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Sample records for techniques molecular beacon

  1. Molecular Beacons in Diagnostics

    OpenAIRE

    Tyagi, Sanjay; Kramer, Fred Russell

    2012-01-01

    Recent technical advances have begun to realize the potential of molecular beacons to test for diverse infections in clinical diagnostic laboratories. These include the ability to test for, and quantify, multiple pathogens in the same clinical sample, and to detect antibiotic resistant strains within hours. The design principles of molecular beacons have also spawned a variety of allied technologies.

  2. Molecular Beacon-Based MicroRNA Imaging During Neurogenesis.

    Science.gov (United States)

    Lee, Jonghwan; Kim, Soonhag

    2016-01-01

    The fluorescence monitoring system for examining endogenous microRNA (miRNA) activity in cellular level provides crucial information on not only understanding a critical role of miRNA involving a variety of biological processes, but also evaluating miRNA expression patterns in a noninvasive manner. In this protocol, we report the details of a new procedure for a molecular beacon-based miRNA monitoring system, which includes the illustration scheme for miRNA detection strategy, exogenous miRNA detection, and measurement of endogenous miRNA expression level during neurogenesis. The fluorescence signal of miR-124a beacon quenched by BHQ2 was gradually recovered as increasing concentration of the miR-124a in tube. The functional work of miR-124a beacon was examined in intracellular environment, allowing for the internalization of the miR-124a beacon by lipofectamine, which resulted in activated fluorescent signals of the miR-124a beacon in the HeLa cells after the addition of synthetic miR-124a. The endogenous miR-124a expression level was detected by miR-124a beacon system during neurogenesis, showing brighter fluorescence intensity in cytoplasmic area of P19 cells after induction of neuronal differentiation by retinoic acid. The molecular beacon based-miRNA detection technique could be applicable to the simultaneous visualization of a variety of miRNA expression patterns using different fluorescence dyes. For the study of examining endogenous miRNA expression level using miRNA-beacon system, if cellular differentiation step is already prepared, transfection step of miR-124a beacon into P19 cells, and acquisition of activated fluorescence signal measured by confocal microscope can be conducted approximately within 6 h.

  3. Diagnosis of Neisseria gonorrhoeae Using Molecular Beacon

    Science.gov (United States)

    Patel, Achchhe Lal; Sonkar, Subash Chandra; Kumari, Indu; Saluja, Daman

    2015-01-01

    Neisseria gonorrhoeae is an important sexually transmitted diseases (STD) causing pathogen worldwide. Due to absence of an affordable diagnostic assay, routine screening of gonococcal infection becomes impossible in developing countries where infection rates are maximum. Treatment is given on the basis of symptoms alone which leads to spread of infection. Thus, development of a rapid, sensitive, specific, and PCR based visual diagnostic assay suitable for developing countries, required for better disease management, is aimed at in present study. Endocervical swabs were collected from patients visiting gynecology department of various hospitals in Delhi. In-house PCR based assay was developed and modified to visual assay using molecular beacon for end-point detection. It was evaluated against Roche AMPLICOR NG kit and rmp gene. Specificity of beacon was confirmed by competition experiments. Diagnostic test was 98.21% specific and 99.59% sensitive whereas negative and positive predicted value were 99.40% and 98.78%, respectively. We also observed that twice the concentration (2X) of premix was stable at 4°C for 4 months and dry swab samples gave concordant results with that of wet swabs. These features make the test best suitable for routine diagnosis of genital infections in developing countries. PMID:25802857

  4. Early Detection of Breast Cancer Using Molecular Beacons

    National Research Council Canada - National Science Library

    Yang, Lily

    2008-01-01

    .... We proposed to use molecular beacon technology to detect the level of expression of several biomarker genes that are highly expressed in breast cancer cells but not in normal breast epithelial cells...

  5. Caged molecular beacons: controlling nucleic acid hybridization with light.

    Science.gov (United States)

    Wang, Chunming; Zhu, Zhi; Song, Yanling; Lin, Hui; Yang, Chaoyong James; Tan, Weihong

    2011-05-28

    We have constructed a novel class of light-activatable caged molecular beacons (cMBs) that are caged by locking two stems with a photo-labile biomolecular interaction or covalent bond. With the cMBs, the nucleic acid hybridization process can be easily controlled with light, which offers the possibility for a high spatiotemporal resolution study of intracellular mRNAs. © The Royal Society of Chemistry 2011

  6. Molecular beacon probes-base multiplex NASBA Real-time for detection of HIV-1 and HCV.

    Science.gov (United States)

    Mohammadi-Yeganeh, S; Paryan, M; Mirab Samiee, S; Kia, V; Rezvan, H

    2012-06-01

    Developed in 1991, nucleic acid sequence-based amplification (NASBA) has been introduced as a rapid molecular diagnostic technique, where it has been shown to give quicker results than PCR, and it can also be more sensitive. This paper describes the development of a molecular beacon-based multiplex NASBA assay for simultaneous detection of HIV-1 and HCV in plasma samples. A well-conserved region in the HIV-1 pol gene and 5'-NCR of HCV genome were used for primers and molecular beacon design. The performance features of HCV/HIV-1 multiplex NASBA assay including analytical sensitivity and specificity, clinical sensitivity and clinical specificity were evaluated. The analysis of scalar concentrations of the samples indicated that the limit of quantification of the assay was beacon probes detected all HCV genotypes and all major variants of HIV-1. This method may represent a relatively inexpensive isothermal method for detection of HIV-1/HCV co-infection in monitoring of patients.

  7. Detection of DNA damage by using hairpin molecular beacon probes and graphene oxide.

    Science.gov (United States)

    Zhou, Jie; Lu, Qian; Tong, Ying; Wei, Wei; Liu, Songqin

    2012-09-15

    A hairpin molecular beacon tagged with carboxyfluorescein in combination with graphene oxide as a quencher reagent was used to detect the DNA damage by chemical reagents. The fluorescence of molecular beacon was quenched sharply by graphene oxide; while in the presence of its complementary DNA the quenching efficiency decreased because their hybridization prevented the strong adsorbability of molecular beacon on graphene oxide. If the complementary DNA was damaged by a chemical reagent and could not form intact duplex structure with molecular beacon, more molecular beacon would adsorb on graphene oxide increasing the quenching efficiency. Thus, damaged DNA could be detected based on different quenching efficiencies afforded by damaged and intact complementary DNA. The damage effects of chlorpyrifos-methyl and three metabolites of styrene such as mandelieaeids, phenylglyoxylieaeids and epoxystyrene on DNA were studied as models. The method for detection of DNA damage was reliable, rapid and simple compared to the biological methods. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. Chimeric peptide beacons: a direct polypeptide analog of DNA molecular beacons†

    OpenAIRE

    Oh, Kenneth J.; Cash, Kevin J.; Lubin, Arica A.; Plaxco, Kevin W.

    2007-01-01

    We have developed a new biosensor architecture, which is comprised of a polypeptide–peptide nucleic acid tri-block copolymer and which we have termed chimeric peptide beacons (CPB), that generates an optical output via a mechanism analogous to that employed in DNA-based molecular beacons.

  9. Synthesis and Characterization of a Magnetically Active 19F Molecular Beacon.

    Science.gov (United States)

    Dempsey, Megan E; Marble, Hetal D; Shen, Tun-Li; Fawzi, Nicolas L; Darling, Eric M

    2018-02-21

    Gene expression is used extensively to describe cellular characteristics and behaviors; however, most methods of assessing gene expression are unsuitable for living samples, requiring destructive processes such as fixation or lysis. Recently, molecular beacons have become a viable tool for live-cell imaging of mRNA molecules in situ. Historically, beacon-mediated imaging has been limited to fluorescence-based approaches. We propose the design and synthesis of a novel molecular beacon for magnetic resonance detection of any desired target nucleotide sequence. The biologically compatible synthesis incorporates commonly used bioconjugation reactions in aqueous conditions and is accessible for laboratories without extensive synthesis capabilities. The resulting beacon uses fluorine ( 19 F) as a reporter, which is broadened, or turned "off", via paramagnetic relaxation enhancement from a stabilized nitroxide radical spin label when the beacon is not bound to its nucleic acid target. Therefore, the 19 F NMR signal of the beacon is quenched in its hairpin conformation when the spin label and the 19 F substituent are held in proximity, but the signal is recovered upon beacon hybridization to its specific complementary nucleotide sequence by physical separation of the radical from the 19 F reporter. This study establishes a path for magnetic resonance-based assessment of specific mRNA expression, providing new possibilities for applying molecular beacon technology in living systems.

  10. Highly sensitive and rapid bacteria detection using molecular beacon-Au nanoparticles hybrid nanoprobes.

    Science.gov (United States)

    Cao, Jing; Feng, Chao; Liu, Yan; Wang, Shouyu; Liu, Fei

    2014-07-15

    Since many diseases are caused by pathogenic bacterial infections, accurate and rapid detection of pathogenic bacteria is in urgent need to timely apply appropriate treatments and to reduce economic costs. To end this, we designed molecular beacon-Au nanoparticle hybrid nanoprobes to improve the bacterial detection efficiency and sensitivity. Here, we show that the designed molecular beacon modified Au nanoparticles could specifically recognize synthetic DNAs targets and can readily detect targets in clinical samples. Moreover, the hybrid nanoprobes can recognize Escherichia coli within an hour at a concentration of 10(2) cfu/ml, which is 1000-folds sensitive than using molecular beacon directly. Our results show that the molecular beacon-Au nanoparticle hybrid nanoprobes have great potential in medical and biological applications. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. High-throughput SNP genotyping: combining tag SNPs and molecular beacons

    CSIR Research Space (South Africa)

    Barreiro, LB

    2009-10-01

    Full Text Available In the last decade, molecular beacons have emerged to become a widely used tool in the multiplex typing of single nucleotide polymorphisms (SNPs). Improvements in detection technologies in instrumentation and chemistries to label these probes have...

  12. Optical Fiber Nanotips Coated with Molecular Beacons for DNA Detection

    Directory of Open Access Journals (Sweden)

    Ambra Giannetti

    2015-04-01

    Full Text Available Optical fiber sensors, thanks to their compactness, fast response and real-time measurements, have a large impact in the fields of life science research, drug discovery and medical diagnostics. In recent years, advances in nanotechnology have resulted in the development of nanotools, capable of entering the single cell, resulting in new nanobiosensors useful for the detection of biomolecules inside living cells. In this paper, we provide an application of a nanotip coupled with molecular beacons (MBs for the detection of DNA. The MBs were characterized by hybridization studies with a complementary target to prove their functionality both free in solution and immobilized onto a solid support. The solid support chosen as substrate for the immobilization of the MBs was a 30 nm tapered tip of an optical fiber, fabricated by chemical etching. With this set-up promising results were obtained and a limit of detection (LOD of 0.57 nM was reached, opening up the possibility of using the proposed nanotip to detect mRNAs inside the cytoplasm of living cells.

  13. Molecular beacon anchored onto a graphene oxide substrate

    Science.gov (United States)

    Darbandi, Arash; Datta, Debopam; Patel, Krunal; Lin, Gary; Stroscio, Michael A.; Dutta, Mitra

    2017-09-01

    In this article, we report a graphene oxide-based nanosensor incorporating semiconductor quantum dots linked to DNA-aptamers that functions as a ‘turn-off’ fluorescent nanosensor for detection of low concentrations of analytes. A specific demonstration of this turn-off aptasensor is presented for the case of the detection of mercury (II) ions. In this system, ensembles of aptamer-based quantum-dot sensors are anchored onto graphene oxide (GO) flakes which provide a platform for analyte detection in the vicinity of GO. Herein, the operation of this ensemble-based nanosensor is demonstrated for mercury ions, which upon addition of mercury, quenching of the emission intensity from the quantum dots is observed due to resonance energy transfer between quantum dots and the gold nanoparticle connected via a mercury target aptamer. A key result is that the usually dominant effect of quenching of the quantum dot due to close proximity to the GO can be reduced to negligible levels by using a linker molecule in conjunctions with the aptamer-based nanosensor. The effect of ionic concentration of the background matrix on the emission intensity was also investigated. The sensor system is found to be highly selective towards mercury and exhibits a linear behavior (r 2 > 0.99) in the nanomolar concentration range. The detection limit of the sensor towards mercury with no GO present was found to be 16.5 nM. With GO attached to molecular beacon via 14 base, 35 base, and 51 base long linker DNA, the detection limit was found to be 38.4 nM, 9.45 nM, and 11.38 nM; respectively.

  14. Quencher-free molecular beacon tethering 7-hydroxycoumarin detects targets through protonation/deprotonation.

    Science.gov (United States)

    Kashida, Hiromu; Yamaguchi, Kyohei; Hara, Yuichi; Asanuma, Hiroyuki

    2012-07-15

    In this study, we synthesized a simple but efficient quencher-free molecular beacon tethering 7-hydroxycoumarin on D-threoninol based on its pK(a) change. The pK(a) of 7-hydroxycoumarin in a single strand was determined as 8.8, whereas that intercalated in the duplex was over 10. This large pK(a) shift (more than 1.2) upon hybridization could be attributed to the anionic and hydrophobic microenvironment inside the DNA duplex. Because 7-hydroxycoumarin quenches its fluorescence upon protonation, the emission intensity of the duplex at pH 8.5 was 1/15 that of the single strand. We applied this quenching mechanism to the preparation of a quencher-free molecular beacon by introducing the dye into the middle of the stem part. In the absence of the target, the stem region formed a duplex and fluorescence was quenched. However, when the target was added, the molecular beacon opened and the dye was deprotonated. As a result, the emission intensity of the molecular beacon with the target was 10 times higher than that without the target. Accordingly, a quencher-free molecular beacon utilizing the pK(a) change was successfully developed. Copyright © 2012 Elsevier Ltd. All rights reserved.

  15. Molecular beacon – tool for real time studying gene activity in stem cells

    DEFF Research Database (Denmark)

    Ilieva, Mirolyuba; Dufva, Martin

    Cells respond to their internal genetic programs and external stimuli by modulating the synthesis of specific mRNAs. Direct observation of mRNA expression in living cells can provide valuable information with regards to understanding fundamental processes such cell differentiation, regeneration...... and cancerogenesis. Molecular beacon technology is based on fluorescence resonance energy transfer (FRET) and the complementary pairing principles. These fluorescent molecular probes are highly specific and sensitive and are one important tool in in vitro diagnostics. Here molecular beacons are used to follow...

  16. Analyte-Triggered DNA-Probe Release from a Triplex Molecular Beacon for Nanopore Sensing.

    Science.gov (United States)

    Guo, Bingyuan; Sheng, Yingying; Zhou, Ke; Liu, Quansheng; Liu, Lei; Wu, Hai-Chen

    2018-03-26

    A new nanopore sensing strategy based on triplex molecular beacon was developed for the detection of specific DNA or multivalent proteins. The sensor is composed of a triplex-forming molecular beacon and a stem-forming DNA component that is modified with a host-guest complex. Upon target DNA hybridizing with the molecular beacon loop or multivalent proteins binding to the recognition elements on the stem, the DNA probe is released and produces highly characteristic current signals when translocated through α-hemolysin. The frequency of current signatures can be used to quantify the concentrations of the target molecules. This sensing approach provides a simple, quick, and modular tool for the detection of specific macromolecules with high sensitivity and excellent selectivity. It may find useful applications in point-of-care diagnostics with a portable nanopore kit in the future. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Quantum dot-based molecular beacon to monitor intracellular microRNAs.

    Science.gov (United States)

    Lee, Jonghwan; Moon, Sung Ung; Lee, Yong Seung; Ali, Bahy A; Al-Khedhairy, Abdulaziz A; Ali, Daoud; Ahmed, Javed; Al Salem, Abdullah M; Kim, Soonhag

    2015-06-02

    Fluorescence monitoring of endogenous microRNA (miRNA or miR) activity related to neuronal development using nano-sized materials provides crucial information on miRNA expression patterns in a noninvasive manner. In this study, we report a new method to monitor intracellular miRNA124a using quantum dot-based molecular beacon (R9-QD-miR124a beacon). The R9-QD-miR124a beacon was constructed using QDs and two probes, miR124a-targeting oligomer and arginine rich cell-penetrating peptide (R9 peptide). The miR124a-targeting oligomer contains a miR124a binging sequence and a black hole quencher 1 (BHQ1). In the absence of target miR124a, the R9-QD-miR124a beacon forms a partial duplex beacon and remained in quenched state because the BHQ1 quenches the fluorescence signal of the R9-QD-miR124a beacon. The binding of miR124a to the miR124a binding sequence of the miR124a-targeting oligomer triggered the separation of the BHQ1 quencher and subsequent signal-on of a red fluorescence signal. Moreover, enhanced cellular uptake was achieved by conjugation with the R9 peptide, which resulted in increased fluorescent signal of the R9-QD-miR124a beacons in P19 cells during neurogenesis due to the endogenous expression of miR124a.

  18. Quantum Dot-Based Molecular Beacon to Monitor Intracellular MicroRNAs

    Directory of Open Access Journals (Sweden)

    Jonghwan Lee

    2015-06-01

    Full Text Available Fluorescence monitoring of endogenous microRNA (miRNA or miR activity related to neuronal development using nano-sized materials provides crucial information on miRNA expression patterns in a noninvasive manner. In this study, we report a new method to monitor intracellular miRNA124a using quantum dot-based molecular beacon (R9-QD-miR124a beacon. The R9-QD-miR124a beacon was constructed using QDs and two probes, miR124a-targeting oligomer and arginine rich cell-penetrating peptide (R9 peptide. The miR124a-targeting oligomer contains a miR124a binging sequence and a black hole quencher 1 (BHQ1. In the absence of target miR124a, the R9-QD-miR124a beacon forms a partial duplex beacon and remained in quenched state because the BHQ1 quenches the fluorescence signal of the R9-QD-miR124a beacon. The binding of miR124a to the miR124a binding sequence of the miR124a-targeting oligomer triggered the separation of the BHQ1 quencher and subsequent signal-on of a red fluorescence signal. Moreover, enhanced cellular uptake was achieved by conjugation with the R9 peptide, which resulted in increased fluorescent signal of the R9-QD-miR124a beacons in P19 cells during neurogenesis due to the endogenous expression of miR124a.

  19. Cleavable DNA-protein hybrid molecular beacon: A novel efficient signal translator for sensitive fluorescence anisotropy bioassay.

    Science.gov (United States)

    Hu, Pan; Yang, Bin

    2016-01-15

    Due to its unique features such as high sensitivity, homogeneous format, and independence on fluorescent intensity, fluorescence anisotropy (FA) assay has become a hotspot of study in oligonucleotide-based bioassays. However, until now most FA probes require carefully customized structure designs, and thus are neither generalizable for different sensing systems nor effective to obtain sufficient signal response. To address this issue, a cleavable DNA-protein hybrid molecular beacon was successfully engineered for signal amplified FA bioassay, via combining the unique stable structure of molecular beacon and the large molecular mass of streptavidin. Compared with single DNA strand probe or conventional molecular beacon, the DNA-protein hybrid molecular beacon exhibited a much higher FA value, which was potential to obtain high signal-background ratio in sensing process. As proof-of-principle, this novel DNA-protein hybrid molecular beacon was further applied for FA bioassay using DNAzyme-Pb(2+) as a model sensing system. This FA assay approach could selectively detect as low as 0.5nM Pb(2+) in buffer solution, and also be successful for real samples analysis with good recovery values. Compatible with most of oligonucleotide probes' designs and enzyme-based signal amplification strategies, the molecular beacon can serve as a novel signal translator to expand the application prospect of FA technology in various bioassays. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Surface-attached molecular beacons light the way for DNA sequencing

    Czech Academy of Sciences Publication Activity Database

    Paleček, Emil

    2004-01-01

    Roč. 22, č. 2 (2004), s. 55-58 ISSN 0167-7799 R&D Projects: GA AV ČR IBS5004355; GA ČR GA204/03/0566 Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular beacon * DNA stem-loop structure * DNA sensors Subject RIV: BO - Biophysics Impact factor: 8.606, year: 2004

  1. A Biofunctional Molecular Beacon for Detecting Single Base Mutations in Cancer Cells

    Directory of Open Access Journals (Sweden)

    Haiyan Dong

    2016-01-01

    Full Text Available The development of a convenient and sensitive biosensing system to detect specific DNA sequences is an important issue in the field of genetic disease therapy. As a classic DNA detection technique, molecular beacon (MB is often used in the biosensing system. However, it has intrinsic drawbacks, including high assay cost, complicated chemical modification, and operational complexity. In this study, we developed a simple and cost-effective label-free multifunctional MB (LMMB by integrating elements of polymerization primer, template, target recognition, and G-quadruplex into one entity to detect target DNA. The core technique was accomplished by introducing a G-hairpin that features fragments of both G-quadruplex and target DNA recognition in the G-hairpin stem. Hybridization between LMMB and target DNA triggered conformational change between the G-hairpin and the common C-hairpin, resulting in significant SYBR-green signal amplification. The hybridization continues to the isothermal circular strand-displacement polymerization and accumulation of the double-stranded fragments, causing the uninterrupted extension of the LMMB without a need of chemical modification and other assistant DNA sequences. The novel and programmable LMMB could detect target DNA with sensitivity at 250 pmol/l with a linear range from 2 to 100 nmol/l and the relative standard deviation of 7.98%. The LMMB could sense a single base mutation from the normal DNA, and polymerase chain reaction (PCR amplicons of the mutant-type cell line from the wild-type one. The total time required for preparation and assaying was only 25 minutes. Apparently, the LMMB shows great potential for detecting DNA and its mutations in biosamples, and therefore it opens up a new prospect for genetic disease therapy.

  2. A distance-dependent metal-enhanced fluorescence sensing platform based on molecular beacon design.

    Science.gov (United States)

    Zhou, Zhenpeng; Huang, Hongduan; Chen, Yang; Liu, Feng; Huang, Cheng Zhi; Li, Na

    2014-02-15

    A new metal-enhanced fluorescence (MEF) based platform was developed on the basis of distance-dependent fluorescence quenching-enhancement effect, which combined the easiness of Ag-thiol chemistry with the MEF property of noble-metal structures as well as the molecular beacon design. For the given sized AgNPs, the fluorescence enhancement factor was found to increase with a d(6) dependency in agreement with fluorescence resonance energy transfer mechanism at shorter distance and decrease with a d(-3) dependency in agreement with plasmonic enhancement mechanism at longer distance between the fluorophore and the AgNP surface. As a proof of concept, the platform was demonstrated by a sensitive detection of mercuric ions, using thymine-containing molecular beacon to tune silver nanoparticle (AgNP)-enhanced fluorescence. Mercuric ions were detected via formation of a thymine-mercuric-thymine structure to open the hairpin, facilitating fluorescence recovery and AgNP enhancement to yield a limit of detection of 1 nM, which is well below the U.S. Environmental Protection Agency regulation of the Maximum Contaminant Level Goal (10nM) in drinking water. Since the AgNP functioned as not only a quencher to reduce the reagent blank signal but also an enhancement substrate to increase fluorescence of the open hairpin when target mercuric ions were present, the quenching-enhancement strategy can greatly improve the detection sensitivity and can in principle be a universal approach for various targets when combined with molecular beacon design. © 2013 Elsevier B.V. All rights reserved.

  3. Enzymatic Amplification of DNA/RNA Hybrid Molecular Beacon Signaling in Nucleic Acid Detection

    OpenAIRE

    Jacroux, Thomas; Rieck, Daniel C.; Cui, Rong; Ouyang, Yexin; Dong, Wen-Ji

    2012-01-01

    A rapid assay operable under isothermal or non-isothermal conditions is described wherein the sensitivity of a typical molecular beacon (MB) system is improved by utilizing thermostable RNase H to enzymatically cleave an MB comprised of a DNA stem and RNA loop (R/D-MB). Upon hybridization of the R/D-MB to target DNA, there was a modest increase in fluorescence intensity (~5.7x above background) due to an opening of the probe and concomitant reduction in the Förster resonance energy transfer e...

  4. Detection of Candida species in pregnant Chinese women with a molecular beacon method.

    Science.gov (United States)

    Zhai, Yanhong; Liu, Jing; Zhou, Li; Ji, Tongzhen; Meng, Lingxin; Gao, Yang; Liu, Ran; Wang, Xiao; Li, Lin; Lu, Binghuai; Cao, Zheng

    2018-04-20

    Candida pathogens are commonly found in women and can cause vulvovaginal candidiasis (VVC), whose infection rate is further increased during pregnancy. We aimed to study the Candida prevalence and strain distribution in pregnant Chinese women with a molecular beacon assay. From March 2016 to February 2017, a total of 993 pregnant women attending routine antenatal visits at the Beijing Obstetrics and Gynecology Hospital were enrolled. For Candida detection and identification, a unique molecular beacon assay was presented and compared with a traditional phenotypic method. Antifungal susceptibility was tested with the following agents: 5-flucytosine, amphotericin B, fluconazole, itraconazole and voriconazole. The prevalence of Candida was found to be 21.8 % when using the molecular method and 15.0 % when using the phenotypic method. The distribution of the Candida spp. was listed in order of decreasing prevalence: Candida albicans (79.8 %), Candida glabrata (13.5 %), Candida parapsilosis (3.7 %), Candida krusei (2.2 %) and Candida tropicalis (1.1 %). We found that 90.7 % of the Candida detection results were consistent between the molecular and the phenotypic methods. In the cases where the sequencing analyses for the Candida isolates resulted in inconsistent identification, the molecular method showed higher sensitivity than the phenotypic method (96.0 vs 64.6 %). C. albicans, C. glabrata and C. parapsilosis were essentially susceptible to all five antifungal agents tested, whereas C. tropicalis and C. krusei were susceptible to voriconazole and amphotericin B. By exhibiting good sensitivity and specificity, the molecular assay may offer a fast and accurate Candida screening platform for pregnant women.

  5. Detection of DNA damage based on metal-mediated molecular beacon and DNA strands displacement reaction

    Science.gov (United States)

    Xiong, Yanxiang; Wei, Min; Wei, Wei; Yin, Lihong; Pu, Yuepu; Liu, Songqin

    2014-01-01

    DNA hairpin structure probes are usually designed by forming intra-molecular duplex based on Watson-Crick hydrogen bonds. In this paper, a molecular beacon based on silver ions-mediated cytosine-Ag+-cytosine base pairs was used to detect DNA. The inherent characteristic of the metal ligation facilitated the design of functional probe and the adjustment of its binding strength compared to traditional DNA hairpin structure probes, which make it be used to detect DNA in a simple, rapid and easy way with the help of DNA strands displacement reaction. The method was sensitive and also possesses the good specificity to differentiate the single base mismatched DNA from the complementary DNA. It was also successfully applied to study the damage effect of classic genotoxicity chemicals such as styrene oxide and sodium arsenite on DNA, which was significant in food science, environmental science and pharmaceutical science.

  6. A quencher-free molecular beacon design based on pyrene excimer fluorescence using pyrene-labeled UNA (unlocked nucleic acid)

    DEFF Research Database (Denmark)

    Karlsen, Kasper Kannegård; Okholm, Anders Hauge; Kjems, Jørgen

    2013-01-01

    A quencher-free molecular beacon capable of generating pyrene excimer fluorescence has been constructed using strategically positioned pyrene-UNA monomers. Hybridization of a fully complementary RNA target was accompanied by a pyrene excimer emission increase of more than 900%, and detection of RNA...

  7. Surveillance technology for HIV-1 subtype C in Ethiopia: an env-based NASBA molecular beacon assay to discriminate between subcluster C and C'

    NARCIS (Netherlands)

    Ayele, Workenesh; Baar, Michel P. de; Goudsmit, Jaap; Kliphuis, Aletta; Tilahun, Tesfaye; Dorigo-Zetsma, Wendelien; Wolday, Dawit; Abebe, Almaz; Mengistu, Yohannes; Pollakis, Georgios

    2005-01-01

    Forty-nine samples with known C2V3 sequences were used for the evaluation of an env-based molecular beacon assay to distinguish between the two genetic subclusters C and C' which characterize the HIV-1 epidemic in Ethiopia. Two subcluster C and two subcluster C' beacons targeting two different loci

  8. A molecular-beacon-based asymmetric PCR assay for easy visualization of amplicons in the diagnosis of trichomoniasis.

    Science.gov (United States)

    Sonkar, Subash C; Sachdev, Divya; Mishra, Prashant K; Kumar, Anita; Mittal, Pratima; Saluja, Daman

    2016-12-15

    The currently available nucleic acid amplification tests (NAATs) for trichomoniasis are accurate, quick and confirmative with superior sensitivity than traditional culture-based microbiology assays. However, these assays are associated with problems of carry over contamination, false positive results, requirement of technical expertise for performance and detection of end product. Hence, a diagnostic assay with easy visualization of the amplified product will be profitable. An in-house, rapid, sensitive, specific molecular-beacon-based PCR assay, using primers against pfoB gene of Trichomonas vaginalis, was developed and evaluated using dry ectocervical swabs (n=392) from symptomatic females with vaginal discharge. Total DNA was isolated and used as template for the PCR assays. The performance and reproducibility of PCR assay was evaluated by composite reference standard (CRS). For easy visualization of the amplified product, molecular-beacon was designed and amplicons were visualized directly using fluorescent handheld dark reader or by Micro-Plate Reader. Molecular-beacons are single-stranded hairpin shaped nucleic acid probes composed of a stem, with fluorophore/quencher pair and a loop region complementary to the desired DNA. The beacon-based PCR assay designed in the present study is highly specific as confirmed by competition experiments and extremely sensitive with detection limit of 20fg of genomic DNA (3-4 pathogens). The minimum infrastructure requirement and ease to perform the assay makes this method highly useful for resource poor countries for better disease management. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Simple fluorescence-based detection of protein kinase A activity using a molecular beacon probe.

    Science.gov (United States)

    Ma, Changbei; Lv, Xiaoyuan; Wang, Kemin; Jin, Shunxin; Liu, Haisheng; Wu, Kefeng; Zeng, Weimin

    2017-11-02

    Protein kinase A was detected by quantifying the amount of ATP used after a protein kinase reaction. The ATP assay was performed using the T4 DNA ligase and a molecular beacon (MB). In the presence of ATP, DNA ligase catalyzed the ligation of short DNA. The ligation product then hybridized to MB, resulting in a fluorescence enhancement of the MB. This assay was capable of determining protein kinase A in the range of 12.5∼150 nM, with a detection limit of 1.25 nM. Furthermore, this assay could also be used to investigate the effect of genistein on protein kinase A. It was a universal, non-radioisotopic, and homogeneous method for assaying protein kinase A.

  10. Facile conversion of ATP-binding RNA aptamer to quencher-free molecular aptamer beacon.

    Science.gov (United States)

    Park, Yoojin; Nim-Anussornkul, Duangrat; Vilaivan, Tirayut; Morii, Takashi; Kim, Byeang Hyean

    2018-01-15

    We have developed RNA-based quencher-free molecular aptamer beacons (RNA-based QF-MABs) for the detection of ATP, taking advantage of the conformational changes associated with ATP binding to the ATP-binding RNA aptamer. The RNA aptamer, with its well-defined structure, was readily converted to the fluorescence sensors by incorporating a fluorophore into the loop region of the hairpin structure. These RNA-based QF-MABs exhibited fluorescence signals in the presence of ATP relative to their low background signals in the absence of ATP. The fluorescence emission intensity increased upon formation of a RNA-based QF-MAB·ATP complex. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop.

    Science.gov (United States)

    Dembska, Anna; Juskowiak, Bernard

    2015-01-01

    In this work, we present a spectral characterization of pH-sensitive system, which combines the i-motif properties with the spatially sensitive fluorescence signal of pyrene molecules attached to hairpin ends. The excimer production (fluorescence max. ∼480 nm) by pyrene labels at the ends of the molecular beacon is driven by pH-dependent i-motif formation in the loop. To illustrate the performance and reversible work of our systems, we performed the experiments with repeatedly pH cycling between pH values of 7.5±0.3 and 6.5±0.3. The sensor gives analytical response in excimer-monomer switching mode in narrow pH range (1.5 pH units) and exhibits high pH resolution (0.1 pH unit). Copyright © 2015 Elsevier B.V. All rights reserved.

  12. [Molecular beacon based PNA-FISH method combined with fluorescence scanning for rapid detection of Listeria monocytogenes].

    Science.gov (United States)

    Wu, Shan; Zhang, Xiaofeng; Shuai, Jiangbing; Li, Ke; Yu, Huizhen; Jin, Chenchen

    2016-07-04

    To simplify the PNA-FISH (Peptide nucleic acid-fluorescence in situ hybridization) test, molecular beacon based PNA probe combined with fluorescence scanning detection technology was applied to replace the original microscope observation to detect Listeria monocytogenes The 5′ end and 3′ end of the L. monocytogenes specific PNA probes were labeled with the fluorescent group and the quenching group respectively, to form a molecular beacon based PNA probe. When PNA probe used for fluorescence scanning and N1 treatment as the control, the false positive rate was 11.4%, and the false negative rate was 0; when N2 treatment as the control, the false positive rate decreased to 4.3%, but the false negative rate rose to 18.6%. When beacon based PNA probe used for fluorescence scanning, taken N1 treatment as blank control, the false positive rate was 8.6%, and the false negative rate was 1.4%; taken N2 treatment as blank control, the false positive rate was 5.7%, and the false negative rate was 1.4%. Compared with PNA probe, molecular beacon based PNA probe can effectively reduce false positives and false negatives. The success rates of hybridization of the two PNA probes were 83.3% and 95.2% respectively; and the rates of the two beacon based PNA probes were 91.7% and 90.5% respectively, which indicated that labeling the both ends of the PNA probe dose not decrease the hybridization rate with the target bacteria. The combination of liquid phase PNA-FISH and fluorescence scanning method, can significantly improve the detection efficiency.

  13. Quantum Dot-Fullerene Based Molecular Beacon Nanosensors for Rapid, Highly Sensitive Nucleic Acid Detection.

    Science.gov (United States)

    Liu, Ye; Kannegulla, Akash; Wu, Bo; Cheng, Li-Jing

    2018-05-15

    Spherical fullerene (C 60 ) can quench the fluorescence of a quantum dot (QD) through energy transfer and charge transfer processes, with the quenching efficiency regulated by the number of proximate C 60 on each QD. With the quenching property and its small size compared with other nanoparticle-based quenchers, it is advantageous to group a QD reporter and multiple C 60 -labeled oligonucleotide probes to construct a molecular beacon (MB) probe for sensitive, robust nucleic acid detection. We demonstrated a rapid, high-sensitivity DNA detection method using the nanosensors composed of QD-C 60 based MBs carried by magnetic nanoparticles (MNPs). The assay was accelerated by first dispersing the nanosensors in analytes for highly efficient DNA capture resulting from short-distance 3-dimensional diffusion of targets to the sensor surface and then concentrating the nanosensors to a substrate by magnetic force to amplify the fluorescence signal for target quantification. The enhanced mass transport enabled a rapid detection (< 10 min) with a small sample volume (1-10 µl). The high signal-to-noise ratio produced by the QD-C 60 pairs and magnetic concentration yielded a detection limit of 100 fM (~106 target DNA copies for a 10 µl analyte). The rapid, sensitive, label-free detection method will benefit the applications in point-of-care molecular diagnostic technologies.

  14. A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms.

    Science.gov (United States)

    Guo, Qingsheng; Bai, Zhixiong; Liu, Yuqian; Sun, Qingjiang

    2016-03-15

    In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Theranostic properties of a survivin-directed molecular beacon in human melanoma cells.

    Directory of Open Access Journals (Sweden)

    Sara Carpi

    Full Text Available Survivin is an inhibitor of apoptosis overexpressed in different types of tumors and undetectable in most terminally differentiated normal tissues. In the current study, we sought to evaluate the in vitro theranostic properties of a molecular beacon-oligodeoxynucleotide (MB that targets survivin mRNA. We used laser scanning confocal microscopy to study MB delivery in living cells and real-time PCR and western blot to assess selective survivin-targeting in human malignant melanoma cells. We further assess the pro-apoptotic effect of MB by measuring internucleosomal DNA fragmentation, dissipation of mitochondrial membrane potential (MMP and changes in nuclear morphology. Transfection of MB into A375 and 501 Mel cells generated high signal intensity from the cytoplasm, while no signal was detected in the extracellular environment and in survivin-negative cells (i.e., human melanocytes and monocytes. MB time dependently decreased survivin mRNA and protein expression in melanoma cells with the maximum effect reached at 72 h. Treatment of melanoma cells with MB induced apoptosis by significant changes in MMP, accumulation of histone-complexed DNA fragments in the cytoplasm and nuclear condensation. MB also enhanced the pro-apoptotic effect of standard chemotherapeutic drugs tested at clinically relevant concentrations. The MB tested in the current study conjugates the ability of imaging with the pharmacological silencing activity against survivin mRNA in human melanoma cells and may represent an innovative approach for cancer diagnosis and treatment.

  16. Recognition of dual targets by a molecular beacon-based sensor: subtyping of influenza A virus.

    Science.gov (United States)

    Lee, Chun-Ching; Liao, Yu-Chieh; Lai, Yu-Hsuan; Lee, Chang-Chun David; Chuang, Min-Chieh

    2015-01-01

    A molecular beacon (MB)-based sensor to offer a decisive answer in combination with information originated from dual-target inputs is designed. The system harnesses an assistant strand and thermodynamically favored designation of unpaired nucleotides (UNs) to process the binary targets in "AND-gate" format and report fluorescence in "off-on" mechanism via a formation of a DNA four-way junction (4WJ). By manipulating composition of the UNs, the dynamic fluorescence difference between the binary targets-coexisting circumstance and any other scenario was maximized. Characteristic equilibrium constant (K), change of entropy (ΔS), and association rate constant (k) between the association ("on") and dissociation ("off") states of the 4WJ were evaluated to understand unfolding behavior of MB in connection to its sensing capability. Favorable MB and UNs were furthermore designed toward analysis of genuine genetic sequences of hemagglutinin (HA) and neuraminidase (NA) in an influenza A H5N2 isolate. The MB-based sensor was demonstrated to yield a linear calibration range from 1.2 to 240 nM and detection limit of 120 pM. Furthermore, high-fidelity subtyping of influenza virus was implemented in a sample of unpurified amplicons. The strategy opens an alternative avenue of MB-based sensors for dual targets toward applications in clinical diagnosis.

