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Sample records for quantitative multiplexed analysis

  1. Guided protein extraction from formalin-fixed tissues for quantitative multiplex analysis avoids detrimental effects of histological stains.

    Science.gov (United States)

    Becker, Karl-Friedrich; Schott, Christina; Becker, Ingrid; Höfler, Heinz

    2008-05-01

    Formalin fixed and paraffin embedded (FFPE) tissues are the basis for histopathological diagnosis of many diseases around the world. For translational research and routine diagnostics, protein analysis from FFPE tissues is very important. We evaluated the potential influence of six histological stains, including hematoxylin (Mayer and Gill), fast red, light green, methyl blue and toluidine blue, for yield, electrophoretic mobility in 1-D gels, and immunoreactivity of proteins isolated from formalin-fixed breast cancer tissues. Proteins extracted from stained FFPE tissues using a recently established technique were compared with proteins obtained from the same tissues but without prior histological staining. Western blot and quantitative protein lysate microarray analysis demonstrated that histological staining can result in decreased protein yield but may not have much influence on immunoreactivity and electrophoretic mobility. Interestingly, not all staining protocols tested are compatible with subsequent protein analysis. The commonly used hematoxylin staining was found to be suitable for multiplexed quantitative protein measurement technologies although protein extraction was less efficient. For best results we suggest a guided protein extraction method, in which an adjacent hematoxylin/eosin-stained tissue section is used to control dissection of an unstained specimen for subsequent protein extraction and quantification for research and diagnosis.

  2. Quantitation of Bt-176 maize genomic sequences by surface plasmon resonance-based biospecific interaction analysis of multiplex polymerase chain reaction (PCR).

    Science.gov (United States)

    Feriotto, Giordana; Gardenghi, Sara; Bianchi, Nicoletta; Gambari, Roberto

    2003-07-30

    Surface plasmon resonance (SPR) based biosensors have been described for the identification of genetically modified organisms (GMO) by biospecific interaction analysis (BIA). This paper describes the design and testing of an SPR-based BIA protocol for quantitative determinations of GMOs. Biotinylated multiplex Polymerase Chain Reaction (PCR) products from nontransgenic maize as well as maize powders containing 0.5 and 2% genetically modified Bt-176 sequences were immobilized on different flow cells of a sensor chip. After immobilization, different oligonucleotide probes recognizing maize zein and Bt-176 sequences were injected. The results obtained were compared with Southern blot analysis and with quantitative real-time PCR assays. It was demonstrated that sequential injections of Bt-176 and zein probes to sensor chip flow cells containing multiplex PCR products allow discrimination between PCR performed using maize genomic DNA containing 0.5% Bt-176 sequences and that performed using maize genomic DNA containing 2% Bt-176 sequences. The efficiency of SPR-based BIA in discriminating material containing different amounts of Bt-176 maize is comparable to real-time quantitative PCR and much more reliable than Southern blotting, which in the past has been used for semiquantitative purposes. Furthermore, the approach allows the BIA assay to be repeated several times on the same multiplex PCR product immobilized on the sensor chip, after washing and regeneration of the flow cell. Finally, it is emphasized that the presented strategy to quantify GMOs could be proposed for all of the SPR-based, commercially available biosensors. Some of these optical SPR-based biosensors use, instead of flow-based sensor chips, stirred microcuvettes, reducing the costs of the experimentation.

  3. In vivo multiplex quantitative analysis of 3 forms of alpha melanocyte stimulating hormone in pituitary of prolyl endopeptidase deficient mice

    Directory of Open Access Journals (Sweden)

    Perroud Bertrand

    2009-06-01

    Full Text Available Abstract Background In vitro reactions are useful to identify putative enzyme substrates, but in vivo validation is required to identify actual enzyme substrates that have biological meaning. To investigate in vivo effects of prolyl endopeptidase (PREP, a serine protease, on alpha melanocyte stimulating hormone (α-MSH, we developed a new mass spectrometry based technique to quantitate, in multiplex, the various forms of α-MSH. Methods Using Multiple Reaction Monitoring (MRM, we analyzed peptide transitions to quantify three different forms of α-MSH. Transitions were first confirmed using standard peptides. Samples were then analyzed by mass spectrometry using a triple quadrupole mass spectrometer, after elution from a reverse phase C18 column by a gradient of acetonitrile. Results We first demonstrate in vitro that PREP digests biological active alpha melanocyte stimulating hormone (α-MSH1–13, by cleaving the terminal amidated valine and releasing a truncated alpha melanocyte stimulating hormone (α-MSH1–12 product – the 12 residues α-MSH form. We then use the technique in vivo to analyze the MRM transitions of the three different forms of α-MSH: the deacetylated α-MSH1–13, the acetylated α-MSH1–13 and the truncated form α-MSH1–12. For this experiment, we used a mouse model (PREP-GT in which the serine protease, prolyl endopeptidase, is deficient due to a genetrap insertion. Here we report that the ratio between acetylated α-MSH1–13 and α-MSH1–12 is significantly increased (P-value = 0.015, N = 6 in the pituitaries of PREP-GT mice when compared to wild type littermates. In addition no significant changes were revealed in the relative level of α-MSH1–13 versus the deacetylated α-MSH1–13. These results combined with the demonstration that PREP digests α-MSH1–13 in vitro, strongly suggest that α-MSH1–13 is an in vivo substrate of PREP. Conclusion The multiplex targeted quantitative peptidomics technique we

  4. A multiplex GC-MS/MS technique for the sensitive and quantitative single-run analysis of acidic phytohormones and related compounds, and its application to Arabidopsis thaliana.

    Science.gov (United States)

    Müller, Axel; Düchting, Petra; Weiler, Elmar W

    2002-11-01

    A highly sensitive and accurate multiplex gas chromatography-tandem mass spectrometry (GC-MS/MS) technique is reported for indole-3-acetic acid, abscisic acid, jasmonic acid, 12-oxo-phytodienoic acid and salicylic acid. The optimized setup allows the routine processing and analysis of up to 60 plant samples of between 20 and 200 mg of fresh weight per day. The protocol was designed and the equipment used was chosen to facilitate implementation of the method into other laboratories and to provide access to state-of-the-art analytical tools for the acidic phytohormones and related signalling molecules. Whole-plant organ-distribution maps for indole-3-acetic acid, abscisic acid, jasmonic acid, 12-oxo-phytodienoic acid and salicylic acid were generated for Arabidopsis thaliana (L.) Heynh. For leaves of A. thaliana, a spatial resolution of hormone quantitation down to approximately 2 mm(2) was achieved.

  5. Multiplexed quantitative analysis of CD3, CD8, and CD20 predicts response to neoadjuvant chemotherapy in breast cancer.

    Science.gov (United States)

    Brown, Jason R; Wimberly, Hallie; Lannin, Donald R; Nixon, Christian; Rimm, David L; Bossuyt, Veerle

    2014-12-01

    Although tumor-infiltrating lymphocytes (TIL) have been associated with response to neoadjuvant therapy, measurement typically is subjective, semiquantitative, and unable to differentiate among subpopulations. Here, we describe a quantitative objective method for analyzing lymphocyte subpopulations and assessing their predictive value. We developed a quantitative immunofluorescence assay to measure stromal expression of CD3, CD8, and CD20 on one slide. We validated this assay by comparison with flow cytometry on tonsil specimens and assessed predictive value in breast cancer on a neoadjuvant cohort (n = 95). Then, each marker was tested for prediction of pathologic complete response (pCR) compared with pathologist estimation of the percentage of lymphocyte infiltrate. The lymphocyte percentage and CD3, CD8, and CD20 proportions were similar between flow cytometry and quantitative immunofluorescence on tonsil specimens. Pathologist TIL count predicted pCR [P = 0.043; OR, 4.77; 95% confidence interval (CI), 1.05-21.6] despite fair interobserver reproducibility (κ = 0.393). Stromal AQUA (automated quantitative analysis) scores for CD3 (P = 0.023; OR, 2.51; 95% CI, 1.13-5.57), CD8 (P = 0.029; OR, 2.00; 95% CI, 1.08-3.72), and CD20 (P = 0.005; OR, 1.80; 95% CI, 1.19-2.72) predicted pCR in univariate analysis. CD20 AQUA score predicted pCR (P = 0.019; OR, 5.37; 95% CI, 1.32-21.8) independently of age, size, nuclear grade, nodal status, ER, PR, HER2, and Ki-67, whereas CD3, CD8, and pathologist estimation did not. We have developed and validated an objective, quantitative assay measuring TILs in breast cancer. Although this work provides analytic validity, future larger studies will be required to prove clinical utility. ©2014 American Association for Cancer Research.

  6. Multiplex real-time quantitative PCR, microscopy and rapid diagnostic immuno-chromatographic tests for the detection of Plasmodium spp: performance, limit of detection analysis and quality assurance

    Directory of Open Access Journals (Sweden)

    Ralevski Filip

    2009-12-01

    Full Text Available Abstract Background Accurate laboratory diagnosis of malaria species in returning travelers is paramount in the treatment of this potentially fatal infectious disease. Materials and methods A total of 466 blood specimens from returning travelers to Africa, Asia, and South/Central America with suspected malaria infection were collected between 2007 and 2009 at the reference public health laboratory. These specimens were assessed by reference microscopy, multipex real-time quantitative polymerase chain reaction (QPCR, and two rapid diagnostic immuno-chromatographic tests (ICT in a blinded manner. Key clinical laboratory parameters such as limit of detection (LOD analysis on clinical specimens by parasite stage, inter-reader variability of ICTs, staffing implications, quality assurance and cost analysis were evaluated. Results QPCR is the most analytically sensitive method (sensitivity 99.41%, followed by CARESTART (sensitivity 88.24%, and BINAXNOW (sensitivity 86.47% for the diagnosis of malaria in returning travelers when compared to reference microscopy. However, microscopy was unable to specifically identify Plasmodia spp. in 18 out of 170 positive samples by QPCR. Moreover, the 17 samples that were negative by microscopy and positive by QPCR were also positive by ICTs. Quality assurance was achieved for QPCR by exchanging a blinded proficiency panel with another reference laboratory. The Kappa value of inter-reader variability among three readers for BINAXNOW and CARESTART was calculated to be 0.872 and 0.898 respectively. Serial dilution studies demonstrated that the QPCR cycle threshold correlates linearly with parasitemia (R2 = 0.9746 in a clinically relevant dynamic range and retains a LOD of 11 rDNA copies/μl for P. falciparum, which was several log lower than reference microscopy and ICTs. LOD for QPCR is affected not only by parasitemia but the parasite stage distribution of each clinical specimen. QPCR was approximately 6-fold more

  7. Quantitative multiplex detection of pathogen biomarkers

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-02-09

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

  8. Quantitative multiplex detection of pathogen biomarkers

    Science.gov (United States)

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

    2014-10-14

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

  9. Microgravity validation of a novel system for RNA isolation and multiplex quantitative real time PCR analysis of gene expression on the International Space Station.

    Science.gov (United States)

    Parra, Macarena; Jung, Jimmy; Boone, Travis D; Tran, Luan; Blaber, Elizabeth A; Brown, Mark; Chin, Matthew; Chinn, Tori; Cohen, Jacob; Doebler, Robert; Hoang, Dzung; Hyde, Elizabeth; Lera, Matthew; Luzod, Louie T; Mallinson, Mark; Marcu, Oana; Mohamedaly, Youssef; Ricco, Antonio J; Rubins, Kathleen; Sgarlato, Gregory D; Talavera, Rafael O; Tong, Peter; Uribe, Eddie; Williams, Jeffrey; Wu, Diana; Yousuf, Rukhsana; Richey, Charles S; Schonfeld, Julie; Almeida, Eduardo A C

    2017-01-01

    The International Space Station (ISS) National Laboratory is dedicated to studying the effects of space on life and physical systems, and to developing new science and technologies for space exploration. A key aspect of achieving these goals is to operate the ISS National Lab more like an Earth-based laboratory, conducting complex end-to-end experimentation, not limited to simple microgravity exposure. Towards that end NASA developed a novel suite of molecular biology laboratory tools, reagents, and methods, named WetLab-2, uniquely designed to operate in microgravity, and to process biological samples for real-time gene expression analysis on-orbit. This includes a novel fluidic RNA Sample Preparation Module and fluid transfer devices, all-in-one lyophilized PCR assays, centrifuge, and a real-time PCR thermal cycler. Here we describe the results from the WetLab-2 validation experiments conducted in microgravity during ISS increment 47/SPX-8. Specifically, quantitative PCR was performed on a concentration series of DNA calibration standards, and Reverse Transcriptase-quantitative PCR was conducted on RNA extracted and purified on-orbit from frozen Escherichia coli and mouse liver tissue. Cycle threshold (Ct) values and PCR efficiencies obtained on-orbit from DNA standards were similar to Earth (1 g) controls. Also, on-orbit multiplex analysis of gene expression from bacterial cells and mammalian tissue RNA samples was successfully conducted in about 3 h, with data transmitted within 2 h of experiment completion. Thermal cycling in microgravity resulted in the trapping of gas bubbles inside septa cap assay tubes, causing small but measurable increases in Ct curve noise and variability. Bubble formation was successfully suppressed in a rapid follow-up on-orbit experiment using standard caps to pressurize PCR tubes and reduce gas release during heating cycles. The WetLab-2 facility now provides a novel operational on-orbit research capability for molecular biology and

  10. Real time quantitative amplification detection on a microarray: towards high multiplex quantitative PCR.

    NARCIS (Netherlands)

    Pierik, A.; Moamfa, M; van Zelst, M.; Clout, D.; Stapert, H.; Dijksman, Johan Frederik; Broer, D.; Wimberger-Friedl, R.

    2012-01-01

    Quantitative real-time polymerase chain reaction (qrtPCR) is widely used as a research and diagnostic tool. Notwithstanding its many powerful features, the method is limited in the degree of multiplexing to about 6 due to spectral overlap of the available fluorophores. A new method is presented that

  11. Analysis and Research of Multiplexing System

    Institute of Scientific and Technical Information of China (English)

    郭惠玲; 王仝杰; 刘越男

    2001-01-01

    The development of optical transmission was summarized. The multiplexing system was show in detail. The concepts, characteristic, key technology, expand trend and application prospect of frequency-division multiplexing, time-division multiplexing, code-division multiplexing and wave-division multiplexing were illustrated.

  12. The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis.

    Science.gov (United States)

    Zhang, Yongjie; Skaar, Ida; Sulyok, Michael; Liu, Xingzhong; Rao, Mingyong; Taylor, John W

    2016-01-01

    Pu-erh is a tea produced in Yunnan, China by microbial fermentation of fresh Camellia sinensis leaves by two processes, the traditional raw fermentation and the faster, ripened fermentation. We characterized fungal and bacterial communities in leaves and both Pu-erhs by high-throughput, rDNA-amplicon sequencing and we characterized the profile of bioactive extrolite mycotoxins in Pu-erh teas by quantitative liquid chromatography-tandem mass spectrometry. We identified 390 fungal and 629 bacterial OTUs from leaves and both Pu-erhs. Major findings are: 1) fungal diversity drops and bacterial diversity rises due to raw or ripened fermentation, 2) fungal and bacterial community composition changes significantly between fresh leaves and both raw and ripened Pu-erh, 3) aging causes significant changes in the microbial community of raw, but not ripened, Pu-erh, and, 4) ripened and well-aged raw Pu-erh have similar microbial communities that are distinct from those of young, raw Ph-erh tea. Twenty-five toxic metabolites, mainly of fungal origin, were detected, with patulin and asperglaucide dominating and at levels supporting the Chinese custom of discarding the first preparation of Pu-erh and using the wet tea to then brew a pot for consumption.

  13. Development and standardization of multiplexed antibody microarrays for use in quantitative proteomics.

    Science.gov (United States)

    Perlee, Lt; Christiansen, J; Dondero, R; Grimwade, B; Lejnine, S; Mullenix, M; Shao, W; Sorette, M; Tchernev, Vt; Patel, Dd; Kingsmore, Sf

    2004-12-15

    BACKGROUND: Quantitative proteomics is an emerging field that encompasses multiplexed measurement of many known proteins in groups of experimental samples in order to identify differences between groups. Antibody arrays are a novel technology that is increasingly being used for quantitative proteomics studies due to highly multiplexed content, scalability, matrix flexibility and economy of sample consumption. Key applications of antibody arrays in quantitative proteomics studies are identification of novel diagnostic assays, biomarker discovery in trials of new drugs, and validation of qualitative proteomics discoveries. These applications require performance benchmarking, standardization and specification. RESULTS: Six dual-antibody, sandwich immunoassay arrays that measure 170 serum or plasma proteins were developed and experimental procedures refined in more than thirty quantitative proteomics studies. This report provides detailed information and specification for manufacture, qualification, assay automation, performance, assay validation and data processing for antibody arrays in large scale quantitative proteomics studies. CONCLUSION: The present report describes development of first generation standards for antibody arrays in quantitative proteomics. Specifically, it describes the requirements of a comprehensive validation program to identify and minimize antibody cross reaction under highly multiplexed conditions; provides the rationale for the application of standardized statistical approaches to manage the data output of highly replicated assays; defines design requirements for controls to normalize sample replicate measurements; emphasizes the importance of stringent quality control testing of reagents and antibody microarrays; recommends the use of real-time monitors to evaluate sensitivity, dynamic range and platform precision; and presents survey procedures to reveal the significance of biomarker findings.

  14. Development and standardization of multiplexed antibody microarrays for use in quantitative proteomics

    Directory of Open Access Journals (Sweden)

    Sorette M

    2004-12-01

    Full Text Available Abstract Background Quantitative proteomics is an emerging field that encompasses multiplexed measurement of many known proteins in groups of experimental samples in order to identify differences between groups. Antibody arrays are a novel technology that is increasingly being used for quantitative proteomics studies due to highly multiplexed content, scalability, matrix flexibility and economy of sample consumption. Key applications of antibody arrays in quantitative proteomics studies are identification of novel diagnostic assays, biomarker discovery in trials of new drugs, and validation of qualitative proteomics discoveries. These applications require performance benchmarking, standardization and specification. Results Six dual-antibody, sandwich immunoassay arrays that measure 170 serum or plasma proteins were developed and experimental procedures refined in more than thirty quantitative proteomics studies. This report provides detailed information and specification for manufacture, qualification, assay automation, performance, assay validation and data processing for antibody arrays in large scale quantitative proteomics studies. Conclusion The present report describes development of first generation standards for antibody arrays in quantitative proteomics. Specifically, it describes the requirements of a comprehensive validation program to identify and minimize antibody cross reaction under highly multiplexed conditions; provides the rationale for the application of standardized statistical approaches to manage the data output of highly replicated assays; defines design requirements for controls to normalize sample replicate measurements; emphasizes the importance of stringent quality control testing of reagents and antibody microarrays; recommends the use of real-time monitors to evaluate sensitivity, dynamic range and platform precision; and presents survey procedures to reveal the significance of biomarker findings.

  15. A Biologist's Field Guide to Multiplexed Quantitative Proteomics.

    Science.gov (United States)

    Bakalarski, Corey E; Kirkpatrick, Donald S

    2016-05-01

    High-throughput genomic and proteomic studies have generated near-comprehensive catalogs of biological constituents within many model systems. Nevertheless, static catalogs are often insufficient to fully describe the dynamic processes that drive biology. Quantitative proteomic techniques address this need by providing insight into closely related biological states such as the stages of a therapeutic response or cellular differentiation. The maturation of quantitative proteomics in recent years has brought about a variety of technologies, each with their own strengths and weaknesses. It can be difficult for those unfamiliar with this evolving landscape to match the experiment at hand with the best tool for the job. Here, we outline quantitative methods for proteomic mass spectrometry and discuss their benefits and weaknesses from the perspective of the biologist aiming to generate meaningful data and address mechanistic questions. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Quantitative investment analysis

    CERN Document Server

    DeFusco, Richard

    2007-01-01

    In the "Second Edition" of "Quantitative Investment Analysis," financial experts Richard DeFusco, Dennis McLeavey, Jerald Pinto, and David Runkle outline the tools and techniques needed to understand and apply quantitative methods to today's investment process.

  17. Multiplexed paper test strip for quantitative bacterial detection.

    Science.gov (United States)

    Hossain, S M Zakir; Ozimok, Cory; Sicard, Clémence; Aguirre, Sergio D; Ali, M Monsur; Li, Yingfu; Brennan, John D

    2012-06-01

    Rapid, sensitive, on-site detection of bacteria without a need for sophisticated equipment or skilled personnel is extremely important in clinical settings and rapid response scenarios, as well as in resource-limited settings. Here, we report a novel approach for selective and ultra-sensitive multiplexed detection of Escherichia coli (non-pathogenic or pathogenic) using a lab-on-paper test strip (bioactive paper) based on intracellular enzyme (β-galactosidase (B-GAL) or β-glucuronidase (GUS)) activity. The test strip is composed of a paper support (0.5 × 8 cm), onto which either 5-bromo-4-chloro-3-indolyl-β-D: -glucuronide sodium salt (XG), chlorophenol red β-galactopyranoside (CPRG) or both and FeCl(3) were entrapped using sol-gel-derived silica inks in different zones via an ink-jet printing technique. The sample was lysed and assayed via lateral flow through the FeCl(3) zone to the substrate area to initiate rapid enzyme hydrolysis of the substrate, causing a change from colorless-to-blue (XG hydrolyzed by GUS, indication of nonpathogenic E. coli) and/or yellow to red-magenta (CPRG hydrolyzed by B-GAL, indication of total coliforms). Using immunomagnetic nanoparticles for selective preconcentration, the limit of detection was ~5 colony-forming units (cfu) per milliliter for E. coli O157:H7 and ~20 cfu/mL for E. coli BL21, within 30 min without cell culturing. Thus, these paper test strips could be suitable for detection of viable total coliforms and pathogens in bathing water samples. Moreover, inclusion of a culturing step allows detection of less than 1 cfu in 100 mL within 8 h, making the paper tests strips relevant for detection of multiple pathogens and total coliform bacteria in beverage and food samples.

  18. Nanoscale Test Strips for Multiplexed Blood Analysis

    Science.gov (United States)

    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

    DEFF Research Database (Denmark)

    2015-01-01

    Algebraic procedures for the analysis of multiple social networks are delivered with this package. Among other things, it is possible to create and manipulate multivariate network data with different formats, and there are effective ways available to treat multiple networks with routines that com......Algebraic procedures for the analysis of multiple social networks are delivered with this package. Among other things, it is possible to create and manipulate multivariate network data with different formats, and there are effective ways available to treat multiple networks with routines...... that combine algebraic systems like the partially ordered semigroup or the semiring structure together with the relational bundles occurring in different types of multivariate network data sets. As well an algebraic approach for two-mode networks is made through Galois derivations between families of the pair...

  20. Multivariate Quantitative Chemical Analysis

    Science.gov (United States)

    Kinchen, David G.; Capezza, Mary

    1995-01-01

    Technique of multivariate quantitative chemical analysis devised for use in determining relative proportions of two components mixed and sprayed together onto object to form thermally insulating foam. Potentially adaptable to other materials, especially in process-monitoring applications in which necessary to know and control critical properties of products via quantitative chemical analyses of products. In addition to chemical composition, also used to determine such physical properties as densities and strengths.

  1. Multivariate Quantitative Chemical Analysis

    Science.gov (United States)

    Kinchen, David G.; Capezza, Mary

    1995-01-01

    Technique of multivariate quantitative chemical analysis devised for use in determining relative proportions of two components mixed and sprayed together onto object to form thermally insulating foam. Potentially adaptable to other materials, especially in process-monitoring applications in which necessary to know and control critical properties of products via quantitative chemical analyses of products. In addition to chemical composition, also used to determine such physical properties as densities and strengths.

  2. Metrics for the analysis of multiplex networks

    CERN Document Server

    Battiston, Federico; Latora, Vito

    2013-01-01

    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 multi-layer 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 multi-layer networks, whose links are either unweighted or weighted. In particular we propose a series of measures to characterise the multiplexity 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, iii) global properties related to the navigability of the multiplex across the different layers. The measures we introduce are validated on a genuine multi-layer dataset of Indonesian terrorists, where information among 78 individuals are recorded with respect to ...

  3. Optimization and analysis of code-division multiplexed TES microcalorimeters

    CERN Document Server

    Fowler, J W; Hilton, G C; Irwin, K D; Schmidt, D R; Stiehl, G M; Swetz, D S; Ullom, J N; Vale., L R

    2011-01-01

    We are developing code-division multiplexing (CDM) systems for transition-edge sensor arrays with the goal of reaching multiplexing factors in the hundreds. We report on x-ray measurements made with a four-channel prototype CDM system that employs a flux-summing architecture, emphasizing data-analysis issues. We describe an empirical method to determine the demodulation matrix that minimizes cross-talk. This CDM system achieves energy resolutions of between 2.3 eV and 3.0 eV FWHM at 5.9 keV.

  4. Quantitative Hydrocarbon Surface Analysis

    Science.gov (United States)

    Douglas, Vonnie M.

    2000-01-01

    The elimination of ozone depleting substances, such as carbon tetrachloride, has resulted in the use of new analytical techniques for cleanliness verification and contamination sampling. The last remaining application at Rocketdyne which required a replacement technique was the quantitative analysis of hydrocarbons by infrared spectrometry. This application, which previously utilized carbon tetrachloride, was successfully modified using the SOC-400, a compact portable FTIR manufactured by Surface Optics Corporation. This instrument can quantitatively measure and identify hydrocarbons from solvent flush of hardware as well as directly analyze the surface of metallic components without the use of ozone depleting chemicals. Several sampling accessories are utilized to perform analysis for various applications.

  5. Familial aggregation of quantitative autistic traits in multiplex versus simplex autism.

    Science.gov (United States)

    Virkud, Yamini V; Todd, Richard D; Abbacchi, Anna M; Zhang, Yi; Constantino, John N

    2009-04-05

    Recent research has suggested that the mode of inheritance for simplex autism (SA, one individual in the family affected) may be distinct from that for multiplex autism (MA, two or more individuals affected). Since sub clinical autistic traits have been observed in "unaffected" relatives of children with autism, we explored whether the distributions of such traits in families supported differential modes of genetic transmission for SA and MA autism. We measured patterns of familial aggregation of quantitative autistic traits (QAT) in children and parents in 80 SA families and 210 MA families, using the Social Responsiveness Scale. When considering all SA and MA siblings who scored below a uniform quantitative (clinical-level) severity threshold, MA brothers exhibited a distinct pathological shift in the distribution, compared to SA brothers (P level of concordant elevation among spousal pairs in this volunteer sample. Among male first degree relatives, there exist distinct patterns of QAT manifestation for simplex versus multiplex autism. These findings are consistent with the results of molecular genetic studies that have suggested differential modes of intergenerational transmission for SA and MA. Characterization of QAT and other endophenotypes among close relatives may be useful for reducing sample heterogeneity in future genetic and neurobiologic studies of autism.

  6. Quantitative characterization of single cells by use of immunocytochemistry combined with multiplex LA-ICP-MS.

    Science.gov (United States)

    Mueller, Larissa; Herrmann, Antje J; Techritz, Sandra; Panne, Ulrich; Jakubowski, Norbert

    2017-05-01

    Actual research demonstrates that LA-ICP-MS is capable of being used as an imaging tool with cellular resolution. The aim of this investigation was the method development for LA-ICP-MS to extend the versatility to quantitative and multiplexing imaging of single eukaryotic cells. For visualization of individual cells selected, lanthanide-labeled antibodies were optimized for immuno-imaging of single cells with LA-ICP-MS. The molar content of the artificial introduced labels per cell was quantified using self-made nitrocellulose-coated slides for matrix-matched calibration and calculated amounts were in the range of 3.1 to 17.8 atmol per cell. Furthermore, the quantification strategy allows a conversion of 2D intensity profiles based on counts per second (cps) to quantitative 2D profiles representing the molar amount of the artificial introduced elemental probes per pixel for each individual cell. Graphical abstract ᅟ.

  7. Single-shot quantitative phase microscopy with color-multiplexed differential phase contrast (cDPC).

    Science.gov (United States)

    Phillips, Zachary F; Chen, Michael; Waller, Laura

    2017-01-01

    We present a new technique for quantitative phase and amplitude microscopy from a single color image with coded illumination. Our system consists of a commercial brightfield microscope with one hardware modification-an inexpensive 3D printed condenser insert. The method, color-multiplexed Differential Phase Contrast (cDPC), is a single-shot variant of Differential Phase Contrast (DPC), which recovers the phase of a sample from images with asymmetric illumination. We employ partially coherent illumination to achieve resolution corresponding to 2× the objective NA. Quantitative phase can then be used to synthesize DIC and phase contrast images or extract shape and density. We demonstrate amplitude and phase recovery at camera-limited frame rates (50 fps) for various in vitro cell samples and c. elegans in a micro-fluidic channel.

  8. Multiplex single particle analysis in microfluidics.

    Science.gov (United States)

    Dannhauser, D; Romeo, G; Causa, F; De Santo, I; Netti, P A

    2014-10-21

    A straightforward way to measure separated micrometric sized particles in microfluidic flow is reported. The light scattering profile (LSP) of each single particle is fully characterized by using a CMOS-camera based small angle light scattering (SALS) apparatus, ranging from 2° up to 30°. To ensure controlled particle passage through the incident laser, a viscoelastic 3D alignment effect by viscoelastic induced particle migration has been implemented in a simple and cost-effective microfluidic device. Different polystyrene particle sizes are measured in microfluidic flows and the obtained scattering signatures are matched with the Lorenz-Mie based scattering theory. The results confirm the possibility of using this apparatus for real multiplex particle analyses in microfluidic particle flows.

  9. The power of multiplexed functional analysis of genetic variants.

    Science.gov (United States)

    Gasperini, Molly; Starita, Lea; Shendure, Jay

    2016-10-01

    New technologies have recently enabled saturation mutagenesis and functional analysis of nearly all possible variants of regulatory elements or proteins of interest in single experiments. Here we discuss the past, present, and future of such multiplexed (functional) assays for variant effects (MAVEs). MAVEs provide detailed insight into sequence-function relationships, and they may prove critical for the prospective clinical interpretation of genetic variants.

  10. Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging.

    Science.gov (United States)

    Bauman, Tyler M; Ricke, Emily A; Drew, Sally A; Huang, Wei; Ricke, William A

    2016-04-08

    Immunohistochemistry is a commonly used clinical and research lab detection technique for investigating protein expression and localization within tissues. Many semi-quantitative systems have been developed for scoring expression using immunohistochemistry, but inherent subjectivity limits reproducibility and accuracy of results. Furthermore, the investigation of spatially overlapping biomarkers such as nuclear transcription factors is difficult with current immunohistochemistry techniques. We have developed and optimized a system for simultaneous investigation of multiple proteins using high throughput methods of multiplexed immunohistochemistry and multispectral imaging. Multiplexed immunohistochemistry is performed by sequential application of primary antibodies with secondary antibodies conjugated to horseradish peroxidase or alkaline phosphatase. Different chromogens are used to detect each protein of interest. Stained slides are loaded into an automated slide scanner and a protocol is created for automated image acquisition. A spectral library is created by staining a set of slides with a single chromogen on each. A subset of representative stained images are imported into multispectral imaging software and an algorithm for distinguishing tissue type is created by defining tissue compartments on images. Subcellular compartments are segmented by using hematoxylin counterstain and adjusting the intrinsic algorithm. Thresholding is applied to determine positivity and protein co-localization. The final algorithm is then applied to the entire set of tissues. Resulting data allows the user to evaluate protein expression based on tissue type (ex. epithelia vs. stroma) and subcellular compartment (nucleus vs. cytoplasm vs. plasma membrane). Co-localization analysis allows for investigation of double-positive, double-negative, and single-positive cell types. Combining multispectral imaging with multiplexed immunohistochemistry and automated image acquisition is an

  11. Quantitative multiplex detection of biomarkers on a waveguide-based biosensor using quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Hongzhi [Los Alamos National Laboratory; Mukundan, Harshini [Los Alamos National Laboratory; Martinez, Jennifer S [Los Alamos National Laboratory; Swanson, Basil I [Los Alamos National Laboratory; Anderson, Aaron S [Los Alamos National Laboratory; Grace, Kevin [Los Alamos National Laboratory

    2009-01-01

    The quantitative, simultaneous detection of multiple biomarkers with high sensitivity and specificity is critical for biomedical diagnostics, drug discovery and biomarker characterization [Wilson 2006, Tok 2006, Straub 2005, Joos 2002, Jani 2000]. Detection systems relying on optical signal transduction are, in general, advantageous because they are fast, portable, inexpensive, sensitive, and have the potential for multiplex detection of analytes of interest. However, conventional immunoassays for the detection of biomarkers, such as the Enzyme Linked Immunosorbant Assays (ELISAs) are semi-quantitative, time consuming and insensitive. ELISA assays are also limited by high non-specific binding, especially when used with complex biological samples such as serum and urine (REF). Organic fluorophores that are commonly used in such applications lack photostability and possess a narrow Stoke's shift that makes simultaneous detection of multiple fluorophores with a single excitation source difficult, thereby restricting their use in multiplex assays. The above limitations with traditional assay platforms have resulted in the increased use of nanotechnology-based tools and techniques in the fields of medical imaging [ref], targeted drug delivery [Caruthers 2007, Liu 2007], and sensing [ref]. One such area of increasing interest is the use of semiconductor quantum dots (QDs) for biomedical research and diagnostics [Gao and Cui 2004, Voura 2004, Michalet 2005, Chan 2002, Jaiswal 2004, Gao 2005, Medintz 2005, So 2006 2006, Wu 2003]. Compared to organic dyes, QDs provide several advantages for use in immunoassay platforms, including broad absorption bands with high extinction coefficients, narrow and symmetric emission bands with high quantum yields, high photostablility, and a large Stokes shift [Michalet 2005, Gu 2002]. These features prompted the use of QDs as probes in biodetection [Michalet 2005, Medintz 2005]. For example, Jaiswal et al. reported long term multiple

  12. Comparison of real-time genotyping and quantitative PCR,multiplex-PCR and sequence analysis for hepatitis B virus genotypes B and C%荧光定量分型PCR、多重PCR和测序检测HBV基因型的方法学比较

    Institute of Scientific and Technical Information of China (English)

    张秀瑜; 赵耀; 张文露; 胡源; 袁作为; 黄爱龙

    2010-01-01

    目的 比较荧光定量分型PCR、直接测序和多重PCR三种HBV基因分型法,对本实验室建立的荧光定量分型PCR方法进行评价.方法 用多重PCR、直接测序和荧光定量分型PCR法检测113份HBV DNA阳性的临床样本.结果 荧光定量分型PCR和直接测序法检出率100%,多重PCR法检出率94.69%,6份样本未能分型.荧光定量分型PCR和多重PCR的Kappa系数0.915,荧光定量分型PCR和直接测序法的Kappa系数0.742,一致性均较好.对B/C基因型混合感染样本,荧光定量分型PCR法检出28例(24.78%),多重PCR法检出19例(16.81%),直接测序法检出13例(11.50%).结论 荧光定量分型PCR分型结果准确可靠,对基因型混合感染样本的检出率明显高于多重PCR及直接测序法,是一种高效、简便、快速、准确的HBV基因分型法,适用于大规模流行病学调查.%Objective To evaluate the real-time genotyping and quantitative PCR(RT-GQ-PCR)method by comparing it with direct sequence analysis and the multiplex-PCR method.Methods RT-GQ-PCR,direct sequence analysis and the multiplex-PCR method were used to detect HBV genotypes of 113 patient samples with HBV-DNA positive.ResultsThe detection rate of RT-GQ-PCR and direct sequence analysis was 100%,and the multiplex-PCR is 94.69%.The concordance between RT-GQ-PCR and the multiplex-PCR is perfect(Kappa value =0.915),and the consistency of RT-GQ-PCR and direct sequence analysis is pretty good(Kappa value = 0.742),specially at detecting single genotype.Twenty-eight samples with genotypes B and C dual infections were detected by RT-GQ-PCR,but only 19 samples by the multiplexPCR and 13 samples by direct sequence analysis.Conclusion The RT-GQ-PCR is convenient,rapid and accurate in HBV genotyping,especially more sensitive than direct sequence analysis and the multiplex-PCR for detecting dual genotypes.The method is applicable for large-scale epidemiological study.

  13. Multiplex enrichment quantitative PCR (ME-qPCR): a high-throughput, highly sensitive detection method for GMO identification.

    Science.gov (United States)

    Fu, Wei; Zhu, Pengyu; Wei, Shuang; Zhixin, Du; Wang, Chenguang; Wu, Xiyang; Li, Feiwu; Zhu, Shuifang

    2017-04-01

    Among all of the high-throughput detection methods, PCR-based methodologies are regarded as the most cost-efficient and feasible methodologies compared with the next-generation sequencing or ChIP-based methods. However, the PCR-based methods can only achieve multiplex detection up to 15-plex due to limitations imposed by the multiplex primer interactions. The detection throughput cannot meet the demands of high-throughput detection, such as SNP or gene expression analysis. Therefore, in our study, we have developed a new high-throughput PCR-based detection method, multiplex enrichment quantitative PCR (ME-qPCR), which is a combination of qPCR and nested PCR. The GMO content detection results in our study showed that ME-qPCR could achieve high-throughput detection up to 26-plex. Compared to the original qPCR, the Ct values of ME-qPCR were lower for the same group, which showed that ME-qPCR sensitivity is higher than the original qPCR. The absolute limit of detection for ME-qPCR could achieve levels as low as a single copy of the plant genome. Moreover, the specificity results showed that no cross-amplification occurred for irrelevant GMO events. After evaluation of all of the parameters, a practical evaluation was performed with different foods. The more stable amplification results, compared to qPCR, showed that ME-qPCR was suitable for GMO detection in foods. In conclusion, ME-qPCR achieved sensitive, high-throughput GMO detection in complex substrates, such as crops or food samples. In the future, ME-qPCR-based GMO content identification may positively impact SNP analysis or multiplex gene expression of food or agricultural samples. Graphical abstract For the first-step amplification, four primers (A, B, C, and D) have been added into the reaction volume. In this manner, four kinds of amplicons have been generated. All of these four amplicons could be regarded as the target of second-step PCR. For the second-step amplification, three parallels have been taken for

  14. Multiplex dipstick immunoassay for semi-quantitative determination of Fusarium mycotoxins in cereals

    Energy Technology Data Exchange (ETDEWEB)

    Lattanzio, Veronica M.T., E-mail: veronica.lattanzio@ispa.cnr.it [National Research Council of Italy, Institute of Sciences of Food Production (ISPA-CNR), Via Amendola 122/O, 70126 Bari (Italy); Nivarlet, Noan [UNISENSOR S.A., Zoning industriel du Dossay, Rue du Dossay no 3, B-4020 Liege (Belgium); Lippolis, Vincenzo; Gatta, Stefania Della [National Research Council of Italy, Institute of Sciences of Food Production (ISPA-CNR), Via Amendola 122/O, 70126 Bari (Italy); Huet, Anne-Catherine; Delahaut, Philippe [Centre d' Economie Rurale (CER Groupe), Rue du Point du Jour no 8, B-6900 Marloie (Belgium); Granier, Benoit [UNISENSOR S.A., Zoning industriel du Dossay, Rue du Dossay no 3, B-4020 Liege (Belgium); Visconti, Angelo [National Research Council of Italy, Institute of Sciences of Food Production (ISPA-CNR), Via Amendola 122/O, 70126 Bari (Italy)

    2012-03-09

    Highlights: Black-Right-Pointing-Pointer We developed a rapid method based on a multiplex dipstick immunoassay. Black-Right-Pointing-Pointer The assay allowed the determination of major Fusarium toxins in wheat, oats, maize. Black-Right-Pointing-Pointer We obtained cut off levels close to EU regulatory levels. - Abstract: A multiplex dipstick immunoassay based method for the simultaneous determination of major Fusarium toxins, namely zearalenone, T-2 and HT-2 toxins, deoxynivalenol and fumonisins in wheat, oats and maize has been developed. The dipstick format was based on an indirect competitive approach. Four test lines (mycotoxin-BSA conjugates) and one control line were located on the strip membrane. Labelled antibodies were freeze-dried within the microwell. Two matrix-related sample preparation protocols have been developed for wheat/oats (not containing fumonisins) and maize (containing fumonisins) respectively. The use of a methanol/water mixture for sample preparation allowed recoveries in the range 73-109% for all mycotoxins in all tested cereals, with relative standard deviation less than 10%. The optimized immunoassay was able to detect target mycotoxins at cut off levels equal to 80% of EU maximum permitted levels, i.e. 280, 400, 1400 and 3200 {mu}g kg{sup -1}, respectively, for zearalenone, T-2/HT-2 toxins, deoxynivalenol and fumonisins in maize, and 80, 400 and 1400 {mu}g kg{sup -1}, respectively, for zearalenone, T-2/HT-2 toxins and deoxynivalenol in wheat and oats. Analysis of naturally contaminated samples resulted in a good agreement between multiplex dipstick and validated confirmatory LC-MS/MS. The percentage of false positive results was less than or equal to 13%, whereas no false negative results were obtained. Data on the presence/absence of 6 mycotoxins at levels close to EU regulatory levels were obtained within 30 min. The proposed immunoassay protocol is rapid, inexpensive, easy-to-use and fit for purpose of rapid screening of mycotoxins

  15. Dynamic multiplexed analysis method using ion mobility spectrometer

    Science.gov (United States)

    Belov, Mikhail E [Richland, WA

    2010-05-18

    A method for multiplexed analysis using ion mobility spectrometer in which the effectiveness and efficiency of the multiplexed method is optimized by automatically adjusting rates of passage of analyte materials through an IMS drift tube during operation of the system. This automatic adjustment is performed by the IMS instrument itself after determining the appropriate levels of adjustment according to the method of the present invention. In one example, the adjustment of the rates of passage for these materials is determined by quantifying the total number of analyte molecules delivered to the ion trap in a preselected period of time, comparing this number to the charge capacity of the ion trap, selecting a gate opening sequence; and implementing the selected gate opening sequence to obtain a preselected rate of analytes within said IMS drift tube.

  16. Capacity analysis of spectrum sharing spatial multiplexing MIMO systems

    KAUST Repository

    Yang, Liang

    2014-12-01

    This paper considers a spectrum sharing (SS) multiple-input multiple-output (MIMO) system operating in a Rayleigh fading environment. First the capacity of a single-user SS spatial multiplexing system is investigated in two scenarios that assume different receivers. To explicitly show the capacity scaling law of SS MIMO systems, some approximate capacity expressions for the two scenarios are derived. Next, we extend our analysis to a multiple user system with zero-forcing receivers (ZF) under spatially-independent scheduling and analyze the sum-rate. Furthermore, we provide an asymptotic sum-rate analysis to investigate the effects of different parameters on the multiuser diversity gain. Our results show that the secondary system with a smaller number of transmit antennas Nt and a larger number of receive antennas Nr can achieve higher capacity at lower interference temperature Q, but at high Q the capacity follows the scaling law of the conventional MIMO systems. However, for a ZF SS spatial multiplexing system, the secondary system with small Nt and large Nr can achieve the highest capacity throughout the entire region of Q. For a ZF SS spatial multiplexing system with scheduling, the asymptotic sum-rate scales like Ntlog2(Q(KNtNp-1)/Nt), where Np denotes the number of antennas of the primary receiver and K represents the number of secondary transmitters.

  17. Quantitative proteomic profiling of breast cancers using a multiplexed microfluidic platform for immunohistochemistry and immunocytochemistry.

    Science.gov (United States)

    Kim, Minseok S; Kwon, Seyong; Kim, Taemin; Lee, Eun Sook; Park, Je-Kyun

    2011-02-01

    This paper describes a multiplexed microfluidic immunohistochemistry (IHC)/immunocytochemistry (ICC) platform for quantitative proteomic profiling in breast cancer samples. Proteomic profiling via ICC was examined for four breast cancer cell lines (AU-565, HCC70, MCF-7, and SK-BR-3). The microfluidic device enabled 20 ICC assays on a biological specimen at the same time and a 16-fold decrease in time consumption, and could be used to quantitatively compare the expression level of each biomarker. The immunohistochemical staining from the microfluidic system showed an accurate localization of protein and comparable quality to that of the conventional IHC method. Although AU-565 and SK-BR-3 cell lines were classified by luminal subtype and adenocarcinomas and were derived from the same patient, weak p63 expression was seen only in SK-BR-3. The HCC70 cell line showed a triple-negative (estrogen receptor-negative/progesterone receptor-negative/human epidermal growth factor receptor 2-negative) phenotype and showed only cytokeratin 5 expression, a representative basal/myoepithelial cell marker. To demonstrate the applicability of the system to clinical samples for proteomic profiling, we were also able to apply this platform to human breast cancer tissue. This result indicates that the microfluidic IHC/ICC platform is useful for accurate histopathological diagnoses using numerous specific biomarkers simultaneously, facilitating the individualization of cancer therapy.

  18. Simultaneous detection, typing and quantitation of oncogenic human papillomavirus by multiplex consensus real-time PCR.

    Science.gov (United States)

    Jenkins, Andrew; Allum, Anne-Gry; Strand, Linda; Aakre, Randi Kersten

    2013-02-01

    A consensus multiplex real-time PCR test (PT13-RT) for the oncogenic human papillomavirus (HPV) types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59 and 66 is described. The test targets the L1 gene. Analytical sensitivity is between 4 and 400 GU (genomic units) in the presence of 500 ng of human DNA, corresponding to 75,000 human cells. HPV types are grouped into multiplex groups of 3 or 4 resulting in the use of 4 wells per sample and permitting up to 24 samples per run (including controls) in a standard 96-well real-time PCR instrument. False negative results are avoided by (a) measuring sample DNA concentration to control that sufficient cellular material is present and (b) including HPV type 6 as a homologous internal control in order to detect PCR inhibition or competition from other (non-oncogenic) HPV types. Analysis time from refrigerator to report is 8 h, including 2.5 h hands-on time. Relative to the HC2 test, the sensitivity and specificity were respectively 98% and 83%, the lower specificity being attributable to the higher analytical sensitivity of PT13-RT. To assess type determination comparison was made with a reversed line-blot test. Type concordance was high (κ=0.79) with discrepancies occurring mostly in multiple-positive samples. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Multiplex time-reducing quantitative polymerase chain reaction assay for determination of telomere length in blood and tissue DNA.

    Science.gov (United States)

    Jiao, Jingjing; Kang, Jing X; Tan, Rui; Wang, Jingdong; Zhang, Yu

    2012-04-01

    In this paper we describe a multiplex time-reducing quantitative polymerase chain reaction (qPCR) method for determination of telomere length. This multiplex qPCR assay enables two pairs of primers to simultaneously amplify telomere and single copy gene (albumin) templates, thus reducing analysis time and labor compared with the previously established singleplex assay. The chemical composition of the master mix and primers for the telomere and albumin were systematically optimized. The thermal cycling program was designed to ensure complete separation of the melting processes of the telomere and albumin. Semi-log standard curves of DNA concentration versus cycle threshold (C (t)) were established, with a linear relationship over an 81-fold DNA concentration range. The well-performed intra-assay (RSD range 2.4-4.7%) and inter-assay (RSD range: 3.1-5.0%) reproducibility were demonstrated to ensure measurement stability. Using wild-type, Lewis lung carcinoma and H22 liver carcinoma C57BL/6 mouse models, significantly different telomere lengths among different DNA samples were not observed in wild-type mice. However, the relative telomere lengths of the tumor DNA in the two strains of tumor-bearing mice were significantly shorter than the lengths in the surrounding non-tumor DNA of tumor-bearing mice and the tissue DNA of wild-type mice. These results suggest that the shortening of telomere lengths may be regarded as an important indicator for cancer control and prevention. Quantification of telomere lengths was further confirmed by the traditional Southern blotting method. This method could be successfully used to reduce the time needed for rapid, precise measurement of telomere lengths in biological samples.

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

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, L.S.; Hoffman, E.P. (Univ. of Pittsburgh Schoool of Medicine, Pittsburgh, PA (United States)); Tarleton, J. (Self Memorial Hospital, Greenwood, SC (United States)); Popovich, B. (Children' s Hosptial and Health Center, San Diego, CA (United States)); Seltzer, W.K. (Univ. of Colorado Health Sciences Center, Denver, CO (United States))

    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.

  1. Multiplex, Quantitative, Reverse Transcription PCR Detection of Influenza Viruses Using Droplet Microfluidic Technology

    Directory of Open Access Journals (Sweden)

    Ravi Prakash

    2014-12-01

    Full Text Available Quantitative, reverse transcription, polymerase chain reaction (qRT-PCR is facilitated by leveraging droplet microfluidic (DMF system, which due to its precision dispensing and sample handling capabilities at microliter and lower volumes has emerged as a popular method for miniaturization of the PCR platform. This work substantially improves and extends the functional capabilities of our previously demonstrated single qRT-PCR micro-chip, which utilized a combination of electrostatic and electrowetting droplet actuation. In the reported work we illustrate a spatially multiplexed micro-device that is capable of conducting up to eight parallel, real-time PCR reactions per usage, with adjustable control on the PCR thermal cycling parameters (both process time and temperature set-points. This micro-device has been utilized to detect and quantify the presence of two clinically relevant respiratory viruses, Influenza A and Influenza B, in human samples (nasopharyngeal swabs, throat swabs. The device performed accurate detection and quantification of the two respiratory viruses, over several orders of RNA copy counts, in unknown (blind panels of extracted patient samples with acceptably high PCR efficiency (>94%. The multi-stage qRT-PCR assays on eight panel patient samples were accomplished within 35–40 min, with a detection limit for the target Influenza virus RNAs estimated to be less than 10 RNA copies per reaction.

  2. A novel multiplex method for the simultaneous detection and relative quantitation of pollen allergens.

    Science.gov (United States)

    Morales, Sonia; Castro, Antonio Jesús; Jimenez-Lopez, Jose Carlos; Florido, Fernando; Rodríguez-García, María Isabel; de Dios Alché, Juan

    2012-05-01

    Standardization of pollen protein extracts is essential in order to ensure efficiency and safety in allergy diagnosis and immunotherapy. In this paper, we have optimized a multiplex Western blotting method for the simultaneous detection of four olive pollen allergens (Ole e 1, Ole e 2, Ole e 5, and Ole e 9) on a single blot using a monoclonal antibody from mouse and three polyclonal antibodies raised in rabbit. We utilized unconjugated Fab antibody fragments for blocking rabbit primary antibodies, and fluorescence-based detection. These changes allowed an accurate and reliable comparative quantitation of these allergens among pollen-protein samples from six olive cultivars. In addition, we also tested the IgE-binding capacity of these pollen extracts by reprobing the same blot with a pool of sera from eight patients allergic to olive and detection with enzyme conjugated antibodies. A noticeable variability regarding allergen content and IgE-reactivity was found among the olive cultivars analyzed. Moreover, we could easily confirm the identity of some of the IgE-binding proteins by simply overlapping both fluorescence and chemiluminescence images. This method is versatile since it can be applied to other allergogenic plant species and extended to other allergens.

  3. A multiplex quantitative real-time polymerase chain reaction panel for detecting neurologic pathogens in dogs with meningoencephalitis

    OpenAIRE

    Han, Jae-Ik; Chang, Dong-Woo; Na, Ki-Jeong

    2015-01-01

    Meningoencephalitis (ME) is a common inflammatory disorder of the central nervous system in dogs. Clinically, ME has both infectious and non-infectious causes. In the present study, a multiplex quantitative real-time polymerase chain reaction (mqPCR) panel was optimized for the detection of eight canine neurologic pathogens (Blastomyces dermatitidis, Cryptococcus spp., Neospora caninum, Borrelia burgdorferi, Bartonella spp., Toxoplasma gondii, Ehrlichia canis, and canine distemper virus [CDV]...

  4. Quantitative Techniques in Volumetric Analysis

    Science.gov (United States)

    Zimmerman, John; Jacobsen, Jerrold J.

    1996-12-01

    Quantitative Techniques in Volumetric Analysis is a visual library of techniques used in making volumetric measurements. This 40-minute VHS videotape is designed as a resource for introducing students to proper volumetric methods and procedures. The entire tape, or relevant segments of the tape, can also be used to review procedures used in subsequent experiments that rely on the traditional art of quantitative analysis laboratory practice. The techniques included are: Quantitative transfer of a solid with a weighing spoon Quantitative transfer of a solid with a finger held weighing bottle Quantitative transfer of a solid with a paper strap held bottle Quantitative transfer of a solid with a spatula Examples of common quantitative weighing errors Quantitative transfer of a solid from dish to beaker to volumetric flask Quantitative transfer of a solid from dish to volumetric flask Volumetric transfer pipet A complete acid-base titration Hand technique variations The conventional view of contemporary quantitative chemical measurement tends to focus on instrumental systems, computers, and robotics. In this view, the analyst is relegated to placing standards and samples on a tray. A robotic arm delivers a sample to the analysis center, while a computer controls the analysis conditions and records the results. In spite of this, it is rare to find an analysis process that does not rely on some aspect of more traditional quantitative analysis techniques, such as careful dilution to the mark of a volumetric flask. Figure 2. Transfer of a solid with a spatula. Clearly, errors in a classical step will affect the quality of the final analysis. Because of this, it is still important for students to master the key elements of the traditional art of quantitative chemical analysis laboratory practice. Some aspects of chemical analysis, like careful rinsing to insure quantitative transfer, are often an automated part of an instrumental process that must be understood by the

  5. Identification of SPRED1 deletions using RT-PCR, multiplex ligation-dependent probe amplification and quantitative PCR.

    Science.gov (United States)

    Spencer, Emily; Davis, Julia; Mikhail, Fady; Fu, Chuanhua; Vijzelaar, Raymon; Zackai, Elaine H; Feret, Holly; Meyn, M Stephen; Shugar, Andrea; Bellus, Gary; Kocsis, Kristina; Kivirikko, Sirpa; Pöyhönen, Minna; Messiaen, Ludwine

    2011-06-01

    Legius syndrome, is a recently identified autosomal dominant disorder caused by loss of function mutations in the SPRED1 gene, with individuals mainly presenting with multiple café-au-lait macules (CALM), freckling and macrocephaly. So far, only SPRED1 point mutations have been identified as the cause of this syndrome. To determine if copy number changes (CNCs) are a cause of Legius syndrome, we have used a Multiplex Ligation-dependent Probe Amplification (MLPA) assay covering all SPRED1 exons in a cohort of 510 NF1-negative patients presenting with multiple CALMs with or without freckling, but no other NF1 diagnostic signs. Four different deletions were identified by MLPA and confirmed by quantitative PCR, reverse transcriptase PCR and/or array CGH: a deletion of exon 1 and the SPRED1 promoter region in a proband and two first-degree relatives; a deletion of the entire SPRED1 gene in a sporadic patient; a deletion of exon 2-6 in a proband and her father; and an ∼6.6 Mb deletion on chromosome 15 that spans SPRED1 in a sporadic patient. Deletions account for ∼10% of the 40 detected SPRED1 mutations in this cohort of 510 individuals. These results indicate the need for dosage analysis to complement sequencing-based SPRED1 mutation analyses.

  6. Air-segmented amplitude-modulated multiplexed flow analysis.

    Science.gov (United States)

    Inui, Koji; Uemura, Takeshi; Ogusu, Takeshi; Takeuchi, Masaki; Tanaka, Hideji

    2011-01-01

    Air-segmentation is applied to amplitude-modulated multiplexed flow analysis, which we proposed recently. Sample solutions, the flow rates of which are varied periodically, are merged with reagent and/or diluent solution. The merged stream is segmented by air-bubbles and, downstream, its absorbance is measured after deaeration. The analytes in the samples are quantified from the amplitudes of the respective wave components in the absorbance. The proposed method is applied to the determinations of a food dye, phosphate ions and nitrite ions. The air-segmentation is effective for limiting amplitude damping through the axial dispersion, resulting in an improvement in sensitivity. This effect is more pronounced at shorter control periods and longer flow path lengths.

  7. Simultaneous quantitative assessment of circulating cell-free mitochondrial and nuclear DNA by multiplex real-time PCR

    Directory of Open Access Journals (Sweden)

    Peng Xia

    2009-01-01

    Full Text Available Quantification of circulating nucleic acids in plasma and serum could be used as a non-invasive diagnostic tool for monitoring a wide variety of diseases and conditions. We describe here a rapid, simple and accurate multiplex real-time PCR method for direct synchronized analysis of circulating cell-free (ccf mitochondrial (mtDNA and nuclear (nDNA DNA in plasma and serum samples. The method is based on one-step multiplex real-time PCR using a FAM-labeled MGB probe and primers to amplify the mtDNA sequence of the ATP 8 gene, and a VIC-labeled MGB probe and primers to amplify the nDNA sequence of the glycerinaldehyde-3-phosphate-dehydrogenase (GAPDH gene, in plasma and serum samples simultaneously. The efficiencies of the multiplex assays were measured in serial dilutions. Based on the simulation of the PCR reaction kinetics, the relative quantities of ccf mtDNA were calculated using a very simple equation. Using our optimised real-time PCR conditions, close to 100% efficiency was obtained from the two assays. The two assays performed in the dilution series showed very good and reproducible correlation to each other. This optimised multiplex real-time PCR protocol can be widely used for synchronized quantification of mtDNA and nDNA in different samples, with a very high rate of efficiency.

  8. Application of a Multiplex Quantitative PCR to Assess Prevalence and Intensity Of Intestinal Parasite Infections in a Controlled Clinical Trial.

    Directory of Open Access Journals (Sweden)

    Stacey Llewellyn

    2016-01-01

    Full Text Available Accurate quantitative assessment of infection with soil transmitted helminths and protozoa is key to the interpretation of epidemiologic studies of these parasites, as well as for monitoring large scale treatment efficacy and effectiveness studies. As morbidity and transmission of helminth infections are directly related to both the prevalence and intensity of infection, there is particular need for improved techniques for assessment of infection intensity for both purposes. The current study aimed to evaluate two multiplex PCR assays to determine prevalence and intensity of intestinal parasite infections, and compare them to standard microscopy.Faecal samples were collected from a total of 680 people, originating from rural communities in Timor-Leste (467 samples and Cambodia (213 samples. DNA was extracted from stool samples and subject to two multiplex real-time PCR reactions the first targeting: Necator americanus, Ancylostoma spp., Ascaris spp., and Trichuris trichiura; and the second Entamoeba histolytica, Cryptosporidium spp., Giardia. duodenalis, and Strongyloides stercoralis. Samples were also subject to sodium nitrate flotation for identification and quantification of STH eggs, and zinc sulphate centrifugal flotation for detection of protozoan parasites. Higher parasite prevalence was detected by multiplex PCR (hookworms 2.9 times higher, Ascaris 1.2, Giardia 1.6, along with superior polyparasitism detection with this effect magnified as the number of parasites present increased (one: 40.2% vs. 38.1%, two: 30.9% vs. 12.9%, three: 7.6% vs. 0.4%, four: 0.4% vs. 0%. Although, all STH positive samples were low intensity infections by microscopy as defined by WHO guidelines the DNA-load detected by multiplex PCR suggested higher intensity infections.Multiplex PCR, in addition to superior sensitivity, enabled more accurate determination of infection intensity for Ascaris, hookworms and Giardia compared to microscopy, especially in samples

  9. Quantitative Risk Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Helms, J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-02-10

    The US energy sector is vulnerable to multiple hazards including both natural disasters and malicious attacks from an intelligent adversary. The question that utility owners, operators and regulators face is how to prioritize their investments to mitigate the risks from a hazard that can have the most impact on the asset of interest. In order to be able to understand their risk landscape and develop a prioritized mitigation strategy, they must quantify risk in a consistent way across all hazards their asset is facing. Without being able to quantitatively measure risk, it is not possible to defensibly prioritize security investments or evaluate trade-offs between security and functionality. Development of a methodology that will consistently measure and quantify risk across different hazards is needed.

  10. Monotowns: A Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Shastitko Andrei

    2016-06-01

    Full Text Available The authors propose an empirical analysis of the current situation in monotowns. The study questions the perceived seriousness of the ‘monotown problem’ as well as the actual challenges it presents. The authors use a cluster analysis to divide monotowns into groups for further structural comparison. The structural differences in the available databases limit the possibilities of empirical analysis. Hence, alternative approaches are required. The authors consider possible reasons for the limitations identified. Special attention is paid to the monotowns that were granted the status of advanced development territories. A comparative analysis makes it possible to study their general characteristics and socioeconomic indicators. The authors apply the theory of opportunistic behaviour to describe potential problems caused by the lack of unified criteria for granting monotowns the status of advanced development territories. The article identifies the main stakeholders and the character of their interaction; it desc ribes a conceptual model built on the principal/agent interactions, and identifies the parametric space of mutually beneficial cooperation. The solution to the principal/agent problem suggested in the article contributes to the development of an alternative approach to the current situation and a rational approach to overcoming the ‘monotown problem’.

  11. Nanoscale Test Strips for Multiplexed Blood Analysis Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of our nanoscale test strips, or nanostrips, is to provide rapid, low-cost, powerful multiplexed analyses in a diminutive form so that whole body health...

  12. Evaluation of multiplex ligation-dependent probe amplification analysis versus multiplex polymerase chain reaction assays in the detection of dystrophin gene rearrangements in an Iranian population subset

    Directory of Open Access Journals (Sweden)

    Nayereh Nouri

    2014-01-01

    Full Text Available Background: The Duchenne muscular dystrophy (DMD gene is located in the short arm of the X chromosome (Xp21. It spans 2.4 Mb of the human genomic DNA and is composed of 79 exons. Mutations in the Dystrophin gene result in DMD and Becker muscular dystrophy. In this study, the efficiency of multiplex ligation-dependent probe amplification (MLPA over multiplex polymerase chain reaction (PCR assays in an Iranian population was investigated. Materials and Methods: Multiplex PCR assays and MLPA analysis were carried out in 74 patients affected with DMD. Results: Multiplex PCR detected deletions in 51% of the patients with DMD. MLPA analysis could determine all the deletions detected by the multiplex PCR. Additionally, MLPA was able to identify one more deletion and duplication in patients without detectable mutations by multiplex PCR. Moreover, MLPA precisely determined the exact size of the deletions. Conclusion: Although MLPA analysis is more sensitive for detection of deletions and duplications in the dystrophin gene, multiplex PCR might be used for the initial analysis of the boys affected with DMD in the Iranian population as it was able to detect 95% of the rearrangements in patients with DMD.

  13. Simultaneous comprehensive multiplex autoantibody analysis for rapidly progressive glomerulonephritis.

    Science.gov (United States)

    Sowa, Mandy; Trezzi, Barbara; Hiemann, Rico; Schierack, Peter; Grossmann, Kai; Scholz, Juliane; Somma, Valentina; Sinico, Renato Alberto; Roggenbuck, Dirk; Radice, Antonella

    2016-11-01

    Rapidly progressive glomerulonephritis (RPGN) is mainly caused by anti-glomerular basement membrane (GBM) antibody-mediated glomerulonephritis, immune-complex or anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides and leads to rapid loss of renal function. Detection of ANCA and autoantibodies (autoAbs) to GBM and dsDNA enables early diagnosis and appropriate treatment of RPGN aiding in preventing end-stage renal disease.Determination of ANCA on neutrophils (ANCA) as well as autoAbs to myeloperoxidase (MPO-ANCA), proteinase 3 (PR3-ANCA), GBM, and dsDNA was performed by the novel multiplex CytoBead technology combining cell- and microbead-based autoAb analyses by automated indirect immunofluorescence (IIF). Forty patients with granulomatosis with polyangiitis (GPA), 48 with microscopic polyangiitis (MPA), 2 with eosinophilic GPA, 42 with systemic lupus erythematosus (SLE), 43 with Goodpasture syndrome (GPS), 57 with infectious diseases (INF), and 55 healthy subjects (HS) were analyzed and findings compared with classical single testing.The CytoBead assay revealed for GPA, MPA, GPS, and SLE the following diagnostic sensitivities and for HS and INF the corresponding specificities: PR3-ANCA, 85.0% and 100.0%; MPO-ANCA, 77.1% and 99.1%; anti-GBM autoAb, 88.4% and 96.4%; anti-dsDNA autoAb, 83.3% and 97.3%; ANCA, 91.1% and 99.1%, respectively. Agreement with classical enzyme-linked immunosorbent assay and IIF was very good for anti-GBM autoAb, MPO-ANCA, PR3-ANCA, and ANCA, respectively. Anti-dsDNA autoAb comparative analysis demonstrated fair agreement only and a significant difference (P = 0.0001).The CytoBead technology provides a unique multiplex reaction environment for simultaneous RPGN-specific autoAb testing. CytoBead RPGN assay is a promising alternative to time-consuming single parameter analysis and, thus, is well suited for emergency situations.

  14. Simultaneous comprehensive multiplex autoantibody analysis for rapidly progressive glomerulonephritis

    Science.gov (United States)

    Sowa, Mandy; Trezzi, Barbara; Hiemann, Rico; Schierack, Peter; Grossmann, Kai; Scholz, Juliane; Somma, Valentina; Sinico, Renato Alberto; Roggenbuck, Dirk; Radice, Antonella

    2016-01-01

    Abstract Rapidly progressive glomerulonephritis (RPGN) is mainly caused by anti-glomerular basement membrane (GBM) antibody-mediated glomerulonephritis, immune-complex or anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides and leads to rapid loss of renal function. Detection of ANCA and autoantibodies (autoAbs) to GBM and dsDNA enables early diagnosis and appropriate treatment of RPGN aiding in preventing end-stage renal disease. Determination of ANCA on neutrophils (ANCA) as well as autoAbs to myeloperoxidase (MPO-ANCA), proteinase 3 (PR3-ANCA), GBM, and dsDNA was performed by the novel multiplex CytoBead technology combining cell- and microbead-based autoAb analyses by automated indirect immunofluorescence (IIF). Forty patients with granulomatosis with polyangiitis (GPA), 48 with microscopic polyangiitis (MPA), 2 with eosinophilic GPA, 42 with systemic lupus erythematosus (SLE), 43 with Goodpasture syndrome (GPS), 57 with infectious diseases (INF), and 55 healthy subjects (HS) were analyzed and findings compared with classical single testing. The CytoBead assay revealed for GPA, MPA, GPS, and SLE the following diagnostic sensitivities and for HS and INF the corresponding specificities: PR3-ANCA, 85.0% and 100.0%; MPO-ANCA, 77.1% and 99.1%; anti-GBM autoAb, 88.4% and 96.4%; anti-dsDNA autoAb, 83.3% and 97.3%; ANCA, 91.1% and 99.1%, respectively. Agreement with classical enzyme-linked immunosorbent assay and IIF was very good for anti-GBM autoAb, MPO-ANCA, PR3-ANCA, and ANCA, respectively. Anti-dsDNA autoAb comparative analysis demonstrated fair agreement only and a significant difference (P = 0.0001). The CytoBead technology provides a unique multiplex reaction environment for simultaneous RPGN-specific autoAb testing. CytoBead RPGN assay is a promising alternative to time-consuming single parameter analysis and, thus, is well suited for emergency situations. PMID:27858870

  15. Analysis of WiMAX Physical Layer Using Spatial Multiplexing

    CERN Document Server

    Sanghoi, Pavani

    2012-01-01

    Broadband Wireless Access (BWA) has emerged as a promising solution for providing last mile internet access technology to provide high speed internet access to the users in the residential as well as in the small and medium sized enterprise sectors. IEEE 802.16e is one of the most promising and attractive candidate among the emerging technologies for broadband wireless access. The emergence of WiMAX protocol has attracted various interests from almost all the fields of wireless communications. MIMO systems which are created according to the IEEE 802.16-2005 standard (WiMAX) under different fading channels can be implemented to get the benefits of both the MIMO and WiMAX technologies. In this paper analysis of higher level of modulations (i.e. M-PSK and M-QAM for different values of M) with different code rates and on WiMAX-MIMO system is presented for Rayleigh channel by focusing on spatial multiplexing MIMO technique. Signal-to Noise Ratio (SNR) vs Bit Error Rate (BER) analysis has been done.

  16. Plasmonic liquid marbles: a miniature substrate-less SERS platform for quantitative and multiplex ultratrace molecular detection.

    Science.gov (United States)

    Lee, Hiang Kwee; Lee, Yih Hong; Phang, In Yee; Wei, Jiaqi; Miao, Yue-E; Liu, Tianxi; Ling, Xing Yi

    2014-05-12

    Inspired by aphids, liquid marbles have been studied extensively and have found application as isolated microreactors, as micropumps, and in sensing. However, current liquid-marble-based sensing methodologies are limited to qualitative colorimetry-based detection. Herein we describe the fabrication of a plasmonic liquid marble as a substrate-less analytical platform which, when coupled with ultrasensitive SERS, enables simultaneous multiplex quantification and the identification of ultratrace analytes across separate phases. Our plasmonic liquid marble demonstrates excellent mechanical stability and is suitable for the quantitative examination of ultratrace analytes, with detection limits as low as 0.3 fmol, which corresponds to an analytical enhancement factor of 5×10(8). The results of our simultaneous detection scheme based on plasmonic liquid marbles and an aqueous-solid-organic interface quantitatively tally with those found for the individual detection of methylene blue and coumarin.

