorescence and epi-white light, every intact bead in the image is accurately extracted and decoded by PC colors, which stand for the target species. This method, which shows high robustness and accuracy under various configurations, eliminates the high hardware requirement of spectroscopy analysis and user-interaction software, and provides adequate supports for the general automated analysis of POCT based on PCBs array. PMID:25341876

  4. Multiplexed detection of lung cancer biomarkers based on quantum dots and microbeads.

    PubMed

    Wu, Simin; Liu, Lifen; Li, Gong; Jing, Fengxiang; Mao, Hongju; Jin, Qinghui; Zhai, Wanyin; Zhang, Hongfeng; Zhao, Jianlong; Jia, Chunping

    2016-08-15

    We have developed a multiplexed fluoroimmunoassay of three lung cancer biomarkers based on multicolor quantum dots (QDs) as detection elements and micro-magnetic beads as immune carriers. QDs have the ability to simplify multiplexed analysis. In our method, the fluorescent signals derived from three cross-talk-free QD conjugated probes with emission maxima at 525, 585 and 625nm could be analyzed to determine the concentrations of the target proteins. With this system, fragments of cytokeratin 19 (CYRFA 21-1), carcinoembryonic antigen (CEA), and neuron-specific enolase (NSE), were simultaneously detected in a single sample with a low detection limit down to the 1.0ng/mL level (364pg/mL for CYRFA 21-1, 38pg/mL for CEA, 370pg/mL for NSE in a single detection). Additional advantages of the presented method include ease of operation, low cost, and a very low sample volume (20µL). PMID:27260434

  5. Image Decoding of Photonic Crystal Beads Array in the Microfluidic Chip for Multiplex Assays

    NASA Astrophysics Data System (ADS)

    Yuan, Junjie; Zhao, Xiangwei; Wang, Xiaoxia; Gu, Zhongze

    2014-10-01

    Along with the miniaturization and intellectualization of biomedical instruments, the increasing demand of health monitoring at anywhere and anytime elevates the need for the development of point of care testing (POCT). Photonic crystal beads (PCBs) as one kind of good encoded microcarriers can be integrated with microfluidic chips in order to realize cost-effective and high sensitive multiplex bioassays. However, there are difficulties in analyzing them towards automated analysis due to the characters of the PCBs and the unique detection manner. In this paper, we propose a strategy to take advantage of automated image processing for the color decoding of the PCBs array in the microfluidic chip for multiplex assays. By processing and alignment of two modal images of epi-fluorescence and epi-white light, every intact bead in the image is accurately extracted and decoded by PC colors, which stand for the target species. This method, which shows high robustness and accuracy under various configurations, eliminates the high hardware requirement of spectroscopy analysis and user-interaction software, and provides adequate supports for the general automated analysis of POCT based on PCBs array.

  6. Multiplexed immunosensing and kinetics monitoring in nanofluidic devices with highly enhanced target capture efficiency.

    PubMed

    Lin, Yii-Lih; Huang, Yen-Jun; Teerapanich, Pattamon; Leïchlé, Thierry; Chou, Chia-Fu

    2016-05-01

    Nanofluidic devices promise high reaction efficiency and fast kinetic responses due to the spatial constriction of transported biomolecules with confined molecular diffusion. However, parallel detection of multiple biomolecules, particularly proteins, in highly confined space remains challenging. This study integrates extended nanofluidics with embedded protein microarray to achieve multiplexed real-time biosensing and kinetics monitoring. Implementation of embedded standard-sized antibody microarray is attained by epoxy-silane surface modification and a room-temperature low-aspect-ratio bonding technique. An effective sample transport is achieved by electrokinetic pumping via electroosmotic flow. Through the nanoslit-based spatial confinement, the antigen-antibody binding reaction is enhanced with ∼100% efficiency and may be directly observed with fluorescence microscopy without the requirement of intermediate washing steps. The image-based data provide numerous spatially distributed reaction kinetic curves and are collectively modeled using a simple one-dimensional convection-reaction model. This study represents an integrated nanofluidic solution for real-time multiplexed immunosensing and kinetics monitoring, starting from device fabrication, protein immobilization, device bonding, sample transport, to data analysis at Péclet number less than 1. PMID:27375819

  7. Extensible Multiplex Real-time PCR of MicroRNA Using Microparticles.

    PubMed

    Jung, Seungwon; Kim, Junsun; Lee, Dong Jin; Oh, Eun Hae; Lim, Hwasup; Kim, Kwang Pyo; Choi, Nakwon; Kim, Tae Song; Kim, Sang Kyung