  17. Design of two and three input molecular logic gates using non-Watson-Crick base pairing-based molecular beacons.

    Science.gov (United States)

    Lin, Jia-Hui; Tseng, Wei-Lung

    2014-03-21

    This study presents a single, resettable, and sensitive molecular beacon (MB) used to operate molecular-scale logic gates. The MB consists of a random DNA sequence, a fluorophore at the 5'-end, and a quencher at the 3'-end. The presence of Hg(2+), Ag(+), and coralyne promoted the formation of stable T-Hg(2+)-T, C-Ag(+)-C, and A2-coralyne-A2 coordination in the MB probe, respectively, thereby driving its conformational change. The metal ion or small molecule-mediated coordination of mismatched DNA brought the fluorophore and the quencher into close proximity, resulting in collisional quenching of fluorescence between the two organic dyes. Because thiol can bind Hg(2+) and remove it from the T-Hg(2+)-T-based MB, adding thiol to a solution of the T-Hg(2+)-T-based MB allowed the fluorophore and the quencher to be widely separated. A similar phenomenon was observed when replacing Hg(2+) with Ag(+). Because Ag(+) strongly binds to iodide, cyanide, and cysteine, they were capable of removing Ag(+) from the C-Ag(+)-C-based MB, restoring the fluorescence of the MB. Moreover, the fluorescence of the A2-coralyne-A2-based MB could be switched on by adding polyadenosine. Using these analytes as inputs and the MB as a signal transducer, we successfully developed a series of two-input, three-input, and set-reset logic gates at the molecular level.

  18. Theragnosis-based combined cancer therapy using doxorubicin-conjugated microRNA-221 molecular beacon.

    Science.gov (United States)

    Lee, Jonghwan; Choi, Kyung-Ju; Moon, Sung Ung; Kim, Soonhag

    2016-01-01

    Recently, microRNA (miRNA or miR) has emerged as a new cancer biomarker because of its high expression level in various cancer types and its role in the control of tumor suppressor genes. In cancer studies, molecular imaging and treatment based on target cancer markers have been combined to facilitate simultaneous cancer diagnosis and therapy. In this study, for combined therapy with diagnosis of cancer, we developed a doxorubicin-conjugated miR-221 molecular beacon (miR-221 DOXO MB) in a single platform composed of three different nucleotides: miR-221 binding sequence, black hole quencher 1 (BHQ1), and doxorubicin binding site. Imaging of endogenous miR-221 was achieved by specific hybridization between miR-221 and the miR-221 binding site in miR-221 DOXO MB. The presence of miR-221 triggered detachment of the quencher oligo and subsequent activation of a fluorescent signal of miR-221 DOXO MB. Simultaneous cancer therapy in C6 astrocytoma cells and nude mice was achieved by inhibition of miRNA-221 function that downregulates tumor suppressor genes. The detection of miR-221 expression and inhibition of miR-221 function by miR-221 DOXO MB provide the feasibility as a cancer theragnostic probe. Furthermore, a cytotoxic effect was induced by unloading of doxorubicin intercalated into miR-221 DOXO MB inside cells. Loss of miR-221 function and cytotoxicity induced by the miR-221 DOXO MB provides combined therapeutic efficacy against cancers. This method could be used as a new theragnostic probe with enhanced therapy to detect and inhibit many cancer-related miRNAs. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Detection of Naja atra Cardiotoxin Using Adenosine-Based Molecular Beacon.

    Science.gov (United States)

    Shi, Yi-Jun; Chen, Ying-Jung; Hu, Wan-Ping; Chang, Long-Sen

    2017-01-07

    This study presents an adenosine (A)-based molecular beacon (MB) for selective detection of Naja atra cardiotoxin (CTX) that functions by utilizing the competitive binding between CTX and the poly(A) stem of MB to coralyne. The 5'- and 3'-end of MB were labeled with a reporter fluorophore and a non-fluorescent quencher, respectively. Coralyne induced formation of the stem-loop MB structure through A₂-coralyne-A₂ coordination, causing fluorescence signal turn-off due to fluorescence resonance energy transfer between the fluorophore and quencher. CTX3 could bind to coralyne. Moreover, CTX3 alone induced the folding of MB structure and quenching of MB fluorescence. Unlike that of snake venom α-neurotoxins, the fluorescence signal of coralyne-MB complexes produced a bell-shaped concentration-dependent curve in the presence of CTX3 and CTX isotoxins; a turn-on fluorescence signal was noted when CTX concentration was ≤80 nM, while a turn-off fluorescence signal was noted with a further increase in toxin concentrations. The fluorescence signal of coralyne-MB complexes yielded a bell-shaped curve in response to varying concentrations of N. atra crude venom but not those of Bungarus multicinctus and Protobothrops mucrosquamatus venoms. Moreover, N. nigricollis venom also functioned as N. atra venom to yield a bell-shaped concentration-dependent curve of MB fluorescence signal, again supporting that the hairpin-shaped MB could detect crude venoms containing CTXs. Taken together, our data validate that a platform composed of coralyne-induced stem-loop MB structure selectively detects CTXs.

  20. G-Quadruplex DNAzyme Molecular Beacon for Amplified Colorimetric Biosensing of Pseudostellaria heterophylla

    Directory of Open Access Journals (Sweden)

    Juan Hu

    2013-01-01

    Full Text Available With an internal transcribed spacer of 18 S, 5.8 S and 26 S nuclear ribosomal DNA (nrDNA ITS as DNA marker, we report a colorimetric approach for authentication of Pseudostellaria heterophylla (PH and its counterfeit species based on the differentiation of the nrDNA ITS sequence. The assay possesses an unlabelled G-quadruplex DNAzyme molecular beacon (MB probe, employing complementary sequence as biorecognition element and 1:1:1:1 split G-quadruplex halves as reporter. In the absence of target DNA (T-DNA, the probe can shape intermolecular G-quadruplex structures capable of binding hemin to form G-quadruplex-hemin DNAzyme and catalyze the oxidation of ABTS2− to blue-green ABTS•− by H2O2. In the presence of T-DNA, T-DNA can hybridize with the complementary sequence to form a duplex structure, hindering the formation of the G-quadruplex structure and resulting in the loss of the catalytic activity. Consequently, a UV-Vis absorption signal decrease is observed in the ABTS2−-H2O2 system. The “turn-off” assay allows the detection of T-DNA from 1.0 × 10−9 to 3.0 × 10−7 mol·L−1 (R2 = 0.9906, with a low detection limit of 3.1 × 10−10 mol·L−1. The present study provides a sensitive and selective method and may serve as a foundation of utilizing the DNAzyme MB sensor for identifying traditional Chinese medicines.

  1. Molecular beacon-based real-time PCR method for detection of porcine DNA in gelatin and gelatin capsules.

    Science.gov (United States)

    Mohamad, Nurhidayatul Asma; Mustafa, Shuhaimi; Khairil Mokhtar, Nur Fadhilah; El Sheikha, Aly Farag

    2018-03-05

    The pharmaceutical industry has boosted gelatin consumption worldwide. This is supported by the availability of cost-effective gelatin production from porcine by-products. However, cross-contamination of gelatin materials, where porcine gelatin was unintentionally included in the other animal sources of gelatin, has caused significant concerns about halal authenticity. The real-time polymerase chain reaction (PCR) has enabled a highly specific and sensitive animal species detection method in various food products. Hence, such a technique was employed in the present study to detect and quantify porcine DNA in gelatin using a molecular beacon probe, with differences in performance between mitochondrial (cytochrome b gene) and chromosomal DNA-(MPRE42 repetitive element) based porcine-specific PCR assays being compared. A higher sensitivity was observed in chromosomal DNA (MPRE-PCR assay), where this assay allows the detection of gelatin DNA at amounts as as low as 1 pg, whereas mitochondrial DNA (CBH-PCR assay) can only detect at levels down to 10 pg of gelatin DNA. When an analysis with commercial gelatin and gelatin capsule samples was conducted, the same result was observed, with a significantly more sensitive detection being provided by the repetitive element of chromosomal DNA. The present study has established highly sensitive DNA-based porcine detection systems derived from chromosomal DNA that are feasible for highly processed products such as gelatin and gelatin capsules containing a minute amount of DNA. This sensitive detection method can also be implemented to assist the halal authentication process of various food products available on the market. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

  2. Application of a molecular beacon based real-time isothermal amplification (MBRTIA) technology for simultaneous detection of Bacillus cereus and Staphylococcus aureus.

    Science.gov (United States)

    Mandappa, I M; Joglekar, Prasanna; Manonmani, H K

    2015-07-01

    A multiplex real-time isothermal amplification assay was developed using molecular beacons for the detection of Bacillus cereus and Staphylococcus aureus by targeting four important virulence genes. A correlation between targeting highly accessible DNA sequences and isothermal amplification based molecular beacon efficiency and sensitivity was demonstrated using phi(Φ)29 DNA polymerase at a constant isothermal temperature of 30 °C. It was very selective and consistently detected down to 10(1) copies of DNA. The specificity and sensitivity of this assay, when tested with pure culture were high, surpassing those of currently used PCR assays for the detection of these organisms. The molecular beacon based real-time isothermal amplification (MBRTIA) assay could be carried out entirely in 96 well plates or well strips, enabling a rapid and high-throughput detection of food borne pathogens.

  3. SOX2 and OCT4 mRNA-Expressing Cells, Detected by Molecular Beacons, Localize to the Center of Neurospheres during Differentiation

    DEFF Research Database (Denmark)

    Ilieva, Mirolyuba; Dufva, Martin

    2013-01-01

    Neurospheres are used as in vitro assay to measure the properties of neural stem cells. To investigate the molecular and phenotypic heterogeneity of neurospheres, molecular beacons (MBs) targeted against the stem cell markers OCT4 and SOX2 were designed, and synthesized with a 2'-O-methyl RNA...

  4. A NASBA on microgel-tethered molecular-beacon microarray for real-time microbial molecular diagnostics.

    Science.gov (United States)

    Ma, Y; Dai, X; Hong, T; Munk, G B; Libera, M

    2016-12-19

    Despite their many advantages and successes, molecular beacon (MB) hybridization probes have not been extensively used in microarray formats because of the complicating probe-substrate interactions that increase the background intensity. We have previously shown that tethering to surface-patterned microgels is an effective means for localizing MB probes to specific surface locations in a microarray format while simultaneously maintaining them in as water-like an environment as possible and minimizing probe-surface interactions. Here we extend this approach to include both real-time detection together with integrated NASBA amplification. We fabricate small (∼250 μm × 250 μm) simplex, duplex, and five-plex assays with microarray spots of controllable size (∼20 μm diameter), position, and shape to detect bacteria and fungi in a bloodstream-infection model. The targets, primers, and microgel-tethered probes can be combined in a single isothermal reaction chamber with no post-amplification labelling. We extract total RNA from clinical blood samples and differentiate between Gram-positive and Gram-negative bloodstream infection in a duplex assay to detect RNA- amplicons. The sensitivity based on our current protocols in a simplex assay to detect specific ribosomal RNA sequences within total RNA extracted from S. aureus and E. coli cultures corresponds to tens of bacteria per ml. We furthermore show that the platform can detect RNA- amplicons from synthetic target DNA with 1 fM sensitivity in sample volumes that contain about 12 000 DNA molecules. These experiments demonstrate an alternative approach that can enable rapid and real-time microarray-based molecular diagnostics.

  5. [Molecular techniques in mycology].

    Science.gov (United States)

    Rodríguez-Tudela, Juan Luis; Cuesta, Isabel; Gómez-López, Alicia; Alastruey-Izquierdo, Ana; Bernal-Martínez, Leticia; Cuenca-Estrella, Manuel

    2008-11-01

    An increasing number of molecular techniques for the diagnosis of fungal infections have been developed in the last few years, due to the growing prevalence of mycoses and the length of time required for diagnosis when classical microbiological methods are used. These methods are designed to resolve the following aspects of mycological diagnosis: a) Identification of fungi to species level by means of sequencing relevant taxonomic targets; b) early clinical diagnosis of invasive fungal infections; c) detection of molecular mechanisms of resistance to antifungal agents; and d) molecular typing of fungi. Currently, these methods are restricted to highly developed laboratories. However, some of these techniques will probably be available in daily clinical practice in the near future.

  6. Studying the influence of stem composition in pH-sensitive molecular beacons onto their sensing properties.

    Science.gov (United States)

    Dembska, Anna; Kierzek, Elzbieta; Juskowiak, Bernard

    2017-10-16

    Intracellular sensing using fluorescent molecular beacons is a potentially useful strategy for real-time, in vivo monitoring of important cellular events. This work is focused on evaluation of pyrene excimer signaling molecular beacons (MBs) for the monitoring of pH changes in vitro as well as inside living cells. The recognition element in our MB called pHSO (pH-sensitive oligonucleotide) is the loop enclosing cytosine-rich fragment that is able to form i-motif structure in a specific pH range. However, alteration of a sequence of the 6 base pairs containing stem of MB allowed the design of pHSO probes that exhibited different dynamic pH range and possessed slightly different transition midpoint between i-motif and open loop configuration. Moreover, this conformational transition was accompanied by spectral changes showing developed probes different pyrene excimer-monomer emission ratio triggered by pH changes. The potential of these MBs for intracellular pH sensing is demonstrated on the example of HeLa cells line. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Molecular Beacon Enables Combination of Highly Processive and Highly Sensitive Rolling Circle Amplification Readouts for Detection of DNA-Modifying Enzymes

    DEFF Research Database (Denmark)

    Kristoffersen, Emil Laust; Gonzales, Maria; Stougaard, Magnus

    2015-01-01

    is separated, giving rise to a fluorescent signal, measurable in pseudo real-time using a qPCR machine or in a fluorimeter. The RCA products in complex with the molecular beacon can subsequently be moved to microscopic slides and analyzed in a fluorescence microscope. We describe the proof of the principle...

  8. Real-time monitoring of disintegration activity of catalytic core domain of HIV-1 integrase using molecular beacon.

    Science.gov (United States)

    Zhang, Da-wei; Zhao, Ming-ming; He, Hong-qiu; Guo, Shun-xing

    2013-09-15

    HIV-1 integrase, an essential enzyme for retroviral replication, is a validated target for anti-HIV therapy development. The catalytic core domain of integrase (IN-CCD) is capable of catalyzing disintegration reaction. In this work, a hairpin-shaped disintegration substrate was designed and validated by enzyme-linked immunosorbent assay; a molecular beacon-based assay was developed for disintegration reaction of IN-CCD. Results showed that the disintegration substrate could be recognized and catalyzed by IN-CCD, and the disintegration reaction can be monitored according to the increase of fluorescent signal. The assay can be applied to real-time detection of disintegration with advantages of simplicity, high sensitivity, and excellent specificity. Copyright © 2013 Elsevier Inc. All rights reserved.

  9. Experimental study of the evanescent-wave photonic sensors response in presence of molecular beacon conformational changes.

    Science.gov (United States)

    Ruiz-Tórtola, Ángela; Prats-Quílez, Francisco; Gónzalez-Lucas, Daniel; Bañuls, María-José; Maquieira, Ángel; Wheeler, Guy; Dalmay, Tamas; Griol, Amadeu; Hurtado, Juan; Bohlmann, Helge; Götzen, Reiner; García-Rupérez, Jaime

    2018-04-17

    An experimental study of the influence of the conformational change suffered by molecular beacon (MB) probes -upon the biorecognition of nucleic acid target oligonucleotides over evanescent wave photonic sensors- is reported. To this end, high sensitivity photonic sensors based on silicon photonic bandgap (PBG) structures were used, where the MB probes were immobilized via their 5' termination. Those MBs incorporate a biotin moiety close to their 3' termination in order to selectively bind a streptavidin molecule to them. The different photonic sensing responses obtained towards the target oligonucleotide detection, when the streptavidin molecule was bound to the MB probes or not, demonstrate the conformational change suffered by the MB upon hybridization, which promotes the displacement of the streptavidin molecule away from the surface of the photonic sensing structure. Schematic diagram of the PBG sensing structure on which the streptavidin-labeled MB probes were immobilized. This article is protected by copyright. All rights reserved.

  10. "Molecular beacon"-hosted thioflavin T: Applications for label-free fluorescent detection of iodide and logic operations.

    Science.gov (United States)

    Li, Yan-Yun; Jiang, Xiao-Qin; Lu, Ling-Fei; Zhang, Min; Shi, Guoyue

    2016-04-01

    In this work, we presented a simple, label-free and rapid-responsive fluorescence assay for iodide (I(-)) detection based on "molecular beacon (MB)"-hosted thioflavin T (ThT), achieving a limit of detection as low as 158 nM. The proposed method exhibited very good selectivity to I(-) ions over other anions interference due to the strong binding force between I(-) ions with Hg(2+). Upon the addition of I(-) ions, it would capture Hg(2+) from a T-Hg(2+)-T complex belonging to the MB-like DNA hairpin structure, which eventually quenched the initial fluorescence as output. In addition, it was successfully applied for operation of an integrated DNA logic gate system and to the determination of I(-) in real samples such as human urine. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. A molecular beacon based on DNA-templated silver nanoclusters for the highly sensitive and selective multiplexed detection of virulence genes.

    Science.gov (United States)

    Han, Dan; Wei, Chunying

    2018-05-01

    In this work, we develop a fluorescent molecular beacon based on the DNA-templated silver nanoclusters (DNA-Ag NCs). The skillfully designed molecular beacon can be conveniently used for detection of diverse virulence genes as long as the corresponding recognition sequences are embedded. Importantly, the constructed detection system allows simultaneous detection of multiple nucleic acids, which is attributed to non-overlapping emission spectra of the as-synthesized silver nanoclusters. Based on the target-induced fluorescence enhancement, three infectious disease-related genes HIV, H1N1, and H5N1 are detected, and the corresponding detection limits are 3.53, 0.12 and 3.95nM, respectively. This design allows specific, versatile and simultaneous detection of diverse targets with easy operation and low cost. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. In-cell protease assay systems based on trans-localizing molecular beacon proteins using HCV protease as a model system.

    Directory of Open Access Journals (Sweden)

    Jeong Hee Kim

    Full Text Available This study describes a sensitive in-cell protease detection system that enables direct fluorescence detection of a target protease and its inhibition inside living cells. This live-cell imaging system provides a fluorescent molecular beacon protein comprised of an intracellular translocation signal sequence, a protease-specific cleavage sequence, and a fluorescent tag sequence(s. The molecular beacon protein is designed to change its intracellular localization upon cleavage by a target protease, i.e., from the cytosol to a subcellular organelle or from a subcellular organelle to the cytosol. Protease activity can be monitored at the single cell level, and accordingly the entire cell population expressing the protease can be accurately enumerated. The clear cellular change in fluorescence pattern makes this system an ideal tool for various life science and drug discovery research, including high throughput and high content screening applications.

  13. Personal Beacon

    Science.gov (United States)

    2000-01-01

    The MicroPLB (personal locator beacon) is a search and rescue satellite-aided tracking (SARSAT) transmitter. When activated it emits a distress signal to a constellation of internationally operated satellites. The endangered person's identity and location anywhere on Earth is automatically forwarded to central monitoring stations around the world. It is accurate to within just a few meters. The user uses the device to download navigation data from a global positioning satellite receiver. After the download is complete, the MicroPLB functions as a self-locating beacon. Also, it is the only PLB to use a safe battery. In the past, other PLB devices have used batteries that have enough volatility to explode with extreme force. It was developed by Microwave Monolithic, Inc. through SBIR funding from Glenn Research Center and Goddard Space Flight Center.

  14. Molecular beacon based biosensor for the sequence-specific detection of DNA using DNA-capped gold nanoparticles-streptavidin conjugates for signal amplification

    International Nuclear Information System (INIS)

    Fang, Xian; Jiang, Wei; Han, Xiaowei; Zhang, Yuzhong

    2013-01-01

    We describe a highly sensitive and selective molecular beacon-based electrochemical impedance biosensor for the sequence-specific detection of DNA. DNA-capped conjugates between gold nanoparticles (Au-NPs) and streptavidin are used for signal amplification. The molecular beacon was labeled with a thiol at its 5′ end and with biotin at its 3′ end, and then immobilized on the surface of a bare gold electrode through the formation of Au-S bonds. Initially, the molecular beacon is present in the “closed” state, and this shields the biotin from being approached by streptavidin due to steric hindrance. In the presence of the target DNA, the target DNA molecules hybridize with the loop and cause a conformational change that moves the biotin away from the surface of the electrode. The biotin thereby becomes accessible for the reporter (the DNA-streptavidin capped Au-NPs), and this results in a distinct increase in electron transfer resistance. Under optimal conditions, the increase in resistance is linearly related to the logarithm of the concentration of complementary target DNA in the range from 1.0 fM to 0.1 μM, with a detection limit of 0.35 fM (at an S/N of 3). This biosensor exhibits good selectivity, and acceptable stability and reproducibility. (author)

  15. Selective amyloid β oligomer assay based on abasic site-containing molecular beacon and enzyme-free amplification.

    Science.gov (United States)

    Zhu, Linling; Zhang, Junying; Wang, Fengyang; Wang, Ya; Lu, Linlin; Feng, Chongchong; Xu, Zhiai; Zhang, Wen

    2016-04-15

    Amyloid-beta (Aβ) oligomers are highly toxic species in the process of Aβ aggregation and are regarded as potent therapeutic targets and diagnostic markers for Alzheimer's disease (AD). Herein, a label-free molecular beacon (MB) system integrated with enzyme-free amplification strategy was developed for simple and highly selective assay of Aβ oligomers. The MB system was constructed with abasic site (AP site)-containing stem-loop DNA and a fluorescent ligand 2-amino-5,6,7-trimethyl-1,8-naphyridine (ATMND), of which the fluorescence was quenched upon binding to the AP site in DNA stem. Enzyme-free amplification was realized by target-triggered continuous opening of two delicately designed MBs (MB1 and MB2). Target DNA hybridization with MB1 and then MB2 resulted in the release of two ATMND molecules in one binding event. Subsequent target recycling could greatly amplify the detection sensitivity due to the greatly enhanced turn-on emission of ATMND fluorescence. Combining with Aβ oligomers aptamers, the strategy was applied to analyze Aβ oligomers and the results showed that it could quantify Aβ oligomers with high selectivity and monitor the Aβ aggregation process. This novel method may be conducive to improve the diagnosis and pathogenic study of Alzheimer's disease. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Novel Molecular Beacon Probe-Based Real-Time RT-PCR Assay for Diagnosis of Crimean-Congo Hemorrhagic Fever Encountered in India

    Directory of Open Access Journals (Sweden)

    Aman Kamboj

    2014-01-01

    Full Text Available Crimean-Congo hemorrhagic fever (CCHF is an emerging zoonotic disease in India and requires immediate detection of infection both for preventing further transmission and for controlling the infection. The present study describes development, optimization, and evaluation of a novel molecular beacon-based real-time RT-PCR assay for rapid, sensitive, and specific diagnosis of Crimean-Congo hemorrhagic fever virus (CCHFV. The developed assay was found to be a better alternative to the reported TaqMan assay for routine diagnosis of CCHF.

  17. Hairpin-Hairpin Molecular Beacon Interactions for Detection of Survivin mRNA in Malignant SW480 Cells.

    Science.gov (United States)

    Ratajczak, Katarzyna; Krazinski, Bartlomiej E; Kowalczyk, Anna E; Dworakowska, Beata; Jakiela, Slawomir; Stobiecka, Magdalena

    2018-05-07

    Cancer biomarkers offer unique prospects for the development of cancer diagnostics and therapy. One of such biomarkers, protein survivin (Sur), exhibits strong antiapoptotic and proliferation-enhancing properties and is heavily expressed in multiple cancers. Thus, it can be utilized to provide new modalities for modulating the cell-growth rate, essential for effective cancer treatment. Herein, we have focused on the development of a new survivin-based cancer detection platform for colorectal cancer cells SW480 using a turn-on fluorescence oligonucleotide molecular beacon (MB) probe, encoded to recognize Sur messenger RNA (mRNA). Contrary to the expectations, we have found that both the complementary target oligonucleotide strands as well as the single- and double-mismatch targets, instead of exhibiting the anticipated simple random conformations, preferentially formed secondary structure motifs by folding into small-loop hairpin structures. Such a conformation may interfere with, or even undermine, the biorecognition process. To gain better understanding of the interactions involved, we have replaced the classical Tyagi-Kramer model of interactions between a straight target oligonucleotide strand and a hairpin MB with a new model to account for the hairpin-hairpin interactions as the biorecognition principle. A detailed mechanism of these interactions has been proposed. Furthermore, in experimental work, we have demonstrated an efficient transfection of malignant SW480 cells with SurMB probes containing a fluorophore Joe (SurMB-Joe) using liposomal nanocarriers. The green emission from SurMB-Joe in transfected cancer cells, due to the hybridization of the SurMB-Joe loop with Sur mRNA hairpin target, corroborates Sur overexpression. On the other hand, healthy human-colon epithelial cells CCD 841 CoN show only negligible expression of survivin mRNA. These experiments provide the proof-of-concept for distinguishing between the cancer and normal cells by the proposed

  18. Voltammetric determination of attomolar levels of a sequence derived from the genom of hepatitis B virus by using molecular beacon mediated circular strand displacement and rolling circle amplification.

    Science.gov (United States)

    Huang, Shan; Feng, Mengmeng; Li, Jiawen; Liu, Yi; Xiao, Qi

    2018-03-03

    The authors describe an electrochemical method for the determination of the single-stranded DNA (ssDNA) oligonucleotide with a sequence derived from the genom of hepatitis B virus (HBV). It is making use of circular strand displacement (CSD) and rolling circle amplification (RCA) strategies mediated by a molecular beacon (MB). This ssDNA hybridizes with the loop portion of the MB immobilized on the surface of a gold electrode, while primer DNA also hybridizes with the rest of partial DNA sequences of MB. This triggers the MB-mediated CSD. The RCA is then initiated to produce a long DNA strand with multiple tandem-repeat sequences, and this results in a significant increase of the differential pulse voltammetric response of the electrochemical probe Methylene Blue at a rather low working potential of -0.24 V (vs. Ag/AgCl). Under optimal experimental conditions, the assay displays an ultrahigh sensitivity (with a 2.6 aM detection limit) and excellent selectivity. Response is linear in the 10 to 700 aM DNA concentration range. Graphical abstract Schematic of a voltammetric method for the determination of attomolar levels of target DNA. It is based on molecular beacon mediated circular strand displacement and rolling circle amplification strategies. Under optimal experimental conditions, the assay displays an ultrahigh sensitivity with a 2.6 aM detection limit and excellent selectivity.

  19. Long-stem shaped multifunctional molecular beacon for highly sensitive nucleic acids determination via intramolecular and intermolecular interactions based strand displacement amplification.

    Science.gov (United States)

    Xu, Jianguo; Zheng, Tingting; Le, Jingqing; Jia, Lee

    2017-11-20

    Occurrence and application of oligonucleotide probes have promoted great progress in the biochemical analysis field due to their unique biological and chemical properties. In this work, a long-stem shaped multifunctional molecular beacon (LS-MMB) that is responsive to a cancer-related gene, p53, is well-prepared. By designing the probe with long-paired bases at its two ends and short-paired bases between the middle region and the 3' end, the LS-MMB is intelligently endowed with the ability to recognize the target analyte, serve as the polymerization primer/template, and signal the hybridization event synchronously, which is distinctly advantageous over the traditional molecular beacons (MBs). Moreover, it is excitingly found that the LS-MMB can be employed to exert intramolecular and intermolecular interactions for strand displacement amplification (SDA) without the involvement of any assistant probes; this therapy results in a really easy and rapid sensing system that provides an extremely low background noise and high target output signal. In this case, an excellent sensitivity and specificity to detect target gene down to picomolar level and resolution to even one nucleotide variation are achieved, respectively. In addition, the application potential for real genomic DNA analysis is realized. We envision that the probe of LS-MMB can act as a universal platform for biosensing and biomedical research.

  20. Molecular detection of Phytophthora ramorum by real-time PCR using Taqman, SYBR Green and molecular beacons with three genes

    Science.gov (United States)

    G.J. Bilodeau; C.A. Lévesque; A.W.A.M. De Cock; C. Duchaine; G. Kristjansson; R.C. Hamelin

    2006-01-01

    Sudden oak death, caused by Phytophthora ramorum, is a severe disease that can affect numerous species of trees and shrubs. This pathogen has been spread via nursery stock, and quarantine measures are currently in place to prevent further spread. Molecular assays have been developed to rapidly detect and identify P. ramorum, but...

  1. Nucleic acid detection using BRET-beacons based on bioluminescent protein-DNA hybrids

    NARCIS (Netherlands)

    Engelen, W.; van de Wiel, K.M.; Meijer, L.H.H.; Saha, B.; Merkx, M.

    2017-01-01

    Bioluminescent molecular beacons have been developed using a modular design approach that relies on BRET between the bright luciferase NanoLuc and a Cy3 acceptor. While classical molecular beacons are hampered by background fluorescence and scattering, these BRET-beacons allow detection of low pM

  2. Hlaallele Detection Using Molecular Techniques

    Directory of Open Access Journals (Sweden)

    Philip A. Dyer

    1993-01-01

    Full Text Available There are now many molecular biological techniques available to define HLA class I and class II alleles. Some of these are also applicable to other human polymorphic genes, in particular to those non-HLA genes encoded within the Mhc. The range of techniques available allows laboratories to choose those most suited to their purpose. The routine laboratory supporting solid organ transplants will need to type large numbers of potential recipients over a period of time, probably using PCR-SSOP while donors will be typed singly and rapidly using PCR-SSP with HLA allele compatibility determined by heteroduplex analysis. Laboratories supporting bone marrow transplantation, where time is less pressing, can choose from the whole range of techniques to determine accurately donor recipient Mhc compatibility. For disease studies, techniques defining precise HLA allele sequence polymorphisms are needed and high sample numbers have to be accommodated. When an association is established allele sequencing has to be used. In the near future, the precise role of HLA alleles in transplantation and disease susceptibility is likely to be established unambiguously.

  3. Information Dissemination in VANETS by Piggybacking on Beacons -- An Analysis of the Impact of Network Parameters

    NARCIS (Netherlands)

    Klein Wolterink, W.; Heijenk, Geert; Karagiannis, Georgios

    2011-01-01

    Piggybacking on beacons is a forwarding technique that is regularly used in vehicular ad-hoc network (VANET) research as a means to disseminate data. With this technique data is attached to and transmitted along with scheduled beacons, without changing the timing of the beacons. In this paper we

  4. Auditory evacuation beacons

    NARCIS (Netherlands)

    Wijngaarden, S.J. van; Bronkhorst, A.W.; Boer, L.C.

    2005-01-01

    Auditory evacuation beacons can be used to guide people to safe exits, even when vision is totally obscured by smoke. Conventional beacons make use of modulated noise signals. Controlled evacuation experiments show that such signals require explicit instructions and are often misunderstood. A new

  5. SOX2 and OCT4 mRNA-expressing cells, detected by molecular beacons, localize to the center of neurospheres during differentiation.

    Directory of Open Access Journals (Sweden)

    Mirolyuba Ilieva

    Full Text Available Neurospheres are used as in vitro assay to measure the properties of neural stem cells. To investigate the molecular and phenotypic heterogeneity of neurospheres, molecular beacons (MBs targeted against the stem cell markers OCT4 and SOX2 were designed, and synthesized with a 2'-O-methyl RNA backbone. OCT4 and SOX2 MBs were transfected into human embryonic mesencephalon derived cells, which spontaneously form neurospheres when grown on poly-L-ornitine/fibronectin matrix and medium complemented with bFGF. OCT4 and SOX2 gene expression were tracked in individual cell using the MBs. Quantitative image analysis every day for seven days showed that the OCT4 and SOX2 mRNA-expressing cells clustered in the centre of the neurospheres cultured in differentiation medium. By contrast, cells at the periphery of the differentiating spheres developed neurite outgrowths and expressed the tyrosine hydroxylase protein, indicating terminal differentiation. Neurospheres cultured in growth medium contained OCT4 and SOX2-positive cells distributed throughout the entire sphere, and no differentiating neurones. Gene expression of SOX2 and OCT4 mRNA detected by MBs correlated well with gene and protein expression measured by qRT-PCR and immunostaining, respectively. These experimental data support the theoretical model that stem cells cluster in the centre of neurospheres, and demonstrate the use of MBs for the spatial localization of specific gene-expressing cells within heterogeneous cell populations.

  6. The G-BHQ synergistic effect: Improved double quenching molecular beacons based on guanine and Black Hole Quencher for sensitive simultaneous detection of two DNAs.

    Science.gov (United States)

    Xiang, Dongshan; Li, Fengquan; Wu, Chenyi; Shi, Boan; Zhai, Kun

    2017-11-01

    We designed two double quenching molecular beacons (MBs) with simple structure based on guanine (G base) and Black Hole Quencher (BHQ), and developed a new analytical method for sensitive simultaneous detection of two DNAs by synchronous fluorescence analysis. In this analytical method, carboxyl fluorescein (FAM) and tetramethyl-6-carboxyrhodamine (TAMRA) were respectively selected as fluorophore of two MBs, Black Hole Quencher 1 (BHQ-1) and Black Hole Quencher 2 (BHQ-2) were respectively selected as organic quencher, and three continuous nucleotides with G base were connected to organic quencher (BHQ-1 and BHQ-2). In the presence of target DNAs, the two MBs hybridize with the corresponding target DNAs, the fluorophores are separated from organic quenchers and G bases, leading to recovery of fluorescence of FAM and TAMRA. Under a certain conditions, the fluorescence intensities of FAM and TAMRA all exhibited good linear dependence on their concentration of target DNAs (T1 and T2) in the range from 4 × 10 -10 to 4 × 10 -8 molL -1 (M). The detection limit (3σ, n = 13) of T1 was 3 × 10 -10 M and that of T2 was 2×10 -10 M, respectively. Compared with the existing analysis methods for multiplex DNA with MBs, this proposed method based on double quenching MBs is not only low fluorescence background, short analytical time and low detection cost, but also easy synthesis and good stability of MB probes. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. A Turn-on Fluorescence Sensor for Heparin Detection Based on a Release of Taiwan Cobra Cardiotoxin from a DNA Aptamer or Adenosine-Based Molecular Beacon.

    Science.gov (United States)

    Shi, Yi-Jun; Wang, Liang-Jun; Lee, Yuan-Chin; Huang, Chia-Hui; Hu, Wan-Ping; Chang, Long-Sen

    2018-02-19

    This study presents two sensitive fluorescent assays for sensing heparin on the basis of the electrostatic interaction between heparin and Naja naja atra cardiotoxin 3 (CTX3). Owing to CTX3-induced folded structure of an adenosine-based molecular beacon (MB) or a DNA aptamer against CTX3, a reduction in the fluorescent signal of the aptamer or MB 5'-end labeled with carboxyfluorescein (FAM) and 3'-end labeled with 4-([4-(dimethylamino)phenyl]azo)-benzoic acid (DABCYL) was observed upon the addition of CTX3. The presence of heparin and formation of the CTX3-heparin complex caused CTX3 detachment from the MB or aptamer, and restoration of FAM fluorescence of the 5'-FAM-and-3'-DABCYL-labeled MB and aptamer was subsequently noted. Moreover, the detection of heparin with these CTX3-aptamer and CTX3-MB sensors showed high sensitivity and selectivity toward heparin over chondroitin sulfate and hyaluronic acid regardless of the presence of plasma. The limit of detection for heparin in plasma was determined to be 16 ng/mL and 15 ng/mL, respectively, at a signal-to-noise ratio of 3. This study validates the practical utility of the CTX3-aptamer and CTX3-MB systems for determining the concentration of heparin in a biological matrix.

  8. Rapid, High-Throughput, and Direct Molecular Beacon Delivery to Human Cancer Cells Using a Nanowire-Incorporated and Pneumatic Pressure-Driven Microdevice.

    Science.gov (United States)

    Kim, Kyung Hoon; Kim, Jung; Choi, Jong Seob; Bae, Sunwoong; Kwon, Donguk; Park, Inkyu; Kim, Do Hyun; Seo, Tae Seok

    2015-12-01

    Tracking and monitoring the intracellular behavior of mRNA is of paramount importance for understanding real-time gene expression in cell biology. To detect specific mRNA sequences, molecular beacons (MBs) have been widely employed as sensing probes. Although numerous strategies for MB delivery into the target cells have been reported, many issues such as the cytotoxicity of the carriers, dependence on the random probability of MB transfer, and critical cellular damage still need to be overcome. Herein, we have developed a nanowire-incorporated and pneumatic pressure-driven microdevice for rapid, high-throughput, and direct MB delivery to human breast cancer MCF-7 cells to monitor survivin mRNA expression. The proposed microdevice is composed of three layers: a pump-associated glass manifold layer, a monolithic polydimethylsiloxane (PDMS) membrane, and a ZnO nanowire-patterned microchannel layer. The MB is immobilized on the ZnO nanowires by disulfide bonding, and the glass manifold and PDMS membrane serve as a microvalve, so that the cellular attachment and detachment on the MB-coated nanowire array can be manipulated. The combination of the nanowire-mediated MB delivery and the microvalve function enable the transfer of MB into the cells in a controllable way with high cell viability and to detect survivin mRNA expression quantitatively after docetaxel treatment. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Nicking endonuclease-assisted signal amplification of a split molecular aptamer beacon for biomolecule detection using graphene oxide as a sensing platform.

    Science.gov (United States)

    Li, Xiang; Ding, Xuelian; Fan, Jing

    2015-12-07

    Sensitive and selective detection of ultralow concentrations of specific biomolecules is important in early clinical diagnoses and biomedical applications. Many types of aptasensors have been developed for the detection of various biomolecules, but usually suffer from false positive signals and high background signals. In this work, we have developed an amplified fluorescence aptasensor platform for ultrasensitive biomolecule detection based on enzyme-assisted target-recycling signal amplification and graphene oxide. By using a split molecular aptamer beacon and a nicking enzyme, the typical problem of false positive signals can be effectively resolved. Only in the presence of a target biomolecule, the sensor system is able to generate a positive signal, which significantly improves the selectivity of the aptasensor. Moreover, using graphene oxide as a super-quencher can effectively reduce the high background signal of a sensing platform. We select vascular endothelial growth factor (VEGF) and adenosine triphosphate (ATP) as model analytes in the current proof-of-concept experiments. It is shown that under optimized conditions, our strategy exhibits high sensitivity and selectivity for the quantification of VEGF and ATP with a low detection limit (1 pM and 4 nM, respectively). In addition, this biosensor has been successfully utilized in the analysis of real biological samples.