  17. Quantitative multiplex quantum dot in-situ hybridisation based gene expression profiling in tissue microarrays identifies prognostic genes in acute myeloid leukaemia

    Energy Technology Data Exchange (ETDEWEB)

    Tholouli, Eleni [Department of Haematology, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL (United Kingdom); MacDermott, Sarah [The Medical School, The University of Manchester, Oxford Road, M13 9PT Manchester (United Kingdom); Hoyland, Judith [School of Biomedicine, Faculty of Medical and Human Sciences, The University of Manchester, Oxford Road, M13 9PT Manchester (United Kingdom); Yin, John Liu [Department of Haematology, Manchester Royal Infirmary, Oxford Road, Manchester, M13 9WL (United Kingdom); Byers, Richard, E-mail: richard.byers@cmft.nhs.uk [School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, The University of Manchester, Stopford Building, Oxford Road, M13 9PT Manchester (United Kingdom)

    2012-08-24

    Highlights: Black-Right-Pointing-Pointer Development of a quantitative high throughput in situ expression profiling method. Black-Right-Pointing-Pointer Application to a tissue microarray of 242 AML bone marrow samples. Black-Right-Pointing-Pointer Identification of HOXA4, HOXA9, Meis1 and DNMT3A as prognostic markers in AML. -- Abstract: Measurement and validation of microarray gene signatures in routine clinical samples is problematic and a rate limiting step in translational research. In order to facilitate measurement of microarray identified gene signatures in routine clinical tissue a novel method combining quantum dot based oligonucleotide in situ hybridisation (QD-ISH) and post-hybridisation spectral image analysis was used for multiplex in-situ transcript detection in archival bone marrow trephine samples from patients with acute myeloid leukaemia (AML). Tissue-microarrays were prepared into which white cell pellets were spiked as a standard. Tissue microarrays were made using routinely processed bone marrow trephines from 242 patients with AML. QD-ISH was performed for six candidate prognostic genes using triplex QD-ISH for DNMT1, DNMT3A, DNMT3B, and for HOXA4, HOXA9, Meis1. Scrambled oligonucleotides were used to correct for background staining followed by normalisation of expression against the expression values for the white cell pellet standard. Survival analysis demonstrated that low expression of HOXA4 was associated with poorer overall survival (p = 0.009), whilst high expression of HOXA9 (p < 0.0001), Meis1 (p = 0.005) and DNMT3A (p = 0.04) were associated with early treatment failure. These results demonstrate application of a standardised, quantitative multiplex QD-ISH method for identification of prognostic markers in formalin-fixed paraffin-embedded clinical samples, facilitating measurement of gene expression signatures in routine clinical samples.

  18. Diagnosis of ocular toxoplasmosis by two polymerase chain reaction (PCR) examinations: qualitative multiplex and quantitative real-time.

    Science.gov (United States)

    Sugita, Sunao; Ogawa, Manabu; Inoue, Shizu; Shimizu, Norio; Mochizuki, Manabu

    2011-09-01

    To establish a two-step polymerase chain reaction (PCR) diagnostic system for ocular toxoplasmosis. A total of 13 ocular fluid samples (11 aqueous humor and 2 vitreous fluid) were collected from 13 patients with clinically suspected ocular toxoplasmosis. Ten ocular samples from other uveitis patients and 20 samples from subjects without ocular inflammation were used as controls. Two polymerase chain reaction (PCR) methods, i.e., qualitative multiplex PCR and quantitative real-time PCR, were used to measure the toxoplasma genome (T. gondii B1 gene). Qualitative multiplex PCR detected T. gondii B1 gene in the ocular fluids of 11 out of 13 patients with clinically suspected ocular toxoplasmosis. In real-time PCR, we detected high copy numbers of T. gondii DNA (5.1 × 10(2)-2.1 × 10(6) copies/mL) in a total of 10 patients (10/13, 77%). Only ocular toxoplasmosis scar lesions were observed in the three real-time PCR-negative patients. PCR assay results for the samples from the two control groups were all negative. The two-step PCR examination to detect toxoplasma DNA is a useful tool for diagnosing ocular toxoplasmosis.

  19. One-step multiplex quantitative RT-PCR for the simultaneous detection of viroids and phytoplasmas of pome fruit trees.

    Science.gov (United States)

    Malandraki, Ioanna; Varveri, Christina; Olmos, Antonio; Vassilakos, Nikon

    2015-03-01

    A one-step multiplex real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) based on TaqMan chemistry was developed for the simultaneous detection of Pear blister canker viroid and Apple scar skin viroid along with universal detection of phytoplasmas, in pome trees. Total nucleic acids (TNAs) extraction was performed according to a modified CTAB protocol. Primers and TaqMan MGB probes for specific detection of the two viroids were designed in this study, whereas for phytoplasma detection published universal primers and probe were used, with the difference that the later was modified to carry a MGB quencher. The pathogens were detected simultaneously in 10-fold serial dilutions of TNAs from infected plant material into TNAs of healthy plant up to dilutions 10(-5) for viroids and 10(-4) for phytoplasmas. The multiplex real-time assay was at least 10 times more sensitive than conventional protocols for viroid and phytoplasma detection. Simultaneous detection of the three targets was achieved in composite samples at least up to a ratio of 1:100 triple-infected to healthy tissue, demonstrating that the developed assay has the potential to be used for rapid and massive screening of viroids and phytoplasmas of pome fruit trees in the frame of certification schemes and surveys.

  20. Multiplexed and quantitative study of biomarker expression in tumor specimens using quantum dots

    Science.gov (United States)

    Wu, Aileen; True, Lawrence; Gao, Xiaohu

    2006-02-01

    When conjugated with targeting molecules, quantum dots (QD) can be used as powerful cancer diagnostic tools providing the molecular profiles of cancer cases based on common clinical biopsies. Such personalized analyses will enable doctors to treat and manage the patients' diseases more effectively. The unique optical properties (e.g., size-tunable emission, simultaneous excitation, high brightness and photostability) of these nanoparticles make them superior to conventionally popular organic fluorophores 1-2. Polymer-encapsulated, antibody-tagged QDs were prepared and used to successfully stain both fixed and live cells as well as clinical formalin-fixed paraffin-embedded (FFPE) tissue sections. In the tissue staining study, QD bioconjugates targeting mutated p53 and early growth response protein (egr-1) were used to examine prostate cancer tissues. The tissue slides were then analyzed with a wavelength-resolved spectrometer to accurately quantify the protein expression levels. In comparison to traditional qualitatively based diagnostic procedures, quantum dot nanotechnology allows for a more quantitative, rigorous and objective analysis of tissue specimens in question. In addition, new developments in imaging instrumentation could automate spectroscopy measurements and data analysis.

  1. A colony multiplex quantitative PCR-Based 3S3DBC method and variations of it for screening DNA libraries.

    Directory of Open Access Journals (Sweden)

    Yang An

    Full Text Available A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After describing pooling strategies and issues that should be considered in DNA library screening, here we report an efficient colony multiplex quantitative PCR-based 3-step, 3-dimension, and binary-code (3S3DBC method we used to screen genes from a planarian genomic DNA fosmid library. This method requires only 3 rounds of PCR reactions and only around 6 hours to distinguish one or more desired clones from a large DNA library. According to the particular situations in different research labs, this method can be further modified and simplified to suit their requirements.

  2. Structure-guided unravelling: Phenolic hydroxyls contribute to reduction of acrylamide using multiplex quantitative structure-activity relationship modelling.

    Science.gov (United States)

    Zhang, Yu; Huang, Mengmeng; Wang, Qiao; Cheng, Jun

    2016-05-15

    We reported a structure-activity relationship study on unravelling phenolic hydroxyls instead of alcoholic hydroxyls contribute to the reduction of acrylamide formation by flavonoids. The dose-dependent study shows a close correlation between the number of phenolic hydroxyls of flavonoids and their reduction effects. In view of positions of hydroxyls, the 3',4'(ortho)-dihydroxyls in B cycle, 3-hydroxyl or hydroxyls of 3-gallate in C cycle, and 5,7(meta)-dihydroxyls in A cycle of flavonoid structures play an important role in the reduction of acrylamide. Flavone C-glycosides are more effective at reducing the formation of acrylamide than flavone O-glycosides when sharing the same aglycone. The current multiplex quantitative structure-activity relationship (QSAR) equations effectively predict the inhibitory rates of acrylamide using selected chemometric parameters (R(2): 0.835-0.938). This pioneer study opens a broad understanding on the chemoprevention of acrylamide contaminants on a structural basis.

  3. Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

    Directory of Open Access Journals (Sweden)

    Takahiro Tsujikawa

    2017-04-01

    Full Text Available Here, we describe a multiplexed immunohistochemical platform with computational image processing workflows, including image cytometry, enabling simultaneous evaluation of 12 biomarkers in one formalin-fixed paraffin-embedded tissue section. To validate this platform, we used tissue microarrays containing 38 archival head and neck squamous cell carcinomas and revealed differential immune profiles based on lymphoid and myeloid cell densities, correlating with human papilloma virus status and prognosis. Based on these results, we investigated 24 pancreatic ductal adenocarcinomas from patients who received neoadjuvant GVAX vaccination and revealed that response to therapy correlated with degree of mono-myelocytic cell density and percentages of CD8+ T cells expressing T cell exhaustion markers. These data highlight the utility of in situ immune monitoring for patient stratification and provide digital image processing pipelines to the community for examining immune complexity in precious tissue sections, where phenotype and tissue architecture are preserved to improve biomarker discovery and assessment.

  4. Bridging Online and Offline Social Networks: Multiplex Analysis

    CERN Document Server

    Filiposka, Sonja; Dimitrova, Tamara; Kocarev, Ljupco

    2016-01-01

    We show that three basic actor characteristics, namely normalized reciprocity, three cycles, and triplets, can be expressed using an unified framework that is based on computing the similarity index between two sets associated with the actor: the set of her/his friends and the set of those considering her/him as a friend. These metrics are extended to multiplex networks and then computed for two friendship networks generated by collecting data from two groups of undergraduate students. We found that in offline communication strong and weak ties are (almost) equally presented, while in online communication weak ties are dominant. Moreover, weak ties are much less reciprocal than strong ties. However, across different layers of the multiplex network reciprocities are preserved, while triads (measured with normalized three cycles and triplets) are not significant.

  5. Bridging online and offline social networks: Multiplex analysis

    Science.gov (United States)

    Filiposka, Sonja; Gajduk, Andrej; Dimitrova, Tamara; Kocarev, Ljupco

    2017-04-01

    We show that three basic actor characteristics, namely normalized reciprocity, three cycles, and triplets, can be expressed using an unified framework that is based on computing the similarity index between two sets associated with the actor: the set of her/his friends and the set of those considering her/him as a friend. These metrics are extended to multiplex networks and then computed for two friendship networks generated by collecting data from two groups of undergraduate students. We found that in offline communication strong and weak ties are (almost) equally presented, while in online communication weak ties are dominant. Moreover, weak ties are much less reciprocal than strong ties. However, across different layers of the multiplex network reciprocities are preserved, while triads (measured with normalized three cycles and triplets) are not significant.

  6. Quantitative analysis of glycated proteins.

    Science.gov (United States)

    Priego-Capote, Feliciano; Ramírez-Boo, María; Finamore, Francesco; Gluck, Florent; Sanchez, Jean-Charles

    2014-02-07

    The proposed protocol presents a comprehensive approach for large-scale qualitative and quantitative analysis of glycated proteins (GP) in complex biological samples including biological fluids and cell lysates such as plasma and red blood cells. The method, named glycation isotopic labeling (GIL), is based on the differential labeling of proteins with isotopic [(13)C6]-glucose, which supports quantitation of the resulting glycated peptides after enzymatic digestion with endoproteinase Glu-C. The key principle of the GIL approach is the detection of doublet signals for each glycated peptide in MS precursor scanning (glycated peptide with in vivo [(12)C6]- and in vitro [(13)C6]-glucose). The mass shift of the doublet signals is +6, +3 or +2 Da depending on the peptide charge state and the number of glycation sites. The intensity ratio between doublet signals generates quantitative information of glycated proteins that can be related to the glycemic state of the studied samples. Tandem mass spectrometry with high-energy collisional dissociation (HCD-MS2) and data-dependent methods with collision-induced dissociation (CID-MS3 neutral loss scan) are used for qualitative analysis.

  7. Detection of free-living amoebae by using multiplex quantitative PCR.

    Science.gov (United States)

    Le Calvez, Thomas; Trouilhé, Marie-Cécile; Humeau, Philippe; Moletta-Denat, Marina; Frère, Jacques; Héchard, Yann

    2012-06-01

    Free-living amoebae (FLA) are protozoa found worldwide in soil and aquatic environments, which are able to colonize man-made water networks. Some FLA have the potential to be pathogenic and others might harbour pathogenic bacteria. Indeed, FLA feed on bacteria, but some bacteria could resist phagocytosis and either survive in FLA or even multiply within FLA. These bacteria are collectively named amoeba resistant bacteria (ARB). The best characterized example is Legionella pneumophila, for which FLA is the main reservoir in the environment. Not only could FLA be a reservoir that protects ARB, some bacteria might become more resistant to treatment and be more virulent. Thus, it is of medical significance to quantify FLA populations in soil, water or the environment. The main limitation for the quantification of FLA is that classical culture is not efficient and reliable for many genera and 'strains'. Thus, several PCR-based quantification methods have been published for various FLA. However, thus far, no method has been published to simultaneously quantify the main FLA genera in the same PCR reaction. In this study, we developed a multiplex qPCR method to detect both Amoebozoan (i.e. Acanthamoeba, Hartmannella and Echinamoeba) and Vahlkampfiidae (i.e. Vahlkampfia and Naegleria) using 18S ribosomal RNA as the target gene. This method was shown to be specific, reliable and sensitive, could be used for the quantification of FLA and is likely to be useful to anticipate risks due to FLA or pathogenic bacteria, such as L. pneumophila.

  8. A multiplex calibrated real-time PCR assay for quantitation of DNA of EBV-1 and 2.

    Science.gov (United States)

    Gatto, Francesca; Cassina, Giulia; Broccolo, Francesco; Morreale, Giuseppe; Lanino, Edoardo; Di Marco, Eddi; Vardas, Efthiya; Bernasconi, Daniela; Buttò, Stefano; Principi, Nicola; Esposito, Susanna; Scarlatti, Gabriella; Lusso, Paolo; Malnati, Mauro S

    2011-12-01

    Accurate and highly sensitive tests for the diagnosis of active Epstein-Barr virus (EBV) infection are essential for the clinical management of individuals infected with EBV. A calibrated quantitative real-time PCR assay for the measurement of EBV DNA of both EBV-1 and 2 subtypes was developed, combining the detection of the EBV DNA and a synthetic DNA calibrator in a multiplex PCR format. The assay displays a wide dynamic range and a high degree of accuracy even in the presence of 1μg of human genomic DNA. This assay measures with the same efficiency EBV DNA from strains prevalent in different geographic areas. The clinical sensitivity and specificity of the system were evaluated by testing 181 peripheral blood mononuclear cell (PBMCs) and plasma specimens obtained from 21 patients subjected to bone marrow transplantation, 70 HIV-seropositive subjects and 23 healthy controls. Patients affected by EBV-associated post-transplant lymphoprolipherative disorders had the highest frequency of EBV detection and the highest viral load. Persons infected with HIV had higher levels of EBV DNA load in PBMCs and a higher frequency of EBV plasma viremia compared to healthy controls. In conclusion, this new assay provides a reliable high-throughput method for the quantitation of EBV DNA in clinical samples.

  9. A Framework for Analysis of Computational Imaging Systems: Role of Signal Prior, Sensor Noise and Multiplexing.

    Science.gov (United States)

    Mitra, Kaushik; Cossairt, Oliver S; Veeraraghavan, Ashok

    2014-10-01

    Over the last decade, a number of computational imaging (CI) systems have been proposed for tasks such as motion deblurring, defocus deblurring and multispectral imaging. These techniques increase the amount of light reaching the sensor via multiplexing and then undo the deleterious effects of multiplexing by appropriate reconstruction algorithms. Given the widespread appeal and the considerable enthusiasm generated by these techniques, a detailed performance analysis of the benefits conferred by this approach is important. Unfortunately, a detailed analysis of CI has proven to be a challenging problem because performance depends equally on three components: (1) the optical multiplexing, (2) the noise characteristics of the sensor, and (3) the reconstruction algorithm which typically uses signal priors. A few recent papers [12], [30], [49] have performed analysis taking multiplexing and noise characteristics into account. However, analysis of CI systems under state-of-the-art reconstruction algorithms, most of which exploit signal prior models, has proven to be unwieldy. In this paper, we present a comprehensive analysis framework incorporating all three components. In order to perform this analysis, we model the signal priors using a Gaussian Mixture Model (GMM). A GMM prior confers two unique characteristics. First, GMM satisfies the universal approximation property which says that any prior density function can be approximated to any fidelity using a GMM with appropriate number of mixtures. Second, a GMM prior lends itself to analytical tractability allowing us to derive simple expressions for the `minimum mean square error' (MMSE) which we use as a metric to characterize the performance of CI systems. We use our framework to analyze several previously proposed CI techniques (focal sweep, flutter shutter, parabolic exposure, etc.), giving conclusive answer to the question: `How much performance gain is due to use of a signal prior and how much is due to

  10. A Multiplexed, Probe-Based Quantitative PCR Assay for DNA of Phytophthora sojae

    Science.gov (United States)

    Phytophthora sojae (Kaufm. & Gerd.) causes seed rot, pre- and post-emergence damping off, and sometimes foliar blight in soybean (Glycine max). Crop loss may approach 100% with susceptible cultivars. We report here the development of a unique quantitative PCR assay specific to DNA of P. sojae, and a...

  11. Blocking Analysis of Time-Division Multiplexed Multicast Switch

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The particular switch concerned here is a Three-Stage Time-space-time (TST) interconnection network and performs the time-division circuit switching. The input and output stages are Time Slot Interchangers (TSI). The central stage is a time-multiplexed switch with two ports per address. By exploiting the channel grouping at the central stage as well as reducing the average loading at each internal frame,the three-stage multicast switch has potential to remove almost all slot contention blockings.

  12. Quantitative Comparison of Tumor Delivery for Multiple Targeted Nanoparticles Simultaneously by Multiplex ICP-MS

    Science.gov (United States)

    Elias, Andrew; Crayton, Samuel H.; Warden-Rothman, Robert; Tsourkas, Andrew

    2014-01-01

    Given the rapidly expanding library of disease biomarkers and targeting agents, the number of unique targeted nanoparticles is growing exponentially. The high variability and expense of animal testing often makes it unfeasible to examine this large number of nanoparticles in vivo. This often leads to the investigation of a single formulation that performed best in vitro. However, nanoparticle performance in vivo depends on many variables, many of which cannot be adequately assessed with cell-based assays. To address this issue, we developed a lanthanide-doped nanoparticle method that allows quantitative comparison of multiple targeted nanoparticles simultaneously. Specifically, superparamagnetic iron oxide (SPIO) nanoparticles with different targeting ligands were created, each with a unique lanthanide dopant. Following the simultaneous injection of the various SPIO compositions into tumor-bearing mice, inductively coupled plasma mass spectroscopy was used to quantitatively and orthogonally assess the concentration of each SPIO composition in serial blood and resected tumor samples. PMID:25068300

  13. Quantitative Comparison of Tumor Delivery for Multiple Targeted Nanoparticles Simultaneously by Multiplex ICP-MS

    Science.gov (United States)

    Elias, Andrew; Crayton, Samuel H.; Warden-Rothman, Robert; Tsourkas, Andrew

    2014-07-01

    Given the rapidly expanding library of disease biomarkers and targeting agents, the number of unique targeted nanoparticles is growing exponentially. The high variability and expense of animal testing often makes it unfeasible to examine this large number of nanoparticles in vivo. This often leads to the investigation of a single formulation that performed best in vitro. However, nanoparticle performance in vivo depends on many variables, many of which cannot be adequately assessed with cell-based assays. To address this issue, we developed a lanthanide-doped nanoparticle method that allows quantitative comparison of multiple targeted nanoparticles simultaneously. Specifically, superparamagnetic iron oxide (SPIO) nanoparticles with different targeting ligands were created, each with a unique lanthanide dopant. Following the simultaneous injection of the various SPIO compositions into tumor-bearing mice, inductively coupled plasma mass spectroscopy was used to quantitatively and orthogonally assess the concentration of each SPIO composition in serial blood and resected tumor samples.

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

    DEFF Research Database (Denmark)

    Berger, Sanne Schou; Lauritsen, Klara Tølbøl; Boas, Ulrik

    2017-01-01

    We have developed and made a preliminary validation of a bead-based multiplexed immunoassay for simultaneous detection of porcine serum antibodies to Actinobacillus pleuropneumoniae serovars 1, 2, 6, 7, and 12. Magnetic fluorescent beads were coupled with A. pleuropneumoniae antigens and tested...... Pathogen Free system. Assay specificities and sensitivities as well as the corresponding cutoff values were determined using receiver operating characteristic (ROC) curve analysis, and the A. pleuropneumoniae multiplex assay showed good correlation with the in-house ELISAs and CF tests with areas under ROC...

  15. A multiplex quantitative real-time polymerase chain reaction panel for detecting neurologic pathogens in dogs with meningoencephalitis.

    Science.gov (United States)

    Han, Jae-Ik; Chang, Dong-Woo; Na, Ki-Jeong

    2015-01-01

    Meningoencephalitis (ME) is a common inflammatory disorder of the central nervous system in dogs. Clinically, ME has both infectious and non-infectious causes. In the present study, a multiplex quantitative real-time polymerase chain reaction (mqPCR) panel was optimized for the detection of eight canine neurologic pathogens (Blastomyces dermatitidis, Cryptococcus spp., Neospora caninum, Borrelia burgdorferi, Bartonella spp., Toxoplasma gondii, Ehrlichia canis, and canine distemper virus [CDV]). The mqPCR panel was subsequently applied to 53 cerebrospinal fluid (CSF) samples collected from dogs with ME. The analytic sensitivity (i.e., limit of detection, expressed as molecules per 1 mL of recombinant vector) was 3.8 for CDV, 3.7 for Ehrlichia canis, 3.7 for Bartonella spp., 3.8 for Borrelia burgdorferi, 3.7 for Blastomyces dermatitidis, 3.7 for Cryptococcus spp., 38 for Neospora caninum, and 3.7 for Toxoplasma gondii. Among the tested CSF samples, seven (15%) were positive for the following pathogens in decreasing order of frequency: Cryptococcus spp. (3/7), Blastomyces dermatitidis (2/7), and Borrelia burgdorferi (2/7). In summary, use of an mqPCR panel with high analytic sensitivity as an initial screen for infectious agents in dogs with ME could facilitate the selection of early treatment strategies and improve outcomes.

  16. High-throughput multiplex quantitative polymerase chain reaction method for Giardia lamblia and Cryptosporidium species detection in stool samples.

    Science.gov (United States)

    Nurminen, Noora; Juuti, Rosa; Oikarinen, Sami; Fan, Yue-Mei; Lehto, Kirsi-Maarit; Mangani, Charles; Maleta, Kenneth; Ashorn, Per; Hyöty, Heikki

    2015-06-01

    Giardia lamblia and Cryptosporidium species belong to a complex group of pathogens that cause diseases hampering development and socioeconomic improvements in the developing countries. Both pathogens are recognized as significant causes of diarrhea and nutritional disorders. However, further studies are needed to clarify the role of parasitic infections, especially asymptomatic infections in malnutrition and stunting. We developed a high-throughput multiplex quantitative polymerase chain reaction (qPCR) method for G. lamblia and Cryptosporidium spp. detection in stool samples. The sensitivity and specificity of the method were ensured by analyzing confirmed positive samples acquired from diagnostics laboratories and participating in an external quality control round. Its capability to detect asymptomatic G. lamblia and Cryptosporidium spp. infections was confirmed by analyzing stool samples collected from 44 asymptomatic 6-month-old infants living in an endemic region in Malawi. Of these, five samples were found to be positive for G. lamblia and two for Cryptosporidium spp. In conclusion, the developed method is suitable for large-scale studies evaluating the occurrence of G. lamblia and Cryptosporidium spp. in endemic regions and for clinical diagnostics of these infections.

  17. A simple method for the evaluation of microfluidic architecture using flow quantitation via a multiplexed fluidic resistance measurement.

    Science.gov (United States)

    Leslie, Daniel C; Melnikoff, Brett A; Marchiarullo, Daniel J; Cash, Devin R; Ferrance, Jerome P; Landers, James P

    2010-08-07

    Quality control of microdevices adds significant costs, in time and money, to any fabrication process. A simple, rapid quantitative method for the post-fabrication characterization of microchannel architecture using the measurement of flow with volumes relevant to microfluidics is presented. By measuring the mass of a dye solution passed through the device, it circumvents traditional gravimetric and interface-tracking methods that suffer from variable evaporation rates and the increased error associated with smaller volumes. The multiplexed fluidic resistance (MFR) measurement method measures flow via stable visible-wavelength dyes, a standard spectrophotometer and common laboratory glassware. Individual dyes are used as molecular markers of flow for individual channels, and in channel architectures where multiple channels terminate at a common reservoir, spectral deconvolution reveals the individual flow contributions. On-chip, this method was found to maintain accurate flow measurement at lower flow rates than the gravimetric approach. Multiple dyes are shown to allow for independent measurement of multiple flows on the same device simultaneously. We demonstrate that this technique is applicable for measuring the fluidic resistance, which is dependent on channel dimensions, in four fluidically connected channels simultaneously, ultimately determining that one chip was partially collapsed and, therefore, unusable for its intended purpose. This method is thus shown to be widely useful in troubleshooting microfluidic flow characteristics.

  18. A multiplex network analysis of the Mexican banking system: link persistence, overlap, and waiting times

    NARCIS (Netherlands)

    Molina-Borboa, J.L.; Martínez-Jaramillo, S.; López-Gallo, F.; van der Leij, M.

    2015-01-01

    This paper analyzes the persistence and overlap of relationships between banks in a multiplex decomposition of the exposures network. Our analysis may be useful for researchers designing stress tests or models in which the behavior of banks is modeled explicitly. This has not been looked at previous

  19. Multiplex SNP analysis on whole genome amplified DNA from archived dried bloodspots, a validation study

    DEFF Research Database (Denmark)

    Tvedegaard, Kristine C.; Parner, Erik; Hooper, Craig W.

    Multiplex SNP analysis on whole genome amplified DNA from archived dried bloodspots, a validation study Kristine C. Tvedegaard,1 Erik Parner,1 Craig W. Hooper,2 Jørn Atterman,1 Niels Gregersen3, Poul Thorsen,1 1Institute of Public Health, NANEA at Department of Epidemiology, University of Aarhus...

  20. Submarine Pipeline Routing Risk Quantitative Analysis

    Institute of Scientific and Technical Information of China (English)

    徐慧; 于莉; 胡云昌; 王金英

    2004-01-01

    A new method for submarine pipeline routing risk quantitative analysis was provided, and the study was developed from qualitative analysis to quantitative analysis.The characteristics of the potential risk of the submarine pipeline system were considered, and grey-mode identification theory was used. The study process was composed of three parts: establishing the indexes system of routing risk quantitative analysis, establishing the model of grey-mode identification for routing risk quantitative analysis, and establishing the standard of mode identification result. It is shown that this model can directly and concisely reflect the hazard degree of the routing through computing example, and prepares the routing selection for the future.

  1. Performance analysis of spatial multiplexing MIMO system with time reversal technology

    Science.gov (United States)

    Shrestha, Sanjeeb; Dou, Zheng; Khan, Zayed

    2013-03-01

    This paper deals with the performance analysis of Spatial Multiplexing(SM) multiple input multiple output (MIMO) system with time reversal (TR) technology. Focus is given on the spatial multiplexing gain of MIMO than the diversity gain aspect with the notion that the idea of diversity is inseparably associated with the uncertainty of the channel. If transmitter knows Channel State Information (CSI) before transmission, potential benefits can be harvested. TR is used here, to provide Channel State Information (CSI) at the transmitter before transmission. With the features of temporal and spatial focusing, TR not only can provide immunity against fading for spatially multiplexed data stream but also help boost its Multi Stream Interference (MSI) limited performance by mitigating it. The performance analysis of SM-MIMOTR is carried out with the aim of average minimum error probability for quantity of interest data rate. The interest date rate is 19.07 Mbps, where as the average minimum error probably is set to be that of Single Input Multi Output (SIMO) maximum ratio combining system (MRC). BER of Single Input Single Output (SISO) system is also simulated for making comparison tangible. Simulation study shows that Bit Error Rate (BER) performance of the system with the data rate of interest nearly coincides with that of SIMO system at the range of 10-15db and is better than SISO in all simulated Eb/No points. Additionally, from the standpoint of tread off curve, between diversity gain and spatial multiplexing gain, the non linearity nature still holds.

  2. Analysis of complex contagions in random multiplex networks

    CERN Document Server

    Yagan, Osman

    2012-01-01

    We study the diffusion of influence in random multiplex networks where links can be of $r$ different types, and for a given content (e.g., rumor, product, political view), each link type is associated with a content dependent parameter $c_i$ in $[0,\\infty]$ that measures the relative bias type-$i$ links have in spreading this content. In this setting, we propose a linear threshold model of contagion where nodes switch state if their "perceived" proportion of active neighbors exceeds a threshold \\tau. Namely, a node connected to $m_i$ active neighbors and $k_i-m_i$ inactive neighbors via type-$i$ links will turn active if $\\sum{c_i m_i}/\\sum{c_i k_i}$ exceeds its threshold \\tau. Under this model, we obtain the condition, probability and expected size of global spreading events. Our results extend the existing work on complex contagions in several directions by i) providing solutions for coupled random networks whose vertices are neither identical nor disjoint, (ii) highlighting the effect of content on the dyn...

  3. Application of a Multiplex Quantitative PCR to Assess Prevalence and Intensity Of Intestinal Parasite Infections in a Controlled Clinical Trial

    DEFF Research Database (Denmark)

    Llewellyn, Stacey; Inpankaew, Tawin; Nery, Susana Vaz;

    2016-01-01

    multiplex real-time PCR reactions the first targeting: Necator americanus, Ancylostoma spp., Ascaris spp., and Trichuris trichiura; and the second Entamoeba histolytica, Cryptosporidium spp., Giardia. duodenalis, and Strongyloides stercoralis. Samples were also subject to sodium nitrate flotation...

  4. A Novel Universal Primer-Multiplex-PCR Method with Sequencing Gel Electrophoresis Analysis

    Science.gov (United States)

    Huang, Kunlun; Zhang, Nan; Yuan, Yanfang; Shang, Ying; Luo, Yunbo

    2012-01-01

    In this study, a novel universal primer-multiplex-PCR (UP-M-PCR) method adding a universal primer (UP) in the multiplex PCR reaction system was described. A universal adapter was designed in the 5′-end of each specific primer pairs which matched with the specific DNA sequences for each template and also used as the universal primer (UP). PCR products were analyzed on sequencing gel electrophoresis (SGE) which had the advantage of exhibiting extraordinary resolution. This method overcame the disadvantages rooted deeply in conventional multiplex PCR such as complex manipulation, lower sensitivity, self-inhibition and amplification disparity resulting from different primers, and it got a high specificity and had a low detection limit of 0.1 ng for single kind of crops when screening the presence of genetically modified (GM) crops in mixture samples. The novel developed multiplex PCR assay with sequencing gel electrophoresis analysis will be useful in many fields, such as verifying the GM status of a sample irrespective of the crop and GM trait and so on. PMID:22272223

  5. DEVELOPMENT OF REAL-TIME MULTIPLEX PCR FOR THE QUANTITATIVE DETERMINATION OF TREC'S AND KREC'S IN WHOLE BLOOD AND IN DRIED BLOOD SPOTS

    Directory of Open Access Journals (Sweden)

    M. A. Gordukova

    2015-01-01

    Full Text Available Primary immunodeficiencies (PID such as severe combined immunodeficiency (SCID and X-linked agammaglobulinemia are characterized by the lack of functional Tand B-cells, respectively. Without early diagnosis and prompt treatment children with PID suffer from severe infectious diseases, leading to their death or disability. Our purpose was developing of simple, inexpensive, high throughput technique based on the quantitative determination of TREC and KREC molecules by real-time PCR, and its validation in a group of children with a verified diagnosis of SCID and X-linked agammaglobulinemia.In this study, we developed and validated multiplex real-time PCR for the TREC’s and KREC’s quantitative analysis. We have shown that linear range of Ct changes depending on the concentrations of targets with a correlation coefficient R2 not worse than 0.98 was observed at concentrations from 109 to 5 × 104 copies per ml. The lowest amount of targets reliably detected in a reaction volume was 10 TREC’s copies, 5 KREC ‘s copies and 5 copies of internal control (IL17RA. We determined the age-depended reference values of TRECs and KRECs in whole blood in 29 boys and 27 girls with normal immunological parameters. The normal cut-offs for TRECs and KRECs were defined in dry blood spots depending on the method of extraction.The proposed method showed 100% diagnostic sensitivity and specificity in the studied group. The method can be proposed as a screening tool for the diagnosis of SCID and X-linked agammaglobulinemia both in whole blood and in the dry blood spots. The further investigation is required with larger number of samples. 

  6. Quantitative imaging of nanometric optical path length modulations by time-averaged heterodyne holography in coherent frequency-division multiplexing regime

    CERN Document Server

    Bruno, Francois; Lesaffre, Max; Verrier, Nicolas; Atlan, Michael

    2013-01-01

    We report a demonstration of amplitude and phase imaging of out-of-plane sinusoidal vibration at nanometer scales with a heterodyne holographic interferometer. Time-averaged holograms of a phase-modulated optical field are recorded with an exposure time much longer than the modulation period. Optical heterodyning, a frequency-conversion process aimed at shifting a given radiofrequency optical side band in the sensor bandwidth, is performed with an off-axis and frequency-shifted optical local oscillator. The originality of the proposed method is to make use of a multiplexed local oscillator to address several optical side bands into the temporal bandwidth of the sensor array. This process is called coherent frequency-division multiplexing. It enables simultaneous recording and pixel-to-pixel division of two side band holograms, which permits quantitative mapping of the modulation depth of local optical path lengths yielding small optical phase modulations. Additionally, a linear frequency chirp ensures the ret...

  7. Identification of species by multiplex analysis of variable-length sequences

    OpenAIRE

    Pereira, Filipe; Carneiro, João; Matthiesen, Rune; van Asch, Barbara; Pinto, Nádia; Gusmão, Leonor; Amorim, António

    2010-01-01

    The quest for a universal and efficient method of identifying species has been a longstanding challenge in biology. Here, we show that accurate identification of species in all domains of life can be accomplished by multiplex analysis of variable-length sequences containing multiple insertion/deletion variants. The new method, called SPInDel, is able to discriminate 93.3% of eukaryotic species from 18 taxonomic groups. We also demonstrate that the identification of prokaryotic and viral speci...

  8. A quantitative multiplex nuclease protection assay reveals immunotoxicity gene expression profiles in the rabbit model for vaginal drug safety evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Fichorova, Raina N., E-mail: rfichorova@rics.bwh.harvard.edu [Laboratory of Genital Tract Biology, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women' s Hospital and Harvard Medical School, Boston, MA (United States); Mendonca, Kevin; Yamamoto, Hidemi S.; Murray, Ryan [Laboratory of Genital Tract Biology, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women' s Hospital and Harvard Medical School, Boston, MA (United States); Chandra, Neelima; Doncel, Gustavo F. [CONRAD, Department of Obstetrics and Gynecology, Eastern Virginia Medical School, Norfolk, VA (United States)

    2015-06-15

    Any vaginal product that alters the mucosal environment and impairs the immune barrier increases the risk of sexually transmitted infections, especially HIV infection, which thrives on mucosal damage and inflammation. The FDA-recommended rabbit vaginal irritation (RVI) model serves as a first line selection tool for vaginal products; however, for decades it has been limited to histopathology scoring, insufficient to select safe anti-HIV microbicides. In this study we incorporate to the RVI model a novel quantitative nuclease protection assay (qNPA) to quantify mRNA levels of 25 genes representing leukocyte differentiation markers, toll-like receptors (TLR), cytokines, chemokines, epithelial repair, microbicidal and vascular markers, by designing two multiplex arrays. Tissue sections were obtained from 36 rabbits (6 per treatment arm) after 14 daily applications of a placebo gel, saline, 4% nonoxynol-9 (N-9), and three combinations of the anti-HIV microbicides tenofovir (TFV) and UC781 in escalating concentrations (highest: 10% TFV + 2.5%UC781). Results showed that increased expression levels of toll-like receptor (TLR)-4, interleukin (IL)-1β, CXCL8, epithelial membrane protein (EMP)-1 (P < 0.05), and decreased levels of TLR2 (P < 0.05), TLR3 and bactericidal permeability increasing protein (BPI) (P < 0.001) were associated with cervicovaginal mucosal alteration (histopathology). Seven markers showed a significant linear trend predicting epithelial damage (up with CD4, IL-1β, CXCL8, CCL2, CCL21, EMP1 and down with BPI). Despite the low tissue damage RVI scores, the high-dose microbicide combination gel caused activation of HIV host cells (SLC and CD4) while N-9 caused proinflammatory gene upregulation (IL-8 and TLR4) suggesting a potential for increasing risk of HIV via different mechanisms depending on the chemical nature of the test product. - Highlights: • A transcriptome nuclease protection assay assessed microbicides for vaginal safety. • Biomarkers were

  9. Application of a Multiplex Quantitative PCR to Assess Prevalence and Intensity Of Intestinal Parasite Infections in a Controlled Clinical Trial

    DEFF Research Database (Denmark)

    Llewellyn, Stacey; Inpankaew, Tawin; Nery, Susana Vaz

    2016-01-01

    multiplex real-time PCR reactions the first targeting: Necator americanus, Ancylostoma spp., Ascaris spp., and Trichuris trichiura; and the second Entamoeba histolytica, Cryptosporidium spp., Giardia. duodenalis, and Strongyloides stercoralis. Samples were also subject to sodium nitrate flotation...... for identification and quantification of STH eggs, and zinc sulphate centrifugal flotation for detection of protozoan parasites. Higher parasite prevalence was detected by multiplex PCR (hookworms 2.9 times higher, Ascaris 1.2, Giardia 1.6, along with superior polyparasitism detection with this effect magnified...

  10. Validation of microsatellite multiplexes for parentage analysis in a coral reef fish (Lutjanus carponotatus, Lutjanidae)

    KAUST Repository

    Harrison, Hugo B.

    2014-05-25

    Parentage analysis is an important tool for identifying connectivity patterns in coral reef fishes, but often requires numerous highly polymorphic markers. We isolated 21 polymorphic microsatellite markers from the stripey snapper, Lutjanus carponotatus and describe their integration into three multiplex PCRs. All markers were highly polymorphic with a mean of 24.9 ± 1.8 SE alleles per locus and an average observed heterozygosity of 0.797 ± 0.038 SE across 285 genotyped individuals. Using a simulated dataset, we conclude that the complete marker set provides sufficient resolution to resolve parent–offspring relationships in natural populations with 99.6 ± 0.1 % accuracy in parentage assignments. This multiplex assay provides an effective means of investigating larval dispersal and population connectivity in this fishery-targeted coral reef fish species and informing the design of marine protected area networks for biodiversity conservation and fisheries management.

  11. Cytokines profiling by multiplex analysis in experimental arthritis: which pathophysiological relevance for articular versus systemic mediators?

    Science.gov (United States)

    Paquet, Joseph; Goebel, Jean-Christophe; Delaunay, Camille; Pinzano, Astrid; Grossin, Laurent; Cournil-Henrionnet, Christel; Gillet, Pierre; Netter, Patrick; Jouzeau, Jean-Yves; Moulin, David

    2012-03-13

    We have taken advantage of the large screening capacity of a multiplex immunoassay to better define the respective contribution of articular versus systemic cytokines in experimental arthritis. We performed a follow up (from 7 hours to 14 days) multiplex analysis of 24 cytokines in synovial fluid and sera of rats developing Antigen-Induced Arthritis (AIA) and confronted their protein level changes with molecular, biochemical, histological and clinical events occurring in the course of the disease. The time-scheduled findings in arthritic joints correlated with time-dependent changes of cytokine amounts in joint effusions but not with their blood levels. From seven hours after sensitization, high levels of chemokines (MCP-1, MIP1α, GRO/KC, RANTES, eotaxin) were found in synovial fluid of arthritic knees whereas perivascular infiltration occurred in the synovium; local release of inflammatory cytokines (IFNγ, IL-1β, IL-6) preceded the spreading of inflammation and resulted in progressive degradation of cartilage and bone. Finally a local overexpression of several cytokines/adipocytokines poorly described in arthritis (IL-13, IL-18, leptin) was observed. Distinct panels of cytokines were found in arthritic fluid during AIA, and the expected effect of mediators correlated well with changes occurring in joint tissues. Moreover, multiplex analysis could be helpful to identify new pathogenic mediators and to elucidate the mechanisms supporting the efficacy of putative targeted therapies.

  12. Development of a Multiplexed, Bead-Based Assessment Tool for Rapid Identification and Quantitation of Microorganisms in Field Samples. Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Lowe, M.; Halden, R.

    2002-10-09

    This was the final report for DOE NABIR grant DE-FG02-01ER63264 (PI Mary Lowe). The grant was entitled ''Development of a Multiplexed Bead-Based Assessment Tool for Rapid Identification and Quantitation of Microorganisms in Field Samples.'' The grant duration was one year. The purpose was to develop a bead-based assay for measuring analyte DNAs in environmental PCR products and to apply the method to a field experiment. The primary experiment was located at the UMTRA Old Rifle site.

  13. Quantitative analysis of saccadic search strategy

    NARCIS (Netherlands)

    Over, E.A.B.

    2007-01-01

    This thesis deals with the quantitative analysis of saccadic search strategy. The goal of the research presented was twofold: 1) to quantify overall characteristics of fixation location and saccade direction, and 2) to identify search strategies, with the use of a quantitative description of eye mov

  14. Quantitative analysis of saccadic search strategy

    NARCIS (Netherlands)

    Over, E.A.B.

    2007-01-01

    This thesis deals with the quantitative analysis of saccadic search strategy. The goal of the research presented was twofold: 1) to quantify overall characteristics of fixation location and saccade direction, and 2) to identify search strategies, with the use of a quantitative description of eye

  15. An investigation of genetic counselors' testing recommendations: pedigree analysis and the use of multiplex breast cancer panel testing.

    Science.gov (United States)

    Lundy, Meghan G; Forman, Andrea; Valverde, Kathleen; Kessler, Lisa

    2014-08-01

    Genetic testing recommendations for hereditary breast and ovarian cancer involve pedigree analysis and consultation of testing guidelines. The testing landscape for hereditary cancer syndromes is shifting as multiplex panel tests become more widely integrated into clinical practice. The purpose of the current study was to assess how genetic counselors utilize pedigrees to make recommendations for genetic testing, to determine consistency of these recommendations with National Comprehensive Cancer Network (NCCN) Guidelines and to explore current use of multiplex panel testing. Sixty-nine genetic counselors were recruited through the National Society of Genetic Counselors Cancer Special Interest Group's Discussion Forum. Participation involved pedigree analysis and completion of an online questionnaire assessing testing recommendations and use of multiplex panel testing. Pedigree analysis and test recommendations were scored for consistency with NCCN guidelines. The average score was 12.83/15 indicating strong consistency with NCCN guidelines. Participants were more likely to consider multiplex testing when pedigrees demonstrated highly penetrant dominant inheritance but were not indicative of a particular syndrome. Participant concerns about multiplex panel testing include limited guidelines for both testing eligibility and medical management. This study demonstrates high utilization of pedigree analysis and raises new questions about its use in multiplex genetic testing.

  16. Detection of gene copy number aberrations in mantle cell lymphoma by a single quantitative multiplex PCR assay: clinicopathological relevance and prognosis value.

    Science.gov (United States)

    Jardin, Fabrice; Picquenot, Jean-Michel; Parmentier, Françoise; Ruminy, Philippe; Cornic, Marie; Penther, Dominique; Bertrand, Philippe; Lanic, Hélène; Cassuto, Ophélie; Humbrecht, Catherine; Lemasle, Emilie; Wautier, Agathe; Bastard, Christian; Tilly, Hervé

    2009-09-01

    The t(11;14)(q13;q32) is the hallmark of mantle cell lymphoma (MCL). Additional genetic alterations occur in the majority of cases. This study aimed to design a polymerase chain reaction (PCR) assay to determine the incidence and relevance of recurrent gene copy number aberrations in this disease. Forty-two MCL cases with frozen- or paraffin-embedded (FFPE) tissues were selected. Three different quantitative Multiplex PCR of Short Fluorescent Fragments (QMPSF) assays were designed to simultaneously analyse eight genes (CDKN2A, RB1, ATM, CDK2, TP53, MYC, CDKN1B, MDM2), to analyse the 9p21 locus (CDKN2A/CDKN2B) and FFPE tissues. Gains of MYC, CDK2, CDKN1B, and MDM2 were observed in 10% of cases. Losses of RB1, CDKN2A, ATM or TP53 were observed in 38%, 31%, 24% and 10% of cases, respectively. Analysis of the 9p21 locus indicated that, in most cases, tumours displayed a complete inactivation of p14(ARF)/p15I(NK4B)/p16I(NK4A). CDKN2A and MYC aberrations were associated with a high MCL international prognostic index (MIPI). CDK2/MDM2 gains and CDKN2A/TP53 losses correlated with an unfavourable outcome. PCR experiments with frozen and FFPE-tissues indicated that our approach is valid in a routine diagnostic setting, providing a powerful tool that could be used for patient stratification in combination with MIPI in future clinical trials.

  17. Multiplexed Volume Bragg Gratings in Narrowand Broad-band Spectral Systems: Analysis and Application

    Science.gov (United States)

    Ingersoll, Gregory B.

    Volume Bragg gratings (VBGs) are important holographic optical elements in many spectral systems. Using multiple volume gratings, whether multiplexed or arranged sequentially, provides advantages to many types of systems in overall efficiency, dispersion performance, flexibility of design, etc. However, the use of multiple gratings---particularly when the gratings are multiplexed in a single holographic optical element (HOE)---is subject to inter-grating coupling effects that ultimately limit system performance. Analyzing these coupling effects requires a more complex mathematical model than the straightforward analysis of a single volume grating. We present a matrix-based algorithm for determining diffraction efficiencies of significant coupled waves in these multiplexed grating holographic optical elements (HOEs). Several carefully constructed experiments with spectrally multiplexed gratings in dichromated gelatin verify our conclusions. Applications of this theory to broad- and narrow-band systems are explored in detailed simulations. Broadband systems include spectrum splitters for diverse-bandgap photovoltaic (PV) cells. Volume Bragg gratings can serve as effective spectrum splitters, but the inherent dispersion of a VBG can be detrimental given a broad-spectrum input. The performance of a holographic spectrum splitter element can be improved by utilizing multiple volume gratings, each operating in a slightly different spectral band. However, care must be taken to avoid inter-grating coupling effects that limit ultimate performance. We explore broadband multi-grating holographic optical elements (HOEs) in sandwiched arrangements where individual single-grating HOEs are placed in series, and in multiplexed arrangements where multiple gratings are recorded in a single HOE. Particle swarm optimization (PSO) is used to tailor these systems to the solar spectrum taking into account both efficiency and dispersion. Both multiplexed and sandwiched two-grating systems

  18. Quantitative Analysis of Face Symmetry.

    Science.gov (United States)

    Tamir, Abraham

    2015-06-01

    The major objective of this article was to report quantitatively the degree of human face symmetry for reported images taken from the Internet. From the original image of a certain person that appears in the center of each triplet, 2 symmetric combinations were constructed that are based on the left part of the image and its mirror image (left-left) and on the right part of the image and its mirror image (right-right). By applying a computer software that enables to determine length, surface area, and perimeter of any geometric shape, the following measurements were obtained for each triplet: face perimeter and area; distance between the pupils; mouth length; its perimeter and area; nose length and face length, usually below the ears; as well as the area and perimeter of the pupils. Then, for each of the above measurements, the value C, which characterizes the degree of symmetry of the real image with respect to the combinations right-right and left-left, was calculated. C appears on the right-hand side below each image. A high value of C indicates a low symmetry, and as the value is decreasing, the symmetry is increasing. The magnitude on the left relates to the pupils and compares the difference between the area and perimeter of the 2 pupils. The major conclusion arrived at here is that the human face is asymmetric to some degree; the degree of asymmetry is reported quantitatively under each portrait.

  19. Multiplex fluorescence melting curve analysis for mutation detection with dual-labeled, self-quenched probes.

    Directory of Open Access Journals (Sweden)

    Qiuying Huang

    Full Text Available Probe-based fluorescence melting curve analysis (FMCA is a powerful tool for mutation detection based on melting temperature generated by thermal denaturation of the probe-target hybrid. Nevertheless, the color multiplexing, probe design, and cross-platform compatibility remain to be limited by using existing probe chemistries. We hereby explored two dual-labeled, self-quenched probes, TaqMan and shared-stem molecular beacons, in their ability to conduct FMCA. Both probes could be directly used for FMCA and readily integrated with closed-tube amplicon hybridization under asymmetric PCR conditions. Improved flexibility of FMCA by using these probes was illustrated in three representative applications of FMCA: mutation scanning, mutation identification and mutation genotyping, all of which achieved improved color-multiplexing with easy probe design and versatile probe combination and all were validated with a large number of real clinical samples. The universal cross-platform compatibility of these probes-based FMCA was also demonstrated by a 4-color mutation genotyping assay performed on five different real-time PCR instruments. The dual-labeled, self-quenched probes offered unprecedented combined advantage of enhanced multiplexing, improved flexibility in probe design, and expanded cross-platform compatibility, which would substantially improve FMCA in mutation detection of various applications.

  20. Mastering Transcription: Multiplexed Analysis of Transcription Start Site Sequences.

    Science.gov (United States)

    Hochschild, Ann

    2015-12-17

    In this issue of Molecular Cell, Vvedenskaya et al. (2015) describe a high-throughput sequencing-based methodology for the massively parallel analysis of transcription from a high-complexity barcoded template library both in vitro and in vivo, providing a powerful new tool for the study of transcription.

  1. Weighted Multiplex Networks

    CERN Document Server

    Menichetti, Giulia; Panzarasa, Pietro; Mondragón, Raúl J; Bianconi, Ginestra

    2013-01-01

    One of the most important challenges in network science is to quantify the information encoded in complex network structures. Disentangling randomness from organizational principles is even more demanding when networks have a multiplex nature. Multiplex networks are multilayer systems of $N$ nodes that can be linked in multiple interacting and co-evolving layers. In these networks, relevant information might not be captured if the single layers were analyzed separately. Here we demonstrate that such partial analysis of layers fails to capture significant correlations between weights and topology of complex multiplex networks. To this end, we study two weighted multiplex co-authorship and citation networks involving the authors included in the American Physical Society. We show that in these networks weights are strongly correlated with multiplex structure, and provide empirical evidence in favor of the advantage of studying weighted measures of multiplex networks, such as multistrength and the inverse multipa...

  2. Development of a novel multiplex DNA microarray for Fusarium graminearum and analysis of azole fungicide responses

    Directory of Open Access Journals (Sweden)

    Deising Holger B

    2011-01-01

    Full Text Available Abstract Background The toxigenic fungal plant pathogen Fusarium graminearum compromises wheat production worldwide. Azole fungicides play a prominent role in controlling this pathogen. Sequencing of its genome stimulated the development of high-throughput technologies to study mechanisms of coping with fungicide stress and adaptation to fungicides at a previously unprecedented precision. DNA-microarrays have been used to analyze genome-wide gene expression patterns and uncovered complex transcriptional responses. A recently developed one-color multiplex array format allowed flexible, effective, and parallel examinations of eight RNA samples. Results We took advantage of the 8 × 15 k Agilent format to design, evaluate, and apply a novel microarray covering the whole F. graminearum genome to analyze transcriptional responses to azole fungicide treatment. Comparative statistical analysis of expression profiles uncovered 1058 genes that were significantly differentially expressed after azole-treatment. Quantitative RT-PCR analysis for 31 selected genes indicated high conformity to results from the microarray hybridization. Among the 596 genes with significantly increased transcript levels, analyses using GeneOntology and FunCat annotations detected the ergosterol-biosynthesis pathway genes as the category most significantly responding, confirming the mode-of-action of azole fungicides. Cyp51A, which is one of the three F. graminearum paralogs of Cyp51 encoding the target of azoles, was the most consistently differentially expressed gene of the entire study. A molecular phylogeny analyzing the relationships of the three CYP51 proteins in the context of 38 fungal genomes belonging to the Pezizomycotina indicated that CYP51C (FGSG_11024 groups with a new clade of CYP51 proteins. The transcriptional profiles for genes encoding ABC transporters and transcription factors suggested several involved in mechanisms alleviating the impact of the fungicide

  3. Quantitative analysis of Boehm's GC

    Institute of Scientific and Technical Information of China (English)

    GUAN Xue-tao; ZHANG Yuan-rui; GOU Xiao-gang; CHENG Xu

    2003-01-01

    The term garbage collection describes the automated process of finding previously allocated memorythatis no longer in use in order to make the memory available to satisfy subsequent allocation requests. Wehave reviewed existing papers and implementations of GC, and especially analyzed Boehm' s C codes, which isa real-time mark-sweep GC running under Linux and ANSI C standard. In this paper, we will quantitatively an-alyze the performance of different configurations of Boehm' s collector subjected to different workloads. Reportedmeasurements demonstrate that a refined garbage collector is a viable alternative to traditional explicit memorymanagement techniques, even for low-level languages. It is more a trade-off for certain system than an all-or-nothing proposition.

  4. Quantitative analysis of qualitative images

    Science.gov (United States)

    Hockney, David; Falco, Charles M.

    2005-03-01

    We show optical evidence that demonstrates artists as early as Jan van Eyck and Robert Campin (c1425) used optical projections as aids for producing their paintings. We also have found optical evidence within works by later artists, including Bermejo (c1475), Lotto (c1525), Caravaggio (c1600), de la Tour (c1650), Chardin (c1750) and Ingres (c1825), demonstrating a continuum in the use of optical projections by artists, along with an evolution in the sophistication of that use. However, even for paintings where we have been able to extract unambiguous, quantitative evidence of the direct use of optical projections for producing certain of the features, this does not mean that paintings are effectively photographs. Because the hand and mind of the artist are intimately involved in the creation process, understanding these complex images requires more than can be obtained from only applying the equations of geometrical optics.

  5. [Clarification of a break-in theft crime by multiplex PCR analysis of cigarette butts].

    Science.gov (United States)

    Hochmeister, M; Haberl, J; Borer, V; Rudin, O; Dirnhofer, R

    1995-01-01

    This paper describes the first use of multiplex PCR amplification kits for the analysis of DNA extracted from cigarette butts in a criminal case. Two suspects could be excluded as potential contributors to the samples, whereas the multi locus PCR-based DNa profile derived from the cigarette butts was consistent with a DNA profile derived from a third suspect. For identity testing in criminal cases where cigarette butts are involved, commercially available PCR amplification kits provide currently the most powerful tool. Furthermore this PCR-based analysis can be implemented into most application orientated laboratories.

  6. Multiplex social ecological network analysis reveals how social changes affect community robustness more than resource depletion.

    Science.gov (United States)

    Baggio, Jacopo A; BurnSilver, Shauna B; Arenas, Alex; Magdanz, James S; Kofinas, Gary P; De Domenico, Manlio

    2016-11-29

    Network analysis provides a powerful tool to analyze complex influences of social and ecological structures on community and household dynamics. Most network studies of social-ecological systems use simple, undirected, unweighted networks. We analyze multiplex, directed, and weighted networks of subsistence food flows collected in three small indigenous communities in Arctic Alaska potentially facing substantial economic and ecological changes. Our analysis of plausible future scenarios suggests that changes to social relations and key households have greater effects on community robustness than changes to specific wild food resources.

  7. A lab-on-a-chip system integrating tissue sample preparation and multiplex RT-qPCR for gene expression analysis in point-of-care hepatotoxicity assessment.

    Science.gov (United States)

    Lim, Geok Soon; Chang, Joseph S; Lei, Zhang; Wu, Ruige; Wang, Zhiping; Cui, Kemi; Wong, Stephen

    2015-10-21

    A truly practical lab-on-a-chip (LOC) system for point-of-care testing (POCT) hepatotoxicity assessment necessitates the embodiment of full-automation, ease-of-use and "sample-in-answer-out" diagnostic capabilities. To date, the reported microfluidic devices for POCT hepatotoxicity assessment remain rudimentary as they largely embody only semi-quantitative or single sample/gene detection capabilities. In this paper, we describe, for the first time, an integrated LOC system that is somewhat close to a practical POCT hepatotoxicity assessment device - it embodies both tissue sample preparation and multiplex real-time RT-PCR. It features semi-automation, is relatively easy to use, and has "sample-in-answer-out" capabilities for multiplex gene expression analysis. Our tissue sample preparation module incorporating both a microhomogenizer and surface-treated paramagnetic microbeads yielded high purity mRNA extracts, considerably better than manual means of extraction. A primer preloading surface treatment procedure and the single-loading inlet on our multiplex real-time RT-PCR module simplify off-chip handling procedures for ease-of-use. To demonstrate the efficacy of our LOC system for POCT hepatotoxicity assessment, we perform a preclinical animal study with the administration of cyclophosphamide, followed by gene expression analysis of two critical protein biomarkers for liver function tests, aspartate transaminase (AST) and alanine transaminase (ALT). Our experimental results depict normalized fold changes of 1.62 and 1.31 for AST and ALT, respectively, illustrating up-regulations in their expression levels and hence validating their selection as critical genes of interest. In short, we illustrate the feasibility of multiplex gene expression analysis in an integrated LOC system as a viable POCT means for hepatotoxicity assessment.

  8. Electrochemical detection of magnetically-entrapped DNA sequences from complex samples by multiplexed enzymatic labelling: Application to a transgenic food/feed quantitative survey.

    Science.gov (United States)

    Manzanares-Palenzuela, C L; Martín-Clemente, J P; Lobo-Castañón, M J; López-Ruiz, B

    2017-03-01

    Monitoring of genetically modified organisms in food and feed demands molecular techniques that deliver accurate quantitative results. Electrochemical DNA detection has been widely described in this field, yet most reports convey qualitative data and application in processed food and feed samples is limited. Herein, the applicability of an electrochemical multiplex assay for DNA quantification in complex samples is assessed. The method consists of the simultaneous magnetic entrapment via sandwich hybridisation of two DNA sequences (event-specific and taxon-specific) onto the surface of magnetic microparticles, followed by bienzymatic labelling. As proof-of-concept, we report its application in a transgenic food/feed survey where relative quantification (two-target approach) of Roundup Ready Soybean® (RRS) was performed in food and feed. Quantitative coupling to end-point PCR was performed and calibration was achieved from 22 and 243 DNA copies spanning two orders of magnitude for the event and taxon-specific sequences, respectively. We collected a total of 33 soybean-containing samples acquired in local supermarkets, four out of which were found to contain undeclared presence of genetically modified soybean. A real-time PCR method was used to verify these findings. High correlation was found between results, indicating the suitability of the proposed multiplex method for food and feed monitoring.

  9. Development and Validation of a Multiplexed Protein Quantitation Assay for the Determination of Three Recombinant Proteins in Soybean Tissues by Liquid Chromatography with Tandem Mass Spectrometry.

    Science.gov (United States)

    Hill, Ryan C; Oman, Trent J; Shan, Guomin; Schafer, Barry; Eble, Julie; Chen, Cynthia

    2015-08-26

    Currently, traditional immunochemistry technologies such as enzyme-linked immunosorbent assays (ELISA) are the predominant analytical tool used to measure levels of recombinant proteins expressed in genetically engineered (GE) plants. Recent advances in agricultural biotechnology have created a need to develop methods capable of selectively detecting and quantifying multiple proteins in complex matrices because of increasing numbers of transgenic proteins being coexpressed or "stacked" to achieve tolerance to multiple herbicides or to provide multiple modes of action for insect control. A multiplexing analytical method utilizing liquid chromatography with tandem mass spectrometry (LC-MS/MS) has been developed and validated to quantify three herbicide-tolerant proteins in soybean tissues: aryloxyalkanoate dioxygenase (AAD-12), 5-enol-pyruvylshikimate-3-phosphate synthase (2mEPSPS), and phosphinothricin acetyltransferase (PAT). Results from the validation showed high recovery and precision over multiple analysts and laboratories. Results from this method were comparable to those obtained with ELISA with respect to protein quantitation, and the described method was demonstrated to be suitable for multiplex quantitation of transgenic proteins in GE crops.

  10. Millstone: software for multiplex microbial genome analysis and engineering.

    Science.gov (United States)

    Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

    2017-05-25

    Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

  11. Cancer detection by quantitative fluorescence image analysis.

    Science.gov (United States)

    Parry, W L; Hemstreet, G P

    1988-02-01

    Quantitative fluorescence image analysis is a rapidly evolving biophysical cytochemical technology with the potential for multiple clinical and basic research applications. We report the application of this technique for bladder cancer detection and discuss its potential usefulness as an adjunct to methods used currently by urologists for the diagnosis and management of bladder cancer. Quantitative fluorescence image analysis is a cytological method that incorporates 2 diagnostic techniques, quantitation of nuclear deoxyribonucleic acid and morphometric analysis, in a single semiautomated system to facilitate the identification of rare events, that is individual cancer cells. When compared to routine cytopathology for detection of bladder cancer in symptomatic patients, quantitative fluorescence image analysis demonstrated greater sensitivity (76 versus 33 per cent) for the detection of low grade transitional cell carcinoma. The specificity of quantitative fluorescence image analysis in a small control group was 94 per cent and with the manual method for quantitation of absolute nuclear fluorescence intensity in the screening of high risk asymptomatic subjects the specificity was 96.7 per cent. The more familiar flow cytometry is another fluorescence technique for measurement of nuclear deoxyribonucleic acid. However, rather than identifying individual cancer cells, flow cytometry identifies cellular pattern distributions, that is the ratio of normal to abnormal cells. Numerous studies by others have shown that flow cytometry is a sensitive method to monitor patients with diagnosed urological disease. Based upon results in separate quantitative fluorescence image analysis and flow cytometry studies, it appears that these 2 fluorescence techniques may be complementary tools for urological screening, diagnosis and management, and that they also may be useful separately or in combination to elucidate the oncogenic process, determine the biological potential of tumors

  12. Rapid, sensitive and real-time multiplexing platform for the analysis of protein and nucleic-acid biomarkers.

    Science.gov (United States)

    Falconnet, Didier; She, Joseph; Tornay, Raphaël; Leimgruber, Elisa; Bernasconi, David; Lagopoulos, Lucienne; Renaud, Philippe; Demierre, Nicolas; van den Bogaard, Patrick

    2015-02-03

    We describe a multiplexing technology, named Evalution, based on novel digitally encoded microparticles in microfluidic channels. Quantitative multiplexing is becoming increasingly important for research and routine clinical diagnostics, but fast, easy-to-use, flexible and highly reproducible technologies are needed to leverage the advantages of multiplexing. The presented technology has been tailored to ensure (i) short assay times and high reproducibility thanks to reaction-limited binding regime, (ii) dynamic control of assay conditions and real-time binding monitoring allowing optimization of multiple parameters within a single assay run, (iii) compatibility with various immunoassay formats such as coflowing the samples and detection antibodies simultaneously and hence simplifying workflows, (iv) analyte quantification based on initial binding rates leading to increased system dynamic range and (v) high sensitivity via enhanced fluorescence collection. These key features are demonstrated with assays for proteins and nucleic acids showing the versatility of this technology.

  13. Investigation of Pokemon-regulated proteins in hepatocellular carcinoma using mass spectrometry-based multiplex quantitative proteomics.

    Science.gov (United States)

    Bi, Xin; Jin, Yibao; Gao, Xiang; Liu, Feng; Gao, Dan; Jiang, Yuyang; Liu, Hongxia

    2013-01-01

    Pokemon is a transcription regulator involved in embryonic development, cellular differentiation and oncogenesis. It is aberrantly overexpressed in multiple human cancers including Hepatocellular carcinoma (HCC) and is considered as a promising biomarker for HCC. In this work, the isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics strategy was used to investigate the proteomic profile associated with Pokemon in human HCC cell line QGY7703 and human hepatocyte line HL7702. Samples were labeled with four-plex iTRAQ reagents followed by two-dimensional liquid chromatography coupled with tandem mass spectrometry analysis. A total of 24 differentially expressed proteins were selected as significant. Nine proteins were potentially up-regulated by Pokemon while 15 proteins were potentially down-regulated and many proteins were previously identified as potential biomarkers for HCC. Gene ontology (GO) term enrichment revealed that the listed proteins were mainly involved in DNA metabolism and biosynthesis process. The changes of glucose-6-phosphate 1-dehydrogenase (G6PD, up-regulated) and ribonucleoside-diphosphate reductase large sub-unit (RIM1, down-regulated) were validated by Western blotting analysis and denoted as Pokemon's function of oncogenesis. We also found that Pokemon potentially repressed the expression of highly clustered proteins (MCM3, MCM5, MCM6, MCM7) which played key roles in promoting DNA replication. Altogether, our results may help better understand the role of Pokemon in HCC and promote the clinical applications.

  14. A multiplexable, microfluidic platform for the rapid quantitation of a biomarker panel for early ovarian cancer detection at the point-of-care.

    Science.gov (United States)

    Shadfan, Basil H; Simmons, Archana R; Simmons, Glennon W; Ho, Andy; Wong, Jorge; Lu, Karen H; Bast, Robert C; McDevitt, John T

    2015-01-01

    Point-of-care (POC) diagnostic platforms have the potential to enable low-cost, large-scale screening. As no single biomarker is shed by all ovarian cancers, multiplexed biomarker panels promise improved sensitivity and specificity to address the unmet need for early detection of ovarian cancer. We have configured the programmable bio-nano-chip (p-BNC)-a multiplexable, microfluidic, modular platform-to quantify a novel multi-marker panel comprising CA125, HE4, MMP-7, and CA72-4. The p-BNC is a bead-based immunoanalyzer system with a credit-card-sized footprint that integrates automated sample metering, bubble and debris removal, reagent storage and waste disposal, permitting POC analysis. Multiplexed p-BNC immunoassays demonstrated high specificity, low cross-reactivity, low limits of detection suitable for early detection, and a short analysis time of 43 minutes. Day-to-day variability, a critical factor for longitudinally monitoring biomarkers, ranged between 5.4% and 10.5%, well below the biologic variation for all four markers. Biomarker concentrations for 31 late-stage sera correlated well (R(2) = 0.71 to 0.93 for various biomarkers) with values obtained on the Luminex platform. In a 31 patient cohort encompassing early- and late-stage ovarian cancers along with benign and healthy controls, the multiplexed p-BNC panel was able to distinguish cases from controls with 68.7% sensitivity at 80% specificity. Utility for longitudinal biomarker monitoring was demonstrated with prediagnostic plasma from 2 cases and 4 controls. Taken together, the p-BNC shows strong promise as a diagnostic tool for large-scale screening that takes advantage of faster results and lower costs while leveraging possible improvement in sensitivity and specificity from biomarker panels.

  15. Analysis of multiplex gene expression maps obtained by voxelation

    Directory of Open Access Journals (Sweden)

    Smith Desmond J

    2009-04-01

    Full Text Available Abstract Background Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. Results To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in

  16. Integration of PCR-Sequencing Analysis with Multiplex Ligation-Dependent Probe Amplification for Diagnosis of Hereditary Fructose Intolerance.

    Science.gov (United States)

    Ferri, Lorenzo; Caciotti, Anna; Cavicchi, Catia; Rigoldi, Miriam; Parini, Rossella; Caserta, Marina; Chibbaro, Guido; Gasperini, Serena; Procopio, Elena; Donati, Maria Alice; Guerrini, Renzo; Morrone, Amelia

    2012-01-01

    Mutations in the ALDOB gene impair the activity of the hepatic aldolase B enzyme, causing hereditary fructose intolerance (HFI), an inherited autosomic recessive disease of carbohydrate metabolism, that can result in hypoglycemia, liver and kidney failure, coma, and death. Noninvasive diagnosis is possible by identifying mutant ALDOB alleles in suspected patients. We report the genetic characterization of a cohort of 18 HFI Caucasian patients, based on PCR-sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA), with the identification of two novel genetic lesions: a small duplication c.940_941dupT (p.Trp314fsX22) and a large deletion encompassing the promoter region and exon 1. MLPA and long range-PCR (LR-PCR) also identified the recently reported g.7840_14288del6448 allele with a surprisingly high frequency (11%) within our patients' cohort. The most common p.Ala150Pro (44%), p.Ala175Asp (19%), p.Asn335Lys (8%), and/or the known c.360-363del4 (5%), p.Tyr204X (2.8%), IVS6 -2A>G (2.8%) mutant alleles were identified in 14 patients at a homozygous or compound-heterozygous level. The integration of PCR-sequencing analysis with exon-dosage tools [MLPA and quantitative fluorescent multiplex-PCR (QFM-PCR)] led to the full genotyping of patients within our cohort and to the identification of the new deletion encompassing the promoter region and exon 1.