    2016-01-01

    Multiplex quantitative real-time PCR (qPCR), which measures multiple DNAs in a given sample, has received significant attention as a mean of verifying the rapidly increasing genetic targets of interest in single phenotype. Here we suggest a readily extensible qPCR for the expression analysis of multiple microRNA (miRNA) targets using microparticles of primer-immobilized networks as discrete reactors. Individual particles, 200~500 μm in diameter, are identified by two-dimensional codes engraved into the particles and the non-fluorescent encoding allows high-fidelity acquisition of signal in real-time PCR. During the course of PCR, the amplicons accumulate in the volume of the particles with high reliability and amplification efficiency over 95%. In a quick assay comprising of tens of particles holding different primers, each particle brings the independent real-time amplification curve representing the quantitative information of each target. Limited amount of sample was analyzed simultaneously in single chamber through this highly multiplexed qPCR; 10 kinds of miRNAs from purified extracellular vesicles (EVs). PMID:26964639

  8. Image Decoding of Photonic Crystal Beads Array in the Microfluidic Chip for Multiplex Assays

    PubMed Central

    Yuan, Junjie; Zhao, Xiangwei; Wang, Xiaoxia; Gu, Zhongze

    2014-01-01

    Along with the miniaturization and intellectualization of biomedical instruments, the increasing demand of health monitoring at anywhere and anytime elevates the need for the development of point of care testing (POCT). Photonic crystal beads (PCBs) as one kind of good encoded microcarriers can be integrated with microfluidic chips in order to realize cost-effective and high sensitive multiplex bioassays. However, there are difficulties in analyzing them towards automated analysis due to the characters of the PCBs and the unique detection manner. In this paper, we propose a strategy to take advantage of automated image processing for the color decoding of the PCBs array in the microfluidic chip for multiplex assays. By processing and alignment of two modal images of epi-fluorescence and epi-white light, every intact bead in the image is accurately extracted and decoded by PC colors, which stand for the target species. This method, which shows high robustness and accuracy under various configurations, eliminates the high hardware requirement of spectroscopy analysis and user-interaction software, and provides adequate supports for the general automated analysis of POCT based on PCBs array. PMID:25341876

  9. Developing rapid, point-of-care, multiplex detection for use in lateral flow devices

    NASA Astrophysics Data System (ADS)

    Rao, R. S.; Albala, J. S.; Lane, S. L.; Matthews, D. L.; Fisher, A. M.; Lambert, J. L.; Coleman, M. A.

    2005-11-01

    Immunoassays have been widely used in commercial, scientific and medical research for detection and quantification of analytes in complex mixtures. There is however a need for a point-of-care, multiplex diagnostic assays capable of providing rapid and quantitative measurements of analytes present in samples that are sufficiently simple to carry out without use of a laboratory or individuals trained in chemical analysis. We are developing a fluorescent lateral flow immunoassay platform to perform simultaneous, multiplexed detection of analytes in a complex fluid mixture along with instrumentation to optically quantitate the analytes in the sample. Our prototype imaging system is based on conventional 16-bit CCD optics, which enables the development of a rugged diagnostic instrument that can be further scaled down for point-of-care applications. We have compared protein microarrays with lateral flow assays (LFAs) to determine the sensitivity of each system for the measurement of distinct proteins in complex samples. We are pursuing the LFA platform such that it can easily be scaled to meet the requirements of any given screening application, and be implemented for use in a medical or surgical setting.

  10. Multiplex variable number of tandem repeats for Oenococcus oeni and applications.

    PubMed

    Claisse, Olivier; Lonvaud-Funel, Aline

    2014-04-01

    Oenococcus oeni is responsible for the malolactic fermentation of wine. Genomic diversity has already been established in this species. In addition, winemakers usually report varying starter-culture efficiency. It is essential to monitor indigenous and selected strains in order to understand strain survival and development during the winemaking process. A previous article described a variable number of tandem repeats (VNTR) scheme, based on five polymorphic loci of the genome. VNTR typing of O. oeni was highly discriminating, faster, and more reliable than the PFGE or MLST methods. The objective of this study was to set up a faster protocol by multiplexing, taking advantage of the high performance of multicolor capillary electrophoresis. The primers were labeled with multiple fluorescent dyes. PCR conditions were adapted by multiplexing amplifications in two separate PCR mixtures for the five loci, both at the same annealing temperature. The resulting assay proved to be robust, accurate, fast and easy to perform. Thanks to this new protocol, all O. oeni strains used in the study were typed using the five tandem repeats (TR). As expected, the primers for the five TR loci were specific to O. oeni. The method was improved to analyze isolated and mixed colonies, as well as bacteria harvested from wine using fast technology for analysis of nucleic acids (FTA(®)) technology. Finally, predictive models were constructed, to predict phylogenetic relationships and associate bacterial strain resistance to freeze-drying with fragment length analysis (FLA) profiles and genotypic and phenotypic characters. PMID:24290630