  10. Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes

    Science.gov (United States)

    Ni, Yanxiang; Cao, Bo; Ma, Tszshan; Niu, Gang; Huo, Yingdong; Huang, Jiandong; Chen, Danni; Liu, Yi; Yu, Bin; Zhang, Michael Q; Niu, Hanben

    2017-01-01

    High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaint probes have enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence. We used three-dimensional stochastic optical reconstruction microscopy (3D-STORM) with optimized imaging conditions to efficiently distinguish sparsely distributed Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and only 29–34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in human or mouse genome, respectively. We demonstrated our MB-based FISH method was capable of visualizing the so far shortest non-repetitive genomic sequence in 3D at super-resolution. DOI: http://dx.doi.org/10.7554/eLife.21660.001 PMID:28485713

  11. Introduction to basic molecular biologic techniques for molecular imaging researches

    International Nuclear Information System (INIS)

    Kang, Joo Hyun

    2004-01-01

    Molecular imaging is a rapidly growing field due to the advances in molecular biology and imaging technologies. With the introduction of imaging reporter genes into the cell, diverse cellular processes can be monitored, quantified and imaged non-invasively in vivo. These processes include the gene expression, protein-protein interactions, signal transduction pathways, and monitoring of cells such as cancer cells, immune cells, and stem cells. In the near future, molecular imaging analysis will allow us to observe the incipience and progression of the disease. These will make us easier to give a diagnosis in the early stage of intractable diseases such as cancer, neuro-degenerative disease, and immunological disorders. Additionally, molecular imaging method will be a valuable tool for the real-time evaluation of cells in molecular biology and the basic biological studies. As newer and more powerful molecular imaging tools become available, it will be necessary to corporate clinicians, molecular biologists and biochemists for the planning, interpretation, and application of these techniques to their fullest potential. In order for such a multidisciplinary team to be effective, it is essential that a common understanding of basic biochemical and molecular biologic techniques is achieved. Basic molecular techniques for molecular imaging methods are presented in this paper

  12. Molecular beacon-decorated polymethylmethacrylate core-shell fluorescent nanoparticles for the detection of survivin mRNA in human cancer cells.

    Science.gov (United States)

    Adinolfi, Barbara; Pellegrino, Mario; Giannetti, Ambra; Tombelli, Sara; Trono, Cosimo; Sotgiu, Giovanna; Varchi, Greta; Ballestri, Marco; Posati, Tamara; Carpi, Sara; Nieri, Paola; Baldini, Francesco

    2017-02-15

    One of the main goals of nanomedicine in cancer is the development of effective drug delivery systems, primarily nanoparticles. Survivin, an overexpressed anti-apoptotic protein in cancer, represents a pharmacological target for therapy and a Molecular Beacon (MB) specific for survivin mRNA is available. In this study, the ability of polymethylmethacrylate nanoparticles (PMMA-NPs) to promote survivin MB uptake in human A549 cells was investigated. Fluorescent and positively charged core PMMA-NPs of nearly 60nm, obtained through an emulsion co-polymerization reaction, and the MB alone were evaluated in solution, for their analytical characterization; then, the MB specificity and functionality were verified after adsorption onto the PMMA-NPs. The carrier ability of PMMA-NPs in A549 was examined by confocal microscopy. With the optimized protocol, a hardly detectable fluorescent signal was obtained after incubation of the cells with the MB alone (fluorescent spots per cell of 1.90±0.40 with a mean area of 1.04±0.20µm 2 ), while bright fluorescent spots inside the cells were evident by using the MB loaded onto the PMMA-NPs. (27.50±2.30 fluorescent spots per cell with a mean area of 2.35±0.16µm 2 ). These results demonstrate the ability of the PMMA-NPs to promote the survivin-MB internalization, suggesting that this complex might represent a promising strategy for intracellular sensing and for the reduction of cancer cell proliferation. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Techniques for Investigating Molecular Toxicology of Nanomaterials.

    Science.gov (United States)

    Wang, Yanli; Li, Chenchen; Yao, Chenjie; Ding, Lin; Lei, Zhendong; Wu, Minghong

    2016-06-01

    Nanotechnology has been a rapidly developing field in the past few decades, resulting in the more and more exposure of nanomaterials to human. The increased applications of nanomaterials for industrial, commercial and life purposes, such as fillers, catalysts, semiconductors, paints, cosmetic additives and drug carriers, have caused both obvious and potential impacts on human health and environment. Nanotoxicology is used to study the safety of nanomaterials and has grown at the historic moment. Molecular toxicology is a new subdiscipline to study the interactions and impacts of materials at the molecular level. To better understand the relationship between the molecular toxicology and nanomaterials, this review summarizes the typical techniques and methods in molecular toxicology which are applied when investigating the toxicology of nanomaterials and include six categories: namely; genetic mutation detection, gene expression analysis, DNA damage detection, chromosomal aberration analysis, proteomics, and metabolomics. Each category involves several experimental techniques and methods.

  14. Robot-Beacon Distributed Range-Only SLAM for Resource-Constrained Operation.

    Science.gov (United States)

    Torres-González, Arturo; Martínez-de Dios, Jose Ramiro; Ollero, Anibal

    2017-04-20

    This work deals with robot-sensor network cooperation where sensor nodes (beacons) are used as landmarks for Range-Only (RO) Simultaneous Localization and Mapping (SLAM). Most existing RO-SLAM techniques consider beacons as passive devices disregarding the sensing, computational and communication capabilities with which they are actually endowed. SLAM is a resource-demanding task. Besides the technological constraints of the robot and beacons, many applications impose further resource consumption limitations. This paper presents a scalable distributed RO-SLAM scheme for resource-constrained operation. It is capable of exploiting robot-beacon cooperation in order to improve SLAM accuracy while meeting a given resource consumption bound expressed as the maximum number of measurements that are integrated in SLAM per iteration. The proposed scheme combines a Sparse Extended Information Filter (SEIF) SLAM method, in which each beacon gathers and integrates robot-beacon and inter-beacon measurements, and a distributed information-driven measurement allocation tool that dynamically selects the measurements that are integrated in SLAM, balancing uncertainty improvement and resource consumption. The scheme adopts a robot-beacon distributed approach in which each beacon participates in the selection, gathering and integration in SLAM of robot-beacon and inter-beacon measurements, resulting in significant estimation accuracies, resource-consumption efficiency and scalability. It has been integrated in an octorotor Unmanned Aerial System (UAS) and evaluated in 3D SLAM outdoor experiments. The experimental results obtained show its performance and robustness and evidence its advantages over existing methods.

  15. Improvement of Leukemia diagnose with molecular techniques

    International Nuclear Information System (INIS)

    Campos Rudin, M.E.

    1997-01-01

    The objective of this study was to contribute with new techniques to the clinical diagnosis and to the monitoring of mycloid chronic leukemias in Costa Rica. The same one achieved to determine that is viable to apply radioactive and non reactive methodologies, for the molecular detection of the Philadelphia chromosome.It also found that the application of techniques of cellular biology, helps to classify better the mycloide leukemias and the chronic mycloproliferatives and miclodisplaced disorders. (S. Grainger) [es

  16. Use of molecular techniques in bioremediation.

    Science.gov (United States)

    Płaza, G; Ulfig, K; Hazen, T C; Brigmon, R L

    2001-01-01

    In a practical sense, biotechnology is concerned with the production of commercial products generated by biological processes. More formally, biotechnology may be defined as "the application of scientific and engineering principles to the processing of material by biological agents to provide goods and services" (Cantor, 2000). From a historical perspective, biotechnology dates back to the time when yeast was first used for beer or wine fermentation, and bacteria were used to make yogurt. In 1972, the birth of recombinant DNA technology moved biotechnology to new heights and led to the establishment of a new industry. Progress in biotechnology has been truly remarkable. Within four years of the discovery of recombinant DNA technology, genetically modified organisms (GMOs) were making human insulin, interferon, and human growth hormone. Now, recombinant DNA technology and its products--GMOs are widely used in environmental biotechnology (Glick and Pasternak, 1988; Cowan, 2000). Bioremediation is one of the most rapidly growing areas of environmental biotechnology. Use of bioremediation for environmental clean up is popular due to low costs and its public acceptability. Indeed, bioremediation stands to benefit greatly and advance even more rapidly with the adoption of molecular techniques developed originally for other areas of biotechnology. The 1990s was the decade of molecular microbial ecology (time of using molecular techniques in environmental biotechnology). Adoption of these molecular techniques made scientists realize that microbial populations in the natural environments are much more diverse than previously thought using traditional culture methods. Using molecular ecological methods, such as direct DNA isolation from environmental samples, denaturing gradient gel electrophoresis (DGGE), PCR methods, nucleic acid hybridization etc., we can now study microbial consortia relevant to pollutant degradation in the environment. These techniques promise to

  17. SU-E-J-257: Image Artifacts Caused by Implanted Calypso Beacons in MRI Studies

    International Nuclear Information System (INIS)

    Amro, H; Chetty, I; Gordon, J; Wen, N

    2014-01-01

    Purpose: The presence of Calypso Beacon-transponders in patients can cause artifacts during MRI imaging studies. This could be a problem for post-treatment follow up of cancer patients using MRI studies to evaluate metastasis and for functional imaging studies.This work assesses (1) the volume immediately surrounding the transponders that will not be visualized by the MRI due to the beacons, and (2) the dependence of the non-visualized volume on beacon orientation, and scanning techniques. Methods: Two phantoms were used in this study (1) water filled box, (2) and a 2300 cc block of pork meat. Calypso beacons were implanted in the phantoms both in parallel and perpendicular orientations with respect to the MR scanner magnetic field. MR image series of the phantom were obtained with on a 1.0T high field open MR-SIM with multiple pulse sequences, for example, T1-weighted fast field echo and T2-weighted turbo spin echo. Results: On average, a no-signal region with 2 cm radius and 3 cm length was measured. Image artifacts are more significant when beacons are placed parallel to scanner magnetic field; the no-signal area around the beacon was about 0.5 cm larger in orthogonal orientation. The no-signal region surrounding the beacons slightly varies in dimension for the different pulse sequences. Conclusion: The use of Calypso beacons can prohibit the use of MRI studies in post-treatment assessments, especially in the immediate region surrounding the implanted beacon. A characterization of the MR scanner by identifying the no-signal regions due to implanted beacons is essential. This may render the use of Calypso beacons useful for some cases and give the treating physician a chance to identify those patients prior to beacon implantation

  18. SU-E-J-257: Image Artifacts Caused by Implanted Calypso Beacons in MRI Studies

    Energy Technology Data Exchange (ETDEWEB)

    Amro, H; Chetty, I; Gordon, J; Wen, N [Henry Ford Health System, Detroit, MI (United States)

    2014-06-01

    Purpose: The presence of Calypso Beacon-transponders in patients can cause artifacts during MRI imaging studies. This could be a problem for post-treatment follow up of cancer patients using MRI studies to evaluate metastasis and for functional imaging studies.This work assesses (1) the volume immediately surrounding the transponders that will not be visualized by the MRI due to the beacons, and (2) the dependence of the non-visualized volume on beacon orientation, and scanning techniques. Methods: Two phantoms were used in this study (1) water filled box, (2) and a 2300 cc block of pork meat. Calypso beacons were implanted in the phantoms both in parallel and perpendicular orientations with respect to the MR scanner magnetic field. MR image series of the phantom were obtained with on a 1.0T high field open MR-SIM with multiple pulse sequences, for example, T1-weighted fast field echo and T2-weighted turbo spin echo. Results: On average, a no-signal region with 2 cm radius and 3 cm length was measured. Image artifacts are more significant when beacons are placed parallel to scanner magnetic field; the no-signal area around the beacon was about 0.5 cm larger in orthogonal orientation. The no-signal region surrounding the beacons slightly varies in dimension for the different pulse sequences. Conclusion: The use of Calypso beacons can prohibit the use of MRI studies in post-treatment assessments, especially in the immediate region surrounding the implanted beacon. A characterization of the MR scanner by identifying the no-signal regions due to implanted beacons is essential. This may render the use of Calypso beacons useful for some cases and give the treating physician a chance to identify those patients prior to beacon implantation.

  19. Improvement of molecular techniques: A multidisciplinar vision

    Directory of Open Access Journals (Sweden)

    Bruno do Amaral Crispim

    2016-08-01

    Full Text Available The advances in molecular technologies since the discovery of the PCR (Polymerase Chain Reaction and their association with the use of molecular markers, allowed a rapid progress in the development of technologies and equipment able to generate and analyze data on a large scale, revolutionizing research that until recently was only based on single marker, like the analysis of Single Nucleotide Polymorphism (SNP, and nowadays with the genomic era is already possible in a few hours genotyping millions or even thousands of SNPs. This evolution has allowed improvements in research to the knowledge of genomes creating expectations and real possibilities of application of these techniques in various fields, from medicine to animal production. These new technologies of molecular analysis of DNA variability determining points of interest in chromosomes, which are technically called as molecular markers. These markers can be used in various applications, including paternity test, construction of genetic maps, mapping of quantitative inheritance of characteristics, isolation of genes, marker-assisted selection and characterization of the genetic diversity of different species. The improvement of sequencing and bioinformatics technologies were crucial to studies with characteristics of interest using high-density genetic information. The SNP genotyping panels stimulated researches in the human area, especially in studies of cancer and exoma, and also in agribusiness, aiming the search for superior genotypes for domestic plants and animals. The differential use of the panels is the possibility to seek complex characteristics, once the wide distribution of markers favors through the linkage disequilibrium, the identification of genomic regions associated with expression phenotypes in study. Therefore, this advance has become essential for greater accuracy and speed in molecular diagnostics, increasing the accuracy in the selection of individuals with

  20. Gold nanoparticle-based beacon to detect STAT5b mRNA expression in living cells: a case optimized by bioinformatics screen

    Directory of Open Access Journals (Sweden)

    Deng D

    2015-04-01

    Full Text Available Dawei Deng,* Yang Li,* Jianpeng Xue, Jie Wang, Guanhua Ai, Xin Li, Yueqing GuDepartment of Biomedical Engineering, China Pharmaceutical University, Nanjing, People’s Republic of China*These authors contributed equally to this workAbstract: Messenger RNA (mRNA, a single-strand ribonucleic acid with functional gene information is usually abnormally expressed in cancer cells and has become a promising biomarker for the study of tumor progress. Hairpin DNA-coated gold nanoparticle (hDAuNP beacon containing a bare gold nanoparticle (AuNP as fluorescence quencher and thiol-terminated fluorescently labeled stem–loop–stem oligonucleotide sequences attached by Au–S bond is currently a new nanoscale biodiagnostic platform capable of mRNA detection, in which the design of the loop region sequence is crucial for hybridizing with the target mRNA. Hence, in this study, to improve the sensitivity and selectivity of hDAuNP beacon simultaneously, the loop region of hairpin DNA was screened by bioinformatics strategy. Here, signal transducer and activator of transcription 5b (STAT5b mRNA was selected and used as a practical example. The results from the combined characterizations using optical techniques, flow cytometry assay, and cell microscopic imaging showed that after optimization, the as-prepared hDAuNP beacon had higher selectivity and sensitivity for the detection of STAT5b mRNA in living cells, as compared with our previous beacon. Thus, the bioinformatics method may be a promising new strategy for assisting in the designing of the hDAuNP beacon, extending its application in the detection of mRNA expression and the resultant mRNA-based biological processes and disease pathogenesis.Keywords: molecular beacon, bioinformatics, gold nanoparticle, STAT5b mRNA, visual detection

  1. Development of Aptamer Beacons for Antemortem Diagnosis of Chronic Wasting Disease

    National Research Council Canada - National Science Library

    Clinkenbeard, Kenneth D

    2005-01-01

    .... Once selected, the CWD aptamers will be configured as aptamer beacons that can act as molecular switches to turn "on" a novel and highly sensitive diagnostic technology termed amplifying fluorescing polymer...

  2. Development of Aptamer Beacons for Antemortem Diagnosis of Chronic Wasting Disease

    National Research Council Canada - National Science Library

    Clinkenbeard, Kenneth

    2004-01-01

    .... Once selected, the CWD aptamers will be configured as aptamer beacons that can act as molecular switches to turn on a novel and highly sensitive diagnostic technology termed amplifying fluorescing polymer. Objective...

  3. COSPAS-SARSAT Beacon Certification Facility

    Data.gov (United States)

    Federal Laboratory Consortium — EPG's COSPAS-SARSAT Beacon Certification Facility is one of five certification facilities in the world. Formal certifications are available for all beacon types and...

  4. Molecular Technique to Understand Deep Microbial Diversity

    Science.gov (United States)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample.

  5. 47 CFR 97.203 - Beacon station.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 5 2010-10-01 2010-10-01 false Beacon station. 97.203 Section 97.203... SERVICE Special Operations § 97.203 Beacon station. (a) Any amateur station licensed to a holder of a Technician, Technician Plus, General, Advanced or Amateur Extra Class operator license may be a beacon. A...

  6. Rapid molecular technique to distinguish Fusarium species

    CSIR Research Space (South Africa)

    Lodolo, EJ

    1993-03-01

    Full Text Available The nuclear DNA (nDNA) of different isolates of three closely related, toxin-producing Fusarium species, F. moniliforme, F. nygamai and F. napiforme, was compared to ascertain the sensitivity of a molecular method to distinguish these three species...

  7. Electroactive crown ester-Cu2+ complex with in-situ modification at molecular beacon probe serving as a facile electrochemical DNA biosensor for the detection of CaMV 35s.

    Science.gov (United States)

    Zhan, Fengping; Liao, Xiaolei; Gao, Feng; Qiu, Weiwei; Wang, Qingxiang

    2017-06-15

    A novel electrochemical DNA biosensor has been facilely constructed by in-situ assembly of electroactive 4'-aminobenzo-18-crown-6-copper(II) complex (AbC-Cu 2+ ) on the free terminal of the hairpin-structured molecule beacon. The 3'-SH modified molecule beacon probe was first immobilized on the gold electrode (AuE) surface through self-assembly chemistry of Au-S bond. Then the crow ester of AbC was covalently coupled with 5'-COOH on the molecule beacon, and served as a platform to attach the Cu 2+ by coordination with ether bond (-O-) of the crown cycle. Thus, an electroactive molecule beacon-based biosensing interface was constructed. In comparison with conventional methods for preparation of electroactive molecule beacon, the approach presented in this work is much simpler, reagent- and labor-saving. Selectivity study shows that the in-situ fabricated electroactive molecule beacon remains excellent recognition ability of pristine molecule beacon probe to well differentiate various DNA fragments. The target DNA can be quantatively determined over the range from 0.10pM to 0.50nM. The detection limit of 0.060pM was estimated based on signal-to-noise ratio of 3. When the biosensor was applied for the detection cauliflower mosaic virus 35s (CaMV 35s) in soybean extraction samples, satisfactory results are achieved. This work opens a new strategy for facilely fabricating electrochemical sensing interface, which also shows great potential in aptasensor and immurosensor fabrication. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Molecular Imprinting Techniques Used for the Preparation of Biosensors

    Directory of Open Access Journals (Sweden)

    Gizem Ertürk

    2017-02-01

    Full Text Available Molecular imprinting is the technology of creating artificial recognition sites in polymeric matrices which are complementary to the template in their size, shape and spatial arrangement of the functional groups. Molecularly imprinted polymers (MIPs and their incorporation with various transducer platforms are among the most promising approaches for detection of several analytes. There are a variety of molecular imprinting techniques used for the preparation of biomimetic sensors including bulk imprinting, surface imprinting (soft lithography, template immobilization, grafting, emulsion polymerization and epitope imprinting. This chapter presents an overview of all of these techniques with examples from particular publications.

  9. [Advances of Molecular Diagnostic Techniques Application in Clinical Diagnosis.

    Science.gov (United States)

    Ying, Bin-Wu

    2016-11-01

    Over the past 20 years,clinical molecular diagnostic technology has made rapid development,and became the most promising field in clinical laboratory medicine.In particular,with the development of genomics,clinical molecular diagnostic methods will reveal the nature of clinical diseases in a deeper level,thus guiding the clinical diagnosis and treatments.Many molecular diagnostic projects have been routinely applied in clinical works.This paper reviews the advances on application of clinical diagnostic techniques in infectious disease,tumor and genetic disorders,including nucleic acid amplification,biochip,next-generation sequencing,and automation molecular system,and so on.

  10. A Measurement Study of BLE iBeacon and Geometric Adjustment Scheme for Indoor Location-Based Mobile Applications

    Directory of Open Access Journals (Sweden)

    Jeongyeup Paek

    2016-01-01

    Full Text Available Bluetooth Low Energy (BLE and the iBeacons have recently gained large interest for enabling various proximity-based application services. Given the ubiquitously deployed nature of Bluetooth devices including mobile smartphones, using BLE and iBeacon technologies seemed to be a promising future to come. This work started off with the belief that this was true: iBeacons could provide us with the accuracy in proximity and distance estimation to enable and simplify the development of many previously difficult applications. However, our empirical studies with three different iBeacon devices from various vendors and two types of smartphone platforms prove that this is not the case. Signal strength readings vary significantly over different iBeacon vendors, mobile platforms, environmental or deployment factors, and usage scenarios. This variability in signal strength naturally complicates the process of extracting an accurate location/proximity estimation in real environments. Our lessons on the limitations of iBeacon technique lead us to design a simple class attendance checking application by performing a simple form of geometric adjustments to compensate for the natural variations in beacon signal strength readings. We believe that the negative observations made in this work can provide future researchers with a reference on how well of a performance to expect from iBeacon devices as they enter their system design phases.

  11. Molecular techniques as complementary tools in orchid mutagenesis

    Energy Technology Data Exchange (ETDEWEB)

    Mohd Nazir Basiran; Sakinah Ariffin [Malaysian Institute for Nuclear Technology Research (MINT), Bangi (Malaysia)

    2002-02-01

    Orchid breeders have always been dependent on hybridization technology to produce new orchid hybrids and varieties. The technology has proven very reliable and easy to use and has produced wide range of successful cultivars with attractive combinations of spray length, bud number, flower colour and form, vase life, fragrance, seasonality, and compactness. By introducing mutagenesis however, wide variations of flower colours, form and size can still be obtained in addition to overcoming the problem of sexual incompatibility and sterility. In addition, complementary use of molecular techniques will allow breeders to target more specific characteristic changes and cut short breeding time. PCR-based techniques used to analyse the DNA of mutagenic clones found polymorphic fragments that can be developed as molecular markers. This paper describes how mutagenesis and molecular techniques can be used to enhance orchid breeding efforts. (author)

  12. An adaptive scheme for robot localization and mapping with dynamically configurable inter-beacon range measurements.

    Science.gov (United States)

    Torres-González, Arturo; Martinez-de Dios, Jose Ramiro; Ollero, Anibal

    2014-04-25

    This work is motivated by robot-sensor network cooperation techniques where sensor nodes (beacons) are used as landmarks for range-only (RO) simultaneous localization and mapping (SLAM). This paper presents a RO-SLAM scheme that actuates over the measurement gathering process using mechanisms that dynamically modify the rate and variety of measurements that are integrated in the SLAM filter. It includes a measurement gathering module that can be configured to collect direct robot-beacon and inter-beacon measurements with different inter-beacon depth levels and at different rates. It also includes a supervision module that monitors the SLAM performance and dynamically selects the measurement gathering configuration balancing SLAM accuracy and resource consumption. The proposed scheme has been applied to an extended Kalman filter SLAM with auxiliary particle filters for beacon initialization (PF-EKF SLAM) and validated with experiments performed in the CONET Integrated Testbed. It achieved lower map and robot errors (34% and 14%, respectively) than traditional methods with a lower computational burden (16%) and similar beacon energy consumption.

  13. A Brief Review of Molecular Techniques to Assess Plant Diversity

    Directory of Open Access Journals (Sweden)

    Ibrahim A. Arif

    2010-05-01

    Full Text Available Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD, amplified fragment length polymorphism (AFLP, microsatellites and single nucleotide polymorphisms (SNP have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species.

  14. A Brief Review of Molecular Techniques to Assess Plant Diversity

    Science.gov (United States)

    Arif, Ibrahim A.; Bakir, Mohammad A.; Khan, Haseeb A.; Al Farhan, Ahmad H.; Al Homaidan, Ali A.; Bahkali, Ali H.; Sadoon, Mohammad Al; Shobrak, Mohammad

    2010-01-01

    Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species. PMID:20559503

  15. The ANTARES optical beacon system

    International Nuclear Information System (INIS)

    Ageron, M.; Aguilar, J.A.; Albert, A.

    2007-01-01

    ANTARES is a neutrino telescope being deployed in the Mediterranean Sea. It consists of a three-dimensional array of photomultiplier tubes that can detect the Cherenkov light induced by charged particles produced in the interactions of neutrinos with the surrounding medium. High angular resolution can be achieved, in particular, when a muon is produced, provided that the Cherenkov photons are detected with sufficient timing precision. Considerations of the intrinsic time uncertainties stemming from the transit time spread in the photomultiplier tubes and the mechanism of transmission of light in sea water lead to the conclusion that a relative time accuracy of the order of 0.5 ns is desirable. Accordingly, different time calibration systems have been developed for the ANTARES telescope. In this article, a system based on Optical Beacons, a set of external and well-controlled pulsed light sources located throughout the detector, is described. This calibration system takes into account the optical properties of sea water, which is used as the detection volume of the ANTARES telescope. The design, tests, construction and first results of the two types of beacons, LED and laser-based, are presented

  16. The ANTARES optical beacon system

    Energy Technology Data Exchange (ETDEWEB)

    Ageron, M. [CPPM - Centre de Physique des Particules de Marseille, CNRS/IN2P3 et Universite de la Mediterranee, 163 Avenue de Luminy, Case 902, 13288 Marseille Cedex 9 (France); Aguilar, J.A. [IFIC - Instituto de Fisica Corpuscular, Edificios de Investigacion de Paterna, CSIC - Universitat de Valencia, Apdo. de Correos 22085, 46071 Valencia (Spain)]. E-mail: J.A.Aguilar@ific.uv.es; Albert, A. [GRPHE - Groupe de Recherche en Physique des Hautes Energies, Universite de Haute Alsace, 61 Rue Albert Camus, 68093 Mulhouse Cedex (France)) (and others)

    2007-08-11

    ANTARES is a neutrino telescope being deployed in the Mediterranean Sea. It consists of a three-dimensional array of photomultiplier tubes that can detect the Cherenkov light induced by charged particles produced in the interactions of neutrinos with the surrounding medium. High angular resolution can be achieved, in particular, when a muon is produced, provided that the Cherenkov photons are detected with sufficient timing precision. Considerations of the intrinsic time uncertainties stemming from the transit time spread in the photomultiplier tubes and the mechanism of transmission of light in sea water lead to the conclusion that a relative time accuracy of the order of 0.5 ns is desirable. Accordingly, different time calibration systems have been developed for the ANTARES telescope. In this article, a system based on Optical Beacons, a set of external and well-controlled pulsed light sources located throughout the detector, is described. This calibration system takes into account the optical properties of sea water, which is used as the detection volume of the ANTARES telescope. The design, tests, construction and first results of the two types of beacons, LED and laser-based, are presented.

  17. The ANTARES optical beacon system

    Science.gov (United States)

    Ageron, M.; Aguilar, J. A.; Albert, A.; Ameli, F.; Anghinolfi, M.; Anton, G.; Anvar, S.; Ardellier-Desages, F.; Aslanides, E.; Aubert, J.-J.; Auer, R.; Barbarito, E.; Basa, S.; Battaglieri, M.; Becherini, Y.; Beltramelli, J.; Bertin, V.; Bigi, A.; Billault, M.; Blaes, R.; de Botton, N.; Bouwhuis, M. C.; Bradbury, S. M.; Bruijn, R.; Brunner, J.; Burgio, G. F.; Busto, J.; Cafagna, F.; Caillat, L.; Calzas, A.; Capone, A.; Caponetto, L.; Carmona, E.; Carr, J.; Cartwright, S. L.; Castel, D.; Castorina, E.; Cavasinni, V.; Cecchini, S.; Ceres, A.; Charvis, P.; Chauchot, P.; Chiarusi, T.; Circella, M.; Colnard, C.; Compère, C.; Coniglione, R.; Cottini, N.; Coyle, P.; Cuneo, S.; Cussatlegras, A.-S.; Damy, G.; van Dantzig, R.; de Bonis, G.; de Marzo, C.; de Vita, R.; Dekeyser, I.; Delagnes, E.; Denans, D.; Deschamps, A.; Destelle, J.-J.; Dinkespieler, B.; Distefano, C.; Donzaud, C.; Drogou, J.-F.; Druillole, F.; Durand, D.; Ernenwein, J.-P.; Escoffier, S.; Falchini, E.; Favard, S.; Fehr, F.; Feinstein, F.; Ferry, S.; Fiorello, C.; Flaminio, V.; Fratini, K.; Fuda, J.-L.; Galeotti, S.; Gallone, J.-M.; Giacomelli, G.; Girard, N.; Gojak, C.; Goret, Ph.; Graf, K.; Hallewell, G.; Harakeh, M. N.; Hartmann, B.; Heijboer, A.; Heine, E.; Hello, Y.; Hernández-Rey, J. J.; Hößl, J.; Hoffman, C.; Hogenbirk, J.; Hubbard, J. R.; Jaquet, M.; Jaspers, M.; de Jong, M.; Jouvenot, F.; Kalantar-Nayestanaki, N.; Kappes, A.; Karg, T.; Katz, U.; Keller, P.; Kok, E.; Kok, H.; Kooijman, P.; Kopper, C.; Korolkova, E. V.; Kouchner, A.; Kretschmer, W.; Kruijer, A.; Kuch, S.; Kudryavstev, V. A.; Lagier, P.; Lahmann, R.; Lamanna, G.; Lamare, P.; Lambard, G.; Languillat, J.-C.; Laschinsky, H.; Lavalle, J.; Le Guen, Y.; Le Provost, H.; Le van Suu, A.; Lefèvre, D.; Legou, T.; Lelaizant, G.; Lim, G.; Lo Presti, D.; Loehner, H.; Loucatos, S.; Louis, F.; Lucarelli, F.; Lyashuk, V.; Marcelin, M.; Margiotta, A.; Masullo, R.; Mazéas, F.; Mazure, A.; McMillan, J. E.; Megna, R.; Melissas, M.; Migneco, E.; Milovanovic, A.; Mongelli, M.; Montaruli, T.; Morganti, M.; Moscoso, L.; Musumeci, M.; Naumann-Godo, M.; Naumann, C.; Niess, V.; Noble, T.; Olivetto, C.; Ostasch, R.; Palanque-Delabrouille, N.; Payre, P.; Peek, H.; Perez, A.; Petta, C.; Piattelli, P.; Pillet, R.; Pineau, J.-P.; Poinsignon, J.; Popa, V.; Pradier, T.; Racca, C.; Randazzo, N.; van Randwijk, J.; Real, D.; van Rens, B.; Réthoré, F.; Rewiersma, P.; Riccobene, G.; Rigaud, V.; Ripani, M.; Roca, V.; Roda, C.; Rolin, J. F.; Rose, H. J.; Rostovtsev, A.; Roux, J.; Ruppi, M.; Russo, G. V.; Rusydi, G.; Salesa, F.; Salomon, K.; Sapienza, P.; Schmitt, F.; Schuller, J.-P.; Shanidze, R.; Sokalski, I.; Spona, T.; Spurio, M.; van der Steenhoven, G.; Stolarczyk, T.; Streeb, K.; Sulak, L.; Taiuti, M.; Tamburini, C.; Tao, C.; Terreni, G.; Thompson, L. F.; Urbano, F.; Valdy, P.; Valente, V.; Vallage, B.; Vaudaine, G.; Venekamp, G.; Verlaat, B.; Vernin, P.; de Vries-Uiterweerd, G.; van Wijk, R.; Wijnker, G.; de Witt Huberts, P.; Wobbe, G.; de Wolf, E.; Yao, A.-F.; Zaborov, D.; Zaccone, H.; Zornoza, J. D.; Zúñiga, J.

    2007-08-01

    ANTARES is a neutrino telescope being deployed in the Mediterranean Sea. It consists of a three-dimensional array of photomultiplier tubes that can detect the Cherenkov light induced by charged particles produced in the interactions of neutrinos with the surrounding medium. High angular resolution can be achieved, in particular, when a muon is produced, provided that the Cherenkov photons are detected with sufficient timing precision. Considerations of the intrinsic time uncertainties stemming from the transit time spread in the photomultiplier tubes and the mechanism of transmission of light in sea water lead to the conclusion that a relative time accuracy of the order of 0.5 ns is desirable. Accordingly, different time calibration systems have been developed for the ANTARES telescope. In this article, a system based on Optical Beacons, a set of external and well-controlled pulsed light sources located throughout the detector, is described. This calibration system takes into account the optical properties of sea water, which is used as the detection volume of the ANTARES telescope. The design, tests, construction and first results of the two types of beacons, LED and laser-based, are presented.

  18. A fermionic molecular dynamics technique to model nuclear matter

    International Nuclear Information System (INIS)

    Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.

    2009-01-01

    Full text: At sub-nuclear densities of about 10 14 g/cm 3 , nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)

  19. Searching for Cost-Optimized Interstellar Beacons

    Science.gov (United States)

    Benford, Gregory; Benford, James; Benford, Dominic

    2010-06-01

    What would SETI beacon transmitters be like if built by civilizations that had a variety of motives but cared about cost? In a companion paper, we presented how, for fixed power density in the far field, a cost-optimum interstellar beacon system could be built. Here, we consider how we should search for a beacon if it were produced by a civilization similar to ours. High-power transmitters could be built for a wide variety of motives other than the need for two-way communication; this would include beacons built to be seen over thousands of light-years. Extraterrestrial beacon builders would likely have to contend with economic pressures just as their terrestrial counterparts do. Cost, spectral lines near 1 GHz, and interstellar scintillation favor radiating frequencies substantially above the classic "water hole." Therefore, the transmission strategy for a distant, cost-conscious beacon would be a rapid scan of the galactic plane with the intent to cover the angular space. Such pulses would be infrequent events for the receiver. Such beacons built by distant, advanced, wealthy societies would have very different characteristics from what SETI researchers seek. Future searches should pay special attention to areas along the galactic disk where SETI searches have seen coherent signals that have not recurred on the limited listening time intervals we have used. We will need to wait for recurring events that may arriarrive in intermittent bursts. Several new SETI search strategies have emerged from these ideas. We propose a new test for beacons that is based on the Life Plane hypotheses.

  20. Deep sea AUV navigation using multiple acoustic beacons

    Science.gov (United States)

    Ji, Da-xiong; Song, Wei; Zhao, Hong-yu; Liu, Jian

    2016-04-01

    Navigation is a critical requirement for the operation of Autonomous Underwater Vehicles (AUVs). To estimate the vehicle position, we present an algorithm using an extended Kalman filter (EKF) to integrate dead-reckoning position with acoustic ranges from multiple beacons pre-deployed in the operating environment. Owing to high latency, variable sound speed multipath transmissions and unreliability in acoustic measurements, outlier recognition techniques are proposed as well. The navigation algorithm has been tested by the recorded data of deep sea AUV during field operations in a variety of environments. Our results show the improved performance over prior techniques based on position computation.

  1. Molecular detection of pathogens in water--the pros and cons of molecular techniques.

    Science.gov (United States)

    Girones, Rosina; Ferrús, Maria Antonia; Alonso, José Luis; Rodriguez-Manzano, Jesus; Calgua, Byron; Corrêa, Adriana de Abreu; Hundesa, Ayalkibet; Carratala, Anna; Bofill-Mas, Sílvia

    2010-08-01

    Pollution of water by sewage and run-off from farms produces a serious public health problem in many countries. Viruses, along with bacteria and protozoa in the intestine or in urine are shed and transported through the sewer system. Even in highly industrialized countries, pathogens, including viruses, are prevalent throughout the environment. Molecular methods are used to monitor viral, bacterial, and protozoan pathogens, and to track pathogen- and source-specific markers in the environment. Molecular techniques, specifically polymerase chain reaction-based methods, provide sensitive, rapid, and quantitative analytical tools with which to study such pathogens, including new or emerging strains. These techniques are used to evaluate the microbiological quality of food and water, and to assess the efficiency of virus removal in drinking and wastewater treatment plants. The range of methods available for the application of molecular techniques has increased, and the costs involved have fallen. These developments have allowed the potential standardization and automation of certain techniques. In some cases they facilitate the identification, genotyping, enumeration, viability assessment, and source-tracking of human and animal contamination. Additionally, recent improvements in detection technologies have allowed the simultaneous detection of multiple targets in a single assay. However, the molecular techniques available today and those under development require further refinement in order to be standardized and applicable to a diversity of matrices. Water disinfection treatments may have an effect on the viability of pathogens and the numbers obtained by molecular techniques may overestimate the quantification of infectious microorganisms. The pros and cons of molecular techniques for the detection and quantification of pathogens in water are discussed. (c) 2010 Elsevier Ltd. All rights reserved.

  2. Molecular biology - Part I: Techniques, terminology, and concepts

    International Nuclear Information System (INIS)

    Brown, J. Martin

    1996-01-01

    Purpose/Objective: One of the barriers to understanding modern molecular biology is the lack of a clear understanding of the relevant terminology, techniques, and concepts. This refresher course is intended to address these deficiencies starting from a basic level. The lecture will cover many of the common uses of recombinant DNA, including gene cloning and manipulation. The goal is to enable the nonspecialist to increase his or her understanding of molecular biology in order to more fully enjoy reading current publications and/or listening seminars. Radiation biologists trying to understand a little more molecular biology should also benefit. The following concepts will be among those explained and illustrated: restriction endonucleases, gel electrophoresis, gene cloning, use of vectors such as plasmids, bacteriophage, cosmids and viruses, cDNA and genomic libraries, Southern, Northern, and Western blotting, fluorescent in situ hybridization, polymerase chain reaction (PCR), gel retardation, and reporter gene assays

  3. Molecular techniques for MRSA typing: current issues and perspectives

    Directory of Open Access Journals (Sweden)

    P. A. Trindade

    Full Text Available Staphylococcus aureus has long been recognised as an important pathogen in human disease. Serious staphylococcal infections can frequently occur in inpatients and may lead to dire consequences, especially as to therapy with antimicrobial agents. The increase in the frequency of Methicillin-Resistant Staphylococcus aureus (MRSA as the causal agent of nosocomial infection and the possibility of emergence of resistance to vancomycin demands a quick and trustworthy characterization of isolates and identification of clonal spread within hospitals. Enough information must be generated to permit the implementation of appropriate measures for control of infection, so that outbreaks can be contained. Molecular typing techniques reviewed in this manuscript include: plasmid profile analysis, analysis of chromosomal DNA after enzymatic restriction, Southern blotting, pulsed field gel electrophoresis (PFGE, techniques involving polymerase chain reaction and multilocus sequence typing (MLST. Repetitive DNA Sequence PCR (rep-PCR may be used for screening due to its practicality, low cost and reproducibility. Because of its high discriminatory power Pulsed-Field Gel Electrophoresis (PFGE still remains the gold standard for MRSA typing. New techniques with higher reproducibility and discriminatory power, such as Multi-Locus Sequence Typing (MLST, are appearing. These are mostly useful for global epidemiology studies. Molecular typing techniques are invaluable tools for the assessment of putative MRSA outbreaks and so should be extensively used for this purpose.