  17. MULTIPLEX ANALYSIS OF BIOMARKERS OF NEOANGIOGENESIS AND INFLAMMATION IN HEART TRANSPLANT RECIPIENTS

    Directory of Open Access Journals (Sweden)

    O. P. Shevchenko

    2015-01-01

    Full Text Available Aim of study: multiplex analysis of the levels of biomarkers of neoangiogenesis and inflammation in cardiac transplant recipients. Materials and methods. 59 pts. with heart failure III–IV according to NYHA FC, waiting for a heart transplant, aged 22 to 73 years, 48 males and 11 females. 41 recipient (30 men and 11 women had dilated cardiomyopathy, 18 – coronary heart disease (CHD. The concentration of VEGF-A, VEGF-D, PlGF, PDGF-BB, FGF, sCD40L, MCP-1 was measured using xMAP technology, the sets of reagents Simplex ProcartaPlexTM (Affymetrix, USA. Results. There are four levels of seven biomarkers of neoangiogenesis and inflammation method for multiplex analysis in patients with heart failure. A year after transplantation, the mean levels of biomarkers VEGF-A (p = 0.001, PDGF-BB (p = 0.018, MCP-1 (p = 0.003 was significantly decreased, and the others had a tendency to decrease relative to the level before transplantation. It was shown individual differences of levels of VEGF-A, VEGF-D and PlGF before and after transplantation. There were found different dynamics of the concentrations of biomarkers and growth factors before and after heart transplantation in patients with cardiovascular complications and without them. Conclusion. Multiplex analysis allows to measure the concentration range of analyte biomarkers of neoangiogenesis, inflammation in one sample of blood serum of patients with severe heart failure and after transplantation. There are marked individual differences in the concentration of biomarkers in different clinical situations that may have clinical significance in the conduct and supervision of recipients after transplantation.

  18. Multiplex high-throughput gene mutation analysis in acute myeloid leukemia.

    Science.gov (United States)

    Dunlap, Jennifer; Beadling, Carol; Warrick, Andrea; Neff, Tanaya; Fleming, William H; Loriaux, Marc; Heinrich, Michael C; Kovacsovics, Tibor; Kelemen, Katalin; Leeborg, Nicky; Gatter, Ken; Braziel, Rita M; Press, Richard; Corless, Christopher L; Fan, Guang

    2012-12-01

    Classification of acute myeloid leukemia increasingly depends on genetic analysis. However, the number of known mutations in acute myeloid leukemia is expanding rapidly. Therefore, we tested a high-throughput screening method for acute myeloid leukemia mutation analysis using a multiplex mass spectrometry-based approach. To our knowledge, this is the first reported application of this approach to genotype leukemias in a clinical setting. One hundred seven acute myeloid leukemia cases were screened for mutations using a panel that covers 344 point mutations across 31 genes known to be associated with leukemia. The analysis was performed by multiplex polymerase chain reaction for mutations in genes of interest followed by primer extension reactions. Products were analyzed on a Sequenom MassARRAY system (San Diego, CA). The multiplex panel yielded mutations in 58% of acute myeloid leukemia cases with normal cytogenetics and 21% of cases with abnormal cytogenetics. Cytogenetics and routine polymerase chain reaction-based screening of NPM1, CEBPA, FLT3-ITD, and KIT was also performed on a subset of cases. When combined with the results of these standard polymerase chain reaction-based tests, the mutation frequency reached 78% in cases with normal cytogenetics. Of these, 42% harbored multiple mutations primarily involving NPM1 with NRAS, KRAS, CEBPA, PTPN11, IDH1, or FLT3. In contrast, cases with abnormal cytogenetics rarely harbored more than 1 mutation (1.5%), suggesting different underlying biology. This study demonstrates the feasibility and utility of broad-based mutation profiling of acute myeloid leukemia in a clinical setting. This approach will be helpful in defining prognostic subgroups of acute myeloid leukemia and contribute to the selection of patients for enrollment into trials with novel inhibitors.

  19. Complete Photoionization Experiments via Ultrafast Coherent Control with Polarization Multiplexing II: Numerics & Analysis Methodologies

    CERN Document Server

    Hockett, P; Lux, C; Baumert, T

    2015-01-01

    The feasibility of complete photoionization experiments, in which the full set of photoionization matrix elements are determined, using multiphoton ionization schemes with polarization-shaped pulses has recently been demonstrated [Hockett et. al., Phys. Rev. Lett. 112, 223001 (2014)]. Here we extend on our previous work to discuss further details of the numerics and analysis methodology utilised, and compare the results directly to new tomographic photoelectron measurements, which provide a more sensitive test of the validity of the results. In so doing we discuss in detail the physics of the photoionziation process, and suggest various avenues and prospects for this coherent multiplexing methodology.

  20. Digital transplantation pathology: combining whole slide imaging, multiplex staining and automated image analysis.

    Science.gov (United States)

    Isse, K; Lesniak, A; Grama, K; Roysam, B; Minervini, M I; Demetris, A J

    2012-01-01

    Conventional histopathology is the gold standard for allograft monitoring, but its value proposition is increasingly questioned. "-Omics" analysis of tissues, peripheral blood and fluids and targeted serologic studies provide mechanistic insights into allograft injury not currently provided by conventional histology. Microscopic biopsy analysis, however, provides valuable and unique information: (a) spatial-temporal relationships; (b) rare events/cells; (c) complex structural context; and (d) integration into a "systems" model. Nevertheless, except for immunostaining, no transformative advancements have "modernized" routine microscopy in over 100 years. Pathologists now team with hardware and software engineers to exploit remarkable developments in digital imaging, nanoparticle multiplex staining, and computational image analysis software to bridge the traditional histology-global "-omic" analyses gap. Included are side-by-side comparisons, objective biopsy finding quantification, multiplexing, automated image analysis, and electronic data and resource sharing. Current utilization for teaching, quality assurance, conferencing, consultations, research and clinical trials is evolving toward implementation for low-volume, high-complexity clinical services like transplantation pathology. Cost, complexities of implementation, fluid/evolving standards, and unsettled medical/legal and regulatory issues remain as challenges. Regardless, challenges will be overcome and these technologies will enable transplant pathologists to increase information extraction from tissue specimens and contribute to cross-platform biomarker discovery for improved outcomes.

  1. Quantitative histogram analysis of images

    Science.gov (United States)

    Holub, Oliver; Ferreira, Sérgio T.

    2006-11-01

    A routine for histogram analysis of images has been written in the object-oriented, graphical development environment LabVIEW. The program converts an RGB bitmap image into an intensity-linear greyscale image according to selectable conversion coefficients. This greyscale image is subsequently analysed by plots of the intensity histogram and probability distribution of brightness, and by calculation of various parameters, including average brightness, standard deviation, variance, minimal and maximal brightness, mode, skewness and kurtosis of the histogram and the median of the probability distribution. The program allows interactive selection of specific regions of interest (ROI) in the image and definition of lower and upper threshold levels (e.g., to permit the removal of a constant background signal). The results of the analysis of multiple images can be conveniently saved and exported for plotting in other programs, which allows fast analysis of relatively large sets of image data. The program file accompanies this manuscript together with a detailed description of two application examples: The analysis of fluorescence microscopy images, specifically of tau-immunofluorescence in primary cultures of rat cortical and hippocampal neurons, and the quantification of protein bands by Western-blot. The possibilities and limitations of this kind of analysis are discussed. Program summaryTitle of program: HAWGC Catalogue identifier: ADXG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXG_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computers: Mobile Intel Pentium III, AMD Duron Installations: No installation necessary—Executable file together with necessary files for LabVIEW Run-time engine Operating systems or monitors under which the program has been tested: WindowsME/2000/XP Programming language used: LabVIEW 7.0 Memory required to execute with typical data:˜16MB for starting and ˜160MB used for

  2. Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants

    Directory of Open Access Journals (Sweden)

    Khatri Purvesh

    2010-10-01

    Full Text Available Abstract Background Combining the results of studies using highly parallelized measurements of gene expression such as microarrays and RNAseq offer unique challenges in meta analysis. Motivated by a need for a deeper understanding of organ transplant rejection, we combine the data from five separate studies to compare acute rejection versus stability after solid organ transplantation, and use this data to examine approaches to multiplex meta analysis. Results We demonstrate that a commonly used parametric effect size estimate approach and a commonly used non-parametric method give very different results in prioritizing genes. The parametric method providing a meta effect estimate was superior at ranking genes based on our gold-standard of identifying immune response genes in the transplant rejection datasets. Conclusion Different methods of multiplex analysis can give substantially different results. The method which is best for any given application will likely depend on the particular domain, and it remains for future work to see if any one method is consistently better at identifying important biological signal across gene expression experiments.

  3. Using multiplex PCR amplification and typing kits for the analysis of DNA evidence in a serial killer case.

    Science.gov (United States)

    Hochmeister, M N; Budowle, B; Eisenberg, A; Borer, U V; Dirnhofer, R

    1996-01-01

    Analysis of DNA evidence in a serial killer case was performed using the AmpliType HLA-DQ alpha-, AmpliType PM-, and the GenePrint STR Multiplex System PCR Amplification Kits. In addition, a sex typing procedure using the X-Y homologous gene amelogenin was carried out. DNA profiles from a single hair with attached sheath material, recovered from underneath the seat cover of the suspect's car seat were compared with DNA profiles derived from reference head hairs from a homicide victim. From the evidentiary sample only 9 ng of human DNA could be recovered. In a sample, where the quantity of DNA becomes a critical issue a powerful route is the simultaneous amplification of several loci (multiplex PCR). This is the first report where commercially available multiplex PCR amplification and typing kits have been introduced for the analysis of DNA evidence in a serial killer case and the analysis has been admitted in court.

  4. C6 Peptide-Based Multiplex Phosphorescence Analysis (PHOSPHAN for Serologic Confirmation of Lyme Borreliosis.

    Directory of Open Access Journals (Sweden)

    Vera G Pomelova

    Full Text Available A single-tier immunoassay using the C6 peptide of VlsE (C6 from Borrelia burgdorferi sensu stricto (Bb has been proposed as a potential alternative to conventional two-tier testing for the serologic diagnosis of Lyme disease in the United States and Europe.To evaluate the performance of C6 peptide based multiplex Phosphorescence Analysis (PHOSPHAN for the serologic confirmation of Lyme borreliosis (LB in Russian patients.Serum samples (n = 351 were collected from 146 patients with erythema migrans (EM; samples from 131 of these patients were taken several times prior to treatment and at different stages of recovery. The control group consisted of 197 healthy blood donors and 31 patients with other diseases, all from the same highly endemic region of Russia. All samples were analyzed by PHOSPHAN for IgM and IgG to Bb C6, recombinant OspC and VlsE proteins, and C6 peptides from B. garinii and B. afzelii.IgM and IgG to Bb C6 were identified in 43 and 95 out of 131 patients (32.8 and 72.5%, respectively; seroconversion of IgM antibodies was observed in about half of the patients (51.2%, and of IgG antibodies, in almost all of them (88.4%. Additional detection of OspC-IgM and VlsE-IgM or IgG to C6 from B. garinii or B. afzelii did not contribute significantly to the overall sensitivity of the multiplex immunoassay.The multiplex phosphorescence immunoassay is a promising method for simultaneously revealing the spectrum of antibodies to several Borrelia antigens. Detection of IgM and IgG to Bb C6 in the sera of EM patients provides effective serologic confirmation of LB and, with high probability, indicates an active infection process.

  5. A laser ablation ICP-MS based method for multiplexed immunoblot analysis: applications to manganese-dependent protein dynamics of photosystem II in barley (Hordeum vulgare L.)

    DEFF Research Database (Denmark)

    de Bang, Thomas Christian; Petersen, Jørgen; Pedas, Pai Rosager

    2015-01-01

    developed a multiplexed antibody-based assay and analysed selected PSII subunits in barley (Hordeum vulgare L.). A selection of antibodies were labelled with specific lanthanides and immunoreacted with thylakoids exposed to Mn deficiency after western blotting. Subsequently, western blot membranes were...... analysed by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), which allowed selective and relative quantitative analysis via the different lanthanides. The method was evaluated against established liquid chromatography electrospray ionization tandem mass spectrometry (LC...

  6. Stand-Sit Microchip for High-Throughput, Multiplexed Analysis of Single Cancer Cells.

    Science.gov (United States)

    Ramirez, Lisa; Herschkowitz, Jason I; Wang, Jun

    2016-01-01

    Cellular heterogeneity in function and response to therapeutics has been a major challenge in cancer treatment. The complex nature of tumor systems calls for the development of advanced multiplexed single-cell tools that can address the heterogeneity issue. However, to date such tools are only available in a laboratory setting and don't have the portability to meet the needs in point-of-care cancer diagnostics. Towards that application, we have developed a portable single-cell system that is comprised of a microchip and an adjustable clamp, so on-chip operation only needs pipetting and adjusting of clamping force. Up to 10 proteins can be quantitated from each cell with hundreds of single-cell assays performed in parallel from one chip operation. We validated the technology and analyzed the oncogenic signatures of cancer stem cells by quantitating both aldehyde dehydrogenase (ALDH) activities and 5 signaling proteins in single MDA-MB-231 breast cancer cells. The technology has also been used to investigate the PI3K pathway activities of brain cancer cells expressing mutant epidermal growth factor receptor (EGFR) after drug intervention targeting EGFR signaling. Our portable single-cell system will potentially have broad application in the preclinical and clinical settings for cancer diagnosis in the future.

  7. Stand-Sit Microchip for High-Throughput, Multiplexed Analysis of Single Cancer Cells

    Science.gov (United States)

    Ramirez, Lisa; Herschkowitz, Jason I.; Wang, Jun

    2016-01-01

    Cellular heterogeneity in function and response to therapeutics has been a major challenge in cancer treatment. The complex nature of tumor systems calls for the development of advanced multiplexed single-cell tools that can address the heterogeneity issue. However, to date such tools are only available in a laboratory setting and don’t have the portability to meet the needs in point-of-care cancer diagnostics. Towards that application, we have developed a portable single-cell system that is comprised of a microchip and an adjustable clamp, so on-chip operation only needs pipetting and adjusting of clamping force. Up to 10 proteins can be quantitated from each cell with hundreds of single-cell assays performed in parallel from one chip operation. We validated the technology and analyzed the oncogenic signatures of cancer stem cells by quantitating both aldehyde dehydrogenase (ALDH) activities and 5 signaling proteins in single MDA-MB-231 breast cancer cells. The technology has also been used to investigate the PI3K pathway activities of brain cancer cells expressing mutant epidermal growth factor receptor (EGFR) after drug intervention targeting EGFR signaling. Our portable single-cell system will potentially have broad application in the preclinical and clinical settings for cancer diagnosis in the future. PMID:27581736

  8. Christhin: Quantitative Analysis of Thin Layer Chromatography

    CERN Document Server

    Barchiesi, Maximiliano; Renaudo, Carlos; Rossi, Pablo; Pramparo, María de Carmen; Nepote, Valeria; Grosso, Nelson Ruben; Gayol, María Fernanda

    2012-01-01

    Manual for Christhin 0.1.36 Christhin (Chromatography Riser Thin) is software developed for the quantitative analysis of data obtained from thin-layer chromatographic techniques (TLC). Once installed on your computer, the program is very easy to use, and provides data quickly and accurately. This manual describes the program, and reading should be enough to use it properly.

  9. Quantitative texture analysis of electrodeposited line patterns

    DEFF Research Database (Denmark)

    Pantleon, Karen; Somers, Marcel A.J.

    2005-01-01

    Free-standing line patterns of Cu and Ni were manufactured by electrochemical deposition into lithographically prepared patterns. Electrodeposition was carried out on top of a highly oriented Au-layer physically vapor deposited on glass. Quantitative texture analysis carried out by means of x...

  10. Quantitative texture analysis of electrodeposited line patterns

    DEFF Research Database (Denmark)

    Pantleon, Karen; Somers, Marcel A.J.

    2005-01-01

    Free-standing line patterns of Cu and Ni were manufactured by electrochemical deposition into lithographically prepared patterns. Electrodeposition was carried out on top of a highly oriented Au-layer physically vapor deposited on glass. Quantitative texture analysis carried out by means of x...

  11. Quantitative analysis of arm movement smoothness

    Science.gov (United States)

    Szczesna, Agnieszka; Błaszczyszyn, Monika

    2017-07-01

    The paper deals with the problem of motion data quantitative smoothness analysis. We investigated values of movement unit, fluidity and jerk for healthy and paralyzed arm of patients with hemiparesis after stroke. Patients were performing drinking task. To validate the approach, movement of 24 patients were captured using optical motion capture system.

  12. Seniors' Online Communities: A Quantitative Content Analysis

    Science.gov (United States)

    Nimrod, Galit

    2010-01-01

    Purpose: To examine the contents and characteristics of seniors' online communities and to explore their potential benefits to older adults. Design and Methods: Quantitative content analysis of a full year's data from 14 leading online communities using a novel computerized system. The overall database included 686,283 messages. Results: There was…

  13. A quantitative approach to scar analysis.

    Science.gov (United States)

    Khorasani, Hooman; Zheng, Zhong; Nguyen, Calvin; Zara, Janette; Zhang, Xinli; Wang, Joyce; Ting, Kang; Soo, Chia

    2011-02-01

    Analysis of collagen architecture is essential to wound healing research. However, to date no consistent methodologies exist for quantitatively assessing dermal collagen architecture in scars. In this study, we developed a standardized approach for quantitative analysis of scar collagen morphology by confocal microscopy using fractal dimension and lacunarity analysis. Full-thickness wounds were created on adult mice, closed by primary intention, and harvested at 14 days after wounding for morphometrics and standard Fourier transform-based scar analysis as well as fractal dimension and lacunarity analysis. In addition, transmission electron microscopy was used to evaluate collagen ultrastructure. We demonstrated that fractal dimension and lacunarity analysis were superior to Fourier transform analysis in discriminating scar versus unwounded tissue in a wild-type mouse model. To fully test the robustness of this scar analysis approach, a fibromodulin-null mouse model that heals with increased scar was also used. Fractal dimension and lacunarity analysis effectively discriminated unwounded fibromodulin-null versus wild-type skin as well as healing fibromodulin-null versus wild-type wounds, whereas Fourier transform analysis failed to do so. Furthermore, fractal dimension and lacunarity data also correlated well with transmission electron microscopy collagen ultrastructure analysis, adding to their validity. These results demonstrate that fractal dimension and lacunarity are more sensitive than Fourier transform analysis for quantification of scar morphology. Copyright © 2011 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  14. Chicken QTL mapping by multiplex PCR

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    To facilitate rapid determination of the chromosomal location of quantitative trait loci, the current approaches to gene mapping are improved using a multiplex PCR technique. The high-throughput linkage analysis method described here allows selection of 178 from 328 microsatellite markers through the multiplex PCR method combined with the semi-automatic fluorescence-labeled DNA analysis technology. Those polymorphism markers are distributed on 23 autosomes and one sex chromosome (chromosome Z), covering 3080cM genetic distance. The average marker density is 18cM, dispersed into 30 different sets. These selected polymorphism microsatellite markers segregate with the family members, following the Mendel's heritage laws, and are very useful for chicken linkage map analysis as well as for the research on some important economic quantitative characters of chicken.

  15. Diversity Analysis of Bit-Interleaved Coded Multiple Beamforming with Orthogonal Frequency Division Multiplexing

    CERN Document Server

    Li, Boyu

    2011-01-01

    Beamforming techniques employing Singular Value Decomposition (SVD) are commonly used in Multi-Input Multi-Output (MIMO) wireless communication systems. For frequency selective channels, Bit-Interleaved Coded Multiple Beamforming with Orthogonal Frequency Division Multiplexing (BICMB-OFDM) can be applied to achieve both spatial diversity and multipath diversity. However, the diversity analysis of BICMB-OFDM is a challenging problem because of its complicated system structure. In this paper, the diversity of BICMB-OFDM is investigated with the consideration of the correlation among subcarrier channels. Based on the analysis, the maximum achievable diversity is derived. Then, a full diversity condition RcSL<=1 is proved, where Rc, S, and L are the code rate, the number of parallel streams, and the number of channel taps, respectively. However, with correlation, the actual diversity is degraded compared to its maximum achievable value. Therefore, two strategies are discussed to combat the diversity degradatio...

  16. Performance analysis of modified Asymmetrically-Clipped Optical Orthogonal Frequency-Division Multiplexing systems

    Science.gov (United States)

    Mohamed, Salma D.; Shalaby, Hossam M. H.; Andonovic, Ivan; Aly, Moustafa H.

    2016-12-01

    A modification to the Asymmetrically-Clipped Optical Orthogonal Frequency-Division Multiplexing (ACO-OFDM) technique is proposed through unipolar encoding. A performance analysis of the Bit Error Rate (BER) is developed and Monte Carlo simulations are carried out to verify the analysis. Results are compared to that of the corresponding ACO-OFDM system under the same bit energy and transmission rate; an improvement of 1 dB is obtained at a BER of 10-4 . In addition, the performance of the proposed system in the presence of atmospheric turbulence is investigated using single-input multiple-output (SIMO) configuration and its performance under that environment is compared to that of ACO-OFDM. Energy improvements of 4 dB and 2.2 dB are obtained at a BER of 10-4 for SIMO systems of 1 and 2 photodetectors at the receiver for the case of strong turbulence, respectively.

  17. Numerical analysis of intermodal delay in few-mode fibers for mode division multiplexing in optical fiber communication systems

    Institute of Scientific and Technical Information of China (English)

    Abid Munir; XIN Xiang-jun; LIU Bo; Abdul Latif; Aftab Hussain; Shahab Ahmad Niazi

    2012-01-01

    In order to achieve higher spectral efficiency,mode division multiplexing (MDM) in few-mode fibers is a new research area.The idea faces lots of technical issues including intermodal delay and mode coupling which limit the achievable length of the system.This paper is designated to complete the analysis of intermodal delay in step-index few-mode fibers.We analyze numerically all the parameters of fiber,which could impact intermodal delay in few-mode fibers and identify the conditions which can increase the number of multiplex modes without significant increase in maximum intermodal delay.

  18. Fully integrated wearable sensor arrays for multiplexed in situ perspiration analysis

    Science.gov (United States)

    Gao, Wei; Emaminejad, Sam; Nyein, Hnin Yin Yin; Challa, Samyuktha; Chen, Kevin; Peck, Austin; Fahad, Hossain M.; Ota, Hiroki; Shiraki, Hiroshi; Kiriya, Daisuke; Lien, Der-Hsien; Brooks, George A.; Davis, Ronald W.; Javey, Ali

    2016-01-01

    Wearable sensor technologies are essential to the realization of personalized medicine through continuously monitoring an individual’s state of health. Sampling human sweat, which is rich in physiological information, could enable non-invasive monitoring. Previously reported sweat-based and other non-invasive biosensors either can only monitor a single analyte at a time or lack on-site signal processing circuitry and sensor calibration mechanisms for accurate analysis of the physiological state. Given the complexity of sweat secretion, simultaneous and multiplexed screening of target biomarkers is critical and requires full system integration to ensure the accuracy of measurements. Here we present a mechanically flexible and fully integrated (that is, no external analysis is needed) sensor array for multiplexed in situ perspiration analysis, which simultaneously and selectively measures sweat metabolites (such as glucose and lactate) and electrolytes (such as sodium and potassium ions), as well as the skin temperature (to calibrate the response of the sensors). Our work bridges the technological gap between signal transduction, conditioning (amplification and filtering), processing and wireless transmission in wearable biosensors by merging plastic-based sensors that interface with the skin with silicon integrated circuits consolidated on a flexible circuit board for complex signal processing. This application could not have been realized using either of these technologies alone owing to their respective inherent limitations. The wearable system is used to measure the detailed sweat profile of human subjects engaged in prolonged indoor and outdoor physical activities, and to make a real-time assessment of the physiological state of the subjects. This platform enables a wide range of personalized diagnostic and physiological monitoring applications.

  19. A Multiplexed Cytokeratin Analysis Using Targeted Mass Spectrometry Reveals Specific Profiles in Cancer-Related Pleural Effusions

    Directory of Open Access Journals (Sweden)

    Dominik Domanski

    2016-07-01

    Full Text Available Pleural effusion (PE, excess fluid in the pleural space, is often observed in lung cancer patients and also forms due to many benign ailments. Classifying it quickly is critical, but this remains an analytical challenge often lengthening the diagnosis process or exposing patients to unnecessary risky invasive procedures. We tested the analysis of PE using a multiplexed cytokeratin (CK panel with targeted mass spectrometry–based quantitation for its rapid classification. CK markers are often assessed in pathological examinations for cancer diagnosis and guiding treatment course. We developed methods to simultaneously quantify 33 CKs in PE using peptide standards for increased analytical specificity and a simple CK enrichment method to detect their low amounts. Analyzing 121 PEs associated with a variety of lung cancers and noncancerous causes, we show that abundance levels of 10 CKs can be related to PE etiology. CK-6, CK-7, CK-8, CK-18, and CK-19 were found at significantly higher levels in cancer-related PEs. Additionally, elevated levels of vimentin and actin differentiated PEs associated with bacterial infections. A classifier algorithm effectively grouped PEs into cancer-related or benign PEs with 81% sensitivity and 79% specificity. A set of undiagnosed PEs showed that our method has potential to shorten PE diagnosis time. For the first time, we show that a cancer-relevant panel of simple-epithelial CK markers currently used in clinical assessment can also be quantitated in PEs. Additionally, while requiring less invasive sampling, our methodology demonstrated a significant ability to identify cancer-related PEs in clinical samples and thus could improve patient care in the future.

  20. A battery-powered notebook thermal cycler for rapid multiplex real-time PCR analysis.

    Science.gov (United States)

    Belgrader, P; Young, S; Yuan, B; Primeau, M; Christel, L A; Pourahmadi, F; Northrup, M A

    2001-01-15

    A compact, real-time PCR instrument was developed for rapid, multiplex analysis of nucleic acids in an inexpensive, portable format. The instrument consists of a notebook computer, two reaction modules with integrated optics for four-color fluorescence detection, batteries, and a battery-charging system. The instrument weighs 3.3 kg, measures 26 x 22 x 7.5 cm, and can run continuously on the internal batteries for 4 h. Independent control of the modules allows differing temperature profiles and detection schemes to be run simultaneously. Results are presented that demonstrate rapid (1) detection and identification of Bacillus subtilis and Bacillus thuringensis spores and (2) characterization of a single nucleotide polymorphism for the hereditary hemochromatosis gene.

  1. Quantitative image analysis of celiac disease.

    Science.gov (United States)

    Ciaccio, Edward J; Bhagat, Govind; Lewis, Suzanne K; Green, Peter H

    2015-03-07

    We outline the use of quantitative techniques that are currently used for analysis of celiac disease. Image processing techniques can be useful to statistically analyze the pixular data of endoscopic images that is acquired with standard or videocapsule endoscopy. It is shown how current techniques have evolved to become more useful for gastroenterologists who seek to understand celiac disease and to screen for it in suspected patients. New directions for focus in the development of methodology for diagnosis and treatment of this disease are suggested. It is evident that there are yet broad areas where there is potential to expand the use of quantitative techniques for improved analysis in suspected or known celiac disease patients.

  2. Quantitative image analysis of celiac disease

    Science.gov (United States)

    Ciaccio, Edward J; Bhagat, Govind; Lewis, Suzanne K; Green, Peter H

    2015-01-01

    We outline the use of quantitative techniques that are currently used for analysis of celiac disease. Image processing techniques can be useful to statistically analyze the pixular data of endoscopic images that is acquired with standard or videocapsule endoscopy. It is shown how current techniques have evolved to become more useful for gastroenterologists who seek to understand celiac disease and to screen for it in suspected patients. New directions for focus in the development of methodology for diagnosis and treatment of this disease are suggested. It is evident that there are yet broad areas where there is potential to expand the use of quantitative techniques for improved analysis in suspected or known celiac disease patients. PMID:25759524

  3. Use of multiplex PCR and PCR restriction enzyme analysis for detection and exploration of the variability in the free-living amoeba Naegleria in the environment.

    Science.gov (United States)

    Pélandakis, Michel; Pernin, Pierre

    2002-04-01

    A multiplex PCR was developed to simultaneously detect Naegleria fowleri and other Naegleria species in the environment. Multiplex PCR was also capable of identifying N. fowleri isolates with internal transcribed spacers of different sizes. In addition, restriction fragment length polymorphism analysis of the PCR product distinguished the main thermophilic Naegleria species from the sampling sites.

  4. Evaluation and subsequent optimizations of the quantitative AmpliSens Florocenosis/Bacterial vaginosis-FRT multiplex real-time PCR assay for diagnosis of bacterial vaginosis.

    Science.gov (United States)

    Rumyantseva, Tatiana; Shipitsyna, Elena; Guschin, Alexander; Unemo, Magnus

    2016-12-01

    Traditional microscopy-based methods for diagnosis of bacterial vaginosis (BV) are underutilized in many settings, and molecular techniques may provide opportunities for rapid, objective, and accurate BV diagnosis. This study evaluated the quantitative AmpliSens Florocenosis/Bacterial vaginosis-FRT multiplex real-time PCR (Florocenosis-BV) assay. Vaginal samples from a previous study including unselected female subjects (n = 163) and using Amsel criteria and 454 pyrosequencing for BV diagnosis were examined with the Florocenosis-BV test and additionally tested for the presence and quantity of Gardnerella vaginalis clades 3 and 4. The Florocenosis-BV assay demonstrated 100% and 98% sensitivity compared with the Amsel criteria and 454 pyrosequencing, respectively, with 91% specificity. The modified Florocenosis-BV assay (detecting also G. vaginalis clades 3 and 4) resulted in 100% sensitivity vs the Amsel criteria and 454 pyrosequencing with specificity of 86% and 88%, respectively. Further optimizations of thresholds for the quantitative parameters used in the kit resulted in 99-100% accuracy vs Amsel criteria and 454 pyrosequencing for selected parameters. The Florocenosis-BV assay is an objective, accurate, sensitive, and specific method for BV diagnosis; however, the performance of the test can be further improved with some minor optimizations. © 2016 APMIS. Published by John Wiley & Sons Ltd.

  5. Simultaneous detection and quantitation of Chikungunya, dengue and West Nile viruses by multiplex RT-PCR assays and dengue virus typing using high resolution melting.

    Science.gov (United States)

    Naze, F; Le Roux, K; Schuffenecker, I; Zeller, H; Staikowsky, F; Grivard, P; Michault, A; Laurent, P

    2009-12-01

    Chikungunya (CHIKV), Dengue (DENV) and West Nile (WNV) viruses are arthropod-borne viruses that are able to emerge or re-emerge in many regions due to climatic changes and increase in travel. Since these viruses produce similar clinical signs it is important for physicians and epidemiologists to differentiate them rapidly. A molecular method was developed for their detection and quantitation in plasma samples and a DENV typing technique were developed. The method consisted in performing two multiplex real-time one-step RT-PCR assays, to detect and quantify the three viruses. Both assays were conducted in a single run, from a single RNA extract containing a unique coextracted and coamplified composite internal control. The quantitation results were close to the best detection thresholds obtained with simplex RT-PCR techniques. The differentiation of DENV types was performed using a High Resolution Melting technique. The assays enable the early diagnosis of the three arboviruses during viremia, including cases of coinfection. The method is rapid, specific and highly sensitive with a potential for clinical diagnosis and epidemiological surveillance. A DENV positive sample can be typed conveniently using the High Resolution Melting technique using the same apparatus.

  6. Tumor cell-collagen interactions: Identification and semi-quantitative evaluation of selectively-expressed genes by combination of differential display- and multiplex-PCR

    Directory of Open Access Journals (Sweden)

    Sirchia Rosalia

    2003-01-01

    Full Text Available It is widely acknowledged that the presence of extracellular matrix components as substrates can drastically modulate the phenotype and gene expression of cultured cells, including tumor cells. A number of published reports indicated that substrates made from two peculiar collagen species, i.e. type V and OF/LB, which are abnormally deposited in the stroma of primary ductal infiltrating carcinoma (d.i.c. of the breast “in vivo,” were able to exert marked and opposite effects on “in vitro” viability, growth and invasiveness of the 8701-BC cell line, isolated from d.i.c.-affected breast epithelium. To complement such functional data on the effect of cell-collagen interactions with information at molecular level, we have utilized a combination of differential display- and semi-quantitative multiplex-PCR techniques with the aim of detecting variations in the expression levels of selected genes by cells maintained in either culture condition. Here we report some prototypical data on the identification and semi-quantitation of three of the differentially-amplified PCR products found, i.e. HSP2A and MSF-B which are up-regulated in cells grown onto OF/LB collagen substrate, and SRCAP which is prominently down-regulated in the presence of type V collagen substrate. This protocol represents a powerful tool for evaluating changes in the levels and patterns of gene expression which can be theoretically adapted to any experimental model system.

  7. Development of a multiplex real-time PCR assay for phylogenetic analysis of Uropathogenic Escherichia coli.

    Science.gov (United States)

    Hasanpour, Mojtaba; Najafi, Akram

    2017-03-28

    Uropathogenic Escherichia coli (UPEC) is among major pathogens causing 80-90% of all episodes of urinary tract infections (UTIs). Recently, E. coli strains are divided into eight main phylogenetic groups including A, B1, B2, C, D, E, F, and clade I. This study was aimed to develop a rapid, sensitive, and specific multiplex real time PCR method capable of detecting phylogenetic groups of E. coli strains. This study was carried out on E. coli strains (isolated from the patient with UTI) in which the presence of all seven target genes had been confirmed in our previous phylogenetic study. An EvaGreen-based singleplex and multiplex real-time PCR with melting curve analysis was designed for simultaneous detection and differentiation of these genes. The primers were selected mainly based on the production of amplicons with melting temperatures (Tm) ranging from 82°C to 93°C and temperature difference of more than 1.5°C between each peak.The multiplex real-time PCR assays that have been developed in the present study were successful in detecting the eight main phylogenetic groups. Seven distinct melting peaks were discriminated, with Tm value of 93±0.8 for arpA, 89.2±0.1for chuA, 86.5±0.1 for yjaA, 82.3±0.2 for TspE4C2, 87.8±0.1for trpAgpC, 85.4±0.6 for arpAgpE genes, and 91±0.5 for the internal control. To our knowledge, this study is the first melting curve-based real-time PCR assay developed for simultaneous and discrete detection of these seven target genes. Our findings showed that this assay has the potential to be a rapid, reliable and cost-effective alternative for routine phylotyping of E. coli strains.

  8. Using Qualitative Hazard Analysis to Guide Quantitative Safety Analysis

    Science.gov (United States)

    Shortle, J. F.; Allocco, M.

    2005-01-01

    Quantitative methods can be beneficial in many types of safety investigations. However, there are many difficulties in using quantitative m ethods. Far example, there may be little relevant data available. This paper proposes a framework for using quantitative hazard analysis to prioritize hazard scenarios most suitable for quantitative mziysis. The framework first categorizes hazard scenarios by severity and likelihood. We then propose another metric "modeling difficulty" that desc ribes the complexity in modeling a given hazard scenario quantitatively. The combined metrics of severity, likelihood, and modeling difficu lty help to prioritize hazard scenarios for which quantitative analys is should be applied. We have applied this methodology to proposed concepts of operations for reduced wake separation for airplane operatio ns at closely spaced parallel runways.

  9. Influence analysis in quantitative trait loci detection.

    Science.gov (United States)

    Dou, Xiaoling; Kuriki, Satoshi; Maeno, Akiteru; Takada, Toyoyuki; Shiroishi, Toshihiko

    2014-07-01

    This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods-the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation-based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics.

  10. Multiplex matrix network analysis of protein complexes in the human TCR signalosome.

    Science.gov (United States)

    Smith, Stephen E P; Neier, Steven C; Reed, Brendan K; Davis, Tessa R; Sinnwell, Jason P; Eckel-Passow, Jeanette E; Sciallis, Gabriel F; Wieland, Carilyn N; Torgerson, Rochelle R; Gil, Diana; Neuhauser, Claudia; Schrum, Adam G

    2016-08-02

    Multiprotein complexes transduce cellular signals through extensive interaction networks, but the ability to analyze these networks in cells from small clinical biopsies is limited. To address this, we applied an adaptable multiplex matrix system to physiologically relevant signaling protein complexes isolated from a cell line or from human patient samples. Focusing on the proximal T cell receptor (TCR) signalosome, we assessed 210 pairs of PiSCES (proteins in shared complexes detected by exposed surface epitopes). Upon stimulation of Jurkat cells with superantigen-loaded antigen-presenting cells, this system produced high-dimensional data that enabled visualization of network activity. A comprehensive analysis platform generated PiSCES biosignatures by applying unsupervised hierarchical clustering, principal component analysis, an adaptive nonparametric with empirical cutoff analysis, and weighted correlation network analysis. We generated PiSCES biosignatures from 4-mm skin punch biopsies from control patients or patients with the autoimmune skin disease alopecia areata. This analysis distinguished disease patients from the controls, detected enhanced basal TCR signaling in the autoimmune patients, and identified a potential signaling network signature that may be indicative of disease. Thus, generation of PiSCES biosignatures represents an approach that can provide information about the activity of protein signaling networks in samples including low-abundance primary cells from clinical biopsies.

  11. Quantitative resilience analysis through control design.

    Energy Technology Data Exchange (ETDEWEB)

    Sunderland, Daniel; Vugrin, Eric D.; Camphouse, Russell Chris (Sandia National Laboratories, Carlsbad, NM)

    2009-09-01

    Critical infrastructure resilience has become a national priority for the U. S. Department of Homeland Security. System resilience has been studied for several decades in many different disciplines, but no standards or unifying methods exist for critical infrastructure resilience analysis. Few quantitative resilience methods exist, and those existing approaches tend to be rather simplistic and, hence, not capable of sufficiently assessing all aspects of critical infrastructure resilience. This report documents the results of a late-start Laboratory Directed Research and Development (LDRD) project that investigated the development of quantitative resilience through application of control design methods. Specifically, we conducted a survey of infrastructure models to assess what types of control design might be applicable for critical infrastructure resilience assessment. As a result of this survey, we developed a decision process that directs the resilience analyst to the control method that is most likely applicable to the system under consideration. Furthermore, we developed optimal control strategies for two sets of representative infrastructure systems to demonstrate how control methods could be used to assess the resilience of the systems to catastrophic disruptions. We present recommendations for future work to continue the development of quantitative resilience analysis methods.

  12. Development of a novel multiplex type-specific quantitative real-time PCR for detection and differentiation of infections with human papillomavirus types HPV2, HPV27, and HPV57.

    Science.gov (United States)

    Hošnjak, Lea; Fujs Komloš, Kristina; Kocjan, Boštjan J; Seme, Katja; Poljak, Mario

    2016-12-01

    The present study describes the development and evaluation of the first multiplex type-specific quantitative real-time PCR (RT-PCR), enabling simple, rapid, sensitive, and specific concurrent detection and differentiation of human papillomavirus (HPV) types HPV2, 27, and 57 in a single PCR reaction. The HPV2/27/57 multiplex RT-PCR with a dynamic range of seven orders of magnitude (discriminating 10 to 108 viral genome equivalents/reaction) has an analytical sensitivity of at least 10 viral copies of each targeted HPV type/reaction, and no cross-reactivities were observed among the included targets. All three primer/probe combinations were efficient in amplifying 500 copies of targeted DNA in a background of 108, 107, 500, 100, and 10 copies of non-targeted viral DNA/reaction, and the performance of the HPV2/27/57 multiplex RT-PCR was additionally not affected by the presence of background human genomic DNA. When testing DNA isolates obtained from fresh-frozen tissue specimens of various children's warts, the results of the HPV2/27/57 multiplex RT-PCR were completely in line with the results of the conventional Low-risk Alpha-PV PCR. The newly developed HPV2/27/57 multiplex RT-PCR is an appropriate test for use in routine clinical laboratory settings and for studies focusing on the molecular epidemiology, pathogenesis, and natural history of HPV2/27/57-related lesions.

  13. Quantitative multiplex assay for simultaneous detection and identification of Indiana and New Jersey serotypes of vesicular stomatitis virus

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Uttenthal, Åse; Fernandez, Jovita;

    2005-01-01

    In order to establish a rapid and reliable system for the detection of vesicular stomatitis virus (VSV), we developed a quantitative reverse transcription-PCR assay for the detection, quantification, and differentiation of the major serotypes, VSV Indiana and VSV New Jersey, using a closed...

  14. Fourier optics analysis of phase-mask-based path-length-multiplexed optical coherence tomography.

    Science.gov (United States)

    Yin, Biwei; Dwelle, Jordan; Wang, Bingqing; Wang, Tianyi; Feldman, Marc D; Rylander, Henry G; Milner, Thomas E

    2015-11-01

    Optical coherence tomography (OCT) is an imaging technique that constructs a depth-resolved image by measuring the optical path-length difference between broadband light backscattered from a sample and a reference surface. For many OCT sample arm optical configurations, sample illumination and backscattered light detection share a common path. When a phase mask is placed in the sample path, features in the detected signal are observed, which suggests that an analysis of a generic common path OCT imaging system is warranted. In this study, we present a Fourier optics analysis using a Fresnel diffraction approximation of an OCT system with a path-length-multiplexing element (PME) inserted in the sample arm optics. The analysis may be generalized for most phase-mask-based OCT systems. A radial-angle-diverse PME is analyzed in detail, and the point spread function, coherent transfer function, sensitivity of backscattering angular diversity detection, and signal formation in terms of sample spatial frequency are simulated and discussed. The analysis reveals important imaging features and application limitations of OCT imaging systems with a phase mask in the sample path optics.

  15. A one-step real-time multiplex PCR for screening Y-chromosomal microdeletions without downstream amplicon size analysis.

    Directory of Open Access Journals (Sweden)

    Viviana Kozina

    Full Text Available BACKGROUND: Y-chromosomal microdeletions (YCMD are one of the major genetic causes for non-obstructive azoospermia. Genetic testing for YCMD by multiplex polymerase chain reaction (PCR is an established method for quick and robust screening of deletions in the AZF regions of the Y-chromosome. Multiplex PCRs have the advantage of including a control gene in every reaction and significantly reducing the number of reactions needed to screen the relevant genomic markers. PRINCIPAL FINDINGS: The widely established "EAA/EMQN best practice guidelines for molecular diagnosis of Y-chromosomal microdeletions (2004" were used as a basis for designing a real-time multiplex PCR system, in which the YCMD can simply be identified by their melting points. For this reason, some AZF primers were substituted by primers for regions in their genomic proximity, and the ZFX/ZFY control primer was exchanged by the AMELX/AMELY control primer. Furthermore, we substituted the classical SybrGreen I dye by the novel and high-performing DNA-binding dye EvaGreen™ and put substantial effort in titrating the primer combinations in respect to optimal melting peak separation and peak size. SIGNIFICANCE: With these changes, we were able to develop a platform-independent and robust real-time based multiplex PCR, which makes the need for amplicon identification by electrophoretic sizing expendable. By using an open-source system for real-time PCR analysis, we further demonstrate the applicability of automated melting point and YCMD detection.

  16. Multiplexed labeling of viable cells for high-throughput analysis of glycine receptor function using flow cytometry.

    Science.gov (United States)

    Gilbert, Daniel F; Wilson, John C; Nink, Virginia; Lynch, Joseph W; Osborne, Geoffrey W

    2009-05-01

    Flow cytometry is an important drug discovery tool because it permits high-content multiparameter analysis of individual cells. A new method dramatically enhanced screening throughput by multiplexing many discrete fixed cell populations; however, this method is not suited to assays requiring functional cellular responses. HEK293 cells were transfected with unique mutant glycine receptors. Mutant receptor expression was confirmed by coexpression of yellow fluorescent protein (YFP). Commercially available cell-permeant dyes were used to label each glycine receptor expressing mutant with a unique optical code. All encoded cell lines were combined in a single tube and analyzed on a flow cytometer simultaneously before and after the addition of glycine receptor agonist. We decoded multiplexed cells that expressed functionally distinct glycine receptor chloride channels and analyzed responses to glycine in terms of chloride-sensitive YFP expression. Here, data provided by flow cytometry can be used to discriminate between functional and nonfunctional mutations in the glycine receptor, a process accelerated by the use of multiplexing. Further, this data correlates to data generated using a microscopy-based technique. The present study demonstrates multiplexed labeling of live cells, to enable cell populations to be subject to further cell culture and experimentation, and compares the results with those obtained using live cell microscopy. (c) 2009 International Society for Advancement of Cytometry.

  17. Inspection, visualisation and analysis of quantitative proteomics data

    OpenAIRE

    Gatto, Laurent

    2016-01-01

    Material Quantitative Proteomics and Data Analysis Course. 4 - 5 April 2016, Queen Hotel, Chester, UK Table D - Inspection, visualisation and analysis of quantitative proteomics data, Laurent Gatto (University of Cambridge)

  18. A microfluidic cigarette smoke collecting platform for simultaneous sample extraction and multiplex analysis.

    Science.gov (United States)

    Hu, Shan-Wen; Xu, Bi-Yi; Qiao, Shu; Zhao, Ge; Xu, Jing-Juan; Chen, Hong-Yuan; Xie, Fu-Wei

    2016-04-01

    In this work, we report a novel microfluidic gas collecting platform aiming at simultaneous sample extraction and multiplex mass spectrometry (MS) analysis. An alveolar-mimicking elastic polydimethylsiloxane (PDMS) structures was designed to move dynamically driven by external pressure. The movement was well tuned both by its amplitude and rhythm following the natural process of human respiration. By integrating the alveolar units into arrays and assembling them to gas channels, a cyclic contraction/expansion system for gas inhale and exhale was successfully constructed. Upon equipping this system with a droplet array on the alveolar array surface, we were able to get information of inhaled smoke in a new strategy. Here, with cigarette smoke as an example, analysis of accumulation for target molecules during passive smoking is taken. Relationships between the breathing times, distances away from smokers and inhaled content of nicotine are clarified. Further, by applying different types of extraction solvent droplets on different locations of the droplet array, simultaneous extraction of nicotine, formaldehyde and caproic acid in sidestream smoke (SS) are realized. Since the extract droplets are spatially separated, they can be directly analyzed by MS which is fast and can rid us of all complex sample separation and purification steps. Combining all these merits, this small, cheap and portable platform might find wide application in inhaled air pollutant analysis both in and outdoors. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. A quasi-quantitative dual multiplexed immunoblot method to simultaneously analyze ATM and H2AX Phosphorylation in human peripheral blood mononuclear cells.

    Science.gov (United States)

    Bakkenist, Christopher J; Czambel, R Kenneth; Hershberger, Pamela A; Tawbi, Hussein; Beumer, Jan H; Schmitz, John C

    2015-01-01

    Pharmacologic inhibition of DNA repair may increase the efficacy of many cytotoxic cancer agents. Inhibitors of DNA repair enzymes including APE1, ATM, ATR, DNA-PK and PARP have been developed and the PARP inhibitor olaparib is the first-in-class approved in Europe and the USA for the treatment of advanced BRCA-mutated ovarian cancer. Sensitive pharmacodynamic (PD) biomarkers are needed to further evaluate the efficacy of inhibitors of DNA repair enzymes in clinical trials. ATM is a protein kinase that mediates cell-cycle checkpoint activation and DNA double-strand break repair. ATM kinase activation at DNA double-strand breaks (DSBs) is associated with intermolecular autophosphorylation on serine-1981. Exquisite sensitivity and high stoichiometry as well as facile extraction suggest that ATM serine-1981 phosphorylation may be a highly dynamic PD biomarker for both ATM kinase inhibitors and radiation- and chemotherapy-induced DSBs. Here we report the pre-clinical analytical validation and fit-for-purpose biomarker method validation of a quasi-quantitative dual multiplexed immunoblot method to simultaneously analyze ATM and H2AX phosphorylation in human peripheral blood mononuclear cells (PBMCs). We explore the dynamics of these phosphorylations in PBMCs exposed to chemotherapeutic agents and DNA repair inhibitors in vitro, and show that ATM serine-1981 phosphorylation is increased in PBMCs in sarcoma patients treated with DNA damaging chemotherapy.

  20. Rapid semi-automated quantitative multiplex tandem PCR (MT-PCR assays for the differential diagnosis of influenza-like illness

    Directory of Open Access Journals (Sweden)

    Dwyer Dominic E

    2010-05-01

    Full Text Available Abstract Background Influenza A, including avian influenza, is a major public health threat in developed and developing countries. Rapid and accurate detection is a key component of strategies to contain spread of infection, and the efficient diagnosis of influenza-like-illness is essential to protect health infrastructure in the event of a major influenza outbreak. Methods We developed a multiplexed PCR (MT-PCR assay for the simultaneous diagnosis of respiratory viruses causing influenza-like illness, including the specific recognition of influenza A haemagglutinin subtypes H1, H3, and H5. We tested several hundred clinical specimens in two diagnostic reference laboratories and compared the results with standard techniques. Results The sensitivity and specificity of these assays was higher than individual assays based on direct antigen detection and standard PCR against a range of control templates and in several hundred clinical specimens. The MT-PCR assays provided differential diagnoses as well as potentially useful quantitation of virus in clinical samples. Conclusions MT-PCR is a potentially powerful tool for the differential diagnosis of influenza-like illness in the clinical diagnostic laboratory.

  1. Accuracy analysis for triangulation and tracking based on time-multiplexed structured light.

    Science.gov (United States)

    Wagner, Benjamin; Stüber, Patrick; Wissel, Tobias; Bruder, Ralf; Schweikard, Achim; Ernst, Floris

    2014-08-01

    The authors' research group is currently developing a new optical head tracking system for intracranial radiosurgery. This tracking system utilizes infrared laser light to measure features of the soft tissue on the patient's forehead. These features are intended to offer highly accurate registration with respect to the rigid skull structure by means of compensating for the soft tissue. In this context, the system also has to be able to quickly generate accurate reconstructions of the skin surface. For this purpose, the authors have developed a laser scanning device which uses time-multiplexed structured light to triangulate surface points. The accuracy of the authors' laser scanning device is analyzed and compared for different triangulation methods. These methods are given by the Linear-Eigen method and a nonlinear least squares method. Since Microsoft's Kinect camera represents an alternative for fast surface reconstruction, the authors' results are also compared to the triangulation accuracy of the Kinect device. Moreover, the authors' laser scanning device was used for tracking of a rigid object to determine how this process is influenced by the remaining triangulation errors. For this experiment, the scanning device was mounted to the end-effector of a robot to be able to calculate a ground truth for the tracking. The analysis of the triangulation accuracy of the authors' laser scanning device revealed a root mean square (RMS) error of 0.16 mm. In comparison, the analysis of the triangulation accuracy of the Kinect device revealed a RMS error of 0.89 mm. It turned out that the remaining triangulation errors only cause small inaccuracies for the tracking of a rigid object. Here, the tracking accuracy was given by a RMS translational error of 0.33 mm and a RMS rotational error of 0.12°. This paper shows that time-multiplexed structured light can be used to generate highly accurate reconstructions of surfaces. Furthermore, the reconstructed point sets can be

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

    Science.gov (United States)

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

    2009-08-31

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

  3. Quantitative analysis of spirality in elliptical galaxies

    CERN Document Server

    Dojcsak, Levente

    2013-01-01

    We use an automated galaxy morphology analysis method to quantitatively measure the spirality of galaxies classified manually as elliptical. The data set used for the analysis consists of 60,518 galaxy images with redshift obtained by the Sloan Digital Sky Survey (SDSS) and classified manually by Galaxy Zoo, as well as the RC3 and NA10 catalogues. We measure the spirality of the galaxies by using the Ganalyzer method, which transforms the galaxy image to its radial intensity plot to detect galaxy spirality that is in many cases difficult to notice by manual observation of the raw galaxy image. Experimental results using manually classified elliptical and S0 galaxies with redshift <0.3 suggest that galaxies classified manually as elliptical and S0 exhibit a nonzero signal for the spirality. These results suggest that the human eye observing the raw galaxy image might not always be the most effective way of detecting spirality and curves in the arms of galaxies.

  4. Quantitative laryngeal electromyography: turns and amplitude analysis.

    Science.gov (United States)

    Statham, Melissa McCarty; Rosen, Clark A; Nandedkar, Sanjeev D; Munin, Michael C

    2010-10-01

    Laryngeal electromyography (LEMG) is primarily a qualitative examination, with no standardized approach to interpretation. The objectives of our study were to establish quantitative norms for motor unit recruitment in controls and to compare with interference pattern analysis in patients with unilateral vocal fold paralysis (VFP). Retrospective case-control study We performed LEMG of the thyroarytenoid-lateral cricoarytenoid muscle complex (TA-LCA) in 21 controls and 16 patients with unilateral VFP. Our standardized protocol used a concentric needle electrode with subjects performing variable force TA-LCA contraction. To quantify the interference pattern density, we measured turns and mean amplitude per turn for ≥10 epochs (each 500 milliseconds). Logarithmic regression analysis between amplitude and turns was used to calculate slope and intercept. Standard deviation was calculated to further define the confidence interval, enabling generation of a linear-scale graphical "cloud" of activity containing ≥90% of data points for controls and patients. Median age of controls and patients was similar (50.7 vs. 48.5 years). In controls, TA-LCA amplitude with variable contraction ranged from 145-1112 μV, and regression analysis comparing mean amplitude per turn to root-mean-square amplitude demonstrated high correlation (R = 0.82). In controls performing variable contraction, median turns per second was significantly higher compared to patients (450 vs. 290, P = .002). We first present interference pattern analysis in the TA-LCA in healthy adults and patients with unilateral VFP. Our findings indicate that motor unit recruitment can be quantitatively measured within the TA-LCA. Additionally, patients with unilateral VFP had significantly reduced turns when compared with controls.

  5. Multiplex quantitative PCR for detection of lower respiratory tract infection and meningitis caused by Streptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis

    Directory of Open Access Journals (Sweden)

    Welinder-Olsson Christina

    2010-12-01

    Full Text Available Abstract Background Streptococcus pneumoniae and Haemophilus influenzae cause pneumonia and as Neisseria meningitidis they are important agents of meningitis. Although several PCR methods have been described for these bacteria the specificity is an underestimated problem. Here we present a quantitative multiplex real-time PCR (qmPCR for detection of S. pneumoniae (9802 gene fragment, H. influenzae (omp P6 gene and N. meningitidis (ctrA gene. The method was evaluated on bronchoalveolar lavage (BAL samples from 156 adults with lower respiratory tract infection (LRTI and 31 controls, and on 87 cerebrospinal fluid (CSF samples from meningitis patients. Results The analytical sensitivity was not affected by using a combined mixture of reagents and a combined DNA standard (S. pneumoniae/H. influenzae/N. meningitidis in single tubes. By blood- and BAL-culture and S. pneumoniae urinary antigen test, S. pneumoniae and H. influenzae were aetiological agents in 21 and 31 of the LTRI patients, respectively. These pathogens were identified by qmPCR in 52 and 72 of the cases, respectively, yielding sensitivities and specificities of 95% and 75% for S. pneumoniae, and 90% and 65% for H. influenzae, respectively. When using a cut-off of 105 genome copies/mL for clinical positivity the sensitivities and specificities were 90% and 80% for S. pneumoniae, and 81% and 85% for H. influenzae, respectively. Of 44 culture negative but qmPCR positive for H. influenzae, 41 were confirmed by fucK PCR as H. influenzae. Of the 103 patients who had taken antibiotics prior to sampling, S. pneumoniae and H. influenzae were identified by culture in 6% and 20% of the cases, respectively, and by the qmPCR in 36% and 53% of the cases, respectively. In 87 CSF samples S. pneumoniae and N. meningitidis were identified by culture and/or 16 S rRNA in 14 and 10 samples and by qmPCR in 14 and 10 samples, respectively, giving a sensitivity of 100% and a specificity of 100% for both

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

    Energy Technology Data Exchange (ETDEWEB)

    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. [Stanford Univ., CA (United States)] [and others

    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.

  7. Rapid microfluidic analysis of a Y-STR multiplex for screening of forensic samples.

    Science.gov (United States)

    Gibson-Daw, Georgiana; Albani, Patricia; Gassmann, Marcus; McCord, Bruce

    2017-02-01

    In this paper, we demonstrate a rapid analysis procedure for use with a small set of rapidly mutating Y chromosomal short tandem repeat (Y-STR) loci that combines both rapid polymerase chain reaction (PCR) and microfluidic separation elements. The procedure involves a high-speed polymerase and a rapid cycling protocol to permit PCR amplification in 16 min. The resultant amplified sample is next analysed using a short 1.8-cm microfluidic electrophoresis system that permits a four-locus Y-STR genotype to be produced in 80 s. The entire procedure takes less than 25 min from sample collection to result. This paper describes the rapid amplification protocol as well as studies of the reproducibility and sensitivity of the procedure and its optimisation. The amplification process utilises a small high-speed thermocycler, microfluidic device and compact laptop, making it portable and potentially useful for rapid, inexpensive on-site genotyping. The four loci used for the multiplex were selected due to their rapid mutation rates and should proved useful in preliminary screening of samples and suspects. Overall, this technique provides a method for rapid sample screening of suspect and crime scene samples in forensic casework. Graphical abstract ᅟ.

  8. Multiplexed transcriptome analysis to detect ALK, ROS1 and RET rearrangements in lung cancer

    Science.gov (United States)

    Rogers, Toni-Maree; Arnau, Gisela Mir; Ryland, Georgina L.; Huang, Stephen; Lira, Maruja E.; Emmanuel, Yvette; Perez, Omar D.; Irwin, Darryl; Fellowes, Andrew P.; Wong, Stephen Q.; Fox, Stephen B.

    2017-01-01

    ALK, ROS1 and RET gene fusions are important predictive biomarkers for tyrosine kinase inhibitors in lung cancer. Currently, the gold standard method for gene fusion detection is Fluorescence In Situ Hybridization (FISH) and while highly sensitive and specific, it is also labour intensive, subjective in analysis, and unable to screen a large numbers of gene fusions. Recent developments in high-throughput transcriptome-based methods may provide a suitable alternative to FISH as they are compatible with multiplexing and diagnostic workflows. However, the concordance between these different methods compared with FISH has not been evaluated. In this study we compared the results from three transcriptome-based platforms (Nanostring Elements, Agena LungFusion panel and ThermoFisher NGS fusion panel) to those obtained from ALK, ROS1 and RET FISH on 51 clinical specimens. Overall agreement of results ranged from 86–96% depending on the platform used. While all platforms were highly sensitive, both the Agena panel and Thermo Fisher NGS fusion panel reported minor fusions that were not detectable by FISH. Our proof–of–principle study illustrates that transcriptome-based analyses are sensitive and robust methods for detecting actionable gene fusions in lung cancer and could provide a robust alternative to FISH testing in the diagnostic setting. PMID:28181564

  9. Quantitative Analysis in Nuclear Medicine Imaging

    CERN Document Server

    2006-01-01

    This book provides a review of image analysis techniques as they are applied in the field of diagnostic and therapeutic nuclear medicine. Driven in part by the remarkable increase in computing power and its ready and inexpensive availability, this is a relatively new yet rapidly expanding field. Likewise, although the use of radionuclides for diagnosis and therapy has origins dating back almost to the discovery of natural radioactivity itself, radionuclide therapy and, in particular, targeted radionuclide therapy has only recently emerged as a promising approach for therapy of cancer and, to a lesser extent, other diseases. As effort has, therefore, been made to place the reviews provided in this book in a broader context. The effort to do this is reflected by the inclusion of introductory chapters that address basic principles of nuclear medicine imaging, followed by overview of issues that are closely related to quantitative nuclear imaging and its potential role in diagnostic and therapeutic applications. ...

  10. Automatic quantitative morphological analysis of interacting galaxies

    CERN Document Server

    Shamir, Lior; Wallin, John

    2013-01-01

    The large number of galaxies imaged by digital sky surveys reinforces the need for computational methods for analyzing galaxy morphology. While the morphology of most galaxies can be associated with a stage on the Hubble sequence, morphology of galaxy mergers is far more complex due to the combination of two or more galaxies with different morphologies and the interaction between them. Here we propose a computational method based on unsupervised machine learning that can quantitatively analyze morphologies of galaxy mergers and associate galaxies by their morphology. The method works by first generating multiple synthetic galaxy models for each galaxy merger, and then extracting a large set of numerical image content descriptors for each galaxy model. These numbers are weighted using Fisher discriminant scores, and then the similarities between the galaxy mergers are deduced using a variation of Weighted Nearest Neighbor analysis such that the Fisher scores are used as weights. The similarities between the ga...

  11. Nonlinear dynamics and quantitative EEG analysis.

    Science.gov (United States)

    Jansen, B H

    1996-01-01

    Quantitative, computerized electroencephalogram (EEG) analysis appears to be based on a phenomenological approach to EEG interpretation, and is primarily rooted in linear systems theory. A fundamentally different approach to computerized EEG analysis, however, is making its way into the laboratories. The basic idea, inspired by recent advances in the area of nonlinear dynamics and chaos theory, is to view an EEG as the output of a deterministic system of relatively simple complexity, but containing nonlinearities. This suggests that studying the geometrical dynamics of EEGs, and the development of neurophysiologically realistic models of EEG generation may produce more successful automated EEG analysis techniques than the classical, stochastic methods. A review of the fundamentals of chaos theory is provided. Evidence supporting the nonlinear dynamics paradigm to EEG interpretation is presented, and the kind of new information that can be extracted from the EEG is discussed. A case is made that a nonlinear dynamic systems viewpoint to EEG generation will profoundly affect the way EEG interpretation is currently done.

  12. Functional Multiplex PageRank

    Science.gov (United States)

    Iacovacci, Jacopo; Rahmede, Christoph; Arenas, Alex; Bianconi, Ginestra

    2016-10-01

    Recently it has been recognized that many complex social, technological and biological networks have a multilayer nature and can be described by multiplex networks. Multiplex networks are formed by a set of nodes connected by links having different connotations forming the different layers of the multiplex. Characterizing the centrality of the nodes in a multiplex network is a challenging task since the centrality of the node naturally depends on the importance associated to links of a certain type. Here we propose to assign to each node of a multiplex network a centrality called Functional Multiplex PageRank that is a function of the weights given to every different pattern of connections (multilinks) existent in the multiplex network between any two nodes. Since multilinks distinguish all the possible ways in which the links in different layers can overlap, the Functional Multiplex PageRank can describe important non-linear effects when large relevance or small relevance is assigned to multilinks with overlap. Here we apply the Functional Page Rank to the multiplex airport networks, to the neuronal network of the nematode C. elegans, and to social collaboration and citation networks between scientists. This analysis reveals important differences existing between the most central nodes of these networks, and the correlations between their so-called pattern to success.

  13. Analysis of Fixed Outage Transmission Schemes: A Finer Look at the Full Multiplexing Point

    CERN Document Server

    Wu, Peng

    2007-01-01

    This paper studies the performance of transmission schemes that have rate that increases with average SNR while maintaining a fixed outage probability. This is in contrast to the classical Zheng-Tse diversity-multiplexing tradeoff (DMT) that focuses on increasing rate and decreasing outage probability. Three different systems are explored: antenna diversity systems, time/frequency diversity systems, and automatic repeat request (ARQ) systems. In order to accurately study performance in the fixed outage setting, it is necesary to go beyond the coarse, asymptotic multiplexing gain metric. In the case of antenna diversity and time/frequency diversity, an affine approximation to high SNR outage capacity (i.e., multiplexing gain plus a power/rate offset) accurately describes performance and shows the very significant benefits of diversity. ARQ is also seen to provide a significant performance advantage, but even an affine approximation to outage capacity is unable to capture this advantage and outage capacity must...

  14. Detection of somatic quantitative genetic alterations by multiplex polymerase chain reaction for the prediction of outcome in diffuse large B-cell lymphomas.

    Science.gov (United States)

    Jardin, Fabrice; Ruminy, Philippe; Kerckaert, Jean-Pierre; Parmentier, Françoise; Picquenot, Jean-Michel; Quief, Sabine; Villenet, Céline; Buchonnet, Gérard; Tosi, Mario; Frebourg, Thierry; Bastard, Christian; Tilly, Hervé

    2008-04-01

    Genomic gains and losses play a crucial role in the development of diffuse large B-cell lymphomas. High resolution array comparative genomic hybridization provides a comprehensive view of these genomic imbalances but is not routinely applicable. We developed a polymerase chain reaction assay to provide information regarding gains or losses of relevant genes and prognosis in diffuse large B-cell lymphomas. Two polymerase chain reaction assays (multiplex polymerase chain reaction of short fluorescent fragments, QMPSF) were designed to detect gains or losses of c-REL, BCL6, SIM1, PTPRK, MYC, CDKN2A, MDM2, CDKN1B, TP53 and BCL2. Array comparative genomic hybridization was simultaneously performed to evaluate the sensitivity and predictive value of the QMPSF assay. The biological and clinical relevance of this assay were assessed. The predictive value of the QMPSF assay for detecting abnormal DNA copy numbers ranged between 88-97%, giving an overall concordance rate of 92% with comparative genomic hybridization results. In 77 cases of diffuse large B-cell lymphomas, gains of MYC, CDKN1B, c-REL and BCL2 were detected in 12%, 40%, 27% and 29%, respectively. TP53 and CDKN2A deletions were observed in 22% and 36% respectively. BCL2 and CDKN2A allelic status correlated with protein expression. TP53 mutations were associated with allelic deletions in 45% of cases. The prognostic value of a single QMPSF assay including TP53, MYC, CDKN2A, SIM1 and CDKN1B was predictive of the outcome independently of the germinal center B-cell like/non-germinal center B-cell like subtype or the International Prognostic Index. QMPSF is a reliable and flexible method for detecting somatic quantitative genetic alterations in diffuse large B-cell lymphomas and could be integrated in future prognostic predictive models.

  15. Comparison of a Multiplex Flow Cytometric Assay with Enzyme-Linked Immunosorbent Assay for Quantitation of Antibodies to Tetanus, Diphtheria, and Haemophilus influenzae Type b

    OpenAIRE

    Pickering, Jerry W.; Martins, Thomas B.; Schroder, M. Carl; Hill, Harry R.

    2002-01-01

    We developed a multiplexed indirect immunofluorescence assay for antibodies to Haemophilus influenza type b (Hib) polysaccharide and the toxoids of Clostridium tetani (Tet) and Corynebacterium diphtheriae (Dip) based on the Luminex multiple-analyte profiling system. A pooled serum standard was calibrated against World Health Organization standards for Dip and Tet and an international standard for Hib. The multiplexed Luminex assay was compared to individual enzyme-linked immunosorbent assays ...

  16. Quantitative risk analysis preoperational of gas pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Manfredi, Carlos; Bispo, Gustavo G.; Esteves, Alvaro [Gie S.A., Buenos Aires (Argentina)

    2009-07-01

    The purpose of this analysis is to predict how it can be affected the individual risk and the public's general security due to the operation of a gas pipeline. In case that the single or social risks are considered intolerable, compared with the international standards, to be recommended measures of mitigation of the risk associated to the operation until levels that can be considered compatible with the best practices in the industry. The quantitative risk analysis calculates the probability of occurrence of an event based on the frequency of occurrence of the same one and it requires a complex mathematical treatment. The present work has as objective to develop a calculation methodology based on the previously mentioned publication. This calculation methodology is centered in defining the frequencies of occurrence of events, according to representative database of each case in study. Besides, it settles down the consequences particularly according to the considerations of each area and the different possibilities of interferences with the gas pipeline in study. For each one of the interferences a typical curve of ignition probabilities is developed in function from the distance to the pipe. (author)

  17. Quantitative analysis of protein turnover in plants.

    Science.gov (United States)

    Nelson, Clark J; Li, Lei; Millar, A Harvey

    2014-03-01

    Proteins are constantly being synthesised and degraded as plant cells age and as plants grow, develop and adapt the proteome. Given that plants develop through a series of events from germination to fruiting and even undertake whole organ senescence, an understanding of protein turnover as a fundamental part of this process in plants is essential. Both synthesis and degradation processes are spatially separated in a cell across its compartmented structure. The majority of protein synthesis occurs in the cytosol, while synthesis of specific components occurs inside plastids and mitochondria. Degradation of proteins occurs in both the cytosol, through the action of the plant proteasome, and in organelles and lytic structures through different protease classes. Tracking the specific synthesis and degradation rate of individual proteins can be undertaken using stable isotope feeding and the ability of peptide MS to track labelled peptide fractions over time. Mathematical modelling can be used to follow the isotope signature of newly synthesised protein as it accumulates and natural abundance proteins as they are lost through degradation. Different technical and biological constraints govern the potential for the use of (13)C, (15)N, (2)H and (18)O for these experiments in complete labelling and partial labelling strategies. Future development of quantitative protein turnover analysis will involve analysis of protein populations in complexes and subcellular compartments, assessing the effect of PTMs and integrating turnover studies into wider system biology study of plants.

  18. Multiplexity and multireciprocity in directed multiplexes

    Science.gov (United States)

    Gemmetto, Valerio; Squartini, Tiziano; Picciolo, Francesco; Ruzzenenti, Franco; Garlaschelli, Diego

    2016-10-01

    Real-world multilayer networks feature nontrivial dependencies among links of different layers. Here we argue that if links are directed, then dependencies are twofold. Besides the ordinary tendency of links of different layers to align as the result of "multiplexity," there is also a tendency to antialign as a result of what we call "multireciprocity," i.e., the fact that links in one layer can be reciprocated by opposite links in a different layer. Multireciprocity generalizes the scalar definition of single-layer reciprocity to that of a square matrix involving all pairs of layers. We introduce multiplexity and multireciprocity matrices for both binary and weighted multiplexes and validate their statistical significance against maximum-entropy null models that filter out the effects of node heterogeneity. We then perform a detailed empirical analysis of the world trade multiplex (WTM), representing the import-export relationships between world countries in different commodities. We show that the WTM exhibits strong multiplexity and multireciprocity, an effect which is, however, largely encoded into the degree or strength sequences of individual layers. The residual effects are still significant and allow us to classify pairs of commodities according to their tendency to be traded together in the same direction and/or in opposite ones. We also find that the multireciprocity of the WTM is significantly lower than the usual reciprocity measured on the aggregate network. Moreover, layers with low (high) internal reciprocity are embedded within sets of layers with comparably low (high) mutual multireciprocity. This suggests that, in the WTM, reciprocity is inherent to groups of related commodities rather than to individual commodities. We discuss the implications for international trade research focusing on product taxonomies, the product space, and fitness and complexity metrics.