  11. Extensible Multiplex Real-time PCR of MicroRNA Using Microparticles

    PubMed Central

    Jung, Seungwon; Kim, Junsun; Lee, Dong Jin; Oh, Eun Hae; Lim, Hwasup; Kim, Kwang Pyo; Choi, Nakwon; Kim, Tae Song; Kim, Sang Kyung

    2016-01-01

    Multiplex quantitative real-time PCR (qPCR), which measures multiple DNAs in a given sample, has received significant attention as a mean of verifying the rapidly increasing genetic targets of interest in single phenotype. Here we suggest a readily extensible qPCR for the expression analysis of multiple microRNA (miRNA) targets using microparticles of primer-immobilized networks as discrete reactors. Individual particles, 200~500 μm in diameter, are identified by two-dimensional codes engraved into the particles and the non-fluorescent encoding allows high-fidelity acquisition of signal in real-time PCR. During the course of PCR, the amplicons accumulate in the volume of the particles with high reliability and amplification efficiency over 95%. In a quick assay comprising of tens of particles holding different primers, each particle brings the independent real-time amplification curve representing the quantitative information of each target. Limited amount of sample was analyzed simultaneously in single chamber through this highly multiplexed qPCR; 10 kinds of miRNAs from purified extracellular vesicles (EVs). PMID:26964639

  12. Profiling Antibodies to Mycobacterium tuberculosis by Multiplex Microbead Suspension Arrays for Serodiagnosis of Tuberculosis▿

    PubMed Central

    Khan, Imran H.; Ravindran, Resmi; Yee, JoAnn; Ziman, Melanie; Lewinsohn, David M.; Gennaro, Marila L.; Flynn, JoAnne L.; Goulding, Celia W.; DeRiemer, Kathryn; Lerche, Nickolas W.; Luciw, Paul A.

    2008-01-01

    Tuberculosis (TB) is a serious global disease. The fatality rate attributed to TB is among the highest of infectious diseases, with approximately 2 million deaths occurring per year worldwide. Identification of individuals infected with Mycobacterium tuberculosis and screening of their immediate contacts is crucial for controlling the spread of TB. Current methods for detection of M. tuberculosis infection are not efficient, in particular, for testing large numbers of samples. We report a novel and efficient multiplex microbead immunoassay (MMIA), based on Luminex technology, for profiling antibodies to M. tuberculosis. Microbead sets identifiable by unique fluorescence were individually coated with each of several M. tuberculosis antigens and tested in multiplex format for antibody detection in the experimental nonhuman primate model of TB. Certain M. tuberculosis antigens, e.g., ESAT-6, CFP-10, and HspX, were included to enhance the specificity of the MMIA, because these antigens are absent in nontuberculous mycobacteria and the vaccine strain Mycobacterium bovis bacillus Calmette-Guérin. The MMIA enabled simultaneous detection of multiple M. tuberculosis plasma antibodies in several cohorts of macaques representing different stages of infection and/or disease. Antibody profiles were defined in early and latent/chronic infection. These proof-of-concept findings demonstrate the potential clinical use of the MMIA. In addition, the MMIA serodetection system has a potential for mining M. tuberculosis open reading frames (about 4,000) to discover novel target proteins for the development of more-comprehensive TB serodiagnostic tests. PMID:18077619

  13. A Multiplex PCR-coupled Liquid Bead Array for the Simultaneous Detection of Four Biothreat Agents

    SciTech Connect

    Wilson, W J; Erler, A M; Nasarabadi, S L; Skowronski, E W; McCready, P M

    2004-02-04

    We have developed a 10-plexed PCR assay coupled to a 12-plexed liquid bead array to rapidly screen environmental samples for B. anthracis, Y. pestis, F. tularensis, and B. melitensis. Highly validated species -specific primer sets were used to simultaneously amplify multiple diagnostic regions unique to each individual pathogen. Resolution of the mix of amplified products was achieved by PCR product hybridization to corresponding probe sequences, attached to unique sets of fluorescent beads. The hybridized beads were processed through a flow cytometer, which detected presence and quantity of each PCR product. The assay was optimized to allow for maximum sensitivity in a multiplexed format. A high- throughput demonstration was performed where 384 simulated environmental samples were spiked with different amounts of B. thuringensis spores and pathogen DNA. The samples were robotically processed to extract DNA and arrayed for multiplexed PCR-liquid bead detection. The assay correctly identified the presence or absence of each pathogen and collected over 3,000 individual data points within a single 8-hour shift for approximately $1.20 per sample in a 10-plexed assay.