  4. Molecular techniques for MRSA typing: current issues and perspectives

    Directory of Open Access Journals (Sweden)

    Trindade P. A.

    2003-01-01

    Full Text Available Staphylococcus aureus has long been recognised as an important pathogen in human disease. Serious staphylococcal infections can frequently occur in inpatients and may lead to dire consequences, especially as to therapy with antimicrobial agents. The increase in the frequency of Methicillin-Resistant Staphylococcus aureus (MRSA as the causal agent of nosocomial infection and the possibility of emergence of resistance to vancomycin demands a quick and trustworthy characterization of isolates and identification of clonal spread within hospitals. Enough information must be generated to permit the implementation of appropriate measures for control of infection, so that outbreaks can be contained. Molecular typing techniques reviewed in this manuscript include: plasmid profile analysis, analysis of chromosomal DNA after enzymatic restriction, Southern blotting, pulsed field gel electrophoresis (PFGE, techniques involving polymerase chain reaction and multilocus sequence typing (MLST. Repetitive DNA Sequence PCR (rep-PCR may be used for screening due to its practicality, low cost and reproducibility. Because of its high discriminatory power Pulsed-Field Gel Electrophoresis (PFGE still remains the gold standard for MRSA typing. New techniques with higher reproducibility and discriminatory power, such as Multi-Locus Sequence Typing (MLST, are appearing. These are mostly useful for global epidemiology studies. Molecular typing techniques are invaluable tools for the assessment of putative MRSA outbreaks and so should be extensively used for this purpose.

  5. Beach Advisory and Closing Online Notification (BEACON) system

    Data.gov (United States)

    U.S. Environmental Protection Agency — Beach Advisory and Closing Online Notification system (BEACON) is a colletion of state and local data reported to EPA about beach closings and advisories. BEACON is...

  6. Improved margin utilization through the use of beacon power distribution surveillance

    International Nuclear Information System (INIS)

    Miller, R. Wade; Boyd, William A.

    2002-01-01

    Core Operations, including fuel cycle costs, can be significantly improved when state of the art surveillance techniques are employed for core power distribution monitoring. Core power distribution monitoring and Technical Specification surveillance are major operational issues at PWR's, particularly in plants with movable in core detectors. Even plants with fixed in core detectors do not always make use of the continuous data that is available. The BEACON TM system (Best Estimate Analysis of Core Operations - Nuclear) is a core monitoring and operational support package developed by Westinghouse for use in PWR plants with fixed or movable in core detectors. BEACON is a real time core monitoring system, which uses existing core instrumentation data and an on-line neutronics model to provide continuous monitored of the core power distribution information. With this information available the BEACON system can be used to continuously monitor core power margin for the plant Tech Spec surveillance requirements and for plant operational guidance

  7. The isolated Leptospira Spp. Identification by molecular biological techniques

    Directory of Open Access Journals (Sweden)

    Duangjai Suwancharoen

    2017-01-01

    Full Text Available Leptospirosis is a zoonotic disease caused by the bacteria of Leptospira spp. Identification of this bacterium relies on serotyping and genotyping. Data base for animal causative serovars in Thailand is limited. As the unknown serovars are found in the laboratory, they need to be sent overseas for referent identification. To reduce the cost, this research intended to develop a leptospiral identification method which is user–friendly and able to classify efficiently. Ten Leptospira isolations were cultured from urine samples. They were identified by three molecular biological techniques, including Pulsed-Field Gel Electrophoresis (PFGE, Variable Number Tandem Repeat (VNTR and Multilocus Sequence Typing (MLST. These methods were developed and compared to find the most suitable one for leptospiral identification. VNTR was found to be inappropriate since it could not identify the agents and it did not show the PCR product. PFGE and MLST gave the same results of the unknown 1 and 2 which were L.weilii sv Samin st Samin. Unknown 4 showed different results by each technique. Unknown 5 to 10 were likely to be L.meyeri sv Ranarum st ICF and Leptonema illini sv Illini st 3055 by PFGE but MLST could not identify the serovar. However, molecular biological technique for Leptospira identification should be done by several methods in order to confirm the result of each other.

  8. BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal M.; Alam, Intikhab; Bajic, Vladimir B.

    2015-01-01

    We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/

  9. 14 CFR 171.269 - Marker beacon performance requirements.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 3 2010-01-01 2010-01-01 false Marker beacon performance requirements. 171.269 Section 171.269 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF... Landing System (ISMLS) § 171.269 Marker beacon performance requirements. ISMLS marker beacon equipment...

  10. Doing Forensic on DTUsat-2 Using the Beacon Counter

    DEFF Research Database (Denmark)

    Fléron, René

    2016-01-01

    DTUsat-2 was launched into a Polar LEO on a Dnepr rocket out of Yasny on 19th June 2014. After the first few days of beacon recording and precise orbit determination it became apparent that all was not nominal. One notable thing was the relatively low beacon count number. The beacon count reflects...

  11. Improvement of Leukemia diagnose with molecular techniques; Mejoran diagnostico de leucemias con tecnicas moleculares

    Energy Technology Data Exchange (ETDEWEB)

    Campos Rudin, M E

    1997-07-01

    The objective of this study was to contribute with new techniques to the clinical diagnosis and to the monitoring of mycloid chronic leukemias in Costa Rica. The same one achieved to determine that is viable to apply radioactive and non reactive methodologies, for the molecular detection of the Philadelphia chromosome.It also found that the application of techniques of cellular biology, helps to classify better the mycloide leukemias and the chronic mycloproliferatives and miclodisplaced disorders. (S. Grainger) [Spanish] El objetivode este estudio fue el de aportar nuevas tecnicas al diagnostico clinico y monitoreo de las leucemias micloides cronicas en Costa Rica. El mismo logro determinar que es viable aplicar metodologias radioactivas y no radioactivas, para la deteccion molecular del cromosoma Filadelfia. Tambien encontro que la aplicacion de tecnicas de biologia celular, ayudan a clasificar mejor las leucemias mieloides y los desordenes cronicos micloproliferativos y myclodisplacicos. (S. Grainger)

  12. Solar powered aviation beacon/landing light

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-07-01

    The objective of the work was to design, develop and test Solar Powered Aviation Landing Lights/Obstruction Beacons. The entire lighting units were to be stand alone devices capable of producing their own individual power supply. The whole process was to be documented to provide insight into the processes and decisions involved. (author)

  13. An analytical model for beaconing in VANETs

    NARCIS (Netherlands)

    van Eenennaam, Martijn; Remke, Anne Katharina Ingrid; Heijenk, Geert

    2012-01-01

    IEEE 802.11 CSMA/CA is generally considered to be well-understood, and many detailed models are available. However, most models focus on Unicast in small-scale W-LAN scenarios. When modelling beaconing in VANETs, the Broadcast nature and the (potentially) large number of nodes cause phenomena

  14. Molecular genetic techniques for gene manipulation in Candida albicans.

    Science.gov (United States)

    Xu, Qiu-Rong; Yan, Lan; Lv, Quan-Zhen; Zhou, Mi; Sui, Xue; Cao, Yong-Bing; Jiang, Yuan-Ying

    2014-05-15

    Candida albicans is one of the most common fungal pathogen in humans due to its high frequency as an opportunistic and pathogenic fungus causing superficial as well as invasive infections in immunocompromised patients. An understanding of gene function in C. albicans is necessary to study the molecular basis of its pathogenesis, virulence and drug resistance. Several manipulation techniques have been used for investigation of gene function in C. albicans, including gene disruption, controlled gene expression, protein tagging, gene reintegration, and overexpression. In this review, the main cassettes containing selectable markers used for gene manipulation in C. albicans are summarized; the advantages and limitations of these cassettes are discussed concerning the influences on the target gene expression and the virulence of the mutant strains.

  15. 76 FR 17625 - Proposed Information Collection; Comment Request; Emergency Beacon Registrations

    Science.gov (United States)

    2011-03-30

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration Proposed Information Collection; Comment Request; Emergency Beacon Registrations AGENCY: National Oceanic and Atmospheric... emergency radio beacon. Persons purchasing a digital distress beacon, operating in the frequency range of...

  16. Localization with a mobile beacon in underwater acoustic sensor networks.

    Science.gov (United States)

    Lee, Sangho; Kim, Kiseon

    2012-01-01

    Localization is one of the most important issues associated with underwater acoustic sensor networks, especially when sensor nodes are randomly deployed. Given that it is difficult to deploy beacon nodes at predetermined locations, localization schemes with a mobile beacon on the sea surface or along the planned path are inherently convenient, accurate, and energy-efficient. In this paper, we propose a new range-free Localization with a Mobile Beacon (LoMoB). The mobile beacon periodically broadcasts a beacon message containing its location. Sensor nodes are individually localized by passively receiving the beacon messages without inter-node communications. For location estimation, a set of potential locations are obtained as candidates for a node's location and then the node's location is determined through the weighted mean of all the potential locations with the weights computed based on residuals.

  17. Localization with a Mobile Beacon in Underwater Acoustic Sensor Networks

    Directory of Open Access Journals (Sweden)

    Sangho Lee

    2012-04-01

    Full Text Available Localization is one of the most important issues associated with underwater acoustic sensor networks, especially when sensor nodes are randomly deployed. Given that it is difficult to deploy beacon nodes at predetermined locations, localization schemes with a mobile beacon on the sea surface or along the planned path are inherently convenient, accurate, and energy-efficient. In this paper, we propose a new range-free Localization with a Mobile Beacon (LoMoB. The mobile beacon periodically broadcasts a beacon message containing its location. Sensor nodes are individually localized by passively receiving the beacon messages without inter-node communications. For location estimation, a set of potential locations are obtained as candidates for a node’s location and then the node’s location is determined through the weighted mean of all the potential locations with the weights computed based on residuals.

  18. High-visibility infrared beacons for IFF and combat ID

    Science.gov (United States)

    Pralle, Martin; Puscasu, Irina; Johnson, Edward; Loges, Peter; Melnyk, James

    2005-05-01

    A new kind of Identification Friend or Foe (IFF) infrared beacon has been demonstrated. The omni-directional beacon consists of a pyramidal array of 1W pulsIR thermal light sources. Operating at a total power of 84W, the beacon can be used to track and identify surface vehicles and personnel with a recognition range of up to 6 miles on the battlefield and in urban environments or the marine boundary layer. Advanced photonic technology enables the beacon to be seen only while using a 3-5 μm or 8-12 μm thermal imaging system. There is no visible or near-IR emission to betray the location of the beacon. The beacon is rugged and will operate from -40 to 50°C ambient temperature, 0-100% relative humidity, 0 - 10,000 ft altitude, and meets MIL-STD 810F and MIL-STD 461E.

  19. Determination of molecular parameters by electron collisions and laser techniques

    International Nuclear Information System (INIS)

    Colon, C.

    1989-01-01

    In this work a general procedure to study diatomic molecules in intermediate coupling scheme has been developed. This study allows to obtain expressions to calculate molecular line strengths and rotational transition intensities. These results are used in a numerical program to synthetize vibrational and rotational band spectra of any diatomic molecule. With this technique the experimental spectra of the first negative system of N 2 + and the fist positive system of N 2 are reproduced theoretically and it is possible to deduce its electronic transition moments values by comparison. Also the method has been applied to compare the synthetized bands with the experimental spectra of the B O u + -- x 1 Σ g + system of Au 2 and the A 2 Σ--- x 2 π system of OH. From these comparison band intensities and electronic moments can be deduced. The branching ratio method to measure the relative spectral response in the 1100-1560 A o =wavelength range of a vacuum uv monochromator has been used. Relative intensity of rotational lines with origine in a common upper vibrational-rotational level of Warner and Lyman systems of H 2 , have been measured. Also in this work, the deexcitation of the B 3 π + (0 + u ), v'=14 level of I 2 after pulsed laser excitation has been studied. The quenching cross sections by collisions with I 2 , H 2 , CO 2 and CH 4 have been determin-ed. (Author)

  20. Photoionization of excited molecular states using multiphoton excitation techniques

    International Nuclear Information System (INIS)

    Dehmer, P.M.; Pratt, S.T.; Dehmer, J.L.

    1984-01-01

    Photoelectron spectra are reported for three photon resonant, four photon ionization of H 2 via the B 1 Σ/sub u/ + , v = 7 (J = 2,4) and C 1 π/sub u'/, v = 0-4 (J = 1) levels and of N 2 via the o 3 1 π/sub u'/, v = 1,2, b 1 π/sub u'/, v = 3-5, and c 1 π/sub u'/, v = 0 levels. The results reflect both the spectroscopy and the dynamics of photoionization of excited molecular states and are discussed in terms of the selection rules for photoionization and the relative probabilities of photoionization from Rydberg and valence states. In some cases, in accordance with the Franck-Condon principle, the results demonstrate that resonant multiphoton ionization through Rydberg states may be a powerful technique for the production of electronic, vibrational, and rotational state selected ions. However, in other cases, systematic departures from Franck-Condon factors are observed, which reflect the more subtle dynamics of excited state photoionization. 23 references, 6 figures, 2 tables

  1. Photoionization of excited molecular states using multiphoton excitation techniques

    International Nuclear Information System (INIS)

    Dehmer, P.M.; Pratt, S.T.; Dehmer, J.L.

    1984-01-01

    Photoelectron spectra are reported for three photon resonant, four photon ionization of H 2 via the B 1 Σ + /sub u/, v = 7 (J = 2,4) and C 1 Pi/sub u/, v = 0-4 (J = 1) levels and of N 2 via the o 3 1 Pi/sub u/, v = 1,2, b 1 Pi/sub u/, v = 3-5, and c 1 Pi/sub u/, v = 0 levels. The results reflect both the spectroscopy and the dynamics of photoionization of excited molecular states and are discussed in terms of the selection rules for photoionization and the relative probabilities of photoionization from Rydberg and valence states. In some cases, in accordance with the Franck-Condon principle, the results demonstrate that resonant multiphoton ionization through Rydberg states may be a powerful technique for the production of electronic, vibrational, and rotational state selected ions. However, in other cases, systematic departures from Franck-Condon factors are observed, which reflect the more subtle dynamics of excited state photoionization

  2. [Molecular techniques applied in species identification of Toxocara].

    Science.gov (United States)

    Fogt, Renata

    2006-01-01

    Toxocarosis is still an important and actual problem in human medicine. It can manifest as visceral (VLM), ocular (OLM) or covert (CT) larva migrans syndroms. Complicated life cycle of Toxocara, lack of easy and practical methods of species differentiation of the adult nematode and embarrassing in recognition of the infection in definitive hosts create difficulties in fighting with the infection. Although studies on human toxocarosis have been continued for over 50 years there is no conclusive answer, which of species--T. canis or T. cati constitutes a greater risk of transmission of the nematode to man. Neither blood serological examinations nor microscopic observations of the morphological features of the nematode give the satisfied answer on the question. Since the 90-ths molecular methods were developed for species identification and became useful tools being widely applied in parasitological diagnosis. This paper cover the survey of methods of DNA analyses used for identification of Toxocara species. The review may be helpful for researchers focused on Toxocara and toxocarosis as well as on detection of new species. The following techniques are described: PCR (Polymerase Chain Reaction), RFLP (Restriction Fragment Length Polymorphism), RAPD (Random Amplified Polymorphic DNA) and SSCP (Single Strand Conformation Polymorphism).

  3. Mechanical Properties of Nanostructured Materials Determined Through Molecular Modeling Techniques

    Science.gov (United States)

    Clancy, Thomas C.; Gates, Thomas S.

    2005-01-01

    The potential for gains in material properties over conventional materials has motivated an effort to develop novel nanostructured materials for aerospace applications. These novel materials typically consist of a polymer matrix reinforced with particles on the nanometer length scale. In this study, molecular modeling is used to construct fully atomistic models of a carbon nanotube embedded in an epoxy polymer matrix. Functionalization of the nanotube which consists of the introduction of direct chemical bonding between the polymer matrix and the nanotube, hence providing a load transfer mechanism, is systematically varied. The relative effectiveness of functionalization in a nanostructured material may depend on a variety of factors related to the details of the chemical bonding and the polymer structure at the nanotube-polymer interface. The objective of this modeling is to determine what influence the details of functionalization of the carbon nanotube with the polymer matrix has on the resulting mechanical properties. By considering a range of degree of functionalization, the structure-property relationships of these materials is examined and mechanical properties of these models are calculated using standard techniques.

  4. Aircraft Position Measurement Using Laser Beacon Optics.

    Science.gov (United States)

    1981-01-01

    8217Comparison of Solar Concentrators .’ Solar Energy, Vol. 10, p. 93, 1976. 7. Winston , R., ’Light Collection Within the Framework of Goemetrical Optics ...8217 J. Optical Society of Am., Vol. 60, p. 245, 1970. 8. Welford, W. T., tics of Nonimaging Concentrators . New York, Academic Press, T978. 9. Bracewell...helicopter pilot and the flight engineer on board the YO-3A. This thesis will concentrate on the development of the laser beacon, the detector optics

  5. Development of a universal RNA beacon for exogenous gene detection.

    Science.gov (United States)

    Guo, Yuanjian; Lu, Zhongju; Cohen, Ira Stephen; Scarlata, Suzanne

    2015-05-01

    Stem cell therapy requires a nontoxic and high-throughput method to achieve a pure cell population to prevent teratomas that can occur if even one cell in the implant has not been transformed. A promising method to detect and separate cells expressing a particular gene is RNA beacon technology. However, developing a successful, specific beacon to a particular transfected gene can take months to develop and in some cases is impossible. Here, we report on an off-the-shelf universal beacon that decreases the time and cost of applying beacon technology to select any living cell population transfected with an exogenous gene. ©AlphaMed Press.

  6. Quantum chemical approaches: semiempirical molecular orbital and hybrid quantum mechanical/molecular mechanical techniques.

    Science.gov (United States)

    Bryce, Richard A; Hillier, Ian H

    2014-01-01

    The use of computational quantum chemical methods to aid drug discovery is surveyed. An overview of the various computational models spanning ab initio, density function theory, semiempirical molecular orbital (MO), and hybrid quantum mechanical (QM)/molecular mechanical (MM) methods is given and their strengths and weaknesses are highlighted, focussing on the challenge of obtaining the accuracy essential for them to make a meaningful contribution to drug discovery. Particular attention is given to hybrid QM/MM and semiempirical MO methods which have the potential to yield the necessary accurate predictions of macromolecular structure and reactivity. These methods are shown to have advanced the study of many aspects of substrate-ligand interactions relevant to drug discovery. Thus, the successful parametrization of semiempirical MO methods and QM/MM methods can be used to model noncovalent substrate-protein interactions, and to lead to improved scoring functions. QM/MM methods can be used in crystal structure refinement and are particularly valuable for modelling covalent protein-ligand interactions and can thus aid the design of transition state analogues. An extensive collection of examples from the areas of metalloenzyme structure, enzyme inhibition, and ligand binding affinities and scoring functions are used to illustrate the power of these techniques.

  7. Molecular Genetics Techniques to Develop New Treatments for Brain Cancers

    Energy Technology Data Exchange (ETDEWEB)

    Fox, Jacob; Fathallan-Shaykh, Hassan

    2006-09-22

    The objectives of this report are: (1) to devise novel molecular gene therapies for malignant brain tumors, (2) advance our understanding of the immune system in the central nervous system; and (3) apply genomics to find molecular probes to diagnose brain tumors, predict prognosis, biological behavior and their response to treatment.

  8. Molecular techniques: An overview of methods for the detection of ...

    African Journals Online (AJOL)

    Several DNA molecular markers are now available for use in surveillance and investigation of food-borne outbreaks that were previously difficult to detect. The results from several sources of literature indicate substantially different degrees of sensitivities between conventional detection methods and molecular-based ...

  9. Assessment of Knowledge of Participants on Basic Molecular Biology Techniques after 5-Day Intensive Molecular Biology Training Workshops in Nigeria

    Science.gov (United States)

    Yisau, J. I.; Adagbada, A. O.; Bamidele, T.; Fowora, M.; Brai, B. I. C.; Adebesin, O.; Bamidele, M.; Fesobi, T.; Nwaokorie, F. O.; Ajayi, A.; Smith, S. I.

    2017-01-01

    The deployment of molecular biology techniques for diagnosis and research in Nigeria is faced with a number of challenges, including the cost of equipment and reagents coupled with the dearth of personnel skilled in the procedures and handling of equipment. Short molecular biology training workshops were conducted at the Nigerian Institute of…

  10. Topical MMP beacon enabled fluorescence-guided resection of oral carcinoma

    Science.gov (United States)

    Burgess, Laura; Chen, Juan; Wolter, Nikolaus E.; Wilson, Brian; Zheng, Gang

    2016-01-01

    Each year almost 300,000 individuals worldwide are diagnosed with oral cancer, more than 90% of these being oral carcinoma [N. Engl. J. Med. 328, 184 19938417385]. Surgical resection is the standard of care, but accurate delineation of the tumor boundaries is challenging, resulting in either under-resection with risk of local recurrence or over-resection with increased functional loss and negative impact on quality of life. This study evaluates, in two pre-clinical in vivo tumor models, the potential of fluorescence-guided resection using molecular beacons activated by metalloproteinases, which are frequently upregulated in human oral cancer. In both models there was rapid (beacon activation upon local application, allowing clear fluoresecence imaging in vivo and confirmed by ex vivo fluorescence microscopy and HPLC, with minimal activation in normal oral tissues. Although the tissue penetration was limited using topical application, these findings support further development of this approach towards translation to first-in-human trials. PMID:27231609

  11. Beach Advisory and Closing Online Notification (BEACON) system

    Science.gov (United States)

    Beach Advisory and Closing Online Notification system (BEACON) is a colletion of state and local data reported to EPA about beach closings and advisories. BEACON is the public-facing query of the Program tracking, Beach Advisories, Water quality standards, and Nutrients database (PRAWN) which tracks beach closing and advisory information.

  12. Element selective detection of molecular species applying chromatographic techniques and diode laser atomic absorption spectrometry.

    Science.gov (United States)

    Kunze, K; Zybin, A; Koch, J; Franzke, J; Miclea, M; Niemax, K

    2004-12-01

    Tunable diode laser atomic absorption spectroscopy (DLAAS) combined with separation techniques and atomization in plasmas and flames is presented as a powerful method for analysis of molecular species. The analytical figures of merit of the technique are demonstrated by the measurement of Cr(VI) and Mn compounds, as well as molecular species including halogen atoms, hydrogen, carbon and sulfur.

  13. Recent progress in satellite radio beacon studies with particular emphasis on the ATS-6 radio beacon experiment

    International Nuclear Information System (INIS)

    Davies, K.

    1980-01-01

    In May 1974 a new era in satellite radio beacon studies of the ionosphere opened with the ATS-6 Radio Beacon Experiment. The history of radio beacon studies up to that time is reviewed briefly and the particular features of the ATS-6 beacon are discussed together with the basic theory required to interpret the measurements. The main emphasis is on the ATS-6 beacon experiment but other beacon data are discussed which provide the necessary background. The diurnal and seasonal variations of the total electron content and the plasmaspheric content are presented for the U.S.A. and Europe. In winter the plasmaspheric content over the Western Hemisphere maximizes at night while in Europe and the Pacific it appears to peak near noon. This is thought to be caused by flow of plasma from the local and conjugate ionospheres. Night maxima of total electron content are found showing that they do not arise from depletions of the plasmaspheric content. The plasmaspheric content is highly sensitive to solar-terrestrial disturbance, it reaches a minimum on the third day of a storm and may take between 10 and 20 days of partial filling and emptying to recover. Travelling disturbances in U.S.A., Europe, and India show similarities of speeds but not of direction. Beacon observations of micropulsations in total content, tropospheric fluctuations and Fresnel diffraction by intense ionospheric irregularities are discussed together with radio wave scintillations and some applications of beacon radio data to communications and navigation. (orig.)

  14. 76 FR 65216 - Beacon Medical Services, LLC, Aurora, CO; Notice of Negative Determination Regarding Application...

    Science.gov (United States)

    2011-10-20

    ... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-80,219] Beacon Medical Services... workers and former workers of Beacon Medical Services, LLC, Aurora, Colorado (Beacon Medical Services... published in the Federal Register on July 8, 2011 (76 FR 40401). The workers of Beacon Medical Services are...

  15. 78 FR 75392 - American Beacon Funds, et al.; Notice of Application

    Science.gov (United States)

    2013-12-11

    ... Asset Management LLC; (b) American Beacon Balanced Fund--the Manager, Barrow, Hanley, Mewhinney... Beacon Funds, et al.; Notice of Application December 5, 2013. AGENCY: Securities and Exchange Commission...) (order). Applicants: American Beacon Funds and American Beacon Select Funds (collectively, the ``Trusts...

  16. Using current molecular techniques for rapid differentiation of ...

    African Journals Online (AJOL)

    Typhoid fever is responsible for the deaths of many people annually. However, conventional and timeconsuming detection methods for Salmonella Typhi still dominate. By using a molecular based approach, it was possible to identify Salmonella Typhi by amplifying two specific genes (viaB and tyv) and by using RFLP ...

  17. Do rufous hummingbirds (Selasphorus rufus) use visual beacons?

    Science.gov (United States)

    Hurly, T Andrew; Franz, Simone; Healy, Susan D

    2010-03-01

    Animals are often assumed to use highly conspicuous features of a goal to head directly to that goal ('beaconing'). In the field it is generally assumed that flowers serve as beacons to guide pollinators. Artificial hummingbird feeders are coloured red to serve a similar function. However, anecdotal reports suggest that hummingbirds return to feeder locations in the absence of the feeder (and thus the beacon). Here we test these reports for the first time in the field, using the natural territories of hummingbirds and manipulating flowers on a scale that is ecologically relevant to the birds. We compared the predictions from two distinct hypotheses as to how hummingbirds might use the visual features of rewards: the distant beacon hypothesis and the local cue hypothesis. In two field experiments, we found no evidence that rufous hummingbirds used a distant visual beacon to guide them to a rewarded location. In no case did birds abandon their approach to the goal location from a distance; rather they demonstrated remarkable accuracy of navigation by approaching to within about 70 cm of a rewarded flower's original location. Proximity varied depending on the size of the training flower: birds flew closer to a previously rewarded location if it had been previously signalled with a small beacon. Additionally, when provided with a beacon at a new location, birds did not fly directly to the new beacon. Taken together, we believe these data demonstrate that these hummingbirds depend little on visual characteristics to beacon to rewarded locations, but rather that they encode surrounding landmarks in order to reach the goal and then use the visual features of the goal as confirmation that they have arrived at the correct location.

  18. Assessment of knowledge of participants on basic molecular biology techniques after 5-day intensive molecular biology training workshops in Nigeria.

    Science.gov (United States)

    Yisau, J I; Adagbada, A O; Bamidele, T; Fowora, M; Brai, B I C; Adebesin, O; Bamidele, M; Fesobi, T; Nwaokorie, F O; Ajayi, A; Smith, S I

    2017-07-08

    The deployment of molecular biology techniques for diagnosis and research in Nigeria is faced with a number of challenges, including the cost of equipment and reagents coupled with the dearth of personnel skilled in the procedures and handling of equipment. Short molecular biology training workshops were conducted at the Nigerian Institute of Medical Research (NIMR), to improve the knowledge and skills of laboratory personnel and academics in health, research, and educational facilities. Five-day molecular biology workshops were conducted annually between 2011 and 2014, with participants drawn from health, research facilities, and the academia. The courses consisted of theoretical and practical sessions. The impact of the workshops on knowledge and skill acquisition was evaluated by pre- and post-tests which consisted of 25 multiple choice and other questions. Sixty-five participants took part in the workshops. The mean knowledge of molecular biology as evaluated by the pre- and post-test assessments were 8.4 (95% CI 7.6-9.1) and 13.0 (95 CI 11.9-14.1), respectively. The mean post-test score was significantly greater than the mean pre-test score (p biology workshop significantly increased the knowledge and skills of participants in molecular biology techniques. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):313-317, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  19. Determining the stereochemical structures of molecular ions by ''Coulomb-explosion'' techniques with fast (MeV) molecular ion beams

    International Nuclear Information System (INIS)

    Gemmell, D.S.

    1980-01-01

    Recent studies on the dissociation of fast (MeV) molecular ion beams in thin foils suggest a novel alternative approach to the determination of molecular ion structures. In this article we review some recent high-resolution studies on the interactions of fast molecular ion beams with solid and gaseous targets and indicate how such studies may be applied to the problem of determining molecular ion structures. The main features of the Coulomb explosion of fast-moving molecular ion projectiles and the manner in which Coulomb-explosion techniques may be applied to the problem (difficult to attack by more conventional means) of determining the stereochemical structures of molecular ions has been described in this paper. Examples have been given of early experiments designed to elicit structure information. The techniques are still in their infancy, and it is to be expected that as both the technology and the analysis are refined, the method will make valuable contributions to the determination of molecular ion structures

  20. Snapshot analysis for rhodium fixed incore detector using BEACON methodology

    International Nuclear Information System (INIS)

    Cha, Kyoon Ho; Choi, Yu Sun; Lee, Eun Ki; Park, Moon Ghu; Morita, Toshio; Heibel, Michael D.

    2004-01-01

    The purpose of this report is to process the rhodium detector data of the Yonggwang nuclear unit 4 cycle 5 core for the measured power distribution by using the BEACON methodology. Rhodium snapshots of the YGN 4 cycle 5 have been analyzed by both BEACON/SPINOVA and CECOR to compare the results of both codes. By analyzing a large number of snapshots obtained during normal plant operation. Reviewing the results of this analysis, the BEACON/SPNOVA can be used for the snapshot analysis of Korean Standard Nuclear Power (KSNP) plants

  1. BEACON TSM application system to the operation of PWR reactors

    International Nuclear Information System (INIS)

    Lozano, J. A.; Mildrum, C.; Serrano, J. F.

    2012-01-01

    BEACON-TSM is an advanced core monitoring system for PWR reactor cores, and also offers the possibility to perform a wide range of predictive calculation in support of reactor operation. BEACON-TSM is presently installed and licensed in the 5 Spanish PWR reactors of standard Westinghouse design. the purpose of this paper is to describe the features of this software system and to show the advantages obtainable by a nuclear power plant from its use. To illustrate the capabilities and benefits of BEACON-TSM two real case reactor operating situations are presented. (Author)

  2. Beacon-S TM: Non-uniform attenuation correction for SPECT imaging. The new medium-energy transmission device for AXIS and IRIX

    International Nuclear Information System (INIS)

    Daniel Gagnon, D.

    1999-01-01

    The paper presents new medium-energy transmission device for SPECT imaging. Beacon-S includes a 356-keV medium energy 133 Ba source with a 10.54-year half-life. Beacon-S provide high-resolution and high-contrast transmission scans. The higher energy of the gamma substantially improves the transmission contrast for larger patients by virtue of better penetration through the body

  3. Using "Pseudomonas Putida xylE" Gene to Teach Molecular Cloning Techniques for Undergraduates

    Science.gov (United States)

    Dong, Xu; Xin, Yi; Ye, Li; Ma, Yufang

    2009-01-01

    We have developed and implemented a serial experiment in molecular cloning laboratory course for undergraduate students majored in biotechnology. "Pseudomonas putida xylE" gene, encoding catechol 2, 3-dioxygenase, was manipulated to learn molecular biology techniques. The integration of cloning, expression, and enzyme assay gave students…

  4. Increased dose near the skin due to electromagnetic surface beacon transponder.

    Science.gov (United States)

    Ahn, Kang-Hyun; Manger, Ryan; Halpern, Howard J; Aydogan, Bulent

    2015-05-08

    The purpose of this study was to evaluate the increased dose near the skin from an electromagnetic surface beacon transponder, which is used for localization and tracking organ motion. The bolus effect due to the copper coil surface beacon was evaluated with radiographic film measurements and Monte Carlo simulations. Various beam incidence angles were evaluated for both 6 MV and 18 MV experimentally. We performed simulations using a general-purpose Monte Carlo code MCNPX (Monte Carlo N-Particle) to supplement the experimental data. We modeled the surface beacon geometry using the actual mass of the glass vial and copper coil placed in its L-shaped polyethylene terephthalate tubing casing. Film dosimetry measured factors of 2.2 and 3.0 enhancement in the surface dose for normally incident 6 MV and 18 MV beams, respectively. Although surface dose further increased with incidence angle, the relative contribution from the bolus effect was reduced at the oblique incidence. The enhancement factors were 1.5 and 1.8 for 6 MV and 18 MV, respectively, at an incidence angle of 60°. Monte Carlo simulation confirmed the experimental results and indicated that the epidermal skin dose can reach approximately 50% of the dose at dmax at normal incidence. The overall effect could be acceptable considering the skin dose enhancement is confined to a small area (~ 1 cm2), and can be further reduced by using an opposite beam technique. Further clinical studies are justified in order to study the dosimetric benefit versus possible cosmetic effects of the surface beacon. One such clinical situation would be intact breast radiation therapy, especially large-breasted women.

  5. Studies of molecular dynamics with neutron scattering techniques. Part of a coordinated programme on neutron scattering techniques

    International Nuclear Information System (INIS)

    Vinhas, L.A.

    1980-05-01

    Molecular dynamics was studied in samples of tert-butanol, cyclohexanol and methanol, using neutron inelastic and quasi-elastic techniques. The frequency spectra of cyclohexanol in crystalline phase were interpreted by assigning individual energy peaks to hindered rotation of molecules, lattice vibration, hydrogen bond stretching and ring bending modes. Neutron quasi-elastic scattering measurements permitted the testing of models for molecular diffusion as a function of temperature. The interpretation of neutron incoherent inelastic scattering on methanol indicated the different modes of molecular dynamics in this material; individual inelastic peaks in the spectra could be assigned to vibrations of crystalline lattice, stretching of hydrogen bond and vibrational and torsional modes of CH 3 OH molecule. The results of the experimental work on tertbutanol indicate two distinct modes of motion in this material: individual molecular librations are superposed to a cooperative rotation diffusion which occurs both in solid and in liquid state

  6. [Etiologic diagnosis in meningitis and encephalitis molecular biology techniques].

    Science.gov (United States)

    Conca, Natalia; Santolaya, María Elena; Farfan, Mauricio J; Cofré, Fernanda; Vergara, Alejandra; Salazar, Liliana; Torres, Juan Pablo

    2016-01-01

    The aetiological study of infections of the central nervous system has traditionally been performed using bacterial cultures and, more recently, using polymerase chain reaction (PCR) for herpes simplex virus (HSV). Bacterial cultures may not have good performance, especially in the context of patients who have received antibiotics prior to sampling, and a request for HSV only by PCR reduces the information to only one aetiological agent. The aim of this study is to determine the infectious causes of meningitis and encephalitis, using traditional microbiology and molecular biology to improve the aetiological diagnosis of these diseases. A prospective study was conducted on 19 patients with suspected meningitis, admitted to the Luis Calvo Mackenna Hospital in Santiago, Chile, from March 1, 2011 to March 30, 2012. After obtaining informed consent, the CSF samples underwent cytochemical study, conventional culture, multiplex PCR for the major producing bacterial meningitis (N. meningitidis, S. pneumoniae, H. influenzae), real-time single PCR for HSV-1 and 2, VZV, EBV, CMV, HHV-6 and enterovirus. Clinical and epidemiological data were also collected from the clinical records. Of the 19 patients analysed, 2 were diagnosed by conventional methods and 7 by adding molecular biology (increase to 37%). Three patients had meningitis due to S. pneumoniae, one due to Enterobacter cloacae, 2 patients meningoencephalitis HSV-1, and one VZV meningitis. The addition of PCR to conventional diagnostic methods in CNS infections increases the probability of finding the causal agent. This allows a more adequate, timely and rational management of the disease. Copyright © 2014. Publicado por Elsevier España, S.L.U.

  7. Evaluation of light-emitting diode beacon light fixtures.

    Science.gov (United States)

    2009-12-01

    Rotating beacons containing filament light sources have long been used on highway maintenance trucks : to indicate the presence of the truck to other drivers. Because of advances in light-emitting diode (LED) : technologies, flashing lights containin...

  8. Evaluation of BEACON-COLSS Core Monitoring System Benefits

    International Nuclear Information System (INIS)

    Kim, Joon Sung; Park, Young Ho; Morita, Toshio; Book, Michael A.

    2005-01-01

    In Korean Standard Nuclear Power Plant COLSS (Core Operating Limit Supervisory System) is used to monitor the DNBR Power Operating Limit (DNBRPOL) and Linear Heat Rate POL (KWPFPOL). Westinghouse and KNFC have developed an upgraded core monitoring system by combining the BEACON TM core monitoring system 1 (Best Estimate Analyzer for Core Operation . Nuclear) and COLSS into an integrated product that is called BEACON-COLSS. BEACON-COLSS generates the 3-D power distribution corrected by the in-core detectors measurements. The 3-D core power distribution methodology in BEACON-COLSS is significantly better than the synthesis methodology in COLSS. BEACONCOLSS uses the CETOP-D 2 thermal hydraulic code instead of CETOP-1. CETOP-D is a multi-channel thermal hydraulics code that will provide more accurate DNBR calculations than the DNBR calculators currently used in COLSS

  9. Pedestrian hybrid beacon guide : recommendations and case study.

    Science.gov (United States)

    2014-01-01

    A pedestrian hybrid beacon (PHB) is a traffic control : device similar to a European pedestrian signal : (PELICAN) that was imported to the US and adapted by : engineers in Arizona to increase motorists awareness of : pedestrian crossings at uncon...