  19. An integrated system of ABO typing and multiplex STR testing for forensic DNA analysis.

    Science.gov (United States)

    Jiang, Xianhua; He, Juan; Jia, Fei; Shen, Hongying; Zhao, Jinling; Chen, Chuguang; Bai, Liping; Liu, Feng; Hou, Guangwei; Guo, Faye

    2012-12-01

    A new amplification system for ABO and STR genotyping in a single reaction has been successfully developed. Two types of information can be obtained from a biological sample at one time. One is the classical information of ABO blood group typing for screening suspects and the other is STR information for individual identification. The system allows for the simultaneous detection of 15 autosomal STR loci (containing all CODIS STR loci as well as Penta D and Penta E), six ABO genotypes (O/O, B/B, A/A, A/O, A/B, and B/O) and the gender-determining locus Amelogenin. Primers are designed so that the amplicons are distributed ranging from 75bp to 500bp within a four-dye fluorescent design, leaving a fourth dye for the internal size standard. With 30 cycles, the results showed that the optimal amount of DNA template for this multiplex ranges from 250pg to 2ng and the lowest detection threshold is 125pg (as low as 63pg for ABO loci). For the DNA template outside the optimal detection range, we could adjust the number of cycles to obtain the robust profiles. Mixture studies showed that over 83% of minor alleles were detected at 1:9 ratios. The full profiles were still observed when 4ng of degraded DNA was digested by DNase I and 1ng undegraded DNA was added to 40μM haematin. Polymerase chain reaction (PCR)-based conditions including the concentrations of primers, magnesium and the Taq polymerase as well as volume, cycle numbers and annealing temperature were examined and optimised. In addition, the system was validated by 364 bloodstain samples and 32 common casework samples. According to the Chinese National Standards and Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, our system demonstrates good detection performance and is an ideal tool for forensic DNA typing with potential application.

  20. Demand and Congestion in Multiplex Transportation Networks

    Science.gov (United States)

    al-Awwad, Zeyad; Jiang, Shan; González, Marta C.

    2016-01-01

    Urban transportation systems are multimodal, sociotechnical systems; however, while their multimodal aspect has received extensive attention in recent literature on multiplex networks, their sociotechnical aspect has been largely neglected. We present the first study of an urban transportation system using multiplex network analysis and validated Origin-Destination travel demand, with Riyadh’s planned metro as a case study. We develop methods for analyzing the impact of additional transportation layers on existing dynamics, and show that demand structure plays key quantitative and qualitative roles. There exist fundamental geometrical limits to the metro’s impact on traffic dynamics, and the bulk of environmental accrue at metro speeds only slightly faster than those planned. We develop a simple model for informing the use of additional, “feeder” layers to maximize reductions in global congestion. Our techniques are computationally practical, easily extensible to arbitrary transportation layers with complex transfer logic, and implementable in open-source software. PMID:27657738

  1. Applying Knowledge of Quantitative Design and Analysis

    Science.gov (United States)

    Baskas, Richard S.

    2011-01-01

    This study compared and contrasted two quantitative scholarly articles in relation to their research designs. Their designs were analyzed by the comparison of research references and research specific vocabulary to describe how various research methods were used. When researching and analyzing quantitative scholarly articles, it is imperative to…

  2. Quantitative color analysis for capillaroscopy image segmentation.

    Science.gov (United States)

    Goffredo, Michela; Schmid, Maurizio; Conforto, Silvia; Amorosi, Beatrice; D'Alessio, Tommaso; Palma, Claudio

    2012-06-01

    This communication introduces a novel approach for quantitatively evaluating the role of color space decomposition in digital nailfold capillaroscopy analysis. It is clinically recognized that any alterations of the capillary pattern, at the periungual skin region, are directly related to dermatologic and rheumatic diseases. The proposed algorithm for the segmentation of digital capillaroscopy images is optimized with respect to the choice of the color space and the contrast variation. Since the color space is a critical factor for segmenting low-contrast images, an exhaustive comparison between different color channels is conducted and a novel color channel combination is presented. Results from images of 15 healthy subjects are compared with annotated data, i.e. selected images approved by clinicians. By comparison, a set of figures of merit, which highlights the algorithm capability to correctly segment capillaries, their shape and their number, is extracted. Experimental tests depict that the optimized procedure for capillaries segmentation, based on a novel color channel combination, presents values of average accuracy higher than 0.8, and extracts capillaries whose shape and granularity are acceptable. The obtained results are particularly encouraging for future developments on the classification of capillary patterns with respect to dermatologic and rheumatic diseases.

  3. Quantitative gold nanoparticle analysis methods: A review.

    Science.gov (United States)

    Yu, Lei; Andriola, Angelo

    2010-08-15

    Research and development in the area of gold nanoparticles' (AuNPs) preparation, characterization, and applications are burgeoning in recent years. Many of the techniques and protocols are very mature, but two major concerns are with the mass domestic production and the consumption of AuNP based products. First, how many AuNPs exist in a dispersion? Second, where are the AuNPs after digestion by the environment and how many are there? To answer these two questions, reliable and reproducible methods are needed to analyze the existence and the population of AuNP in samples. This review summarized the most recent chemical and particle quantitative analysis methods that have been used to characterize the concentration (in number of moles of gold per liter) or population (in number of particles per mL) of AuNPs. The methods summarized in this review include, mass spectroscopy, electroanalytical methods, spectroscopic methods, and particle counting methods. These methods may count the number of AuNP directly or analyze the total concentration of element gold in an AuNP dispersion.

  4. Quantitative Risk Analysis: Method And Process

    Directory of Open Access Journals (Sweden)

    Anass BAYAGA

    2010-03-01

    Full Text Available Recent and past studies (King III report, 2009: 73-75; Stoney 2007;Committee of Sponsoring Organisation-COSO, 2004, Bartell, 2003; Liebenberg and Hoyt, 2003; Reason, 2000; Markowitz 1957 lament that although, the introduction of quantifying risk to enhance degree of objectivity in finance for instance was quite parallel to its development in the manufacturing industry, it is not the same in Higher Education Institution (HEI. In this regard, the objective of the paper was to demonstrate the methods and process of Quantitative Risk Analysis (QRA through likelihood of occurrence of risk (phase I. This paper serves as first of a two-phased study, which sampled hundred (100 risk analysts in a University in the greater Eastern Cape Province of South Africa.The analysis of likelihood of occurrence of risk by logistic regression and percentages were conducted to investigate whether there were a significant difference or not between groups (analyst in respect of QRA.The Hosmer and Lemeshow test was non-significant with a chi-square(X2 =8.181; p = 0.300, which indicated that there was a good model fit, since the data did not significantly deviate from the model. The study concluded that to derive an overall likelihood rating that indicated the probability that a potential risk may be exercised within the construct of an associated threat environment, the following governing factors must be considered: (1 threat source motivation and capability (2 nature of the vulnerability (3 existence and effectiveness of current controls (methods and process.

  5. Quantitative risks analysis of maritime terminal petrochemical

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Leandro Silveira; Leal, Cesar A. [Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil). Programa de Pos-Graduacao em Engenharia Mecanica (PROMEC)]. E-mail: leandro19889900@yahoo.com.br

    2008-07-01

    This work consists of the application of a computer program (RISKAN) developed for studies of quantification of industrial risks and also a revision of the models used in the program. As part the evaluation made, a test was performed with the application of the computer program to estimate the risks for a marine terminal for storage of petrochemical products, in the city of Rio Grande, Brazil. Thus, as part of the work, it was performed a Quantitative Risk Analysis associated to the terminal, both for the workers and for the population nearby, with a verification of acceptability using the tolerability limits established by the State Licensing Agency (FEPAM-RS). In the risk analysis methodology used internationally, the most used way of presenting results of social risks is in the graphical form with the use of the FN curves and for the individual risk it is common the use of the iso-risk curves traced on the map of the area where is the plant. In the beginning of the study, both a historical analysis of accidents and use of the technique of Preliminary Analysis of Risks were made in order to aid in the process of identification of the possible scenarios of accidents related to the activities in the terminal. After identifying the initiating events, their frequencies or probabilities of occurrence were estimated and followed by the calculations of the physical effects and deaths, with the use, inside the computer program, of published models of Prins Mauritz Laboratory and of American Institute of Chemical Engineers. The average social risk obtained for the external populations was of 8.7x10{sup -7} fatality.year{sup -1} and for the internal population (people working inside the terminal), 3.2x10{sup -4} fatality.year-1. The accident scenario that most contributed to the social risk was death due to exposure to the thermal radiation caused by pool fire, with 84.3% of the total estimated for external populations and 82.9% for the people inside the terminal. The

  6. The use of different multiplex PCRs for twin zygosity determination and its application in forensic trace analysis.

    Science.gov (United States)

    von Wurmb-Schwark, Nicole; Schwark, Thorsten; Christiansen, Lene; Lorenz, Delia; Oehmichen, Manfred

    2004-04-01

    STR typing becomes more and more valuable for different approaches of science. It revolutionized determining of zygosity in twin research and it is very often the only possibility for discrimination in forensic trace analysis. In this study 55 twin pairs from Denmark were genetically investigated to determine their zygosity. For analysis two multiplex PCR kits, the AmpFlSTR Identifiler kit, which comprises 15 loci plus the amelogenin gender determination and the Powerplex ES kit with eight different loci were employed. For a forensic approach every twin pair was regarded as being a forensic trace analysis, i.e. suspect or victim/biological trace and then we determined the security and precision with that a match of genetic patterns or an exclusion could be observed. Sixty percent of the twin pairs were di- and 40% monozygotic. There were no differences in zygosity determination between the two multiplex kits. The lowest number of exclusions by determining dizygosity was four loci for the Identifiler and three for Powerplex ES kit, the highest was 13 (Identifiler) and eight (Powerplex). It could be shown that the highly discriminative multiplex PCR kits gave matching probabilities of over 99.999999% (calculation based on data for unrelated individuals) even when only five or six STRs could be determined (assuming a trace analysis with some non-detectable STRs and therefore an incomplete genetic pattern). No questionable results regarding zygosity of the twin pairs were obtained even when only eight loci (using the Powerplex ES kit) were investigated. The simulated forensic results showed that matching probabilities should always be handled with care to not possibly come to wrong conclusions concerning the origin of the biological trace.

  7. Quantitative high-resolution melting analysis for detecting adulterations.

    Science.gov (United States)

    Mader, Eduard; Ruzicka, Joana; Schmiderer, Corinna; Novak, Johannes

    2011-02-01

    Admixtures of different plant species are a common problem in raw materials for medicinal use. Two exemplary assays were developed to admixtures in Helleborus niger with high-resolution melting analysis. HRM proved to be a very sensitive tool in detecting admixtures, able to detect a ratio of 1:1000 with unknown species, and of 1:200,000 with Veratrum nigrum. The example proves the ability of HRM for quantification in multiplex PCR. The method is not limited to detecting adulterations. It can also be used to quantify a specific target by integrating a second amplicon in the assay as internal standard. Copyright © 2010 Elsevier Inc. All rights reserved.

  8. Multiplex cytokine analysis of dermal interstitial blister fluid defines local disease mechanisms in systemic sclerosis.

    Science.gov (United States)

    Clark, Kristina En; Lopez, Henry; Abdi, Bahja Ahmed; Guerra, Sandra G; Shiwen, Xu; Khan, Korsa; Etomi, Oseme; Martin, George R; Abraham, David J; Denton, Christopher P; Stratton, Richard J

    2015-03-23

    Clinical diversity in systemic sclerosis (SSc) reflects multifaceted pathogenesis and the effect of key growth factors or cytokines operating within a disease-specific microenvironment. Dermal interstitial fluid sampling offers the potential to examine local mechanisms and identify proteins expressed within lesional tissue. We used multiplex cytokine analysis to profile the inflammatory and immune activity in the lesions of SSc patients. Dermal interstitial fluid sample from the involved forearm skin, and synchronous plasma samples were collected from SSc patients (n = 26, diffuse cutaneous SSc (DcSSc) n = 20, limited cutaneous SSc (LcSSc) n = 6), and healthy controls (HC) (n = 10) and profiled by Luminex® array for inflammatory cytokines, chemokines, and growth factors. Luminex® profiling of the dermal blister fluid showed increased inflammatory cytokines (median interleukin ( IL)-6 in SSc 39.78 pg/ml, HC 5.51 pg/ml, p = 0.01, median IL-15 in SSc 6.27 pg/ml, HC 4.38 pg/ml, p = 0.03), chemokines (monocyte chemotactic protein (MCP)-3 9.81 pg/ml in SSc, 7.18 pg/ml HC, p = 0.04), and profibrotic growth factors (platelet derived growth factor (PDGF)-AA 10.38 pg/ml versus 6.94 pg/ml in HC, p = 0.03). In general dermal fluid and plasma cytokine levels did not correlate, consistent with predominantly local production of these factors within the dermal lesions, rather than leakage from the serum. In hierarchical clustering and network analysis IL-6 emerged as a key central mediator. Our data confirm that an immuno-inflammatory environment and aberrant vascular repair are intimately linked to fibroblast activation in lesional skin in SSc. This non-invasive method could be used to profile disease activity in the clinic, and identifies key inflammatory or pro-fibrotic proteins that might be targeted therapeutically. Distinct subgroups of SSc may be defined that show innate or adaptive immune cytokine signatures.

  9. The new challenges of multiplex networks: Measures and models

    Science.gov (United States)

    Battiston, Federico; Nicosia, Vincenzo; Latora, Vito

    2017-02-01

    What do societies, the Internet, and the human brain have in common? They are all examples of complex relational systems, whose emerging behaviours are largely determined by the non-trivial networks of interactions among their constituents, namely individuals, computers, or neurons, rather than only by the properties of the units themselves. In the last two decades, network scientists have proposed models of increasing complexity to better understand real-world systems. Only recently we have realised that multiplexity, i.e. the coexistence of several types of interactions among the constituents of a complex system, is responsible for substantial qualitative and quantitative differences in the type and variety of behaviours that a complex system can exhibit. As a consequence, multilayer and multiplex networks have become a hot topic in complexity science. Here we provide an overview of some of the measures proposed so far to characterise the structure of multiplex networks, and a selection of models aiming at reproducing those structural properties and quantifying their statistical significance. Focusing on a subset of relevant topics, this brief review is a quite comprehensive introduction to the most basic tools for the analysis of multiplex networks observed in the real-world. The wide applicability of multiplex networks as a framework to model complex systems in different fields, from biology to social sciences, and the colloquial tone of the paper will make it an interesting read for researchers working on both theoretical and experimental analysis of networked systems.

  10. Sum-rate analysis of spectrum sharing spatial multiplexing MIMO systems with zero-forcing and multiuser diversity

    KAUST Repository

    Yang, Liang

    2013-06-01

    This paper considers a multiuser spectrum sharing (SS) multiple-input multiple-output (MIMO) system with zero-forcing (ZF) operating in a Rayleigh fading environment. We provide an asymptotic sum-rate analysis to investigate the effects of different parameters on the multiuser diversity gain. For a ZF SS spatial multiplexing system with scheduling, the asymptotic sum-rate scales like Nt log2(Q(Nt Np√K - 1)/N t), where Np denotes the number of antennas of primary receiver, Q is the interference temperature, and K represents the number of secondary transmitters. © 2013 IEEE.

  11. Development of genomic microsatellite multiplex PCR using dye-labeled universal primer and its validation in pedigree analysis of Pacific oyster ( Crassostrea gigas)

    Science.gov (United States)

    Liu, Ting; Li, Qi; Song, Junlin; Yu, Hong

    2017-02-01

    There is an increasing requirement for traceability of aquaculture products, both for consumer protection and for food safety. There are high error rates in the conventional traceability systems depending on physical labels. Genetic traceability technique depending on DNA-based tracking system can overcome this problem. Genealogy information is essential for genetic traceability, and microsatellite DNA marker is a good choice for pedigree analysis. As increasing genotyping throughput of microsatellites, microsatellite multiplex PCR has become a fast and cost-effective technique. As a commercially important cultured aquatic species, Pacific oyster Crassostrea gigas has the highest global production. The objective of this study was to develop microsatellite multiplex PCR panels with dye-labeled universal primer for pedigree analysis in C. gigas, and these multiplex PCRs were validated using 12 full-sib families with known pedigrees. Here we developed six informative multiplex PCRs using 18 genomic microsatellites in C. gigas. Each multiplex panel contained a single universal primer M13(-21) used as a tail on each locus-specific forward primer and a single universal primer M13(-21) labeled with fluorophores. The polymorphisms of the markers were moderate, with an average of 10.3 alleles per locus and average polymorphic information content of 0.740. The observed heterozygosity per locus ranged from 0.492 to 0.822. Cervus simulations revealed that the six panels would still be of great value when massive families were analysed. Pedigree analysis of real offspring demonstrated that 100% of the offspring were unambiguously allocated to their parents when two multiplex PCRs were used. The six sets of multiplex PCRs can be an important tool for tracing cultured individuals, population genetic analysis, and selective breeding program in C. gigas.

  12. Wireless Network Code Design and Performance Analysis using Diversity-Multiplexing Tradeoff

    CERN Document Server

    Topakkaya, Hakan

    2010-01-01

    Network coding and cooperative communication have received considerable attention from the research community recently in order to mitigate the adverse effects of fading in wireless transmissions and at the same time to achieve high throughput and better spectral efficiency. In this work, we design and analyze deterministic and random network coding schemes for a cooperative communication setup with multiple sources and destinations. We show that our schemes outperform conventional cooperation in terms of the diversity-multiplexing tradeoff (DMT). Specifically, it achieves the full-diversity order at the expense of a slightly reduced multiplexing rate. We establish the link between the parity-check matrix for a $(N+M,M,N+1)$ systematic MDS code and the network coding coefficients in a cooperative communication system of $N$ source-destination pairs and $M$ relays. We present two ways to generate the network coding matrix: using the Cauchy matrices and the Vandermonde matrices, and establish that they both off...

  13. Human Y chromosome microdeletion analysis by PCR multiplex protocols identifying only clinically relevant AZF microdeletions.

    Science.gov (United States)

    Vogt, Peter H; Bender, Ulrike

    2013-01-01

    PCR multiplex assays are the method of choice for quickly revealing genomic microdeletions in the large repetitive genomic sequence blocks on the long arm of the human Y chromosome. They harbor the Azoospermia Factor (AZF) genes, which cause male infertility when functionally disrupted. These protein encoding Y genes are expressed exclusively or predominantly during male germ cell development, i.e., at different phases of human spermatogenesis. They are located in three distinct genomic sequence regions designated AZFa, AZFb, and AZFc, respectively. Complete deletion of an AZF region, also called "classical" AZF microdeletion, is always associated with male infertility and a distinct testicular pathology. Partial AZF deletions including single AZF Y genes can cause the same testicular pathology as the corresponding complete deletion (e.g., DDX3Y gene deletions in AZFa), or might not be associated with male infertility at all (e.g., some BPY2, CDY1, DAZ gene deletions in AZFc). We therefore propose that a PCR multiplex assay aimed to reduce only those AZF microdeletions causing a specific testicular pathology-thus relevant for clinical applications. It only includes Sequence Tagged Site (STS) deletion markers inside the exon structures of the Y genes known to be expressed in male germ cells and located in the three AZF regions. They were integrated in a robust standard protocol for four PCR multiplex mixtures which also include the basic principles of quality control according to the strict guidelines of the European Molecular Genetics Quality Network (EMQN: http://www.emqn.org). In case all Y genes of one AZF region are deleted the molecular extension of this AZF microdeletion is diagnosed to be yes or no comparable to that of the "classical" AZF microdeletion by an additional PCR multiplex assay analyzing the putative AZF breakpoint borderlines.

  14. Quantitative Data Analysis--In the Graduate Curriculum

    Science.gov (United States)

    Albers, Michael J.

    2017-01-01

    A quantitative research study collects numerical data that must be analyzed to help draw the study's conclusions. Teaching quantitative data analysis is not teaching number crunching, but teaching a way of critical thinking for how to analyze the data. The goal of data analysis is to reveal the underlying patterns, trends, and relationships of a…

  15. The Curriculum in Quantitative Analysis: Results of a Survey.

    Science.gov (United States)

    Locke, David C.; Grossman, William E. L.

    1987-01-01

    Reports on the results of a survey of college level instructors of quantitative analysis courses. Discusses what topics are taught in such courses, how much weight is given to these topics, and which experiments are used in the laboratory. Poses some basic questions about the curriculum in quantitative analysis. (TW)

  16. Multiplex Quantitative Histologic Analysis of Human Breast Cancer Cell Signaling and Cell Fate

    Science.gov (United States)

    2010-05-01

    P. Lewis , B. S. Manjunath, and S. K. Fisher, “Automated tool for the detection of cell nuclei in digital microscopic images: Application to retinal...set model and some applications to Mumford -Shah image segmentation,” IEEE Trans. Image Process., vol. 15, no. 5, pp. 1171–1181, May 2006. [37] N. R

  17. Diversity-Multiplexing Tradeoff via Asymptotic Analysis of Large MIMO Systems

    CERN Document Server

    Loyka, Sergey

    2007-01-01

    Diversity-multiplexing tradeoff (DMT) presents a compact framework to compare various MIMO systems and channels in terms of the two main advantages they provide (i.e. high data rate and/or low error rate). This tradeoff was characterized asymptotically (SNR-> infinity) for i.i.d. Rayleigh fading channel by Zheng and Tse [1]. The asymptotic DMT overestimates the finite-SNR one [2]. In this paper, using the recent results on the asymptotic (in the number of antennas) outage capacity distribution, we derive and analyze the finite-SNR DMT for a broad class of channels (not necessarily Rayleigh fading). Based on this, we give the convergence conditions for the asymptotic DMT to be approached by the finite-SNR one. The multiplexing gain definition is shown to affect critically the convergence point: when the multiplexing gain is defined via the mean (ergodic) capacity, the convergence takes place at realistic SNR values. Furthermore, in this case the diversity gain can also be used to estimate the outage probabilit...

  18. Metal-organic framework-based molecular beacons for multiplexed DNA detection by synchronous fluorescence analysis.

    Science.gov (United States)

    Ye, Tai; Liu, Yufei; Luo, Ming; Xiang, Xia; Ji, Xinghu; Zhou, Guohua; He, Zhike

    2014-04-07

    We report a new sensor combined two dimensional metal-organic framework (MOF), N,N-bis(2-hydroxy-ethyl)dithiooxamidato copper(II) (H2dtoaCu), with the hairpin-structured oligonucleotides and demonstrate its feasibility in detecting multiplexed sequence-specific DNA. The key component of this sensor (MOF-MBs) is the hairpin-structured fluorescent oligonucleotide that allows the MOFs to function as both a "nanoscaffold" for the oligonucleotide and a "nanoquencher" of the fluorophore. An oligonucleotide sequence fragment of wild-type HBV (T1) and a reverse-transcription oligonucleotide sequence of RNA fragment of HIV (T2) were used as model systems. While in the presence of the targets, the fluorescence of dyes was recovered by forming a double strand structure. Multiplex DNA detection can be realized by synchronous scanning fluorescence spectrometry, and there was no cross reaction between the two probes. Under the optimum conditions, the fluorescence intensities of two dyes all exhibit good linear dependence on their target DNA concentration in the range of 1-10 nM with the detection limit of 0.87 nM and 0.22 nM for T1 and T2, respectively. As a proof of concept, the MOF-MBs have been successfully used as a potential sensing platform for simultaneous detection of multiplexed DNA.

  19. Multiplex Ligation-Dependent Probe Amplification Technique for Copy Number Analysis on Small Amounts of DNA Material

    DEFF Research Database (Denmark)

    Sørensen, Karina; Andersen, Paal; Larsen, Lars;

    2008-01-01

    The multiplex ligation-dependent probe amplification (MLPA) technique is a sensitive technique for relative quantification of up to 50 different nucleic acid sequences in a single reaction, and the technique is routinely used for copy number analysis in various syndromes and diseases. The aim...... of the study was to exploit the potential of MLPA when the DNA material is limited. The DNA concentration required in standard MLPA analysis is not attainable from dried blood spot samples (DBSS) often used in neonatal screening programs. A novel design of MLPA probes has been developed to permit for MLPA...... analysis on small amounts of DNA. Six patients with congenital adrenal hyperplasia (CAH) were used in this study. DNA was extracted from both whole blood and DBSS and subjected to MLPA analysis using normal and modified probes. Results were analyzed using GeneMarker and manual Excel analysis. A total...

  20. Combination and Integration of Qualitative and Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Philipp Mayring

    2001-02-01

    Full Text Available In this paper, I am going to outline ways of combining qualitative and quantitative steps of analysis on five levels. On the technical level, programs for the computer-aided analysis of qualitative data offer various combinations. Where the data are concerned, the employment of categories (for instance by using qualitative content analysis allows for combining qualitative and quantitative forms of data analysis. On the individual level, the creation of types and the inductive generalisation of cases allow for proceeding from individual case material to quantitative generalisations. As for research design, different models can be distinguished (preliminary study, generalisation, elaboration, triangulation which combine qualitative and quantitative steps of analysis. Where the logic of research is concerned, it can be shown that an extended process model which combined qualitative and quantitative research can be appropriate and thus lead to an integration of the two approaches. URN: urn:nbn:de:0114-fqs010162

  1. Quantitative analysis of four protein biomarkers: An automated microfluidic cartridge-based method and its comparison to colorimetric ELISA.

    Science.gov (United States)

    Dysinger, Mark; Marusov, Greg; Fraser, Stephanie

    2017-09-13

    Biomarker quantitation with ligand binding assays has matured greatly in recent years. This maturation has been partly in response to demands for more data points from fewer samples or less available sample volume. Multiplexing offers opportunities to acquire data for multiple analytes from single sample assay iterations, but has its own unique challenges and limitations. ProteinSimple has developed Simple Plex™, an automated immunoassay platform consisting of microfluidic cartridge-based assays run on the Ella instrument. Ella subverts traditional multiplexing challenges by rapidly performing triplicate measurements of up to four different analytes simultaneously, each in their own respective assay vessels and all from a single sample. Here we describe a comparison of the Simple Plex platform versus colorimetric ELISA and their respective abilities to quantitate four common biomarkers (MCP-1/CCL2, VEGF-A, TNF-α, and IL-6) from twenty-eight healthy individual donor plasma samples. Each biomarker was tested on the two platforms on each of two days. Ella analysis required significantly reduced sample volume, manual steps, and total time. Overall, Ella was able to quantify results for all twenty-eight samples for each of the four biomarkers. In contrast, ELISA was able to measure quantifiable results within respective calibration curve ranges for MCP-1/CCL2 (96% of samples) and VEGFA (7% of samples). For TNF-α and IL-6, ELISA was not sensitive enough to quantify any samples in the assay ranges. This stark difference in quantitative results underscores Ella's ability to multiplex without compromising sensitivity, and has far reaching potential for biomarker panel measurement in support of diagnosis, prognosis, and monitoring of disease. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Design of multiplex calibrant plasmids, their use in GMO detection and the limit of their applicability for quantitative purposes owing to competition effects.

    Science.gov (United States)

    Debode, Frédéric; Marien, Aline; Janssen, Eric; Berben, Gilbert

    2010-03-01

    Five double-target multiplex plasmids to be used as calibrants for GMO quantification were constructed. They were composed of two modified targets associated in tandem in the same plasmid: (1) a part of the soybean lectin gene and (2) a part of the transgenic construction of the GTS40-3-2 event. Modifications were performed in such a way that each target could be amplified with the same primers as those for the original target from which they were derived but such that each was specifically detected with an appropriate probe. Sequence modifications were done to keep the parameters of the new target as similar as possible to those of its original sequence. The plasmids were designed to be used either in separate reactions or in multiplex reactions. Evidence is given that with each of the five different plasmids used in separate wells as a calibrant for a different copy number, a calibration curve can be built. When the targets were amplified together (in multiplex) and at different concentrations inside the same well, the calibration curves showed that there was a competition effect between the targets and this limits the range of copy numbers for calibration over a maximum of 2 orders of magnitude. Another possible application of multiplex plasmids is discussed.

  3. Some Epistemological Considerations Concerning Quantitative Analysis

    Science.gov (United States)

    Dobrescu, Emilian

    2008-01-01

    This article presents the author's address at the 2007 "Journal of Applied Quantitative Methods" ("JAQM") prize awarding festivity. The festivity was included in the opening of the 4th International Conference on Applied Statistics, November 22, 2008, Bucharest, Romania. In the address, the author reflects on three theses that…

  4. Experimental Design and Multiplexed Modeling Using Titrimetry and Spreadsheets

    Science.gov (United States)

    Harrington, Peter De B.; Kolbrich, Erin; Cline, Jennifer

    2002-07-01

    The topics of experimental design and modeling are important for inclusion in the undergraduate curriculum. Many general chemistry and quantitative analysis courses introduce students to spreadsheet programs, such as MS Excel. Students in the laboratory sections of these courses use titrimetry as a quantitative measurement method. Unfortunately, the only model that students may be exposed to in introductory chemistry courses is the working curve that uses the linear model. A novel experiment based on a multiplex model has been devised for titrating several vinegar samples at a time. The multiplex titration can be applied to many other routine determinations. An experimental design model is fit to titrimetric measurements using the MS Excel LINEST function to estimate concentration from each sample. This experiment provides valuable lessons in error analysis, Class A glassware tolerances, experimental simulation, statistics, modeling, and experimental design.

  5. MicroRNA expression analysis and Multiplex ligation-dependent probe amplification in metastatic and non-metastatic uveal melanoma

    DEFF Research Database (Denmark)

    Larsen, Ann-Cathrine; Holst, Line; Kaczkowski, Bogumil

    2014-01-01

    Purpose: To determine the association of microRNA expression and chromosomal changes with metastasis and survival in uveal melanoma (UM). Methods: Thirty-six patients with UM were selected based on the metastatic status, and clinicopathological data were collected. Multiplex ligation......-dependent probe amplification (MLPA) was used to identify chromosomal changes. Chromosomal changes and clinicopathological data were correlated with survival and metastasis. The microRNA expression was analysed in 26 of the 36 archived UM samples. Unsupervised analysis, differential expression analysis and Cox...... regression analysis were performed to determine the association with metastasis and survival. Results: Metastasis and metastatic death occurred in 20 patients, two patients died of other causes and one patient of unknown causes. A significant association between increasing size category (p = 0.002, log...

  6. [Microarray analytic system for multiplex analysis by real-time polymerase chain reaction with reagents immobilized in microreactors].

    Science.gov (United States)

    Navolotskiĭ, D V; Perchik, A V; Mark'ianov, I A; Ganeev, A A; Sliadnev, M N

    2011-01-01

    A microarray analytic system that uses a silicon chip with immobilized in microreactor test-system for multiplex analysis of DNA by real-time polymerase chain reaction (RT-PCR) was developed and optimized. We suggested the method of immobilization of PCR-components of a test-system, chose the stabilizer, and conducted the optimization of the composition of reaction mixture to achieve permanent stability of a microarray. We conducted optimization of preparation of samples using magnetic sorbent and indicated that, with 2.6 x 10(4) copies/ml, 60 min are necessary to obtain positive identification including time for preparation of model probes. The abilities of the created system were demonstrated on the example of microarray analysis of samples with different content of DNA, low absolute limits of identification (20 DNA copies in microreactor), and high reproducibility of the analysis.

  7. Laser capture microdissection and multiplex-tandem PCR analysis of proximal tubular epithelial cell signaling in human kidney disease.

    Science.gov (United States)

    Wilkinson, Ray; Wang, Xiangju; Kassianos, Andrew J; Zuryn, Steven; Roper, Kathrein E; Osborne, Andrew; Sampangi, Sandeep; Francis, Leo; Raghunath, Vishwas; Healy, Helen

    2014-01-01

    Interstitial fibrosis, a histological process common to many kidney diseases, is the precursor state to end stage kidney disease, a devastating and costly outcome for the patient and the health system. Fibrosis is historically associated with chronic kidney disease (CKD) but emerging evidence is now linking many forms of acute kidney disease (AKD) with the development of CKD. Indeed, we and others have observed at least some degree of fibrosis in up to 50% of clinically defined cases of AKD. Epithelial cells of the proximal tubule (PTEC) are central in the development of kidney interstitial fibrosis. We combine the novel techniques of laser capture microdissection and multiplex-tandem PCR to identify and quantitate "real time" gene transcription profiles of purified PTEC isolated from human kidney biopsies that describe signaling pathways associated with this pathological fibrotic process. Our results: (i) confirm previous in-vitro and animal model studies; kidney injury molecule-1 is up-regulated in patients with acute tubular injury, inflammation, neutrophil infiltration and a range of chronic disease diagnoses, (ii) provide data to inform treatment; complement component 3 expression correlates with inflammation and acute tubular injury, (iii) identify potential new biomarkers; proline 4-hydroxylase transcription is down-regulated and vimentin is up-regulated across kidney diseases, (iv) describe previously unrecognized feedback mechanisms within PTEC; Smad-3 is down-regulated in many kidney diseases suggesting a possible negative feedback loop for TGF-β in the disease state, whilst tight junction protein-1 is up-regulated in many kidney diseases, suggesting feedback interactions with vimentin expression. These data demonstrate that the combined techniques of laser capture microdissection and multiplex-tandem PCR have the power to study molecular signaling within single cell populations derived from clinically sourced tissue.

  8. Laser capture microdissection and multiplex-tandem PCR analysis of proximal tubular epithelial cell signaling in human kidney disease.

    Directory of Open Access Journals (Sweden)

    Ray Wilkinson

    Full Text Available Interstitial fibrosis, a histological process common to many kidney diseases, is the precursor state to end stage kidney disease, a devastating and costly outcome for the patient and the health system. Fibrosis is historically associated with chronic kidney disease (CKD but emerging evidence is now linking many forms of acute kidney disease (AKD with the development of CKD. Indeed, we and others have observed at least some degree of fibrosis in up to 50% of clinically defined cases of AKD. Epithelial cells of the proximal tubule (PTEC are central in the development of kidney interstitial fibrosis. We combine the novel techniques of laser capture microdissection and multiplex-tandem PCR to identify and quantitate "real time" gene transcription profiles of purified PTEC isolated from human kidney biopsies that describe signaling pathways associated with this pathological fibrotic process. Our results: (i confirm previous in-vitro and animal model studies; kidney injury molecule-1 is up-regulated in patients with acute tubular injury, inflammation, neutrophil infiltration and a range of chronic disease diagnoses, (ii provide data to inform treatment; complement component 3 expression correlates with inflammation and acute tubular injury, (iii identify potential new biomarkers; proline 4-hydroxylase transcription is down-regulated and vimentin is up-regulated across kidney diseases, (iv describe previously unrecognized feedback mechanisms within PTEC; Smad-3 is down-regulated in many kidney diseases suggesting a possible negative feedback loop for TGF-β in the disease state, whilst tight junction protein-1 is up-regulated in many kidney diseases, suggesting feedback interactions with vimentin expression. These data demonstrate that the combined techniques of laser capture microdissection and multiplex-tandem PCR have the power to study molecular signaling within single cell populations derived from clinically sourced tissue.

  9. On-Chip integration of sample pretreatment and Multiplex polymerase chain reaction (PCR) for DNA analysis

    DEFF Research Database (Denmark)

    Brivio, Monica; Snakenborg, Detlef; Søgaard, E.

    2008-01-01

    In this paper we present a modular lab-on-a-chip system for integrated sample pre-treatment (PT) by magnetophoresis and DNA amplification by polymerase chain reaction (PCR). It consists of a polymer-based microfluidic chip mounted on a custom-made thermocycler (Figure 1) and includes a simple...... and efficient method for switching the liquid flow between the PT and PCR chamber. Purification of human genomic DNA from EDTA-treated blood and multiplex PCR were successfully carried out on-chip using the developed lab-on-a-chip system....

  10. The Microwave SQUID Multiplexer

    Science.gov (United States)

    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

  11. Finite-SNR Diversity-Multiplexing Tradeoff via Asymptotic Analysis of Large MIMO Systems

    CERN Document Server

    Loyka, Sergey

    2010-01-01

    Diversity-multiplexing tradeoff (DMT) was characterized asymptotically (SNR-> infinity) for i.i.d. Rayleigh fading channel by Zheng and Tse [1]. The SNR-asymptotic DMT overestimates the finite-SNR one [2]. This paper outlines a number of additional limitations and difficulties of the DMT framework and discusses their implications. Using the recent results on the size-asymptotic (in the number of antennas) outage capacity distribution, the finite-SNR, size-asymptotic DMT is derived for a broad class of fading distributions. The SNR range over which the finite-SNR DMT is accurately approximated by the SNR-asymptotic one is characterized. The multiplexing gain definition is shown to affect critically this range and thus should be carefully selected, so that the SNR-asymptotic DMT is an accurate approximation at realistic SNR values and thus has operational significance to be used as a design criteria. The finite SNR diversity gain is shown to decrease with correlation and power imbalance in a broad class of fadi...

  12. Structural and quantitative analysis of Equisetum alkaloids.

    Science.gov (United States)

    Cramer, Luise; Ernst, Ludger; Lubienski, Marcus; Papke, Uli; Schiebel, Hans-Martin; Jerz, Gerold; Beuerle, Till

    2015-08-01

    Equisetum palustre L. is known for its toxicity for livestock. Several studies in the past addressed the isolation and identification of the responsible alkaloids. So far, palustrine (1) and N(5)-formylpalustrine (2) are known alkaloids of E. palustre. A HPLC-ESI-MS/MS method in combination with simple sample work-up was developed to identify and quantitate Equisetum alkaloids. Besides the two known alkaloids six related alkaloids were detected in different Equisetum samples. The structure of the alkaloid palustridiene (3) was derived by comprehensive 1D and 2D NMR experiments. N(5)-Acetylpalustrine (4) was also thoroughly characterized by NMR for the first time. The structure of N(5)-formylpalustridiene (5) is proposed based on mass spectrometry results. Twenty-two E. palustre samples were screened by a HPLC-ESI-MS/MS method after development of a simple sample work-up and in most cases the set of all eight alkaloids were detected in all parts of the plant. A high variability of the alkaloid content and distribution was found depending on plant organ, plant origin and season ranging from 88 to 597mg/kg dried weight. However, palustrine (1) and the alkaloid palustridiene (3) always represented the main alkaloids. For the first time, a comprehensive identification, quantitation and distribution of Equisetum alkaloids was achieved.

  13. Energy Dispersive Spectrometry and Quantitative Analysis Short Course. Introduction to X-ray Energy Dispersive Spectrometry and Quantitative Analysis

    Science.gov (United States)

    Carpenter, Paul; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    This course will cover practical applications of the energy-dispersive spectrometer (EDS) to x-ray microanalysis. Topics covered will include detector technology, advances in pulse processing, resolution and performance monitoring, detector modeling, peak deconvolution and fitting, qualitative and quantitative analysis, compositional mapping, and standards. An emphasis will be placed on use of the EDS for quantitative analysis, with discussion of typical problems encountered in the analysis of a wide range of materials and sample geometries.

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

    Science.gov (United States)

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

    2013-06-01

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

  15. Performance analysis of long reach colorless wavelength division multiplexed-orthogonal frequency division multiplexing-passive optical network with broadcast capability

    Science.gov (United States)

    Pandey, Gaurav; Goel, Aditya

    2016-07-01

    A colorless wavelength division multiplexed-orthogonal frequency division multiplexing-passive optical network (WDM-OFDM-PON) is presented, which is capable of supporting symmetric 10 Gbps downlink direct detection (DD) OFDM unicast signal, broadcast signal, and uplink on-off keying (OOK) signal up to 60 km that includes both single mode and dispersion compensation fiber. At each optical network unit (ONU), DD has been used to receive downlink unicast and broadcast OFDM data. A delay interferometer (DI) has been used at a central office to achieve 10 Gbps uplink signal transmission over 60 km distance utilizing a reflective semiconductor optical amplifier (bandwidth=1.5 GHz) at the ONU because DI works as a vestigial sideband filter and an optical equalizer. Broadcast channel does not affect the system performance because it generates a limited interference of the order of 0.1 to 0.28 dB to downlink and uplink channels, and this interference is distributed to every ONU. For bit error rate of 10-9, the receiver sensitivity of -24, -23.1, and -20.14 dBm is achieved by simulating downlink OFDM unicast channels, OFDM broadcast channel, and uplink OOK unicast channels, respectively, for a symmetric data rate of 10 Gbps over 60 km.

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

    Science.gov (United States)

    Zhao, Ming; Li, Yu; Peng, Leilei

    2014-09-22

    We report a fast non-iterative lifetime data analysis method for the Fourier multiplexed frequency-sweeping confocal FLIM (Fm-FLIM) system [Opt. Express 22, 10221 (2014)]. 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.

  17. China ASON Network Migration Scenarios and Their Quantitative Analysis

    Institute of Scientific and Technical Information of China (English)

    Soichiro; Araki; Itaru; Nishioka; Yoshihiko; Suemura

    2003-01-01

    This paper proposes two migration scenarios from China ring networks to ASON mesh networks. In our quantitative analysis with ASON/GMPLS simulator, a subnetwork protection scheme achieved best balanced performance in resource utilization and restoration time.

  18. China ASON Network Migration Scenarios and Their Quantitative Analysis

    Institute of Scientific and Technical Information of China (English)

    Guoying Zhang; Soichiro Araki; Itaru Nishioka; Yoshihiko Suemura

    2003-01-01

    This paper proposes two migration scenarios from China rin g networks to ASON mesh networks . In our quantitative analysis with ASON/GMPLS simulator, a subnetwork protection scheme achieved best balanced performance in resource utilization and restoration time.

  19. Quantitative and qualitative analysis of sterols/sterolins and ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-06-03

    Jun 3, 2008 ... Quantitative and qualitative analysis of sterols/sterolins ... method was developed to identify and quantify sterols (especially β-sitosterol) in chloroform extracts of ... Studies with phytosterols, especially β-sitosterol, have.

  20. Development and validation of a quantitative PCR assay using multiplexed hydrolysis probes for detection and quantification of Theileria orientalis isolates and differentiation of clinically relevant subtypes.

    Science.gov (United States)

    Bogema, D R; Deutscher, A T; Fell, S; Collins, D; Eamens, G J; Jenkins, C

    2015-03-01

    Theileria orientalis is an emerging pathogen of cattle in Asia, Australia, and New Zealand. This organism is a vector-borne hemoprotozoan that causes clinical disease characterized by anemia, abortion, and death, as well as persistent subclinical infections. Molecular methods of diagnosis are preferred due to their sensitivity and utility in differentiating between pathogenic and apathogenic genotypes. Conventional PCR (cPCR) assays for T. orientalis detection and typing are laborious and do not provide an estimate of parasite load. Current real-time PCR assays cannot differentiate between clinically relevant and benign genotypes or are only semiquantitative without a defined clinical threshold. Here, we developed and validated a hydrolysis probe quantitative PCR (qPCR) assay which universally detects and quantifies T. orientalis and identifies the clinically associated Ikeda and Chitose genotypes (UIC assay). Comparison of the UIC assay results with previously validated universal and genotype-specific cPCR results demonstrated that qPCR detects and differentiates T. orientalis with high sensitivity and specificiy. Comparison of quantitative results based on percent parasitemia, determined via blood film analysis and packed cell volume (PCV) revealed significant positive and negative correlations, respectively. One-way analysis of variance (ANOVA) indicated that blood samples from animals with clinical signs of disease contained statistically higher concentrations of T. orientalis DNA than animals with subclinical infections. We propose clinical thresholds to assist in classifying high-, moderate-, and low-level infections and describe how parasite load and the presence of the Ikeda and Chitose genotypes relate to disease.

  1. Quantitative Models and Analysis for Reactive Systems

    DEFF Research Database (Denmark)

    Thrane, Claus

    phones and websites. Acknowledging that now more than ever, systems come in contact with the physical world, we need to revise the way we construct models and verification algorithms, to take into account the behavior of systems in the presence of approximate, or quantitative information, provided...... by the environment in which they are embedded. This thesis studies the semantics and properties of a model-based framework for re- active systems, in which models and specifications are assumed to contain quantifiable information, such as references to time or energy. Our goal is to develop a theory of approximation......, by studying how small changes to our models affect the verification results. A key source of motivation for this work can be found in The Embedded Systems Design Challenge [HS06] posed by Thomas A. Henzinger and Joseph Sifakis. It contains a call for advances in the state-of-the-art of systems verification...

  2. Quantitative Models and Analysis for Reactive Systems

    DEFF Research Database (Denmark)

    Thrane, Claus

    phones and websites. Acknowledging that now more than ever, systems come in contact with the physical world, we need to revise the way we construct models and verification algorithms, to take into account the behavior of systems in the presence of approximate, or quantitative information, provided......, allowing verification procedures to quantify judgements, on how suitable a model is for a given specification — hence mitigating the usual harsh distinction between satisfactory and non-satisfactory system designs. This information, among other things, allows us to evaluate the robustness of our framework......, by studying how small changes to our models affect the verification results. A key source of motivation for this work can be found in The Embedded Systems Design Challenge [HS06] posed by Thomas A. Henzinger and Joseph Sifakis. It contains a call for advances in the state-of-the-art of systems verification...

  3. Towards a quantitative OCT image analysis.

    Directory of Open Access Journals (Sweden)

    Marina Garcia Garrido

    Full Text Available Optical coherence tomography (OCT is an invaluable diagnostic tool for the detection and follow-up of retinal pathology in patients and experimental disease models. However, as morphological structures and layering in health as well as their alterations in disease are complex, segmentation procedures have not yet reached a satisfactory level of performance. Therefore, raw images and qualitative data are commonly used in clinical and scientific reports. Here, we assess the value of OCT reflectivity profiles as a basis for a quantitative characterization of the retinal status in a cross-species comparative study.Spectral-Domain Optical Coherence Tomography (OCT, confocal Scanning-Laser Ophthalmoscopy (SLO, and Fluorescein Angiography (FA were performed in mice (Mus musculus, gerbils (Gerbillus perpadillus, and cynomolgus monkeys (Macaca fascicularis using the Heidelberg Engineering Spectralis system, and additional SLOs and FAs were obtained with the HRA I (same manufacturer. Reflectivity profiles were extracted from 8-bit greyscale OCT images using the ImageJ software package (http://rsb.info.nih.gov/ij/.Reflectivity profiles obtained from OCT scans of all three animal species correlated well with ex vivo histomorphometric data. Each of the retinal layers showed a typical pattern that varied in relative size and degree of reflectivity across species. In general, plexiform layers showed a higher level of reflectivity than nuclear layers. A comparison of reflectivity profiles from specialized retinal regions (e.g. visual streak in gerbils, fovea in non-human primates with respective regions of human retina revealed multiple similarities. In a model of Retinitis Pigmentosa (RP, the value of reflectivity profiles for the follow-up of therapeutic interventions was demonstrated.OCT reflectivity profiles provide a detailed, quantitative description of retinal layers and structures including specialized retinal regions. Our results highlight the

  4. Quantitative data analysis in education a critical introduction using SPSS

    CERN Document Server

    Connolly, Paul

    2007-01-01

    This book provides a refreshing and user-friendly guide to quantitative data analysis in education for students and researchers. It assumes absolutely no prior knowledge of quantitative methods or statistics. Beginning with the very basics, it provides the reader with the knowledge and skills necessary to be able to undertake routine quantitative data analysis to a level expected of published research. Rather than focusing on teaching statistics through mathematical formulae, the book places an emphasis on using SPSS to gain a real feel for the data and an intuitive grasp of t

  5. Joint association analysis of bivariate quantitative and qualitative traits.

    Science.gov (United States)

    Yuan, Mengdie; Diao, Guoqing

    2011-11-29

    Univariate genome-wide association analysis of quantitative and qualitative traits has been investigated extensively in the literature. In the presence of correlated phenotypes, it is more intuitive to analyze all phenotypes simultaneously. We describe an efficient likelihood-based approach for the joint association analysis of quantitative and qualitative traits in unrelated individuals. We assume a probit model for the qualitative trait, under which an unobserved latent variable and a prespecified threshold determine the value of the qualitative trait. To jointly model the quantitative and qualitative traits, we assume that the quantitative trait and the latent variable follow a bivariate normal distribution. The latent variable is allowed to be correlated with the quantitative phenotype. Simultaneous modeling of the quantitative and qualitative traits allows us to make more precise inference on the pleiotropic genetic effects. We derive likelihood ratio tests for the testing of genetic effects. An application to the Genetic Analysis Workshop 17 data is provided. The new method yields reasonable power and meaningful results for the joint association analysis of the quantitative trait Q1 and the qualitative trait disease status at SNPs with not too small MAF.

  6. Development of qualitative and quantitative PCR analysis for meat adulteration from RNA samples.

    Science.gov (United States)

    Cheng, Jai-Hong; Chou, Hsiao-Ting; Lee, Meng-Shiou; Sheu, Shyang-Chwen

    2016-02-01

    Total RNA samples were used to establish qualitative and quantitative PCR-based methods for assessing meat adulteration. The primers were designed based on the mRNA sequences of troponin I (TnI), mitochondrial ribosomal protein (MRP) and tropomodulin genes to distinguish chicken, pork, goat, beef and ostrich. There was no cross reaction between the primers, and the detection limit of the cDNA template was 0.01 and 20 ng in simplex PCR and multiplex PCR, respectively. In the low temperature storage test, the detection limits of cDNA template with 10 and 1 ng were determined at 4 °C and -80 °C. In quantitative assay, the precision of real-time PCR analysis expressed as a coefficient of variation (CV) ranged from 0.25% to 5.24% and the trueness, expressed as an error, ranged from 0.28% to 6.98% for adulteration. Thus, herein, we provided alternative tools for the assessment of meat adulteration using mRNA-based PCR methods. Copyright © 2015. Published by Elsevier Ltd.

  7. Analysis of Doppler-effeet on satellite constellations with wavelength division multiplexing architectures

    Institute of Scientific and Technical Information of China (English)

    Qinglong Yang; Liying Tan; Jing Ma

    2009-01-01

    With the development of optical space communications, a global space-based optical backbone network is currently proposed by using broadband laser inter-satellite links (ISLs) which enable routing traffic through the space. Satellite optical networking techniques based on wavelength division multiplexing (WDM) ISLs can transit significantly high data rates signals. In this letter, a new function of wavelength excursion due to Doppler-effect is developed for the ISLs, considering the conception of pointing ahead mechanism. The characteristic of wavelength excursion induced by Doppler-effect is examined in one of low earth orbit (LEO) satellite constellation networks named the next-generation LEO system (NeLS) with WDM ISLs assumed, and the influence on its communications caused by wavelength excursion is analyzed.

  8. Optimality analysis of multiplex A-TIG welding flux for nickel-base superalloy

    Institute of Scientific and Technical Information of China (English)

    Fan Chenglei; Yang Chunli; Liang Yingchun; Lin Sanbao; Yu Xiang

    2007-01-01

    Orthogonal experiment is employed to study a new kind of multiplex flux for nickel-base superalloy. This activated TIG welding flux is composed of NaF, MgF2 and CaF2, and their proportion is 5:4:1. Compared with conventional TIG welding, the penetration increases 164% by the action of the flux. Tensile test result indicates that the fracture strength of the mixed flux A-TIG weld bead is higher than base metal, and it increases along with the decrement of the welding current. The average extensibility of the weldment is beyond 100%, which means perfect ductility. Metallographs elucidate that there exist lots of deep and evenly distributed dimples on the fracture section of weld bead while on that of base metal there only exists a few shallow dimples and massive tearing ridge.

  9. Deletion Analysis Of The Duchenne/Becker Muscular Dystrophy Gene Using Multiplex Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Dastur P

    2004-01-01

    Full Text Available The diagnosis of Duchenna Muscular Dystrophy (DMD and Becker Muscular Dystorphy (BMD is mainly based on clinical profile, serum CPK values, muscle biopsy and immunostaining for dystrophin. This was done in 100 unrelated patients using 19 exons including the promoter region in two sets of multiplex polymerase chain reaction (PCR. These primers amplify most of the exons in the deletion prone ′hot spot′ regions allowing determinations of deletion end points. Intragenic deletions were detected in 74 patients indicating that the use of PCR- based assays will allow deletion detection help in prenatal diagnosis for most of the DMD/BMD patients. The frequency of deletions observed in the present study was 74%.

  10. Analysis of dystrophin gene deletions by multiplex PCR in eastern India

    Directory of Open Access Journals (Sweden)

    Basak Jayasri

    2006-01-01

    Full Text Available The most common genetic neuromuscular disease of childhood, Duchenne and Becker muscular dystrophy (DMD/BMD is caused by deletion, duplication or point mutation of the dystrophin gene located at Xp 21.2. In the present study DNA from seventy unrelated patients clinically diagnosed as having DMD/BMD referred from different parts of West Bengal, a few other states and Bangladesh are analyzed using the multiplex polymerase chain reaction (m-PCR to screen for exon deletions and its distribution within the dystrophin gene. Out of seventy patients forty six (63% showed large intragenic deletion in the dystrophin gene. About 79% of these deletions are located in the hot spot region i.e., between exon 42 to 53. This is the first report of frequency and distribution of deletion in dystrophin gene in eastern Indian DMD/BMD population.

  11. Deletion Analysis Of The Duchenne/Becker Muscular Dystrophy Gene Using Multiplex Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Dastur R

    2003-01-01

    Full Text Available The diagnosis of Duchenne Muscular Dystrophy (DMD and Becker Muscular Dystrophy (BMD is mainly based on clinical profile, serum CPK values, muscle biopsy and immunostaining for dystrophin. Most recent and accurate method for diagnosing DMD/BMD is by detection of mutations in the DMD gene. This was done in 100 unrelated patients using 19 exons including the promoter region in two sets of multiplex polymerase chain reaction (PCR. These primers amplify most of the exons in the deletion prone ′hotspot′ regions allowing determination of deletion end point. Intragenic deletions were detected in 74 patients indicating that the use of PCR-based assays will allow deletion detection help in prenatal diagnosis for most of the DMD/BMD patients. The frequency of deletions observed in the present study was 74%.

  12. Usefulness of three-channel multiplex real-time PCR and melting curve analysis for simultaneous detection and identification of the Mycobacterium tuberculosis complex and nontuberculous mycobacteria.

    Science.gov (United States)

    Hong, Yun Ji; Chung, Young Hoon; Kim, Taek Soo; Song, Sang Hoon; Park, Kyoung Un; Yim, Jae Joon; Song, Junghan; Lee, Jae Ho; Kim, Eui Chong

    2011-11-01

    We attempted to determine the benefits of three-channel multiplex real-time PCR and melting curve analysis not only in detecting and distinguishing between nontuberculous mycobacteria (NTM) and the Mycobacterium tuberculosis complex but also in identifying NTM to the species level.

  13. Novel multiplex format of an extended multilocus variable-number-tandem-repeat analysis of Clostridium difficile correlates with tandem repeat sequence typing.

    Science.gov (United States)

    Jensen, Mie Birgitte Frid; Engberg, Jørgen; Larsson, Jonas T; Olsen, Katharina E P; Torpdahl, Mia

    2015-03-01

    Subtyping of Clostridium difficile is crucial for outbreak investigations. An extended multilocus variable-number tandem-repeat analysis (eMLVA) of 14 variable number tandem repeat (VNTR) loci was validated in multiplex format compatible with a routine typing laboratory and showed excellent concordance with tandem repeat sequence typing (TRST) and high discriminatory power.

  14. Multiple quantitative trait analysis using bayesian networks.

    Science.gov (United States)

    Scutari, Marco; Howell, Phil; Balding, David J; Mackay, Ian

    2014-09-01

    Models for genome-wide prediction and association studies usually target a single phenotypic trait. However, in animal and plant genetics it is common to record information on multiple phenotypes for each individual that will be genotyped. Modeling traits individually disregards the fact that they are most likely associated due to pleiotropy and shared biological basis, thus providing only a partial, confounded view of genetic effects and phenotypic interactions. In this article we use data from a Multiparent Advanced Generation Inter-Cross (MAGIC) winter wheat population to explore Bayesian networks as a convenient and interpretable framework for the simultaneous modeling of multiple quantitative traits. We show that they are equivalent to multivariate genetic best linear unbiased prediction (GBLUP) and that they are competitive with single-trait elastic net and single-trait GBLUP in predictive performance. Finally, we discuss their relationship with other additive-effects models and their advantages in inference and interpretation. MAGIC populations provide an ideal setting for this kind of investigation because the very low population structure and large sample size result in predictive models with good power and limited confounding due to relatedness.

  15. Performance Analysis of the Multiband Orthogonal Frequency Division Multiplexing Ultra-Wideband Systems for Multipath Fading and Multiuser Interference Channels

    Directory of Open Access Journals (Sweden)

    Yuan Ouyang

    2015-01-01

    Full Text Available This paper presents the performance analysis of the multiband orthogonal frequency division multiplexing (MB-OFDM ultra-wideband (UWB systems for multipath fading and multiuser interference channels. A closed form approximation of the BER performance of the MB-OFDM UWB system with multiple interferences is proposed. Based on the derived approximation, the effects on the BER performance for the choice of the codeword constraint lengths of the convolutional encoder, the length of the cyclic prefix, and the multiuser environments of two or more interferers are thoroughly discussed. Four UWB multipath fading channels are also investigated for the BER performance of the MB-OFDM UWB system. The simulated results provide us with useful information to appropriately choose the parameters of the MB-OFDM UWB system for the sake of achieving the BER performance that conforms to requirement of the FCC standards.

  16. Multiplex agarose gel electrophoresis system for variable number of tandem repeats genotyping: analysis example using Mycobacterium tuberculosis.

    Science.gov (United States)

    Wada, Takayuki; Maeda, Shinji

    2013-04-01

    As one genotyping method for Mycobacterium tuberculosis, variable number of tandem repeats (VNTR) is a promising tool to trace the undefined transmission of tuberculosis, but it often requires large equipment such as a genetic analyzer for DNA fragment analysis or CE system to conduct systematic analyses. For convenient genotyping at low cost in laboratories, we designed a multiplex PCR system that is applicable to agarose gel electrophoresis using fluorescent PCR primers. For tuberculosis genotyping by VNTR, the copy quantities of minisatellite DNA must be determined in more than 12 loci. The system can halve laborious electrophoresis processes by presenting an image of two VNTR amplicons on a single lane. No expensive equipment is necessary for this method. Therefore, it is useful even in developing countries. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Multiplex analysis of polyA-linked sequences (MAPS): an RNA-seq strategy to profile poly(A+) RNA.

    Science.gov (United States)

    Zhou, Yu; Li, Hai-Ri; Huang, Jie; Jin, Ge; Fu, Xiang-Dong

    2014-01-01

    We summarize 12 experimental methods that have been developed for profiling gene expression by focusing on the 3'-end of poly(A+) mRNA, distilling both common and unique features. Of this family of methods, we provide detailed protocol for MAPS, a method we believe is the simplest and most cost-effective for profiling gene expression and quantifying alternative polyadenylation events by oligo-dT priming followed by random priming and deep sequencing. This method also enables library multiplexing by using a set of bar coding primers during PCR amplification. We also provide a general guideline for analysis of the data generated by MAPS by using the software package maps3end.

  18. Simultaneous determination of nitrite and nitrate ions by air-segmented amplitude-modulated multiplexed flow analysis.

    Science.gov (United States)

    Yoshida, Haruka; Inui, Koji; Takeuchi, Masaki; Tanaka, Hideji

    2012-01-01

    The concept of amplitude-modulated multiplexed flow analysis has been extended to the simultaneous determination of multiple analytes in a sample. A sample solution containing nitrite and nitrate ions is delivered from two channels, but the flow rates are varied at different frequencies. One of the channels has a reduction column for converting nitrate ions to nitrite ions. Downstream, the absorbance of the diazo-coupling product is monitored after the merging of both solutions with a Griess reagent. The signal is analyzed by a fast Fourier transform (FFT) in real time. From the thus-obtained amplitude, a µmol dm(-3) level of the ions can be determined. The introduction of air bubbles is effective to reduce any axial dispersion, and hence to improve the sensitivity.

  19. Applied quantitative analysis in the social sciences

    CERN Document Server

    Petscher, Yaacov; Compton, Donald L

    2013-01-01

    To say that complex data analyses are ubiquitous in the education and social sciences might be an understatement. Funding agencies and peer-review journals alike require that researchers use the most appropriate models and methods for explaining phenomena. Univariate and multivariate data structures often require the application of more rigorous methods than basic correlational or analysis of variance models. Additionally, though a vast set of resources may exist on how to run analysis, difficulties may be encountered when explicit direction is not provided as to how one should run a model

  20. Quantitative analysis of probabilistic BPMN workflows

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2012-01-01

    We present a framework for modelling and analysis of realworld business workflows. We present a formalised core subset of the Business Process Modelling and Notation (BPMN) and then proceed to extend this language with probabilistic nondeterministic branching and general-purpose reward annotations...... of events, reward-based properties and best- and worst- case scenarios. We develop a simple example of medical workflow and demonstrate the utility of this analysis in accurate provisioning of drug stocks. Finally, we suggest a path to building upon these techniques to cover the entire BPMN language, allow...

  1. The quantitative failure of human reliability analysis

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, C.T.

    1995-07-01

    This philosophical treatise argues the merits of Human Reliability Analysis (HRA) in the context of the nuclear power industry. Actually, the author attacks historic and current HRA as having failed in informing policy makers who make decisions based on risk that humans contribute to systems performance. He argues for an HRA based on Bayesian (fact-based) inferential statistics, which advocates a systems analysis process that employs cogent heuristics when using opinion, and tempers itself with a rational debate over the weight given subjective and empirical probabilities.

  2. Multiplexed operation of a micromachined ultrasonic droplet ejector array.

    Science.gov (United States)

    Forbes, Thomas P; Degertekin, F Levent; Fedorov, Andrei G

    2007-10-01

    A dual-sample ultrasonic droplet ejector array is developed for use as a soft-ionization ion source for multiplexed mass spectrometry (MS). Such a multiplexed ion source aims to reduce MS analysis time for multiple analyte streams, as well as allow for the synchronized ejection of the sample(s) and an internal standard for quantitative results and mass calibration. Multiplexing is achieved at the device level by division of the fluid reservoir and separating the active electrodes of the piezoelectric transducer for isolated application of ultrasonic wave energy to each domain. The transducer is mechanically shaped to further reduce the acoustical crosstalk between the domains. Device design is performed using finite-element analysis simulations and supported by experimental characterization. Isolated ejection of approximately 5 microm diameter water droplets from individual domains in the micromachined droplet ejector array at around 1 MHz frequency is demonstrated by experiments. The proof-of-concept demonstration using a dual-sample device also shows potential for multiplexing with larger numbers of analytes.

  3. Quantitative analysis of cascade impactor samples - revisited

    Science.gov (United States)

    Orlić , I.; Chiam, S. Y.; Sanchez, J. L.; Tang, S. M.

    1999-04-01

    Concentrations of aerosols collected in Singapore during the three months long haze period that affected the whole South-East Asian region in 1997 are reported. Aerosol samples were continuously collected by using a fine aerosol sampler (PM2.5) and occasionally with a single orifice cascade impactor (CI) sampler. Our results show that in the fine fraction (<2.5 μm) the concentrations of two well-known biomass burning products, i.e. K and S were generally increased by a factor 2-3 compared to the non-hazy periods. However, a discrepancy was noticed, at least for elements with lower atomic number (Ti and below) between the results obtained by the fine aerosol sampler and the cascade impactor. Careful analysis by means of Nuclear Microscopy, in particular by the Scanning Transmission Ion Microscopy (STIM) technique, revealed that thicknesses of the lower CI stages exceeded thick target limits for 2 MeV protons. Detailed depth profiles of all CI stages were therefore measured using the STIM technique and concentrations corrected for absorption and proton energy loss. After correcting results for the actual sample thickness, concentrations of all major elements (S, Cl, K, Ca) agreed much better with the PM2.5 results. The importance of implementing thick target corrections in analysis of CI samples, especially those collected in the urban environments, is emphasized. Broad beam PIXE analysis approach is certainly not adequate in these cases.

  4. Quantitative analysis of Li by PIGE technique

    Science.gov (United States)

    Fonseca, M.; Mateus, R.; Santos, C.; Cruz, J.; Silva, H.; Luis, H.; Martins, L.; Jesus, A. P.

    2017-09-01

    In this work, the cross section of the reactions 7Li(p,pγ)7Li (γ - 478 keV) at the proton energy range 2.0-4.2 MeV was measured. The measurements were carried out at the 3 MV Tandem Accelerator at the CTN/IST Laboratory in Lisbon. To validate the obtained results, calculated gamma-ray yields were compared, at several proton energy values, with experimental yields for thick samples made of inorganic compounds containing lithium. In order to quantify the light elements present in the samples, we used a standard free method for PIGE in thick samples, based on a code - Emitted Radiation Yield Analysis (ERYA), which integrates the nuclear reaction excitation function along the depth of the sample. We also demonstrated the capacity of the technique for analysis of Li ores, as Spodumene, Lithium Muscovite and Holmquistite, and Li-alloys for plasma facing materials showing that this is a reliable and accurate method for PIGE analysis of Li in thick samples.

  5. Quantitative MRI analysis of dynamic enhancement of focal liver lesions

    Directory of Open Access Journals (Sweden)

    S. S. Bagnenko

    2012-01-01

    Full Text Available In our study 45 patients with different focal liver lesions (110 nodules were examined using high field MR-system (1,5 T. During this investigation quantitative MRI analysis of dynamic enhancement of various hepatic lesions and parenchymatous organs of abdomen were performed. It was shown that quantitative evaluation of enhanced MRI improves understanding of vascular transformation processes in pathologic hepatic focuses and in liver itself that is important for differential diagnoses of these diseases.

  6. Financial indicators for municipalities: a quantitative analysis

    Directory of Open Access Journals (Sweden)

    Sreĉko Devjak

    2009-12-01

    Full Text Available From the characterization of Local Authority financing models and structures in Portugal and Slovenia, a set of financial and generic budget indicators has been established. These indicators may be used in a comparative analysis considering the Bragança District in Portugal, and municipalities of similar population size in Slovenia. The research identified significant differences, in terms of financing sources due to some discrepancies on financial models and competences of municipalities on each country. The results show that Portuguese and Slovenian municipalities, in 2003, for the economy indicator, had similar ranking behaviour, but in 2004, they changed this behaviour.

  7. QUANTITATIVE ANALYSIS OF DRAWING TUBES MICROSTRUCTURE

    Directory of Open Access Journals (Sweden)

    Maroš Martinkovič

    2009-05-01

    Full Text Available Final properties of forming pieces are affected by production, at first conditions of mechanical working. Application of stereology methods to statistic reconstruction of three-dimensional plastic deformed material structure by bulk forming led to detail analysis of material structure changes. The microstructure of cold drawing tubes from STN 411353 steel was analyzed. Grain boundaries orientation was measured on perpendicular and parallel section of tubes with different degree of deformation. Macroscopic deformation leads to grain boundaries deformation and these ones were compared.

  8. Event History Analysis in Quantitative Genetics

    DEFF Research Database (Denmark)

    Maia, Rafael Pimentel

    Event history analysis is a clas of statistical methods specially designed to analyze time-to-event characteristics, e.g. the time until death. The aim of the thesis was to present adequate multivariate versions of mixed survival models that properly represent the genetic aspects related to a given...... time-to-event characteristic of interest. Real genetic longevity studies based on female animals of different species (sows, dairy cows, and sheep) exemplifies the use of the methods. Moreover these studies allow to understand som genetic mechanisms related to the lenght of the productive life...

  9. Chromatic Image Analysis For Quantitative Thermal Mapping

    Science.gov (United States)

    Buck, Gregory M.

    1995-01-01

    Chromatic image analysis system (CIAS) developed for use in noncontact measurements of temperatures on aerothermodynamic models in hypersonic wind tunnels. Based on concept of temperature coupled to shift in color spectrum for optical measurement. Video camera images fluorescence emitted by phosphor-coated model at two wavelengths. Temperature map of model then computed from relative brightnesses in video images of model at those wavelengths. Eliminates need for intrusive, time-consuming, contact temperature measurements by gauges, making it possible to map temperatures on complex surfaces in timely manner and at reduced cost.

  10. Segmentation and Quantitative Analysis of Epithelial Tissues.

    Science.gov (United States)

    Aigouy, Benoit; Umetsu, Daiki; Eaton, Suzanne

    2016-01-01

    Epithelia are tissues that regulate exchanges with the environment. They are very dynamic and can acquire virtually any shape; at the cellular level, they are composed of cells tightly connected by junctions. Most often epithelia are amenable to live imaging; however, the large number of cells composing an epithelium and the absence of informatics tools dedicated to epithelial analysis largely prevented tissue scale studies. Here we present Tissue Analyzer, a free tool that can be used to segment and analyze epithelial cells and monitor tissue dynamics.

  11. Differentiation of Campylobacter jejuni and Campylobacter coli Using Multiplex-PCR and High Resolution Melt Curve Analysis.

    Science.gov (United States)

    Banowary, Banya; Dang, Van Tuan; Sarker, Subir; Connolly, Joanne H; Chenu, Jeremy; Groves, Peter; Ayton, Michelle; Raidal, Shane; Devi, Aruna; Vanniasinkam, Thiru; Ghorashi, Seyed A

    2015-01-01

    Campylobacter spp. are important causes of bacterial gastroenteritis in humans in developed countries. Among Campylobacter spp. Campylobacter jejuni (C. jejuni) and C. coli are the most common causes of human infection. In this study, a multiplex PCR (mPCR) and high resolution melt (HRM) curve analysis were optimized for simultaneous detection and differentiation of C. jejuni and C. coli isolates. A segment of the hippuricase gene (hipO) of C. jejuni and putative aspartokinase (asp) gene of C. coli were amplified from 26 Campylobacter isolates and amplicons were subjected to HRM curve analysis. The mPCR-HRM was able to differentiate between C. jejuni and C. coli species. All DNA amplicons generated by mPCR were sequenced. Analysis of the nucleotide sequences from each isolate revealed that the HRM curves were correlated with the nucleotide sequences of the amplicons. Minor variation in melting point temperatures of C. coli or C. jejuni isolates was also observed and enabled some intraspecies differentiation between C. coli and/or C. jejuni isolates. The potential of PCR-HRM curve analysis for the detection and speciation of Campylobacter in additional human clinical specimens and chicken swab samples was also confirmed. The sensitivity and specificity of the test were found to be 100% and 92%, respectively. The results indicated that mPCR followed by HRM curve analysis provides a rapid (8 hours) technique for differentiation between C. jejuni and C. coli isolates.