  14. A novel, one-step amplification and oligonucleotide ligation procedure for multiplex genetic typing

    SciTech Connect

    Eggerding, F.A.

    1994-09-01

    A new technique, coupled amplification and oligonucleotide ligation (CAL), has been developed for simultaneous multiplex amplification and genotyping of DNA. CAL is a biphasic method which combines in one assay DNA amplification by the polymerase chain reaction (PCR) with DNA genotyping by the oligonucleotide ligation assay (OLA). By virtue of a difference in the melting temperatures of PCR primer-target DNA and OLA probe-target DNA hybrids, the method allows preferential amplification of DNA during stage I and oligonucleotide ligation during stage II of the reaction. In stage I target DNA is amplified using high-melting primers in a two-step PCR cycle that employs a 72{degrees}C anneal-elongation step. In stage II genotyping of PCR products by competitive oligonucleotide ligation with oligonucleotide probes located between PCR primers is accomplished by several cycles of denaturation at 94{degrees}C followed by anneal-ligation at 55{degrees}C. Ligation products are fluorochrome-labeled at their 3{prime}-ends and analyzed electrophoretically on a fluorescent DNA sequencer. The CAL procedure has been used for multiplex detection of 30 cystic fibrosis mutations and for analysis of ras gene point mutations. Because mutation detection occurs concurrently with target amplification, the technique is rapid, highly sensitive and specific, easily automatable, and requires minimal sample processing.

  15. Design and implementation of an integrated magnetic spectrometer for multiplexed biosensing.

    PubMed

    Sideris, Constantine; Hajimiri, Ali

    2013-12-01

    Magnetic spectroscopy allows for characterization of the magnetic susceptibility of magnetic beads across a broad frequency range. This enables differentiation and quantification of multiple beads of varying types concurrently present in the active volume of a sensor's surface. A magnetic spectrometer can be used for multi-probe tagging and identification akin to multi-color fluorescent bio-sensing. We propose a new sensing methodology to perform magnetic spectroscopy and analyze various important design parameters such as SNR and gain uniformity. We present a proof-of-concept design of a fully integrated CMOS magnetic spectrometer that can detect, quantify, and characterize magnetic materials in the 1.1 GHz to 3.3 GHz frequency range, where we demonstrate magnetic multiplexing capability using a mixture of two different kinds of magnetic beads. The sensor consumes less than 2 mW of DC power within the whole frequency range, requires no external biasing magnetic fields, is implemented in a standard CMOS process, and can be powered and operated completely from a USB interface. The magnetic spectrometer not only increases the throughput and multiplexing of biosensing experiments for a given sensor area, but also can enable additional applications, such as magnetic flow cytometry and signal-collocation assays of multiple probes. PMID:24473542

  16. Multiplexed Detection of Cytokines Based on Dual Bar-Code Strategy and Single-Molecule Counting.

    PubMed

    Li, Wei; Jiang, Wei; Dai, Shuang; Wang, Lei

    2016-02-01

    Cytokines play important roles in the immune system and have been regarded as biomarkers. While single cytokine is not specific and accurate enough to meet the strict diagnosis in practice, in this work, we constructed a multiplexed detection method for cytokines based on dual bar-code strategy and single-molecule counting. Taking interferon-γ (IFN-γ) and tumor necrosis factor-α (TNF-α) as model analytes, first, the magnetic nanobead was functionalized with the second antibody and primary bar-code strands, forming a magnetic nanoprobe. Then, through the specific reaction of the second antibody and the antigen that fixed by the primary antibody, sandwich-type immunocomplex was formed on the substrate. Next, the primary bar-code strands as amplification units triggered multibranched hybridization chain reaction (mHCR), producing nicked double-stranded polymers with multiple branched arms, which were served as secondary bar-code strands. Finally, the secondary bar-code strands hybridized with the multimolecule labeled fluorescence probes, generating enhanced fluorescence signals. The numbers of fluorescence dots were counted one by one for quantification with epi-fluorescence microscope. By integrating the primary and secondary bar-code-based amplification strategy and the multimolecule labeled fluorescence probes, this method displayed an excellent sensitivity with the detection limits were both 5 fM. Unlike the typical bar-code assay that the bar-code strands should be released and identified on a microarray, this method is more direct. Moreover, because of the selective immune reaction and the dual bar-code mechanism, the resulting method could detect the two targets simultaneously. Multiple analysis in human serum was also performed, suggesting that our strategy was reliable and had a great potential application in early clinical diagnosis. PMID:26721199