  10. Detecting Molecular Properties by Various Laser-Based Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hsin, Tse-Ming [Iowa State Univ., Ames, IA (United States)

    2007-01-01

    Four different laser-based techniques were applied to study physical and chemical characteristics of biomolecules and dye molecules. These techniques are liole burning spectroscopy, single molecule spectroscopy, time-resolved coherent anti-Stokes Raman spectroscopy and laser-induced fluorescence microscopy. Results from hole burning and single molecule spectroscopy suggested that two antenna states (C708 & C714) of photosystem I from cyanobacterium Synechocystis PCC 6803 are connected by effective energy transfer and the corresponding energy transfer time is ~6 ps. In addition, results from hole burning spectroscopy indicated that the chlorophyll dimer of the C714 state has a large distribution of the dimer geometry. Direct observation of vibrational peaks and evolution of coumarin 153 in the electronic excited state was demonstrated by using the fs/ps CARS, a variation of time-resolved coherent anti-Stokes Raman spectroscopy. In three different solvents, methanol, acetonitrile, and butanol, a vibration peak related to the stretch of the carbonyl group exhibits different relaxation dynamics. Laser-induced fluorescence microscopy, along with the biomimetic containers-liposomes, allows the measurement of the enzymatic activity of individual alkaline phosphatase from bovine intestinal mucosa without potential interferences from glass surfaces. The result showed a wide distribution of the enzyme reactivity. Protein structural variation is one of the major reasons that are responsible for this highly heterogeneous behavior.

  11. A heuristic evaluation of the Facebook's advertising tool beacon

    OpenAIRE

    Jamal, A; Cole, M

    2009-01-01

    Interface usability is critical to the successful adoption of information systems. The aim of this study is to evaluate interface of Facebook's advertising tool Beacon by using privacy heuristics [4]. Beacon represents an interesting case study because of the negative media and user backlash it received. The findings of heuristic evaluation suggest violation of privacy heuristics [4]. Here, analysis identified concerns about user choice and consent, integrity and security of data, and awarene...

  12. Beacon-Colss core monitoring system application and benefits

    International Nuclear Information System (INIS)

    Boyd, W.A.; Yoon, T.Y.

    2005-01-01

    Westinghouse and KNFC are creating an upgraded core monitoring system by merging the BEACON system (best estimate analyzer for core operation-nuclear) and COLSS (core operating limit supervisory system) into an integrated product. Although both BEACON and COLSS are core monitoring systems that have been in operation at many plants for a number of years, they each have some features and capabilities that are not in the other. Therefore it has been decided to incorporate portions of COLSS into the beacon system to create an optional level to support core monitoring applications on selected combustion engineering (C-E) designed plants. This optional level in the beacon system will be called BEACON-COLSS and will allow the beacon system to monitor the LCO's and Tech Spec limits at CE plants that currently use COLSS. This paper will present the structure of the new core monitoring system and the benefits it achieves for current COLSS plants, i.e., CE plants in the US and KSNP (Korean standard nuclear power plant). (authors)

  13. Detection of multidrug resistance using molecular nuclear technique

    International Nuclear Information System (INIS)

    Lee, Jae Tae; Ahn, Byeong Cheol

    2004-01-01

    Although the outcome of cancer patients after cytotoxic chemotherapy is related diverse mechanisms, multidrug resistance (MDR) for chemotherapeutic drugs due to cellular P-glycoprotein (Pgp) or multidrug-resistance associated protein (MRP) is most important factor in the chemotherapy failure to cancer. A large number of pharmacologic compounds, including verapamil, quinidine, tamoxifen, cyclosporin A and quinolone derivatives have been reported to overcome MDR. Single photon emission computed tomography (SPECT) and positron emission tomography (PET) are available for the detection of Pgp and MRP-mediated transporter. 99 m-Tc-MIBI and other 99 m-Tc-radiopharmaceuticals are substrates for Pgp and MRP, and have been used in clinical studies for tumor imaging, and to visualize blockade of Pgp-mediated transport after modulation of Pgp pump. Colchicine, verapamil and daunorubicin labeled with 11 C have been evaluated for the quantification of Pgp-mediated transport with PET in vivo and reported to be feasible substrates with which to image Pgp function in tumors. Leukotrienes are specific substrates for MRP and N-( 11 C)acetyl-leukotriene E4 provides an opportunity to study MRP function non-invasively in vivo. SPECT and PET pharmaceuticals have successfully used to evaluate pharmacologic effects of MDR modulators. Imaging of MDR and reversal of MDR with bioluminescence in a living animal is also evaluated for future clinical trial. We have described recent advances in molecular imaging of MDR and reviewed recent publications regarding feasibility of SPECT and PET imaging to study the functionality of MDR transporters in vivo

  14. Utility of the molecular biology techniques to the analytical control of the microbiological quality of waters

    International Nuclear Information System (INIS)

    Codony, F.; Martin Perez, L.; Morato, J.; Dominguez Gual, M. C.

    2009-01-01

    The molecular biology techniques made accessible to the water industry the ability to detect and quantify, in a few hours, any organism known. given this scenario, it is important to realize the strengths and weaknesses of these techniques to get a better picture of the scope of its implementation and its most that probably usefulness. We must be familiar with these techniques to understand the results and properly evaluate its detection limit. (Author) 4 refs.

  15. Status of biotechnology with emphasis on molecular techniques for mutation breeding in the Philippines

    Energy Technology Data Exchange (ETDEWEB)

    Lapade, A.G.; Nazarea, T.Y.; Veluz, A.M.S.; Marbella, L.J.; Nato, A.Q.; Coloma, C.B. Jr.; Asencion, A.B. [Philippine Nuclear Research Institute, Commonwealth Avenue, Quezon (Philippines)

    2002-02-01

    This paper summarizes the status of biotechnology with emphasis on molecular techniques for plant breeding in the Philippines. Several molecular and in-vitro culture techniques are integrated in plant breeding for crop improvement at PNRI, UPLB, IRRI and PhilRice. At IRRI, PCR techniques, RFLP and RAPD, PCR techniques, RFLP and RAPD were developed to establish high density molecular maps, determine breadth and diversity of germplasm and characterize alien introgression. The molecular maps have identified DNA sequence of resistance genes of HYVs and NPTs to abiotic and biotic stresses, the major achievement is the development of high density molecular maps in rice with at least 2000 markers. The biotechnology program at PhilRice for varietal improvement includes: (1) utilization of molecular marker technology such gene mapping of desired traits in rice, analysis of genetic relationships of germplasm materials and breeding lines through DNA fingerprinting and genetic diversity studies and development and application of marker aided selection for disease resistance (RTD and BLB); (2) application of in-vitro techniques in the development of lines with tolerance to adverse conditions; (3) molecular cloning of important genes for RTD resistance; (4) genetic transformation for male sterility and resistance to sheath blight and stem borers; and (5) transfer of disease resistance from wild species to cultivated varieties. In IPB, molecular markers:microsatellites or SSR, AFLP and RGA are being used for mapping and diversity studies in coconut, mango, banana, mungbean, corn and tomato. Mutation breeding at PNRI using gamma radiation has resulted in the development of crop varieties with desirable traits. The use of AFLP coupled to PCR is being used to study polymorphism in plant variants of radiation-induced mutants of rice, pineapple and ornamentals. (author)

  16. Practical Fingerprinting Localization for Indoor Positioning System by Using Beacons

    Directory of Open Access Journals (Sweden)

    Santosh Subedi

    2017-01-01

    Full Text Available Recent developments in the fields of smartphones and wireless communication technologies such as beacons, Wi-Fi, and ultra-wideband have made it possible to realize indoor positioning system (IPS with a few meters of accuracy. In this paper, an improvement over traditional fingerprinting localization is proposed by combining it with weighted centroid localization (WCL. The proposed localization method reduces the total number of fingerprint reference points over the localization space, thus minimizing both the time required for reading radio frequency signals and the number of reference points needed during the fingerprinting learning process, which eventually makes the process less time-consuming. The proposed positioning has two major steps of operation. In the first step, we have realized fingerprinting that utilizes lightly populated reference points (RPs and WCL individually. Using the location estimated at the first step, WCL is run again for the final location estimation. The proposed localization technique reduces the number of required fingerprint RPs by more than 40% compared to normal fingerprinting localization method with a similar localization estimation error.

  17. Molecular detection of drug resistance in microbes by isotopic techniques: The IAEA experience

    International Nuclear Information System (INIS)

    Dar, L.; Boussaha, A.; Padhy, A.K.; Khan, B.

    2003-01-01

    The International Atomic Energy Agency (IAEA) supports various programmes on the uses of radionuclide techniques in the management of human communicable diseases. An important issue, being addressed through several technology transfer projects, is the detection of drug resistance in microbes by radioisotope based molecular-biology diagnostic procedures. The techniques employed include dot blot hybridisation with P-32 labelled oligonucleotide probes to detect point mutations, associated with drug resistance, in microbial genes amplified by the polymerase chain reaction (PCR). Molecular methods have been used for the detection of drug resistance in the malarial parasite, Plasmodium falciparum, and in Mycobacterium tuberculosis. Radioisotope based molecular-biology methods have been demonstrated to have comparative advantages in being sensitive, specific, cost-effective, and suitable for application to large-scale molecular surveillance for drug resistance. (author)

  18. Gold nanoparticle-based beacon to detect STAT5b mRNA expression in living cells: a case optimized by bioinformatics screen.

    Science.gov (United States)

    Deng, Dawei; Li, Yang; Xue, Jianpeng; Wang, Jie; Ai, Guanhua; Li, Xin; Gu, Yueqing

    2015-01-01

    Messenger RNA (mRNA), a single-strand ribonucleic acid with functional gene information is usually abnormally expressed in cancer cells and has become a promising biomarker for the study of tumor progress. Hairpin DNA-coated gold nanoparticle (hDAuNP) beacon containing a bare gold nanoparticle (AuNP) as fluorescence quencher and thiol-terminated fluorescently labeled stem-loop-stem oligonucleotide sequences attached by Au-S bond is currently a new nanoscale biodiagnostic platform capable of mRNA detection, in which the design of the loop region sequence is crucial for hybridizing with the target mRNA. Hence, in this study, to improve the sensitivity and selectivity of hDAuNP beacon simultaneously, the loop region of hairpin DNA was screened by bioinformatics strategy. Here, signal transducer and activator of transcription 5b (STAT5b) mRNA was selected and used as a practical example. The results from the combined characterizations using optical techniques, flow cytometry assay, and cell microscopic imaging showed that after optimization, the as-prepared hDAuNP beacon had higher selectivity and sensitivity for the detection of STAT5b mRNA in living cells, as compared with our previous beacon. Thus, the bioinformatics method may be a promising new strategy for assisting in the designing of the hDAuNP beacon, extending its application in the detection of mRNA expression and the resultant mRNA-based biological processes and disease pathogenesis.

  19. The role and future of in-vitro isotopic techniques in molecular biology

    International Nuclear Information System (INIS)

    Dar, L.; Khan, B.K.

    2004-01-01

    In this review we discuss isotopic in-vitro molecular biology techniques, and their advantages and applications. Isotopic methods have helped to shape molecular biology since its early days. Despite the availability of non-isotopic alternatives, isotopic methods continue to be used in molecular biology due to certain advantages, especially related to sensitivity and cost-effectiveness. Numerous techniques involving the use of isotopes help in the characterization of genes, including the detection of single nucleotide polymorphisms (SNPs) or mutations. Other isotopic molecular methods are utilized to study the phenotypic expression of gene sequences and their mutation. Emerging branches of molecular biology like functional genomics and proteomics are extremely important for exploiting the rapidly growing data derived from whole genomic sequencing of human and microbial genomes. Recent molecular biology applications like the high-throughput array techniques are relevant in the context of both structural and functional genomics. In proteomics, stable isotope based technology has found applications in the analysis of protein structure and interactions. (author)

  20. Induced mutations and molecular techniques for crop improvement. Proceedings of an international symposium

    International Nuclear Information System (INIS)

    1995-01-01

    The symposium was aimed at reviewing current aspects of mutation and molecular biology techniques for use in crop improvement and to bridge the gap between practical plant breeding and molecular laboratory techniques. Over the past few years, many transgenic plants have been developed in important crops such as rice, wheat, maize, soybean, banana, cassava and cotton, as well as in many food, industrial and pharmaceutical plant species. More than 180 participants from 48 countries of which 31 were from developing countries, attended which provided a forum for the discussion of problems related to crop improvement world wide, and their possible solutions. Refs, figs and tabs

  1. Molecular Detection of Antimicrobial Resistance

    Science.gov (United States)

    Fluit, Ad C.; Visser, Maarten R.; Schmitz, Franz-Josef

    2001-01-01

    The determination of antimicrobial susceptibility of a clinical isolate, especially with increasing resistance, is often crucial for the optimal antimicrobial therapy of infected patients. Nucleic acid-based assays for the detection of resistance may offer advantages over phenotypic assays. Examples are the detection of the methicillin resistance-encoding mecA gene in staphylococci, rifampin resistance in Mycobacterium tuberculosis, and the spread of resistance determinants across the globe. However, molecular assays for the detection of resistance have a number of limitations. New resistance mechanisms may be missed, and in some cases the number of different genes makes generating an assay too costly to compete with phenotypic assays. In addition, proper quality control for molecular assays poses a problem for many laboratories, and this results in questionable results at best. The development of new molecular techniques, e.g., PCR using molecular beacons and DNA chips, expands the possibilities for monitoring resistance. Although molecular techniques for the detection of antimicrobial resistance clearly are winning a place in routine diagnostics, phenotypic assays are still the method of choice for most resistance determinations. In this review, we describe the applications of molecular techniques for the detection of antimicrobial resistance and the current state of the art. PMID:11585788

  2. The use of BEACON monitoring in plant power uprates

    International Nuclear Information System (INIS)

    Miller, Wade

    2003-01-01

    BEACON is the core support software technology that provides Utilities with continuous 3-D core power distribution monitoring, operational analysis capability, and operations support capability. BEACON monitoring delivers quantifiable plant margins for both reload design and plant operations improvement. When linked to Plant Power Upratings, BEACON permits an improvement in fuel cycle economics through higher peaking factors, higher power levels and higher discharge burnups. Operational flexibility of Uprated Plants is enhanced through elimination of axial power shape and core power tilt specifications. Also, the number of flux maps for these plants is reduced and local power is monitored continuously, permitting faster power escalation. Integrated 3-D power distribution analysis capabilities provide core designers with historical margin data that permits a reduction in core follow requirements as well as reduced curve book data related scope. Examples of specific Uprated Plant applications will be discussed. In anticipation of future needs of Uprated Plants, plans to integrate the technology of BEACON with COLSS are being executed. Finally, the capability to monitor Crud Induced Power Shift (axial offset) is also planned for incorporation into BEACON in the near future and will be discussed

  3. Current status of molecular biological techniques for plant breeding in the Republic of Korea

    Energy Technology Data Exchange (ETDEWEB)

    Sohn, Seong-Han; Lee, Si-Myung; Park, Bum-Seok; Yun, In-Sun; Goo, Doe-Hoe; Kim, Seok-Dong [Rural Development Administration, National Institute of Agricultural Science and Technology, Suwon (Korea)

    2002-02-01

    Classical plant breeding has played an important role in developing new varieties in current agriculture. For decades, the technique of cross-pollination has been popular for breeding in cereal and horticultural crops to introduce special traits. However, recently the molecular techniques get widely accepted as an alternative tool in both introducing a useful trait for developing the new cultivars and investigating the characteristics of a trait in plant, like the identification of a gene. Using the advanced molecular technique, several genetically modified (GM) crops (e.g., Roundup Ready Soybean, YieldGard, LibertyLink etc.) became commercially cultivated and appeared in the global market since 1996. The GM crops, commercially available at the moment, could be regarded as successful achievements in history of crop breeding conferring the specific gene into economically valuable crops to make them better. Along with such achievements, on the other hand these new crops have also caused the controversial debate on the safety of GM crops as human consumption and environmental release as well. Nevertheless, molecular techniques are widespread and popular in both investigating the basic science of plant biology and breeding new varieties compared to their conventional counterparts. Thus, the Department of Bioresources at the National Institute of Agricultural Science and Technology (NIAST) has been using the molecular biological techniques as a complimentary tool for the improvement of crop varieties for almost two decades. (author)

  4. Palindromic Molecule Beacon-Based Cascade Amplification for Colorimetric Detection of Cancer Genes.

    Science.gov (United States)

    Shen, Zhi-Fa; Li, Feng; Jiang, Yi-Fan; Chen, Chang; Xu, Huo; Li, Cong-Cong; Yang, Zhe; Wu, Zai-Sheng

    2018-03-06

    A highly sensitive and selective colorimetric assay based on a multifunctional molecular beacon with palindromic tail (PMB) was proposed for the detection of target p53 gene. The PMB probe can serve as recognition element, primer, and polymerization template and contains a nicking site and a C-rich region complementary to a DNAzyme. In the presence of target DNA, the hairpin of PMB is opened, and the released palindromic tails intermolecularly hybridize with each other, triggering the autonomous polymerization/nicking/displacement cycles. Although only one type of probe is involved, the system can execute triple and continuous polymerization strand displacement amplifications, generating large amounts of G-quadruplex fragments. These G-rich fragments can bind to hemin and form the DNAzymes that possess the catalytic activity similar to horseradish peroxidase, catalyzing the oxidation of ABTS by H 2 O 2 and producing the colorimetric signal. Utilizing the newly proposed sensing system, target DNA can be detected down to 10 pM with a linear response range from 10 pM to 200 nM, and mutant target DNAs are able to be distinguished even by the naked eye. The desirable detection sensitivity, high specificity, and operation convenience without any separation step and chemical modification demonstrate that the palindromic molecular beacon holds the potential for detecting and monitoring a variety of nucleic acid-related biomarkers.

  5. Hardware Implementation of A Non-RLL Soft-decoding Beacon-based Visible Light Communication Receiver

    OpenAIRE

    Nguyen, Duc-Phuc; Le, Dinh-Dung; Tran, Thi-Hong; Huynh, Huu-Thuan; Nakashima, Yasuhiko

    2018-01-01

    Visible light communication (VLC)-based beacon systems, which usually transmit identification (ID) information in small-size data frames are applied widely in indoor localization applications. There is one fact that flicker of LED light should be avoid in any VLC systems. Current flicker mitigation solutions based on run-length limited (RLL) codes suffer from reduced code rates, or are limited to hard-decoding forward error correction (FEC) decoders. Recently, soft-decoding techniques of RLL-...

  6. 14 CFR 171.321 - DME and marker beacon performance requirements.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 3 2010-01-01 2010-01-01 false DME and marker beacon performance... (MLS) § 171.321 DME and marker beacon performance requirements. (a) The DME equipment must meet the..._regulations/ibr_locations.html. (b) MLS marker beacon equipment must meet the performance requirements...

  7. 33 CFR 149.580 - What are the requirements for a radar beacon?

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false What are the requirements for a radar beacon? 149.580 Section 149.580 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF... Navigation Miscellaneous § 149.580 What are the requirements for a radar beacon? (a) A radar beacon (RACON...

  8. 77 FR 41271 - Safety Zone; Newburgh to Beacon Swim, Newburgh, Hudson River, NY

    Science.gov (United States)

    2012-07-13

    ... 1625-AA00 Safety Zone; Newburgh to Beacon Swim, Newburgh, Hudson River, NY AGENCY: Coast Guard, DHS... navigable waters of the Hudson River, NY in the vicinity of Newburgh, NY for the annual Newburgh Beacon Swim... Beacon Swim is an annual recurring event that has a permanent safety zone found at 33 CFR 165.160. The...

  9. Comparison of classical and molecular techniques for the determination of microbial biodiversity in Mediterranean crop soils

    Energy Technology Data Exchange (ETDEWEB)

    Munoz, A.; Lopez-Pineiro, A.; Ramirez, M.

    2009-07-01

    Soil microbe ecology has lately become increasingly important in the study of soil microbe populations. direct extraction of soil bacteria DNA allows PCR and DGGE analyses for the microorganism identification of these complex samples, avoiding the need for time-consuming culture-dependent techniques. The aim of the present study was to compare the two techniques (culture-dependent and molecular culture-independent) in four different plots of maize (Zea mays L.) crop under irrigation in south-western Spain. (Author)

  10. Exploring the transformative potential of Bluetooth beacons in higher education

    Directory of Open Access Journals (Sweden)

    Kieran McDonald

    2016-11-01

    Full Text Available The growing ubiquity of smartphones and tablet devices integrated into personal, social and professional life, facilitated by expansive communication networks globally, has the potential to disrupt higher education. Academics and students are considering the future possibilities of exploiting these tools and utilising networks to consolidate and expand knowledge, enhancing learning gain. Bluetooth beacon technology has been developed by both Apple and Google as a way to situate digital information within physical spaces, and this paper reflects on a beacon intervention in a contemporary art school in higher education conducted by the authors intended to develop a situated community of practice in Art & Design. The paper describes the project, including relevant theoretical foundations and background to the beacon technology, with regards to the potential of using these devices to create a connected learning community by enhancing learning and facilitating knowledge creation in a borderless learning space.

  11. Detection of thermocouple malfunction in the Beacon system

    International Nuclear Information System (INIS)

    Morita, T.; Heibel, M.D.; Congedo, T.V.

    1992-01-01

    The BEACON system uses Core Exit Thermocouples (T/C) extensively for continuous radial power distribution monitoring. The T/C's are used to adjust the reference power distribution generated by the BEACON system to match the current radial power distribution. T/C reliability, repeatability, and relative accuracy have been very satisfactory. However, it is very important to detect any T/C malfunctions during operation, since a T/C signal change caused by an undetected malfunction can lead to serious errors in the radial power distribution developed by BEACON. A simple procedure has been developed which is capable of discriminating between changes in T/C signals caused by actual changes in reactor conditions and signal changes caused by T/C malfunctions

  12. Comparison of BEACON and COMPARE reactor cavity subcompartment analyses

    International Nuclear Information System (INIS)

    Burkett, M.W.; Idar, E.S.; Gido, R.G.; Lime, J.F.; Koestel, A.

    1984-04-01

    In this study, a more advanced best-estimate containment code, BEACON-MOD3A, was ued to calculate force and moment loads resulting from a high-energy blowdown for two reactor cavity geometries previously analyzed with the licensing computer code COMPARE-MOD1A. The BEACON force and moment loads were compared with the COMPARE results to determine the safety margins provided by the COMPARE code. The forces and moments calculated by the codes were found to be different, although not in any consistent manner, for the two reactor cavity geometries studied. Therefore, generic summary statements regarding margins cannot be made because of the effects of the detailed physical configuration. However, differences in the BEACON and COMPARE calculated forces and moments can be attributed to differences in the modeling assumptions used in the codes and the analyses

  13. Some early results from the ATS-6 radio beacon experiment

    International Nuclear Information System (INIS)

    Davies, K.; Fritz, R.B.; Grubb, R.N.; Jones, J.E.

    1975-01-01

    The multifrequency satellite radio beacon enables the measurement of the columnar electron content of the ionosphere and plasmasphere along the ray path and its spatial and temporal structure. Measurements include modulation phase, Faraday rotation, and amplitude. The characteristics of the beacon transmitter and its design are presented together with the design of the Boulder receiver and antennas and the calibration procedures. A shape factor F is defined which depends on the electron density and geomagnetic field distributions. It is found that F varies by about 30 percent from day to night. It is shown that the ratio of the plasmaspheric content to total content varies from about 0.08 during the day to about 0.35 at night. Other examples which are presented to illustrate the uses of the radio beacon include sunrise effects, solar flare enhancements of total content, and the ionospheric storms of early July 1974

  14. Molecular techniques for the identification and detection of microorganisms relevant for the food industry

    NARCIS (Netherlands)

    Klijn, N.

    1996-01-01

    The research described in this thesis concerns the development and application in food microbiology of molecular identification and detection techniques based on 16S rRNA sequences. The technologies developed were applied to study the microbial ecology of two groups of bacteria, namely

  15. Studies of Phase Transformation in Molecular Crystals Using the Positron Annihilation Technique

    DEFF Research Database (Denmark)

    Eldrup, Morten Mostgaard; Lightbody, David; Sherwood, John N.

    1980-01-01

    An examination has been made of the brittle/plastic phase transformation in the molecular crystals cyclohexane, DL-camphene and succinonitrile using the positron annihilation technique. In each material, the transition is characterized by a distinct increase in ortho-positronium lifetime. The inf...

  16. Intelligent Techniques Using Molecular Data Analysis in Leukaemia: An Opportunity for Personalized Medicine Support System.

    Science.gov (United States)

    Banjar, Haneen; Adelson, David; Brown, Fred; Chaudhri, Naeem

    2017-01-01

    The use of intelligent techniques in medicine has brought a ray of hope in terms of treating leukaemia patients. Personalized treatment uses patient's genetic profile to select a mode of treatment. This process makes use of molecular technology and machine learning, to determine the most suitable approach to treating a leukaemia patient. Until now, no reviews have been published from a computational perspective concerning the development of personalized medicine intelligent techniques for leukaemia patients using molecular data analysis. This review studies the published empirical research on personalized medicine in leukaemia and synthesizes findings across studies related to intelligence techniques in leukaemia, with specific attention to particular categories of these studies to help identify opportunities for further research into personalized medicine support systems in chronic myeloid leukaemia. A systematic search was carried out to identify studies using intelligence techniques in leukaemia and to categorize these studies based on leukaemia type and also the task, data source, and purpose of the studies. Most studies used molecular data analysis for personalized medicine, but future advancement for leukaemia patients requires molecular models that use advanced machine-learning methods to automate decision-making in treatment management to deliver supportive medical information to the patient in clinical practice.

  17. BEACON: automated tool for Bacterial GEnome Annotation ComparisON.

    Science.gov (United States)

    Kalkatawi, Manal; Alam, Intikhab; Bajic, Vladimir B

    2015-08-18

    Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON's utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27%, while the number of genes without any function assignment is reduced. We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/ .

  18. Beacon communities' public health initiatives: a case study analysis.

    Science.gov (United States)

    Massoudi, Barbara L; Marcial, Laura H; Haque, Saira; Bailey, Robert; Chester, Kelley; Cunningham, Shellery; Riley, Amanda; Soper, Paula

    2014-01-01

    The Beacon Communities for Public Health (BCPH) project was launched in 2011 to gain a better understanding of the range of activities currently being conducted in population- and public health by the Beacon Communities. The project highlighted the successes and challenges of these efforts with the aim of sharing this information broadly among the public health community. The Beacon Community Program, designed to showcase technology-enabled, community-based initiatives to improve outcomes, focused on: building and strengthening health information technology (IT) infrastructure and exchange capabilities; translating investments in health IT to measureable improvements in cost, quality, and population health; and, developing innovative approaches to performance measurement, technology, and care delivery. Four multimethod case studies were conducted based on a modified sociotechnical framework to learn more about public health initiative implementation and use in the Beacon Communities. Our methodological approach included using document review and semistructured key informant interviews. NACCHO Model Practice Program criteria were used to select the public health initiatives included in the case studies. Despite differences among the case studies, common barriers and facilitators were found to be present in all areas of the sociotechnical framework application including structure, people, technology, tasks, overarching considerations, and sustainability. Overall, there were many more facilitators (range = 7-14) present for each Beacon compared to barriers (range = 4-6). Four influential promising practices were identified through the work: forging strong and sustainable partnerships; ensuring a good task-technology fit and a flexible and iterative design; fostering technology acceptance; and, providing education and demonstrating value. A common weakness was the lack of a framework or model for the Beacon Communities evaluation work. Sharing a framework or approach

  19. Beacon Communities’ Public Health Initiatives: A Case Study Analysis

    Science.gov (United States)

    Massoudi, Barbara L.; Marcial, Laura H.; Haque, Saira; Bailey, Robert; Chester, Kelley; Cunningham, Shellery; Riley, Amanda; Soper, Paula

    2014-01-01

    Introduction: The Beacon Communities for Public Health (BCPH) project was launched in 2011 to gain a better understanding of the range of activities currently being conducted in population- and public health by the Beacon Communities. The project highlighted the successes and challenges of these efforts with the aim of sharing this information broadly among the public health community. Background: The Beacon Community Program, designed to showcase technology-enabled, community-based initiatives to improve outcomes, focused on: building and strengthening health information technology (IT) infrastructure and exchange capabilities; translating investments in health IT to measureable improvements in cost, quality, and population health; and, developing innovative approaches to performance measurement, technology, and care delivery. Methods: Four multimethod case studies were conducted based on a modified sociotechnical framework to learn more about public health initiative implementation and use in the Beacon Communities. Our methodological approach included using document review and semistructured key informant interviews. NACCHO Model Practice Program criteria were used to select the public health initiatives included in the case studies. Findings: Despite differences among the case studies, common barriers and facilitators were found to be present in all areas of the sociotechnical framework application including structure, people, technology, tasks, overarching considerations, and sustainability. Overall, there were many more facilitators (range = 7–14) present for each Beacon compared to barriers (range = 4–6). Discussion: Four influential promising practices were identified through the work: forging strong and sustainable partnerships; ensuring a good task-technology fit and a flexible and iterative design; fostering technology acceptance; and, providing education and demonstrating value. Conclusions: A common weakness was the lack of a framework or model for

  20. Frequency Estimator Performance for a Software-Based Beacon Receiver

    Science.gov (United States)

    Zemba, Michael J.; Morse, Jacquelynne Rose; Nessel, James A.; Miranda, Felix

    2014-01-01

    As propagation terminals have evolved, their design has trended more toward a software-based approach that facilitates convenient adjustment and customization of the receiver algorithms. One potential improvement is the implementation of a frequency estimation algorithm, through which the primary frequency component of the received signal can be estimated with a much greater resolution than with a simple peak search of the FFT spectrum. To select an estimator for usage in a QV-band beacon receiver, analysis of six frequency estimators was conducted to characterize their effectiveness as they relate to beacon receiver design.

  1. Early Detection of Breast Cancer Using Molecular Beacons

    Science.gov (United States)

    2008-01-01

    therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. We thank Dr. Toncred Styblo and Beth...charges. This article must therefore be hereby marked “ advertisement ” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. 1 To whom...Ambrosini, G., Adida , C., and Altieri, D. C. (1997) Nat. Med. 3, 917–921 17. Tanaka, K., Iwamoto, S., Gon, G., Nohara, T., Iwamoto,M., andTanigawa, N

  2. New frontiers of molecular beacons: signal amplification and nanomachines

    DEFF Research Database (Denmark)

    Della Vedova, Paolo

    2013-01-01

    by two complementary strands (stem), conjugated respectively with a fluorophore and a quencher. Upon hybridization with complementary target, the stem bonds break, parting the fluorophore from the quencher and resulting in a detectable signal. This thesis is divided in two major sections. The first...

  3. Optimalization of Beacon Selection for Localization in Wireless AD-HOC Networks

    Directory of Open Access Journals (Sweden)

    Martin Matula

    2008-01-01

    Full Text Available In this paper we engage in optimalization of convenient beacons for localization position of a node in the ad-hoc network. An algorithm designed by us localizes position of moving or static node by RSS (Received Signal Strength method and trilateration. At first, localization of unknown node runs by combination of all beacons. Than optimalizating algorithmreduces the number of beacons (and repeats localization, while only three left. Its reduction is based on highest levels of received signal strength. It is only when signals are from the nearest beacons. Position localizating exactness is statistically interpreted from all localization by beacons combination and its repeating.

  4. Performance of the NASA Beacon Receiver for the Alphasat Aldo Paraboni TDP5 Propagation Experiment

    Science.gov (United States)

    Nessel, James; Morse, Jacquelynne; Zemba, Michael; Riva, Carlo; Luini, Lorenzo

    2015-01-01

    NASA Glenn Research Center (GRC) and the Politecnico di Milano (POLIMI) have initiated a joint propagation campaign within the framework of the Alphasat propagation experiment to characterize rain attenuation, scintillation, and gaseous absorption effects of the atmosphere in the 40 gigahertz band. NASA GRC has developed and installed a K/Q-band (20/40 gigahertz) beacon receiver at the POLIMI campus in Milan, Italy, which receives the 20/40 gigahertz signals broadcast from the Alphasat Aldo Paraboni Technology Demonstration Payload (TDP) no. 5 beacon payload. The primary goal of these measurements is to develop a physical model to improve predictions of communications systems performance within the Q-band. Herein, we describe the design and preliminary performance of the NASA propagation terminal, which has been installed and operating in Milan since June 2014. The receiver is based upon a validated Fast Fourier Transform (FFT) I/Q digital design approach utilized in other operational NASA propagation terminals, but has been modified to employ power measurement via a frequency estimation technique and to coherently track and measure the amplitude of the 20/40 gigahertz beacon signals. The system consists of a 1.2-meter K-band and a 0.6-meter Q-band Cassegrain reflector employing synchronous open-loop tracking to track the inclined orbit of the Alphasat satellite. An 8 hertz sampling rate is implemented to characterize scintillation effects, with a 1-hertz measurement bandwidth dynamic range of 45 decibels. A weather station with an optical disdrometer is also installed to characterize rain drop size distribution for correlation with physical based models.

  5. Preliminary Results of the NASA Beacon Receiver for Alphasat Aldo Paraboni TDP5 Propagation Experiment

    Science.gov (United States)

    Nessel, James; Morse, Jacquelynne; Zemba, Michael; Riva, Carlo; Luini, Lorenzo

    2014-01-01

    NASA Glenn Research Center (GRC) and the Politecnico di Milano (POLIMI) have initiated a joint propagation campaign within the framework of the Alphasat propagation experiment to characterize rain attenuation, scintillation, and gaseous absorption effects of the atmosphere in the 40 GHz band. NASA GRC has developed and installed a K/Q-band (20/40 GHz) beacon receiver at the POLIMI campus in Milan, Italy, which receives the 20/40 GHz signals broadcast from the Alphasat Aldo Paraboni TDP#5 beacon payload. The primary goal of these measurements is to develop a physical model to improve predictions of communications systems performance within the Q-band. Herein, we describe the design and preliminary performance of the NASA propagation terminal, which has been installed and operating in Milan since May 2014. The receiver is based upon a validated Fast Fourier Transform (FFT) I/Q digital design approach utilized in other operational NASA propagation terminals, but has been modified to employ power measurement via a frequency estimation technique and to coherently track and measure the amplitude of the 20/40 GHz beacon signals. The system consists of a 1.2-m K-band and a 0.6-m Qband Cassegrain reflector employing synchronous open-loop tracking to track the inclined orbit of the Alphasat satellite. An 8 Hz sampling rate is implemented to characterize scintillation effects, with a 1-Hz measurement bandwidth dynamic range of 45 dB. A weather station with an optical disdrometer is also installed to characterize rain drop size distribution for correlation with physical based models.

  6. Overshadowing of geometric cues by a beacon in a spatial navigation task.

    Science.gov (United States)

    Redhead, Edward S; Hamilton, Derek A; Parker, Matthew O; Chan, Wai; Allison, Craig

    2013-06-01

    In three experiments, we examined whether overshadowing of geometric cues by a discrete landmark (beacon) is due to the relative saliences of the cues. Using a virtual water maze task, human participants were required to locate a platform marked by a beacon in a distinctively shaped pool. In Experiment 1, the beacon overshadowed geometric cues in a trapezium, but not in an isosceles triangle. The longer escape latencies during acquisition in the trapezium control group with no beacon suggest that the geometric cues in the trapezium were less salient than those in the triangle. In Experiment 2, we evaluated whether generalization decrement, caused by the removal of the beacon at test, could account for overshadowing. An additional beacon was placed in an alternative corner. For the control groups, the beacons were identical; for the overshadow groups, they were visually unique. Overshadowing was again found in the trapezium. In Experiment 3, we tested whether the absence of overshadowing in the triangle was due to the geometric cues being more salient than the beacon. Following training, the beacon was relocated to a different corner. Participants approached the beacon rather than the trained platform corner, suggesting that the beacon was more salient. These results suggest that associative processes do not fully explain cue competition in the spatial domain.

  7. The BEACON on-line core monitoring system. Functional upgrades and applications

    International Nuclear Information System (INIS)

    Boyd, W.A.; Miller, R.W.

    1997-01-01

    The BEACON TM core monitor system has been in commercial operation since 1989 and was licensed by the USNRC for on-line core power distribution and thermal power limit monitoring in 1994. Since that time BEACON has been installed at 17 plants. Each of these customers has a different perspective on the use of data from BEACON and a different approach on the application of BEACON to support their plant operations. To support these varied needs and approaches the BEACON system has been divided into three operational levels to better match the system functions to the customer needs and approaches to system integration. Based on customer feedback, the BEACON system was upgraded in some areas and streamlined in other areas to better support the needs of each customer. The three operational levels of the BEACON system, the major product upgrades and system evolution that has taken place to support the needs and applications of our customers are discussed. (authors)

  8. Techniques for Maximizing the Performance of Molecular Pathology Testing: Responsibilities of All Pathologists

    Directory of Open Access Journals (Sweden)

    Evren UZUN

    2018-05-01

    Full Text Available Molecular pathological analysis has an expanding role in patient diagnosis and management. The performance of these techniques relies on excellent laboratory procedures. However, the crucial step is obtaining the best samples for molecular analysis. Archiving and selection of these are the responsibilities of all pathologists even if they are not working at a center with molecular pathological facilities. This review focuses on the features of different types of materials for molecular pathological analysis. Many steps that might affect the results, including communication between the pathologist and the oncology team, features of different types of materials (cytological, tissue blocks, biopsy, circulating tumor cells (CTCs and cell-free circulating nucleic acids, effects of tissue processing, methods for selecting the best material, and tissue saving and tumor enrichment methods are discussed. The procedures for referral to a center for molecular pathological analysis are also mentioned. Awareness of the importance of the cytopathological and histopathological material of the patients for future molecular pathological analysis by pathologists is of the utmost importance.

  9. Remarks on the observability of single beacon underwater navigation

    DEFF Research Database (Denmark)

    Jouffroy, Jerome; Ross, Andrew

    This paper contributes a simple and intuitive result in the analysis of underwater navigation using a single ranging beacon. This analysis should help with the design of small and lightweight underwater vehicles by reducing the amount of instrumentation required for accurate navigation. The concept...

  10. The Westinghouse BEACON on-line core monitoring system

    International Nuclear Information System (INIS)

    Buechel, Robert J.; Boyd, William A.; Casadei, Alberto L.