  12. A Comparative Assessment of Greek Universities' Efficiency Using Quantitative Analysis

    Science.gov (United States)

    Katharaki, Maria; Katharakis, George

    2010-01-01

    In part due to the increased demand for higher education, typical evaluation frameworks for universities often address the key issue of available resource utilisation. This study seeks to estimate the efficiency of 20 public universities in Greece through quantitative analysis (including performance indicators, data envelopment analysis (DEA) and…

  13. A Comparative Assessment of Greek Universities' Efficiency Using Quantitative Analysis

    Science.gov (United States)

    Katharaki, Maria; Katharakis, George

    2010-01-01

    In part due to the increased demand for higher education, typical evaluation frameworks for universities often address the key issue of available resource utilisation. This study seeks to estimate the efficiency of 20 public universities in Greece through quantitative analysis (including performance indicators, data envelopment analysis (DEA) and…

  14. The multiplex dependency structure of financial markets

    CERN Document Server

    Musmeci, Nicoló; Aste, Tomaso; Di Matteo, Tiziana; Latora, Vito

    2016-01-01

    We propose here a multiplex network approach to investigate simultaneously different types of dependency in complex data sets. In particular, we consider multiplex networks made of four layers corresponding respectively to linear, non-linear, tail, and partial correlations among a set of financial time series. We construct the sparse graph on each layer using a standard network filtering procedure, and we then analyse the structural properties of the obtained multiplex networks. The study of the time evolution of the multiplex constructed from financial data uncovers important changes in intrinsically multiplex properties of the network, and such changes are associated with periods of financial stress. We observe that some features are unique to the multiplex structure and would not be visible otherwise by the separate analysis of the single-layer networks corresponding to each dependency measure.

  15. Optimized Protocol for Quantitative Multiple Reaction Monitoring-Based Proteomic Analysis of Formalin-Fixed, Paraffin-Embedded Tissues.

    Science.gov (United States)

    Kennedy, Jacob J; Whiteaker, Jeffrey R; Schoenherr, Regine M; Yan, Ping; Allison, Kimberly; Shipley, Melissa; Lerch, Melissa; Hoofnagle, Andrew N; Baird, Geoffrey Stuart; Paulovich, Amanda G

    2016-08-01

    Despite a clinical, economic, and regulatory imperative to develop companion diagnostics, precious few new biomarkers have been successfully translated into clinical use, due in part to inadequate protein assay technologies to support large-scale testing of hundreds of candidate biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues. Although the feasibility of using targeted, multiple reaction monitoring mass spectrometry (MRM-MS) for quantitative analyses of FFPE tissues has been demonstrated, protocols have not been systematically optimized for robust quantification across a large number of analytes, nor has the performance of peptide immuno-MRM been evaluated. To address this gap, we used a test battery approach coupled to MRM-MS with the addition of stable isotope-labeled standard peptides (targeting 512 analytes) to quantitatively evaluate the performance of three extraction protocols in combination with three trypsin digestion protocols (i.e., nine processes). A process based on RapiGest buffer extraction and urea-based digestion was identified to enable similar quantitation results from FFPE and frozen tissues. Using the optimized protocols for MRM-based analysis of FFPE tissues, median precision was 11.4% (across 249 analytes). There was excellent correlation between measurements made on matched FFPE and frozen tissues, both for direct MRM analysis (R(2) = 0.94) and immuno-MRM (R(2) = 0.89). The optimized process enables highly reproducible, multiplex, standardizable, quantitative MRM in archival tissue specimens.

  16. Coupled wave analysis of holographically induced transparency (HIT) generated by two multiplexed volume gratings.

    Science.gov (United States)

    Carretero, Luis; Blaya, Salvador; Acebal, Pablo; Fimia, Antonio; Madrigal, Roque; Murciano, Angel

    2011-04-11

    We present a holographic system that can be used to manipulate the group velocity of light pulses. The proposed structure is based on the multiplexing of two sequential holographic volume gratings, one in transmission and the other in reflection geometry, where one of the recording beams must be the same for both structures. As in other systems such as grating induced transparency (GIT) or coupled-resonator-induced transparency (CRIT), by using the coupled wave theory it is shown that this holographic structure represents a classical analogue of the electromagnetically induced transparency (EIT). Analytical expressions were obtained for the transmittance induced at the forbidden band (spectral hole) and conditions where the group velocity was slowed down were analyzed. Moreover, the propagation of Gaussian pulses is analyzed for this system by obtaining, after further approximations, analytical expressions for the distortion of the transmitted field. As a result, we demonstrate the conditions where the transmitted pulse is slowed down and its shape is only slightly distorted. Finally, by comparing with the exact solutions obtained, the range of validity of all the analytical formulae was verified, demonstrating that the error is very low.

  17. Analysis of Dystrophin Gene Deletions by Multiplex PCR in Moroccan Patients

    Directory of Open Access Journals (Sweden)

    Aziza Sbiti

    2002-01-01

    Full Text Available Duchenne and Becker muscular dystrophy (DMD and BMD are X-linked diseases resulting from a defect in the dystrophin gene located on Xp21. DMD is the most frequent neuromuscular disease in humans (1/3500 male newborn. Deletions in the dystrophin gene represent 65% of mutations in DMD/BMD patients. We have analyzed DNA from 72 Moroccan patients with DMD/BMD using the multiplex polymerase chain reaction (PCR to screen for exon deletions within the dystrophin gene, and to estimate the frequency of these abnormalities. We found dystrophin gene deletions in 37 cases. Therefore the frequency in Moroccan DMD/BMD patients is about 51.3%. All deletions were clustered in the two known hot-spots regions, and in 81% of cases deletions were detected in the region from exon 43 to exon 52. These findings are comparable to those reported in other studies. It is important to note that in our population, we can first search for deletions of DMD gene in the most frequently deleted exons determined by this study. This may facilitate the molecular diagnosis of DMD and BMD in our country.

  18. Improvement and Analysis of Carrier-Interferometry Orthogonal Frequency Division Multiplexing System

    Institute of Scientific and Technical Information of China (English)

    HE Jian-hui; QUAN Zi-yi; MEN Ai-dong

    2005-01-01

    This paper proposes to use Fast Fourier Transform (FFT)/Inverse Fast Fourier Transform (IFFT), instead of vector-matrix multiplication, to implement the spreading/despreading in Carrier-Interferometry Orthogonal Frequency Division Multiplexing (CI/OFDM) and Pseudo-Orthogonal Carrier-Interferometry OFDM (PO-CI/OFDM). That can improve the signal processing efficiency of CI/OFDM and PO-CI/OFDM systems by about 2N/log2N and 2N/(1+log2N) times respectively and dose not make any difference to the system function and performance. Moreover, the efficiency benefits will increase with the increase of the number of sub-carriers. In addition to that, we point out that the transmitter of CI/OFDM is actually technically equivalent to that of a single-carrier system with cyclic-prefix and the receiver of CI/OFDM is a typical OFDM receiver with CI despreading. Hence the low Peak-to-Average Power Ratio (PAPR) property and high anti-fading performance of CI/OFDM system can be well explained.

  19. Structural model analysis of multiple quantitative traits.

    Directory of Open Access Journals (Sweden)

    Renhua Li

    2006-07-01

    Full Text Available We introduce a method for the analysis of multilocus, multitrait genetic data that provides an intuitive and precise characterization of genetic architecture. We show that it is possible to infer the magnitude and direction of causal relationships among multiple correlated phenotypes and illustrate the technique using body composition and bone density data from mouse intercross populations. Using these techniques we are able to distinguish genetic loci that affect adiposity from those that affect overall body size and thus reveal a shortcoming of standardized measures such as body mass index that are widely used in obesity research. The identification of causal networks sheds light on the nature of genetic heterogeneity and pleiotropy in complex genetic systems.

  20. Quantitative Analysis of Seismicity in Iran

    Science.gov (United States)

    Raeesi, Mohammad; Zarifi, Zoya; Nilfouroushan, Faramarz; Boroujeni, Samar Amini; Tiampo, Kristy

    2017-03-01

    We use historical and recent major earthquakes and GPS geodetic data to compute seismic strain rate, geodetic slip deficit, static stress drop, the parameters of the magnitude-frequency distribution and geodetic strain rate in the Iranian Plateau to identify seismically mature fault segments and regions. Our analysis suggests that 11 fault segments are in the mature stage of the earthquake cycle, with the possibility of generating major earthquakes. These faults primarily are located in the north and the east of Iran. Four seismically mature regions in southern Iran with the potential for damaging strong earthquakes are also identified. We also delineate four additional fault segments in Iran that can generate major earthquakes without robust clues to their maturity.The most important fault segment in this study is the strike-slip system near the capital city of Tehran, with the potential to cause more than one million fatalities.

  1. Quantitative Analysis of Seismicity in Iran

    Science.gov (United States)

    Raeesi, Mohammad; Zarifi, Zoya; Nilfouroushan, Faramarz; Boroujeni, Samar Amini; Tiampo, Kristy

    2016-12-01

    We use historical and recent major earthquakes and GPS geodetic data to compute seismic strain rate, geodetic slip deficit, static stress drop, the parameters of the magnitude-frequency distribution and geodetic strain rate in the Iranian Plateau to identify seismically mature fault segments and regions. Our analysis suggests that 11 fault segments are in the mature stage of the earthquake cycle, with the possibility of generating major earthquakes. These faults primarily are located in the north and the east of Iran. Four seismically mature regions in southern Iran with the potential for damaging strong earthquakes are also identified. We also delineate four additional fault segments in Iran that can generate major earthquakes without robust clues to their maturity.The most important fault segment in this study is the strike-slip system near the capital city of Tehran, with the potential to cause more than one million fatalities.

  2. Setting up Multiplex Panels for Genetic Testing of Familial Hy¬pertrophic Cardiomyopathy Based on Linkage Analysis

    Directory of Open Access Journals (Sweden)

    Hoorieh SAGHAFI

    2016-03-01

    Full Text Available 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. Keywords: Cardiomyopathy, Hypertrophic, Genetic linkage, Diagnosis 

  3. Quantitative analysis of forest fire extinction efficiency

    Directory of Open Access Journals (Sweden)

    Miguel E. Castillo-Soto

    2015-08-01

    Full Text Available Aim of study: Evaluate the economic extinction efficiency of forest fires, based on the study of fire combat undertaken by aerial and terrestrial means. Area of study, materials and methods: Approximately 112,000 hectares in Chile. Records of 5,876 forest fires that occurred between 1998 and 2009 were analyzed. The area further provides a validation sector for results, by incorporating databases for the years 2010 and 2012. The criteria used for measuring extinction efficiency were economic value of forestry resources, Contraction Factor analysis and definition of the extinction costs function. Main results: It is possible to establish a relationship between burnt area, extinction costs and economic losses. The method proposed may be used and adapted to other fire situations, requiring unit costs for aerial and terrestrial operations, economic value of the property to be protected and speed attributes of fire spread in free advance. Research highlights: The determination of extinction efficiency in containment works of forest fires and potential projection of losses, different types of plant fuel and local conditions favoring the spread of fire broaden the admissible ranges of a, φ and Ce considerably.

  4. Uncertainty of quantitative microbiological methods of pharmaceutical analysis.

    Science.gov (United States)

    Gunar, O V; Sakhno, N G

    2015-12-30

    The total uncertainty of quantitative microbiological methods, used in pharmaceutical analysis, consists of several components. The analysis of the most important sources of the quantitative microbiological methods variability demonstrated no effect of culture media and plate-count techniques in the estimation of microbial count while the highly significant effect of other factors (type of microorganism, pharmaceutical product and individual reading and interpreting errors) was established. The most appropriate method of statistical analysis of such data was ANOVA which enabled not only the effect of individual factors to be estimated but also their interactions. Considering all the elements of uncertainty and combining them mathematically the combined relative uncertainty of the test results was estimated both for method of quantitative examination of non-sterile pharmaceuticals and microbial count technique without any product. These data did not exceed 35%, appropriated for a traditional plate count methods.

  5. Quantitative methods for the analysis of electron microscope images

    DEFF Research Database (Denmark)

    Skands, Peter Ulrik Vallø

    1996-01-01

    The topic of this thesis is an general introduction to quantitative methods for the analysis of digital microscope images. The images presented are primarily been acquired from Scanning Electron Microscopes (SEM) and interfermeter microscopes (IFM). The topic is approached though several examples...... foundation of the thesis fall in the areas of: 1) Mathematical Morphology; 2) Distance transforms and applications; and 3) Fractal geometry. Image analysis opens in general the possibility of a quantitative and statistical well founded measurement of digital microscope images. Herein lies also the conditions...

  6. Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an O-18-Labeled “Universal” Reference Sample

    Energy Technology Data Exchange (ETDEWEB)

    Qian, Weijun; Liu, Tao; Petyuk, Vladislav A.; Gritsenko, Marina A.; Petritis, Brianne O.; Polpitiya, Ashoka D.; Kaushal, Amit; Xiao, Wenzhong; Finnerty, Celeste C.; Jescheke, Marc G.; Jaitly, Navdeep; Monroe, Matthew E.; Moore, Ronald J.; Moldawer, Lyle L.; Davis, Ronald W.; Tompkins, Ronald G.; Hemdon, David N.; Camp, David G.; Smith, Richard D.

    2009-01-01

    Quantitative comparison of protein abundances across a relatively large number of patient samples is an important challenge for clinical proteomic applications. Herein we describe a dual-quantitation strategy that allows the simultaneous integration of complementary label-free and stable isotope labeling based approaches without increasing the number of LC-MS analyses. The approach utilizes a stable isotope 18O-labeled “universal” reference sample as a comprehensive set of internal standards spiked into each individually processed unlabeled patient sample. The quantitative data are based on both the direct 16O-MS intensities for label-free quantitation and the 16O/18O isotopic peptide pair ratios that compare each patient sample to the identical labeled reference. The effectiveness of this dual-quantitation approach for large scale quantitative proteomics is demonstrated by the application to a set of 38 clinical plasma samples from surviving and non-surviving severe burn patients. With the coupling of immunoaffinity depletion, cysteinyl-peptide enrichment based fractionation, high resolution LC-MS measurements, and the dual-quantitation approach, a total of 318 proteins were confidently quantified with at least two peptides and 263 proteins were quantified by both approaches. The strategy also enabled a direct comparison between the two approaches with the labeling approach showing significantly better precision in quantitation while the label-free approach resulted in more protein identifications. The relative abundance differences determined by the two approaches also show strong correlation. Finally, the dual-quantitation strategy allowed us to identify more candidate protein biomarkers, illustrating the complementary nature of the two quantitative methods.

  7. Issues in Quantitative Analysis of Ultraviolet Imager (UV) Data: Airglow

    Science.gov (United States)

    Germany, G. A.; Richards, P. G.; Spann, J. F.; Brittnacher, M. J.; Parks, G. K.

    1999-01-01

    The GGS Ultraviolet Imager (UVI) has proven to be especially valuable in correlative substorm, auroral morphology, and extended statistical studies of the auroral regions. Such studies are based on knowledge of the location, spatial, and temporal behavior of auroral emissions. More quantitative studies, based on absolute radiometric intensities from UVI images, require a more intimate knowledge of the instrument behavior and data processing requirements and are inherently more difficult than studies based on relative knowledge of the oval location. In this study, UVI airglow observations are analyzed and compared with model predictions to illustrate issues that arise in quantitative analysis of UVI images. These issues include instrument calibration, long term changes in sensitivity, and imager flat field response as well as proper background correction. Airglow emissions are chosen for this study because of their relatively straightforward modeling requirements and because of their implications for thermospheric compositional studies. The analysis issues discussed here, however, are identical to those faced in quantitative auroral studies.

  8. Issues in Quantitative Analysis of Ultraviolet Imager (UV) Data: Airglow

    Science.gov (United States)

    Germany, G. A.; Richards, P. G.; Spann, J. F.; Brittnacher, M. J.; Parks, G. K.

    1999-01-01

    The GGS Ultraviolet Imager (UVI) has proven to be especially valuable in correlative substorm, auroral morphology, and extended statistical studies of the auroral regions. Such studies are based on knowledge of the location, spatial, and temporal behavior of auroral emissions. More quantitative studies, based on absolute radiometric intensities from UVI images, require a more intimate knowledge of the instrument behavior and data processing requirements and are inherently more difficult than studies based on relative knowledge of the oval location. In this study, UVI airglow observations are analyzed and compared with model predictions to illustrate issues that arise in quantitative analysis of UVI images. These issues include instrument calibration, long term changes in sensitivity, and imager flat field response as well as proper background correction. Airglow emissions are chosen for this study because of their relatively straightforward modeling requirements and because of their implications for thermospheric compositional studies. The analysis issues discussed here, however, are identical to those faced in quantitative auroral studies.

  9. Use of stable isotope dimethyl labeling coupled to selected reaction monitoring to enhance throughput by multiplexing relative quantitation of targeted proteins.

    Science.gov (United States)

    Aye, Thin Thin; Low, Teck Yew; Bjørlykke, Yngvild; Barsnes, Harald; Heck, Albert J R; Berven, Frode S

    2012-06-05

    In this manuscript, we present a proof-of-concept study for targeted relative protein quantitation workflow using chemical labeling in the form of dimethylation, coupled with selected reaction monitoring (dimethyl-SRM). We first demonstrate close to complete isotope incorporation for all peptides tested. The accuracy, reproducibility, and linear dynamic range of quantitation are further assessed based on known ratios of nonhuman standard proteins spiked into human cerebrospinal fluid (CSF) as a model complex matrix. Quantitation reproducibility below 20% (CV < 20%) was obtained for analyte concentrations present at a dynamic range of 4 orders of magnitude lower than that of the background proteins. An error of less than 15% was observed when measuring the abundance of 44 out of 45 major human plasma proteins. Dimethyl-SRM was further examined by comparing the relative quantitation of eight proteins in human CSF with the relative quantitation obtained using synthetic heavy peptides coupled to stable isotope dilution-SRM (SID-SRM). Comparison between the two methods reveals that the correlation between dimethyl-SRM and SID-SRM is within 0.3-33% variation, demonstrating the accuracy of relative quantitation using dimethyl-SRM. Dimethyl labeling coupled with SRM provides a fast, convenient, and cost-effective alternative for relative quantitation of a large number of candidate proteins/peptides.

  10. Accuracy of Image Analysis in Quantitative Study of Cement Paste

    Directory of Open Access Journals (Sweden)

    Feng Shu-Xia

    2016-01-01

    Full Text Available Quantitative study on cement paste especially blended cement paste has been a hot and difficult issue over the years, and the technique of backscattered electron image analysis showed unique advantages in this field. This paper compared the test results of cement hydration degree, Ca(OH2 content and pore size distribution in pure pastes by image analysis and other methods. Then the accuracy of qualitative study by image analysis was analyzed. The results showed that image analysis technique had displayed higher accuracy in quantifying cement hydration degree and Ca(OH2 content than non-evaporable water test and thermal analysis respectively.

  11. Longitudinal study of a heteroplasmic 3460 Leber hereditary optic neuropathy family by multiplexed primer-extension analysis and nucleotide sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, S.S.; Fahy, E. [Applied Genetics, San Diego, CA (United States); Bodis-Wollner, I. [State Univ. of New York College of Optometry, New York, NY (United States)] [and others

    1996-02-01

    Nucleotide-sequencing and multiplexed primer-extension assays have been used to quantitate the mutant-allele frequency in 14 maternal relatives, spanning three generations, from a family that is heteroplasmic for the primary Leber hereditary optic neuropathy (LHON) mutation at nucleotide 3460 of the mitochondrial genome. There was excellent agreement between the values that were obtained with the two different methods. The longitudinal study shows that the mutant-allele frequency was constant within individual family members over a sampling period of 3.5 years. Second, although there was an overall increase in the mutant-allele frequency in successive generations, segregation in the direction of the mutant allele was not invariant, and there was one instance in which there was a significant decrease in the frequency from parent to offspring. From these two sets of results, and from previous studies of heteroplasmic LHON families, we conclude that there is no evidence for a marked selective pressure that determines the replication, segregation, or transmission of primary LHON mutations to white blood cells and platelets. Instead, the mtDNA molecules are most likely to replicate and segregate under conditions of random drift at the cellular level. Finally, the pattern of transmission in this maternal lineage is compatible with a developmental bottleneck model in which the number of mitochondrial units of segregation in the female germ line is relatively small in relation to the number of mtDNA molecules within a cell. However, this is not an invariant pattern for humans, and simple models of mitochondrial gene transmission are inappropriate at the present time. 37 refs., 4 figs., 1 tab.

  12. Correlation of maple sap composition with bacterial and fungal communities determined by multiplex automated ribosomal intergenic spacer analysis (MARISA).

    Science.gov (United States)

    Filteau, Marie; Lagacé, Luc; LaPointe, Gisèle; Roy, Denis

    2011-08-01

    During collection, maple sap is contaminated by bacteria and fungi that subsequently colonize the tubing system. The bacterial microbiota has been more characterized than the fungal microbiota, but the impact of both components on maple sap quality remains unclear. This study focused on identifying bacterial and fungal members of maple sap and correlating microbiota composition with maple sap properties. A multiplex automated ribosomal intergenic spacer analysis (MARISA) method was developed to presumptively identify bacterial and fungal members of maple sap samples collected from 19 production sites during the tapping period. Results indicate that the fungal community of maple sap is mainly composed of yeast related to Mrakia sp., Mrakiella sp., Guehomyces pullulans, Cryptococcus victoriae and Williopsis saturnus. Mrakia, Mrakiella and Guehomyces peaks were identified in samples of all production sites and can be considered dominant and stable members of the fungal microbiota of maple sap. A multivariate analysis based on MARISA profiles and maple sap chemical composition data showed correlations between Candida sake, Janthinobacterium lividum, Williopsis sp., Leuconostoc mesenteroides, Mrakia sp., Rhodococcus sp., Pseudomonas tolaasii, G. pullulans and maple sap composition at different flow periods. This study provides new insights on the relationship between microbial community and maple sap quality.

  13. Air segmented amplitude modulated multiplexed flow analysis with software-based phase recognition: determination of phosphate ion.

    Science.gov (United States)

    Ogusu, Takeshi; Uchimoto, Katsuya; Takeuchi, Masaki; Tanaka, Hideji

    2014-01-01

    Amplitude modulated multiplexed flow analysis (AMMFA) has been improved by introducing air segmentation and software-based phase recognition. Sample solutions, the flow rates of which are respectively varied at different frequencies, are merged. Air is introduced to the merged liquid stream in order to limit the dispersion of analytes within each liquid segment separated by air bubbles. The stream is led to a detector with no physical deaeration. Air signals are distinguished from liquid signals through the analysis of detector output signals, and are suppressed down to the level of liquid signals. Resulting signals are smoothed based on moving average computation. Thus processed signals are analyzed by fast Fourier transform. The analytes in the samples are respectively determined from the amplitudes of the corresponding wave components obtained. The developed system has been applied to the simultaneous determinations of phosphate ions in water samples by a Malachite Green method. The linearity of the analytical curve (0.0-31.0 μmol dm(-3)) is good (r(2)>0.999) and the detection limit (3.3 σ) at the modulation period of 30s is 0.52 μmol dm(-3). Good recoveries around 100% have been obtained for phosphate ions spiked into real water samples.

  14. Rapid multiplex analysis of lipid raft components with single-cell resolution.

    Science.gov (United States)

    Schatzlmaier, Philipp; Supper, Verena; Göschl, Lisa; Zwirzitz, Alexander; Eckerstorfer, Paul; Ellmeier, Wilfried; Huppa, Johannes B; Stockinger, Hannes

    2015-09-22

    Lipid rafts, a distinct class of highly dynamic cell membrane microdomains, are integral to cell homeostasis, differentiation, and signaling. However, their quantitative examination is challenging when working with rare cells, developmentally heterogeneous cell populations, or molecules that only associate weakly with lipid rafts. We present a fast biochemical method, which is based on lipid raft components associating with the nucleus upon partial lysis during centrifugation through nonionic detergent. Requiring little starting material or effort, our protocol enabled the multidimensional flow cytometric quantitation of raft-resident proteins with single-cell resolution, thereby assessing the membrane components from a few cells in complex cell populations, as well as their dynamics resulting from cell signaling, differentiation, or genetic mutation.

  15. Quantitative analysis of microtubule transport in growing nerve processes

    DEFF Research Database (Denmark)

    Ma*, Ytao; Shakiryanova*, Dinara; Vardya, Irina;

    2004-01-01

    the translocation of MT plus ends in the axonal shaft by expressing GFP-EB1 in Xenopus embryo neurons in culture. Formal quantitative analysis of MT assembly/disassembly indicated that none of the MTs in the axonal shaft were rapidly transported. Our results suggest that transport of axonal MTs is not required...

  16. Quantitative Analysis of Complex Tropical Forest Stands: A Review ...

    African Journals Online (AJOL)

    FIRST LADY

    The importance of data analysis in quantitative assessment of natural resources ... 350 km long extends from the eastern border of Sierra Leone all the way to. Ghana. .... consider whether data will likely fit the assumptions of a selected model. ... These tests are not alternatives to parametric tests, but rather are a means of.

  17. Analysis of Forecasting Sales By Using Quantitative And Qualitative Methods

    Directory of Open Access Journals (Sweden)

    B. Rama Sanjeeva Sresta,

    2016-09-01

    Full Text Available This paper focuses on analysis of forecasting sales using quantitative and qualitative methods. This forecast should be able to help create a model for measuring a successes and setting goals from financial and operational view points. The resulting model should tell if we have met our goals with respect to measures, targets, initiatives.

  18. Insights Into Quantitative Biology: analysis of cellular adaptation

    OpenAIRE

    Agoni, Valentina

    2013-01-01

    In the last years many powerful techniques have emerged to measure protein interactions as well as gene expression. Many progresses have been done since the introduction of these techniques but not toward quantitative analysis of data. In this paper we show how to study cellular adaptation and how to detect cellular subpopulations. Moreover we go deeper in analyzing signal transduction pathways dynamics.

  19. On-Orbit Quantitative Real-Time Gene Expression Analysis Using the Wetlab-2 System

    Science.gov (United States)

    Parra, Macarena; Jung, Jimmy; Almeida, Eduardo; Boone, Travis; Tran, Luan; Schonfeld, Julie

    2015-01-01

    NASA Ames Research Center's WetLab-2 Project enables on-orbit quantitative Reverse Transcriptase PCR (qRT-PCR) analysis without the need for sample return. The WetLab-2 system is capable of processing sample types ranging from microbial cultures to animal tissues dissected on-orbit. The project developed a RNA preparation module that can lyse cells and extract RNA of sufficient quality and quantity for use as templates in qRT-PCR reactions. Our protocol has the advantage of using non-toxic chemicals and does not require alcohols or other organics. The resulting RNA is dispensed into reaction tubes that contain all lyophilized reagents needed to perform qRT-PCR reactions. System operations require simple and limited crew actions including syringe pushes, valve turns and pipette dispenses. The project selected the Cepheid SmartCycler (TradeMark), a Commercial-Off-The-Shelf (COTS) qRT-PCR unit, because of its advantages including rugged modular design, low power consumption, rapid thermal ramp times and four-color multiplex detection. Single tube multiplex assays can be used to normalize for RNA concentration and integrity, and to study multiple genes of interest in each module. The WetLab-2 system can downlink data from the ISS to the ground after a completed run and uplink new thermal cycling programs. The ability to conduct qRT-PCR and generate results on-orbit is an important step towards utilizing the ISS as a National Laboratory facility. Specifically, the ability to get on-orbit data will provide investigators with the opportunity to adjust experimental parameters in real time without the need for sample return and re-flight. On orbit gene expression analysis can also eliminate the confounding effects on gene expression of reentry stresses and shock acting on live cells and organisms or the concern of RNA degradation of fixed samples and provide on-orbit gene expression benchmarking prior to sample return. Finally, the system can also be used for analysis of

  20. Quantitating the subtleties of microglial morphology with fractal analysis.

    Science.gov (United States)

    Karperien, Audrey; Ahammer, Helmut; Jelinek, Herbert F

    2013-01-01

    It is well established that microglial form and function are inextricably linked. In recent years, the traditional view that microglial form ranges between "ramified resting" and "activated amoeboid" has been emphasized through advancing imaging techniques that point to microglial form being highly dynamic even within the currently accepted morphological categories. Moreover, microglia adopt meaningful intermediate forms between categories, with considerable crossover in function and varying morphologies as they cycle, migrate, wave, phagocytose, and extend and retract fine and gross processes. From a quantitative perspective, it is problematic to measure such variability using traditional methods, but one way of quantitating such detail is through fractal analysis. The techniques of fractal analysis have been used for quantitating microglial morphology, to categorize gross differences but also to differentiate subtle differences (e.g., amongst ramified cells). Multifractal analysis in particular is one technique of fractal analysis that may be useful for identifying intermediate forms. Here we review current trends and methods of fractal analysis, focusing on box counting analysis, including lacunarity and multifractal analysis, as applied to microglial morphology.

  1. Quantitating the Subtleties of Microglial Morphology with Fractal Analysis

    Directory of Open Access Journals (Sweden)

    Audrey eKarperien

    2013-01-01

    Full Text Available It is well established that microglial form and function are inextricably linked. In recent years, the traditional view that microglial form ranges between "ramified resting" and "activated amoeboid" has been emphasized through advancing imaging techniques that point to microglial form being highly dynamic even within the currently accepted morphological categories. Moreover, microglia adopt meaningful intermediate forms between categories, with considerable crossover in function and varying morphologies as they cycle, migrate, wave, phagocytose, and extend and retract fine and gross processes. From a quantitative perspective, it is problematic to measure such variability using traditional methods, but one way of quantitating such detail is through fractal analysis. The techniques of fractal analysis have been used for quantitating microglial morphology, to categorize gross differences but also to differentiate subtle differences (e.g., amongst ramified cells. Multifractal analysis in particular is one technique of fractal analysis that may be useful for identifying intermediate forms. Here we review current trends and methods of fractal analysis, focusing on box counting analysis, including lacunarity and multifractal analysis, as applied to microglial morphology.

  2. Simultaneous confirmatory analysis of different transgenic maize (zea mays) lines using multiplex polymerase chain reaction-restriction analysis and capillary gel electrophoresis with laser induced fluorescence detection.

    Science.gov (United States)

    García-Cañas, Virginia; Cifuentes, Alejandro

    2008-09-24

    A novel analytical procedure based on the combination of multiplex PCR, restriction analysis, and CGE-LIF to unambiguosly and simultaneously confirm the presence of multiple lines of genetically modified corn is proposed. This methodology is based on the amplification of event-specific DNA regions by multiplex PCR using 6-FAM-labeled primers. Subsequently, PCR products are digested by a mixture containing specific restriction endonucleases. Thus, restriction endonucleases selectively recognize DNA target sequences contained in the PCR products and cleave the double-stranded DNA at a given cleavage site. Next, the restriction digest is analyzed by CGE-LIF corroborating the length of the expected restriction fragments, confirming (or not) the existence of GMOs. For accurate size determination of the DNA fragments by CGE-LIF a special standard DNA mixture was produced in this laboratory for calibration. The suitability of this mixture for size determination of labeled DNA fragments is also demonstrated. The usefulness of the proposed methodology is demonstrated through the simultaneous detection and confirmatory analysis of samples containing 0.5% of GA21 and MON863 maize plus an endogenous gene of maize as control.

  3. Quantitative transverse flow assessment using OCT speckle decorrelation analysis

    Science.gov (United States)

    Liu, Xuan; Huang, Yong; Ramella-Roman, Jessica C.; Kang, Jin U.

    2013-03-01

    In this study, we demonstrate the use of inter-Ascan speckle decorrelation analysis of optical coherence tomography (OCT) to assess fluid flow. This method allows quantitative measurement of fluid flow in a plane normal to the scanning beam. To validate this method, OCT images were obtained from a micro fluid channel with bovine milk flowing at different speeds. We also imaged a blood vessel from in vivo animal models and performed speckle analysis to asses blood flow.

  4. Quantitative numerical analysis of transient IR-experiments on buildings

    Science.gov (United States)

    Maierhofer, Ch.; Wiggenhauser, H.; Brink, A.; Röllig, M.

    2004-12-01

    Impulse-thermography has been established as a fast and reliable tool in many areas of non-destructive testing. In recent years several investigations have been done to apply active thermography to civil engineering. For quantitative investigations in this area of application, finite difference calculations have been performed for systematic studies on the influence of environmental conditions, heating power and time, defect depth and size and thermal properties of the bulk material (concrete). The comparison of simulated and experimental data enables the quantitative analysis of defects.

  5. Quantitative analysis of culture using millions of digitized books.

    Science.gov (United States)

    Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva Presser; Veres, Adrian; Gray, Matthew K; Pickett, Joseph P; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A; Aiden, Erez Lieberman

    2011-01-14

    We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of 'culturomics,' focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. Culturomics extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities.

  6. Quantitative analysis of culture using millions of digitized books

    Science.gov (United States)

    Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva P.; Veres, Adrian; Gray, Matthew K.; Pickett, Joseph P.; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A.; Aiden, Erez Lieberman

    2011-01-01

    We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of ‘culturomics’, focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. ‘Culturomics’ extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities. PMID:21163965

  7. Spotsizer: High-throughput quantitative analysis of microbial growth

    Science.gov (United States)

    Jeffares, Daniel C.; Arzhaeva, Yulia; Bähler, Jürg

    2017-01-01

    Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although computational tools for acquiring quantitative measurements of microbial colonies have been developed, their utility can be compromised by inflexible input image requirements, non-trivial installation procedures, or complicated operation. Here, we present the Spotsizer software tool for automated colony size measurements in images of robotically arrayed microbial colonies. Spotsizer features a convenient graphical user interface (GUI), has both single-image and batch-processing capabilities, and works with multiple input image formats and different colony grid types. We demonstrate how Spotsizer can be used for high-throughput quantitative analysis of fission yeast growth. The user-friendly Spotsizer tool provides rapid, accurate, and robust quantitative analyses of microbial growth in a high-throughput format. Spotsizer is freely available at https://data.csiro.au/dap/landingpage?pid=csiro:15330 under a proprietary CSIRO license. PMID:27712582

  8. A strategy to apply quantitative epistasis analysis on developmental traits.

    Science.gov (United States)

    Labocha, Marta K; Yuan, Wang; Aleman-Meza, Boanerges; Zhong, Weiwei

    2017-05-15

    Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits. In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement. Using two different C. elegans developmental phenotypes, body length and sex ratio, as examples, we showed that this method could accommodate various metazoan phenotypes with performances comparable to those methods in single cell growth studies. Comparing with qualitative observations, this method of quantitative epistasis enabled detection of new interactions involving subtle phenotypes. For example, several sex-ratio genes were found to interact with brc-1 and brd-1, the orthologs of the human breast cancer genes BRCA1 and BARD1, respectively. We confirmed the brc-1 interactions with the following genes in DNA damage response: C34F6.1, him-3 (ortholog of HORMAD1, HORMAD2), sdc-1, and set-2 (ortholog of SETD1A, SETD1B, KMT2C, KMT2D), validating the effectiveness of our method in detecting genetic interactions. We developed a reliable, high-throughput method for quantitative epistasis analysis of developmental phenotypes.

  9. Molecular differentiation of Opisthorchis viverrini and Clonorchis sinensis eggs by multiplex real-time PCR with high resolution melting analysis.

    Science.gov (United States)

    Kaewkong, Worasak; Intapan, Pewpan M; Sanpool, Oranuch; Janwan, Penchom; Thanchomnang, Tongjit; Laummaunwai, Porntip; Lulitanond, Viraphong; Doanh, Pham Ngoc; Maleewong, Wanchai

    2013-12-01

    Opisthorchis viverrini and Clonorchis sinensis are parasites known to be carcinogenic and causative agents of cholangiocarcinoma in Asia. The standard method for diagnosis for those parasite infections is stool examination to detect parasite eggs. However, the method has low sensitivity, and eggs of O. viverrini and C. sinensis are difficult to distinguish from each other and from those of some other trematodes. Here, we report a multiplex real-time PCR coupled with high resolution melting (HRM) analysis for the differentiation of O. viverrini and C. sinensis eggs in fecal samples. Using 2 pairs of species-specific primers, DNA sequences from a portion of the mitochondrial NADH dehydrogenase subunit 2 (nad 2) gene, were amplified to generate 209 and 165 bp products for O. viverrini and C. sinensis, respectively. The distinct characteristics of HRM patterns were analyzed, and the melting temperatures peaked at 82.4±0.09℃ and 85.9±0.08℃ for O. viverrini and C. sinensis, respectively. This technique was able to detect as few as 1 egg of O. viverrini and 2 eggs of C. sinensis in a 150 mg fecal sample, which is equivalent to 7 and 14 eggs per gram of feces, respectively. The method is species-specific, rapid, simple, and does not require fluorescent probes or post-PCR processing for discrimination of eggs of the 2 species. It offers a new tool for differentiation and detection of Asian liver fluke infections in stool specimens.

  10. Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an 18O-Labeled “Universal” Reference Sample

    Science.gov (United States)

    Qian, Wei-Jun; Liu, Tao; Petyuk, Vladislav A.; Gritsenko, Marina A.; Petritis, Brianne O.; Polpitiya, Ashoka D.; Kaushal, Amit; Xiao, Wenzhong; Finnerty, Celeste C.; Jeschke, Marc G.; Jaitly, Navdeep; Monroe, Matthew E.; Moore, Ronald J.; Moldawer, Lyle L.; Davis, Ronald W.; Tompkins, Ronald G.; Herndon, David N.; Camp, David G.; Smith, Richard D.

    2009-01-01

    The quantitative comparison of protein abundances across a large number of biological or patient samples represents an important proteomics challenge that needs to be addressed for proteomics discovery applications. Herein, we describe a strategy that incorporates a stable isotope 18O-labeled ″universal″ reference sample as a comprehensive set of internal standards for analyzing large sample sets quantitatively. As a pooled sample, the 18O-labeled ″universal″ reference sample is spiked into each individually processed unlabeled biological sample and the peptide/protein abundances are quantified based on 16O/18O isotopic peptide pair abundance ratios that compare each unlabeled sample to the identical reference sample. This approach also allows for the direct application of label-free quantitation across the sample set simultaneously along with the labeling-approach (i.e., dual-quantitation) since each biological sample is unlabeled except for the labeled reference sample that is used as internal standards. The effectiveness of this approach for large-scale quantitative proteomics is demonstrated by its application to a set of 18 plasma samples from severe burn patients. When immunoaffinity depletion and cysteinyl-peptide enrichment-based fractionation with high resolution LC-MS measurements were combined, a total of 312 plasma proteins were confidently identified and quantified with a minimum of two unique peptides per protein. The isotope labeling data was directly compared with the label-free 16O-MS intensity data extracted from the same data sets. The results showed that the 18O reference-based labeling approach had significantly better quantitative precision compared to the label-free approach. The relative abundance differences determined by the two approaches also displayed strong correlation, illustrating the complementary nature of the two quantitative methods. The simplicity of including the 18O-reference for accurate quantitation makes this

  11. Quantitative nanoscale analysis in 3D using electron tomography

    Energy Technology Data Exchange (ETDEWEB)

    Kuebel, Christian [Karlsruhe Institute of Technology, INT, 76344 Eggenstein-Leopoldshafen (Germany)

    2011-07-01

    State-of-the-art electron tomography has been established as a powerful tool to image complex structures with nanometer resolution in 3D. Especially STEM tomography is used extensively in materials science in such diverse areas as catalysis, semiconductor materials, and polymer composites mainly providing qualitative information on morphology, shape and distribution of materials. However, for an increasing number of studies quantitative information, e.g. surface area, fractal dimensions, particle distribution or porosity are needed. A quantitative analysis is typically performed after segmenting the tomographic data, which is one of the main sources of error for the quantification. In addition to noise, systematic errors due to the missing wedge and due to artifacts from the reconstruction algorithm itself are responsible for these segmentation errors and improved algorithms are needed. This presentation will provide an overview of the possibilities and limitations of quantitative nanoscale analysis by electron tomography. Using catalysts and nano composites as applications examples, intensities and intensity variations observed for the 3D volume reconstructed by WBP and SIRT will be quantitatively compared to alternative reconstruction algorithms; implications for quantification of electron (or X-ray) tomographic data will be discussed and illustrated for quantification of particle size distributions, particle correlations, surface area, and fractal dimensions in 3D.

  12. Evaluation and Design Space Exploration of a Time-Division Multiplexed NoC on FPGA for Image Analysis Applications

    Directory of Open Access Journals (Sweden)

    Houzet Dominique

    2009-01-01

    Full Text Available Abstract The aim of this paper is to present an adaptable Fat Tree NoC architecture for Field Programmable Gate Array (FPGA designed for image analysis applications. Traditional Network on Chip (NoC is not optimal for dataflow applications with large amount of data. On the opposite, point-to-point communications are designed from the algorithm requirements but they are expensives in terms of resource and wire. We propose a dedicated communication architecture for image analysis algorithms. This communication mechanism is a generic NoC infrastructure dedicated to dataflow image processing applications, mixing circuit-switching and packet-switching communications. The complete architecture integrates two dedicated communication architectures and reusable IP blocks. Communications are based on the NoC concept to support the high bandwidth required for a large number and type of data. For data communication inside the architecture, an efficient time-division multiplexed (TDM architecture is proposed. This NoC uses a Fat Tree (FT topology with Virtual Channels (VCs and flit packet-switching with fixed routes. Two versions of the NoC are presented in this paper. The results of their implementations and their Design Space Exploration (DSE on Altera Stratix II are analyzed and compared with a point-to-point communication and illustrated with a multispectral image application. Results show that a point-to-point communication scheme is not efficient for large amount of multispectral image data communications. An NoC architecture uses only 10% of the memory blocks required for a point-to-point architecture but seven times more logic elements. This resource allocation is more adapted to image analysis algorithms as memory elements are a critical point in embedded architectures. An FT NoC-based communication scheme for data transfers provides a more appropriate solution for resource allocation.

  13. Evaluation and Design Space Exploration of a Time-Division Multiplexed NoC on FPGA for Image Analysis Applications

    Directory of Open Access Journals (Sweden)

    Dominique Houzet

    2009-01-01

    Full Text Available The aim of this paper is to present an adaptable Fat Tree NoC architecture for Field Programmable Gate Array (FPGA designed for image analysis applications. Traditional Network on Chip (NoC is not optimal for dataflow applications with large amount of data. On the opposite, point-to-point communications are designed from the algorithm requirements but they are expensives in terms of resource and wire. We propose a dedicated communication architecture for image analysis algorithms. This communication mechanism is a generic NoC infrastructure dedicated to dataflow image processing applications, mixing circuit-switching and packet-switching communications. The complete architecture integrates two dedicated communication architectures and reusable IP blocks. Communications are based on the NoC concept to support the high bandwidth required for a large number and type of data. For data communication inside the architecture, an efficient time-division multiplexed (TDM architecture is proposed. This NoC uses a Fat Tree (FT topology with Virtual Channels (VCs and flit packet-switching with fixed routes. Two versions of the NoC are presented in this paper. The results of their implementations and their Design Space Exploration (DSE on Altera Stratix II are analyzed and compared with a point-to-point communication and illustrated with a multispectral image application. Results show that a point-to-point communication scheme is not efficient for large amount of multispectral image data communications. An NoC architecture uses only 10% of the memory blocks required for a point-to-point architecture but seven times more logic elements. This resource allocation is more adapted to image analysis algorithms as memory elements are a critical point in embedded architectures. An FT NoC-based communication scheme for data transfers provides a more appropriate solution for resource allocation.

  14. Some selected quantitative methods of thermal image analysis in Matlab.

    Science.gov (United States)

    Koprowski, Robert

    2016-05-01

    The paper presents a new algorithm based on some selected automatic quantitative methods for analysing thermal images. It shows the practical implementation of these image analysis methods in Matlab. It enables to perform fully automated and reproducible measurements of selected parameters in thermal images. The paper also shows two examples of the use of the proposed image analysis methods for the area of ​​the skin of a human foot and face. The full source code of the developed application is also provided as an attachment. The main window of the program during dynamic analysis of the foot thermal image.

  15. Data from quantitative label free proteomics analysis of rat spleen

    Directory of Open Access Journals (Sweden)

    Khadar Dudekula

    2016-09-01

    Full Text Available The dataset presented in this work has been obtained using a label-free quantitative proteomic analysis of rat spleen. A robust method for extraction of proteins from rat spleen tissue and LC-MS-MS analysis was developed using a urea and SDS-based buffer. Different fractionation methods were compared. A total of 3484 different proteins were identified from the pool of all experiments run in this study (a total of 2460 proteins with at least two peptides. A total of 1822 proteins were identified from nine non-fractionated pulse gels, 2288 proteins and 2864 proteins were identified by SDS-PAGE fractionation into three and five fractions respectively. The proteomics data are deposited in ProteomeXchange Consortium via PRIDE PXD003520, Progenesis and Maxquant output are presented in the supported information. The generated list of proteins under different regimes of fractionation allow assessing the nature of the identified proteins; variability in the quantitative analysis associated with the different sampling strategy and allow defining a proper number of replicates for future quantitative analysis.

  16. Data from quantitative label free proteomics analysis of rat spleen.

    Science.gov (United States)

    Dudekula, Khadar; Le Bihan, Thierry

    2016-09-01

    The dataset presented in this work has been obtained using a label-free quantitative proteomic analysis of rat spleen. A robust method for extraction of proteins from rat spleen tissue and LC-MS-MS analysis was developed using a urea and SDS-based buffer. Different fractionation methods were compared. A total of 3484 different proteins were identified from the pool of all experiments run in this study (a total of 2460 proteins with at least two peptides). A total of 1822 proteins were identified from nine non-fractionated pulse gels, 2288 proteins and 2864 proteins were identified by SDS-PAGE fractionation into three and five fractions respectively. The proteomics data are deposited in ProteomeXchange Consortium via PRIDE PXD003520, Progenesis and Maxquant output are presented in the supported information. The generated list of proteins under different regimes of fractionation allow assessing the nature of the identified proteins; variability in the quantitative analysis associated with the different sampling strategy and allow defining a proper number of replicates for future quantitative analysis.

  17. An improved quantitative analysis method for plant cortical microtubules.

    Science.gov (United States)

    Lu, Yi; Huang, Chenyang; Wang, Jia; Shang, Peng

    2014-01-01

    The arrangement of plant cortical microtubules can reflect the physiological state of cells. However, little attention has been paid to the image quantitative analysis of plant cortical microtubules so far. In this paper, Bidimensional Empirical Mode Decomposition (BEMD) algorithm was applied in the image preprocessing of the original microtubule image. And then Intrinsic Mode Function 1 (IMF1) image obtained by decomposition was selected to do the texture analysis based on Grey-Level Cooccurrence Matrix (GLCM) algorithm. Meanwhile, in order to further verify its reliability, the proposed texture analysis method was utilized to distinguish different images of Arabidopsis microtubules. The results showed that the effect of BEMD algorithm on edge preserving accompanied with noise reduction was positive, and the geometrical characteristic of the texture was obvious. Four texture parameters extracted by GLCM perfectly reflected the different arrangements between the two images of cortical microtubules. In summary, the results indicate that this method is feasible and effective for the image quantitative analysis of plant cortical microtubules. It not only provides a new quantitative approach for the comprehensive study of the role played by microtubules in cell life activities but also supplies references for other similar studies.

  18. An Improved Quantitative Analysis Method for Plant Cortical Microtubules

    Directory of Open Access Journals (Sweden)

    Yi Lu

    2014-01-01

    Full Text Available The arrangement of plant cortical microtubules can reflect the physiological state of cells. However, little attention has been paid to the image quantitative analysis of plant cortical microtubules so far. In this paper, Bidimensional Empirical Mode Decomposition (BEMD algorithm was applied in the image preprocessing of the original microtubule image. And then Intrinsic Mode Function 1 (IMF1 image obtained by decomposition was selected to do the texture analysis based on Grey-Level Cooccurrence Matrix (GLCM algorithm. Meanwhile, in order to further verify its reliability, the proposed texture analysis method was utilized to distinguish different images of Arabidopsis microtubules. The results showed that the effect of BEMD algorithm on edge preserving accompanied with noise reduction was positive, and the geometrical characteristic of the texture was obvious. Four texture parameters extracted by GLCM perfectly reflected the different arrangements between the two images of cortical microtubules. In summary, the results indicate that this method is feasible and effective for the image quantitative analysis of plant cortical microtubules. It not only provides a new quantitative approach for the comprehensive study of the role played by microtubules in cell life activities but also supplies references for other similar studies.

  19. Quantitative risk analysis of oil storage facilities in seismic areas.

    Science.gov (United States)

    Fabbrocino, Giovanni; Iervolino, Iunio; Orlando, Francesca; Salzano, Ernesto

    2005-08-31

    Quantitative risk analysis (QRA) of industrial facilities has to take into account multiple hazards threatening critical equipment. Nevertheless, engineering procedures able to evaluate quantitatively the effect of seismic action are not well established. Indeed, relevant industrial accidents may be triggered by loss of containment following ground shaking or other relevant natural hazards, either directly or through cascade effects ('domino effects'). The issue of integrating structural seismic risk into quantitative probabilistic seismic risk analysis (QpsRA) is addressed in this paper by a representative study case regarding an oil storage plant with a number of atmospheric steel tanks containing flammable substances. Empirical seismic fragility curves and probit functions, properly defined both for building-like and non building-like industrial components, have been crossed with outcomes of probabilistic seismic hazard analysis (PSHA) for a test site located in south Italy. Once the seismic failure probabilities have been quantified, consequence analysis has been performed for those events which may be triggered by the loss of containment following seismic action. Results are combined by means of a specific developed code in terms of local risk contour plots, i.e. the contour line for the probability of fatal injures at any point (x, y) in the analysed area. Finally, a comparison with QRA obtained by considering only process-related top events is reported for reference.

  20. A multiplex fluorescent quantitative PCR method for detection of three rodent-carrying pathogens%多重荧光定量PCR检测鼠感染3种病原体的方法

    Institute of Scientific and Technical Information of China (English)

    吉尚志; 杨宇; 王静; 王振东; 纪海波

    2011-01-01

    目的 建立多重荧光定量PCR快速检测以鼠为宿主伯氏疏螺旋体、弓形虫和恶性疟原虫的方法,对预防3种病原体引发的疫情具有重要意义.方法 通过设计特异性引物和探针,扩增伯氏疏螺旋体23S rRNA基因,弓形虫的B1基因和恶性疟原虫的SSU基因,采用倍比梯度稀释法检测该体系的灵敏度,以另外8种以鼠为宿主的致病菌评价检测体系的特异性;建立了同时感染3种病原体的鼠全血模拟样本检测试验,以验证方法的适用性.结果 建立自鼠血液模拟样本中同时检测伯氏疏螺旋体、弓形虫和恶性疟原虫的多重荧光定量PCR方法,检测3种病原体的灵敏度分别为5.5、12.8、17.2拷贝/μl,特异性强.结论 建立了多重荧光定量PCR检测伯氏疏螺旋体、弓形虫和恶性疟原虫方法,缩短了检测时间,在疾病防控等方面有很好的应用前景.%Objective To develop a multiplex fluorescenct quantitative PCR assay for rapid and simultaneous detection of Borrelia burgdorferi, Toxoplasma gondii and Plasmodium falciparm carried by rodents. Methods Specific primers and probes were designed to amplify the 23S rRNA gene of B. Burgdorferi, the B1 gene of T. Gondii and the SSU gene of P. Falciparm. The sensitivity of the assay was detected by the fold dilution method. The other eight strains of rodent-bome bacteria were used to examine the specificity of the assay. The method was evaluated to detect B. Burgdorferi, T. Gondii and P. Falciparm simultaneously in mice blood. Results A highly sensitive and specific multiplex fluorescent quantitative PCR assay was established for detection of B. Burgdorferi, T. Gondii and P. Falciparm. The sensitivity was 5.5 copies/u,l for B. Burgdorferi, 12.8 copies/u,l for T. Gondii and 17.2 copies/|xl for P. Falciparm. Conclusion A multiplex fluorescent quantitative PCR assay was developed for detection of B. Burgdorferi, T. Gondii and P. Falciparm, significantly reducing the time

  1. Multiplexed Colorimetric Solid-Phase Extraction

    Science.gov (United States)

    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).

  2. Qualitative and quantitative stability analysis of penta-rhythmic circuits

    Science.gov (United States)

    Schwabedal, Justus T. C.; Knapper, Drake E.; Shilnikov, Andrey L.

    2016-12-01

    Inhibitory circuits of relaxation oscillators are often-used models for dynamics of biological networks. We present a qualitative and quantitative stability analysis of such a circuit constituted by three generic oscillators (of a Fitzhugh-Nagumo type) as its nodes coupled reciprocally. Depending on inhibitory strengths, and parameters of individual oscillators, the circuit exhibits polyrhythmicity of up to five simultaneously stable rhythms. With methods of bifurcation analysis and phase reduction, we investigate qualitative changes in stability of these circuit rhythms for a wide range of parameters. Furthermore, we quantify robustness of the rhythms maintained under random perturbations by monitoring phase diffusion in the circuit. Our findings allow us to describe how circuit dynamics relate to dynamics of individual nodes. We also find that quantitative and qualitative stability properties of polyrhythmicity do not always align.

  3. Quantitative analysis of myocardial tissue with digital autofluorescence microscopy

    DEFF Research Database (Denmark)

    Jensen, Thomas; Holten-Rossing, Henrik; Svendsen, Ida M H;

    2016-01-01

    BACKGROUND: The opportunity offered by whole slide scanners of automated histological analysis implies an ever increasing importance of digital pathology. To go beyond the importance of conventional pathology, however, digital pathology may need a basic histological starting point similar...... to that of hematoxylin and eosin staining in conventional pathology. This study presents an automated fluorescence-based microscopy approach providing highly detailed morphological data from unstained microsections. This data may provide a basic histological starting point from which further digital analysis including...... staining may benefit. METHODS: This study explores the inherent tissue fluorescence, also known as autofluorescence, as a mean to quantitate cardiac tissue components in histological microsections. Data acquisition using a commercially available whole slide scanner and an image-based quantitation algorithm...

  4. Quantitative and qualitative analysis and interpretation of CT perfusion imaging.

    Science.gov (United States)

    Valdiviezo, Carolina; Ambrose, Marietta; Mehra, Vishal; Lardo, Albert C; Lima, Joao A C; George, Richard T

    2010-12-01

    Coronary artery disease (CAD) remains the leading cause of death in the United States. Rest and stress myocardial perfusion imaging has an important role in the non-invasive risk stratification of patients with CAD. However, diagnostic accuracies have been limited, which has led to the development of several myocardial perfusion imaging techniques. Among them, myocardial computed tomography perfusion imaging (CTP) is especially interesting as it has the unique capability of providing anatomic- as well as coronary stenosis-related functional data when combined with computed tomography angiography (CTA). The primary aim of this article is to review the qualitative, semi-quantitative, and quantitative analysis approaches to CTP imaging. In doing so, we will describe the image data required for each analysis and discuss the advantages and disadvantages of each approach.

  5. A fast and reliable readout method for quantitative analysis of surface-enhanced Raman scattering nanoprobes on chip surface.

    Science.gov (United States)

    Chang, Hyejin; Kang, Homan; Jeong, Sinyoung; Ko, Eunbyeol; Lee, Yoon-Sik; Lee, Ho-Young; Jeong, Dae Hong

    2015-05-01

    Surface-enhanced Raman scattering techniques have been widely used for bioanalysis due to its high sensitivity and multiplex capacity. However, the point-scanning method using a micro-Raman system, which is the most common method in the literature, has a disadvantage of extremely long measurement time for on-chip immunoassay adopting a large chip area of approximately 1-mm scale and confocal beam point of ca. 1-μm size. Alternative methods such as sampled spot scan with high confocality and large-area scan method with enlarged field of view and low confocality have been utilized in order to minimize the measurement time practically. In this study, we analyzed the two methods in respect of signal-to-noise ratio and sampling-led signal fluctuations to obtain insights into a fast and reliable readout strategy. On this basis, we proposed a methodology for fast and reliable quantitative measurement of the whole chip area. The proposed method adopted a raster scan covering a full area of 100 μm × 100 μm region as a proof-of-concept experiment while accumulating signals in the CCD detector for single spectrum per frame. One single scan with 10 s over 100 μm × 100 μm area yielded much higher sensitivity compared to sampled spot scanning measurements and no signal fluctuations attributed to sampled spot scan. This readout method is able to serve as one of key technologies that will bring quantitative multiplexed detection and analysis into practice.

  6. A fast and reliable readout method for quantitative analysis of surface-enhanced Raman scattering nanoprobes on chip surface

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Hyejin; Jeong, Sinyoung; Ko, Eunbyeol; Jeong, Dae Hong, E-mail: yslee@snu.ac.kr, E-mail: debobkr@gmail.com, E-mail: jeongdh@snu.ac.kr [Department of Chemistry Education, Seoul National University, Seoul 151-742 (Korea, Republic of); Kang, Homan [Interdisciplinary Program in Nano-Science and Technology, Seoul National University, Seoul 151-742 (Korea, Republic of); Lee, Yoon-Sik, E-mail: yslee@snu.ac.kr, E-mail: debobkr@gmail.com, E-mail: jeongdh@snu.ac.kr [Interdisciplinary Program in Nano-Science and Technology, Seoul National University, Seoul 151-742 (Korea, Republic of); School of Chemical and Biological Engineering, Seoul National University, Seoul 151-742 (Korea, Republic of); Lee, Ho-Young, E-mail: yslee@snu.ac.kr, E-mail: debobkr@gmail.com, E-mail: jeongdh@snu.ac.kr [Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seongnam 463-707 (Korea, Republic of)

    2015-05-15

    Surface-enhanced Raman scattering techniques have been widely used for bioanalysis due to its high sensitivity and multiplex capacity. However, the point-scanning method using a micro-Raman system, which is the most common method in the literature, has a disadvantage of extremely long measurement time for on-chip immunoassay adopting a large chip area of approximately 1-mm scale and confocal beam point of ca. 1-μm size. Alternative methods such as sampled spot scan with high confocality and large-area scan method with enlarged field of view and low confocality have been utilized in order to minimize the measurement time practically. In this study, we analyzed the two methods in respect of signal-to-noise ratio and sampling-led signal fluctuations to obtain insights into a fast and reliable readout strategy. On this basis, we proposed a methodology for fast and reliable quantitative measurement of the whole chip area. The proposed method adopted a raster scan covering a full area of 100 μm × 100 μm region as a proof-of-concept experiment while accumulating signals in the CCD detector for single spectrum per frame. One single scan with 10 s over 100 μm × 100 μm area yielded much higher sensitivity compared to sampled spot scanning measurements and no signal fluctuations attributed to sampled spot scan. This readout method is able to serve as one of key technologies that will bring quantitative multiplexed detection and analysis into practice.

  7. QuantUM: Quantitative Safety Analysis of UML Models

    Directory of Open Access Journals (Sweden)

    Florian Leitner-Fischer

    2011-07-01

    Full Text Available When developing a safety-critical system it is essential to obtain an assessment of different design alternatives. In particular, an early safety assessment of the architectural design of a system is desirable. In spite of the plethora of available formal quantitative analysis methods it is still difficult for software and system architects to integrate these techniques into their every day work. This is mainly due to the lack of methods that can be directly applied to architecture level models, for instance given as UML diagrams. Also, it is necessary that the description methods used do not require a profound knowledge of formal methods. Our approach bridges this gap and improves the integration of quantitative safety analysis methods into the development process. All inputs of the analysis are specified at the level of a UML model. This model is then automatically translated into the analysis model, and the results of the analysis are consequently represented on the level of the UML model. Thus the analysis model and the formal methods used during the analysis are hidden from the user. We illustrate the usefulness of our approach using an industrial strength case study.

  8. Country Risk Analysis: A Survey of the Quantitative Methods

    OpenAIRE

    Hiranya K Nath

    2008-01-01

    With globalization and financial integration, there has been rapid growth of international lending and foreign direct investment (FDI). In view of this emerging trend, country risk analysis has become extremely important for the international creditors and investors. This paper briefly discusses the concepts and definitions, and presents a survey of the quantitative methods that are used to address various issues related to country risk. It also gives a summary review of selected empirical st...

  9. Quantitative Proteomic Approaches for Analysis of Protein S-Nitrosylation.

    Science.gov (United States)

    Qu, Zhe; Greenlief, C Michael; Gu, Zezong

    2016-01-01

    S-Nitrosylation is a redox-based post-translational modification of a protein in response to nitric oxide (NO) signaling, and it participates in a variety of processes in diverse biological systems. The significance of this type of protein modification in health and diseases is increasingly recognized. In the central nervous system, aberrant S-nitrosylation, due to excessive NO production, is known to cause protein misfolding, mitochondrial dysfunction, transcriptional dysregulation, and neuronal death. This leads to an altered physiological state and consequently contributes to pathogenesis of neurodegenerative disorders. To date, much effort has been made to understand the mechanisms underlying protein S-nitrosylation, and several approaches have been developed to unveil S-nitrosylated proteins from different organisms. Interest in determining the dynamic changes of protein S-nitrosylation under different physiological and pathophysiological conditions has underscored the need for the development of quantitative proteomic approaches. Currently, both gel-based and gel-free mass spectrometry-based quantitative methods are widely used, and they each have advantages and disadvantages but may also be used together to produce complementary data. This review evaluates current available quantitative proteomic techniques for the analysis of protein S-nitrosylation and highlights recent advances, with emphasis on applications in neurodegenerative diseases. An important goal is to provide a comprehensive guide of feasible quantitative proteomic methodologies for examining protein S-nitrosylation in research to yield insights into disease mechanisms, diagnostic biomarkers, and drug discovery.

  10. Comprehensive Quantitative Analysis of SQ Injection Using Multiple Chromatographic Technologies.

    Science.gov (United States)

    Chau, Siu-Leung; Huang, Zhi-Bing; Song, Yan-Gang; Yue, Rui-Qi; Ho, Alan; Lin, Chao-Zhan; Huang, Wen-Hua; Han, Quan-Bin

    2016-08-19

    Quality control of Chinese medicine injections remains a challenge due to our poor knowledge of their complex chemical profile. This study aims to investigate the chemical composition of one of the best-selling injections, Shenqi Fuzheng (SQ) injection (SQI), via a full component quantitative analysis. A total of 15 representative small molecular components of SQI were simultaneously determined using ultra-high performance liquid chromatography (UHPLC) coupled with quadrupole tandem time-of-flight mass spectrometry (Q-TOF-MS); saccharide composition of SQI was also quantitatively determined by high performance liquid chromatography (HPLC) with evaporative light scattering detector (ELSD) on an amino column before and after acid hydrolysis. The existence of polysaccharides was also examined on a gel permeation chromatography column. The method was well validated in terms of linearity, sensitivity, precision, accuracy and stability, and was successfully applied to analyze 13 SQI samples. The results demonstrate that up to 94.69% (w/w) of this injection product are quantitatively determined, in which small molecules and monosaccharide/sucrose account for 0.18%-0.21%, and 53.49%-58.2%, respectively. The quantitative information contributes to accumulating scientific evidence to better understand the therapy efficacy and safety of complex Chinese medicine injections.

  11. Comprehensive Quantitative Analysis of SQ Injection Using Multiple Chromatographic Technologies

    Directory of Open Access Journals (Sweden)

    Siu-Leung Chau

    2016-08-01

    Full Text Available Quality control of Chinese medicine injections remains a challenge due to our poor knowledge of their complex chemical profile. This study aims to investigate the chemical composition of one of the best-selling injections, Shenqi Fuzheng (SQ injection (SQI, via a full component quantitative analysis. A total of 15 representative small molecular components of SQI were simultaneously determined using ultra-high performance liquid chromatography (UHPLC coupled with quadrupole tandem time-of-flight mass spectrometry (Q-TOF-MS; saccharide composition of SQI was also quantitatively determined by high performance liquid chromatography (HPLC with evaporative light scattering detector (ELSD on an amino column before and after acid hydrolysis. The existence of polysaccharides was also examined on a gel permeation chromatography column. The method was well validated in terms of linearity, sensitivity, precision, accuracy and stability, and was successfully applied to analyze 13 SQI samples. The results demonstrate that up to 94.69% (w/w of this injection product are quantitatively determined, in which small molecules and monosaccharide/sucrose account for 0.18%–0.21%, and 53.49%–58.2%, respectively. The quantitative information contributes to accumulating scientific evidence to better understand the therapy efficacy and safety of complex Chinese medicine injections.

  12. Quantitative analysis for nonlinear fluorescent spectra based on edges matching

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A novel spectra-edge-matching approach is proposed for the quantitative analysis of the nonlinear fluorescence spectra of the air impurities excited by a femtosecond laser.The fluorescence spectra are first denoised and compressed,both by wavelet transform,and several peak groups are then picked from each spectrum according to a threshold of intensity and are used to extract the spectral features through principal component analysis.It is indicated that the first two principle components actually cover up to 98% of the total information and are sufficient for the final concentration analysis.The analysis reveals a monotone relationship between the spectra intensity and the concentration of the air impurities,suggesting that the femtosecond laser induced fluorescence spectroscopy along with the proposed spectra analysis method can become a powerful tool for monitoring environmental pollutants.

  13. Multiplexity and multireciprocity in directed multiplexes

    CERN Document Server

    Gemmetto, Valerio; Picciolo, Francesco; Ruzzenenti, Franco; Garlaschelli, Diego

    2014-01-01

    In the last few years, the study of multi-layer complex networks has received significant attention. In this work, we provide new measures to analyse dependencies between directed links in different layers of multiplex networks. We show that this requires more than a straightforward extension of the corresponding multiplexity measures that have been developed for undirected multiplexes. In particular, one should take into account the effects of reciprocity, i.e. the tendency of pairs of vertices to establish mutual connections. It is well known that reciprocity is a crucial property of many directed single-layer networks, affecting several dynamical processes taking place on such systems. Here we extend this quantity to directed multiplexes and introduce the notion of multireciprocity, defined as the tendency of links in one layer to be reciprocated by links in a different layer. We introduce multireciprocity measures valid for both binary and weighted networks and then validate these novel quantities on the ...

  14. Quantitative gait analysis following hemispherotomy for Rasmussen′s encephalitis

    Directory of Open Access Journals (Sweden)

    Santhosh George Thomas

    2007-01-01

    Full Text Available Peri-insular hemispherotomy is a form of disconnective hemispherectomy involving complete disconnection of all ascending / descending and commisural connections of one hemisphere. We report a case of a seven and a half year old child with intractable epilepsy due to Rasmussen′s encephalitis who underwent peri-insular hemispherotomy and achieved complete freedom from seizures. Quantitative gait analysis was used to describe the changes in the kinematic and kinetic parameters of gait with surface electromyographs 18 months after surgery. The focus of this paper is to highlight the utility of gait analysis following hemispherotomy with a view to directing postsurgical motor training and rehabilitation.

  15. A Quantitative Method for Microtubule Analysis in Fluorescence Images.

    Science.gov (United States)

    Lan, Xiaodong; Li, Lingfei; Hu, Jiongyu; Zhang, Qiong; Dang, Yongming; Huang, Yuesheng

    2015-12-01

    Microtubule analysis is of significant value for a better understanding of normal and pathological cellular processes. Although immunofluorescence microscopic techniques have proven useful in the study of microtubules, comparative results commonly rely on a descriptive and subjective visual analysis. We developed an objective and quantitative method based on image processing and analysis of fluorescently labeled microtubular patterns in cultured cells. We used a multi-parameter approach by analyzing four quantifiable characteristics to compose our quantitative feature set. Then we interpreted specific changes in the parameters and revealed the contribution of each feature set using principal component analysis. In addition, we verified that different treatment groups could be clearly discriminated using principal components of the multi-parameter model. High predictive accuracy of four commonly used multi-classification methods confirmed our method. These results demonstrated the effectiveness and efficiency of our method in the analysis of microtubules in fluorescence images. Application of the analytical methods presented here provides information concerning the organization and modification of microtubules, and could aid in the further understanding of structural and functional aspects of microtubules under normal and pathological conditions.

  16. Quantitative Phosphoproteomic Analysis of T-Cell Receptor Signaling.

    Science.gov (United States)

    Ahsan, Nagib; Salomon, Arthur R

    2017-01-01

    TCR signaling critically depends on protein phosphorylation across many proteins. Localization of each phosphorylation event relative to the T-cell receptor (TCR) and canonical T-cell signaling proteins will provide clues about the structure of TCR signaling networks. Quantitative phosphoproteomic analysis by mass spectrometry provides a wide-scale view of cellular phosphorylation networks. However, analysis of phosphorylation by mass spectrometry is still challenging due to the relative low abundance of phosphorylated proteins relative to all proteins and the extraordinary diversity of phosphorylation sites across the proteome. Highly selective enrichment of phosphorylated peptides is essential to provide the most comprehensive view of the phosphoproteome. Optimization of phosphopeptide enrichment methods coupled with highly sensitive mass spectrometry workflows significantly improves the sequencing depth of the phosphoproteome to over 10,000 unique phosphorylation sites from complex cell lysates. Here we describe a step-by-step method for phosphoproteomic analysis that has achieved widespread success for identification of serine, threonine, and tyrosine phosphorylation. Reproducible quantification of relative phosphopeptide abundance is provided by intensity-based label-free quantitation. An ideal set of mass spectrometry analysis parameters is also provided that optimize the yield of identified sites. We also provide guidelines for the bioinformatic analysis of this type of data to assess the quality of the data and to comply with proteomic data reporting requirements.