  17. Multiplexed, rapid point of care platform to quantify allergen-specific IgE.

    PubMed

    Monroe, M R; Reddington, A P; Cretich, M; Chiari, M; Little, F; Ünlü, M S

    2011-01-01

    Variation of probe immobilization on microarrays hinders the ability to make high quality, assertive and statistically relevant conclusions needed in the healthcare setting. To address this problem, we have developed a calibrated, compact, inexpensive, multiplexed, dual modality point-of-care detection platform that calibrates and correlates surface probe density measured label-free to captured labeled secondary antibody, is independent of chip-to-chip variability, and improves upon existing diagnostic technology. We have identified four major technological advantages of our proposed platform: the capability to perform single spot analysis based on the fluorophore used for detection, a 10-fold gain in fluorescence signal due to optimized substrate, a calibrated, quantitative method that uses the combined fluorescent and label-free modalities to accurately measure the density of probe and bound target for a variety of systems, and a compact measurement platform offering reliable and rapid results at the doctor's office. Already, we have formulated over a 90% linear correlation between the amount of probe bound to surface and the resulting fluorescence of captured target for IgG, β-lactoglobulin, Ara h 1 peanut allergen, and Phl 5a Timothy grass allergen. PMID:22254352

  18. Linkage arms for minimizing piston wobble

    SciTech Connect

    Langstroth, S.W.

    1992-07-28

    This patent describes an internal combustion engine having a block within which at least one piston is attached to a crankshaft by a connecting rod between the crankpin of the crankshaft and the wrist pin of the piston. This patent describes improvement in a fixed gear concentric with the axis of the crankshaft and coupled to the block; a follower gear concentric with the crankpin; at least one intermediate gear coupling the fixed gear to the follower gear; wherein the ratio of the gears is such that the follower gear orbits the fixed gear and does not rotate; and linkage arms interconnecting the follower gear and the piston for preventing the rotation of the piston about the wrist pin.

  19. Linkage of PRA models. Phase 1, Results

    SciTech Connect

    Smith, C.L.; Knudsen, J.K.; Kelly, D.L.

    1995-12-01

    The goal of the Phase I work of the ``Linkage of PRA Models`` project was to postulate methods of providing guidance for US Nuclear Regulator Commission (NRC) personnel on the selection and usage of probabilistic risk assessment (PRA) models that are best suited to the analysis they are performing. In particular, methods and associated features are provided for (a) the selection of an appropriate PRA model for a particular analysis, (b) complementary evaluation tools for the analysis, and (c) a PRA model cross-referencing method. As part of this work, three areas adjoining ``linking`` analyses to PRA models were investigated: (a) the PRA models that are currently available, (b) the various types of analyses that are performed within the NRC, and (c) the difficulty in trying to provide a ``generic`` classification scheme to groups plants based upon a particular plant attribute.

  20. A simple heuristic for blindfolded record linkage

    PubMed Central

    Lowe, Henry; Das, Amar; Ferris, Todd

    2012-01-01

    Objectives To address the challenge of balancing privacy with the need to create cross-site research registry records on individual patients, while matching the data for a given patient as he or she moves between participating sites. To evaluate the strategy of generating anonymous identifiers based on real identifiers in such a way that the chances of a shared patient being accurately identified were maximized, and the chances of incorrectly joining two records belonging to different people were minimized. Methods Our hypothesis was that most variation in names occurs after the first two letters, and that date of birth is highly reliable, so a single match variable consisting of a hashed string built from the first two letters of the patient's first and last names plus their date of birth would have the desired characteristics. We compared and contrasted the match algorithm characteristics (rate of false positive v. rate of false negative) for our chosen variable against both Social Security Numbers and full names. Results In a data set of 19 000 records, a derived match variable consisting of a 2-character prefix from both first and last names combined with date of birth has a 97% sensitivity; by contrast, an anonymized identifier based on the patient's full names and date of birth has a sensitivity of only 87% and SSN has sensitivity 86%. Conclusion The approach we describe is most useful in situations where privacy policies preclude the full exchange of the identifiers required by more sophisticated and sensitive linkage algorithms. For data sets of sufficiently high quality this effective approach, while producing a lower rate of matching than more complex algorithms, has the merit of being easy to explain to institutional review boards, adheres to the minimum necessary rule of the HIPAA privacy rule, and is faster and less cumbersome to implement than a full probabilistic linkage. PMID:22298567