    1995-01-01

    BEACON (Best Estimate Analysis of Core Operations - Nuclear), a core monitoring and operational support package developed by Westinghouse, has been installed at many operating PWRs worldwide. The BEACON system is a real-time monitoring system which can be used in plants with both fixed and movable incore detector systems and utilizes an on-line nodal model combined with core instrumentation data to provide continuous core power distribution monitoring. In addition, accurate core-predictive capabilities utilizing a full core nodal model updated according to plant operating history can be made to provide operational support. Core history information is kept and displayed to help operators anticipate core behavior and take pro-active control actions. The BEACON system has been licensed by the U.S. Nuclear Regulatory Commission for direct, continuous monitoring of DNBR and peak linear heat rate. This allows BEACON to be integrated into the plant technical specifications to permit significant relaxation of operating limitations defined by conventional technical specifications. (author). 4 refs, 2 figs, 1 tab

  11. On the Efficiency of Secure Beaconing in VANETs

    NARCIS (Netherlands)

    Schoch, Elmar; Kargl, Frank

    Direct inter-vehicle communication enables numerous safety applications like intersection collision warning. Beacons - periodic one-hop link-layer broadcast messages containing, e.g., location, heading, and speed - are the basis for many such applications. For security, current work often requires

  12. Smartphone-Based Indoor Localization with Bluetooth Low Energy Beacons

    Directory of Open Access Journals (Sweden)

    Yuan Zhuang

    2016-04-01

    Full Text Available Indoor wireless localization using Bluetooth Low Energy (BLE beacons has attracted considerable attention after the release of the BLE protocol. In this paper, we propose an algorithm that uses the combination of channel-separate polynomial regression model (PRM, channel-separate fingerprinting (FP, outlier detection and extended Kalman filtering (EKF for smartphone-based indoor localization with BLE beacons. The proposed algorithm uses FP and PRM to estimate the target’s location and the distances between the target and BLE beacons respectively. We compare the performance of distance estimation that uses separate PRM for three advertisement channels (i.e., the separate strategy with that use an aggregate PRM generated through the combination of information from all channels (i.e., the aggregate strategy. The performance of FP-based location estimation results of the separate strategy and the aggregate strategy are also compared. It was found that the separate strategy can provide higher accuracy; thus, it is preferred to adopt PRM and FP for each BLE advertisement channel separately. Furthermore, to enhance the robustness of the algorithm, a two-level outlier detection mechanism is designed. Distance and location estimates obtained from PRM and FP are passed to the first outlier detection to generate improved distance estimates for the EKF. After the EKF process, the second outlier detection algorithm based on statistical testing is further performed to remove the outliers. The proposed algorithm was evaluated by various field experiments. Results show that the proposed algorithm achieved the accuracy of <2.56 m at 90% of the time with dense deployment of BLE beacons (1 beacon per 9 m, which performs 35.82% better than <3.99 m from the Propagation Model (PM + EKF algorithm and 15.77% more accurate than <3.04 m from the FP + EKF algorithm. With sparse deployment (1 beacon per 18 m, the proposed algorithm achieves the accuracies of <3.88 m at

  13. BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal M.

    2015-08-18

    Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/

  14. Smartphone-Based Indoor Localization with Bluetooth Low Energy Beacons.

    Science.gov (United States)

    Zhuang, Yuan; Yang, Jun; Li, You; Qi, Longning; El-Sheimy, Naser

    2016-04-26

    Indoor wireless localization using Bluetooth Low Energy (BLE) beacons has attracted considerable attention after the release of the BLE protocol. In this paper, we propose an algorithm that uses the combination of channel-separate polynomial regression model (PRM), channel-separate fingerprinting (FP), outlier detection and extended Kalman filtering (EKF) for smartphone-based indoor localization with BLE beacons. The proposed algorithm uses FP and PRM to estimate the target's location and the distances between the target and BLE beacons respectively. We compare the performance of distance estimation that uses separate PRM for three advertisement channels (i.e., the separate strategy) with that use an aggregate PRM generated through the combination of information from all channels (i.e., the aggregate strategy). The performance of FP-based location estimation results of the separate strategy and the aggregate strategy are also compared. It was found that the separate strategy can provide higher accuracy; thus, it is preferred to adopt PRM and FP for each BLE advertisement channel separately. Furthermore, to enhance the robustness of the algorithm, a two-level outlier detection mechanism is designed. Distance and location estimates obtained from PRM and FP are passed to the first outlier detection to generate improved distance estimates for the EKF. After the EKF process, the second outlier detection algorithm based on statistical testing is further performed to remove the outliers. The proposed algorithm was evaluated by various field experiments. Results show that the proposed algorithm achieved the accuracy of EKF algorithm and 15.77% more accurate than EKF algorithm. With sparse deployment (1 beacon per 18 m), the proposed algorithm achieves the accuracies of EKF algorithm and 21.41% better than EKF algorithm. Therefore, the proposed algorithm is especially useful to improve the localization accuracy in environments with sparse beacon deployment.

  15. Characterization-Based Molecular Design of Bio-Fuel Additives Using Chemometric and Property Clustering Techniques

    International Nuclear Information System (INIS)

    Hada, Subin; Solvason, Charles C.; Eden, Mario R.

    2014-01-01

    In this work, multivariate characterization data such as infrared spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis allowed capturing important features of the molecular architecture from enormous amount of complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods based on characterization (cGCM) data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive, which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

  16. [Molecular classification of breast cancer patients obtained through the technique of chromogenic in situ hybridization (CISH)].

    Science.gov (United States)

    Fernández, Angel; Reigosa, Aldo

    2013-12-01

    Breast cancer is a heterogeneous disease composed of a growing number of biological subtypes, with substantial variability of the disease progression within each category. The aim of this research was to classify the samples object of study according to the molecular classes of breast cancer: luminal A, luminal B, HER2 and triple negative, as a result of the state of HER2 amplification obtained by the technique of chromogenic in situ hybridization (CISH). The sample consisted of 200 biopsies fixed in 10% formalin, processed by standard techniques up to paraffin embedding, corresponding to patients diagnosed with invasive ductal carcinoma of the breast. These biopsies were obtained from patients from private practice and the Institute of Oncology "Dr. Miguel Pérez Carreño", for immunohistochemistry (IHC) of hormone receptors and HER2 made in the Hospital Metropolitano del Norte, Valencia, Venezuela. The molecular classification of the patient's tumors considering the expression of estrogen and progesterone receptors by IHC and HER2 amplification by CISH, allowed those cases originally classified as unknown, since they had an indeterminate (2+) outcome for HER2 expression by IHC, to be grouped into the different molecular classes. Also, this classification permitted that some cases, initially considered as belonging to a molecular class, were assigned to another class, after the revaluation of the HER2 status by CISH.

  17. Characterization-Based Molecular Design of Bio-Fuel Additives Using Chemometric and Property Clustering Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hada, Subin; Solvason, Charles C.; Eden, Mario R., E-mail: edenmar@auburn.edu [Department of Chemical Engineering, Auburn University, Auburn, AL (United States)

    2014-06-10

    In this work, multivariate characterization data such as infrared spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis allowed capturing important features of the molecular architecture from enormous amount of complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods based on characterization (cGCM) data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive, which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

  18. Characterization-Based Molecular Design of Biofuel Additives Using Chemometric and Property Clustering Techniques

    Directory of Open Access Journals (Sweden)

    Subin eHada

    2014-06-01

    Full Text Available In this work, multivariate characterization data such as infrared (IR spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis (PCA allowed capturing important features of the molecular architecture from complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods (GCM based on characterization data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.

  19. Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques.

    Science.gov (United States)

    Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M; Prates, Luciana L; Yu, Peiqiang

    2017-08-05

    The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HED N/OM ), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    CSIR Research Space (South Africa)

    Barros, E

    2010-05-01

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

  1. SPECT and PET Serve as Molecular Imaging Techniques and in Vivo Biomarkers for Brain Metastases

    Science.gov (United States)

    Palumbo, Barbara; Buresta, Tommaso; Nuvoli, Susanna; Spanu, Angela; Schillaci, Orazio; Fravolini, Mario Luca; Palumbo, Isabella

    2014-01-01

    Nuclear medicine techniques (single photon emission computerized tomography, SPECT, and positron emission tomography, PET) represent molecular imaging tools, able to provide in vivo biomarkers of different diseases. To investigate brain tumours and metastases many different radiopharmaceuticals imaged by SPECT and PET can be used. In this review the main and most promising radiopharmaceuticals available to detect brain metastases are reported. Furthermore the diagnostic contribution of the combination of SPECT and PET data with radiological findings (magnetic resonance imaging, MRI) is discussed. PMID:24897023

  2. Kinetic and Diagnostic Studies of Molecular Plasmas Using Laser Absorption Techniques

    International Nuclear Information System (INIS)

    Welzel, S; Rousseau, A; Davies, P B; Roepcke, J

    2007-01-01

    Within the last decade mid infrared absorption spectroscopy between 3 and 20 μm, known as Infrared Laser Absorption Spectroscopy (IRLAS) and based on tuneable semiconductor lasers, namely lead salt diode lasers, often called tuneable diode lasers (TDL), and quantum cascade lasers (QCL) has progressed considerably as a powerful diagnostic technique for in situ studies of the fundamental physics and chemistry of molecular plasmas. The increasing interest in processing plasmas containing hydrocarbons, fluorocarbons, organo-silicon and boron compounds has lead to further applications of IRLAS because most of these compounds and their decomposition products are infrared active. IRLAS provides a means of determining the absolute concentrations of the ground states of stable and transient molecular species, which is of particular importance for the investigation of reaction kinetics. Information about gas temperature and population densities can also be derived from IRLAS measurements. A variety of free radicals and molecular ions have been detected, especially using TDLs. Since plasmas with molecular feed gases are used in many applications such as thin film deposition, semiconductor processing, surface activation and cleaning, and materials and waste treatment, this has stimulated the adaptation of infrared spectroscopic techniques to industrial requirements. The recent development of QCLs offers an attractive new option for the monitoring and control of industrial plasma processes as well as for highly time-resolved studies on the kinetics of plasma processes. The aim of the present article is threefold: (i) to review recent achievements in our understanding of molecular phenomena in plasmas (ii) to report on selected studies of the spectroscopic properties and kinetic behaviour of radicals, and (iii) to describe the current status of advanced instrumentation for TDLAS in the mid infrared

  3. Synchrotron-Based Microspectroscopic Analysis of Molecular and Biopolymer Structures Using Multivariate Techniques and Advanced Multi-Components Modeling

    International Nuclear Information System (INIS)

    Yu, P.

    2008-01-01

    More recently, advanced synchrotron radiation-based bioanalytical technique (SRFTIRM) has been applied as a novel non-invasive analysis tool to study molecular, functional group and biopolymer chemistry, nutrient make-up and structural conformation in biomaterials. This novel synchrotron technique, taking advantage of bright synchrotron light (which is million times brighter than sunlight), is capable of exploring the biomaterials at molecular and cellular levels. However, with the synchrotron RFTIRM technique, a large number of molecular spectral data are usually collected. The objective of this article was to illustrate how to use two multivariate statistical techniques: (1) agglomerative hierarchical cluster analysis (AHCA) and (2) principal component analysis (PCA) and two advanced multicomponent modeling methods: (1) Gaussian and (2) Lorentzian multi-component peak modeling for molecular spectrum analysis of bio-tissues. The studies indicated that the two multivariate analyses (AHCA, PCA) are able to create molecular spectral corrections by including not just one intensity or frequency point of a molecular spectrum, but by utilizing the entire spectral information. Gaussian and Lorentzian modeling techniques are able to quantify spectral omponent peaks of molecular structure, functional group and biopolymer. By application of these four statistical methods of the multivariate techniques and Gaussian and Lorentzian modeling, inherent molecular structures, functional group and biopolymer onformation between and among biological samples can be quantified, discriminated and classified with great efficiency.

  4. Experience of molecular monitoring techniques in upstream oil and gas operations

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, Anthony F.; Anfindsen, Hilde; Liengen, Turid; Molid, Solfrid [Statoil ASA (Denmark)

    2011-07-01

    For a numbers of years, molecular monitoring tools have been used in upstream oil and gas operations but the results have given only limited added value. This paper discusses the various techniques available for upstream molecular monitoring which provides scope for identification of microbial influenced problems. The methodology, which consists of analyzing solid samples using traditional as well as molecular techniques, is detailed. Two cases were studied with the objective of determining if microbial contamination was contributing to the problem. The first case was a study of amorphous deposits in production wells and mainly iron sulphide was found. The second study was of amorphous deposits in water injection wells and the analysis showed typical components of drilling and completion fluids with some organic material. Two more cases, corrosion of tubing in a water injection well and flow line corrosion, are discussed and the results are given. From the study, it can be concluded that failure can be due to several factors, chemical and biological.

  5. [Application of molecular diagnostic techniques in precision medicine of personalized treatment for colorectal cancer].

    Science.gov (United States)

    Fu, Ji; Lin, Guole

    2016-01-01

    Precision medicine is to customize the treatment options for individual patient based on the personal genome information. Colorectal cancer (CRC) is one of the most common cancer worldwide. Molecular heterogeneity of CRC, which includes the MSI phenotype, hypermutation phenotype, and their relationship with clinical preferences, is believed to be one of the main factors responsible for the considerable variability in treatment response. The development of powerful next-generation sequencing (NGS) technologies allows us to further understand the biological behavior of colorectal cancer, and to analyze the prognosis and chemotherapeutic drug reactions by molecular diagnostic techniques, which can guide the clinical treatment. This paper will introduce the new findings in this field. Meanwhile we integrate the new progress of key pathways including EGFR, RAS, PI3K/AKT and VEGF, and the experience in selective patients through associated molecular diagnostic screening who gain better efficacy after target therapy. The technique for detecting circulating tumor DNA (ctDNA) is introduced here as well, which can identify patients with high risk for recurrence, and demonstrate the risk of chemotherapy resistance. Mechanism of tumor drug resistance may be revealed by dynamic observation of gene alteration during treatment.

  6. Isothermal amplification detection of nucleic acids by a double-nicked beacon.

    Science.gov (United States)

    Shi, Chao; Zhou, Meiling; Pan, Mei; Zhong, Guilin; Ma, Cuiping

    2016-03-01

    Isothermal and rapid amplification detection of nucleic acids is an important technology in environmental monitoring, foodborne pathogen detection, and point-of-care clinical diagnostics. Here we have developed a novel method of isothermal signal amplification for single-stranded DNA (ssDNA) detection. The ssDNA target could be used as an initiator, coupled with a double-nicked molecular beacon, to originate amplification cycles, achieving cascade signal amplification. In addition, the method showed good specificity and strong anti-jamming capability. Overall, it is a one-pot and isothermal strand displacement amplification method without the requirement of a stepwise procedure, which greatly simplifies the experimental procedure and decreases the probability of contamination of samples. With its advantages, the method would be very useful to detect nucleic acids in point-of-care or field use. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Nanomechanical DNA origami 'single-molecule beacons' directly imaged by atomic force microscopy

    Science.gov (United States)

    Kuzuya, Akinori; Sakai, Yusuke; Yamazaki, Takahiro; Xu, Yan; Komiyama, Makoto

    2011-01-01

    DNA origami involves the folding of long single-stranded DNA into designed structures with the aid of short staple strands; such structures may enable the development of useful nanomechanical DNA devices. Here we develop versatile sensing systems for a variety of chemical and biological targets at molecular resolution. We have designed functional nanomechanical DNA origami devices that can be used as 'single-molecule beacons', and function as pinching devices. Using 'DNA origami pliers' and 'DNA origami forceps', which consist of two levers ~170 nm long connected at a fulcrum, various single-molecule inorganic and organic targets ranging from metal ions to proteins can be visually detected using atomic force microscopy by a shape transition of the origami devices. Any detection mechanism suitable for the target of interest, pinching, zipping or unzipping, can be chosen and used orthogonally with differently shaped origami devices in the same mixture using a single platform. PMID:21863016

  8. Beacon-based tourist information system to identify visiting trends of tourists

    Directory of Open Access Journals (Sweden)

    Akihiro Yamaguchi

    2017-11-01

    Full Text Available In this study, we propose a system that provides tourist information and obtains trends of visiting tourists using beacons and cloud service. As part of our research, we are working on the promotion of local area tourism in cooperation with a local community. A low energy Bluetooth device is used as a beacon to transmit a universally unique identifier. In addition, beacons are placed at sightseeing spots and tourist facilities. Our proposed system comprises two application programs; one is a client-side application program that provides area-specific tourist information corresponding to the detected beacon. The other is a server-side application to record time and location information of the detected beacons. In this paper, we describe the scheme of our system, and present the results of experiments conducted using the prototype system in the local tourist area. In addition, we discuss an open platform for information collection services using beacons.

  9. A new crossed molecular beam apparatus using time-sliced ion velocity imaging technique

    International Nuclear Information System (INIS)

    Wu Guorong; Zhang Weiqing; Pan Huilin; Shuai Quan; Jiang Bo; Dai Dongxu; Yang Xueming

    2008-01-01

    A new crossed molecular beam apparatus has been constructed for investigating polyatomic chemical reactions using the time-sliced ion velocity map imaging technique. A unique design is adopted for one of the two beam sources and allows us to set up the molecular beam source either horizontally or vertically. This can be conveniently used to produce versatile atomic or radical beams from photodissociation and as well as electric discharge. Intensive H-atom beam source with high speed ratio was produced by photodissociation of the HI molecule and was reacted with the CD 4 molecule. Vibrational-state resolved HD product distribution was measured by detecting the CD 3 product. Preliminary results were also reported on the F+SiH 4 reaction using the discharged F atom beam. These results demonstrate that this new instrument is a powerful tool for investigating chemical dynamics of polyatomic reactions.

  10. Gas Source Techniques for Molecular Beam Epitaxy of Highly Mismatched Ge Alloys

    Directory of Open Access Journals (Sweden)

    Chad A. Stephenson

    2016-12-01

    Full Text Available Ge and its alloys are attractive candidates for a laser compatible with silicon integrated circuits. Dilute germanium carbide (Ge1−xCx offers a particularly interesting prospect. By using a precursor gas with a Ge4C core, C can be preferentially incorporated in substitutional sites, suppressing interstitial and C cluster defects. We present a method of reproducible and upscalable gas synthesis of tetrakis(germylmethane, or (H3Ge4C, followed by the design of a hybrid gas/solid-source molecular beam epitaxy system and subsequent growth of defect-free Ge1−xCx by molecular beam epitaxy (MBE. Secondary ion mass spectroscopy, transmission electron microscopy and contactless electroreflectance confirm the presence of carbon with very high crystal quality resulting in a decrease in the direct bandgap energy. This technique has broad applicability to growth of highly mismatched alloys by MBE.

  11. Sensitivity of field tests, serological and molecular techniques for Plum Pox Virus detection in various tissues

    Directory of Open Access Journals (Sweden)

    Mojca VIRŠČEK MARN

    2015-12-01

    Full Text Available Sensitivity of field tests (AgriStrip  and Immunochromato, DAS-ELISA, two step RT-PCR and real-time RT-PCR for Plum pox virus (PPV detection was tested in various tissues of apricot, peach, plum and damson plum trees infected with isolates belonging to PPV-D, PPV-M or PPV-Rec, the three strains present in Slovenia. Flowers of apricot and plum in full bloom proved to be a very good source for detection of PPV. PPV could be detected with all tested techniques in symptomatic parts of leaves in May and with one exception even in the beginning of August, but it was not detected in asymptomatic leaves using field tests, DAS-ELISA and partly also molecular techniques. PPV was detected only in some of the samples of asymptomatic parts of the leaves with symptoms and of stalks by field tests and DAS-ELISA. Infections were not detected in buds in August using field tests or DAS-ELISA. Field tests are useful for confirmation of the PPV infection in symptomatic leaves, but in tissues without symptoms DAS-ELISA should be combined or replaced by molecular techniques.

  12. Coulomb-explosion technique for determining geometrical structures of molecular ions

    International Nuclear Information System (INIS)

    Gemmell, D.S.

    1981-01-01

    Traditional experimental techniques (e.g. studies on photon absorption or emission) for determining the sterochemical structures of neutral molecules are extremeley difficult to apply to molecular ions because of problems in obtaining a sufficient spatial density of the ions to be studied. Recent high-resolution measurements on the energy and angle distributions of the fragments produced when fast (MeV) molecular-ion beams from an electrostatic accelerator dissociate (Coulomb explode) in thin foils and in gases, offer promising possibilities for deducing the sterochemical structures of the molecular ions constituting the incident beams. Bond lengths have been determined in this way for several diatomic projectiles (H 2+ , HeH + , CH + , NH + , OH + , N 2+ , O 2+ , etc.) with an accuracy of approx. 0.01 A. H 3+ has been demonstrated (for the first time) to be equilateral triangular and the interproton distance measured. Measurements on single fragments from CO 2+ , N 2 O + , C 3 H 3+ , and CH/sub n/ + have revealed the gross structures of the projectiles. An apparatus has recently been constructed at Argonne to permit precise measurements on fragments in coincidence. The apparatus has been tested on a known structure (OH 2+ ). The O-H bond length was found to be 1.0 +- 0.04 A and the H-O-H bond angle was measured as 110 --- 2 0 . These values are in excellent agreement with those found in optical experiments (0.999 A and 110.5 0 ). This Coulomb explosion technique can be expected to be refined in accuracy and to be extended to a wide range of molecular ions whose structures are inaccessible by other means

  13. Q-Band (37-41 GHz) Satellite Beacon Architecture for RF Propagation Experiments

    Science.gov (United States)

    Simmons, Rainee N.; Wintucky, Edwin G.

    2012-01-01

    In this paper, the design of a beacon transmitter that will be flown as a hosted payload on a geostationary satellite to enable propagation experiments at Q-band (37-41 GHz) frequencies is presented. The beacon uses a phased locked loop stabilized dielectric resonator oscillator and a solid-state power amplifier to achieve the desired output power. The satellite beacon antenna is configured as an offset-fed cut-paraboloidal reflector.

  14. Q-Band (37 to 41 GHz) Satellite Beacon Architecture for RF Propagation Experiments

    Science.gov (United States)

    Simons, Rainee N.; Wintucky, Edwin G.

    2014-01-01

    In this paper, the design of a beacon transmitter that will be flown as a hosted payload on a geostationary satellite to enable propagation experiments at Q-band (37 to 41 GHz) frequencies is presented. The beacon uses a phased locked loop stabilized dielectric resonator oscillator and a solid-state power amplifier to achieve the desired output power. The satellite beacon antenna is configured as an offset-fed cutparaboloidal reflector.

  15. An Analysis of the Optimal Placement of Beacon in Bluetooth-INS Indoor Localization

    OpenAIRE

    Zhao, Xinyu; Ruan, Ling; Zhang, Ling; Long, Yi; Cheng, Fei

    2018-01-01

    The placement of Bluetooth beacon has immediate impact on the accuracy and stability of indoor positioning. Affected by the shelter of building and human, Bluetooth shows uncertain spatial transmission characteristics. Therefore, the scientific deployment of the beacon nodes is closely related to the indoor space environment. In the study of positioning technology using Bluetooth, some scholars have discussed the deployment of Bluetooth beacon in different scenarios. In the principle of avoid...

  16. Remote sensing of the ionosphere using satellite radio beacons

    International Nuclear Information System (INIS)

    Davies, Kenneth

    1991-01-01

    Since the launch of Sputnik I in 1957, satellite radio beacons have been used to measure the total electron content of the ionosphere. A review of the role of satellite beacons in studies of the vertical and spatial structure of the total electron content and on the occurrence of plasma irregularities, both of which affect transionospheric radio signals, is presented. Measurements of Faraday rotation and time of flight give information on the topside of the ionosphere and on the protonosphere. Morphological studies show that the slab thickness of the ionosphere depends on the solar index but is approximately independent of geographical location. Scintillation of amplitude, phase, polarization, and angle provide information on plasma irregularity occurrence in space and time. (author). 23 refs., 16 figs ., 4 tabs

  17. Nanosecond and femtosecond mass spectroscopic analysis of a molecular beam produced by the spray-jet technique

    International Nuclear Information System (INIS)

    Yamada, Toshiki; Shinohara, Hidenori; Kamikado, Toshiya; Okuno, Yoshishige; Suzuki, Hitoshi; Mashiko, Shinro; Yokoyama, Shiyoshi

    2008-01-01

    The spray-jet molecular beam apparatus enabled us to produce a molecular beam of non-volatile molecules under high vacuum from a sprayed mist of sample solutions. The apparatus has been used in spectroscopic studies and as a means of molecular beam deposition. We analyzed the molecular beam, consisting of non-volatile, solvent, and carrier-gas molecules, by using femtosecond- and nanosecond- laser mass spectroscopy. The information thus obtained provided insight into the molecular beam produced by the spray-jet technique

  18. Spectroscopic and molecular docking techniques study of the interaction between oxymetholone and human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Madrakian, Tayyebeh, E-mail: madrakian@basu.ac.ir; Bagheri, Habibollah; Afkhami, Abbas; Soleimani, Mohammad

    2014-11-15

    In this study, the binding of oxymetholone (OXM), a doping drug, to human serum albumin (HSA) was explored at pH 7.40 by spectroscopic methods including spectrofluorimetry, three dimensional excitation–emission matrix (3D EEM), UV–vis absorption, resonance rayleigh scattering (RRS) and molecular docking. The fluorescence results showed that there was a considerable quenching of the intrinsic fluorescence of HSA upon binding to OXM by static quenching mechanism. The Stern–Volmer quenching constants (K{sub SV}) between OXM and HSA at three different temperatures 295, 303, 308 K, were obtained as 4.63×10{sup 4}, 3.05×10{sup 4} and 1.49×10{sup 4} L mol{sup −1}, respectively. Furthermore this interaction was confirmed by UV–vis spectrophotometric and RRS techniques. The binding site number, n, apparent binding constant, K{sub b}, and corresponding thermodynamic parameters (ΔS, ΔH and ΔG) were measured at different temperatures. The Van der Waals and hydrogen-bond forces were found to stabilize OXM–HSA complex. The distance (r) between the donor and acceptor was obtained from Förster's theory of fluorescence resonance energy transfer (FRET) and found to be 1.67 nm. The 3D EEM showed that OXM slightly changes the secondary structure of HSA. Furthermore, the molecular docking was employed for identification of drug binding sites and interaction of OXM with amino acid residues. - Highlights: • The binding of OXM as a doping drug with HSA was studied by different techniques. • The binding constant of HSA–OXM was calculated. • The binding site of OXM on HSA was characterized with molecular docking. • The thermodynamic parameters were calculated according to fluorescence technique.

  19. Aftermath of bustamante attack on genomic beacon service.

    Science.gov (United States)

    Aziz, Md Momin Al; Ghasemi, Reza; Waliullah, Md; Mohammed, Noman

    2017-07-26

    With the enormous need for federated eco-system for holding global genomic and clinical data, Global Alliance for Genomic and Health (GA4GH) has created an international website called beacon service which allows a researcher to find out whether a specific dataset can be utilized to his or her research beforehand. This simple webservice is quite useful as it allows queries like whether a certain position of a target chromosome has a specific nucleotide. However, the increased integration of individuals genomic data into clinical practice and research raised serious privacy concern. Though the answer of such queries are yes or no in Bacon network, it results in serious privacy implication as demonstrated in a recent work from Shringarpure and Bustamante. In their attack model, the authors demonstrated that with a limited number of queries, presence of an individual in any dataset can be determined. We propose two lightweight algorithms (based on randomized response) which captures the efficacy while preserving the privacy of the participants in a genomic beacon service. We also elaborate the strength and weakness of the attack by explaining some of their statistical and mathematical models using real world genomic database. We extend their experimental simulations for different adversarial assumptions and parameters. We experimentally evaluated the solutions on the original attack model with different parameters for better understanding of the privacy and utility tradeoffs provided by these two methods. Also, the statistical analysis further elaborates the different aspects of the prior attack which leads to a better risk management for the participants in a beacon service. The differentially private and lightweight solutions discussed here will make the attack much difficult to succeed while maintaining the fundamental motivation of beacon database network.

  20. Radio beacon synchronization in coherent receivers for nanosatellite applications

    OpenAIRE

    Camps Llorente, Daniel; Piera González, Joan

    2017-01-01

    This document presents a study about the Radio beacon synchronization in coherent receivers for nanosatellite applications. First of all, it is studied the history of these nanosatellites and their actual role in the Aerospace industry, considering their low cost compared to bigger satellites and also because of their availability for all types of companies and people (as universities). These nanosatellites have a wide range of applications, and lots of them depend on the imagination of the u...

  1. Beta aerosols beacon, a truly portable continuous air monitor

    International Nuclear Information System (INIS)

    Prince, R.P.; Garber, F.W.

    1987-01-01

    The Beta Aerosols Beacon (BAB) is a portable (57 lbs) continuous air monitor designed to detect airborne radiation. Utilizing solid state detectors has eliminated the use of lead shielding usually necessary for achieving accurate readings in high background areas, making the monitor lightweight as well as portable. The size of a small suitcase, it can be carried into confined work areas, eliminating the requirement for workers to wear respirators for many maintenance tasks. This paper describes the operation and applications of the BAB

  2. Performance of MAC protocols in beaconing Mobile Adhoc Multibroadcast Networks

    OpenAIRE

    Rico García, Cristina; Lehner, Andreas; Robertson, Patrick; Strang, Thomas

    2010-01-01

    The investigation of infrastructureless safety applications in dierent transportation systems is a hot research topic. The nodes in thevnetwork are designed to advertise to the rest of the nodes informationabout the current traffic situation by means of short beacon messages containing speed, direction, positions and other relevant safety information. The scheduling should be organized by the MAC layer so that the transmitted messages arrive successfully as soon as possible at the recei...

  3. SPECT and PET Serve as Molecular Imaging Techniques and in Vivo Biomarkers for Brain Metastases

    Directory of Open Access Journals (Sweden)

    Barbara Palumbo

    2014-06-01

    Full Text Available Nuclear medicine techniques (single photon emission computerized tomography, SPECT, and positron emission tomography, PET represent molecular imaging tools, able to provide in vivo biomarkers of different diseases. To investigate brain tumours and metastases many different radiopharmaceuticals imaged by SPECT and PET can be used. In this review the main and most promising radiopharmaceuticals available to detect brain metastases are reported. Furthermore the diagnostic contribution of the combination of SPECT and PET data with radiological findings (magnetic resonance imaging, MRI is discussed.

  4. Distributed Beacon Requirements for Branch Point Tolerant Laser Beam Compensation in Extended Atmospheric Turbulence

    National Research Council Canada - National Science Library

    Zetterlind, Virgil

    2002-01-01

    .... A least squares reconstructor is implemented for comparison. System performance is presented for various scenarios, including correction time-delays, wave-front sensor noise, and extended beacons...

  5. Rayleigh beacon for measuring the surface profile of a radio telescope.

    Science.gov (United States)

    Padin, S

    2014-12-01

    Millimeter-wavelength Rayleigh scattering from water droplets in a cloud is proposed as a means of generating a bright beacon for measuring the surface profile of a radio telescope. A λ=3  mm transmitter, with an output power of a few watts, illuminating a stratiform cloud, can generate a beacon with the same flux as Mars in 10 GHz bandwidth, but the beacon has a narrow line width, so it is extremely bright. The key advantage of the beacon is that it can be used at any time, and positioned anywhere in the sky, as long as there are clouds.

  6. a Search for New Physics with the Beacon Mission

    Science.gov (United States)

    Turyshev, Slava G.; Shao, Michael; Girerd, André; Lane, Benjamin

    The primary objective of the Beyond Einstein Advanced Coherent Optical Network (BEACON) mission is a search for new physics beyond general relativity by measuring the curvature of relativistic space-time around the Earth. This curvature is characterized by the Eddington parameter γ — the most fundamental relativistic gravity parameter and a direct measure for the presence of new physical interactions. BEACON will achieve an accuracy of 1 × 10-9 in measuring the parameter γ, thereby going a factor of 30,000 beyond the present best result involving the Cassini spacecraft. Secondary mission objectives include: (i) a direct measurement of the "frame-dragging" and geodetic precessions in the Earth's rotational gravitomagnetic field, to 0.05% and 0.03% accuracy respectively, (ii) the first measurement of gravity's nonlinear effects on light and the corresponding second order spatial metric's effects to 0.01% accuracy. BEACON will lead to robust advances in tests of fundamental physics — this mission could discover a violation or extension of general relativity and/or reveal the presence of an additional long range interaction in physics. It will provide crucial information to separate modern scalar-tensor theories of gravity from general relativity, probe possible ways for gravity quantization, and test modern theories of cosmological evolution.

  7. Adapting Mobile Beacon-Assisted Localization in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Wei Dong

    2009-04-01

    Full Text Available The ability to automatically locate sensor nodes is essential in many Wireless Sensor Network (WSN applications. To reduce the number of beacons, many mobile-assisted approaches have been proposed. Current mobile-assisted approaches for localization require special hardware or belong to centralized localization algorithms involving some deterministic approaches due to the fact that they explicitly consider the impreciseness of location estimates. In this paper, we first propose a range-free, distributed and probabilistic Mobile Beacon-assisted Localization (MBL approach for static WSNs. Then, we propose another approach based on MBL, called Adapting MBL (A-MBL, to increase the efficiency and accuracy of MBL by adapting the size of sample sets and the parameter of the dynamic model during the estimation process. Evaluation results show that the accuracy of MBL and A-MBL outperform both Mobile and Static sensor network Localization (MSL and Arrival and Departure Overlap (ADO when both of them use only a single mobile beacon for localization in static WSNs.

  8. Adapting mobile beacon-assisted localization in wireless sensor networks.

    Science.gov (United States)

    Teng, Guodong; Zheng, Kougen; Dong, Wei

    2009-01-01

    The ability to automatically locate sensor nodes is essential in many Wireless Sensor Network (WSN) applications. To reduce the number of beacons, many mobile-assisted approaches have been proposed. Current mobile-assisted approaches for localization require special hardware or belong to centralized localization algorithms involving some deterministic approaches due to the fact that they explicitly consider the impreciseness of location estimates. In this paper, we first propose a range-free, distributed and probabilistic Mobile Beacon-assisted Localization (MBL) approach for static WSNs. Then, we propose another approach based on MBL, called Adapting MBL (A-MBL), to increase the efficiency and accuracy of MBL by adapting the size of sample sets and the parameter of the dynamic model during the estimation process. Evaluation results show that the accuracy of MBL and A-MBL outperform both Mobile and Static sensor network Localization (MSL) and Arrival and Departure Overlap (ADO) when both of them use only a single mobile beacon for localization in static WSNs.

  9. Impact of beacon wavelength on phase-compensation performance

    Science.gov (United States)

    Enterline, Allison A.; Spencer, Mark F.; Burrell, Derek J.; Brennan, Terry J.

    2017-09-01

    This study evaluates the effects of beacon-wavelength mismatch on phase-compensation performance. In general, beacon-wavelength mismatch occurs at the system level because the beacon-illuminator laser (BIL) and high-energy laser (HEL) are often at different wavelengths. Such is the case, for example, when using an aperture sharing element to isolate the beam-control sensor suite from the blinding nature of the HEL. With that said, this study uses the WavePlex Toolbox in MATLAB® to model ideal spherical wave propagation through various atmospheric-turbulence conditions. To quantify phase-compensation performance, we also model a nominal adaptive-optics (AO) system. We achieve correction from a Shack-Hartmann wavefront sensor and continuous-face-sheet deformable mirror using a least-squares phase reconstruction algorithm in the Fried geometry and a leaky integrator control law. To this end, we plot the power in the bucket metric as a function of BIL-HEL wavelength difference. Our initial results show that positive BIL-HEL wavelength differences achieve better phase compensation performance compared to negative BIL-HEL wavelength differences (i.e., red BILs outperform blue BILs). This outcome is consistent with past results.

  10. Gender identification of Grasshopper Sparrows comparing behavioral, morphological, and molecular techniques

    Science.gov (United States)

    Ammer, F.K.; Wood, P.B.; McPherson, R.J.

    2008-01-01

    Correct gender identification in monomorphic species is often difficult especially if males and females do not display obvious behavioral and breeding differences. We compared gender specific morphology and behavior with recently developed DNA techniques for gender identification in the monomorphic Grasshopper Sparrow (Ammodramus savannarum). Gender was ascertained with DNA in 213 individuals using the 2550F/2718R primer set and 3% agarose gel electrophoresis. Field observations using behavior and breeding characteristics to identify gender matched DNA analyses with 100% accuracy for adult males and females. Gender was identified with DNA for all captured juveniles that did not display gender specific traits or behaviors in the field. The molecular techniques used offered a high level of accuracy and may be useful in studies of dispersal mechanisms and winter assemblage composition in monomorphic species.

  11. Study of DNA interactions with bifenthrin by spectroscopic techniques and molecular modeling

    Science.gov (United States)

    Zhu, Pan; Zhang, Guowen; Ma, Yadi; Zhang, Yepeng; Miao, Hong; Wu, Yongning

    2013-08-01

    The interaction between bifenthrin (BF) and calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) was investigated by UV-vis absorption, fluorescence, circular dichroism (CD), and Fourier transform infrared (FT-IR) spectroscopy, coupled with viscosity measurements and molecular docking techniques. It was found that BF molecular could intercalate into the base pairs of ctDNA as evidenced by significant increases in absorption intensity, fluorescence polarization and relative viscosity of ctDNA, decrease in iodide quenching effect, and induced CD spectral changes. The association constant of BF with ctDNA was evaluated to be in the order of 104 L mol-1. Thermodynamic analysis of the binding data obtained at different temperatures suggested that the binding process was primarily driven by hydrogen bonds and van der Waals forces, as the values of the enthalpy change (ΔH) and the entropy change (ΔS) were calculated to be -31.13 ± 1.89 kJ mol-1 and -22.79 ± 1.21 J mol-1 K-1, respectively. The results of FT-IR spectra and molecular docking showed that a specific binding mainly existed between BF and adenine and guanine bases.

  12. Nonculture molecular techniques for diagnosis of bacterial disease in animals: a diagnostic laboratory perspective.

    Science.gov (United States)

    Cai, H Y; Caswell, J L; Prescott, J F

    2014-03-01

    The past decade has seen remarkable technical advances in infectious disease diagnosis, and the pace of innovation is likely to continue. Many of these techniques are well suited to pathogen identification directly from pathologic or clinical samples, which is the focus of this review. Polymerase chain reaction (PCR) and gene sequencing are now routinely performed on frozen or fixed tissues for diagnosis of bacterial infections of animals. These assays are most useful for pathogens that are difficult to culture or identify phenotypically, when propagation poses a biosafety hazard, or when suitable fresh tissue is not available. Multiplex PCR assays, DNA microarrays, in situ hybridization, massive parallel DNA sequencing, microbiome profiling, molecular typing of pathogens, identification of antimicrobial resistance genes, and mass spectrometry are additional emerging technologies for the diagnosis of bacterial infections from pathologic and clinical samples in animals. These technical advances come, however, with 2 caveats. First, in the age of molecular diagnosis, quality control has become more important than ever to identify and control for the presence of inhibitors, cross-contamination, inadequate templates from diagnostic specimens, and other causes of erroneous microbial identifications. Second, the attraction of these technologic advances can obscure the reality that medical diagnoses cannot be made on the basis of molecular testing alone but instead through integrated consideration of clinical, pathologic, and laboratory findings. Proper validation of the method is required. It is critical that veterinary diagnosticians understand not only the value but also the limitations of these technical advances for routine diagnosis of infectious disease.