  17. What Really Happens in Quantitative Group Research? Results of a Content Analysis of Recent Quantitative Research in "JSGW"

    Science.gov (United States)

    Boyle, Lauren H.; Whittaker, Tiffany A.; Eyal, Maytal; McCarthy, Christopher J.

    2017-01-01

    The authors conducted a content analysis on quantitative studies published in "The Journal for Specialists in Group Work" ("JSGW") between 2012 and 2015. This brief report provides a general overview of the current practices of quantitative group research in counseling. The following study characteristics are reported and…

  18. ROLE OF MULTIPLEX CYTOKINE ANALYSIS IN THE EVALUATION OF THE EFFICACY OF RITUXIMAB DURING TREATMENT FOR RHEUMATOID ARTHRITIS

    Directory of Open Access Journals (Sweden)

    A. A. Novikov

    2011-01-01

    Full Text Available Along with its basic activity in removing B-lymphocytes, rituximab (RTM causes depletion of a population of CD20+ T cells that can pro- duce a variety of immunoregulatory and proinflammatory cytokines and chemokines. Objective: to define a role of multiplex cytokine analysis in the evaluation of the efficiency of using RMT in rheumatoid arthritis (RA. Subjects and methods. Thirty-four patients with the valid diagnosis of RA according to the ACR criteria of 1987 were examined. The con- centrations of cytokines were measured using the xMAP technology (27-plex. Results and discussion. In the group of patients with a clinical response to therapy with the gene engineering biological agent, there was a decrease in the concentrations of interleukins (IL 1β, 1ra, 2, 4, 6, 9, and 13, granulocyte macrophage colony-stimulating factor (GM- CSF, γ-interferon (IFN-γ, monocyte chemoattractant 1 at week 8 of therapy; that in IL 1β, 1ra, 2, 5, 6, 9, 10, 12, 13, and 15, fibroblast growth factor 2 (FGF-2, GM-CSF, IFN-γ, and tumor necrosis factor-α at week 24, and that in IL-9 at week 40. The no-clinical response group showed a reduction in GM-CSF at week 8 and in IL-2 and macrophage inflammatory protein 1β (MIP-1β at week 40, and an increase in IL-8 at week 8. At week 8 after drug infusion, the elevated levels of IL-17 and MIP-1β can be identified as possible early pre- dictors of a response (at week 40. Comparison of the baseline cytokine levels in the groups with different clinical response demonstrated a more than three-fold increase in the concentrations of IL 4, 5, 7, 8, 10, 12, 13, 15, 17, IFN-γ, and vascular endothelial growth factor, and IL-8 at weeks 8 and 40, respectively. 

  19. Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories.

    Science.gov (United States)

    White, Douglas E; Sylvester, Jonathan B; Levario, Thomas J; Lu, Hang; Streelman, J Todd; McDevitt, Todd C; Kemp, Melissa L

    2015-07-01

    Interrogating fundamental cell biology principles that govern tissue morphogenesis is critical to better understanding of developmental biology and engineering novel multicellular systems. Recently, functional micro-tissues derived from pluripotent embryonic stem cell (ESC) aggregates have provided novel platforms for experimental investigation; however elucidating the factors directing emergent spatial phenotypic patterns remains a significant challenge. Computational modelling techniques offer a unique complementary approach to probe mechanisms regulating morphogenic processes and provide a wealth of spatio-temporal data, but quantitative analysis of simulations and comparison to experimental data is extremely difficult. Quantitative descriptions of spatial phenomena across multiple systems and scales would enable unprecedented comparisons of computational simulations with experimental systems, thereby leveraging the inherent power of computational methods to interrogate the mechanisms governing emergent properties of multicellular biology. To address these challenges, we developed a portable pattern recognition pipeline consisting of: the conversion of cellular images into networks, extraction of novel features via network analysis, and generation of morphogenic trajectories. This novel methodology enabled the quantitative description of morphogenic pattern trajectories that could be compared across diverse systems: computational modelling of multicellular structures, differentiation of stem cell aggregates, and gastrulation of cichlid fish. Moreover, this method identified novel spatio-temporal features associated with different stages of embryo gastrulation, and elucidated a complex paracrine mechanism capable of explaining spatiotemporal pattern kinetic differences in ESC aggregates of different sizes.

  20. Multivariate analysis of quantitative traits can effectively classify rapeseed germplasm

    Directory of Open Access Journals (Sweden)

    Jankulovska Mirjana

    2014-01-01

    Full Text Available In this study, the use of different multivariate approaches to classify rapeseed genotypes based on quantitative traits has been presented. Tree regression analysis, PCA analysis and two-way cluster analysis were applied in order todescribe and understand the extent of genetic variability in spring rapeseed genotype by trait data. The traits which highly influenced seed and oil yield in rapeseed were successfully identified by the tree regression analysis. Principal predictor for both response variables was number of pods per plant (NP. NP and 1000 seed weight could help in the selection of high yielding genotypes. High values for both traits and oil content could lead to high oil yielding genotypes. These traits may serve as indirect selection criteria and can lead to improvement of seed and oil yield in rapeseed. Quantitative traits that explained most of the variability in the studied germplasm were classified using principal component analysis. In this data set, five PCs were identified, out of which the first three PCs explained 63% of the total variance. It helped in facilitating the choice of variables based on which the genotypes’ clustering could be performed. The two-way cluster analysissimultaneously clustered genotypes and quantitative traits. The final number of clusters was determined using bootstrapping technique. This approach provided clear overview on the variability of the analyzed genotypes. The genotypes that have similar performance regarding the traits included in this study can be easily detected on the heatmap. Genotypes grouped in the clusters 1 and 8 had high values for seed and oil yield, and relatively short vegetative growth duration period and those in cluster 9, combined moderate to low values for vegetative growth duration and moderate to high seed and oil yield. These genotypes should be further exploited and implemented in the rapeseed breeding program. The combined application of these multivariate methods

  1. Mini-Column Ion-Exchange Separation and Atomic Absorption Quantitation of Nickel, Cobalt, and Iron: An Undergraduate Quantitative Analysis Experiment.

    Science.gov (United States)

    Anderson, James L.; And Others

    1980-01-01

    Presents an undergraduate quantitative analysis experiment, describing an atomic absorption quantitation scheme that is fast, sensitive and comparatively simple relative to other titration experiments. (CS)

  2. Segregation Analysis on Genetic System of Quantitative Traits in Plants

    Institute of Scientific and Technical Information of China (English)

    Gai Junyi

    2006-01-01

    Based on the traditional polygene inheritance model of quantitative traits,the author suggests the major gene and polygene mixed inheritance model.The model was considered as a general one,while the pure major gene and pure polygene inheritance model was a specific case of the general model.Based on the proposed theory,the author established the segregation analysis procedure to study the genetic system of quantitative traits of plants.At present,this procedure can be used to evaluate the genetic effect of individual major genes (up to two to three major genes),the collective genetic effect of polygene,and their heritability value.This paper introduces how to establish the procedure,its main achievements,and its applications.An example is given to illustrate the steps,methods,and effectiveness of the procedure.

  3. Analysis of quantitative pore features based on mathematical morphology

    Institute of Scientific and Technical Information of China (English)

    QI Heng-nian; CHEN Feng-nong; WANG Hang-jun

    2008-01-01

    Wood identification is a basic technique of wood science and industry. Pore features are among the most important identification features for hardwoods. We have used a method based on an analysis of quantitative pore feature, which differs from traditional qualitative methods. We applies mathematical morphology methods such as dilation and erosion, open and close transformation of wood cross-sections, image repairing, noise filtering and edge detection to segment the pores from their background. Then the mean square errors (MSE) of pores were computed to describe the distribution of pores. Our experiment shows that it is easy to classift the pore features into three basic types, just as in traditional qualitative methods, but with the use of MSE of pores. This quantitative method improves wood identification considerably.

  4. Low-volume multiplexed proteolytic activity assay and inhibitor analysis through a pico-injector array.

    Science.gov (United States)

    Ng, Ee Xien; Miller, Miles A; Jing, Tengyang; Lauffenburger, Doug A; Chen, Chia-Hung

    2015-02-21

    Secreted active proteases, from families of enzymes such as matrix metalloproteinases (MMPs) and ADAMs (a disintegrin and metalloproteinases), participate in diverse pathological processes. To simultaneously measure multiple specific protease activities, a series of parallel enzyme reactions combined with a series of inhibitor analyses for proteolytic activity matrix analysis (PrAMA) are essential but limited due to the sample quantity requirements and the complexity of performing multiple reactions. To address these issues, we developed a pico-injector array to generate 72 different reactions in picoliter-volume droplets by controlling the sequence of combinational injections, which allowed simultaneous recording of a wide range of multiple enzyme reactions and measurement of inhibitor effects using small sample volumes (~10 μL). Multiple MMP activities were simultaneously determined by 9 different substrates and 2 inhibitors using injections from a pico-injector array. Due to the advantages of inhibitor analysis, the MMP/ADAM activities of MDA-MB-231, a breast cancer cell line, were characterized with high MMP-2, MMP-3 and ADAM-10 activity. This platform could be customized for a wide range of applications that also require multiple reactions with inhibitor analysis to enhance the sensitivity by encapsulating different chemical sensors.

  5. Multiplex PCR analysis of fumonisin biosynthetic genes in fumonisin-nonproducing Aspergillus niger and A. awamori strains

    Science.gov (United States)

    In order to determine the genetic basis for loss of fumonisin B¬2 (FB2) biosynthesis in FB2 non-producing A. niger strains, we developed multiplex PCR primer sets to amplify fragments of eight fumonisin biosynthetic pathway (fum) genes. Fragments of all eight fum genes were amplified in FB2-produci...

  6. Sandpiles on multiplex networks

    CERN Document Server

    Lee, Kyu-Min; Kim, I -M

    2011-01-01

    We introduce the sandpile model on multiplex networks with more than one type of edges and investigate its scaling and dynamical behaviors. We find that the introduction of multiplexity does not alter the scaling behavior of avalanche dynamics; the system is critical with the asymptotic power-law avalanche size distribution with exponent $\\tau = 3/2$ on duplex random networks. Detailed cascade dynamics, however, is affected by the multiplex coupling. For example, higher-degree nodes such as hubs in scale-free networks fail more often in the multiplex dynamics than in the simplex network counterpart in which different types of edges are simply aggregated. Our results suggest that multiplex modeling would be necessary in order to gain better understanding of cascading failure phenomena of real-world multiplex complex systems, such as the global economic crisis.

  7. Rapid diagnosis of Down's and Edward's syndrome by multiplex real-time quantitative PCR%多重实时定量PCR快速诊断唐氏及爱德华综合征

    Institute of Scientific and Technical Information of China (English)

    眭建忠; 张慧敏; 孙筱放

    2010-01-01

    Objective To establish a multiplex real-time quantitative PCR method for diagnosis of Down's and Edward's syndrome. Methods The sequences of the amyloid precursor protein gene (APP)in the Down's region of chromosome 21 and the thymidylate synthetase gene (TYMS) on chromosome 18 were co-amplified in the same tube. The relative quantitative index △CT value was used to differentiate Down's and Edward's syndrome patient from healthy individual. Four groups of samples, including 36 blood samples from normal controls (group A), 15 amniotic fluid samples from normal pregnancies (group B), 21 samples from patients with Down's syndrome (group C) and 6 samples from patients with Edward's syndrome (group D), were investigated in the study. Results The mean△CT values of the four groups were -0.48±0.15,-0.49±0.12,- 1.26±0.17 and 0.25±0.12 respectively. The △CT value from group B was not different from that from group A (P>0.05). However, the△CT values from group C and group D were significantly different from that from group A (P<0.01), and no overlapping was observed.Conclusion The △CT values from multiplex real-time quantitative PCR could be used to rapidly diagnose Down' s and Edward's syndrome simultaneously.%目的 建立多重实时定量聚合酶链反应(real-time quantitative polymerase chain reaction,RTqPCR)技术,快速分子诊断唐氏及爱德华综合征.方法 应用PCR方法同时扩增位于21号染色体上的淀粉样前蛋白基因(amyloid precursor protein gene,APP)和18号染色体上的胸苷酸合成酶基因(thymidylate synthetase gene,TYMS),以相对定量指标△CT值区分唐氏、爱德华综合征及正常人.用此方法检测4组样本:36名正常人外周血(A组)、15名正常核型的羊水细胞(B组)、21例唐氏综合征(C组)和6例爱德华综合征(D组).结果 A~D 4组样本△CT均值分别为-0.48±0.15、-0.49±0.12、-1.26±0.17和0.25±0.12.B组与A组间差异无统计学意义(P>0.05);C组与A组、D组

  8. Multiplex PCR followed by restriction length polymorphism analysis for the subtyping of bovine herpesvirus 5 isolates

    OpenAIRE

    Maidana; Morano, C.D.; Cianfrinid; de Campos, F.; Roehe, P.M.; Siedler, B.; G. De Stefano; Mauroy, Axel; Thiry, Etienne; Romera, S. A.

    2013-01-01

    Abstract Background: Several types and subtypes of bovine herpesviruses 1 and 5 (BoHV-1 and BoHV-5) have been associated to different clinical conditions of cattle, making type/subtype differentiation essential to understand the pathogenesis and epidemiology of BoHV infections. BoHV-5 subtyping is currently carried out by BstEII restriction enzyme analysis (REA) of the complete virus genome. This method allowed the description of three subtypes, one of which is the most widespread while ...

  9. Quantitative risk analysis as a basis for emergency planning

    Energy Technology Data Exchange (ETDEWEB)

    Yogui, Regiane Tiemi Teruya [Bureau Veritas do Brasil, Rio de Janeiro, RJ (Brazil); Macedo, Eduardo Soares de [Instituto de Pesquisas Tecnologicas (IPT), Sao Paulo, SP (Brazil)

    2009-07-01

    Several environmental accidents happened in Brazil and in the world during the 70's and 80's. This strongly motivated the preparation for emergencies in the chemical and petrochemical industries. Environmental accidents affect the environment and the communities that are neighbor to the industrial facilities. The present study aims at subsidizing and providing orientation to develop Emergency Planning from the data obtained on Quantitative Risk Analysis, elaborated according to the Technical Standard P4.261/03 from CETESB (Sao Paulo Environmental Agency). It was observed, during the development of the research, that the data generated on these studies need a complementation and a deeper analysis, so that it is possible to use them on the Emergency Plans. The main issues that were analyzed and discussed on this study were the reevaluation of hazard identification for the emergency plans, the consequences and vulnerability analysis for the response planning, the risk communication, and the preparation to respond to the emergencies of the communities exposed to manageable risks. As a result, the study intends to improve the interpretation and use of the data deriving from the Quantitative Risk Analysis to develop the emergency plans. (author)

  10. Quantitative analysis of in vivo confocal microscopy images: a review.

    Science.gov (United States)

    Patel, Dipika V; McGhee, Charles N

    2013-01-01

    In vivo confocal microscopy (IVCM) is a non-invasive method of examining the living human cornea. The recent trend towards quantitative studies using IVCM has led to the development of a variety of methods for quantifying image parameters. When selecting IVCM images for quantitative analysis, it is important to be consistent regarding the location, depth, and quality of images. All images should be de-identified, randomized, and calibrated prior to analysis. Numerous image analysis software are available, each with their own advantages and disadvantages. Criteria for analyzing corneal epithelium, sub-basal nerves, keratocytes, endothelium, and immune/inflammatory cells have been developed, although there is inconsistency among research groups regarding parameter definition. The quantification of stromal nerve parameters, however, remains a challenge. Most studies report lower inter-observer repeatability compared with intra-observer repeatability, and observer experience is known to be an important factor. Standardization of IVCM image analysis through the use of a reading center would be crucial for any future large, multi-centre clinical trials using IVCM.

  11. Multiplexed high-content analysis of mitochondrial morphofunction using live-cell microscopy.

    Science.gov (United States)

    Iannetti, Eligio F; Smeitink, Jan A M; Beyrath, Julien; Willems, Peter H G M; Koopman, Werner J H

    2016-09-01

    Mitochondria have a central role in cellular (patho)physiology, and they display a highly variable morphology that is probably coupled to their functional state. Here we present a protocol that allows unbiased and automated quantification of mitochondrial 'morphofunction' (i.e., morphology and membrane potential), cellular parameters (size, confluence) and nuclear parameters (number, morphology) in intact living primary human skin fibroblasts (PHSFs). Cells are cultured in 96-well plates and stained with tetramethyl rhodamine methyl ester (TMRM), calcein-AM (acetoxy-methyl ester) and Hoechst 33258. Next, multispectral fluorescence images are acquired using automated microscopy and processed to extract 44 descriptors. Subsequently, the descriptor data are subjected to a quality control (QC) algorithm based upon principal component analysis (PCA) and interpreted using univariate, bivariate and multivariate analysis. The protocol requires a time investment of ∼4 h distributed over 2 d. Although it is specifically developed for PHSFs, which are widely used in preclinical research, the protocol is portable to other cell types and can be scaled up for implementation in high-content screening.

  12. Multiplexed LC-MS/MS analysis of horse plasma proteins to study doping in sport.

    Science.gov (United States)

    Barton, Chris; Beck, Paul; Kay, Richard; Teale, Phil; Roberts, Jane

    2009-06-01

    The development of protein biomarkers for the indirect detection of doping in horse is a potential solution to doping threats such as gene and protein doping. A method for biomarker candidate discovery in horse plasma is presented using targeted analysis of proteotypic peptides from horse proteins. These peptides were first identified in a novel list of the abundant proteins in horse plasma. To monitor these peptides, an LC-MS/MS method using multiple reaction monitoring was developed to study the quantity of 49 proteins in horse plasma in a single run. The method was optimised and validated, and then applied to a population of race-horses to study protein variance within a population. The method was finally applied to longitudinal time courses of horse plasma collected after administration of an anabolic steroid to demonstrate utility for hypothesis-driven discovery of doping biomarker candidates.

  13. Quantitative phosphoproteomic analysis using iTRAQ method.

    Science.gov (United States)

    Asano, Tomoya; Nishiuchi, Takumi

    2014-01-01

    The MAPK (mitogen-activated kinase) cascade plays important roles in plant perception of and reaction to developmental and environmental cues. Phosphoproteomics are useful to identify target proteins regulated by MAPK-dependent signaling pathway. Here, we introduce the quantitative phosphoproteomic analysis using a chemical labeling method. The isobaric tag for relative and absolute quantitation (iTRAQ) method is a MS-based technique to quantify protein expression among up to eight different samples in one experiment. In this technique, peptides were labeled by some stable isotope-coded covalent tags. We perform quantitative phosphoproteomics comparing Arabidopsis wild type and a stress-responsive mapkk mutant after phytotoxin treatment. To comprehensively identify the downstream phosphoproteins of MAPKK, total proteins were extracted from phytotoxin-treated wild-type and mapkk mutant plants. The phosphoproteins were purified by Pro-Q(®) Diamond Phosphoprotein Enrichment Kit and were digested with trypsin. Resulting peptides were labeled with iTRAQ reagents and were quantified and identified by MALDI TOF/TOF analyzer. We identified many phosphoproteins that were decreased in the mapkk mutant compared with wild type.

  14. A quantitative analysis of IRAS maps of molecular clouds

    Science.gov (United States)

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-01-01

    We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

  15. Simulating realistic predator signatures in quantitative fatty acid signature analysis

    Science.gov (United States)

    Bromaghin, Jeffrey F.

    2015-01-01

    Diet estimation is an important field within quantitative ecology, providing critical insights into many aspects of ecology and community dynamics. Quantitative fatty acid signature analysis (QFASA) is a prominent method of diet estimation, particularly for marine mammal and bird species. Investigators using QFASA commonly use computer simulation to evaluate statistical characteristics of diet estimators for the populations they study. Similar computer simulations have been used to explore and compare the performance of different variations of the original QFASA diet estimator. In both cases, computer simulations involve bootstrap sampling prey signature data to construct pseudo-predator signatures with known properties. However, bootstrap sample sizes have been selected arbitrarily and pseudo-predator signatures therefore may not have realistic properties. I develop an algorithm to objectively establish bootstrap sample sizes that generates pseudo-predator signatures with realistic properties, thereby enhancing the utility of computer simulation for assessing QFASA estimator performance. The algorithm also appears to be computationally efficient, resulting in bootstrap sample sizes that are smaller than those commonly used. I illustrate the algorithm with an example using data from Chukchi Sea polar bears (Ursus maritimus) and their marine mammal prey. The concepts underlying the approach may have value in other areas of quantitative ecology in which bootstrap samples are post-processed prior to their use.

  16. Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization

    Directory of Open Access Journals (Sweden)

    Peterhansel Christoph

    2007-09-01

    Full Text Available Abstract Background Chromatin remodeling, histone modifications and other chromatin-related processes play a crucial role in gene regulation. A very useful technique to study these processes is chromatin immunoprecipitation (ChIP. ChIP is widely used for a few model systems, including Arabidopsis, but establishment of the technique for other organisms is still remarkably challenging. Furthermore, quantitative analysis of the precipitated material and normalization of the data is often underestimated, negatively affecting data quality. Results We developed a robust ChIP protocol, using maize (Zea mays as a model system, and present a general strategy to systematically optimize this protocol for any type of tissue. We propose endogenous controls for active and for repressed chromatin, and discuss various other controls that are essential for successful ChIP experiments. We experienced that the use of quantitative PCR (QPCR is crucial for obtaining high quality ChIP data and we explain why. The method of data normalization has a major impact on the quality of ChIP analyses. Therefore, we analyzed different normalization strategies, resulting in a thorough discussion of the advantages and drawbacks of the various approaches. Conclusion Here we provide a robust ChIP protocol and strategy to optimize the protocol for any type of tissue; we argue that quantitative real-time PCR (QPCR is the best method to analyze the precipitates, and present comprehensive insights into data normalization.

  17. Fluorescent foci quantitation for high-throughput analysis

    Science.gov (United States)

    Ledesma-Fernández, Elena; Thorpe, Peter H.

    2015-01-01

    A number of cellular proteins localize to discrete foci within cells, for example DNA repair proteins, microtubule organizing centers, P bodies or kinetochores. It is often possible to measure the fluorescence emission from tagged proteins within these foci as a surrogate for the concentration of that specific protein. We wished to develop tools that would allow quantitation of fluorescence foci intensities in high-throughput studies. As proof of principle we have examined the kinetochore, a large multi-subunit complex that is critical for the accurate segregation of chromosomes during cell division. Kinetochore perturbations lead to aneuploidy, which is a hallmark of cancer cells. Hence, understanding kinetochore homeostasis and regulation are important for a global understanding of cell division and genome integrity. The 16 budding yeast kinetochores colocalize within the nucleus to form a single focus. Here we have created a set of freely-available tools to allow high-throughput quantitation of kinetochore foci fluorescence. We use this ‘FociQuant’ tool to compare methods of kinetochore quantitation and we show proof of principle that FociQuant can be used to identify changes in kinetochore protein levels in a mutant that affects kinetochore function. This analysis can be applied to any protein that forms discrete foci in cells. PMID:26290880

  18. Analysis of alternative splicing events for cancer diagnosis using a multiplexing nanophotonic biosensor.

    Science.gov (United States)

    Huertas, César S; Domínguez-Zotes, Santos; Lechuga, Laura M

    2017-01-25

    Personalized medicine is a promising tool not only for prevention, screening and development of more efficient treatment strategies, but also for diminishing the side effects caused by current therapies. Deciphering gene regulation pathways provides a reliable prognostic analysis to elucidate the origin of grave diseases and facilitate the selection of the most adequate treatment for each individual. Alternative splicing of mRNA precursors is one of these gene regulation pathways and enables cells to generate different protein outputs from the same gene depending on their developmental or homeostatic status. Its deregulation is strongly linked to disease onset and progression constituting a relevant and innovative class of biomarker. Herein we report a highly selective and sensitive nanophotonic biosensor based on the direct monitoring of the aberrant alternative splicing of Fas gene. Unlike conventional methods, the nanobiosensor performs a real-time detection of the specific isoforms in the fM-pM range without any cDNA synthesis or PCR amplification requirements. The nanobiosensor has been proven isoform-specific with no crosshybridization, greatly minimizing detection biases. The demonstrated high sensitivity and specificity make our nanobiosensor ideal for examining significant tumor-associated expression shifts of alternatively spliced isoforms for the early and accurate theranostics of cancer.

  19. Serological Analysis of Tuberculosis in Goats by Use of the Enferplex Caprine TB Multiplex Test.

    Science.gov (United States)

    O'Brien, Amanda; Whelan, Clare; Clarke, John B; Hayton, Alastair; Watt, Neil J; Harkiss, Gordon D

    2017-02-01

    Tuberculosis in goats is usually diagnosed clinically, at postmortem, or by a positive skin test. However, none of these approaches detects all infected animals. Serology offers an additional tool to identify infected animals missed by current tests. We describe the use of the Enferplex Caprine TB serology test to aid the management of a large dairy goat herd undergoing a tuberculosis breakdown. Initial skin and serology testing showed that IgG antibodies were present in both serum and milk from 100% of skin test-positive animals and in serum and milk from 77.8 and 95.4% of skin test-negative animals, respectively. A good correlation was observed between serum and milk antibody levels. The herd had been vaccinated against Mycobacterium avium subsp. paratuberculosis, but no direct serological cross-reactions were found. Subsequent skin testing revealed 13.7% positive animals, 64.9% of which were antibody positive, while 42.1% of skin test-negative animals were seropositive. Antibody responses remained high 1 month later (57.1% positive), and the herd was slaughtered. Postmortem analysis of 20 skin test-negative goats revealed visible lesions in 6 animals, all of which had antibodies to six Mycobacterium bovis antigens. The results provide indirect evidence that serology testing with serum or milk could be a useful tool in the diagnosis and management of tuberculosis in goats. Copyright © 2017 American Society for Microbiology.

  20. Quantitative multiphase analysis of archaeological bronzes by neutron diffraction

    CERN Document Server

    Siano, S; Celli, M; Pini, R; Salimbeni, R; Zoppi, M; Kockelmann, W A; Iozzo, M; Miccio, M; Moze, O

    2002-01-01

    In this paper, we report the first investigation on the potentials of neutron diffraction to characterize archaeological bronze artifacts. The preliminary feasibility of phase and structural analysis was demonstrated on standardised specimens with a typical bronze alloy composition. These were realised through different hardening and annealing cycles, simulating possible ancient working techniques. The Bragg peak widths that resulted were strictly dependent on the working treatment, thus providing an important analytical element to investigate ancient making techniques. The diagnostic criteria developed on the standardised specimens were then applied to study two Etruscan museum pieces. Quantitative multiphase analysis by Rietveld refinement of the diffraction patterns was successfully demonstrated. Furthermore, the analysis of patterns associated with different artifact elements also yielded evidence for some peculiar perspective of the neutron diffraction diagnostics in archeometric applications. (orig.)

  1. QUANTITATIVE METHODOLOGY FOR STABILITY ANALYSIS OF NONLINEAR ROTOR SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    ZHENG Hui-ping; XUE Yu-sheng; CHEN Yu-shu

    2005-01-01

    Rotor-bearings systems applied widely in industry are nonlinear dynamic systems of multi-degree-of-freedom. Modem concepts on design and maintenance call for quantitative stability analysis. Using trajectory based stability-preserving and dimensional-reduction, a quanttative stability analysis method for rotor systems is presented. At first, an n-dimensional nonlinear non-autonomous rotor system is decoupled into n subsystems after numerical integration. Each of them has only onedegree-of-freedom and contains time-varying parameters to represent all other state variables. In this way, n-dimensional trajectory is mapped into a set of one-dimensional trajectories. Dynamic central point (DCP) of a subsystem is then defined on the extended phase plane, namely, force-position plane. Characteristics of curves on the extended phase plane and the DCP's kinetic energy difference sequence for general motion in rotor systems are studied. The corresponding stability margins of trajectory are evaluated quantitatively. By means of the margin and its sensitivity analysis, the critical parameters of the period doubling bifurcation and the Hopf bifurcation in a flexible rotor supported by two short journal beatings with nonlinear suspensionare are determined.

  2. Quantitative Analysis of Polarimetric Model-Based Decomposition Methods

    Directory of Open Access Journals (Sweden)

    Qinghua Xie

    2016-11-01

    Full Text Available In this paper, we analyze the robustness of the parameter inversion provided by general polarimetric model-based decomposition methods from the perspective of a quantitative application. The general model and algorithm we have studied is the method proposed recently by Chen et al., which makes use of the complete polarimetric information and outperforms traditional decomposition methods in terms of feature extraction from land covers. Nevertheless, a quantitative analysis on the retrieved parameters from that approach suggests that further investigations are required in order to fully confirm the links between a physically-based model (i.e., approaches derived from the Freeman–Durden concept and its outputs as intermediate products before any biophysical parameter retrieval is addressed. To this aim, we propose some modifications on the optimization algorithm employed for model inversion, including redefined boundary conditions, transformation of variables, and a different strategy for values initialization. A number of Monte Carlo simulation tests for typical scenarios are carried out and show that the parameter estimation accuracy of the proposed method is significantly increased with respect to the original implementation. Fully polarimetric airborne datasets at L-band acquired by German Aerospace Center’s (DLR’s experimental synthetic aperture radar (E-SAR system were also used for testing purposes. The results show different qualitative descriptions of the same cover from six different model-based methods. According to the Bragg coefficient ratio (i.e., β , they are prone to provide wrong numerical inversion results, which could prevent any subsequent quantitative characterization of specific areas in the scene. Besides the particular improvements proposed over an existing polarimetric inversion method, this paper is aimed at pointing out the necessity of checking quantitatively the accuracy of model-based PolSAR techniques for a

  3. European Identity in Russian Regions Bordering on Finland: Quantitative Analysis

    OpenAIRE

    A. O. Domanov

    2014-01-01

    Th e quantitative analysis of an opinion poll conducted in October 2013 in three Russian cities located near Finnish border (St-Petersburg, Kronstadt and Vyborg) explores European identity of their citizens. Th is area was chosen to illustrate the crucial importance of space interpretation in spatial identity formation by using critical geopolitical approach. Th e study shows how diff erent images of space on the same territory act as intermediate variables between objective territorial chara...

  4. Quantitative analysis of sideband coupling in photoinduced force microscopy

    Science.gov (United States)

    Jahng, Junghoon; Kim, Bongsu; Lee, Eun Seong; Potma, Eric Olaf

    2016-11-01

    We present a theoretical and experimental analysis of the cantilever motions detected in photoinduced force microscopy (PiFM) using the sideband coupling detection scheme. In sideband coupling, the cantilever dynamics are probed at a combination frequency of a fundamental mechanical eigenmode and the modulation frequency of the laser beam. Using this detection mode, we develop a method for reconstructing the modulated photoinduced force gradient from experimental parameters in a quantitative manner. We show evidence, both theoretically and experimentally, that the sideband coupling detection mode provides PiFM images with superior contrast compared to images obtained when detecting the cantilever motions directly at the laser modulation frequency.

  5. Quantitative and comparative analysis of hyperspectral data fusion performance

    Institute of Scientific and Technical Information of China (English)

    王强; 张晔; 李硕; 沈毅

    2002-01-01

    Hyperspectral data fusion technique is the key to hyperspectral data processing in recent years. Manyfusion methods have been proposed, but little research has been done to evaluate the performances of differentdata fusion methods. In order to meet the urgent need, quantitative correlation analysis (QCA) is proposed toanalyse and compare the performances of different fusion methods directly from data before and after fusion. Ex-periment results show that the new method is effective and the results of comparison are in agreement with theresults of application.

  6. Quantitative chemical analysis of ocular melanosomes in the TEM.

    Science.gov (United States)

    Eibl, O; Schultheiss, S; Blitgen-Heinecke, P; Schraermeyer, U

    2006-01-01

    Melanosomes in retinal tissues of a human, monkey and rat were analyzed by EDX in the TEM. Samples were prepared by ultramicrotomy at different thicknesses. The material was mounted on Al grids and samples were analyzed in a Zeiss 912 TEM equipped with an Omega filter and EDX detector with ultrathin window. Melanosomes consist of C and O as main components, mole fractions are about 90 and 3-10 at.%, respectively, and small mole fraction ratios, between 2 and 0.1 at.%, of Na, Mg, K, Si, P, S, Cl, Ca. All elements were measured quantitatively by standardless EDX with high precision. Mole fractions of transition metals Fe, Cu and Zn were also measured. For Fe a mole fraction ratio of less than 0.1at.% was found and gives the melanin its paramagnetic properties. Its mole fraction is however close to or below the minimum detectable mass fraction of the used equipment. Only in the human eye and only in the retinal pigment epitelium (rpe) the mole fractions of Zn (0.1 at.% or 5000 microg/g) and Cu were clearly beyond the minimum detectable mass fraction. In the rat and monkey eye the mole fraction of Zn was at or below the minimum detectable mass fraction and could not be measured quantitatively. The obtained results yielded the chemical composition of the melanosomes in the choroidal tissue and the retinal pigment epitelium (rpe) of the three different species. The results of the chemical analysis are discussed by mole fraction correlation diagrams. Similarities and differences between the different species are outlined. Correlation behavior was found to hold over species, e.g. the Ca-O correlation. It indicates that Ca is bound to oxygen rich sites in the melanin. These are the first quantitative analyses of melanosomes by EDX reported so far. The quantitative chemical analysis should open a deeper understanding of the metabolic processes in the eye that are of central importance for the understanding of a large number of eye-related diseases. The chemical analysis also

  7. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    Directory of Open Access Journals (Sweden)

    Venkatesha R. Hathwar

    2015-09-01

    Full Text Available Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ...Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.

  8. Quantitative analysis on electrooculography (EOG) for neurodegenerative disease

    Science.gov (United States)

    Liu, Chang-Chia; Chaovalitwongse, W. Art; Pardalos, Panos M.; Seref, Onur; Xanthopoulos, Petros; Sackellares, J. C.; Skidmore, Frank M.

    2007-11-01

    Many studies have documented abnormal horizontal and vertical eye movements in human neurodegenerative disease as well as during altered states of consciousness (including drowsiness and intoxication) in healthy adults. Eye movement measurement may play an important role measuring the progress of neurodegenerative diseases and state of alertness in healthy individuals. There are several techniques for measuring eye movement, Infrared detection technique (IR). Video-oculography (VOG), Scleral eye coil and EOG. Among those available recording techniques, EOG is a major source for monitoring the abnormal eye movement. In this real-time quantitative analysis study, the methods which can capture the characteristic of the eye movement were proposed to accurately categorize the state of neurodegenerative subjects. The EOG recordings were taken while 5 tested subjects were watching a short (>120 s) animation clip. In response to the animated clip the participants executed a number of eye movements, including vertical smooth pursued (SVP), horizontal smooth pursued (HVP) and random saccades (RS). Detection of abnormalities in ocular movement may improve our diagnosis and understanding a neurodegenerative disease and altered states of consciousness. A standard real-time quantitative analysis will improve detection and provide a better understanding of pathology in these disorders.

  9. Quantitative analysis in outcome assessment of instrumented lumbosacral arthrodesis.

    Science.gov (United States)

    Champain, Sabina; Mazel, Christian; Mitulescu, Anca; Skalli, Wafa

    2007-08-01

    The outcome assessment in instrumented lumbosacral fusion mostly focuses on clinical criteria, complications and scores, with a high variability of imaging means, methods of fusion grading and parameters describing degenerative changes, making comparisons between studies difficult. The aim of this retrospective evaluation was to evaluate the interest of quantified radiographic analysis of lumbar spine in global outcome assessment and to highlight the key biomechanical factors involved. Clinical data and Beaujon-Lassale scores were collected for 49 patients who underwent lumbosacral arthrodesis after prior lumbar discectomy (mean follow-up: 5 years). Sagittal standing and lumbar flexion-extension X-ray films allowed quantifying vertebral, lumbar, pelvic and kinematic parameters of the lumbar spine, which were compared to reference values. Statistics were performed to assess evolution for all variables. At long-term follow-up, 90% of patients presented satisfactory clinical outcomes, associated to normal sagittal alignment; vertebral parameters objectified adjacent level degeneration in four cases (8%). Clinical outcome was correlated (r = 0.8) with fusion that was confirmed in 80% of cases, doubtful in 16% and pseudarthrosis seemed to occur in 4% (2) of cases. In addition to clinical data (outcomes comparable to the literature), quantitative analysis accurately described lumbar spine geometry and kinematics, highlighting parameters related to adjacent level's degeneration and a significant correlation between clinical outcome and fusion. Furthermore, criteria proposed to quantitatively evaluate fusion from lumbar dynamic radiographs seem to be appropriate and in agreement with surgeon's qualitative grading in 87% of cases.

  10. Super-multiplex vibrational imaging

    Science.gov (United States)

    Wei, Lu; Chen, Zhixing; Shi, Lixue; Long, Rong; Anzalone, Andrew V.; Zhang, Luyuan; Hu, Fanghao; Yuste, Rafael; Cornish, Virginia W.; Min, Wei

    2017-04-01

    The ability to visualize directly a large number of distinct molecular species inside cells is increasingly essential for understanding complex systems and processes. Even though existing methods have successfully been used to explore structure-function relationships in nervous systems, to profile RNA in situ, to reveal the heterogeneity of tumour microenvironments and to study dynamic macromolecular assembly, it remains challenging to image many species with high selectivity and sensitivity under biological conditions. For instance, fluorescence microscopy faces a ‘colour barrier’, owing to the intrinsically broad (about 1,500 inverse centimetres) and featureless nature of fluorescence spectra that limits the number of resolvable colours to two to five (or seven to nine if using complicated instrumentation and analysis). Spontaneous Raman microscopy probes vibrational transitions with much narrower resonances (peak width of about 10 inverse centimetres) and so does not suffer from this problem, but weak signals make many bio-imaging applications impossible. Although surface-enhanced Raman scattering offers high sensitivity and multiplicity, it cannot be readily used to image specific molecular targets quantitatively inside live cells. Here we use stimulated Raman scattering under electronic pre-resonance conditions to image target molecules inside living cells with very high vibrational selectivity and sensitivity (down to 250 nanomolar with a time constant of 1 millisecond). We create a palette of triple-bond-conjugated near-infrared dyes that each displays a single peak in the cell-silent Raman spectral window; when combined with available fluorescent probes, this palette provides 24 resolvable colours, with the potential for further expansion. Proof-of-principle experiments on neuronal co-cultures and brain tissues reveal cell-type-dependent heterogeneities in DNA and protein metabolism under physiological and pathological conditions, underscoring the

  11. Quantitative Analysis of the Interdisciplinarity of Applied Mathematics.

    Science.gov (United States)

    Xie, Zheng; Duan, Xiaojun; Ouyang, Zhenzheng; Zhang, Pengyuan

    2015-01-01

    The increasing use of mathematical techniques in scientific research leads to the interdisciplinarity of applied mathematics. This viewpoint is validated quantitatively here by statistical and network analysis on the corpus PNAS 1999-2013. A network describing the interdisciplinary relationships between disciplines in a panoramic view is built based on the corpus. Specific network indicators show the hub role of applied mathematics in interdisciplinary research. The statistical analysis on the corpus content finds that algorithms, a primary topic of applied mathematics, positively correlates, increasingly co-occurs, and has an equilibrium relationship in the long-run with certain typical research paradigms and methodologies. The finding can be understood as an intrinsic cause of the interdisciplinarity of applied mathematics.

  12. Fusing Quantitative Requirements Analysis with Model-based Systems Engineering

    Science.gov (United States)

    Cornford, Steven L.; Feather, Martin S.; Heron, Vance A.; Jenkins, J. Steven

    2006-01-01

    A vision is presented for fusing quantitative requirements analysis with model-based systems engineering. This vision draws upon and combines emergent themes in the engineering milieu. "Requirements engineering" provides means to explicitly represent requirements (both functional and non-functional) as constraints and preferences on acceptable solutions, and emphasizes early-lifecycle review, analysis and verification of design and development plans. "Design by shopping" emphasizes revealing the space of options available from which to choose (without presuming that all selection criteria have previously been elicited), and provides means to make understandable the range of choices and their ramifications. "Model-based engineering" emphasizes the goal of utilizing a formal representation of all aspects of system design, from development through operations, and provides powerful tool suites that support the practical application of these principles. A first step prototype towards this vision is described, embodying the key capabilities. Illustrations, implications, further challenges and opportunities are outlined.

  13. Quantitative Phase Analysis by the Rietveld Method for Forensic Science.

    Science.gov (United States)

    Deng, Fei; Lin, Xiaodong; He, Yonghong; Li, Shu; Zi, Run; Lai, Shijun

    2015-07-01

    Quantitative phase analysis (QPA) is helpful to determine the type attribute of the object because it could present the content of the constituents. QPA by Rietveld method requires neither measurement of calibration data nor the use of an internal standard; however, the approximate crystal structure of each phase in a mixture is necessary. In this study, 8 synthetic mixtures composed of potassium nitrate and sulfur were analyzed by Rietveld QPA method. The Rietveld refinement was accomplished with a material analysis using diffraction program and evaluated by three agreement indices. Results showed that Rietveld QPA yielded precise results, with errors generally less than 2.0% absolute. In addition, a criminal case which was broken successfully with the help of Rietveld QPA method was also introduced. This method will allow forensic investigators to acquire detailed information of the material evidence, which could point out the direction for case detection and court proceedings.

  14. [Quantitative analysis of butachlor, oxadiazon and simetryn by gas chromatography].

    Science.gov (United States)

    Liu, F; Mu, W; Wang, J

    1999-03-01

    The quantitative analysis of the ingredients in 26% B-O-S (butachlor, oxadiazon and simetryn) emulsion by gas chromatographic method was carried out with a 5% SE-30 on Chromosorb AW DMCS, 2 m x 3 mm i.d., glass column at column temperature of 210 degrees C and detector temperature of 230 degrees C. The internal standard is di-n-butyl sebacate. The retentions of simetryn, internal standard, butachlor and oxadiazon were 6.5, 8.3, 9.9 and 11.9 min respectively. This method has a recovery of 98.62%-100.77% and the coefficients of variation of this analysis of butachlor, oxadiazon and simetryn were 0.46%, 0.32% and 0.57% respectively. All coefficients of linear correlation were higher than 0.999.

  15. Fusing Quantitative Requirements Analysis with Model-based Systems Engineering

    Science.gov (United States)

    Cornford, Steven L.; Feather, Martin S.; Heron, Vance A.; Jenkins, J. Steven

    2006-01-01

    A vision is presented for fusing quantitative requirements analysis with model-based systems engineering. This vision draws upon and combines emergent themes in the engineering milieu. "Requirements engineering" provides means to explicitly represent requirements (both functional and non-functional) as constraints and preferences on acceptable solutions, and emphasizes early-lifecycle review, analysis and verification of design and development plans. "Design by shopping" emphasizes revealing the space of options available from which to choose (without presuming that all selection criteria have previously been elicited), and provides means to make understandable the range of choices and their ramifications. "Model-based engineering" emphasizes the goal of utilizing a formal representation of all aspects of system design, from development through operations, and provides powerful tool suites that support the practical application of these principles. A first step prototype towards this vision is described, embodying the key capabilities. Illustrations, implications, further challenges and opportunities are outlined.

  16. [Quantitative analysis of transformer oil dissolved gases using FTIR].

    Science.gov (United States)

    Zhao, An-xin; Tang, Xiao-jun; Wang, Er-zhen; Zhang, Zhong-hua; Liu, Jun-hua

    2013-09-01

    For the defects of requiring carrier gas and regular calibration, and low safety using chromatography to on line monitor transformer dissolved gases, it was attempted to establish a dissolved gas analysis system based on Fourier transform infrared spectroscopy. Taking into account the small amount of characteristic gases, many components, detection limit and safety requirements and the difficulty of degasser to put an end to the presence of interference gas, the quantitative analysis model was established based on sparse partial least squares, piecewise section correction and feature variable extraction algorithm using improvement TR regularization. With the characteristic gas of CH4, C2H6, C2H6, and CO2, the results show that using FTIR meets DGA requirements with the spectrum wave number resolution of 1 cm(-1) and optical path of 10 cm.

  17. Rapid ultrasonic isothermal amplification of DNA with multiplexed melting analysis – applications in the clinical diagnosis of sexually transmitted diseases.

    Science.gov (United States)

    Xu, Gaolian; Gunson, Rory N; Cooper, Jonathan M; Reboud, Julien

    2015-02-14

    We describe a nucleic acid testing (NAT) platform for infectious disease diagnostics at the point-of-care, using surface acoustic waves (SAW) to perform a multiplexed loop-mediated isothermal amplification (LAMP) test for sexually transmitted diseases. The ultrasonic actuation not only enables faster NAT reactions but also provides a route towards integrating low-cost, low-power molecular diagnostics into disposable sensors.

  18. Quantitative morphometric analysis for the tectonic characterisation of northern Tunisia.

    Science.gov (United States)

    Camafort, Miquel; Pérez-Peña, José Vicente; Booth-Rea, Guillermo; Ranero, César R.; Gràcia, Eulàlia; Azañón, José Miguel; Melki, Fetheddine; Ouadday, Mohamed

    2016-04-01

    Northern Tunisia is characterized by low deformation rates and low to moderate seismicity. Although instrumental seismicity reaches maximum magnitudes of Mw 5.5, some historical earthquakes have occurred with catastrophic consequences in this region. Aiming to improve our knowledge of active tectonics in Tunisia, we carried out both a quantitative morphometric analysis and field study in the north-western region. We applied different morphometric tools, like river profiles, knickpoint analysis, hypsometric curves and integrals and drainage pattern anomalies in order to differentiate between zones with high or low recent tectonic activity. This analysis helps identifying uplift and subsidence zones, which we relate to fault activity. Several active faults in a sparse distribution were identified. A selected sector was studied with a field campaign to test the results obtained with the quantitative analysis. During the fieldwork we identified geological evidence of recent activity and a considerable seismogenic potential along El Alia-Teboursouk (ETF) and Dkhila (DF) faults. The ETF fault could be responsible of one of the most devastating historical earthquakes in northern Tunisia that destroyed Utique in 412 A.D. Geological evidence include fluvial terraces folded by faults, striated and cracked pebbles, clastic dikes, sand volcanoes, coseismic cracks, etc. Although not reflected in the instrumental seismicity, our results support an important seismic hazard, evidenced by the several active tectonic structures identified and the two seismogenic faults described. After obtaining the current active tectonic framework of Tunisia we discuss our results within the western Mediterranean trying to contribute to the understanding of the western Mediterranean tectonic context. With our results, we suggest that the main reason explaining the sparse and scarce seismicity of the area in contrast with the adjacent parts of the Nubia-Eurasia boundary is due to its extended

  19. High Throughput In Situ DDA Analysis of Neuropeptides by Coupling Novel Multiplex Mass Spectrometric Imaging (MSI) with Gas-Phase Fractionation

    Science.gov (United States)

    OuYang, Chuanzi; Chen, Bingming; Li, Lingjun

    2015-12-01

    Matrix-assisted laser desorption/ionization (MALDI) mass spectrometric imaging (MSI) is a powerful tool to map the spatial distribution of biomolecules on tissue sections. Recent developments of hybrid MS instruments allow combination of different types of data acquisition by various mass analyzers into a single MSI analysis, which reduces experimental time and sample consumptions. Here, using the well-characterized crustacean nervous system as a test-bed, we explore the utility of high resolution and accurate mass (HRAM) MALDI Orbitrap platform for enhanced in situ characterization of the neuropeptidome with improved chemical information. Specifically, we report on a multiplex-MSI method, which combines HRAM MSI with data dependent acquisition (DDA) tandem MS analysis in a single experiment. This method enables simultaneous mapping of neuropeptide distribution, sequence validation, and novel neuropeptide discovery in crustacean neuronal tissues. To enhance the dynamic range and efficiency of in situ DDA, we introduced a novel approach of fractionating full m/z range into several sub-mass ranges and embedding the setup using the multiplex-DDA-MSI scan events to generate pseudo fractionation before MS/MS scans. The division of entire m/z into multiple segments of m/z sub-ranges for MS interrogation greatly decreased the complexity of molecular species from tissue samples and the heterogeneity of the distribution and variation of intensities of m/z peaks. By carefully optimizing the experimental conditions such as the dynamic exclusion, the multiplex-DDA-MSI approach demonstrates better performance with broader precursor coverage, less biased MS/MS scans towards high abundance molecules, and improved quality of tandem mass spectra for low intensity molecular species.

  20. Glioblastoma multiforme: exploratory radiogenomic analysis by using quantitative image features.

    Science.gov (United States)

    Gevaert, Olivier; Mitchell, Lex A; Achrol, Achal S; Xu, Jiajing; Echegaray, Sebastian; Steinberg, Gary K; Cheshier, Samuel H; Napel, Sandy; Zaharchuk, Greg; Plevritis, Sylvia K

    2014-10-01

    To derive quantitative image features from magnetic resonance (MR) images that characterize the radiographic phenotype of glioblastoma multiforme (GBM) lesions and to create radiogenomic maps associating these features with various molecular data. Clinical, molecular, and MR imaging data for GBMs in 55 patients were obtained from the Cancer Genome Atlas and the Cancer Imaging Archive after local ethics committee and institutional review board approval. Regions of interest (ROIs) corresponding to enhancing necrotic portions of tumor and peritumoral edema were drawn, and quantitative image features were derived from these ROIs. Robust quantitative image features were defined on the basis of an intraclass correlation coefficient of 0.6 for a digital algorithmic modification and a test-retest analysis. The robust features were visualized by using hierarchic clustering and were correlated with survival by using Cox proportional hazards modeling. Next, these robust image features were correlated with manual radiologist annotations from the Visually Accessible Rembrandt Images (VASARI) feature set and GBM molecular subgroups by using nonparametric statistical tests. A bioinformatic algorithm was used to create gene expression modules, defined as a set of coexpressed genes together with a multivariate model of cancer driver genes predictive of the module's expression pattern. Modules were correlated with robust image features by using the Spearman correlation test to create radiogenomic maps and to link robust image features with molecular pathways. Eighteen image features passed the robustness analysis and were further analyzed for the three types of ROIs, for a total of 54 image features. Three enhancement features were significantly correlated with survival, 77 significant correlations were found between robust quantitative features and the VASARI feature set, and seven image features were correlated with molecular subgroups (P < .05 for all). A radiogenomics map was

  1. Multiparent intercross populations in analysis of quantitative traits

    Indian Academy of Sciences (India)

    Sujay Rakshit; Arunita Rakshit; J. V. Patil

    2011-04-01

    Most traits of interest to medical, agricultural and animal scientists show continuous variation and complex mode of inheritance. DNA-based markers are being deployed to analyse such complex traits, that are known as quantitative trait loci (QTL). In conventional QTL analysis, F2, backcross populations, recombinant inbred lines, backcross inbred lines and double haploids from biparental crosses are commonly used. Introgression lines and near isogenic lines are also being used for QTL analysis. However, such populations have major limitations like predominantly relying on the recombination events taking place in the F1 generation and mapping of only the allelic pairs present in the two parents. The second generation mapping resources like association mapping, nested association mapping and multiparent intercross populations potentially address the major limitations of available mapping resources. The potential of multiparent intercross populations in gene mapping has been discussed here. In such populations both linkage and association analysis can be conductted without encountering the limitations of structured populations. In such populations, larger genetic variation in the germplasm is accessed and various allelic and cytoplasmic interactions are assessed. For all practical purposes, across crop species, use of eight founders and a fixed population of 1000 individuals are most appropriate. Limitations with multiparent intercross populations are that they require longer time and more resource to be generated and they are likely to show extensive segregation for developmental traits, limiting their use in the analysis of complex traits. However, multiparent intercross population resources are likely to bring a paradigm shift towards QTL analysis in plant species.

  2. Phenotypic analysis of Arabidopsis mutants: quantitative analysis of root growth.

    Science.gov (United States)

    Doerner, Peter

    2008-03-01

    INTRODUCTIONThe growth of plant roots is very easy to measure and is particularly straightforward in Arabidopsis thaliana, because the increase in organ size is essentially restricted to one dimension. The precise measurement of root apical growth can be used to accurately determine growth activity (the rate of growth at a given time) during development in mutants, transgenic backgrounds, or in response to experimental treatments. Root growth is measured in a number of ways, the simplest of which is to grow the seedlings in a Petri dish and record the position of the advancing root tip at appropriate time points. The increase in root length is measured with a ruler and the data are entered into Microsoft Excel for analysis. When dealing with large numbers of seedlings, however, this procedure can be tedious, as well as inaccurate. An alternative approach, described in this protocol, uses "snapshots" of the growing plants, which are taken using gel-documentation equipment (i.e., a video camera with a frame-grabber unit, now commonly used to capture images from ethidium-bromide-stained electrophoresis gels). The images are analyzed using publicly available software (NIH-Image), which allows the user simply to cut and paste data into Microsoft Excel.

  3. Epistasis analysis for quantitative traits by functional regression model.

    Science.gov (United States)

    Zhang, Futao; Boerwinkle, Eric; Xiong, Momiao

    2014-06-01

    The critical barrier in interaction analysis for rare variants is that most traditional statistical methods for testing interactions were originally designed for testing the interaction between common variants and are difficult to apply to rare variants because of their prohibitive computational time and poor ability. The great challenges for successful detection of interactions with next-generation sequencing (NGS) data are (1) lack of methods for interaction analysis with rare variants, (2) severe multiple testing, and (3) time-consuming computations. To meet these challenges, we shift the paradigm of interaction analysis between two loci to interaction analysis between two sets of loci or genomic regions and collectively test interactions between all possible pairs of SNPs within two genomic regions. In other words, we take a genome region as a basic unit of interaction analysis and use high-dimensional data reduction and functional data analysis techniques to develop a novel functional regression model to collectively test interactions between all possible pairs of single nucleotide polymorphisms (SNPs) within two genome regions. By intensive simulations, we demonstrate that the functional regression models for interaction analysis of the quantitative trait have the correct type 1 error rates and a much better ability to detect interactions than the current pairwise interaction analysis. The proposed method was applied to exome sequence data from the NHLBI's Exome Sequencing Project (ESP) and CHARGE-S study. We discovered 27 pairs of genes showing significant interactions after applying the Bonferroni correction (P-values < 4.58 × 10(-10)) in the ESP, and 11 were replicated in the CHARGE-S study.

  4. The analysis of high explosives by liquid chromatography/electrospray ionization mass spectrometry: multiplexed detection of negative ion adducts.

    Science.gov (United States)

    Mathis, John A; McCord, Bruce R

    2005-01-01

    The negative ion electrospray ionization mass spectrometric (ESI-MS) detection of adducts of high explosives with chloride, formate, acetate, and nitrate was used to demonstrate the gas-phase interaction of neutral explosives with these anions. The relative intensities of the adduct species were determined to compare the competitive formation of the selected high explosives and anions. The relative stability of the adduct species varies, yielding preferential formation of certain anionic adducts with different high explosives. To exploit this effect, an isocratic high-performance liquid chromatography (HPLC)/ESI-MS method was developed and used for the simultaneous analysis of high explosives using two different techniques for the addition of the anionic additives; pre- and post-column. The results show that the pre-column approach provides similar results with improved selectivity for specific explosives. By detecting characteristic adduct species for each explosive, this method provides a qualitative and quantitative approach for the analysis and identification of high explosives.

  5. Quantitative CT analysis of small pulmonary vessels in lymphangioleiomyomatosis

    Energy Technology Data Exchange (ETDEWEB)

    Ando, Katsutoshi, E-mail: kando@juntendo.ac.jp [Department of Internal Medicine, Division of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); Tobino, Kazunori [Department of Respiratory Medicine, Iizuka Hospital, 3-83 Yoshio-Machi, Iizuka-City, Fukuoka 820-8505 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); Kurihara, Masatoshi; Kataoka, Hideyuki [Pneumothorax Center, Nissan Tamagawa Hospital, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); Doi, Tokuhide [Fukuoka Clinic, 7-18-11 Umeda, Adachi-Ku, Tokyo 123-0851 (Japan); Hoshika, Yoshito [Department of Internal Medicine, Division of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan); Takahashi, Kazuhisa [Department of Internal Medicine, Division of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421 (Japan); Seyama, Kuniaki [Department of Internal Medicine, Division of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421 (Japan); The Study Group of Pneumothorax and Cystic Lung Diseases, 4-8-1 Seta, Setagaya-Ku, Tokyo 158-0095 (Japan)

    2012-12-15

    Backgrounds: Lymphangioleiomyomatosis (LAM) is a destructive lung disease that share clinical, physiologic, and radiologic features with chronic obstructive pulmonary disease (COPD). This study aims to identify those features that are unique to LAM by using quantitative CT analysis. Methods: We measured total cross-sectional areas of small pulmonary vessels (CSA) less than 5 mm{sup 2} and 5–10 mm{sup 2} and calculated percentages of those lung areas (%CSA), respectively, in 50 LAM and 42 COPD patients. The extent of cystic destruction (LAA%) and mean parenchymal CT value were also calculated and correlated with pulmonary function. Results: The diffusing capacity for carbon monoxide/alveolar volume (DL{sub CO}/VA %predicted) was similar for both groups (LAM, 44.4 ± 19.8% vs. COPD, 45.7 ± 16.0%, p = 0.763), but less tissue damage occurred in LAM than COPD (LAA% 21.7 ± 16.3% vs. 29.3 ± 17.0; p < 0.05). Pulmonary function correlated negatively with LAA% (p < 0.001) in both groups, yet the correlation with %CSA was significant only in COPD (p < 0.001). When the same analysis was conducted in two groups with equal levels of LAA% and DL{sub CO}/VA %predicted, %CSA and mean parenchymal CT value were still greater for LAM than COPD (p < 0.05). Conclusions: Quantitative CT analysis revealing a correlation between cystic destruction and CSA in COPD but not LAM indicates that this approach successfully reflects different mechanisms governing the two pathologic courses. Such determinations of small pulmonary vessel density may serve to differentiate LAM from COPD even in patients with severe lung destruction.

  6. The Quantitative Analysis of Chennai Automotive Industry Cluster

    Science.gov (United States)

    Bhaskaran, Ethirajan

    2016-07-01

    Chennai, also called as Detroit of India due to presence of Automotive Industry producing over 40 % of the India's vehicle and components. During 2001-2002, the Automotive Component Industries (ACI) in Ambattur, Thirumalizai and Thirumudivakkam Industrial Estate, Chennai has faced problems on infrastructure, technology, procurement, production and marketing. The objective is to study the Quantitative Performance of Chennai Automotive Industry Cluster before (2001-2002) and after the CDA (2008-2009). The methodology adopted is collection of primary data from 100 ACI using quantitative questionnaire and analyzing using Correlation Analysis (CA), Regression Analysis (RA), Friedman Test (FMT), and Kruskall Wallis Test (KWT).The CA computed for the different set of variables reveals that there is high degree of relationship between the variables studied. The RA models constructed establish the strong relationship between the dependent variable and a host of independent variables. The models proposed here reveal the approximate relationship in a closer form. KWT proves, there is no significant difference between three locations clusters with respect to: Net Profit, Production Cost, Marketing Costs, Procurement Costs and Gross Output. This supports that each location has contributed for development of automobile component cluster uniformly. The FMT proves, there is no significant difference between industrial units in respect of cost like Production, Infrastructure, Technology, Marketing and Net Profit. To conclude, the Automotive Industries have fully utilized the Physical Infrastructure and Centralised Facilities by adopting CDA and now exporting their products to North America, South America, Europe, Australia, Africa and Asia. The value chain analysis models have been implemented in all the cluster units. This Cluster Development Approach (CDA) model can be implemented in industries of under developed and developing countries for cost reduction and productivity

  7. QuASAR: quantitative allele-specific analysis of reads.

    Science.gov (United States)

    Harvey, Chris T; Moyerbrailean, Gregory A; Davis, Gordon O; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2015-04-15

    Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. http://github.com/piquelab/QuASAR. fluca@wayne.edu or rpique@wayne.edu Supplementary Material is available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  8. Quantitative modeling and data analysis of SELEX experiments

    Science.gov (United States)

    Djordjevic, Marko; Sengupta, Anirvan M.

    2006-03-01

    SELEX (systematic evolution of ligands by exponential enrichment) is an experimental procedure that allows the extraction, from an initially random pool of DNA, of those oligomers with high affinity for a given DNA-binding protein. We address what is a suitable experimental and computational procedure to infer parameters of transcription factor-DNA interaction from SELEX experiments. To answer this, we use a biophysical model of transcription factor-DNA interactions to quantitatively model SELEX. We show that a standard procedure is unsuitable for obtaining accurate interaction parameters. However, we theoretically show that a modified experiment in which chemical potential is fixed through different rounds of the experiment allows robust generation of an appropriate dataset. Based on our quantitative model, we propose a novel bioinformatic method of data analysis for such a modified experiment and apply it to extract the interaction parameters for a mammalian transcription factor CTF/NFI. From a practical point of view, our method results in a significantly improved false positive/false negative trade-off, as compared to both the standard information theory based method and a widely used empirically formulated procedure.

  9. Quantitative analysis of multiple sclerosis: a feasibility study

    Science.gov (United States)

    Li, Lihong; Li, Xiang; Wei, Xinzhou; Sturm, Deborah; Lu, Hongbing; Liang, Zhengrong

    2006-03-01

    Multiple Sclerosis (MS) is an inflammatory and demyelinating disorder of the central nervous system with a presumed immune-mediated etiology. For treatment of MS, the measurements of white matter (WM), gray matter (GM), and cerebral spinal fluid (CSF) are often used in conjunction with clinical evaluation to provide a more objective measure of MS burden. In this paper, we apply a new unifying automatic mixture-based algorithm for segmentation of brain tissues to quantitatively analyze MS. The method takes into account the following effects that commonly appear in MR imaging: 1) The MR data is modeled as a stochastic process with an inherent inhomogeneity effect of smoothly varying intensity; 2) A new partial volume (PV) model is built in establishing the maximum a posterior (MAP) segmentation scheme; 3) Noise artifacts are minimized by a priori Markov random field (MRF) penalty indicating neighborhood correlation from tissue mixture. The volumes of brain tissues (WM, GM) and CSF are extracted from the mixture-based segmentation. Experimental results of feasibility studies on quantitative analysis of MS are presented.

  10. Quantitative colorimetric-imaging analysis of nickel in iron meteorites.

    Science.gov (United States)

    Zamora, L Lahuerta; López, P Alemán; Fos, G M Antón; Algarra, R Martín; Romero, A M Mellado; Calatayud, J Martínez

    2011-02-15

    A quantitative analytical imaging approach for determining the nickel content of metallic meteorites is proposed. The approach uses a digital image of a series of standard solutions of the nickel-dimethylglyoxime coloured chelate and a meteorite sample solution subjected to the same treatment as the nickel standards for quantitation. The image is processed with suitable software to assign a colour-dependent numerical value (analytical signal) to each standard. Such a value is directly proportional to the analyte concentration, which facilitates construction of a calibration graph where the value for the unknown sample can be interpolated to calculate the nickel content of the meteorite. The results thus obtained were validated by comparison with the official, ISO-endorsed spectrophotometric method for nickel. The proposed method is fairly simple and inexpensive; in fact, it uses a commercially available digital camera as measuring instrument and the images it provides are processed with highly user-friendly public domain software (specifically, ImageJ, developed by the National Institutes of Health and freely available for download on the Internet). In a scenario dominated by increasingly sophisticated and expensive equipment, the proposed method provides a cost-effective alternative based on simple, robust hardware that is affordable and can be readily accessed worldwide. This can be especially advantageous for countries were available resources for analytical equipment investments are scant. The proposed method is essentially an adaptation of classical chemical analysis to current, straightforward, robust, cost-effective instrumentation. Copyright © 2010 Elsevier B.V. All rights reserved.

  11. Quantitative analysis of tumor burden in mouse lung via MRI.

    Science.gov (United States)

    Tidwell, Vanessa K; Garbow, Joel R; Krupnick, Alexander S; Engelbach, John A; Nehorai, Arye

    2012-02-01

    Lung cancer is the leading cause of cancer death in the United States. Despite recent advances in screening protocols, the majority of patients still present with advanced or disseminated disease. Preclinical rodent models provide a unique opportunity to test novel therapeutic drugs for targeting lung cancer. Respiratory-gated MRI is a key tool for quantitatively measuring lung-tumor burden and monitoring the time-course progression of individual tumors in mouse models of primary and metastatic lung cancer. However, quantitative analysis of lung-tumor burden in mice by MRI presents significant challenges. Herein, a method for measuring tumor burden based upon average lung-image intensity is described and validated. The method requires accurate lung segmentation; its efficiency and throughput would be greatly aided by the ability to automatically segment the lungs. A technique for automated lung segmentation in the presence of varying tumor burden levels is presented. The method includes development of a new, two-dimensional parametric model of the mouse lungs and a multi-faceted cost function to optimally fit the model parameters to each image. Results demonstrate a strong correlation (0.93), comparable with that of fully manual expert segmentation, between the automated method's tumor-burden metric and the tumor burden measured by lung weight.

  12. The Impact of Arithmetic Skills on Mastery of Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Bruce K. Blaylock

    2012-01-01

    Full Text Available Over the past several years math education has moved from a period where all math calculations were done by hand to an era where most calculations are done using a calculator or computer. There are certainly benefits to this approach, but when one concomitantly recognizes the declining scores on national standardized mathematics exams, it raises the question, “Could the lack of technology-assisted arithmetic manipulation skills have a carryover to understanding higher-level mathematical concepts or is it just a spurious correlation?” Eighty-seven students were tested for their ability to do simple arithmetic and algebra by hand. These scores were then regressed on three important areas of quantitative analysis: recognizing the appropriate tool to use in an analysis, creating a model to carry out the analysis, and interpreting the results of the analysis. The study revealed a significant relationship between the ability to accurately do arithmetic calculations and the ability to recognize the appropriate tool and creating a model. It found no significant relationship between results interpretation and arithmetic skills.

  13. Analysis of generalized interictal discharges using quantitative EEG.

    Science.gov (United States)

    da Silva Braga, Aline Marques; Fujisao, Elaine Keiko; Betting, Luiz Eduardo

    2014-12-01

    Experimental evidence from animal models of the absence seizures suggests a focal source for the initiation of generalized spike-and-wave (GSW) discharges. Furthermore, clinical studies indicate that patients diagnosed with idiopathic generalized epilepsy (IGE) exhibit focal electroencephalographic abnormalities, which involve the thalamo-cortical circuitry. This circuitry is a key network that has been implicated in the initiation of generalized discharges, and may contribute to the pathophysiology of GSW discharges. Quantitative electroencephalogram (qEEG) analysis may be able to detect abnormalities associated with the initiation of GSW discharges. The objective of this study was to determine whether interictal GSW discharges exhibit focal characteristics using qEEG analysis. In this study, 75 EEG recordings from 64 patients were analyzed. All EEG recordings analyzed contained at least one GSW discharge. EEG recordings were obtained by a 22-channel recorder with electrodes positioned according to the international 10-20 system of electrode placement. EEG activity was recorded for 20 min including photic stimulation and hyperventilation. The EEG recordings were visually inspected, and the first unequivocally confirmed generalized spike was marked for each discharge. Three methods of source imaging analysis were applied: dipole source imaging (DSI), classical LORETA analysis recursively applied (CLARA), and equivalent dipole of independent components with cluster analysis. A total of 753 GSW discharges were identified and spatiotemporally analyzed. Source evaluation analysis using all three techniques revealed that the frontal lobe was the principal source of GSW discharges (70%), followed by the parietal and occipital lobes (14%), and the basal ganglia (12%). The main anatomical sources of GSW discharges were the anterior cingulate cortex (36%) and the medial frontal gyrus (23%). Source analysis did not reveal a common focal source of GSW discharges. However

  14. Detection of viable enterotoxin-producing Bacillus cereus and analysis of toxigenicity from ready-to-eat foods and infant formula milk powder by multiplex PCR.

    Science.gov (United States)

    Zhang, Zhihong; Feng, Lixia; Xu, Hengyi; Liu, Chengwei; Shah, Nagendra P; Wei, Hua

    2016-02-01

    Bacillus cereus is responsible for several outbreaks of foodborne diseases due to its emetic toxin and enterotoxin. Enterotoxins, cytotoxin K (CytK), nonhemolytic enterotoxin (Nhe), and hemolysin BL (Hbl), have been recorded in several diarrheal cases due to food poisoning from B. cereus. The objective of this study was to develop a rapid and accurate method that combines multiplex PCR with propidium monoazide to selectively detect viable cells of enterotoxin-producing B. cereus in milk powder, noodles, and rice, and investigate the distribution of enterotoxins in 62 strains of B. cereus in Jiangxi province, China. The specificity of primers of 3 enterotoxins (i.e., cytK, nheA, and hblD) of B. cereus was verified by inclusivity and exclusivity tests using single PCR. Upon optimization of multiplex PCR conditions, it was found that the detection limit of viable cells was 10(2) cfu/mL of B. cereus in pure culture. By enrichment for 3 or 4 h and propidium monoazide pretreatment, a protocol for detection of viable cells as low as 2.2×10(1) cfu/g in spiked food (e.g., milk powder, noodles, and rice) was established and proved valid even under the interference of non-Bacillus cereus at as high as 10(5) cfu/g. Moreover, the protocol based on multiplex PCR for detection was applied for the analysis of distribution of toxin gene of B. cereus, and the results showed a regional feature for toxin gene distribution, indicating that potential toxigenicity of B. cereus should be evaluated further.

  15. ANALYSIS OF REDUCTION IN COMPLEXITY OF MULTIPLE INPUT- MULTIPLE OUTPUT-ORTHOGONAL FREQUENCY DIVISION MULTIPLEXING SYSTEMS WITH CARRIER FREQUENCY OFFSET ESTIMATION AND CORRECTION

    Directory of Open Access Journals (Sweden)

    Sabitha Gauni

    2014-01-01

    Full Text Available Orthogonal Frequency Division Multiplexing (OFDM is a promising research area in Wireless Communication for high data rates. The Multiple Input-Multiple Output (MIMO technology when incorporated with the OFDM system promise a significant boost in the performance. But, the MIMO-OFDM systems are very sensitive to Carrier Frequency Offset (CFO as it deteriorates the system performance with the rise of Inter-Carrier-Interference (ICI. A theoretical analysis to evaluate the performance of Orthogonal Frequency Division Multiplexing (OFDM systems is done here, under the combined influence of Phase Offset and Frequency Offset over Rayleigh, Weibull and Nakagami fading channels using Binary Phase Shift Keying (BPSK Modulation. The analysis of increase in Bit Error Rate (BER caused by the presence of Phase Offset and Frequency Offset is evaluated assuming Gaussian probability density function. Hence the estimation and correction of CFO plays a vital role in MIMO-OFDM systems. A method for CFO estimation and correction is analyzed in the MIMO-OFDM system with 16-QAM modulation. In non-pilot-aided systems the CFO acquisition is done using Maximum Likelihood Estimation (MLE algorithm. The proposed scheme uses the same block for CFO correction of MIMO-OFDM symbols. Since the same phase calculation block is used for the ML estimation along with the acquisition, the computational cost and the complexity of implementation is reduced.

  16. Quantitative microstructure analysis of polymer-modified mortars.

    Science.gov (United States)

    Jenni, A; Herwegh, M; Zurbriggen, R; Aberle, T; Holzer, L

    2003-11-01

    Digital light, fluorescence and electron microscopy in combination with wavelength-dispersive spectroscopy were used to visualize individual polymers, air voids, cement phases and filler minerals in a polymer-modified cementitious tile adhesive. In order to investigate the evolution and processes involved in formation of the mortar microstructure, quantifications of the phase distribution in the mortar were performed including phase-specific imaging and digital image analysis. The required sample preparation techniques and imaging related topics are discussed. As a form of case study, the different techniques were applied to obtain a quantitative characterization of a specific mortar mixture. The results indicate that the mortar fractionates during different stages ranging from the early fresh mortar until the final hardened mortar stage. This induces process-dependent enrichments of the phases at specific locations in the mortar. The approach presented provides important information for a comprehensive understanding of the functionality of polymer-modified mortars.

  17. Ozone Determination: A Comparison of Quantitative Analysis Methods

    Directory of Open Access Journals (Sweden)

    Rachmat Triandi Tjahjanto

    2012-10-01

    Full Text Available A comparison of ozone quantitative analysis methods by using spectrophotometric and volumetric method has been studied. The aim of this research is to determine the better method by considering the effect of reagent concentration and volume on the measured ozone concentration. Ozone which was analyzed in this research was synthesized from air, then it is used to ozonize methyl orange and potassium iodide solutions at different concentration and volume. Ozonation was held for 20 minutes with 363 mL/minutes air flow rates. The concentrations of ozonized methyl orange and potassium iodide solutions was analyzed by spectrophotometric and volumetric method, respectively. The result of this research shows that concentration and volume of reagent having an effect on the measured ozone concentration. Based on the results of both methods, it can be concluded that volumetric method is better than spectrophotometric method.

  18. Quantitative genetic analysis of injury liability in infants and toddlers

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, K.; Matheny, A.P. Jr. [Univ. of Louisville Medical School, KY (United States)

    1995-02-27

    A threshold model of latent liability was applied to infant and toddler twin data on total count of injuries sustained during the interval from birth to 36 months of age. A quantitative genetic analysis of estimated twin correlations in injury liability indicated strong genetic dominance effects, but no additive genetic variance was detected. Because interpretations involving overdominance have little research support, the results may be due to low order epistasis or other interaction effects. Boys had more injuries than girls, but this effect was found only for groups whose parents were prompted and questioned in detail about their children`s injuries. Activity and impulsivity are two behavioral predictors of childhood injury, and the results are discussed in relation to animal research on infant and adult activity levels, and impulsivity in adult humans. Genetic epidemiological approaches to childhood injury should aid in targeting higher risk children for preventive intervention. 30 refs., 4 figs., 3 tabs.

  19. Quantitative analysis of gallstones using laser-induced breakdown spectroscopy.

    Science.gov (United States)

    Singh, Vivek K; Singh, Vinita; Rai, Awadhesh K; Thakur, Surya N; Rai, Pradeep K; Singh, Jagdish P

    2008-11-01

    The utility of laser-induced breakdown spectroscopy (LIBS) for categorizing different types of gallbladder stone has been demonstrated by analyzing their major and minor constituents. LIBS spectra of three types of gallstone have been recorded in the 200-900 nm spectral region. Calcium is found to be the major element in all types of gallbladder stone. The spectrophotometric method has been used to classify the stones. A calibration-free LIBS method has been used for the quantitative analysis of metal elements, and the results have been compared with those obtained from inductively coupled plasma atomic emission spectroscopy (ICP-AES) measurements. The single-shot LIBS spectra from different points on the cross section (in steps of 0.5 mm from one end to the other) of gallstones have also been recorded to study the variation of constituents from the center to the surface. The presence of different metal elements and their possible role in gallstone formation is discussed.

  20. Quantitative image analysis of WE43-T6 cracking behavior

    Science.gov (United States)

    Ahmad, A.; Yahya, Z.

    2013-06-01

    Environment-assisted cracking of WE43 cast magnesium (4.2 wt.% Yt, 2.3 wt.% Nd, 0.7% Zr, 0.8% HRE) in the T6 peak-aged condition was induced in ambient air in notched specimens. The mechanism of fracture was studied using electron backscatter diffraction, serial sectioning and in situ observations of crack propagation. The intermetallic (rare earthed-enriched divorced intermetallic retained at grain boundaries and predominantly at triple points) material was found to play a significant role in initiating cracks which leads to failure of this material. Quantitative measurements were required for this project. The populations of the intermetallic and clusters of intermetallic particles were analyzed using image analysis of metallographic images. This is part of the work to generate a theoretical model of the effect of notch geometry on the static fatigue strength of this material.

  1. qfasar: quantitative fatty acid signature analysis with R

    Science.gov (United States)

    Bromaghin, Jeffrey

    2017-01-01

    Knowledge of predator diets provides essential insights into their ecology, yet diet estimation is challenging and remains an active area of research.Quantitative fatty acid signature analysis (QFASA) is a popular method of estimating diet composition that continues to be investigated and extended. However, software to implement QFASA has only recently become publicly available.I summarize a new R package, qfasar, for diet estimation using QFASA methods. The package also provides functionality to evaluate and potentially improve the performance of a library of prey signature data, compute goodness-of-fit diagnostics, and support simulation-based research. Several procedures in the package have not previously been published.qfasar makes traditional and recently published QFASA diet estimation methods accessible to ecologists for the first time. Use of the package is illustrated with signature data from Chukchi Sea polar bears and potential prey species.

  2. Large-Scale Quantitative Analysis of Painting Arts

    Science.gov (United States)

    Kim, Daniel; Son, Seung-Woo; Jeong, Hawoong

    2014-12-01

    Scientists have made efforts to understand the beauty of painting art in their own languages. As digital image acquisition of painting arts has made rapid progress, researchers have come to a point where it is possible to perform statistical analysis of a large-scale database of artistic paints to make a bridge between art and science. Using digital image processing techniques, we investigate three quantitative measures of images - the usage of individual colors, the variety of colors, and the roughness of the brightness. We found a difference in color usage between classical paintings and photographs, and a significantly low color variety of the medieval period. Interestingly, moreover, the increment of roughness exponent as painting techniques such as chiaroscuro and sfumato have advanced is consistent with historical circumstances.

  3. Quantitative analysis of forest island pattern in selected Ohio landscapes

    Energy Technology Data Exchange (ETDEWEB)

    Bowen, G.W.; Burgess, R.L.

    1981-07-01

    The purpose of this study was to quantitatively describe the various aspects of regional distribution patterns of forest islands and relate those patterns to other landscape features. Several maps showing the forest cover of various counties in Ohio were selected as representative examples of forest patterns to be quantified. Ten thousand hectare study areas (landscapes) were delineated on each map. A total of 15 landscapes representing a wide variety of forest island patterns was chosen. Data were converted into a series of continuous variables which contained information pertinent to the sizes, shape, numbers, and spacing of woodlots within a landscape. The continuous variables were used in a factor analysis to describe the variation among landscapes in terms of forest island pattern. The results showed that forest island patterns are related to topography and other environmental features correlated with topography.

  4. Quantitative analysis of secretome from adipocytes regulated by insulin

    Institute of Scientific and Technical Information of China (English)

    Hu Zhou; Yuanyuan Xiao; Rongxia Li; Shangyu Hong; Sujun Li; Lianshui Wang; Rong Zeng; Kan Liao

    2009-01-01

    Adipocyte is not only a central player involved in storage and release of energy, but also in regulation of energy metabolism in other organs via secretion of pep-tides and proteins. During the pathogenesis of insulin resistance and type 2 diabetes, adipocytes are subjected to the increased levels of insulin, which may have a major impact on the secretion of adipokines. We have undertaken cleavable isotope-coded affinity tag (clCAT) and label-free quantitation approaches to identify and quantify secretory factors that are differen-tially secreted by 3T3-LI adipocytes with or without insulin treatment. Combination of clCAT and label-free results, there are 317 proteins predicted or annotated as secretory proteins. Among these secretory proteins, 179 proteins and 53 proteins were significantly up-regulated and down-regulated, respectively. A total of 77 reported adipokines were quantified in our study, such as adiponectin, cathepsin D, cystatin C, resistin, and transferrin. Western blot analysis of these adipo-kines confirmed the quantitative results from mass spectrometry, and revealed individualized secreting pat-terns of these proteins by increasing insulin dose. In addition, 240 proteins were newly identified and quanti-fied as secreted proteins from 3T3-L1 adipocytes in our study, most of which were up-regulated upon insulin treatment. Further comprehensive bioinformatics analysis revealed that the secretory proteins in extra-cellular matrix-receptor interaction pathway and glycan structure degradation pathway were significantly up-regulated by insulin stimulation.

  5. PIQMIe: A web server for semi-quantitative proteomics data management and analysis

    NARCIS (Netherlands)

    A. Kuzniar (Arnold); R. Kanaar (Roland)

    2014-01-01

    textabstractWe present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates pept

  6. Multiplex tokamak power plant

    Energy Technology Data Exchange (ETDEWEB)

    Dabiri, A.E.

    1986-07-01

    The concept of multiplexing for a fusion power core as an option for producing power is explored. Superconducting, as well as normal magnet, coils in either first or second stability regimes are considered. The results show that multiplex plants with superconducting magnets operating in the second stability regime could be competitive with the single-unit plants in some unit sizes. The key issues that impact the expected benefits of multiplexing must be investigated further. These are factory fabrication, economy of scale, the extent of equipment sharing, inherent safety, maintainability, and utility load management.

  7. Automatic quantitative analysis of cardiac MR perfusion images

    Science.gov (United States)

    Breeuwer, Marcel M.; Spreeuwers, Luuk J.; Quist, Marcel J.

    2001-07-01

    Magnetic Resonance Imaging (MRI) is a powerful technique for imaging cardiovascular diseases. The introduction of cardiovascular MRI into clinical practice is however hampered by the lack of efficient and accurate image analysis methods. This paper focuses on the evaluation of blood perfusion in the myocardium (the heart muscle) from MR images, using contrast-enhanced ECG-triggered MRI. We have developed an automatic quantitative analysis method, which works as follows. First, image registration is used to compensate for translation and rotation of the myocardium over time. Next, the boundaries of the myocardium are detected and for each position within the myocardium a time-intensity profile is constructed. The time interval during which the contrast agent passes for the first time through the left ventricle and the myocardium is detected and various parameters are measured from the time-intensity profiles in this interval. The measured parameters are visualized as color overlays on the original images. Analysis results are stored, so that they can later on be compared for different stress levels of the heart. The method is described in detail in this paper and preliminary validation results are presented.

  8. QTL analysis for some quantitative traits in bread wheat

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Quantitative trait loci (QTL) analysis was conducted in bread wheat for 14 important traits utilizing data from four different mapping populations involving different approaches of QTL analysis. Analysis for grain protein content (GPC) suggested that the major part of genetic variation for this trait is due to environmental interactions. In contrast, pre-harvest sprouting tolerance (PHST) was controlled mainly by main effect QTL (M-QTL) with very little genetic variation due to environmental interactions; a major QTL for PHST was detected on chromosome arm 3AL. For grain weight, one QTL each was detected on chromosome arms 1AS, 2BS and 7AS. QTL for 4 growth related traits taken together detected by different methods ranged from 37 to 40; nine QTL that were detected by single-locus as well as two-locus analyses were all M-QTL. Similarly, single-locus and two-locus QTL analyses for seven yield and yield contributing traits in two populations respectively allowed detection of 25 and 50 QTL by composite interval mapping (CIM), 16 and 25 QTL by multiple-trait composite interval mapping (MCIM) and 38 and 37 QTL by two-locus analyses. These studies should prove useful in QTL cloning and wheat improvement through marker aided selection.

  9. Quantitative polymerase chain reaction analysis by deconvolution of internal standard.

    Science.gov (United States)

    Hirakawa, Yasuko; Medh, Rheem D; Metzenberg, Stan

    2010-04-29

    Quantitative Polymerase Chain Reaction (qPCR) is a collection of methods for estimating the number of copies of a specific DNA template in a sample, but one that is not universally accepted because it can lead to highly inaccurate (albeit precise) results. The fundamental problem is that qPCR methods use mathematical models that explicitly or implicitly apply an estimate of amplification efficiency, the error of which is compounded in the analysis to unacceptable levels. We present a new method of qPCR analysis that is efficiency-independent and yields accurate and precise results in controlled experiments. The method depends on a computer-assisted deconvolution that finds the point of concordant amplification behavior between the "unknown" template and an admixed amplicon standard. We apply the method to demonstrate dexamethasone-induced changes in gene expression in lymphoblastic leukemia cell lines. This method of qPCR analysis does not use any explicit or implicit measure of efficiency, and may therefore be immune to problems inherent in other qPCR approaches. It yields an estimate of absolute initial copy number of template, and controlled tests show it generates accurate results.

  10. Quantitative polymerase chain reaction analysis by deconvolution of internal standard

    Directory of Open Access Journals (Sweden)

    Metzenberg Stan

    2010-04-01

    Full Text Available Abstract Background Quantitative Polymerase Chain Reaction (qPCR is a collection of methods for estimating the number of copies of a specific DNA template in a sample, but one that is not universally accepted because it can lead to highly inaccurate (albeit precise results. The fundamental problem is that qPCR methods use mathematical models that explicitly or implicitly apply an estimate of amplification efficiency, the error of which is compounded in the analysis to unacceptable levels. Results We present a new method of qPCR analysis that is efficiency-independent and yields accurate and precise results in controlled experiments. The method depends on a computer-assisted deconvolution that finds the point of concordant amplification behavior between the "unknown" template and an admixed amplicon standard. We apply the method to demonstrate dexamethasone-induced changes in gene expression in lymphoblastic leukemia cell lines. Conclusions This method of qPCR analysis does not use any explicit or implicit measure of efficiency, and may therefore be immune to problems inherent in other qPCR approaches. It yields an estimate of absolute initial copy number of template, and controlled tests show it generates accurate results.

  11. Multiplexed DNA-modified electrodes.

    Science.gov (United States)

    Slinker, Jason D; Muren, Natalie B; Gorodetsky, Alon A; Barton, Jacqueline K

    2010-03-03

    We report the use of silicon chips with 16 DNA-modified electrodes (DME chips) utilizing DNA-mediated charge transport for multiplexed detection of DNA and DNA-binding protein targets. Four DNA sequences were simultaneously distinguished on a single DME chip with 4-fold redundancy, including one incorporating a single base mismatch. These chips also enabled investigation of the sequence-specific activity of the restriction enzyme Alu1. DME chips supported dense DNA monolayer formation with high reproducibility, as confirmed by statistical comparison to commercially available rod electrodes. The working electrode areas on the chips were reduced to 10 microm in diameter, revealing microelectrode behavior that is beneficial for high sensitivity and rapid kinetic analysis. These results illustrate how DME chips facilitate sensitive and selective detection of DNA and DNA-binding protein targets in a robust and internally standardized multiplexed format.

  12. An approach for quantitative image quality analysis for CT

    Science.gov (United States)

    Rahimi, Amir; Cochran, Joe; Mooney, Doug; Regensburger, Joe

    2016-03-01

    An objective and standardized approach to assess image quality of Compute Tomography (CT) systems is required in a wide variety of imaging processes to identify CT systems appropriate for a given application. We present an overview of the framework we have developed to help standardize and to objectively assess CT image quality for different models of CT scanners used for security applications. Within this framework, we have developed methods to quantitatively measure metrics that should correlate with feature identification, detection accuracy and precision, and image registration capabilities of CT machines and to identify strengths and weaknesses in different CT imaging technologies in transportation security. To that end we have designed, developed and constructed phantoms that allow for systematic and repeatable measurements of roughly 88 image quality metrics, representing modulation transfer function, noise equivalent quanta, noise power spectra, slice sensitivity profiles, streak artifacts, CT number uniformity, CT number consistency, object length accuracy, CT number path length consistency, and object registration. Furthermore, we have developed a sophisticated MATLAB based image analysis tool kit to analyze CT generated images of phantoms and report these metrics in a format that is standardized across the considered models of CT scanners, allowing for comparative image quality analysis within a CT model or between different CT models. In addition, we have developed a modified sparse principal component analysis (SPCA) method to generate a modified set of PCA components as compared to the standard principal component analysis (PCA) with sparse loadings in conjunction with Hotelling T2 statistical analysis method to compare, qualify, and detect faults in the tested systems.

  13. Multiplexed magnetic nanoparticle-antibody conjugates (MNPs-ABS) based prognostic detection of ovarian cancer biomarkers, CA-125, β-2M and ApoA1 using fluorescence spectroscopy with comparison of surface plasmon resonance (SPR) analysis.

    Science.gov (United States)

    Pal, Manoj K; Rashid, Mohammad; Bisht, Manisha

    2015-11-15

    A multiplexed MNPs-Abs based fluorescence spectroscopic system in analysis of serum biomarkers; CA-125, β2-M and ApoA1 for the early detection of ovarian cancer was first time proposed. The lowest detection limits measured in multiplexed setup were 0.26 U/mL, 0.55 ng/mL and 7.7 ng/mL respectively for CA-125, β2-M and ApoA1. A comparative real sample analysis of healthy normal (Control), benign and ovarian cancer patients with SPR has also been done to validate the process. Moreover CA-125 detection only confirms 50-60% of early stage disease. This multiplexed system achieved sensitivity and specificity up to 94% and 98% respectively to distinguish early stage ovarian cancer patients from healthy individuals.

  14. Multiplex detection of food allergens and gluten.

    Science.gov (United States)

    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.

  15. Development of analytical methods for multiplex bio-assay with inductively coupled plasma mass spectrometry.

    Science.gov (United States)

    Ornatsky, Olga I; Kinach, Robert; Bandura, Dmitry R; Lou, Xudong; Tanner, Scott D; Baranov, Vladimir I; Nitz, Mark; Winnik, Mitchell A

    2008-01-01

    Advances in the development of highly multiplexed bio-analytical assays with inductively coupled plasma mass spectrometry (ICP-MS) detection are discussed. Use of novel reagents specifically designed for immunological methods utilizing elemental analysis is presented. The major steps of method development, including selection of elements for tags, validation of tagged reagents, and examples of multiplexed assays, are considered in detail. The paper further describes experimental protocols for elemental tagging of antibodies, immunostaining of live and fixed human leukemia cells, and preparation of samples for ICP-MS analysis. Quantitative analysis of surface antigens on model cell lines using a cocktail of seven lanthanide labeled antibodies demonstrated high specificity and concordance with conventional immunophenotyping.

  16. Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae).

    Science.gov (United States)

    Harrison, Hugo B; Feldheim, Kevin A; Jones, Geoffrey P; Ma, Kayan; Mansour, Hicham; Perumal, Sadhasivam; Williamson, David H; Berumen, Michael L

    2014-06-01

    Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent-offspring relationships in natural populations, with over 99.6% accuracy in parent-offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28-96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species.

  17. Identification of snails within the Bulinus africanus group from East Africa by multiplex SNaPshotäanalysis of single nucleotide polymorphisms within the cytochrome oxidase subunit I

    Directory of Open Access Journals (Sweden)

    Stothard JR

    2002-01-01

    Full Text Available Identification of populations of Bulinus nasutus and B. globosus from East Africa is unreliable using characters of the shell. In this paper, a molecular method of identification is presented for each species based on DNA sequence variation within the mitochondrial cytochrome oxidase subunit I (COI as detected by a novel multiplexed SNaPshotTM assay. In total, snails from 7 localities from coastal Kenya were typed using this assay and variation within shell morphology was compared to reference material from Zanzibar. Four locations were found to contain B. nasutus and 2 locations were found to contain B. globosus. A mixed population containing both B. nasutus and B. globosus was found at Kinango. Morphometric variation between samples was considerable and UPGMA cluster analysis failed to differentiate species. The multiplex SNaPshotTM assay is an important development for more precise methods of identification of B. africanus group snails. The assay could be further broadened for identification of other snail intermediate host species.

  18. Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae)

    KAUST Repository

    Harrison, H.B.

    2014-04-24

    Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent-offspring relationships in natural populations, with over 99.6% accuracy in parent-offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28-96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species. 2014 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

  19. Quantitative DNA methylation analysis of candidate genes in cervical cancer.

    Directory of Open Access Journals (Sweden)

    Erin M Siegel

    Full Text Available Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2. A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97-1.00, p-value = 0.003. Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated.

  20. Quantitative analysis and parametric display of regional myocardial mechanics

    Science.gov (United States)

    Eusemann, Christian D.; Bellemann, Matthias E.; Robb, Richard A.

    2000-04-01

    Quantitative assessment of regional heart motion has significant potential for more accurate diagnosis of heart disease and/or cardiac irregularities. Local heart motion may be studied from medical imaging sequences. Using functional parametric mapping, regional myocardial motion during a cardiac cycle can be color mapped onto a deformable heart model to obtain better understanding of the structure- to-function relationships in the myocardium, including regional patterns of akinesis or diskinesis associated with ischemia or infarction. In this study, 3D reconstructions were obtained from the Dynamic Spatial Reconstructor at 15 time points throughout one cardiac cycle of pre-infarct and post-infarct hearts. Deformable models were created from the 3D images for each time point of the cardiac cycles. Form these polygonal models, regional excursions and velocities of each vertex representing a unit of myocardium were calculated for successive time-intervals. The calculated results were visualized through model animations and/or specially formatted static images. The time point of regional maximum velocity and excursion of myocardium through the cardiac cycle was displayed using color mapping. The absolute value of regional maximum velocity and maximum excursion were displayed in a similar manner. Using animations, the local myocardial velocity changes were visualized as color changes on the cardiac surface during the cardiac cycle. Moreover, the magnitude and direction of motion for individual segments of myocardium could be displayed. Comparison of these dynamic parametric displays suggest that the ability to encode quantitative functional information on dynamic cardiac anatomy enhances the diagnostic value of 4D images of the heart. Myocardial mechanics quantified this way adds a new dimension to the analysis of cardiac functional disease, including regional patterns of akinesis and diskinesis associated with ischemia and infarction. Similarly, disturbances in

  1. Quantitative analysis with the optoacoustic/ultrasound system OPUS

    Science.gov (United States)

    Haisch, Christoph; Zell, Karin; Sperl, Jonathan; Vogel, Mika W.; Niessner, Reinhard

    2009-02-01

    The OPUS (Optoacoustic plus Ultrasound) system is a combination of a medical ultrasound scanner with a highrepetition rate, wavelength-tunable laser system and a suitable triggering interface to synchronize the laser and the ultrasound system. The pulsed laser generates an optoacoustic (OA), or photoacoustic (PA), signal which is detected by the ultrasound system. Alternatively, imaging in conventional ultrasound mode can be performed. Both imaging modes can be superimposed. The laser light is coupled into the tissue laterally, parallel to the ultrasound transducer, which does not require for any major modification to the transducer or the ultrasound beam forming. This was a basic requirement on the instrument, as the intention of the project was to establish the optoacoustic imaging modality as add-on to a conventional standard ultrasound instrument. We believe that this approach may foster the introduction of OA imaging as routine tool in medical diagnosis. Another key aspect of the project was to exploit the capabilities of OA imaging for quantitative analysis. The intention of the presented work is to summarize all steps necessary to extract the significant information from the PA raw data, which are required for the quantification of local absorber distributions. We show results of spatially resolved absorption measurements in scattering samples and a comparison of four different image reconstruction algorithms, regarding their influence on lateral resolution as well as on the signal to noise ratio for different sample depths and absorption values. The reconstruction algorithms are based on Fourier transformation, on a generalized 2D Hough transformation, on circular back-projection and the classical delay-and-sum approach which is implemented in most ultrasound scanners. Furthermore, we discuss the influence of a newly developed laser source, combining diode and flash lamp pumping. Compared to all-flash-lamp pumped systems it features a significantly higher

  2. Quantitative DNA methylation analysis of candidate genes in cervical cancer.

    Science.gov (United States)

    Siegel, Erin M; Riggs, Bridget M; Delmas, Amber L; Koch, Abby; Hakam, Ardeshir; Brown, Kevin D

    2015-01-01

    Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2). A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site) per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC) of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97-1.00, p-value = 0.003). Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated.

  3. Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling.

    Science.gov (United States)

    Wandinger, Sebastian K; Lahortiga, Idoya; Jacobs, Kris; Klammer, Martin; Jordan, Nicole; Elschenbroich, Sarah; Parade, Marc; Jacoby, Edgar; Linders, Joannes T M; Brehmer, Dirk; Cools, Jan; Daub, Henrik

    2016-01-01

    The four members of the epidermal growth factor receptor (EGFR/ERBB) family form homo- and heterodimers which mediate ligand-specific regulation of many key cellular processes in normal and cancer tissues. While signaling through the EGFR has been extensively studied on the molecular level, signal transduction through ERBB3/ERBB4 heterodimers is less well understood. Here, we generated isogenic mouse Ba/F3 cells that express full-length and functional membrane-integrated ERBB3 and ERBB4 or ERBB4 alone, to serve as a defined cellular model for biological and phosphoproteomics analysis of ERBB3/ERBB4 signaling. ERBB3 co-expression significantly enhanced Ba/F3 cell proliferation upon neuregulin-1 (NRG1) treatment. For comprehensive signaling studies we performed quantitative mass spectrometry (MS) experiments to compare the basal ERBB3/ERBB4 cell phosphoproteome to NRG1 treatment of ERBB3/ERBB4 and ERBB4 cells. We employed a workflow comprising differential isotope labeling with mTRAQ reagents followed by chromatographic peptide separation and final phosphopeptide enrichment prior to MS analysis. Overall, we identified 9686 phosphorylation sites which could be confidently localized to specific residues. Statistical analysis of three replicate experiments revealed 492 phosphorylation sites which were significantly changed in NRG1-treated ERBB3/ERBB4 cells. Bioinformatics data analysis recapitulated regulation of mitogen-activated protein kinase and Akt pathways, but also indicated signaling links to cytoskeletal functions and nuclear biology. Comparative assessment of NRG1-stimulated ERBB4 Ba/F3 cells revealed that ERBB3 did not trigger defined signaling pathways but more broadly enhanced phosphoproteome regulation in cells expressing both receptors. In conclusion, our data provide the first global picture of ERBB3/ERBB4 signaling and provide numerous potential starting points for further mechanistic studies.

  4. Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling.

    Directory of Open Access Journals (Sweden)

    Sebastian K Wandinger

    Full Text Available The four members of the epidermal growth factor receptor (EGFR/ERBB family form homo- and heterodimers which mediate ligand-specific regulation of many key cellular processes in normal and cancer tissues. While signaling through the EGFR has been extensively studied on the molecular level, signal transduction through ERBB3/ERBB4 heterodimers is less well understood. Here, we generated isogenic mouse Ba/F3 cells that express full-length and functional membrane-integrated ERBB3 and ERBB4 or ERBB4 alone, to serve as a defined cellular model for biological and phosphoproteomics analysis of ERBB3/ERBB4 signaling. ERBB3 co-expression significantly enhanced Ba/F3 cell proliferation upon neuregulin-1 (NRG1 treatment. For comprehensive signaling studies we performed quantitative mass spectrometry (MS experiments to compare the basal ERBB3/ERBB4 cell phosphoproteome to NRG1 treatment of ERBB3/ERBB4 and ERBB4 cells. We employed a workflow comprising differential isotope labeling with mTRAQ reagents followed by chromatographic peptide separation and final phosphopeptide enrichment prior to MS analysis. Overall, we identified 9686 phosphorylation sites which could be confidently localized to specific residues. Statistical analysis of three replicate experiments revealed 492 phosphorylation sites which were significantly changed in NRG1-treated ERBB3/ERBB4 cells. Bioinformatics data analysis recapitulated regulation of mitogen-activated protein kinase and Akt pathways, but also indicated signaling links to cytoskeletal functions and nuclear biology. Comparative assessment of NRG1-stimulated ERBB4 Ba/F3 cells revealed that ERBB3 did not trigger defined signaling pathways but more broadly enhanced phosphoproteome regulation in cells expressing both receptors. In conclusion, our data provide the first global picture of ERBB3/ERBB4 signaling and provide numerous potential starting points for further mechanistic studies.

  5. Quantitative analysis of cryptic splicing associated with TDP-43 depletion.

    Science.gov (United States)

    Humphrey, Jack; Emmett, Warren; Fratta, Pietro; Isaacs, Adrian M; Plagnol, Vincent

    2017-05-26

    Reliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). TDP-43 depletion causes the aberrant inclusion of cryptic exons into a range of transcripts, but their extent, relevance to disease pathogenesis and whether they are caused by other RNA-binding proteins implicated in ALS/FTD are unknown. We developed an analysis pipeline to discover and quantify cryptic exon inclusion and applied it to publicly available human and murine RNA-sequencing data. We detected widespread cryptic splicing in TDP-43 depletion datasets but almost none in another ALS/FTD-linked protein FUS. Sequence motif and iCLIP analysis of cryptic exons demonstrated that they are bound by TDP-43. Unlike the cryptic exons seen in hnRNP C depletion, those repressed by TDP-43 cannot be linked to transposable elements. Cryptic exons are poorly conserved and inclusion overwhelmingly leads to nonsense-mediated decay of the host transcript, with reduced transcript levels observed in differential expression analysis. RNA-protein interaction data on 73 different RNA-binding proteins showed that, in addition to TDP-43, 7 specifically bind TDP-43 linked cryptic exons. This suggests that TDP-43 competes with other splicing factors for binding to cryptic exons and can repress cryptic exon inclusion. Our quantitative analysis pipeline confirms the presence of cryptic exons during the depletion of TDP-43 but not FUS providing new insight into to RNA-processing dysfunction as a cause or consequence in ALS/FTD.

  6. A computational tool for quantitative analysis of vascular networks.

    Directory of Open Access Journals (Sweden)

    Enrique Zudaire

    Full Text Available Angiogenesis is the generation of mature vascular networks from pre-existing vessels. Angiogenesis is crucial during the organism' development, for wound healing and for the female reproductive cycle. Several murine experimental systems are well suited for studying developmental and pathological angiogenesis. They include the embryonic hindbrain, the post-natal retina and allantois explants. In these systems vascular networks are visualised by appropriate staining procedures followed by microscopical analysis. Nevertheless, quantitative assessment of angiogenesis is hampered by the lack of readily available, standardized metrics and software analysis tools. Non-automated protocols are being used widely and they are, in general, time--and labour intensive, prone to human error and do not permit computation of complex spatial metrics. We have developed a light-weight, user friendly software, AngioTool, which allows for quick, hands-off and reproducible quantification of vascular networks in microscopic images. AngioTool computes several morphological and spatial parameters including the area covered by a vascular network, the number of vessels, vessel length, vascular density and lacunarity. In addition, AngioTool calculates the so-called "branching index" (branch points/unit area, providing a measurement of the sprouting activity of a specimen of interest. We have validated AngioTool using images of embryonic murine hindbrains, post-natal retinas and allantois explants. AngioTool is open source and can be downloaded free of charge.

  7. Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Zhe; Wu, Chaochao; Xie, Fang; Slysz, Gordon W.; Tolic, Nikola; Monroe, Matthew E.; Petyuk, Vladislav A.; Payne, Samuel H.; Fujimoto, Grant M.; Moore, Ronald J.; Fillmore, Thomas L.; Schepmoes, Athena A.; Levine, Douglas; Townsend, Reid; Davies, Sherri; Li, Shunqiang; Ellis, Matthew; Boja, Emily; Rivers, Robert; Rodriguez, Henry; Rodland, Karin D.; Liu, Tao; Smith, Richard D.

    2015-01-02

    Aberrant degradation of proteins is associated with many pathological states, including cancers. Mass spectrometric analysis of tumor peptidomes, the intracellular and intercellular products of protein degradation, has the potential to provide biological insights on proteolytic processing in cancer. However, attempts to use the information on these smaller protein degradation products from tumors for biomarker discovery and cancer biology studies have been fairly limited to date, largely due to the lack of effective approaches for robust peptidomics identification and quantification, and the prevalence of confounding factors and biases associated with sample handling and processing. Herein, we have developed an effective and robust analytical platform for comprehensive analyses of tissue peptidomes, which is suitable for high throughput quantitative studies. The reproducibility and coverage of the platform, as well as the suitability of clinical ovarian tumor and patient-derived breast tumor xenograft samples with post-excision delay of up to 60 min before freezing for peptidomics analysis, have been demonstrated. Moreover, our data also show that the peptidomics profiles can effectively separate breast cancer subtypes, reflecting tumor-associated protease activities. Peptidomics complements results obtainable from conventional bottom-up proteomics, and provides insights not readily obtainable from such approaches.

  8. Correlation between two methods of florbetapir PET quantitative analysis.

    Science.gov (United States)

    Breault, Christopher; Piper, Jonathan; Joshi, Abhinay D; Pirozzi, Sara D; Nelson, Aaron S; Lu, Ming; Pontecorvo, Michael J; Mintun, Mark A; Devous, Michael D

    2017-01-01

    This study evaluated performance of a commercially available standardized software program for calculation of florbetapir PET standard uptake value ratios (SUVr) in comparison with an established research method. Florbetapir PET images for 183 subjects clinically diagnosed as cognitively normal (CN), mild cognitive impairment (MCI) or probable Alzheimer's disease (AD) (45 AD, 60 MCI, and 78 CN) were evaluated using two software processing algorithms. The research method uses a single florbetapir PET template generated by averaging both amyloid positive and amyloid negative registered brains together. The commercial software simultaneously optimizes the registration between the florbetapir PET images and three templates: amyloid negative, amyloid positive, and an average. Cortical average SUVr values were calculated across six predefined anatomic regions with respect to the whole cerebellum reference region. SUVr values were well correlated between the two methods (r2 = 0.98). The relationship between the methods computed from the regression analysis is: Commercial method SUVr = (0.9757*Research SUVr) + 0.0299. A previously defined cutoff SUVr of 1.1 for distinguishing amyloid positivity by the research method corresponded to 1.1 (95% CI = 1.098, 1.11) for the commercial method. This study suggests that the commercial method is comparable to the published research method of SUVr analysis for florbetapir PET images, thus facilitating the potential use of standardized quantitative approaches to PET amyloid imaging.

  9. Quantitative evaluation of midpalatal suture maturation via fractal analysis

    Science.gov (United States)

    Kwak, Kyoung Ho; Kim, Yong-Il; Kim, Yong-Deok

    2016-01-01

    Objective The purpose of this study was to determine whether the results of fractal analysis can be used as criteria for midpalatal suture maturation evaluation. Methods The study included 131 subjects aged over 18 years of age (range 18.1–53.4 years) who underwent cone-beam computed tomography. Skeletonized images of the midpalatal suture were obtained via image processing software and used to calculate fractal dimensions. Correlations between maturation stage and fractal dimensions were calculated using Spearman's correlation coefficient. Optimal fractal dimension cut-off values were determined using a receiver operating characteristic curve. Results The distribution of maturation stages of the midpalatal suture according to the cervical vertebrae maturation index was highly variable, and there was a strong negative correlation between maturation stage and fractal dimension (−0.623, p Fractal dimension was a statistically significant indicator of dichotomous results with regard to maturation stage (area under curve = 0.794, p fractal dimension was used to predict the resulting variable that splits maturation stages into ABC and D or E yielded an optimal fractal dimension cut-off value of 1.0235. Conclusions There was a strong negative correlation between fractal dimension and midpalatal suture maturation. Fractal analysis is an objective quantitative method, and therefore we suggest that it may be useful for the evaluation of midpalatal suture maturation. PMID:27668195

  10. Therapeutic electrical stimulation for spasticity: quantitative gait analysis.

    Science.gov (United States)

    Pease, W S

    1998-01-01

    Improvement in motor function following electrical stimulation is related to strengthening of the stimulated spastic muscle and inhibition of the antagonist. A 26-year-old man with familial spastic paraparesis presented with gait dysfunction and bilateral lower limb spastic muscle tone. Clinically, muscle strength and sensation were normal. He was considered appropriate for a trial of therapeutic electrical stimulation following failed trials of physical therapy and baclofen. No other treatment was used concurrent with the electrical stimulation. Before treatment, quantitative gait analysis revealed 63% of normal velocity and a crouched gait pattern, associated with excessive electromyographic activity in the hamstrings and gastrocnemius muscles. Based on these findings, bilateral stimulation of the quadriceps and anterior compartment musculature was performed two to three times per week for three months. Repeat gait analysis was conducted three weeks after the cessation of stimulation treatment. A 27% increase in velocity was noted associated with an increase in both cadence and right step length. Right hip and bilateral knee stance motion returned to normal (rather than "crouched"). No change in the timing of dynamic electromyographic activity was seen. These findings suggest a role for the use of electrical stimulation for rehabilitation of spasticity. The specific mechanism of this improvement remains uncertain.

  11. Rapid high-throughput analysis of DNaseI hypersensitive sites using a modified Multiplex Ligation-dependent Probe Amplification approach

    Directory of Open Access Journals (Sweden)

    Sinclair Andrew H

    2009-09-01

    Full Text Available Abstract Background Mapping DNaseI hypersensitive sites is commonly used to identify regulatory regions in the genome. However, currently available methods are either time consuming and laborious, expensive or require large numbers of cells. We aimed to develop a quick and straightforward method for the analysis of DNaseI hypersensitive sites that overcomes these problems. Results We have developed a modified Multiplex Ligation-dependent Probe Amplification (MLPA approach for the identification and analysis of genomic regulatory regions. The utility of this approach was demonstrated by simultaneously analysing 20 loci from the ENCODE project for DNaseI hypersensitivity in a range of different cell lines. We were able to obtain reproducible results with as little as 5 × 104 cells per DNaseI treatment. Our results broadly matched those previously reported by the ENCODE project, and both technical and biological replicates showed high correlations, indicating the sensitivity and reproducibility of this method. Conclusion This new method will considerably facilitate the identification and analysis of DNaseI hypersensitive sites. Due to the multiplexing potential of MLPA (up to 50 loci can be examined it is possible to analyse dozens of DNaseI hypersensitive sites in a single reaction. Furthermore, the high sensitivity of MLPA means that fewer than 105 cells per DNaseI treatment can be used, allowing the discovery and analysis of tissue specific regulatory regions without the need for pooling. This method is quick and easy and results can be obtained within 48 hours after harvesting of cells or tissues. As no special equipment is required, this method can be applied by any laboratory interested in the analysis of DNaseI hypersensitive regions.

  12. Genetic analysis of eight population groups living in Taiwan using a 13 X-chromosomal STR loci multiplex system.

    Science.gov (United States)

    Hwa, Hsiao-Lin; Lee, James Chun-I; Chang, Yih-Yuan; Yin, Hsiang-Yi; Chen, Ya-Hui; Tseng, Li-Hui; Su, Yi-Ning; Ko, Tsang-Ming

    2011-01-01

    A 13 X-chromosomal short tandem repeat (STR) multiplex system (DXS6807, DXS8378, DSX9902, DXS7132, DXS9898, DXS6809, DXS6789, DXS7424, DXS101, GATA172D05, HPRTB, DXS8377, and DXS7423) was tested on 1,037 DNA samples from eight population groups currently living in Taiwan. Different distributions of the allelic frequencies in different populations were presented. DXS8377 and DXS101 were the two most polymorphic loci in these eight populations, whereas DXS7423 was the least informative marker in most of the populations studied. The genetic distances between the populations and the constructed phylogenetic tree revealed a long genetic distance between Asian and Caucasian populations as well as isolation of the Tao population. The phylogenetic tree grouped populations into clusters compatible with their ethnogeographic relationships. This 13 X-chromosomal short tandem repeat multiplex system offers a considerable number of polymorphic patterns in different populations. This system can be useful in forensic identification casework and ethnogeographic research.

  13. Multiplex RT-PCR method for the analysis of the expression of human sialyltransferases: application to breast cancer cells.

    Science.gov (United States)

    Recchi, M A; Harduin-Lepers, A; Boilly-Marer, Y; Verbert, A; Delannoy, P

    1998-01-01

    In many cases of human cancer, the appearance of hypersialylated glycan structures is related to a precise stage of the disease; this may depend on altered regulation of one or more sialyltransferases genes. Since several distinct sialyltransferase enzymes arising from different unique genes transfer sialic acid residues in the same linkage onto the same acceptor, it is impossible to precisely determine which enzyme is involved in the observed phenotype based on enzymatic assays. We have developed a very sensitive and highly reproducible multiplex reverse transcriptase-polymerase chain reaction technique in order to monitor the expression of four human sialyltransferases genes ST6Gal I, ST3Gal I, ST3Gal III and ST3Gal IV in small cell samples. Multiplex PCR amplification using specific primers for each sialyltransferase and detection of amplification products by polyacrylamide gel electrophoresis is a method that is fast and easy to handle and has proven to be useful for establishing sialyltransferase patterns of expression in breast immortalized cell line HBL100 as well as in breast cancer cell lines MCF-7/6, MCF-7/AZ and MDA.

  14. Analysis of Performance Limitations in Fiber Bragg Grating Based Optical Add-Drop Multiplexer due to Crosstalk

    Directory of Open Access Journals (Sweden)

    Md. Mahiuddin

    2012-03-01

    Full Text Available Abstract— Wavelength  division  multiplexing  (WDM optical networks  are  attracting  more  and  more attention because of their ability to provide  increased capacity and  flexibility. Optical add-drop multiplexer (OADM  becomes  a  key  component  to  add  or  drop wavelengths  in  high  bit  rate  optical  networks. Crosstalk  in OADM  often degrades  the performance of WDM  system  drastically.  In  this  article,  we  have developed  analytical model  for  low  crosstalk  of  fiber Bragg  grating  based  OADM  with  isolator. We  have also  derived  analytical  expressions  for  relative intensity noise (RIN, bit error rate (BER and power penalty to evaluate the performance limitations of this OADM. Results show that crosstalk, RIN and BER of the  proposed  OADM  are significantly  lower  and provide better performance than the existing OADMs.

  15. Applying Qualitative Hazard Analysis to Support Quantitative Safety Analysis for Proposed Reduced Wake Separation Conops

    Science.gov (United States)

    Shortle, John F.; Allocco, Michael

    2005-01-01

    This paper describes a scenario-driven hazard analysis process to identify, eliminate, and control safety-related risks. Within this process, we develop selective criteria to determine the applicability of applying engineering modeling to hypothesized hazard scenarios. This provides a basis for evaluating and prioritizing the scenarios as candidates for further quantitative analysis. We have applied this methodology to proposed concepts of operations for reduced wake separation for closely spaced parallel runways. For arrivals, the process identified 43 core hazard scenarios. Of these, we classified 12 as appropriate for further quantitative modeling, 24 that should be mitigated through controls, recommendations, and / or procedures (that is, scenarios not appropriate for quantitative modeling), and 7 that have the lowest priority for further analysis.

  16. Evaluating the Quantitative Capabilities of Metagenomic Analysis Software.

    Science.gov (United States)

    Kerepesi, Csaba; Grolmusz, Vince

    2016-05-01

    DNA sequencing technologies are applied widely and frequently today to describe metagenomes, i.e., microbial communities in environmental or clinical samples, without the need for culturing them. These technologies usually return short (100-300 base-pairs long) DNA reads, and these reads are processed by metagenomic analysis software that assign phylogenetic composition-information to the dataset. Here we evaluate three metagenomic analysis software (AmphoraNet--a webserver implementation of AMPHORA2--, MG-RAST, and MEGAN5) for their capabilities of assigning quantitative phylogenetic information for the data, describing the frequency of appearance of the microorganisms of the same taxa in the sample. The difficulties of the task arise from the fact that longer genomes produce more reads from the same organism than shorter genomes, and some software assign higher frequencies to species with longer genomes than to those with shorter ones. This phenomenon is called the "genome length bias." Dozens of complex artificial metagenome benchmarks can be found in the literature. Because of the complexity of those benchmarks, it is usually difficult to judge the resistance of a metagenomic software to this "genome length bias." Therefore, we have made a simple benchmark for the evaluation of the "taxon-counting" in a metagenomic sample: we have taken the same number of copies of three full bacterial genomes of different lengths, break them up randomly to short reads of average length of 150 bp, and mixed the reads, creating our simple benchmark. Because of its simplicity, the benchmark is not supposed to serve as a mock metagenome, but if a software fails on that simple task, it will surely fail on most real metagenomes. We applied three software for the benchmark. The ideal quantitative solution would assign the same proportion to the three bacterial taxa. We have found that AMPHORA2/AmphoraNet gave the most accurate results and the other two software were under

  17. Quantitative analysis of left ventricular strain using cardiac computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Buss, Sebastian J., E-mail: sebastian.buss@med.uni-heidelberg.de [Department of Cardiology, University of Heidelberg, 69120 Heidelberg (Germany); Schulz, Felix; Mereles, Derliz [Department of Cardiology, University of Heidelberg, 69120 Heidelberg (Germany); Hosch, Waldemar [Department of Diagnostic and Interventional Radiology, University of Heidelberg, 69120 Heidelberg (Germany); Galuschky, Christian; Schummers, Georg; Stapf, Daniel [TomTec Imaging Systems GmbH, Munich (Germany); Hofmann, Nina; Giannitsis, Evangelos; Hardt, Stefan E. [Department of Cardiology, University of Heidelberg, 69120 Heidelberg (Germany); Kauczor, Hans-Ulrich [Department of Diagnostic and Interventional Radiology, University of Heidelberg, 69120 Heidelberg (Germany); Katus, Hugo A.; Korosoglou, Grigorios [Department of Cardiology, University of Heidelberg, 69120 Heidelberg (Germany)

    2014-03-15

    Objectives: To investigate whether cardiac computed tomography (CCT) can determine left ventricular (LV) radial, circumferential and longitudinal myocardial deformation in comparison to two-dimensional echocardiography in patients with congestive heart failure. Background: Echocardiography allows for accurate assessment of strain with high temporal resolution. A reduced strain is associated with a poor prognosis in cardiomyopathies. However, strain imaging is limited in patients with poor echogenic windows, so that, in selected cases, tomographic imaging techniques may be preferable for the evaluation of myocardial deformation. Methods: Consecutive patients (n = 27) with congestive heart failure who underwent a clinically indicated ECG-gated contrast-enhanced 64-slice dual-source CCT for the evaluation of the cardiac veins prior to cardiac resynchronization therapy (CRT) were included. All patients underwent additional echocardiography. LV radial, circumferential and longitudinal strain and strain rates were analyzed in identical midventricular short axis, 4-, 2- and 3-chamber views for both modalities using the same prototype software algorithm (feature tracking). Time for analysis was assessed for both modalities. Results: Close correlations were observed for both techniques regarding global strain (r = 0.93, r = 0.87 and r = 0.84 for radial, circumferential and longitudinal strain, respectively, p < 0.001 for all). Similar trends were observed for regional radial, longitudinal and circumferential strain (r = 0.88, r = 0.84 and r = 0.94, respectively, p < 0.001 for all). The number of non-diagnostic myocardial segments was significantly higher with echocardiography than with CCT (9.6% versus 1.9%, p < 0.001). In addition, the required time for complete quantitative strain analysis was significantly shorter for CCT compared to echocardiography (877 ± 119 s per patient versus 1105 ± 258 s per patient, p < 0.001). Conclusion: Quantitative assessment of LV strain

  18. Automated quantitative gait analysis in animal models of movement disorders

    Directory of Open Access Journals (Sweden)

    Vandeputte Caroline

    2010-08-01

    Full Text Available Abstract Background Accurate and reproducible behavioral tests in animal models are of major importance in the development and evaluation of new therapies for central nervous system disease. In this study we investigated for the first time gait parameters of rat models for Parkinson's disease (PD, Huntington's disease (HD and stroke using the Catwalk method, a novel automated gait analysis test. Static and dynamic gait parameters were measured in all animal models, and these data were compared to readouts of established behavioral tests, such as the cylinder test in the PD and stroke rats and the rotarod tests for the HD group. Results Hemiparkinsonian rats were generated by unilateral injection of the neurotoxin 6-hydroxydopamine in the striatum or in the medial forebrain bundle. For Huntington's disease, a transgenic rat model expressing a truncated huntingtin fragment with multiple CAG repeats was used. Thirdly, a stroke model was generated by a photothrombotic induced infarct in the right sensorimotor cortex. We found that multiple gait parameters were significantly altered in all three disease models compared to their respective controls. Behavioural deficits could be efficiently measured using the cylinder test in the PD and stroke animals, and in the case of the PD model, the deficits in gait essentially confirmed results obtained by the cylinder test. However, in the HD model and the stroke model the Catwalk analysis proved more sensitive than the rotarod test and also added new and more detailed information on specific gait parameters. Conclusion The automated quantitative gait analysis test may be a useful tool to study both motor impairment and recovery associated with various neurological motor disorders.

  19. Quantitative assessment of hip osteoarthritis based on image texture analysis.

    Science.gov (United States)

    Boniatis, I S; Costaridou, L I; Cavouras, D A; Panagiotopoulos, E C; Panayiotakis, G S

    2006-03-01

    A non-invasive method was developed to investigate the potential capacity of digital image texture analysis in evaluating the severity of hip osteoarthritis (OA) and in monitoring its progression. 19 textural features evaluating patterns of pixel intensity fluctuations were extracted from 64 images of radiographic hip joint spaces (HJS), corresponding to 32 patients with verified unilateral or bilateral OA. Images were enhanced employing custom developed software for the delineation of the articular margins on digitized pelvic radiographs. The severity of OA for each patient was assessed by expert orthopaedists employing the Kellgren and Lawrence (KL) scale. Additionally, an index expressing HJS-narrowing was computed considering patients from the unilateral OA-group. A textural feature that quantified pixel distribution non-uniformity (grey level non-uniformity, GLNU) demonstrated the strongest correlation with the HJS-narrowing index among all extracted features and utilized in further analysis. Classification rules employing GLNU feature were introduced to characterize a hip as normal or osteoarthritic and to assign it to one of three severity categories, formed in accordance with the KL scale. Application of the proposed rules resulted in relatively high classification accuracies in characterizing a hip as normal or osteoarthritic (90.6%) and in assigning it to the correct KL scale category (88.9%). Furthermore, the strong correlation between the HJS-narrowing index and the pathological GLNU (r = -0.9, p<0.001) was utilized to provide percentages quantifying hip OA-severity. Texture analysis may contribute in the quantitative assessment of OA-severity, in the monitoring of OA-progression and in the evaluation of a chondroprotective therapy.

  20. Nanotechnology patents in the automotive industry (a quantitative & qualitative analysis).

    Science.gov (United States)

    Prasad, Raghavendra; Bandyopadhyay, Tapas K

    2014-01-01

    The aim of the article is to present a trend in patent filings for application of nanotechnology to the automobile sector across the world, using the keyword-based patent search. Overviews of the patents related to nano technology in the automobile industry have been provided. The current work has started from the worldwide patent search to find the patents on nanotechnology in the automobile industry and classify the patents according to the various parts of an automobile to which they are related and the solutions which they are providing. In the next step various graphs have been produced to get an insight into various trends. In next step, analysis of patents in various classifications, have been performed. The trends shown in graphs provide the quantitative analysis whereas; the qualitative analysis has been done in another section. The classifications of patents based on the solution they provide have been performed by reading the claims, titles, abstract and full texts separately. Patentability of nano technology inventions have been discussed in a view to give an idea of requirements and statutory bars to the patentability of nanotechnology inventions. Another objective of the current work is to suggest appropriate framework for the companies regarding use of nano technology in the automobile industry and a suggestive strategy for patenting of the inventions related to the same. For example, US Patent, with patent number US2008-019426A1 discusses the invention related to Lubricant composition. This patent has been studied and classified to fall under classification of automobile parts. After studying this patent, it is deduced that, the problem of friction in engine is being solved by this patent. One classification is the "automobile part" based while other is the basis of "problem being solved". Hence, two classifications, namely reduction in friction and engine were created. Similarly, after studying all the patents, a similar matrix has been created.

  1. Communicability reveals a transition to coordinated behavior in multiplex networks

    CERN Document Server

    Estrada, Ernesto

    2013-01-01

    We analyse 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.

  2. Communicability reveals a transition to coordinated behavior in multiplex networks

    Science.gov (United States)

    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.

  3. A novel method based on click chemistry, which overcomes limitations of cell cycle analysis by classical determination of BrdU incorporation, allowing multiplex antibody staining.

    Science.gov (United States)

    Cappella, Paolo; Gasparri, Fabio; Pulici, Maurizio; Moll, Jürgen

    2008-07-01

    Quantification of BrdU incorporation into DNA is a widely used technique to assess the cell cycle status of cells. DNA denaturation is required for BrdU detection with the drawback that most protein epitopes are destroyed and classical antibody staining techniques for multiplex analysis are not possible. To address this issue we have developed a novel method that overcomes the DNA denaturation step but still allows detection of BrdU. Cells were pulsed for a short time by 5-ethynyl-2'-deoxyuridine, which is incorporated into DNA. The exposed nucleotide alkyne group of DNA was then derivatized in physiologic conditions by the copper (I)-catalyzed azide-alkyne cycloaddition (CuAAC) using BrdU azides. The resulting DNA-bound bromouracil moiety was subsequently detected by commercial anti-BrdU mAb without the need for a denaturation step. Continuous labeling with EdU showed a slightly increased anti-proliferative activity compared to BrdU. However, using a lower concentration of EdU for labeling can compensate for this. Alkynyl tags could be detected quickly by a highly specific reaction using BrdU azides. Fluorescence quenching by the DNA dye PI using both BrdU azides was negligible. Our labeling method is suitable for FCM and HCA and shows a higher signal to noise ratio than other methods. This method also allowed multiplex analysis by simultaneous detection of EdU-BrdU, caspase-3, and phospho-histone 3 mAbs, proving sensitivity and feasibility of this new technique. In addition, it has the potential for use in vivo, as exemplified for bone marrow studies. We have established a new method to determine the position of cells in the cell cycle. This is superior when compared to traditional BrdU detection since it allows multiplex analysis, is more sensitive and shows less quenching with PI. The method provides new opportunities to investigate changes in protein expression at different cell cycle stages using pulse labeling experiments.

  4. Quantitative analysis of polymorphic mixtures of ranitidine hydrochloride by Raman spectroscopy and principal components analysis.

    Science.gov (United States)

    Pratiwi, Destari; Fawcett, J Paul; Gordon, Keith C; Rades, Thomas

    2002-11-01

    Ranitidine hydrochloride exists as two polymorphs, forms I and II, both of which are used to manufacture commercial tablets. Raman spectroscopy can be used to differentiate the two forms but univariate methods of quantitative analysis of one polymorph as an impurity in the other lack sensitivity. We have applied principal components analysis (PCA) of Raman spectra to binary mixtures of the two polymorphs and to binary mixtures prepared by adding one polymorph to powdered tablets of the other. Based on absorption measurements of seven spectral regions, it was found that >97% of the spectral variation was accounted for by three principal components. Quantitative calibration models generated by multiple linear regression predicted a detection limit and quantitation limit for either forms I or II in mixtures of the two of 0.6 and 1.8%, respectively. This study demonstrates that PCA of Raman spectroscopic data provides a sensitive method for the quantitative analysis of polymorphic impurities of drugs in commercial tablets with a quantitation limit of less than 2%.

  5. Quantitative risk analysis of urban flooding in lowland areas

    NARCIS (Netherlands)

    Ten Veldhuis, J.A.E.

    2010-01-01

    Urban flood risk analyses suffer from a lack of quantitative historical data on flooding incidents. Data collection takes place on an ad hoc basis and is usually restricted to severe events. The resulting data deficiency renders quantitative assessment of urban flood risks uncertain. The study repor

  6. A Novel Quantitative Analysis Model for Information System Survivability Based on Conflict Analysis

    Institute of Scientific and Technical Information of China (English)

    WANG Jian; WANG Huiqiang; ZHAO Guosheng

    2007-01-01

    This paper describes a novel quantitative analysis model for system survivability based on conflict analysis, which provides a direct-viewing survivable situation. Based on the three-dimensional state space of conflict, each player's efficiency matrix on its credible motion set can be obtained. The player whose desire is the strongest in all initiates the moving and the overall state transition matrix of information system may be achieved. In addition, the process of modeling and stability analysis of conflict can be converted into a Markov analysis process, thus the obtained results with occurring probability of each feasible situation will help the players to quantitatively judge the probability of their pursuing situations in conflict. Compared with the existing methods which are limited to post-explanation of system's survivable situation, the proposed model is relatively suitable for quantitatively analyzing and forecasting the future development situation of system survivability. The experimental results show that the model may be effectively applied to quantitative analysis for survivability. Moreover, there will be a good application prospect in practice.

  7. APPLICATION OF NEOTAME IN CATCHUP: QUANTITATIVE DESCRIPTIVE AND PHYSICOCHEMICAL ANALYSIS

    Directory of Open Access Journals (Sweden)

    G. C. M. C. BANNWART

    2008-11-01

    Full Text Available

    In this study, fi ve prototypes of catchup were developed by replacing partially or totally the sucrose in the formulation by the sweetener Neotame (NTM. These prototypes were evaluated for their physicochemical characteristics and sensory profi le (Quantitative Descriptive Analysis. The main sensory differences observed among the prototypes were regarding to color, consistency, mouthfeel, sweet taste and tomato taste, for which lower means were obtained as the sugar level was decreased, and also in terms of salty taste, that had higher means with the decrease of sugar. In terms of bitter and sweetener aftertastes, the prototype 100% sweetened with NTM presented the higher mean score, but with no signifi cant difference when compared to other prototypes containing sucrose, for bitter taste, however, it had the highest mean score, statistically different from all the other prototypes. In terms of physicochemical characteristics, the differences were mainly in terms of consistency, solids and color. Despite the differences observed among the prototypes as the sugar level was reduced, it was concluded that NTM is a suitable sweetener for catchup, both for use in reduced calories and no sugar versions.

  8. Quantitative Analysis of AGV System in FMS Cell Layout

    Directory of Open Access Journals (Sweden)

    B. Ramana

    1997-01-01

    Full Text Available Material handling is a specialised activity for a modern manufacturing concern. Automated guided vehicles (AGVs are invariably used for material handling in flexible manufacturing Systems (FMSs due to their flexibility. The quantitative analysis of an AGV system is useful for determining the material flow rates, operation times, length of delivery, length of empty move of AGV and the number of AGVs required for a typical FMS cell layout. The efficiency of the material handling system, such as AGV can be improved by reducing the length of empty move. The length of empty move of AGV depends upon despatching and scheduling methods. If these methods of AGVs are not properly planned, the length of empty move of AGV is greater than the length of delivery .This results in increase in material handling time which in turn increases the number of AGVs required in FMS cell. This paper presents a method for optimising the length of empty travel of AGV in a typical FMS cell layout.

  9. Early child grammars: qualitative and quantitative analysis of morphosyntactic production.

    Science.gov (United States)

    Legendre, Géraldine

    2006-09-10

    This article reports on a series of 5 analyses of spontaneous production of verbal inflection (tense and person-number agreement) by 2-year-olds acquiring French as a native language. A formal analysis of the qualitative and quantitative results is developed using the unique resources of Optimality Theory (OT; Prince & Smolensky, 2004). It is argued that acquisition of morphosyntax proceeds via overlapping grammars (rather than through abrupt changes), which OT formalizes in terms of partial rather than total constraint rankings. Initially, economy of structure constraints take priority over faithfulness constraints that demand faithful expression of a speaker's intent, resulting in child production of tense that is comparable in level to that of child-directed speech. Using the independent Predominant Length of Utterance measure of syntactic development proposed in Vainikka, Legendre, and Todorova (1999), production of agreement is shown first to lag behind tense then to compete with tense at an intermediate stage of development. As the child's development progresses, faithfulness constraints become more dominant, and the overall production of tense and agreement becomes adult-like.

  10. Quantitative produced water analysis using mobile 1H NMR

    Science.gov (United States)

    Wagner, Lisabeth; Kalli, Chris; Fridjonsson, Einar O.; May, Eric F.; Stanwix, Paul L.; Graham, Brendan F.; Carroll, Matthew R. J.; Johns, Michael L.

    2016-10-01

    Measurement of oil contamination of produced water is required in the oil and gas industry to the (ppm) level prior to discharge in order to meet typical environmental legislative requirements. Here we present the use of compact, mobile 1H nuclear magnetic resonance (NMR) spectroscopy, in combination with solid phase extraction (SPE), to meet this metrology need. The NMR hardware employed featured a sufficiently homogeneous magnetic field, such that chemical shift differences could be used to unambiguously differentiate, and hence quantitatively detect, the required oil and solvent NMR signals. A solvent system consisting of 1% v/v chloroform in tetrachloroethylene was deployed, this provided a comparable 1H NMR signal intensity for the oil and the solvent (chloroform) and hence an internal reference 1H signal from the chloroform resulting in the measurement being effectively self-calibrating. The measurement process was applied to water contaminated with hexane or crude oil over the range 1-30 ppm. The results were validated against known solubility limits as well as infrared analysis and gas chromatography.

  11. Quantitative analysis of brain magnetic resonance imaging for hepatic encephalopathy

    Science.gov (United States)

    Syh, Hon-Wei; Chu, Wei-Kom; Ong, Chin-Sing

    1992-06-01

    High intensity lesions around ventricles have recently been observed in T1-weighted brain magnetic resonance images for patients suffering hepatic encephalopathy. The exact etiology that causes magnetic resonance imaging (MRI) gray scale changes has not been totally understood. The objective of our study was to investigate, through quantitative means, (1) the amount of changes to brain white matter due to the disease process, and (2) the extent and distribution of these high intensity lesions, since it is believed that the abnormality may not be entirely limited to the white matter only. Eleven patients with proven haptic encephalopathy and three normal persons without any evidence of liver abnormality constituted our current data base. Trans-axial, sagittal, and coronal brain MRI were obtained on a 1.5 Tesla scanner. All processing was carried out on a microcomputer-based image analysis system in an off-line manner. Histograms were decomposed into regular brain tissues and lesions. Gray scale ranges coded as lesion were then brought back to original images to identify distribution of abnormality. Our results indicated the disease process involved pallidus, mesencephalon, and subthalamic regions.

  12. European Identity in Russian Regions Bordering on Finland: Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    A. O. Domanov

    2014-01-01

    Full Text Available Th e quantitative analysis of an opinion poll conducted in October 2013 in three Russian cities located near Finnish border (St-Petersburg, Kronstadt and Vyborg explores European identity of their citizens. Th is area was chosen to illustrate the crucial importance of space interpretation in spatial identity formation by using critical geopolitical approach. Th e study shows how diff erent images of space on the same territory act as intermediate variables between objective territorial characteristics and citizens’ identities. As the geographical position at the border of Russia provides the citizens with geopolitical alternatives to identify their location as a fortress defending the nation (as in the case of Kronstadt or a bridge between cultures, the given study allows us to compare reasons for these geopolitical choices of inhabitants. Furthermore, the research aims at bridging the gap in the studies of European and multiple identity in Russian regions and provides Northwest Russian perspective on the perpetual discussion about subjective Eastern border of Europe.

  13. Quantitative analysis of plasma interleiukin-6 by immunoassay on microchip

    Science.gov (United States)

    Abe, K.; Hashimoto, Y.; Yatsushiro, S.; Yamamura, S.; Tanaka, M.; Ooie, T.; Baba, Y.; Kataoka, M.

    2012-03-01

    Sandwich enzyme-linked immunoassay (ELISA) is one of the most frequently employed assays for clinical diagnosis, since this enables the investigator to identify specific protein biomarkers. However, the conventional assay using a 96-well microtitration plate is time- and sample-consuming, and therefore is not suitable for rapid diagnosis. To overcome these drawbacks, we performed a sandwich ELISA on a microchip. We employed the piezoelectric inkjet printing for deposition and fixation of 1st antibody on the microchannnel surface (300 μm width and 100 μm depth). Model analyte was interleukin-6 (IL-6) which was one of the inflammatory cytokine. After blocking the microchannel, antigen, biotin-labeled 2nd antibody, and avidin-labeled peroxidase were infused into the microchannel and incubated for 20 min, 10 min, and 5 min, respectively. This assay could detect 2 pg/ml and quantitatively measure the range of 0-32 pg/ml. Liner regression analysis of plasma IL-6 concentration obtained by microchip and conventional methods exhibited a significant relationship (R2 = 0.9964). This assay reduced the time for the antigen-antibody reaction to 1/6, and the consumption of samples and reagents to 1/50 compared with the conventional method. This assay enables us to determine plasma IL-6 with accuracy, high sensitivity, time saving ability, and low consumption of sample and reagents, and thus will be applicable to clinic diagnosis.

  14. Quantitative image analysis of HIV-1 infection in lymphoid tissue

    Energy Technology Data Exchange (ETDEWEB)

    Haase, A.T.; Zupancic, M.; Cavert, W. [Univ. of Minnesota Medical School, Minneapolis, MN (United States)] [and others

    1996-11-08

    Tracking human immunodeficiency virus-type 1 (HIV-1) infection at the cellular level in tissue reservoirs provides opportunities to better understand the pathogenesis of infection and to rationally design and monitor therapy. A quantitative technique was developed to determine viral burden in two important cellular compartments in lymphoid developed to determine viral burden in two important cellular compartments in lymphoid tissues. Image analysis and in situ hybridization were combined to show that in the presymptomatic stages of infection there is a large, relatively stable pool of virions on the surfaces of follicular dendritic cells and a smaller pool of productivity infected cells. Despite evidence of constraints on HIV-1 replication in the infected cell population in lymphoid tissues, estimates of the numbers of these cells and the virus they could produce are consistent with the quantities of virus that have been detected in the bloodstream. The cellular sources of virus production and storage in lymphoid tissues can now be studied with this approach over the course of infection and treatment. 22 refs., 2 figs., 2 tabs.

  15. Full-Range Public Health Leadership, Part 1: Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Erik L. Carlton

    2015-04-01

    Full Text Available Background. Workforce and leadership development are central to the future of public health. However, public health has been slow to translate and apply leadership models from other professions and to incorporate local perspectives in understanding public health leadership. Purpose. This study utilized the full-range leadership model in order to examine public health leadership. Specifically, it sought to measure leadership styles among local health department directors and to understand the context of leadership local health departments.Methods. Leadership styles among local health department directors (n=13 were examined using survey methodology. Quantitative analysis methods included descriptive statistics, boxplots, and Pearson bivariate correlations using SPSS v18.0. Findings. Self-reported leadership styles were highly correlated to leadership outcomes at the organizational level. However, they were not related to county health rankings. Results suggest the preeminence of leader behaviors and providing individual consideration to staff as compared to idealized attributes of leaders, intellectual stimulation, or inspirational motivation. Implications. Holistic leadership assessment instruments, such as the Multifactor Leadership Questionnaire (MLQ can be useful in assessing public health leaders approaches and outcomes. Comprehensive, 360-degree reviews may be especially helpful. Further research is needed to examine the effectiveness of public health leadership development models, as well as the extent that public health leadership impacts public health outcomes.

  16. Quantitative Analysis and Comparisons of EPON Protection Schemes

    Institute of Scientific and Technical Information of China (English)

    CHENHong; JINDepeng; ZENGLieguang; SULi

    2005-01-01

    This paper presents the relationship between the intensity of network damage and the network survivability. Then a method for quantitatively analyzing the survivability of tree network is studied. Based on the analysis, the survivability of Ethernet passive optical network (EPON) with three kinds of protection schemes (i.e., Trunk-fiber protection scheme, Node-fiber protection scheme, and Bus-fiber protection) is discussed. Following this, the comparisons of the survivability among these three kinds of protection schemes of F.PON are put forward. The simulation results show that, when the coverage area is the same, the survivability of EPON with Node-fiber protection scheme is better than that of EPON with Trunk-fiber protection scheme, and when the number and distribution of Optical network unit (ONU) are the same, the survivability of EPON with Bus-fiber protection scheme is better than that of EPON with Nodefiber protection scheme. Under the same constraints, the needed fiber of EPON with Bus-fiber protection scheme is the least when there are more than 12 ONU nodes. These results are useful not only for forecasting and evaluating the survivability of EPON access network, but also for its topology design.