  13. Microbiological studies to select compatible rhizobia for application in wastelands using molecular and nuclear techniques

    International Nuclear Information System (INIS)

    Abdel Raouf, A.M.N

    2010-01-01

    The present work aimed at utilization of wastelands and improving their fertility status through the following topics:1- Isolation and identification of rhizobia from wastelands, then selecting the most resistant isolate to saline conditions.2- Studying the effect of radiation on the most salt tolerant rhizobia and marketing rhizobia using molecular and microbiological techniques.3- Identification and culturing of selected compatible rhizobia to be used in application experiments as a bio fertilizer to inoculate the leguminous crops in order to improve the efficiency of the Rhizobium-legume symbiosis and reclamation of wastelands.4- Application of molecular and nuclear techniques such 16S ribosomal RNA and studying the sequence for these strains for comparison between the most potent rhizobia.5- Determination of protein profile for the most potent rhizobia to throw light about similarities between these strains.6- Attempts to apply polymerase chain reaction (PCR) and use primers for differentiation between the most potent rhizobia.7- Experimental fields for growing some leguminous plants inoculated with irradiated and non-irradiated rhizobia and irrigated with different concentrations of sea water and their effects on growth and total N content of plants.

  14. Proceedings of the FNCA workshop on plant mutation breeding 2001. Molecular biological techniques

    International Nuclear Information System (INIS)

    Kume, Tamikazu; Watanabe, Kazuo; Tano, Shigemitsu

    2002-02-01

    The FNCA (Forum for Nuclear Cooperation in Asia) Workshop on Plant Mutation Breeding was held on 20-24 August 2001 in Bangkok, Thailand. The Workshop was sponsored by the Ministry of Education, Culture, Sports, Science and Technology (MEXT). The Kasetsart University (KU), the Office of Atomic Energy for Peace (OAEP) and Department of Agriculture (DOA) acted as local host and the organizer with the cooperation of the Ministry of Agriculture, Forestry and Fisheries (MAFF) of Japan, the Japan Atomic Industrial Forum (JAIF) and Japan Atomic Energy Research Institute (JAERI). The Workshop was attended by two participants, a Project Leader and an expert on molecular biological techniques for plant mutation breeding, from each of the participating countries, i.e. China, Indonesia, Malaysia, the Philippines and Vietnam. One participant from the Republic of Korea, nine participants from Japan and thirteen participants from Thailand including three invited speakers attended the Workshop. Eleven papers including three invited papers on the current status of molecular biological techniques for plant mutation breeding were presented. Discussions were focused to further regional cooperation, to review and discuss results of past activities. The Medium-Term Plan of the project on the application of radiation and radioisotopes for agriculture in participating countries of Regional Nuclear Cooperation Activities (RNCA) was formulated and agreed. This proceeding compiles the invited and contributed papers that were submitted from the speakers. (author)

  15. X-ray Constrained Extremely Localized Molecular Orbitals: Theory and Critical Assessment of the New Technique.

    Science.gov (United States)

    Genoni, Alessandro

    2013-07-09

    Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.

  16. Experimental investigations of micro-scale flow and heat transfer phenomena by using molecular tagging techniques

    International Nuclear Information System (INIS)

    Hu, Hui; Jin, Zheyan; Lum, Chee; Nocera, Daniel; Koochesfahani, Manoochehr

    2010-01-01

    Recent progress made in the development of novel molecule-based flow diagnostic techniques, including molecular tagging velocimetry (MTV) and lifetime-based molecular tagging thermometry (MTT), to achieve simultaneous measurements of multiple important flow variables for micro-flows and micro-scale heat transfer studies is reported in this study. The focus of the work described here is the particular class of molecular tagging tracers that relies on phosphorescence. Instead of using tiny particles, especially designed phosphorescent molecules, which can be turned into long-lasting glowing marks upon excitation by photons of appropriate wavelength, are used as tracers for both flow velocity and temperature measurements. A pulsed laser is used to 'tag' the tracer molecules in the regions of interest, and the tagged molecules are imaged at two successive times within the photoluminescence lifetime of the tracer molecules. The measured Lagrangian displacement of the tagged molecules provides the estimate of the fluid velocity. The simultaneous temperature measurement is achieved by taking advantage of the temperature dependence of phosphorescence lifetime, which is estimated from the intensity ratio of the tagged molecules in the acquired two phosphorescence images. The implementation and application of the molecular tagging approach for micro-scale thermal flow studies are demonstrated by two examples. The first example is to conduct simultaneous flow velocity and temperature measurements inside a microchannel to quantify the transient behavior of electroosmotic flow (EOF) to elucidate underlying physics associated with the effects of Joule heating on electrokinematically driven flows. The second example is to examine the time evolution of the unsteady heat transfer and phase changing process inside micro-sized, icing water droplets, which is pertinent to the ice formation and accretion processes as water droplets impinge onto cold wind turbine blades

  17. Molecular dynamics in porous media studied by nuclear magnetic resonance techniques

    International Nuclear Information System (INIS)

    Mattea, C.

    2006-01-01

    Field cycling NMR relaxometry was used to study dynamics of fluids under confinement in different scenarios: fluids flowing through porous media, fluids partially filling porous media and polymer melts in nanoscopic pores. Diffusion in partially filled porous media was also studied with the aid of an NMR diffusometry technique. It is shown that hydrodynamic flow influences the spin-lattice relaxation rate of water confined in mesoscopic porous media under certain conditions. The effect is predicted by an analytical theory and Monte Carlo simulations, and confirmed experimentally by field-cycling NMR relaxometry. Field-cycling NMR relaxometry has been applied to polar and non polar adsorbates in partially filled silica porous glasses. The dependence of the spin-lattice relaxation rate on the filling degree shows that limits for slow and fast exchange between different phases can be distinguished and identified depending on the pore size and polarity of the solvents. Diffusion in the same unsaturated systems was studied with the aid of NMR diffusometry technique. The effective diffusion coefficient of solvents with different polarities displays opposite tendencies as a function of the liquid content. A two-phase fast exchange model including Knudsen and ordinary diffusion and different effective tortuosities is presented accounting for these phenomena. In the case of polymer melts confined in narrow artificial tubes of a porous solid matrix with variable diameter (9 to 57 nm), the characteristics of reptation were experimentally verified using proton field cycling NMR relaxometry technique. This observation is independent of the molecular mass and pore size. In bulk, the same polymer melts show either Rouse or renormalized Rouse dynamics, depending on the molecular mass. The polymers under confinement show features specific for reptation even with a pore diameter 15 times larger than the Flory radius while bulk melts of the same polymers do not. (orig.)

  18. Role of Artificial Intelligence Techniques (Automatic Classifiers) in Molecular Imaging Modalities in Neurodegenerative Diseases.

    Science.gov (United States)

    Cascianelli, Silvia; Scialpi, Michele; Amici, Serena; Forini, Nevio; Minestrini, Matteo; Fravolini, Mario Luca; Sinzinger, Helmut; Schillaci, Orazio; Palumbo, Barbara

    2017-01-01

    Artificial Intelligence (AI) is a very active Computer Science research field aiming to develop systems that mimic human intelligence and is helpful in many human activities, including Medicine. In this review we presented some examples of the exploiting of AI techniques, in particular automatic classifiers such as Artificial Neural Network (ANN), Support Vector Machine (SVM), Classification Tree (ClT) and ensemble methods like Random Forest (RF), able to analyze findings obtained by positron emission tomography (PET) or single-photon emission tomography (SPECT) scans of patients with Neurodegenerative Diseases, in particular Alzheimer's Disease. We also focused our attention on techniques applied in order to preprocess data and reduce their dimensionality via feature selection or projection in a more representative domain (Principal Component Analysis - PCA - or Partial Least Squares - PLS - are examples of such methods); this is a crucial step while dealing with medical data, since it is necessary to compress patient information and retain only the most useful in order to discriminate subjects into normal and pathological classes. Main literature papers on the application of these techniques to classify patients with neurodegenerative disease extracting data from molecular imaging modalities are reported, showing that the increasing development of computer aided diagnosis systems is very promising to contribute to the diagnostic process.

  19. Weak beacon detection for air-to-ground optical wireless link establishment.

    Science.gov (United States)

    Han, Yaoqiang; Dang, Anhong; Tang, Junxiong; Guo, Hong

    2010-02-01

    In an air-to-ground free-space optical communication system, strong background interference seriously affects the beacon detection, which makes it difficult to establish the optical link. In this paper, we propose a correlation beacon detection scheme under strong background interference conditions. As opposed to traditional beacon detection schemes, the beacon is modulated by an m-sequence at the transmitting terminal with a digital differential matched filter (DDMF) array introduced at the receiving end to detect the modulated beacon. This scheme is capable of suppressing both strong interference and noise by correlation reception of the received image sequence. In addition, the DDMF array enables each pixel of the image sensor to have its own DDMF of the same structure to process its received image sequence in parallel, thus it makes fast beacon detection possible. Theoretical analysis and an outdoor experiment have been demonstrated and show that the proposed scheme can realize fast and effective beacon detection under strong background interference conditions. Consequently, the required beacon transmission power can also be reduced dramatically.

  20. Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language.

    Science.gov (United States)

    Elmarakeby, Haitham; Arefiyan, Mostafa; Myers, Elijah; Li, Song; Grene, Ruth; Heath, Lenwood S

    2017-12-01

    The Beacon Editor is a cross-platform desktop application for the creation and modification of signal transduction pathways using the Systems Biology Graphical Notation Activity Flow (SBGN-AF) language. Prompted by biologists' requests for enhancements, the Beacon Editor includes numerous powerful features for the benefit of creation and presentation.

  1. 46 CFR 169.555 - Emergency position indicating radio beacon (EPIRB).

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Emergency position indicating radio beacon (EPIRB). 169.555 Section 169.555 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) NAUTICAL SCHOOLS... Emergency position indicating radio beacon (EPIRB). (a) Each vessel certificated for exposed waters must...

  2. 46 CFR 169.831 - Emergency position indicating radio beacon (EPIRB).

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Emergency position indicating radio beacon (EPIRB). 169.831 Section 169.831 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) NAUTICAL SCHOOLS... radio beacon (EPIRB). The master shall ensure that— (a) The EPIRB required in § 169.555 of this...

  3. What Happened to the Beacon Schools? Policy Reform and Educational Equity

    Science.gov (United States)

    Smith, Emma

    2015-01-01

    This paper considers the impact of the Beacon schools initiative on the social and academic characteristics of secondary schools in England. The Beacon schools programme ran from 1998 to 2004 and epitomised the (then) Labour government's focus on school improvement through diversity, collaboration and partnership. This paper looks at variation in…

  4. 46 CFR 169.744 - Emergency position indicating radio beacon (EPIRB).

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Emergency position indicating radio beacon (EPIRB). 169.744 Section 169.744 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) NAUTICAL SCHOOLS... position indicating radio beacon (EPIRB). Each EPIRB must be marked with the vessel's name. ...

  5. Detecting and Preventing Beacon Replay Attacks in Receiver-Initiated MAC Protocols for Energy Efficient WSNs

    DEFF Research Database (Denmark)

    Di Mauro, Alessio; Fafoutis, Xenofon; Mödersheim, Sebastian Alexander

    2013-01-01

    In receiver-initiated MAC protocols for Wireless Sensor Networks (WSNs), communication is initiated by the receiver of the data through beacons containing the receiver's identity. In this paper, we consider the case of a network intruder that captures and replays such beacons towards legitimate...

  6. Beacon- and Schema-Based Method for Recognizing Algorithms from Students' Source Code

    Science.gov (United States)

    Taherkhani, Ahmad; Malmi, Lauri

    2013-01-01

    In this paper, we present a method for recognizing algorithms from students programming submissions coded in Java. The method is based on the concept of "programming schemas" and "beacons". Schemas are high-level programming knowledge with detailed knowledge abstracted out, and beacons are statements that imply specific…

  7. Crowdsourcing for Context: Regarding Privacy in Beacon Encounters via Contextual Integrity

    Directory of Open Access Journals (Sweden)

    Bello-Ogunu Emmanuel

    2016-07-01

    Full Text Available Research shows that context is important to the privacy perceptions associated with technology. With Bluetooth Low Energy beacons, one of the latest technologies for providing proximity and indoor tracking, the current identifiers that characterize a beacon are not sufficient for ordinary users to make informed privacy decisions about the location information that could be shared. One solution would be to have standardized category and privacy labels, produced by beacon providers or an independent third-party. An alternative solution is to find an approach driven by users, for users. In this paper, we propose a novel crowdsourcing based approach to introduce elements of context in beacon encounters.We demonstrate the effectiveness of this approach through a user study, where participants use a crowd-based mobile app designed to collect beacon category and privacy information as a scavenger hunt game. Results show that our approach was effective in helping users label beacons according to the specific context of a given beacon encounter, as well as the privacy perceptions associated with it. This labeling was done with an accuracy of 92%, and with an acceptance rate of 82% of all recommended crowd labels. Lastly, we conclusively show how crowdsourcing for context can be used towards a user-centric framework for privacy management during beacon encounters.

  8. Het effect van beacons in de ByAmfi Store gemeten, geanalyseerd en ontmaskerd

    NARCIS (Netherlands)

    Moes, Anne; van Vliet, Harry

    2015-01-01

    Volgens meerdere marketeers zijn beacons ‘the next big thing’; en grote retailers als de Bijenkorf zetten beacons al in. Klanten kopen namelijk steeds meer via internet, en winkels zoeken daarom naar manieren om een beleving te bieden, zodat klanten naar de winkel blijven komen.

  9. Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques.

    Science.gov (United States)

    Rajendiran, Nivedita; Durrant, Jacob D

    2018-05-05

    Molecular dynamics (MD) simulations provide critical insights into many biological mechanisms. Programs such as VMD, Chimera, and PyMOL can produce impressive simulation visualizations, but they lack many advanced rendering algorithms common in the film and video-game industries. In contrast, the modeling program Blender includes such algorithms but cannot import MD-simulation data. MD trajectories often require many gigabytes of memory/disk space, complicating Blender import. We present Pyrite, a Blender plugin that overcomes these limitations. Pyrite allows researchers to visualize MD simulations within Blender, with full access to Blender's cutting-edge rendering techniques. We expect Pyrite-generated images to appeal to students and non-specialists alike. A copy of the plugin is available at http://durrantlab.com/pyrite/, released under the terms of the GNU General Public License Version 3. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  10. Vibrio parahaemolyticus: A Review on the Pathogenesis, Prevalence and Advance Molecular Identification Techniques

    Directory of Open Access Journals (Sweden)

    Vengadesh eLetchumanan

    2014-12-01

    Full Text Available Vibrio parahaemolyticus is a Gram-negative halophilic bacterium that is found in estuarine, marine and coastal environments. Vibrio parahaemolyticus is the leading causal agent of human acute gastroenteritis following the consumption of raw, undercooked or mishandled marine products. In rare cases, Vibrio parahaemolyticus causes wound infection, ear infection or septicaemia in individuals with pre-existing medical conditions. Vibrio parahaemolyticus has two hemolysins virulence factors that are thermostable direct hemolysin (tdh-a pore-forming protein that contributes to the invasiveness of the bacterium in humans, and TDH-related hemolysin (trh, which plays a similar role as thermostable direct hemolysin (tdh in the disease pathogenesis. In addition, the bacterium is also encodes for adhesions and type III secretion systems (T3SS1 and T3SS2 to ensure its survival in the environment. This review aims at discussing the Vibrio parahemolyticus growth and characteristics, pathogenesis, prevalence and advances in molecular identification techniques.

  11. Sex determination of Pohnpei Micronesian kingfishers using morphological and molecular genetic techniques

    Science.gov (United States)

    Kesler, Dylan C.; Lopes, I.F.; Haig, Susan M.

    2006-01-01

    Conservation-oriented studies of Micronesian Kingfishers (Todiramphus cinnamominus) have been hindered by a lack of basic natural history information, despite the status of the Guam subspecies (T. c. cinnamominus) as one of the most endangered species in the world. We used tissue samples and morphometric measures from museum specimens and wild-captured Pohnpei Micronesian Kingfishers (T. c. reichenbachii) to develop methods for sex determination. We present a modified molecular protocol and a discriminant function that yields the probability that a particular individual is male or female. Our results revealed that females were significantly larger than males, and the discriminant function correctly predicted sex in 73% (30/41) of the individuals. The sex of 86% (18/21) of individuals was correctly assigned when a moderate reliability threshold was set. Sex determination using molecular genetic techniques was more reliable than methods based on morphology. Our results will facilitate recovery efforts for the critically endangered Guam Micronesian Kingfisher and provide a basis for sex determination in the 11 other endangered congeners in the Pacific Basin.

  12. Multiparticle 3D imaging technique to study the structure of molecular ions

    International Nuclear Information System (INIS)

    Koenig, W.; Faibis, A.; Kanter, E.P.; Vager, Z.; Zabransky, B.J.

    1984-01-01

    When energetic molecular ions (E/sub ion/ = 0.1 to 0.5 MeV/amu) pass through thin solid targets a Coulomb explosion ensues due to the rapid (approx. 10 -17 s) stripping of the valence electrons. This process has been successfully used to derive stereochemical information on diatomic and on selected triatomic ions. In order to investigate more complex molecular ions as well as to obtain more accurate and detailed structure information, a large area, multiparticle, position- and time-sensitive detector has been developed to detect all atomic fragments in coincidence. The requirement of multiparticle detection independent of the relative particle positions leads to a rather complex data-readout and -reduction system containing approx. 650 analog-to-digital conversions per event. The system relies heavily on techniques developed for high energy physics experiments during recent years. The single event resolution of the apparatus with respect to bond-lengths and -angles has been studied by Monte Carlo simulations and is typically a few percent

  13. Exploration of disulfiram dealings with calf thymus DNA using spectroscopic, electrochemical and molecular docking techniques

    International Nuclear Information System (INIS)

    Subastri, A.; Durga, A.; Harikrishna, K.; Sureshkumar, M.; Jeevaratnam, K.; Girish, K.S.; Thirunavukkarasu, C.

    2016-01-01

    Disulfiram (C 10 H 20 N 2 S 4 ) is an acetaldehyde dehydrogenase inhibitor used in the treatment of chronic alcoholism and it has also been subjected to the clinical trial for cancer in recent times. However, there is no report on the binding effect of this emerging drug with DNA. Hence, the present investigation was taken up to study the binding effect of disulfiram on DNA under physiological conditions. UV–vis absorption spectroscopy, fluorescence emission spectroscopy, circular dichroism spectroscopy, cyclic voltammetry and molecular docking techniques were employed to determine the interaction mode of disulfiram with DNA. Further, DNA cleavage property of disulfiram was carried out by using agarose gel electrophoresis. The UV–vis absorption, emission and cyclic voltammetry measurements revealed that disulfiram showed the intercalative mode of interaction with DNA. The circular dichroism study exhibited structural changes of partial transition from B-conformation to A-conformation in DNA upon addition of disulfiram. Molecular docking study of disulfiram with DNA depicted intercalative mode of binding by formation of hydrogen and hydrophobic interaction along with docking score of −3.07 kcal/mol. The DNA cleavage study revealed that low concentration of disulfiram (50 µM) protected the DNA from oxidative damage sequentially, while high concentration of disulfiram (100 µM) showed less protective activity. Conversely, it caused DNA damage in the presence of hydroxyl radical oxidative system. Hence, the results obtained from the present investigations provide detailed discernment into DNA interaction effects of disulfiram.

  14. Non-linear optical techniques and optical properties of condensed molecular systems

    Science.gov (United States)

    Citroni, Margherita

    2013-06-01

    Structure, dynamics, and optical properties of molecular systems can be largely modified by the applied pressure, with remarkable consequences on their chemical stability. Several examples of selective reactions yielding technologically attractive products can be cited, which are particularly efficient when photochemical effects are exploited in conjunction with the structural conditions attained at high density. Non-linear optical techniques are a basic tool to unveil key aspects of the chemical reactivity and dynamic properties of molecules. Their application to high-pressure samples is experimentally challenging, mainly because of the small sample dimensions and of the non-linear effects generated in the anvil materials. In this talk I will present results on the electronic spectra of several aromatic crystals obtained through two-photon induced fluorescence and two-photon excitation profiles measured as a function of pressure (typically up to about 25 GPa), and discuss the relationship between the pressure-induced modifications of the electronic structure and the chemical reactivity at high pressure. I will also present the first successful pump-probe infrared measurement performed as a function of pressure on a condensed molecular system. The system under examination is liquid water, in a sapphire anvil cell, up to 1 GPa along isotherms at 298 and 363 K. These measurements give a new enlightening insight into the dynamical properties of low- and high-density water allowing a definition of the two structures.

  15. Application of molecular techniques for the assessment of microorganism diversity on cultural heritage objects.

    Science.gov (United States)

    Otlewska, Anna; Adamiak, Justyna; Gutarowska, Beata

    2014-01-01

    As a result of their unpredictable ability to adapt to varying environmental conditions, microorganisms inhabit different types of biological niches on Earth. Owing to the key role of microorganisms in many biogeochemical processes, trends in modern microbiology emphasize the need to know and understand the structure and function of complex microbial communities. This is particularly important if the strategy relates to microbial communities that cause biodeterioration of materials that constitute our cultural heritage. Until recently, the detection and identification of microorganisms inhabiting objects of cultural value was based only on cultivation-dependent methods. In spite of many advantages, these methods provide limited information because they identify only viable organisms capable of growth under standard laboratory conditions. However, in order to carry out proper conservation and renovation, it is necessary to know the complete composition of microbial communities and their activity. This paper presents and characterizes modern techniques such as genetic fingerprinting and clone library construction for the assessment of microbial diversity based on molecular biology. Molecular methods represent a favourable alternative to culture-dependent methods and make it possible to assess the biodiversity of microorganisms inhabiting technical materials and cultural heritage objects.

  16. Molecular techniques to distinguish morphologically similar Hydrilla verticillata, Egeria densa, Elodea nuttallii, and Elodea canadensis

    Science.gov (United States)

    Rybicki, Nancy B.; Kirshtein, Julie D.; Voytek, Mary A.

    2013-01-01

    The four submerged aquatic species, hydrilla (Hydrilla verticillata [monoecious and dioecious]), Brazilian waterweed (Egeria densa), Canadian waterweed (Elodea canadensis), and western waterweed (Elodea nuttallii), are difficult to positively identify because of their morphological similarity to each other, resulting in possible misidentification. This limits our ability to understand their past and present distribution, which is important in aquatic plant management. We investigated a molecular technique to identify these species, which are problematic because of their invasive nature on multiple continents. Approximately 100 samples of these species, ranging in age from 40-yr-old herbarium samples to recently collected plants, were collected from regions across the United States. The distribution and range of the samples collected in this research were compared to those reported in the literature. We confirmed information on the current wide distribution of both hydrilla biotypes in the United States and discovered that hydrilla had actually invaded the waterways near Washington, DC 6 yr earlier than originally reported. In addition, we found evidence of the confusion, dating back to the 1980s, between Canadian waterweed and western waterweed in the mid-Atlantic region of the United States. Canadian waterweed was previously reported as common and western waterweed as rare; however, our samples indicate the opposite is true. This information indicates there is a need for investigators to anticipate the spread of hydrilla populations to northern U.S. waterways, where it will compete with existing plant species, including Canadian and western waterweeds. Our ability to confirm distribution and pace of spread of invasive and noninvasive species will improve with increased application of molecular techniques.

  17. Uncertainty analysis for the BEACON-COLSS core monitoring system application

    International Nuclear Information System (INIS)

    Morita, T.; Boyd, W.A.; Seong, K.B.

    2005-01-01

    This paper will cover the measurement uncertainty analysis of BEACON-COLSS core monitoring system. The uncertainty evaluation is made by using a BEACON-COLSS simulation program. By simulating the BEACON on-line operation for analytically generated reactor conditions, accuracy of the 'Measured' results can be evaluated by comparing to analytically generated 'Truth'. The DNB power margin is evaluated based on the Combustion Engineering's Modified Statistical Combination of Uncertainties (MSCU) using the CETOPD code for the DNBR calculation. A BEACON-COLSS simulation program for the uncertainty evaluation function has been established for plant applications. Qualification work has been completed for two Combustion Engineering plants. Results of the BEACON-COLSS measured peaking factors and DNBR power margin are plant type dependent and are applicable to reload cores as long as the core geometry and detector layout are unchanged. (authors)

  18. Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks.

    Science.gov (United States)

    Raisaro, Jean Louis; Tramèr, Florian; Ji, Zhanglong; Bu, Diyue; Zhao, Yongan; Carey, Knox; Lloyd, David; Sofia, Heidi; Baker, Dixie; Flicek, Paul; Shringarpure, Suyash; Bustamante, Carlos; Wang, Shuang; Jiang, Xiaoqian; Ohno-Machado, Lucila; Tang, Haixu; Wang, XiaoFeng; Hubaux, Jean-Pierre

    2017-07-01

    The Global Alliance for Genomics and Health (GA4GH) created the Beacon Project as a means of testing the willingness of data holders to share genetic data in the simplest technical context-a query for the presence of a specified nucleotide at a given position within a chromosome. Each participating site (or "beacon") is responsible for assuring that genomic data are exposed through the Beacon service only with the permission of the individual to whom the data pertains and in accordance with the GA4GH policy and standards.While recognizing the inference risks associated with large-scale data aggregation, and the fact that some beacons contain sensitive phenotypic associations that increase privacy risk, the GA4GH adjudged the risk of re-identification based on the binary yes/no allele-presence query responses as acceptable. However, recent work demonstrated that, given a beacon with specific characteristics (including relatively small sample size and an adversary who possesses an individual's whole genome sequence), the individual's membership in a beacon can be inferred through repeated queries for variants present in the individual's genome.In this paper, we propose three practical strategies for reducing re-identification risks in beacons. The first two strategies manipulate the beacon such that the presence of rare alleles is obscured; the third strategy budgets the number of accesses per user for each individual genome. Using a beacon containing data from the 1000 Genomes Project, we demonstrate that the proposed strategies can effectively reduce re-identification risk in beacon-like datasets. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association.

  19. An Interactive Real-Time Locating System Based on Bluetooth Low-Energy Beacon Network †.

    Science.gov (United States)

    Lin, You-Wei; Lin, Chi-Yi

    2018-05-21

    The ubiquity of Bluetooth-enabled smartphones and peripherals has brought tremendous convenience to our daily life. In recent years, Bluetooth beacons have also been gaining popularity in implementing a variety of innovative location-based services such as self-guided systems in exhibition centers. However, the broadcast-based beacon technology can only provide unidirectional communication. In case smartphone users would like to respond to the beacon messages, they have to rely on their own mobile Internet connections to send the information back to the backend system. Nevertheless, mobile Internet services may not be always available or too costly. In this work, we develop a real-time locating system based only on the Bluetooth low energy (BLE) technology to support interactive communications by combining the broadcast and mesh topology options to extend the applicability of beacon solutions. Specifically, we turn the smartphone into a beacon device and augment the beacon devices with the capability of forming a mesh network. The implementation result shows that our beacon devices can detect the presence of specific users at specific locations, and then the presence state can be sent to the application server via the relay of beacon devices. Moreover, the application server can send personalized location-based messages to the users, again via the relay of beacon devices. With the capability of relaying messages between the beacon devices, it would be convenient for developers to implement a variety of interactive applications such as tracking VIP customers at the airport, or tracking an elder with Alzheimer’s disease in the neighborhood.

  20. An Interactive Real-Time Locating System Based on Bluetooth Low-Energy Beacon Network †

    Directory of Open Access Journals (Sweden)

    You-Wei Lin

    2018-05-01

    Full Text Available The ubiquity of Bluetooth-enabled smartphones and peripherals has brought tremendous convenience to our daily life. In recent years, Bluetooth beacons have also been gaining popularity in implementing a variety of innovative location-based services such as self-guided systems in exhibition centers. However, the broadcast-based beacon technology can only provide unidirectional communication. In case smartphone users would like to respond to the beacon messages, they have to rely on their own mobile Internet connections to send the information back to the backend system. Nevertheless, mobile Internet services may not be always available or too costly. In this work, we develop a real-time locating system based only on the Bluetooth low energy (BLE technology to support interactive communications by combining the broadcast and mesh topology options to extend the applicability of beacon solutions. Specifically, we turn the smartphone into a beacon device and augment the beacon devices with the capability of forming a mesh network. The implementation result shows that our beacon devices can detect the presence of specific users at specific locations, and then the presence state can be sent to the application server via the relay of beacon devices. Moreover, the application server can send personalized location-based messages to the users, again via the relay of beacon devices. With the capability of relaying messages between the beacon devices, it would be convenient for developers to implement a variety of interactive applications such as tracking VIP customers at the airport, or tracking an elder with Alzheimer’s disease in the neighborhood.

  1. Determination of BEACON Coupling Coefficients using data from Xenon transient

    International Nuclear Information System (INIS)

    Bozic, M.; Kurincic, B.

    2007-01-01

    NEK uses BEACO TM code (BEACO TM - Westinghouse Best Estimate Analyzer for Core Operating Nuclear) for core monitoring, analysis and core behaviour prediction. Coupling Coefficients determine relationship between core response and excore instrumentation. Measured power distribution using incore moveable detectors during Xenon transient with sufficient power axial offset change is the most important data for further analysis. Classic methodology and BEACO TM Conservative methodology using established Coupling Coefficients are compared on NPP Krsko case. BEACON TM Conservative methodology with predefined Coupling Coefficients is used as a surveillance tool for verification of relationship between core and excore instrumentation during power operation. (author)

  2. Beacon-teknologi - fremtidens kundebehandling eller en trussel for personvernet?

    OpenAIRE

    Jyrkinen, Anna; Kamås, Kamilla

    2016-01-01

    Smarttelefoner har blitt en naturlig del av våre liv. Alt man gjør på smarttelefonen, blir lagret som såkalte “big data”. Dette er verdifull informasjon for bedrifter, da de får mer detaljert bilde av hva forbrukere ser, eller holder på med i det virkelige liv. Det kan oppstå et dilemma ved hvor langt selskapene er villige til å strekke seg, for å samle inn informasjon om sine kunder. Beacons er en ny teknologiform og fungerer via små apparater som kommuniserer med kunder gjenn...

  3. Identification of Viable Helicobacter pylori in Drinking Water Supplies by Cultural and Molecular Techniques.

    Science.gov (United States)

    Santiago, Paula; Moreno, Yolanda; Ferrús, M Antonía

    2015-08-01

    Helicobacter pylori is one of the most common causes of chronic bacterial infection in humans, directly related to peptic ulcer and gastric cancer. It has been suggested that H. pylori can be acquired through different transmission routes, including water. In this study, culture and qPCR were used to detect and identify the presence of H. pylori in drinking water. Furthermore, the combined techniques PMA-qPCR and DVC-FISH were applied for detection of viable cells of H. pylori. Among 24 drinking water samples, 16 samples were positive for the presence of H. pylori, but viable cells were only detected in six samples. Characteristic colonies, covered by a mass of bacterial unspecific growth, were observed on selective agar plates from an only sample, after enrichment. The mixed culture was submitted to DVC-FISH and qPCR analysis, followed by sequencing of the amplicons. Molecular techniques confirmed the growth of H. pylori on the agar plate. Our results demonstrate for the first time that H. pylori can survive and be potentially infective in drinking water, showing that water distribution systems could be a potential route for H. pylori transmission. © 2015 John Wiley & Sons Ltd.

  4. The use of molecular imaging combined with genomic techniques to understand the heterogeneity in cancer metastasis

    Science.gov (United States)

    Chowdhury, R; Ganeshan, B; Irshad, S; Lawler, K; Eisenblätter, M; Milewicz, H; Rodriguez-Justo, M; Miles, K; Ellis, P; Groves, A; Punwani, S

    2014-01-01

    Tumour heterogeneity has, in recent times, come to play a vital role in how we understand and treat cancers; however, the clinical translation of this has lagged behind advances in research. Although significant advancements in oncological management have been made, personalized care remains an elusive goal. Inter- and intratumour heterogeneity, particularly in the clinical setting, has been difficult to quantify and therefore to treat. The histological quantification of heterogeneity of tumours can be a logistical and clinical challenge. The ability to examine not just the whole tumour but also all the molecular variations of metastatic disease in a patient is obviously difficult with current histological techniques. Advances in imaging techniques and novel applications, alongside our understanding of tumour heterogeneity, have opened up a plethora of non-invasive biomarker potential to examine tumours, their heterogeneity and the clinical translation. This review will focus on how various imaging methods that allow for quantification of metastatic tumour heterogeneity, along with the potential of developing imaging, integrated with other in vitro diagnostic approaches such as genomics and exosome analyses, have the potential role as a non-invasive biomarker for guiding the treatment algorithm. PMID:24597512

  5. Nuclear science fights malaria. Radiation and molecular techniques can play targeted roles

    International Nuclear Information System (INIS)

    Groth, Steffen; Khan, Baldip; Robinson, Alan; Hendrichs, Jorge

    2001-01-01

    Malaria is the most important insect transmitted disease. Globally there are 300 to 500 million clinical cases of malaria a year. They result in two million deaths per year (one every 30 seconds), more than 90% of which occur in sub-Saharan Africa. More than 90% of those affected are children less than five years old. The economic impact of the disease is felt disproportionately by poor families who may spend a fourth of their annual income on prevention and control measures. The causative agents are parasites of the genus Plasmodium and they are transmitted only by female mosquitoes of the genus Anopheles. Among key strategies to control malaria are the surveillance of anti-malarial drug efficacy through monitoring the levels of drug resistance, and the reduction of mosquito populations. Nuclear techniques can play important roles in these efforts to combat malaria. This article reports on IAEA activities associated with drug-resistant malaria and describes how molecular methods making use of radioactive isotopes can provide a great advantage in the diagnosis of resistance. The article further presents the IAEA's plans for initiating a research programme to assess the feasibility of developing the Sterile Insect Technique (SIT) as a complementary method to control the vector of malaria

  6. Exploration of the speleotherapeutic potential through the cellular and molecular biology techniques

    Directory of Open Access Journals (Sweden)

    Munteanu Constantin

    2011-02-01

    Full Text Available Objective: Exploring the speleotherapy effects on morphology and physiology of dermal and pulmonary fibroblast obtained from Wistar rats tissue in normal conditions and after induction of experimental “astma” awareness with ovalbumin. Materials and methods: Before initiation of dermal and pulmonary fibroblast cultures, 60 of Wistar rats 75-100 g were divided into two groups: control and sensitized with ovalalbumin. 10 animals of each group were sent to Cacica and Dej salt mines and maintained in a speleotherapy regime. Another 10 animals in each group were monitored separately in INRMFB Biobase . Dermal and pulmonary fibroblast cultures were initiated by enzymatic techniques from appropriate tissue taken of each group Wistar rats. Morphological monitoring was done by phase contast microscopy; biochemical and molecular changes of cultures obtained from animals treated speleothropic compared to control, was experimental establised by electrophoresis and Western Blotting techniques.Results: Experimental data revealed the expression of several proteins after the speleotherapeutic treatment. These data were analysed compared with control, using a specific software.Conclusions: Speleotherapeutic treatment of Wistar rats caused significant differences in morphology and protein expression of dermal and pulmonary fibroblatst grown in the laboratory. These differences support the protective effects of speleotherapy compared with data obtained from animals untreated and sensitized with ovalbumin, having induced experimental asthma status.

  7. Low-mass molecular dynamics simulation: A simple and generic technique to enhance configurational sampling

    Energy Technology Data Exchange (ETDEWEB)

    Pang, Yuan-Ping, E-mail: pang@mayo.edu

    2014-09-26

    Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.

  8. Overview of on-line core monitoring system BEACON

    International Nuclear Information System (INIS)

    Dai Qing; Chen Xiaosong

    2013-01-01

    After more than 20 years of development, key technologies embedded with such system have reached a certain degree of maturity among some foreign countries. However, domestically, there is no comparable system yet. Through in-depth research and analysis on the most widely used core monitoring system in the world, BEACON, it's hope that this will provide guidance on our independent development of the first core monitoring system in China. Excore detectors, core outlet thermocouples and incore movable detectors are used to provide measure data on the status of the core for BEACON. Under the assumption of nodal homogeneity, an effective fast group model is used to solve the diffusion equation, followed by core-wise interpolation by Green's function. Finally, reconstruction of a calculated core is fitted with measured data using the surface spline function. The most significant technological advances are core monitoring during unstable core conditions, the use of nodal expansion method to improve accuracy and the adoption of single point calibration to increase the period of recalibration for the whole core. (authors)

  9. Water absorption length measurement with the ANTARES optical beacon system

    International Nuclear Information System (INIS)

    Yepes-Ramirez, Harold

    2011-01-01

    ANTARES is a neutrino telescope located in the Mediterranean Sea with the aim of detecting high energy neutrinos of extra-terrestrial origin. It consists of a three dimensional array on 12 detection lines of photomultiplier tubes (PMTs) able to detect the Cherenkov light induced by muons produced in the interaction of neutrinos with the surrounding water and seabed. To reach the best angular resolution, good time and positioning calibrations are required. The propagation of Cherenkov photons strongly depends on the optical properties of the sea water, which has an impact on the reconstruction efficiency. The determination of the optical parameters, as the absorption and scattering lengths, is crucial to calculate properly the effective area and the angular resolution of the detector. The ANTARES optical beacon system consists of pulsed and fast, well controlled light sources distributed throughout the detector to carry out in situ the relative time calibration of the detector components. In this contribution we show some results on the sea water optical properties and their stability measured with the optical beacon system.

  10. Design and implementation of Bluetooth beacon in mobile payment system

    Science.gov (United States)

    Han, Tiantian; Ding, Lei

    2017-08-01

    The current line of payment means, mainly in the following ways, cash payment, credit card payment, WeChat Alipay sweep payment. There are many inconvenience in Cash payment, large amounts of cash inconvenience to carry, count the money to spend time and effort, true and false banknotes difficult to distinguish, ticket settlement easy to go wrong. Credit card payment is relatively time-consuming, and WeChat Alipay sweep payment need to sweep. Therefore, the design of a convenient, fast payment to meet the line to pay the demand is particularly important. Based on the characteristics of BLE Bluetooth wireless communication technology, this paper designs a kind of payment method based on Bluetooth beacon. Through the Bluetooth beacon broadcast consumption, consumers only need to open the relevant APP in the Android client, and you can get Bluetooth via mobile phone Bluetooth the amount of consumption of the standard broadcast, in accordance with the corresponding payment platform to complete the payment process, which pay less time to improve the efficiency of payment.