  17. Quantitative analysis of regulatory flexibility under changing environmental conditions

    Science.gov (United States)

    Edwards, Kieron D; Akman, Ozgur E; Knox, Kirsten; Lumsden, Peter J; Thomson, Adrian W; Brown, Paul E; Pokhilko, Alexandra; Kozma-Bognar, Laszlo; Nagy, Ferenc; Rand, David A; Millar, Andrew J

    2010-01-01

    The circadian clock controls 24-h rhythms in many biological processes, allowing appropriate timing of biological rhythms relative to dawn and dusk. Known clock circuits include multiple, interlocked feedback loops. Theory suggested that multiple loops contribute the flexibility for molecular rhythms to track multiple phases of the external cycle. Clear dawn- and dusk-tracking rhythms illustrate the flexibility of timing in Ipomoea nil. Molecular clock components in Arabidopsis thaliana showed complex, photoperiod-dependent regulation, which was analysed by comparison with three contrasting models. A simple, quantitative measure, Dusk Sensitivity, was introduced to compare the behaviour of clock models with varying loop complexity. Evening-expressed clock genes showed photoperiod-dependent dusk sensitivity, as predicted by the three-loop model, whereas the one- and two-loop models tracked dawn and dusk, respectively. Output genes for starch degradation achieved dusk-tracking expression through light regulation, rather than a dusk-tracking rhythm. Model analysis predicted which biochemical processes could be manipulated to extend dusk tracking. Our results reveal how an operating principle of biological regulators applies specifically to the plant circadian clock. PMID:21045818

  18. Quantitative analysis of piperine in ayurvedic formulation by UV Spectrophotometry

    Directory of Open Access Journals (Sweden)

    Gupta Vishvnath

    2011-02-01

    Full Text Available A simple and reproducible UV- spectrophotometric method for the quantitative determination of piperine in Sitopaladi churna (STPLC were developed and validated in the present work. The parameters linearity, precision , accuracy, and standard error were studies according to indian herbal pharmacopiea. In this present study a new, simple, rapid, sensitive, precise and economic spectrophotometric method in ultraviolet region has been developed for the determination of piperine in market and laboratory herbal formulation of Sitopaladi churna. which were procured and purchased respectively from the local market and they were evaluated as per Indian herbal Pharmacopoeia and WHO guidelines. The concentration of piperine present in raw material of PSC was found to be 1.45±0.014 w/w in piper longum fruits. Piperine has the maximum wavelength at 342.5 nm and hence the UV spectrophotometric method was performed at 342.5 nm. The samples were prepared in methanol and methos obeys Beers law in concentration ranges employed for evaluation. The content of piperine in ayurvedic formulation was determined. The result of analysis have been validated statistically and recovery studies confirmed the accuracy of the proposed method. Hence the proposed method can be used for the reliable quantification of Piperine in crude drug and its herbal formulation.

  19. A Quantitative Analysis of Photovoltaic Modules Using Halved Cells

    Directory of Open Access Journals (Sweden)

    S. Guo

    2013-01-01

    Full Text Available In a silicon wafer-based photovoltaic (PV module, significant power is lost due to current transport through the ribbons interconnecting neighbour cells. Using halved cells in PV modules is an effective method to reduce the resistive power loss which has already been applied by some major PV manufacturers (Mitsubishi, BP Solar in their commercial available PV modules. As a consequence, quantitative analysis of PV modules using halved cells is needed. In this paper we investigate theoretically and experimentally the difference between modules made with halved and full-size solar cells. Theoretically, we find an improvement in fill factor of 1.8% absolute and output power of 90 mW for the halved cell minimodule. Experimentally, we find an improvement in fill factor of 1.3% absolute and output power of 60 mW for the halved cell module. Also, we investigate theoretically how this effect confers to the case of large-size modules. It is found that the performance increment of halved cell PV modules is even higher for high-efficiency solar cells. After that, the resistive loss of large-size modules with different interconnection schemes is analysed. Finally, factors influencing the performance and cost of industrial halved cell PV modules are discussed.

  20. Quantitative analysis of 3-OH oxylipins in fermentation yeast.

    Science.gov (United States)

    Potter, Greg; Xia, Wei; Budge, Suzanne M; Speers, R Alex

    2017-02-01

    Despite the ubiquitous distribution of oxylipins in plants, animals, and microbes, and the application of numerous analytical techniques to study these molecules, 3-OH oxylipins have never been quantitatively assayed in yeasts. The formation of heptafluorobutyrate methyl ester derivatives and subsequent analysis with gas chromatography - negative chemical ionization - mass spectrometry allowed for the first determination of yeast 3-OH oxylipins. The concentration of 3-OH 10:0 (0.68-4.82 ng/mg dry cell mass) in the SMA strain of Saccharomyces pastorianus grown in laboratory-scale beverage fermentations was elevated relative to oxylipin concentrations in plant tissues and macroalgae. In fermenting yeasts, the onset of 3-OH oxylipin formation has been related to fermentation progression and flocculation initiation. When the SMA strain was grown in laboratory-scale fermentations, the maximal sugar consumption rate preceded the lowest concentration of 3-OH 10:0 by ∼4.5 h and a distinct increase in 3-OH 10:0 concentration by ∼16.5 h.

  1. 2D-electrophoresis and multiplex immunoassay proteomic analysis of different body fluids and cellular components reveal known and novel markers for extended fasting

    Directory of Open Access Journals (Sweden)

    Evelo Chris T

    2011-03-01

    Full Text Available Abstract Background Proteomic technologies applied for profiling human biofluids and blood cells are considered to reveal new biomarkers of exposure or provide insights into novel mechanisms of adaptation. Methods Both a non-targeted (classical 2D-electrophoresis combined with mass spectrometry as well as a targeted proteomic approach (multiplex immunoassay were applied to investigate how fasting for 36 h, as compared to 12 h, affects the proteome of platelets, peripheral blood mononuclear cells (PBMC, plasma, urine and saliva collected from ten healthy volunteers. Results Between-subject variability was highest in the plasma proteome and lowest in the PBMC proteome. Random Forests analysis performed on the entire dataset revealed that changes in the level of the RhoGDI2 protein in PBMC and plasma ApoA4 levels were the two most obvious biomarkers of an extended fasting. Random Forests (RF analysis of the multiplex immunoassay data revealed leptin and MMP-3 as biomarkers for extended fasting. However, high between-subject variability may have masked the extended fasting effects in the proteome of the biofluids and blood cells. Conclusions Identification of significantly changed proteins in biofluids and blood cells using a non-targeted approach, together with the outcome of targeted analysis revealed both known and novel markers for a 36 h fasting period, including the cellular proteins RhoGDI2 and CLIC1, and plasma proteins ApoA4, leptin and MMP-3. The PBMC proteome exhibited the lowest between-subject variability and therefore these cells appear to represent the best biosamples for biomarker discovery in human nutrigenomics.

  2. Development of a multiplex loop-mediated isothermal amplification method for the simultaneous detection of Salmonella spp. and Vibrio parahaemolyticus

    Science.gov (United States)

    Liu, Ningwei; Zou, Dayang; Dong, Derong; Yang, Zhan; Ao, Da; Liu, Wei; Huang, Liuyu

    2017-01-01

    Rapid detection of food-borne pathogens is important in the food industry, to monitor and prevent the spread of these pathogens through contaminated food products. We therefore established a multiplex real-time loop-mediated isothermal amplification (LAMP) assay to simultaneously detect and distinguish Salmonella spp. and Vibrio parahaemolyticus DNA in a single reaction. Two target sequences, one specific for Salmonella and the other specific for Vibrio parahaemolyticus, were amplified by specific LAMP primers in the same reaction tube. After amplification at 65 °C for 60 min, the amplified products were subjected to melting curve analysis and thus could be distinguished based on the different melting temperatures (Tm values) of the two specifically amplified products. The specificity of the multiplex LAMP assay was evaluated using 19 known bacterial strains, including one V. parahaemolyticus and seven Salmonella spp. strains. The multiplex LAMP showed 100% inclusivity and exclusivity, and a detection limit similar to that of multiplex PCR. In addition, we observed and corrected preferential amplification induced by what we call LAMP selection in the multiplex LAMP reaction. In conclusion, our assay was rapid, specific, and quantitative, making it a useful tool for the food industry. PMID:28349967

  3. Communication about vaccinations in Italian websites: a quantitative analysis.

    Science.gov (United States)

    Tafuri, Silvio; Gallone, Maria S; Gallone, Maria F; Zorico, Ivan; Aiello, Valeria; Germinario, Cinzia

    2014-01-01

    Babies' parents and people who look for information about vaccination often visit anti-vaccine movement's websites, blogs by naturopathic physicians or natural and alternative medicine practitioners. The aim of this work is to provide a quantitative analysis on the type of information available to Italian people regarding vaccination and a quality analysis of websites retrieved through our searches. A quality score was created to evaluate the technical level of websites. A research was performed through Yahoo, Google, and MSN using the keywords "vaccine" and "vaccination," with the function "OR" in order to identify the most frequently used websites. The 2 keywords were input in Italian, and the first 15 pages retrieved by each search engine were analyzed. 149 websites were selected through this methodology. Fifty-three per cent of the websites belonged to associations, groups, or scientific companies, 32.2% (n = 48) consisted of a personal blog and 14.8% (n = 22) belonged to some of the National Health System offices. Among all analyzed websites, 15.4% (n = 23) came from anti-vaccine movement groups. 37.6% reported webmaster name, 67.8% webmaster e-mail, 28.6% indicated the date of the last update and 46.6% the author's name. The quality score for government sites was higher on average than anti-vaccine websites; although, government sites don't use Web 2.0 functions, as the forums.: National Health System institutions who have to promote vaccination cannot avoid investing in web communication because it cannot be managed by private efforts but must be the result of Public Health, private and scientific association, and social movement synergy.

  4. Automated high multiplex qPCR platform for simultaneous detection and quantification of multiple nucleic acid targets.

    Science.gov (United States)

    Hlousek, Louis; Voronov, Sergey; Diankov, Vesselin; Leblang, Amy B; Wells, Patrick J; Ford, Donna M; Nolling, Jork; Hart, Kyle W; Espinoza, Patricio A; Bristol, Michael R; Tsongalis, Gregory J; Yen-Lieberman, Belinda; Slepnev, Vladimir I; Kong, Lilly I; Lee, Ming-Chou

    2012-05-01

    Quantitative PCR (qPCR) using real-time detection of amplification is limited to a small number of targets within a single reaction. The ICEPlex system, using our scalable target analysis routine (STAR) technology, was developed to provide an automated, high multiplexing PCR solution. ICEPlex combines PCR thermal cycling with dynamic, sequential amplicon separation by capillary electrophoresis and two-color quantitative detection in a single integrated system. In contrast to probe-based qPCR, ICEPlex directly measures amplicon accumulation through incorporation of labeled primers. Three orders of magnitude of optical detection range and at least 7 logs of detectable target concentration range are demonstrated. The system can separate more than 50 amplicons per color channel, ranging from 100 to 500 bases, providing broad multiplexing capabilities for a wide spectrum of nucleic acid amplification applications. ICEPlex can be used for analysis of viral DNA or RNA targets, detection of genetic variants, and for reverse-transcriptase PCR gene expression panels.

  5. Quantitative Analysis of Periodontal Pathogens Using Real-Time Polymerase Chain Reaction (PCR).

    Science.gov (United States)

    Marin, Mª José; Figuero, Elena; Herrera, David; Sanz, Mariano

    2017-01-01

    The quantitative polymerase chain reaction (qPCR) is a variant of PCR aimed to detect and quantify a targeted DNA molecule through the addition of probes labeled with fluorescent molecules that emit fluorescence within each amplification cycle, what results in fluorescence values proportional to the amount of accumulated PCR product. This chapter presents the detailed procedures for quantification of different periodontal pathogens (Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Tannerella forsythia, Campylobacter rectus, and Fusobacterium spp.) using qPCR. It also includes the description of the most frequent problems encountered and how to solve them. In addition, a detailed protocol for multiplex qPCR to detect and quantify P. gingivalis and A. actinomycetemcomitans is included.

  6. A quantitative analysis of Salmonella Typhimurium metabolism during infection

    OpenAIRE

    Steeb, Benjamin

    2012-01-01

    In this thesis, Salmonella metabolism during infection was investigated. The goal was to gain a quantitative and comprehensive understanding of Salmonella in vivo nutrient supply, utilization and growth. To achieve this goal, we used a combined experimental / in silico approach. First, we generated a reconstruction of Salmonella metabolism ([1], see 2.1). This reconstruction was then combined with in vivo data from experimental mutant phenotypes to build a comprehensive quantitative in viv...

  7. Quantitative analysis of flavanones and chalcones from willow bark.

    Science.gov (United States)

    Freischmidt, A; Untergehrer, M; Ziegler, J; Knuth, S; Okpanyi, S; Müller, J; Kelber, O; Weiser, D; Jürgenliemk, G

    2015-09-01

    Willow bark extracts are used for the treatment of fever, pain and inflammation. Recent clinical and pharmacological research revealed that not only the salicylic alcohol derivatives, but also the polyphenols significantly contribute to these effects. Quantitative analysis of the European Pharmacopoeia still focuses on the determination of the salicylic alcohol derivatives. The objective of the present study was the development of an effective quantification method for the determination of as many flavanone and chalcone glycosides as possible in Salix purpurea and other Salix species as well as commercial preparations thereof. As Salix species contain a diverse spectrum of the glycosidated flavanones naringenin, eriodictyol, and the chalcone chalconaringenin, a subsequent acidic and enzymatic hydrolysis was developed to yield naringenin and eriodictyol as aglycones, which were quantified by HPLC. The 5-O-glucosides were cleaved with 11.5% TFA before subsequent hydrolysis of the 7-O-glucosides with an almond β-glucosidase at pH 6-7. The method was validated with regard to LOD, LOQ, intraday and interday precision, accuracy, stability, recovery, time of hydrolysis, robustness and applicability to extracts. All 5-O- and 7-O-glucosides of naringenin, eriodictyol and chalconaringenin were completely hydrolysed and converted to naringenin and eriodictyol. The LOD of the HPLC method was 0.77 μM of naringenin and 0.45 μM of eriodictyol. The LOQ was 2.34 μM of naringenin and 1.35 μM for eriodictyol. The method is robust with regard to sample weight, but susceptible concerning enzyme deterioration. The developed method is applicable to the determination of flavanone and chalcone glycosides in willow bark and corresponding preparations.

  8. Quantitative Financial Analysis of Alternative Energy Efficiency Shareholder Incentive Mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Cappers, Peter; Goldman, Charles; Chait, Michele; Edgar, George; Schlegel, Jeff; Shirley, Wayne

    2008-08-03

    Rising energy prices and climate change are central issues in the debate about our nation's energy policy. Many are demanding increased energy efficiency as a way to help reduce greenhouse gas emissions and lower the total cost of electricity and energy services for consumers and businesses. Yet, as the National Action Plan on Energy Efficiency (NAPEE) pointed out, many utilities continue to shy away from seriously expanding their energy efficiency program offerings because they claim there is insufficient profit-motivation, or even a financial disincentive, when compared to supply-side investments. With the recent introduction of Duke Energy's Save-a-Watt incentive mechanism and ongoing discussions about decoupling, regulators and policymakers are now faced with an expanded and diverse landscape of financial incentive mechanisms, Determining the 'right' way forward to promote deep and sustainable demand side resource programs is challenging. Due to the renaissance that energy efficiency is currently experiencing, many want to better understand the tradeoffs in stakeholder benefits between these alternative incentive structures before aggressively embarking on a path for which course corrections can be time-consuming and costly. Using a prototypical Southwest utility and a publicly available financial model, we show how various stakeholders (e.g. shareholders, ratepayers, etc.) are affected by these different types of shareholder incentive mechanisms under varying assumptions about program portfolios. This quantitative analysis compares the financial consequences associated with a wide range of alternative incentive structures. The results will help regulators and policymakers better understand the financial implications of DSR program incentive regulation.

  9. Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis

    Science.gov (United States)

    De la Fuente, Ildefonso M.; Cortes, Jesus M.

    2012-01-01

    The understanding of the effective functionality that governs the enzymatic self-organized processes in cellular conditions is a crucial topic in the post-genomic era. In recent studies, Transfer Entropy has been proposed as a rigorous, robust and self-consistent method for the causal quantification of the functional information flow among nonlinear processes. Here, in order to quantify the functional connectivity for the glycolytic enzymes in dissipative conditions we have analyzed different catalytic patterns using the technique of Transfer Entropy. The data were obtained by means of a yeast glycolytic model formed by three delay differential equations where the enzymatic rate equations of the irreversible stages have been explicitly considered. These enzymatic activity functions were previously modeled and tested experimentally by other different groups. The results show the emergence of a new kind of dynamical functional structure, characterized by changing connectivity flows and a metabolic invariant that constrains the activity of the irreversible enzymes. In addition to the classical topological structure characterized by the specific location of enzymes, substrates, products and feedback-regulatory metabolites, an effective functional structure emerges in the modeled glycolytic system, which is dynamical and characterized by notable variations of the functional interactions. The dynamical structure also exhibits a metabolic invariant which constrains the functional attributes of the enzymes. Finally, in accordance with the classical biochemical studies, our numerical analysis reveals in a quantitative manner that the enzyme phosphofructokinase is the key-core of the metabolic system, behaving for all conditions as the main source of the effective causal flows in yeast glycolysis. PMID:22393350

  10. Descriptive quantitative analysis of hallux abductovalgus transverse plane radiographic parameters.

    Science.gov (United States)

    Meyr, Andrew J; Myers, Adam; Pontious, Jane

    2014-01-01

    Although the transverse plane radiographic parameters of the first intermetatarsal angle (IMA), hallux abductus angle (HAA), and the metatarsal-sesamoid position (MSP) form the basis of preoperative procedure selection and postoperative surgical evaluation of the hallux abductovalgus deformity, the so-called normal values of these measurements have not been well established. The objectives of the present study were to (1) evaluate the descriptive statistics of the first IMA, HAA, and MSP from a large patient population and (2) to determine an objective basis for defining "normal" versus "abnormal" measurements. Anteroposterior foot radiographs from 373 consecutive patients without a history of previous foot and ankle surgery and/or trauma were evaluated for the measurements of the first IMA, HAA, and MSP. The results revealed a mean measurement of 9.93°, 17.59°, and position 3.63 for the first IMA, HAA, and MSP, respectively. An advanced descriptive analysis demonstrated data characteristics of both parametric and nonparametric distributions. Furthermore, clear differentiations in deformity progression were appreciated when the variables were graphically depicted against each other. This could represent a quantitative basis for defining "normal" versus "abnormal" values. From the results of the present study, we have concluded that these radiographic parameters can be more conservatively reported and analyzed using nonparametric descriptive and comparative statistics within medical studies and that the combination of a first IMA, HAA, and MSP at or greater than approximately 10°, 18°, and position 4, respectively, appears to be an objective "tipping point" in terms of deformity progression and might represent an upper limit of acceptable in terms of surgical deformity correction.

  11. A qualitative and quantitative analysis of vegetable pricing in supermarket

    Science.gov (United States)

    Miranda, Suci

    2017-06-01

    The purpose of this study is to analyze the variables affecting the determination of the sale price of vegetable which is constant over time in a supermarket qualitatively and quantitavely. It focuses on the non-organic vegetable with a fixed selling price over time such as spinach, beet, and parsley. In qualitative analysis, the sale price determination is influenced by the vegetable characteristics: (1) vegetable segmentation (low to high daily consumed); (2) vegetable age (how long it can last related to freshness); which both characteristic relates to the inventory management and ultimately to the sale price in supermarket. While quantitatively, the vegetables are divided into two categories: the leaf vegetable group that the leaves are eaten as a vegetable with the aging product (a) = 0 and the shelf life (t) = 0, and the non-leafy vegetable group with the aging group (a) = a+1 and the shelf life (t) = t+1. The vegetable age (a) = 0 means they only last for one day when they are ordered then they have to terminate. Whereas a+1 is that they have a longer life for more than a day such as beet, white radish, and string beans. The shelf life refers to how long it will be placed in a shelf in supermarket in line with the vegetable age. According to the cost plus pricing method using full price costing approach, production costs, non-production costs, and markup are adjusted differently for each category. There is a holding cost added to the sale price of the non-leafy vegetable, yet it is assumed a 0 holding cost for the leafy vegetable category. The amount of expected margin of each category is correlated to the vegetable characteristics.

  12. Hydrocarbons on Phoebe, Iapetus, and Hyperion: Quantitative Analysis

    Science.gov (United States)

    Cruikshank, Dale P.; MoreauDalleOre, Cristina; Pendleton, Yvonne J.; Clark, Roger Nelson

    2012-01-01

    We present a quantitative analysis of the hydrocarbon spectral bands measured on three of Saturn's satellites, Phoebe, Iaperus, and Hyperion. These bands, measured with the Cassini Visible-Infrared Mapping Spectrometer on close fly-by's of these satellites, are the C-H stretching modes of aromatic hydrocarbons at approximately 3.28 micrometers (approximately 3050 per centimeter), and the are four blended bands of aliphatic -CH2- and -CH3 in the range approximately 3.36-3.52 micrometers (approximately 2980- 2840 per centimeter) bably indicating the presence of polycyclic aromatic hydrocarbons (PAH), is unusually strong in comparison to the aliphatic bands, resulting in a unique signarure among Solar System bodies measured so far, and as such offers a means of comparison among the three satellites. The ratio of the C-H bands in aromatic molecules to those in aliphatic molecules in the surface materials of Phoebe, NAro:NAliph approximately 24; for Hyperion the value is approximately 12, while laperus shows an intermediate value. In view of the trend of the evolution (dehydrogenation by heat and radiation) of aliphatic complexes toward more compact molecules and eventually to aromatics, the relative abundances of aliphatic -CH2- and -CH3- is an indication of the lengths of the molecular chain structures, hence the degree of modification of the original material. We derive CH2:CH3 approximately 2.2 in the spectrum of low-albedo material on laperus; this value is the same within measurement errors to the ratio in the diffuse interstellar medium. The similarity in the spectral signatures of the three satellites, plus the apparent weak trend of aromatic/aliphatic abundance from Phoebe to Hyperion, is consistent with, and effectively confirms that the source of the hydrocarbon-bearing material is Phoebe, and that the appearance of that material on the other two satellites arises from the deposition of the inward-spiraling dust that populates the Phoebe ring.

  13. Functional Multiplex PageRank

    CERN Document Server

    Iacovacci, Jacopo; Arenas, Alex; Bianconi, Ginestra

    2016-01-01

    Recently it has been recognized that many complex social, technological and biological networks have a multilayer nature and can be described by multiplex networks. Multiplex networks are formed by a set of nodes connected by links having different connotations forming the different layers of the multiplex. Characterizing the centrality of the nodes in a multiplex network is a challenging task since the centrality of the node naturally depends on the importance associated to links of a certain type. Here we propose to assign to each node of a multiplex network a centrality called Functional Multiplex PageRank that is a function of the weights given to every different pattern of connections (multilinks) existent in the multiplex network between any two nodes. Since multilinks distinguish all the possible ways in which the links in different layers can overlap, the Functional Multiplex PageRank can describe important non-linear effects when large relevance or small relevance is assigned to multilinks with overl...

  14. Quantitative PCR analysis of salivary pathogen burden in periodontitis.

    Science.gov (United States)

    Salminen, Aino; Kopra, K A Elisa; Hyvärinen, Kati; Paju, Susanna; Mäntylä, Päivi; Buhlin, Kåre; Nieminen, Markku S; Sinisalo, Juha; Pussinen, Pirkko J

    2015-01-01

    Our aim was to investigate the value of salivary concentrations of four major periodontal pathogens and their combination in diagnostics of periodontitis. The Parogene study included 462 dentate subjects (mean age 62.9 ± 9.2 years) with coronary artery disease (CAD) diagnosis who underwent an extensive clinical and radiographic oral examination. Salivary levels of four major periodontal bacteria were measured by quantitative real-time PCR (qPCR). Median salivary concentrations of Porphyromonas gingivalis, Tannerella forsythia, and Prevotella intermedia, as well as the sum of the concentrations of the four bacteria, were higher in subjects with moderate to severe periodontitis compared to subjects with no to mild periodontitis. Median salivary Aggregatibacter actinomycetemcomitans concentrations did not differ significantly between the subjects with no to mild periodontitis and subjects with moderate to severe periodontitis. In logistic regression analysis adjusted for age, gender, diabetes, and the number of teeth and implants, high salivary concentrations of P. gingivalis, T. forsythia, and P. intermedia were significantly associated with moderate to severe periodontitis. When looking at different clinical and radiographic parameters of periodontitis, high concentrations of P. gingivalis and T. forsythia were significantly associated with the number of 4-5 mm periodontal pockets, ≥6 mm pockets, and alveolar bone loss (ABL). High level of T. forsythia was associated also with bleeding on probing (BOP). The combination of the four bacteria, i.e., the bacterial burden index, was associated with moderate to severe periodontitis with an odds ratio (OR) of 2.40 (95% CI 1.39-4.13). When A. actinomycetemcomitans was excluded from the combination of the bacteria, the OR was improved to 2.61 (95% CI 1.51-4.52). The highest OR 3.59 (95% CI 1.94-6.63) was achieved when P. intermedia was further excluded from the combination and only the levels of P. gingivalis and T

  15. Universal platform for quantitative analysis of DNA transposition

    Directory of Open Access Journals (Sweden)

    Pajunen Maria I

    2010-11-01

    Full Text Available Abstract Background Completed genome projects have revealed an astonishing diversity of transposable genetic elements, implying the existence of novel element families yet to be discovered from diverse life forms. Concurrently, several better understood transposon systems have been exploited as efficient tools in molecular biology and genomics applications. Characterization of new mobile elements and improvement of the existing transposition technology platforms warrant easy-to-use assays for the quantitative analysis of DNA transposition. Results Here we developed a universal in vivo platform for the analysis of transposition frequency with class II mobile elements, i.e., DNA transposons. For each particular transposon system, cloning of the transposon ends and the cognate transposase gene, in three consecutive steps, generates a multifunctional plasmid, which drives inducible expression of the transposase gene and includes a mobilisable lacZ-containing reporter transposon. The assay scores transposition events as blue microcolonies, papillae, growing within otherwise whitish Escherichia coli colonies on indicator plates. We developed the assay using phage Mu transposition as a test model and validated the platform using various MuA transposase mutants. For further validation and to illustrate universality, we introduced IS903 transposition system components into the assay. The developed assay is adjustable to a desired level of initial transposition via the control of a plasmid-borne E. coli arabinose promoter. In practice, the transposition frequency is modulated by varying the concentration of arabinose or glucose in the growth medium. We show that variable levels of transpositional activity can be analysed, thus enabling straightforward screens for hyper- or hypoactive transposase mutants, regardless of the original wild-type activity level. Conclusions The established universal papillation assay platform should be widely applicable to a

  16. Quantitative PCR analysis of salivary pathogen burden in periodontitis

    Directory of Open Access Journals (Sweden)

    Aino eSalminen

    2015-10-01

    Full Text Available Our aim was to investigate the value of salivary concentrations of four major periodontal pathogens and their combination in diagnostics of periodontitis. The Parogene study included 462 dentate subjects (mean age 62.9±9.2 years with coronary artery disease diagnosis who underwent an extensive clinical and radiographic oral examination. Salivary levels of four major periodontal bacteria were measured by quantitative real-time PCR. Median salivary concentrations of P. gingivalis, T. forsythia, and P. intermedia, as well as the sum of the concentrations of the four bacteria, were higher in subjects with moderate to severe periodontitis compared to subjects with no to mild periodontitis. Median salivary A. actinomycetemcomitans concentrations did not differ significantly between the subjects with no to mild periodontitis and subjects with moderate to severe periodontitis. In logistic regression analysis adjusted for age, gender, diabetes, and the number of teeth and implants, high salivary concentrations of P. gingivalis, T. forsythia, and P. intermedia were significantly associated with moderate to severe periodontitis. When looking at different clinical and radiographic parameters of periodontitis, high concentrations of P. gingivalis and T. forsythia were significantly associated with the number of 4-5 mm periodontal pockets, ≥ 6 mm pockets, and alveolar bone loss (ABL. High level of T. forsythia was associated also with bleeding on probing (BOP. The combination of the four bacteria, i.e. the bacterial burden index, was associated with moderate to severe periodontitis with an odds ratio (OR of 2.40 (95% CI 1.39–4.13. When A. actinomycetemcomitans was excluded from the combination of the bacteria, the OR was improved to 2.61 (95% CI 1.51–4.52. The highest odds ratio 3.59 (95% CI 1.94–6.63 was achieved when P. intermedia was further excluded from the combination and only the levels of P. gingivalis and T. forsythia were used. Salivary

  17. Quantitative analysis of genomic element interactions by molecular colony technique.

    Science.gov (United States)

    Gavrilov, Alexey A; Chetverina, Helena V; Chermnykh, Elina S; Razin, Sergey V; Chetverin, Alexander B

    2014-03-01

    Distant genomic elements were found to interact within the folded eukaryotic genome. However, the used experimental approach (chromosome conformation capture, 3C) enables neither determination of the percentage of cells in which the interactions occur nor demonstration of simultaneous interaction of >2 genomic elements. Each of the above can be done using in-gel replication of interacting DNA segments, the technique reported here. Chromatin fragments released from formaldehyde-cross-linked cells by sodium dodecyl sulfate extraction and sonication are distributed in a polyacrylamide gel layer followed by amplification of selected test regions directly in the gel by multiplex polymerase chain reaction. The fragments that have been cross-linked and separate fragments give rise to multi- and monocomponent molecular colonies, respectively, which can be distinguished and counted. Using in-gel replication of interacting DNA segments, we demonstrate that in the material from mouse erythroid cells, the majority of fragments containing the promoters of active β-globin genes and their remote enhancers do not form complexes stable enough to survive sodium dodecyl sulfate extraction and sonication. This indicates that either these elements do not interact directly in the majority of cells at a given time moment, or the formed DNA-protein complex cannot be stabilized by formaldehyde cross-linking.

  18. Analysis of Spontaneous,gamma ray-and ethylnitrosourea-induced hprt mutants in HL-60 cells With multiplex PCR

    Institute of Scientific and Technical Information of China (English)

    Sheng-Xue Liu; Jia Cao; Hui An; Hua-Min Shun; Lu-Jun Yang; Yong Liu

    2003-01-01

    AIM: To explore the molecular spectra and mechanism of human hypoxanthine guanine phosphoribosyl transferase (hprt) gene mutation induced by ethyluitrosourea (ENU) and 60Co γ-rays.METHODS: Independent human promyelocytic leukemia cells (HL-60) mutants at the hprt locus were isolated from untreated, ethyluitrosourea (ENU) and 60Co γ-ray-exposed cells, respectively, and verified by two-way screening. The genetic changes underlying the mutation were determined by multiplex polymerase chain reaction (PCR) amplification and electrophoresis technique.RESULTS: With dosage increased, survival rate of plated cell reduced (in the group with dosage of ENU with 100-200μg/ml, P<0.01; in the group with dosage of 60Co γ-ray with 2-4 Gy, P<0.05) and mutational frequency increased (in the group of ENU 12.5-200.0 μg/ml, P<0.05; in the group of 60Co γ-ray with 1-4 Gy, P<0.05) significantly. In the 13spontaneous mutants analyzed, 92.3 % of mutant clones did not show any change in number or size of exon, a single exon was lost in 7.7 %, and no evidence indicated total gene deletion occurred in nine hprt exons. However, deletions were found in 79.7 % of ENU-induced mutations (62.5-89.4 %,P<0.01) and in 61.7 % of gamma-ray-induced mutations (28.6-76.5 %, P<0.01). There were deletion mutations in all 9 exons of hprt gene and the most of induced mutations were chain deletion with multiplex exons (97.9 % in gammaray-induced mutants, 88.1% in ENU-induced mutants).CONCLUSION: The spectra of spontaneous mutations differs completely from that induced by EUN or 60Co γ-ray.Although both ENU and γ-ray can cause destruction of genetic structure, mechanism of mutagenesis between them may be different.

  19. A Quantitative Analysis of the Behavioral Checklist of the Movement ABC Motor Test

    Science.gov (United States)

    Ruiz, Luis Miguel; Gomez, Marta; Graupera, Jose Luis; Gutierrez, Melchor; Linaza, Jose Luis

    2007-01-01

    The fifth section of the Henderson and Sugden's Movement ABC Checklist is part of the general Checklist that accompanies The Movement ABC Battery. The authors maintain that the analysis of this section must be mainly qualitative instead of quantitative. The main objective of this study was to employ a quantitative analysis of this behavioural…

  20. [Bibliometric analysis of bacterial quantitative proteomics in English literatures].

    Science.gov (United States)

    Zhang, Xin; She, Danyang; Liu, Youning; Wang, Rui; Di, Xiuzhen; Liang, Beibei; Wang, Yue

    2014-07-01

    To analyze the worldwide advances on bacterial quantitative proteomics over the past fifteen years with bibliometric approach. Literature retrieval was conducted throughout the databases of Pubmed, Embase and Science citation index (SCI), using "bacterium" and "quantitative proteomics" as the key words. The deadline is July 2013. We sorted and analyzed these articles with Endnote X6 from the aspects of published year, the first author, name of journal, published institution, cited frequency and publication type. 932 English articles were included in our research after deleting the duplicates. The first article on bacterial quantitative proteomics was reported in 1999. The maximal publications were 163 related articles in 2012. Up till July 2013, authors from more than 23 countries and regions have published articles in this field. China ranks the fourth. The main publication type is original articles. The most frequently cited article is entitled with "Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition" by Silva JC, Gorenstein MV, Li GZ, et al in Mol Cell Proteomics 2006. The most productive author is Smith RD from Biological Sciences Division, Pac. Northwest National Laboratory. The top journal publishing bacterial quantitative proteomics is Proteomics. More and more researchers pay attention to quantitative proteomics which will be widely used in bacteriology.

  1. Geographical classification of Epimedium based on HPLC fingerprint analysis combined with multi-ingredients quantitative analysis.

    Science.gov (United States)

    Xu, Ning; Zhou, Guofu; Li, Xiaojuan; Lu, Heng; Meng, Fanyun; Zhai, Huaqiang

    2017-05-01

    A reliable and comprehensive method for identifying the origin and assessing the quality of Epimedium has been developed. The method is based on analysis of HPLC fingerprints, combined with similarity analysis, hierarchical cluster analysis (HCA), principal component analysis (PCA) and multi-ingredient quantitative analysis. Nineteen batches of Epimedium, collected from different areas in the western regions of China, were used to establish the fingerprints and 18 peaks were selected for the analysis. Similarity analysis, HCA and PCA all classified the 19 areas into three groups. Simultaneous quantification of the five major bioactive ingredients in the Epimedium samples was also carried out to confirm the consistency of the quality tests. These methods were successfully used to identify the geographical origin of the Epimedium samples and to evaluate their quality.

  2. Multiplex sequencing of pooled mitochondrial genomes-a crucial step toward biodiversity analysis using mito-metagenomics.

    Science.gov (United States)

    Tang, Min; Tan, Meihua; Meng, Guanliang; Yang, Shenzhou; Su, Xu; Liu, Shanlin; Song, Wenhui; Li, Yiyuan; Wu, Qiong; Zhang, Aibing; Zhou, Xin

    2014-12-16

    The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species >15 kb and the remaining >10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.

  3. Performance Analysis of Diversity and Multiplexing Tradeoff and Distributed Space-Time Block Code in Cooperative MIMO Networks

    Directory of Open Access Journals (Sweden)

    Xiaorong Xu

    2009-08-01

    Full Text Available Cooperative MIMO network, which consists of multiple relay nodes equipped with a single antenna, is introduced in this paper. Virtual MIMO is examined with multi-relay cooperative communication. Performances of Distributed Space-Time Block Code (DSTBC in cooperative MIMO are analyzed and compared with general cooperative diversity protocols. Diversity multiplexing tradeoff (DMT, outage probability of DSTBC and pair-wise error probability (PEP of virtual MIMO with DSTBC are derived in detail with equation denotation presented. Numerical Results of DMT and outage performance indicate that, DSTBC could provide full spatial diversity in two cooperative nodes, and it outperforms other cooperative protocols such as Amplify-and-Forward (AF and Selection Decode and Forward (SDF with the increase of cooperative nodes. Meanwhile, Monte Carlo simulation of average error performance in cooperative MIMO network reveal that, with the increase of cooperative nodes, DSTBC could obtain both spatial diversity gain and coded gain. In addition, higher order modulation with the increased number of relays could also enhance BER performance in multi-relay cooperative MIMO network. Theoretical results are confirmed by means of simulations.

  4. Molecular analysis of THH-induced mutations at HPRT locus in human promyelocytic leukemia cells with multiplex polymerase chain reaction

    Institute of Scientific and Technical Information of China (English)

    LIU Sheng-xue; CAO Jia; AN Hui

    2002-01-01

    Objective: To study the genotoxicity and antitumor activity of a Chinese medicinal herb, Tripterygium Hypoglaucum (Level) Hutch (THH). Methods: The genotoxicity and antitumor activity of TH-H were investigated in human promyelocytic leukemia cells on the mutation of hypoxanthine-guanine phosphoribosyl transferase (HPRT) gene by using single cell clone culture, two-way screening counting, multiplex PCR amplification and gel electrophoresis. Results: The results showed that different mutant spectra existed between the spontaneous mutation and induced mutation by THH. Only 7. 7% (1/13) of spontaneous mutants showed deletion mutations, whereas the induced mutants included 46.6% (27/58) deletions. Mapping of all intragenic deletion breakpoints showed a random distribution in all 9 exons, but toward the 3'-end of the HPRT gene. Deletion of exon 1 only appeared when whole gene was deleted. Deletions of exon 7/8 and 9 often showed linkage deletions (71.4%). Conclusion: THH can induce the mutation, mainly deletions, of HPRT gene in human promyelocytic leukemia cells.

  5. Electrochemical sensor for multiplex screening of genetically modified DNA: identification of biotech crops by logic-based biomolecular analysis.

    Science.gov (United States)

    Liao, Wei-Ching; Chuang, Min-Chieh; Ho, Ja-An Annie

    2013-12-15

    Genetically modified (GM) technique, one of the modern biomolecular engineering technologies, has been deemed as profitable strategy to fight against global starvation. Yet rapid and reliable analytical method is deficient to evaluate the quality and potential risk of such resulting GM products. We herein present a biomolecular analytical system constructed with distinct biochemical activities to expedite the computational detection of genetically modified organisms (GMOs). The computational mechanism provides an alternative to the complex procedures commonly involved in the screening of GMOs. Given that the bioanalytical system is capable of processing promoter, coding and species genes, affirmative interpretations succeed to identify specified GM event in terms of both electrochemical and optical fashions. The biomolecular computational assay exhibits detection capability of genetically modified DNA below sub-nanomolar level and is found interference-free by abundant coexistence of non-GM DNA. This bioanalytical system, furthermore, sophisticates in array fashion operating multiplex screening against variable GM events. Such a biomolecular computational assay and biosensor holds great promise for rapid, cost-effective, and high-fidelity screening of GMO. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. Quantitative Analysis by Isotopic Dilution Using Mass Spectroscopy: The Determination of Caffeine by GC-MS.

    Science.gov (United States)

    Hill, Devon W.; And Others

    1988-01-01

    Describes a laboratory technique for quantitative analysis of caffeine by an isotopic dilution method for coupled gas chromatography-mass spectroscopy. Discusses caffeine analysis and experimental methodology. Lists sample caffeine concentrations found in common products. (MVL)

  7. Quantitative analysis of norfloxacin by 1H NMR and HPLC.

    Science.gov (United States)

    Frackowiak, Anita; Kokot, Zenon J

    2012-01-01

    1H NMR and developed previously HPLC methods were applied to quantitative determination of norfloxacin in veterinary solution form for pigeon. Changes in concentration can lead to significant changes in the 1H chemical shifts of non-exchangeable aromatic protons as a result of extensive self-association phenomena. This chemical shift variation of protons was analyzed and applied in the quantitative determination of norfloxacin. The method is simple, rapid, precise and accurate, and can be used for quality control of this drug.

  8. Multiplexed coding in the human basal ganglia

    Science.gov (United States)

    Andres, D. S.; Cerquetti, D.; Merello, M.

    2016-04-01

    A classic controversy in neuroscience is whether information carried by spike trains is encoded by a time averaged measure (e.g. a rate code), or by complex time patterns (i.e. a time code). Here we apply a tool to quantitatively analyze the neural code. We make use of an algorithm based on the calculation of the temporal structure function, which permits to distinguish what scales of a signal are dominated by a complex temporal organization or a randomly generated process. In terms of the neural code, this kind of analysis makes it possible to detect temporal scales at which a time patterns coding scheme or alternatively a rate code are present. Additionally, finding the temporal scale at which the correlation between interspike intervals fades, the length of the basic information unit of the code can be established, and hence the word length of the code can be found. We apply this algorithm to neuronal recordings obtained from the Globus Pallidus pars interna from a human patient with Parkinson’s disease, and show that a time pattern coding and a rate coding scheme co-exist at different temporal scales, offering a new example of multiplexed neuronal coding.

  9. Quantitative analysis of sensor for pressure waveform measurement

    Directory of Open Access Journals (Sweden)

    Tyan Chu-Chang

    2010-01-01

    Full Text Available Abstract Background Arterial pressure waveforms contain important diagnostic and physiological information since their contour depends on a healthy cardiovascular system 1. A sensor was placed at the measured artery and some contact pressure was used to measure the pressure waveform. However, where is the location of the sensor just about enough to detect a complete pressure waveform for the diagnosis? How much contact pressure is needed over the pulse point? These two problems still remain unresolved. Method In this study, we propose a quantitative analysis to evaluate the pressure waveform for locating the position and applying the appropriate force between the sensor and the radial artery. The two-axis mechanism and the modified sensor have been designed to estimate the radial arterial width and detect the contact pressure. The template matching method was used to analyze the pressure waveform. In the X-axis scan, we found that the arterial diameter changed waveform (ADCW and the pressure waveform would change from small to large and then back to small again when the sensor was moved across the radial artery. In the Z-axis scan, we also found that the ADCW and the pressure waveform would change from small to large and then back to small again when the applied contact pressure continuously increased. Results In the X-axis scan, the template correlation coefficients of the left and right boundaries of the radial arterial width were 0.987 ± 0.016 and 0.978 ± 0.028, respectively. In the Z-axis scan, when the excessive contact pressure was more than 100 mm Hg, the template correlation was below 0.983. In applying force, when using the maximum amplitude as the criteria level, the lower contact pressure (r = 0.988 ± 0.004 was better than the higher contact pressure (r = 0.976 ± 0.012. Conclusions Although, the optimal detective position has to be close to the middle of the radial arterial, the pressure waveform also has a good completeness with

  10. Quantitative analysis of autophagy using advanced 3D fluorescence microscopy.

    Science.gov (United States)

    Changou, Chun A; Wolfson, Deanna L; Ahluwalia, Balpreet Singh; Bold, Richard J; Kung, Hsing-Jien; Chuang, Frank Y S

    2013-05-03

    Prostate cancer is the leading form of malignancies among men in the U.S. While surgery carries a significant risk of impotence and incontinence, traditional chemotherapeutic approaches have been largely unsuccessful. Hormone therapy is effective at early stage, but often fails with the eventual development of hormone-refractory tumors. We have been interested in developing therapeutics targeting specific metabolic deficiency of tumor cells. We recently showed that prostate tumor cells specifically lack an enzyme (argininosuccinate synthase, or ASS) involved in the synthesis of the amino acid arginine(1). This condition causes the tumor cells to become dependent on exogenous arginine, and they undergo metabolic stress when free arginine is depleted by arginine deiminase (ADI)(1,10). Indeed, we have shown that human prostate cancer cells CWR22Rv1 are effectively killed by ADI with caspase-independent apoptosis and aggressive autophagy (or macroautophagy)(1,2,3). Autophagy is an evolutionarily-conserved process that allows cells to metabolize unwanted proteins by lysosomal breakdown during nutritional starvation(4,5). Although the essential components of this pathway are well-characterized(6,7,8,9), many aspects of the molecular mechanism are still unclear - in particular, what is the role of autophagy in the death-response of prostate cancer cells after ADI treatment? In order to address this question, we required an experimental method to measure the level and extent of autophagic response in cells - and since there are no known molecular markers that can accurately track this process, we chose to develop an imaging-based approach, using quantitative 3D fluorescence microscopy(11,12). Using CWR22Rv1 cells specifically-labeled with fluorescent probes for autophagosomes and lysosomes, we show that 3D image stacks acquired with either widefield deconvolution microscopy (and later, with super-resolution, structured-illumination microscopy) can clearly capture the early

  11. Microchromatography of hemoglobins. VIII. A general qualitative and quantitative method in plastic drinking straws and the quantitative analysis of Hb-F.

    Science.gov (United States)

    Schroeder, W A; Pace, L A

    1978-03-01

    The microchromatographic procedure for the quantitative analysis of the hemoglobin components in a hemolysate uses columns of DEAE-cellulose in a plastic drinking straw with a glycine-KCN-NaCl developer. Not only may the method be used for the quantitative analysis of Hb-F but also for the analysis of the varied components in mixtures of hemoglobins.

  12. Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM analysis [v1; ref status: indexed, http://f1000r.es/2hj

    Directory of Open Access Journals (Sweden)

    Erin K. Hanson

    2013-12-01

    Full Text Available Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE or quantitative RT-PCR (qRT-PCR platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions, IL1F7 (skin, ALAS2 (blood, MMP10 (menstrual blood, HTN3 (saliva and TGM4 (semen.  The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green. Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively

  13. Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM analysis [v2; ref status: indexed, http://f1000r.es/314

    Directory of Open Access Journals (Sweden)

    Erin K. Hanson

    2014-02-01

    Full Text Available Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE or quantitative RT-PCR (qRT-PCR platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions, IL1F7 (skin, ALAS2 (blood, MMP10 (menstrual blood, HTN3 (saliva and TGM4 (semen.  The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green. Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively

  14. Quantitative Analysis and Design of a Rudder Roll Damping Controller

    DEFF Research Database (Denmark)

    Hearns, G.; Blanke, M.

    1998-01-01

    A rudder roll damping controller is designed using Quantitative feedback theory to be robust for changes in the ships metacentric height. The analytical constraint due to the non-minimum phase behaviour of the rudder to roll is analysed using the Poisson Integral Formula and it is shown how...

  15. Quantitative analysis of distributed control paradigms of robot swarms

    DEFF Research Database (Denmark)

    Ngo, Trung Dung

    2010-01-01

    describe the physical and simulated robots, experiment scenario, and experiment setup. Third, we present our robot controllers based on behaviour based and neural network based paradigms. Fourth, we graphically show their experiment results and quantitatively analyse the results in comparison of the two...

  16. Teaching Quantitative Reasoning for Nonscience Majors through Carbon Footprint Analysis

    Science.gov (United States)

    Boose, David L.

    2014-01-01

    Quantitative reasoning is a key intellectual skill, applicable across disciplines and best taught in the context of authentic, relevant problems. Here, I describe and assess a laboratory exercise that has students calculate their "carbon footprint" and evaluate the impacts of various behavior choices on that footprint. Students gather…

  17. Quantitative security analysis for multi-threaded programs

    NARCIS (Netherlands)

    Ngo, Tri Minh; Huisman, Marieke

    2013-01-01

    Quantitative theories of information flow give us an approach to relax the absolute confidentiality properties that are difficult to satisfy for many practical programs. The classical information-theoretic approaches for sequential programs, where the program is modeled as a communication channel wi

  18. Quantitative and Qualitative Analysis of Biomarkers in Fusarium verticillioides

    Science.gov (United States)

    In this study, a combination HPLC-DART-TOF-MS system was utilized to identify and quantitatively analyze carbohydrates in wild type and mutant strains of Fusarium verticillioides. Carbohydrate fractions were isolated from F. verticillioides cellular extracts by HPLC using a cation-exchange size-excl...

  19. Multiplex editing system

    DEFF Research Database (Denmark)

    2015-01-01

    The present invention relates to a multiplex editing system. The system allows multiple editing of nucleic acid sequences such as genomic sequences, such as knockins of genes of interest in a genome, knockouts of genomic sequences and/or allele replacement. Also provided herein are a method...... for editing nucleic acids and a cell comprising a stably integrated endonuclease....

  20. Multiplex PageRank

    CERN Document Server

    Halu, Arda; Pansaraza, 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 in...

  1. Arthrogryposis multiplex congenita

    DEFF Research Database (Denmark)

    Linnet, Karen Markussen; Balslev, Thomas; Møller-Madsen, Bjarne

    2015-01-01

    Arthrogryposis multiplex congenita (AMC) is a sign rather than a diagnosis. It implies contractures in multiple body areas and occurs in 1:3,000-5,000 live births. Primary aetiologies include neuropathic, myopathic, metabolic, end plate and vascular disorder affecting the developing foetus...

  2. Structural and Quantitative Analysis of Three C-Glycosylflavones by Variable Temperature Proton Quantitative Nuclear Magnetic Resonance

    Directory of Open Access Journals (Sweden)

    Jing Liu

    2017-01-01

    Full Text Available Quantitative nuclear magnetic resonance is a powerful tool in drug analysis because of its speed, precision, and efficiency. In present study, the application of variable temperature proton quantitative nuclear magnetic resonance (VT-1H-qNMR for the calibration of three C-glycosylflavones including orientin, isoorientin, and schaftoside as reference substances was reported. Since there was conformational equilibrium due to the restricted rotation around the C(sp3-C(sp2 bond in C-glycosylflavones, the conformational behaviors were investigated by VT-NMR and verified by molecular mechanics (MM calculation. The VT-1H-qNMR method was validated including the linearity, limit of quantification, precision, and stability. The results were consistent with those obtained from mass balance approach. VT-1H-qNMR can be deployed as an effective tool in analyzing C-glycosylflavones.

  3. Structural and Quantitative Analysis of Three C-Glycosylflavones by Variable Temperature Proton Quantitative Nuclear Magnetic Resonance

    Science.gov (United States)

    Liu, Yang; Dai, Zhong

    2017-01-01

    Quantitative nuclear magnetic resonance is a powerful tool in drug analysis because of its speed, precision, and efficiency. In present study, the application of variable temperature proton quantitative nuclear magnetic resonance (VT-1H-qNMR) for the calibration of three C-glycosylflavones including orientin, isoorientin, and schaftoside as reference substances was reported. Since there was conformational equilibrium due to the restricted rotation around the C(sp3)-C(sp2) bond in C-glycosylflavones, the conformational behaviors were investigated by VT-NMR and verified by molecular mechanics (MM) calculation. The VT-1H-qNMR method was validated including the linearity, limit of quantification, precision, and stability. The results were consistent with those obtained from mass balance approach. VT-1H-qNMR can be deployed as an effective tool in analyzing C-glycosylflavones. PMID:28243484

  4. Cytokine and chemokine profiles of aqueous humor and serum in horses with uveitis measured using multiplex bead immunoassay analysis.

    Science.gov (United States)

    Curto, Elizabeth; Messenger, Kristen M; Salmon, Jacklyn H; Gilger, Brian C

    2016-12-01

    To determine whether horses with clinically diagnosed Equine Recurrent Uveitis (ERU) and those with Leptospirosis infection have a specific cytokine profile in their aqueous humor (AH) and serum that differs from horses with uveitis secondary to other ocular inflammatory processes and from horses with normal eyes. Twenty-five client-owned horses with uveitis that were presented to the North Carolina State University Ophthalmology Service, and four University-owned horses without history or clinical signs of ocular disease. Samples of AH and serum were obtained from horses with ERU (n=13), acute or non-recurrent uveitis (UV; n=7), uveitis secondary to infectious keratitis (IK; n=5), and normal eyes (N; n=4). Cytokine levels in AH and serum were quantified using a multiplex bead immunoassay. Leptospiral antibody titers in serum and AH and PCR for Leptospiral DNA in AH were performed. In the AH of horses with ERU, increased levels of IL-1a, IL-4, IL-6, IL-8, IL-12p70, FGF-2, G-CSF, and RANTES were measured compared to UV, IK and N eyes, but the differences were not significant. However, IL-10 was significantly higher in ERU eyes compared to IK and N (P=0.029; 0.013), and IP-10 in ERU eyes was significantly higher than in UV and N (P=0.004). Furthermore, MCP-1 was significantly higher in ERU than N (P=0.04). In the serum, increased levels of IL-1a, IL-4, IL-6, IL-8, IL-12p70, fractalkine, and G-CSF were measured in horses with ERU, but the levels were not significantly higher than those observed in UV, IK, or N horses. However, serum IP-10 levels in horses with ERU were significantly higher than in UV and N horses (P=0.005) and MCP-1 levels were significantly higher in ERU than N (P=0.03). Horses with marked ocular inflammation had significantly higher serum levels of G-CSF, IL-1a, fractalkine, IL-13, IL-4, IL-17a, IL-12p70, IFN-γ, and MCP-1. Elevated IL-10 in AH was significantly associated with disease chronicity, both overall and in ERU eyes (P=0.049), and in

  5. 2D Gel-Based Multiplexed Proteomic Analysis during Larval Development and Metamorphosis of the Biofouling Polychaete Tubeworm Hydroides elegans

    KAUST Repository

    Zhang, Yu

    2010-09-03

    Larval settlement and metamorphosis of a common biofouling polychaete worm, Hydroides elegans, involve remarkable structural and physiological changes during this pelagic to sessile habitat shift. The endogenous protein molecules and post-translational modifications that drive this larval transition process are not only of interest to ecologists but also to the antifouling paint industry, which aims to control the settlement of this biofouling species on man-made structures (e.g., ship hulls). On the basis of our recent proteomic studies, we hypothesize that rapid larval settlement of H. elegans could be mediated through changes in phosphorylation status of proteins rather than extensive de novo synthesis of proteins. To test this hypothesis, 2D gel-based multiplexed proteomics technology was used to monitor the changes in protein expression and phosphorylation status during larval development and metamorphosis of H. elegans. The protein expression profiles of larvae before and after they reached competency to attach and metamorphose were similar in terms of major proteins, but the percentage of phosphorylated proteins increased from 41% to 49% after competency. Notably, both the protein and phosphoprotein profiles of the metamorphosed individuals (adult) were distinctly different from that of the larvae, with only 40% of the proteins phosphorylated in the adult stage. The intensity ratio of all phosphoprotein spots to all total protein spots was also the highest in the competent larval stage. Overall, our results indicated that the level of protein phosphorylation might play a crucial role in the initiation of larval settlement and metamorphosis. © 2010 American Chemical Society.

  6. Performance Analysis on 16-Channels Wavelength Division Multiplexing in Free Space Optical Transmission under Tropical Regions Environment

    Directory of Open Access Journals (Sweden)

    Ratna K.Z. Sahbudin

    2012-01-01

    Full Text Available Problem statement: Wavelength-Division-Multiplexing (WDM is a promising technique for meeting the growing demand for increased bandwidth and various types of services in the optical access network. For wide area or metropolitan networks, fibers are deployed to provide huge bandwidth. In access networks, the fiber-to-the-home will partially solve the last mile problem. However, some environmentally sensitive area such as housing areas, tower buildings and national parks are not allowed to deploy fibers. Therefore, Radio Frequency (RF is normally used to overcome this problem. The incompatibility of RF and optical channels is now widely believed to be the limiting factor in efforts to further increase transport capabilities. Free Space Optical (FSO communication is the technology that can address any connectivity needed in optical networks, such as core, edge, or access networks. Approach: In this project, the simulation software namely Optical System version 7 is used to simulate the design of WDM in FSO transmission. The total losses that have been considered in this design are geometric loss, transmitter and receiver loss and atmospheric attenuation which focus on nonselective scattering during heavy rainfall condition in Malaysian environment. Malaysian weather data are used to reflect the conditions particularly in tropical regions. Results: We have presented the results of 16-channels WDM at 100-GHz channel spacing. The simulated results show that this system can support a higher bit rate up to 2.5 Gbps over 2.4 km distance. Conclusion: Simulation results showed that WDM FSO system may be a good candidate to solve the last mile problem and also it has capability to accommodate the channels more than 16. By introducing the error correction code or balance detection, the transmission distance might be increased further.

  7. Development and validation of a multiplex methylation specific PCR-coupled liquid bead array for liquid biopsy analysis.

    Science.gov (United States)

    Parisi, C; Mastoraki, S; Markou, A; Strati, A; Chimonidou, M; Georgoulias, V; Lianidou, E S

    2016-10-01

    Liquid biopsy is based on minimally invasive blood tests and has the potential to characterize the evolution of a solid tumor in real time, by extracting molecular information from circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA). Epigenetic silencing of tumor and metastasis suppressor genes plays a key role in survival and metastatic potential of cancer cells. Our group was the first to show the presence of epigenetic alterations in CTCs. We present the development and analytical validation of a highly specific and sensitive Multiplex Methylation Specific PCR-coupled liquid bead array (MMSPA) for the simultaneous detection of the methylation status of three tumor and metastasis suppressor genes (CST6, SOX17 and BRMS1) in liquid biopsy material (CTCs, corresponding ctDNA) and paired primary breast tumors. In the EpCAM-positive CTCs fraction we observed methylation of: a) CST6, in 11/30(37%) and 11/30(37%), b) BRMS1 in 8/30(27%) and 11/30(37%) c) SOX17 in 8/30(27%) and 13/30(43%) early breast cancer patients and patients with verified metastasis respectively. In ctDNA we observed methylation of: a) CST6, in 5/30(17%) and 10/31(32%), b) BRMS1 in 8/30 (27%) and 8/31 (26%) c) SOX17 in 5/30(17%) and 13/31(42%) early breast cancer patients and patients with verified metastasis respectively. Our results indicate a high cancerous load at the epigenetic level in EpCAM-positive CTCs fractions and corresponding ctDNA in breast cancer. The main principle of the developed methodology has the potential to be extended in a large number of gene-targets and be applied in many types of cancer. Copyright © 2016. Published by Elsevier B.V.

  8. Multiplex PCR system for rapid detection of pathogens in patients with presumed sepsis - a systemic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Shy-Shin Chang

    Full Text Available BACKGROUND: Blood culture is viewed as the golden standard for the diagnosis of sepsis but suffers from low sensitivity and long turnaround time. LightCycler SeptiFast (LC-SF is a real-time multiplex polymerase chain reaction test able to detect 25 common pathogens responsible for bloodstream infections within hours. We aim to assess the accuracy of LC-SF by systematically reviewing the published studies. METHOD: Related literature on Medline, Embase, and Cochrane databases was searched up to October 2012 for studies utilizing LC-SF to diagnose suspected sepsis and that provided sufficient data to construct two-by-two tables. RESULTS: A total of 34 studies enrolling 6012 patients of suspected sepsis were included. The overall sensitivity and specificity for LC-SF to detect bacteremia or fungemia was 0·75 (95% CI: 0·65-0·83 and 0·92 (95%CI:0·90-0·95, respectively. LC-SF had a high positive likelihood ratio (10·10 and a moderate negative likelihood ratio (0·27. Specifically, LC-SF had a sensitivity of 0·80 (95%CI: 0·70-0·88 and a specificity of 0·95(95%CI: 0·93-0·97 for the bacteremia outcome, and a sensitivity of 0·61 (95%CI: 0·48-0·72 and a specificity of 0·99 (95%CI: 0·99-0·99 for the fungemia outcome. High heterogeneity was found in the bacteremia outcome subgroup but not in the fungemia outcome subgroup. CONCLUSION: LC-SF is of high rule-in value for early detection of septic patients. In a population with low pretest probability, LC-SF test can still provide valuable information for ruling out bacteremia or fungemia.

  9. Extracting information from multiplex networks.

    Science.gov (United States)

    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.

  10. Extracting information from multiplex networks

    Science.gov (United States)

    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.

  11. Low-cost, multiplexed biosensor for disease diagnosis

    Science.gov (United States)

    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.

  12. Quantitative analysis of immobilized metalloenzymes by atomic absorption spectroscopy.

    Science.gov (United States)

    Opwis, Klaus; Knittel, Dierk; Schollmeyer, Eckhard

    2004-12-01

    A new, sensitive assay for the quantitative determination of immobilized metal containing enzymes has been developed using atomic absorption spectroscopy (AAS). In contrast with conventionally used indirect methods the described quantitative AAS assay for metalloenzymes allows more exact analyses, because the carrier material with the enzyme is investigated directly. As an example, the validity and reliability of the method was examined by fixing the iron-containing enzyme catalase on cotton fabrics using different immobilization techniques. Sample preparation was carried out by dissolving the loaded fabrics in sulfuric acid before oxidising the residues with hydrogen peroxide. The iron concentrations were determined by flame atomic absorption spectrometry after calibration of the spectrometer with solutions of the free enzyme at different concentrations.

  13. Research on Petroleum Reservoir Diagenesis and Damage Using EDS Quantitative Analysis Method With Standard Samples

    Institute of Scientific and Technical Information of China (English)

    包书景; 陈文学; 等

    2000-01-01

    In recent years,the X-ray spectrometer has been devekloped not only just in enhancing resolution,but also towards dynamic analysis.Computer modeling processing,sampled quantitative analysis and supra-light element analysis.With the gradual sophistication of the quantitative analysis system software,the rationality and accuracy of the established sample deferential document have become the most important guarantee to the reliability of sample quantitative analysis.This work is an important technical subject in China Petroleum Reservoir Research.Through two years of research and experimental work,the EDS quantitative analysis method for petroleum geolgey and resevoir research has been established.and referential documents for five mineral(silicate,etc).specimen standards have been compiled.Closely combining the shape characters and compositional characters of the minerals together and applying them into reservoir diagenetic research and prevention of oil formations from damage,we have obtained obvious geological effects.

  14. Quantitative analysis of pheromone-binding protein specificity

    OpenAIRE

    Katti, S.; Lokhande, N.; D González; Cassill, A.; Renthal, R

    2012-01-01

    Many pheromones have very low water solubility, posing experimental difficulties for quantitative binding measurements. A new method is presented for determining thermodynamically valid dissociation constants for ligands binding to pheromone-binding proteins (OBPs), using β-cyclodextrin as a solubilizer and transfer agent. The method is applied to LUSH, a Drosophila OBP that binds the pheromone 11-cis vaccenyl acetate (cVA). Refolding of LUSH expressed in E. coli was assessed by measuring N-p...

  15. Public Library System in Ankara: A Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Bülent Yılmaz

    2014-12-01

    Full Text Available This study investigates 42 public libraries in 25 central districts within the boundaries of Ankara Metropolitan Municipality in respect of five factors according to national and international standards quantitatively. The findings show that public libraries in Ankara are insufficient with respect to the number of buildings, users, staff and collection and also in terms of standards. Therefore, it has been suggested that an urgent planning is necessary for public libraries in Ankara.

  16. Quantitative Trait Locus Analysis of the Early Domestication of Sunflower

    OpenAIRE

    David M Wills; Burke, John M.

    2007-01-01

    Genetic analyses of the domestication syndrome have revealed that domestication-related traits typically have a very similar genetic architecture across most crops, being conditioned by a small number of quantitative trait loci (QTL), each with a relatively large effect on the phenotype. To date, the domestication of sunflower (Helianthus annuus L.) stands as the only counterexample to this pattern. In previous work involving a cross between wild sunflower (also H. annuus) and a highly improv...

  17. Fluorescent microscopy approaches of quantitative soil microbial analysis

    Science.gov (United States)

    Ivanov, Konstantin; Polyanskaya, Lubov

    2015-04-01

    Classical fluorescent microscopy method was used during the last decades in various microbiological studies of terrestrial ecosystems. The method provides representative results and simple application which is allow to use it both as routine part of amplitudinous research and in small-scaled laboratories. Furthermore, depending on research targets a lot of modifications of fluorescent microscopy method were established. Combination and comparison of several approaches is an opportunity of quantitative estimation of microbial community in soil. The first analytical part of the study was dedicated to soil bacterial density estimation by fluorescent microscopy in dynamic of several 30-days experiments. The purpose of research was estimation of changes in soil bacterial community on the different soil horizons under aerobic and anaerobic conditions with adding nutrients in two experimental sets: cellulose and chitin. Was modified the nalidixic acid method for inhibition of DNA division of gram-negative bacteria, and the method provides the quantification of this bacterial group by fluorescent microscopy. Established approach allowed to estimate 3-4 times more cells of gram-negative bacteria in soil. The functions of actinomyces in soil polymer destruction are traditionally considered as dominant in comparison to gram-negative bacterial group. However, quantification of gram-negative bacteria in chernozem and peatland provides underestimation of classical notion for this bacterial group. Chitin introduction had no positive effect to gram-negative bacterial population density changes in chernozem but concurrently this nutrient provided the fast growing dynamics at the first 3 days of experiment both under aerobic and anaerobic conditions. This is confirming chitinolytic activity of gram-negative bacteria in soil organic matter decomposition. At the next part of research modified method for soil gram-negative bacteria quantification was compared to fluorescent in situ

  18. The effects of selection on linkage analysis for quantitative traits.

    Science.gov (United States)

    Mackinnon, M J; Georges, M A

    1992-12-01

    The effects of within-sample selection on the outcome of analyses detecting linkage between genetic markers and quantitative traits were studied. It was found that selection by truncation for the trait of interest significantly reduces the differences between marker genotype means thus reducing the power to detect linked quantitative trait loci (QTL). The size of this reduction is a function of proportion selected, the magnitude of the QTL effect, recombination rate between the marker locus and the QTL, and the allele frequency of the QTL. Proportion selected was the most influential of these factors on bias, e.g., for an allele substitution effect of one standard deviation unit, selecting the top 80%, 50% or 20% of the population required 2, 6 or 24 times the number of progeny, respectively, to offset the loss of power caused by this selection. The effect on power was approximately linear with respect to the size of gene effect, almost invariant to recombination rate, and a complex function of QTL allele frequency. It was concluded that experimental samples from animal populations which have been subjected to even minor amounts of selection will be inefficient in yielding information on linkage between markers and loci influencing the quantitative trait under selection.

  19. The usefulness of 3D quantitative analysis with using MRI for measuring osteonecrosis of the femoral head

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Ji Young; Lee, Sun Wha [Ewha Womans University College of Medicine, Seoul (Korea, Republic of); Park, Youn Soo [Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of)

    2006-11-15

    We wanted to evaluate the usefulness of MRI 3D quantitative analysis for measuring osteonecrosis of the femoral head in comparison with MRI 2D quantitative analysis and quantitative analysis of the specimen. For 3 months at our hospital, 14 femoral head specimens with osteonecrosis were obtained after total hip arthroplasty. The patients preoperative MRIs were retrospectively reviewed for quantitative analysis of the size of the necrosis. Each necrotic fraction of the femoral head was measured by 2D quantitative analysis with using mid-coronal and mid-sagittal MRIs, and by 3D quantitative analysis with using serial continuous coronal MRIs and 3D reconstruction software. The necrotic fraction of the specimen was physically measured by the fluid displacement method. The necrotic fraction according to MRI 2D or 3D quantitative analysis was compared with that of the specimen by using Spearman's correlation test. On the correlative analysis, the necrotic fraction by MRI 2D quantitative analysis and quantitative analysis of the specimen showed moderate correlation (r = 0.657); on the other hand, the necrotic fraction by MRI 3D quantitative analysis and quantitative analysis of the specimen demonstrated a strong correlation (r = 0.952) ({rho} < 0.05). MRI 3D quantitative analysis was more accurate than 2D quantitative analysis using MRI for measuring osteonecrosis of the femoral head. Therefore, it may be useful for predicting the clinical outcome and deciding the proper treatment option.

  20. Quantitation of DNA methylation by melt curve analysis

    Directory of Open Access Journals (Sweden)

    Jones Michael E

    2009-04-01

    Full Text Available Abstract Background Methylation of DNA is a common mechanism for silencing genes, and aberrant methylation is increasingly being implicated in many diseases such as cancer. There is a need for robust, inexpensive methods to quantitate methylation across a region containing a number of CpGs. We describe and validate a rapid, in-tube method to quantitate DNA methylation using the melt data obtained following amplification of bisulfite modified DNA in a real-time thermocycler. Methods We first describe a mathematical method to normalise the raw fluorescence data generated by heating the amplified bisulfite modified DNA. From this normalised data the temperatures at which melting begins and finishes can be calculated, which reflect the less and more methylated template molecules present respectively. Also the T50, the temperature at which half the amplicons are melted, which represents the summative methylation of all the CpGs in the template mixture, can be calculated. These parameters describe the methylation characteristics of the region amplified in the original sample. Results For validation we used synthesized oligonucleotides and DNA from fresh cells and formalin fixed paraffin embedded tissue, each with known methylation. Using our quantitation we could distinguish between unmethylated, partially methylated and fully methylated oligonucleotides mixed in varying ratios. There was a linear relationship between T50 and the dilution of methylated into unmethylated DNA. We could quantitate the change in methylation over time in cell lines treated with the demethylating drug 5-aza-2'-deoxycytidine, and the differences in methylation associated with complete, clonal or no loss of MGMT expression in formalin fixed paraffin embedded tissues. Conclusion We have validated a rapid, simple in-tube method to quantify methylation which is robust and reproducible, utilizes easily designed primers and does not need proprietary algorithms or software. The