  11. Molecular Imaging of Tumors Using a Quantitative T1 Mapping Technique via Magnetic Resonance Imaging

    Directory of Open Access Journals (Sweden)

    Kelsey Herrmann

    2015-07-01

    Full Text Available Magnetic resonance imaging (MRI of glioblastoma multiforme (GBM with molecular imaging agents would allow for the specific localization of brain tumors. Prior studies using T1-weighted MR imaging demonstrated that the SBK2-Tris-(Gd-DOTA3 molecular imaging agent labeled heterotopic xenograft models of brain tumors more intensely than non-specific contrast agents using conventional T1-weighted imaging techniques. In this study, we used a dynamic quantitative T1 mapping strategy to more objectively compare intra-tumoral retention of the SBK2-Tris-(Gd-DOTA3 agent over time in comparison to non-targeted control agents. Our results demonstrate that the targeted SBK2-Tris-(Gd-DOTA3 agent, a scrambled-Tris-(Gd-DOTA3 control agent, and the non-specific clinical contrast agent Optimark™ all enhanced flank tumors of human glioma cells with similar maximal changes on T1 mapping. However, the retention of the agents differs. The non-specific agents show significant recovery within 20 min by an increase in T1 while the specific agent SBK2-Tris-(Gd-DOTA3 is retained in the tumors and shows little recovery over 60 min. The retention effect is demonstrated by percent change in T1 values and slope calculations as well as by calculations of gadolinium concentration in tumor compared to muscle. Quantitative T1 mapping demonstrates the superior binding and retention in tumors of the SBK2-Tris-(Gd-DOTA3 agent over time compared to the non-specific contrast agent currently in clinical use.

  12. Exploration of disulfiram dealings with calf thymus DNA using spectroscopic, electrochemical and molecular docking techniques

    Energy Technology Data Exchange (ETDEWEB)

    Subastri, A.; Durga, A. [Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014 (India); Harikrishna, K.; Sureshkumar, M. [Centre for Bioinformatics, Pondicherry University, Puducherry 605014 (India); Jeevaratnam, K. [Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014 (India); Girish, K.S. [Department of Studies & Research in Biochemistry, Tumkur University, Tumkur, Karnataka (India); Thirunavukkarasu, C., E-mail: tchinnasamy@hotmail.com [Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry 605014 (India)

    2016-02-15

    Disulfiram (C{sub 10}H{sub 20}N{sub 2}S{sub 4}) is an acetaldehyde dehydrogenase inhibitor used in the treatment of chronic alcoholism and it has also been subjected to the clinical trial for cancer in recent times. However, there is no report on the binding effect of this emerging drug with DNA. Hence, the present investigation was taken up to study the binding effect of disulfiram on DNA under physiological conditions. UV–vis absorption spectroscopy, fluorescence emission spectroscopy, circular dichroism spectroscopy, cyclic voltammetry and molecular docking techniques were employed to determine the interaction mode of disulfiram with DNA. Further, DNA cleavage property of disulfiram was carried out by using agarose gel electrophoresis. The UV–vis absorption, emission and cyclic voltammetry measurements revealed that disulfiram showed the intercalative mode of interaction with DNA. The circular dichroism study exhibited structural changes of partial transition from B-conformation to A-conformation in DNA upon addition of disulfiram. Molecular docking study of disulfiram with DNA depicted intercalative mode of binding by formation of hydrogen and hydrophobic interaction along with docking score of −3.07 kcal/mol. The DNA cleavage study revealed that low concentration of disulfiram (50 µM) protected the DNA from oxidative damage sequentially, while high concentration of disulfiram (100 µM) showed less protective activity. Conversely, it caused DNA damage in the presence of hydroxyl radical oxidative system. Hence, the results obtained from the present investigations provide detailed discernment into DNA interaction effects of disulfiram.

  13. Biomechanical testing of new meniscal repair techniques containing ultra high-molecular weight polyethylene suture.

    Science.gov (United States)

    Barber, F Alan; Herbert, Morley A; Schroeder, F Alexander; Aziz-Jacobo, Jorge; Sutker, Michael J

    2009-09-01

    To evaluate the biomechanical characteristics of current meniscal repair techniques containing ultra high-molecular weight polyethylene (UHMWPE) suture with and without cyclic loading. Vertical longitudinal cuts made in porcine menisci were secured with a single repair device. Noncycled and cycled (500 cycles) biomechanical tests were performed on the following groups: group 1, No. 2-0 Mersilene vertical suture (Ethicon, Somerville, NJ); group 2, No. 2-0 Orthocord vertical suture (DePuy Mitek, Westwood, MA); group 3, No. 0 Ultrabraid vertical suture (Smith & Nephew Endoscopy, Andover, MA); group 4, No. 2-0 FiberWire vertical suture (Arthrex, Naples, FL); group 5, vertically oriented mattress suture by use of an Ultra FasT-Fix device (Smith & Nephew Endoscopy) with No. 0 Ultrabraid; group 6, vertically oriented mattress suture by use of a RapidLoc A2 device (DePuy Mitek) with No. 2-0 Orthocord suture; group 7, vertically oriented stitch by use of a MaxFire device with MaxBraid PE suture (Biomet Sports Medicine, Warsaw, IN); and group 8, an obliquely oriented stitch of No. 0 UHMWPE suture inserted by use of a CrossFix device (Cayenne Medical, Scottsdale, AZ). Endpoints were failure loads, failure modes, stiffness, and cyclic displacement. Mean single-pull loads were calculated for Ultra FasT-Fix (121 N), FiberWire (110 N), MaxFire (130 N), Mersilene (84 N), Orthocord (124 N), RapidLoc A2 (86 N), CrossFix (77 N), and Ultrabraid (109 N). After 500 cyclic loads, the Orthocord (222 N) repair was stronger than the others: Ultra FasT-Fix (110 N), FiberWire (117 N), MaxFire (132 N), Mersilene (89 N), RapidLoc A2 (108 N), CrossFix (95 N), and Ultrabraid (126 N) (P Fix, RapidLoc A2, and MaxFire) were comparable to the isolated UHMWPE-containing suture repairs on single-failure load testing. UHMWPE-containing suture repairs are stronger than braided polyester suture repairs, but pure UHMWPE suture (Ultrabraid) elongated more during cycling. Orthocord suture is significantly

  14. Molecular basis of structural make-up of feeds in relation to nutrient absorption in ruminants, revealed with advanced molecular spectroscopy: A review on techniques and models

    Energy Technology Data Exchange (ETDEWEB)

    Rahman, Md. Mostafizar [Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Yu, Peiqiang [Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

    2017-01-31

    Progress in ruminant feed research is no more feasible only based on wet chemical analysis, which is merely able to provide information on chemical composition of feeds regardless of their digestive features and nutritive value in ruminants. Studying internal structural make-up of functional groups/feed nutrients is often vital for understanding the digestive behaviors and nutritive values of feeds in ruminant because the intrinsic structure of feed nutrients is more related to its overall absorption. In this article, the detail information on the recent developments in molecular spectroscopic techniques to reveal microstructural information of feed nutrients and the use of nutrition models in regards to ruminant feed research was reviewed. The emphasis of this review was on (1) the technological progress in the use of molecular spectroscopic techniques in ruminant feed research; (2) revealing spectral analysis of functional groups of biomolecules/feed nutrients; (3) the use of advanced nutrition models for better prediction of nutrient availability in ruminant systems; and (4) the application of these molecular techniques and combination of nutrient models in cereals, co-products and pulse crop research. The information described in this article will promote better insight in the progress of research on molecular structural make-up of feed nutrients in ruminants.

  15. Power-Efficient Beacon Recognition Method Based on Periodic Wake-Up for Industrial Wireless Devices.

    Science.gov (United States)

    Song, Soonyong; Lee, Donghun; Jang, Ingook; Choi, Jinchul; Son, Youngsung

    2018-04-17

    Energy harvester-integrated wireless devices are attractive for generating semi-permanent power from wasted energy in industrial environments. The energy-harvesting wireless devices may have difficulty in their communication with access points due to insufficient power supply for beacon recognition during network initialization. In this manuscript, we propose a novel method of beacon recognition based on wake-up control to reduce instantaneous power consumption in the initialization procedure. The proposed method applies a moving window for the periodic wake-up of the wireless devices. For unsynchronized wireless devices, beacons are always located in the same positions within each beacon interval even though the starting offsets are unknown. Using these characteristics, the moving window checks the existence of the beacon associated withspecified resources in a beacon interval, checks again for neighboring resources at the next beacon interval, and so on. This method can reduce instantaneous power and generates a surplus of charging time. Thus, the proposed method alleviates the problems of power insufficiency in the network initialization. The feasibility of the proposed method is evaluated using computer simulations of power shortage in various energy-harvesting conditions.

  16. DNA aptamer beacon assay for C-telopeptide and handheld fluorometer to monitor bone resorption.

    Science.gov (United States)

    Bruno, John Gordon; Carrillo, Maria P; Phillips, Taylor; Hanson, Douglas; Bohmann, Jonathan A

    2011-09-01

    A novel DNA aptamer beacon is described for quantification of a 26-amino acid C-telopeptide (CTx) of human type I bone collagen. One aptamer sequence and its reverse complement dominated the aptamer pool (31.6% of sequenced clones). Secondary structures of these aptamers were examined for potential binding pockets. Three-dimensional computer models which analyzed docking topologies and binding energies were in agreement with empirical fluorescence experiments used to select one candidate loop for beacon assay development. All loop structures from the aptamer finalists were end-labeled with TYE 665 and Iowa Black quencher for comparison of beacon fluorescence levels as a function of CTx concentration. The optimal beacon, designated CTx 2R-2h yielded a low ng/ml limit of detection using a commercially available handheld fluorometer. The CTx aptamer beacon bound full-length 26-amino acid CTx peptide, but not a shorter 8-amino acid segment of CTx peptide which is a common target for commercial CTx ELISA kits. The prototype assay was shown to detect CTx peptide from human urine after creatinine and urea were removed by size-exclusion chromatography to prevent nonspecific denaturing of the aptamer beacon. This work demonstrates the potential of aptamer beacons to be utilized for rapid and sensitive bone health monitoring in a handheld or point-of-care format.

  17. Pedestrian and motorists' actions at pedestrian hybrid beacon sites: findings from a pilot study.

    Science.gov (United States)

    Pulugurtha, Srinivas S; Self, Debbie R

    2015-01-01

    This paper focuses on an analysis of pedestrian and motorists' actions at sites with pedestrian hybrid beacons and assesses their effectiveness in improving the safety of pedestrians. Descriptive and statistical analyses (one-tail two-sample T-test and two-proportion Z-test) were conducted using field data collected during morning and evening peak hours at three study sites in the city of Charlotte, NC, before and after the installation of pedestrian hybrid beacons. Further, an analysis was conducted to assess the change in pedestrian and motorists' actions over time (before the installation; 1 month, 3 months, 6 months, and 12 months after the installation). Results showed an increase in average traffic speed at one of the pedestrian hybrid beacon sites while no specific trends were observed at the other two pedestrian hybrid beacon sites. A decrease in the number of motorists not yielding to pedestrians, pedestrians trapped in the middle of the street, and pedestrian-vehicle conflicts were observed at all the three pedestrian hybrid beacon sites. The installation of pedestrian hybrid beacons did not have a negative effect on pedestrian actions at two out of the three sites. Improvements seem to be relatively more consistent 3 months after the installation of the pedestrian hybrid beacon.

  18. A Partnership Training Program in Breast Cancer Research Using Molecular Imaging Techniques

    National Research Council Canada - National Science Library

    Wang, Paul C

    2006-01-01

    In the first year of this training grant, five faculty members from different departments at the Howard University were trained in molecular imaging with the faculty at the In Vivo Cellular Molecular...

  19. A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device.

    Science.gov (United States)

    Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia

    2013-12-20

    A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

  20. A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device

    International Nuclear Information System (INIS)

    Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia

    2013-01-01

    A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology. (paper)

  1. A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device

    Science.gov (United States)

    Lambropoulos, Nicholas A.; Reimers, Jeffrey R.; Crossley, Maxwell J.; Hush, Noel S.; Silverbrook, Kia

    2013-12-01

    A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

  2. Probing spatial locality in ionic liquids with the grand canonical adaptive resolution molecular dynamics technique

    Science.gov (United States)

    Shadrack Jabes, B.; Krekeler, C.; Klein, R.; Delle Site, L.

    2018-05-01

    We employ the Grand Canonical Adaptive Resolution Simulation (GC-AdResS) molecular dynamics technique to test the spatial locality of the 1-ethyl 3-methyl imidazolium chloride liquid. In GC-AdResS, atomistic details are kept only in an open sub-region of the system while the environment is treated at coarse-grained level; thus, if spatial quantities calculated in such a sub-region agree with the equivalent quantities calculated in a full atomistic simulation, then the atomistic degrees of freedom outside the sub-region play a negligible role. The size of the sub-region fixes the degree of spatial locality of a certain quantity. We show that even for sub-regions whose radius corresponds to the size of a few molecules, spatial properties are reasonably reproduced thus suggesting a higher degree of spatial locality, a hypothesis put forward also by other researchers and that seems to play an important role for the characterization of fundamental properties of a large class of ionic liquids.

  3. Detection of human filarial parasite Brugia malayi in dogs by histochemical staining and molecular techniques.

    Science.gov (United States)

    Ambily, V R; Pillai, Usha Narayana; Arun, R; Pramod, S; Jayakumar, K M

    2011-09-27

    Human filariasis caused by Brugia malayi is still a public health problem in many countries of Asia including India, Indonesia, Malaysia and Thailand. The World Health Organization (WHO) has targeted to eliminate filariasis by the year 2020 by Mass annual single dose Diethylcarbamazine Administration (MDA). Results of the MDA programme after the first phase was less satisfactory than expected. Malayan filariasis caused by B. malayi is endemic in the south of Thailand where domestic cat serves as the major reservoir host. There is no report about the occurrence of B. malayi in dogs. The present work was carried out to find out the incidence of microfilariasis in dogs and also to detect the presence of human filarial infection in dogs, if any. One hundred dogs above 6 months of age presented to the veterinary college Hospital, Mannuthy, Kerala, with clinical signs suggestive of microfilariasis - fever, anorexia, conjunctivitis, limb and scrotal oedema - were screened for microfilariae by wet film examination. Positive cases were subjected to Giemsa staining, histochemical staining and molecular techniques. Results of the study showed that 80% of dogs had microfilariasis; out of which 20% had sheathed microfilaria. Giemsa and histochemical staining character, PCR and sequencing confirmed it as B. malayi. High prevalence of B. malayi in dogs in this study emphasized the possible role of dogs in transmission of human filariasis. Copyright © 2011 Elsevier B.V. All rights reserved.

  4. New understanding of rhizosphere processes enabled by advances in molecular and spatially resolved techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hess, Nancy J.; Paša-Tolić, Ljiljana; Bailey, Vanessa L.; Dohnalkova, Alice C.

    2017-06-01

    Understanding the role played by microorganisms within soil systems is challenged by the unique intersection of physics, chemistry, mineralogy and biology in fostering habitat for soil microbial communities. To address these challenges will require observations across multiple spatial and temporal scales to capture the dynamics and emergent behavior from complex and interdependent processes. The heterogeneity and complexity of the rhizosphere require advanced techniques that press the simultaneous frontiers of spatial resolution, analyte sensitivity and specificity, reproducibility, large dynamic range, and high throughput. Fortunately many exciting technical advancements are now available to inform and guide the development of new hypotheses. The aim of this Special issue is to provide a holistic view of the rhizosphere in the perspective of modern molecular biology methodologies that enabled a highly-focused, detailed view on the processes in the rhizosphere, including numerous, strong and complex interactions between plant roots, soil constituents and microorganisms. We discuss the current rhizosphere research challenges and knowledge gaps, as well as perspectives and approaches using newly available state-of-the-art toolboxes. These new approaches and methodologies allow the study of rhizosphere processes and properties, and rhizosphere as a central component of ecosystems and biogeochemical cycles.

  5. Ex vivo irradiation of human blood to determine DNA damage using molecular techniques

    International Nuclear Information System (INIS)

    Montes, Angel; Agapito, Juan

    2014-01-01

    Biological dosimetry is the assessment of absorbed dose in individuals exposed to ionizing radiation from blood samples based on the radiation induced damage in cellular DNA. The aim of this study was to determine the damage in the DNA through the assessment of an experimental ex vivo assay using irradiated samples of human blood cells. For this purpose, blood samples were irradiated at low doses (<100 mGy) considering the following parameters: blood volume (3mL), temperature (37 °C) and incubation time (0.5, 2, 4, 8 and 24 h). Dose values were: 0, 12.5, 25 and 50 mGy using Cesium -137 gamma rays at 662 keV and a dose rate of 38.46 mGy/h. The qualitative damage in the genomic DNA was determined using agarose gel electrophoresis and polymerase chain reaction (PCR) for the p53 gene in a sequence of 133 pb of exon 7, related to the protein that acts in the cell repair process. The results of the qualitative analysis showed no degradation of genomic DNA; also an increase in the DNA concentration was observed up to the fourth hour of incubation, finding maximum values for all doses in the two samples. As a conclusion, the effects of ionizing radiation at doses used in this experiment do not generate a detectable damage, by means of molecular techniques such as those used in the present study. (authors).

  6. Easy-to-Build Satellite Beacon Receiver for Propagation Experimentation at Millimeter Bands

    Directory of Open Access Journals (Sweden)

    F. Machado

    2014-04-01

    Full Text Available This paper describes the design and development of a digital satellite beacon receiver for propagation experimentation. Satellite beacons are frequently available for pointing large antennas, but such signals can be used for measuring rain attenuation and other phenomena as, for example, tropospheric scintillation. A fairly inexpensive beacon receiver has been built using off-the-shelf parts. This instrument is not at all bulky making it suitable for easy transportation. This article analyzes the receiver specifications, describes in detail its structure and presents some operational test results.

  7. Tight Bounds for Beacon-Based Coverage in Simple Rectilinear Polygons

    KAUST Repository

    Bae, Sang Won; Shin, Chan-Su; Vigneron, Antoine E.

    2016-01-01

    We establish tight bounds for beacon-based coverage problems. In particular, we show that $$\\lfloor \\frac{n}{6} \\rfloor $$⌊n6⌋ beacons are always sufficient and sometimes necessary to cover a simple rectilinear polygon P with n vertices. When P is monotone and rectilinear, we prove that this bound becomes $$\\lfloor \\frac{n+4}{8} \\rfloor $$⌊n+48⌋. We also present an optimal linear-time algorithm for computing the beacon kernel of P.

  8. Tight Bounds for Beacon-Based Coverage in Simple Rectilinear Polygons

    KAUST Repository

    Bae, Sang Won

    2016-03-21

    We establish tight bounds for beacon-based coverage problems. In particular, we show that $$\\\\lfloor \\\\frac{n}{6} \\ floor $$⌊n6⌋ beacons are always sufficient and sometimes necessary to cover a simple rectilinear polygon P with n vertices. When P is monotone and rectilinear, we prove that this bound becomes $$\\\\lfloor \\\\frac{n+4}{8} \\ floor $$⌊n+48⌋. We also present an optimal linear-time algorithm for computing the beacon kernel of P.

  9. Clinical and molecular analyses of Beckwith-Wiedemann syndrome: Comparison between spontaneous conception and assisted reproduction techniques.

    Science.gov (United States)

    Tenorio, Jair; Romanelli, Valeria; Martin-Trujillo, Alex; Fernández, García-Moya; Segovia, Mabel; Perandones, Claudia; Pérez Jurado, Luis A; Esteller, Manel; Fraga, Mario; Arias, Pedro; Gordo, Gema; Dapía, Irene; Mena, Rocío; Palomares, María; Pérez de Nanclares, Guiomar; Nevado, Julián; García-Miñaur, Sixto; Santos-Simarro, Fernando; Martinez-Glez, Víctor; Vallespín, Elena; Monk, David; Lapunzina, Pablo

    2016-10-01

    Beckwith-Wiedemann syndrome (BWS) is an overgrowth syndrome characterized by an excessive prenatal and postnatal growth, macrosomia, macroglossia, and hemihyperplasia. The molecular basis of this syndrome is complex and heterogeneous, involving genes located at 11p15.5. BWS is correlated with assisted reproductive techniques. BWS in individuals born following assisted reproductive techniques has been found to occur four to nine times higher compared to children with to BWS born after spontaneous conception. Here, we report a series of 187 patients with to BWS born either after assisted reproductive techniques or conceived naturally. Eighty-eight percent of BWS patients born via assisted reproductive techniques had hypomethylation of KCNQ1OT1:TSS-DMR in comparison with 49% for patients with BWS conceived naturally. None of the patients with BWS born via assisted reproductive techniques had hypermethylation of H19/IGF2:IG-DMR, neither CDKN1 C mutations nor patUPD11. We did not find differences in the frequency of multi-locus imprinting disturbances between groups. Patients with BWS born via assisted reproductive techniques had an increased frequency of advanced bone age, congenital heart disease, and decreased frequency of earlobe anomalies but these differences may be explained by the different molecular background compared to those with BWS and spontaneous fertilization. We conclude there is a correlation of the molecular etiology of BWS with the type of conception. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  10. Improvement of the inlet system for the spray-jet technique for use in spectroscopic studies and molecular deposition

    International Nuclear Information System (INIS)

    Yamada, Toshiki; Shinohara, Hidenori; Mashiko, Shinro

    2006-01-01

    We previously developed a molecular beam apparatus with a spray-jet technique in order to produce a molecular beam of non-volatile molecules in vacuum from the sprayed mist of a sample solution. The apparatus is for use in spectroscopic studies or a means of molecular deposition. The spray-jet inlet system consisted of an ultrasonic nebulizer, an inlet chamber and a pulsed nozzle. In the present paper, further improvements to the spray-jet inlet system are reported. The main improvement is the introduction of a pneumatic nebulizer to replace the previous ultrasonic nebulizer. The efficiency of molecular beam generation was evaluated on the basis of the signal intensity of the resonantly enhanced multiphoton ionization time-of-flight mass (REMPI-TOFMS) spectra for a Rhodamine B/methanol solution and the amount of sample consumed. The introduction of the pneumatic nebulizer increased the efficiency by a factor of 20

  11. Identification of microorganisms involved in nitrogen removal from wastewater treatment systems by means of molecular biology techniques

    International Nuclear Information System (INIS)

    Figueroa, M.; Alonso-Gutierrez, J.; Campos, J. L.; Mendez, R.; Mosquera-Corral, A.

    2010-01-01

    The identification of the main bacteria populations present in the granular biomass from a biological reactor treating wastewater has been performed by applying two different molecular biology techniques. By means of the DGGE technique five different genera of heterotrophic bacteria (Thiothrix, Thauera, Cloroflexi, Comamonas y Zoogloea) and one of ammonia oxidizing bacteria (Nitrosomanas) were identified. The FISH technique, based on microscopy, allowed the in situ visualization and quantification of those microorganisms. Special attention was paid to filamentous bacteria distribution (Thiothrix and Cloroflexi) which could exert a structural function in aerobic granular sludge. (Author) 26 refs.

  12. New technique of identifying the hierarchy of dynamic domains in proteins using a method of molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Yesylevskyy S. O.

    2010-04-01

    Full Text Available Aim. Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD simulations. The goal of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed

  13. Design and Implementation of Distress Prevention System using a Beacon

    Directory of Open Access Journals (Sweden)

    Lee Imsu

    2016-01-01

    Full Text Available It was proven that human accidents due to mountain climbing occupy large proportion of recently occurred man-made disasters. This paper designed and implemented an application that tells users about a variety of accidents that frequently occur in mountain and shows dynamic information about mountain climbing. It designed ‘distress prevention system using beacon’. When using beacon, it can dynamically express information without using GPS. It has advantage of supporting BLE and has little Smartphone battery consumption. The application was developed based on Android as a prototype. We expect that the application developed in this paper can contribute to the protection of precious lives by helping quick rescue in case of emergency such as distress. Manager of mountain can control data regarding the mountain climbing accident where the related functions are provided through view and user authority setup in DBMS.

  14. Beacons of discovery the worldwide science of particle physics

    CERN Document Server

    International Committee for Future Accelerators (ICFA)

    2011-01-01

    To discover what our world is made of and how it works at the most fundamental level is the challenge of particle physics. The tools of particle physics—experiments at particle accelerators and underground laboratories, together with observations of space—bring opportunities for discovery never before within reach. Thousands of scientists from universities and laboratories around the world collaborate to design, build and use unique detectors and accelerators to explore the fundamental physics of matter, energy, space and time. Together, in a common world-wide program of discovery, they provide a deep understanding of the world around us and countless benefits to society. Beacons of Discovery presents a vision of the global science of particle physics at the dawn of a new light on the mystery and beauty of the universe.

  15. BEACON: An application of nodal methods for operational support

    International Nuclear Information System (INIS)

    Boyd, W.A.; Nguyen, T.Q.

    1992-01-01

    A practical application of nodal methods is on-line plant operational support. However, to enable plant personnel to take full advantage of a nodal model to support plant operations, (a) a core nodal model must always be up to date with the current core history and conditions, (b) the nodal methods must be fast enough to allow numerous core calculations to be performed in minutes to support engineering decisions, and (c) the system must be easily accessible to engineering personnel at the reactor, their offices, or any other location considered appropriate. A core operational support package developed by Westinghouse called BEACON (best estimate analysis of core operations - nuclear) has been installed at several plants. Results from these plants and numerous in-core flux maps analyzed have demonstrated the accuracy of the model and the effectiveness of the methodology

  16. Seamless Guidance System Combining GPS, BLE Beacon, and NFC Technologies

    Directory of Open Access Journals (Sweden)

    Rung-Shiang Cheng

    2016-01-01

    Full Text Available Users rely increasingly on Location-Based Services (LBS and automated navigation/guidance systems nowadays. However, while such services are easily implemented in outdoor environments using Global Positioning System (GPS technology, a requirement still exists for accurate localization and guidance schemes in indoor settings. Accordingly, the present study proposes a system based on GPS, Bluetooth Low Energy (BLE beacons, and Near Field Communication (NFC technology. Through establishing graphic information and the design of algorithm, this study develops a guidance system for indoors and outdoors on smart phones, wishing to give user perfect smart life through this system. The proposed system is implemented on a smart phone and evaluated on a student campus environment. The experimental results confirm the ability of the proposed app to switch automatically from an outdoor mode to an indoor mode and to guide the user to requested target destination via the shortest possible route.

  17. NPP Grassland: Beacon Hill, U.K., 1972-1993, R1

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set contains two ASCII text files, one providing productivity measurements for a chalk grassland on Beacon Hill, West Sussex, U.K. (50.92 N, -0.85 W) and...

  18. Evaluation of light-emitting diode beacon light fixtures : final report.

    Science.gov (United States)

    2009-12-01

    Rotating beacons containing filament light sources have long been used on highway maintenance trucks : to indicate the presence of the truck to other drivers. Because of advances in light-emitting diode (LED) : technologies, flashing lights containin...

  19. Multi-kW Uplink Fiber-Laser Beacon with Agile Signal Format, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration —  Laser beacons with scalable powers are needed for ground to deep-space optical communication uplinks. They serve as absolute reference for tracking of spacecraft...

  20. Multi-kW Uplink Fiber-Laser Beacon with Agile Signal Format, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Uplink Laser Beacons for deep-space communication, can benefit greatly from migration to the 1010-1030nm wavelengths, via use of Silicon-APDs on the spacecraft...

  1. BEACON: A Summary Framework to Overcome Potential Reimbursement Hurdles.

    Science.gov (United States)

    Dunlop, William C N; Mullins, C Daniel; Pirk, Olaf; Goeree, Ron; Postma, Maarten J; Enstone, Ashley; Heron, Louise

    2016-10-01

    To provide a framework for addressing payers' criteria during the development of pharmaceuticals. A conceptual framework was presented to an international health economic expert panel for discussion. A structured literature search (from 2010 to May 2015), using the following databases in Ovid: Medline(®) and Medline(®) In-Process (PubMed), Embase (Ovid), EconLit (EBSCOhost) and the National Health Service Economic Evaluation Database (NHS EED), and a 'grey literature' search, were conducted to identify existing criteria from the payer perspective. The criteria assessed by existing frameworks and guidelines were collated; the most commonly reported criteria were considered for inclusion in the framework. A mnemonic was conceived as a memory aide to summarise these criteria. Overall, 41 publications were identified as potentially relevant to the objective. Following further screening, 26 were excluded upon full-text review on the basis of no framework presented (n = 13), redundancy (n = 11) or abstract only (n = 2). Frameworks that captured criteria developed for or utilised by the pharmaceutical industry (n = 5) and reimbursement guidance (n = 10) were reviewed. The most commonly identified criteria-unmet need/patient burden, safety, efficacy, quality-of-life outcomes, environment, evidence quality, budget impact and comparator-were incorporated into the summary framework. For ease of communication, the following mnemonic was developed: BEACON (Burden/target population, Environment, Affordability/value, Comparator, Outcomes, Number of studies/quality of evidence). The BEACON framework aims to capture the 'essence' of payer requirements by addressing the most commonly described criteria requested by payers regarding the introduction of a new pharmaceutical.

  2. Remote tracking of a magnetic receiver using low frequency beacons

    International Nuclear Information System (INIS)

    Sheinker, Arie; Ginzburg, Boris; Salomonski, Nizan; Frumkis, Lev; Kaplan, Ben-Zion

    2014-01-01

    Low frequency magnetic fields feature high penetration ability, which allows communication, localization, and tracking in environments where radio or acoustic waves are blocked or distorted by multipath interferences. In the present work, we propose a method for tracking a magnetic receiver using beacons of low frequency magnetic field, where the receiver includes a tri-axial search-coil magnetometer. Measuring the beacons’ magnetic fields and calculating the total-field signals enables localization without restrictions on magnetometer orientation, allowing on-the-move tracking. The total-field signals are used by a global search method, e.g., simulated annealing (SA) algorithm, to localize the receiver. The magnetic field produced by each beacon has a dipole structure and is governed by the beacon’s position and magnetic moment. We have investigated two different methods for estimating beacons’ magnetic moments prior to localization. The first method requires directional measurements, whereas for the second method the total-field signal is used. Effectiveness of these methods has been proved in numerous field tests. In the present work, we introduce a method for tracking a moving receiver by successive localizations. Using previous localization as a starting point of the search method for the next localization can reduce execution time and chances for divergence. The proposed method has been tested using numerous computer simulations. Successful system operation has been verified in field conditions. The good tracking capability together with simple implementation makes the proposed method attractive for real-time, low power field applications, such as mobile robots navigation. (paper)

  3. Improving adherence to the Epic Beacon ambulatory workflow.

    Science.gov (United States)

    Chackunkal, Ellen; Dhanapal Vogel, Vishnuprabha; Grycki, Meredith; Kostoff, Diana

    2017-06-01

    Computerized physician order entry has been shown to significantly improve chemotherapy safety by reducing the number of prescribing errors. Epic's Beacon Oncology Information System of computerized physician order entry and electronic medication administration was implemented in Henry Ford Health System's ambulatory oncology infusion centers on 9 November 2013. Since that time, compliance to the infusion workflow had not been assessed. The objective of this study was to optimize the current workflow and improve the compliance to this workflow in the ambulatory oncology setting. This study was a retrospective, quasi-experimental study which analyzed the composite workflow compliance rate of patient encounters from 9 to 23 November 2014. Based on this analysis, an intervention was identified and implemented in February 2015 to improve workflow compliance. The primary endpoint was to compare the composite compliance rate to the Beacon workflow before and after a pharmacy-initiated intervention. The intervention, which was education of infusion center staff, was initiated by ambulatory-based, oncology pharmacists and implemented by a multi-disciplinary team of pharmacists and nurses. The composite compliance rate was then reassessed for patient encounters from 2 to 13 March 2015 in order to analyze the effects of the determined intervention on compliance. The initial analysis in November 2014 revealed a composite compliance rate of 38%, and data analysis after the intervention revealed a statistically significant increase in the composite compliance rate to 83% ( p < 0.001). This study supports a pharmacist-initiated educational intervention can improve compliance to an ambulatory, oncology infusion workflow.

  4. Perancangan Prototipe Receiver Beacon Black Box Locator Acoustic 37,5 kHz Pingers

    OpenAIRE

    RUSTAMAJI RUSTAMAJI; PAULINE RAHMIATI; SARAH PERMATASARI

    2016-01-01

    ABSTRAK Ketika suatu pesawat terbang mengalami kecelakaan terjatuh ke dalam air, maka lokasi keberadaannya dapat dideteksi oleh alat yang disebut receiver beacon black box locator acoustic (pingers receiver). Pingers receiver berfungsi untuk menerima sinyal dengan frekuensi 37,5 kHz ± 1 kHz dari pingers transmitter atau Underwater Locator Beacon (ULB) yang berada pada black box pesawat. Dalam penelitian ini dibuat perancangan pingers receiver yang tersusun dari rangkaian Band Pass Filter (BPF...

  5. The technologist's role in nuclear medicine in development of centellographic techniques, x-ray guides surgery and molecular techniques

    International Nuclear Information System (INIS)

    Alvarez, Bettina; Juri, Cecilia; Manrique, Gonzalo; Andruskevicius, Patricia; Canepa, Jorge; Coppe, Fatima; Cuervo, Aurora; Lopez, Andrea; Gonzalez, Mirta; Guissoli, Patricia; Rodriguez, Sergio

    2006-01-01

    In our center the Technician in Nuclear Medicine participates in the development and evaluation of Nuclear Medicine and Molecular Biology linked methodologies, with the strategy of the sentinel lymph node (SLN). The aim of the present work is to validate nuclear and molecular methods, using known clinical and prognostic illness parameters. We included prospectively 40 patients with clinically localized melanoma, with an average of 3.6 mm (status: 0.5-15.0 mm) Breslow thickness. The middle age of the patients was 54.2 years (status: 24-82 years), 25 females and 15 males. The tracer used was 99mTc labeled albumin nanocolloid, doing a lymphoscintigraphy 16-18 hours before the surgery, with a total dose of 111-185 MBq. Sequential images were acquired every 5 minutes in a gamma camera during an hour post injection or until drainage was visualized. Once a SLN was located, we did an orthogonal view to locate the nodals in the three-dimensional space. The nodal territories identified by means of lymphoscintigraphy were explored surgically employing an intraoperative gamma probe. Nodal and adjacent tissue radioactivity was measured in vivo and verified ex vivo after the resection. A relation of counts node/background bigger than 2 in vivo and bigger than 10 ex vivo was established in order to consider a node SLN. The SLNs were analyzed by means of histopathology and in 14 patients the expression was studied also using RT-PCR, employing TIR, MART-1 and MIA as markers, in a single-step protocol with 35 cycles of amplification. The experiments were done in duplicates and they included positive and negative control panels. SLN was identified in 38/39 surgical patients (97.4 %), each patient presenting an average of 1.3 nodal. Nodal metastasis were diagnosed by histopathology in 9 patients (24 %). A significant correlation was stated between the metastasis commitment of the SLN and the illness relapsing (p=0.019) during the follow up of 40.8 months (status: 6.7-94.6 months

  6. Serum inverts and improves the fluorescence response of an aptamer beacon to various vitamin D analytes.

    Science.gov (United States)

    Bruno, John G; Carrillo, Maria P; Phillips, Taylor; Edge, Allison

    2012-01-01

    A dominant aptamer loop structure from a library of nearly 100 candidate aptamer sequences developed against immobilized 25-hydroxyvitamin D(3) (calcidiol) was converted into a 5'-TYE 665 and 3'-Iowa black-labelled aptamer beacon. The aptamer beacon exhibited a mild 'lights on' reaction in buffer as a function of increasing concentrations of several vitamin D analogues and metabolites, with a limit of detection of approximately 200 ng/mL, and was not specific for any particular congener. In 10% or 50% human serum, the same aptamer beacon inverted its fluorescence behaviour to become a more intense 'lights off' reaction with an improved limit of detection in the range 4-16 ng/mL. We hypothesized that this drastic change in fluorescence behaviour was due to the presence of creatinine and urea in serum, which might destabilize the quenched beacon, causing an increase in fluorescence followed by decreasing fluorescence as a function of vitamin D concentrations that may bind and quench increasingly greater fractions of the denatured beacons. However, the results of several control experiments in the presence of physiological or greater concentrations of creatinine and urea, alone or combined in buffer, failed to produce the beacon fluorescence inversion. Other possible mechanistic hypotheses are also discussed. Copyright © 2011 John Wiley & Sons, Ltd.

  7. Supporting Beacon and Event-Driven Messages in Vehicular Platoons through Token-Based Strategies.

    Science.gov (United States)

    Balador, Ali; Uhlemann, Elisabeth; Calafate, Carlos T; Cano, Juan-Carlos

    2018-03-23

    Timely and reliable inter-vehicle communications is a critical requirement to support traffic safety applications, such as vehicle platooning. Furthermore, low-delay communications allow the platoon to react quickly to unexpected events. In this scope, having a predictable and highly effective medium access control (MAC) method is of utmost importance. However, the currently available IEEE 802.11p technology is unable to adequately address these challenges. In this paper, we propose a MAC method especially adapted to platoons, able to transmit beacons within the required time constraints, but with a higher reliability level than IEEE 802.11p, while concurrently enabling efficient dissemination of event-driven messages. The protocol circulates the token within the platoon not in a round-robin fashion, but based on beacon data age, i.e., the time that has passed since the previous collection of status information, thereby automatically offering repeated beacon transmission opportunities for increased reliability. In addition, we propose three different methods for supporting event-driven messages co-existing with beacons. Analysis and simulation results in single and multi-hop scenarios showed that, by providing non-competitive channel access and frequent retransmission opportunities, our protocol can offer beacon delivery within one beacon generation interval while fulfilling the requirements on low-delay dissemination of event-driven messages for traffic safety applications.

  8. Supporting Beacon and Event-Driven Messages in Vehicular Platoons through Token-Based Strategies

    Directory of Open Access Journals (Sweden)

    Ali Balador

    2018-03-01

    Full Text Available Timely and reliable inter-vehicle communications is a critical requirement to support traffic safety applications, such as vehicle platooning. Furthermore, low-delay communications allow the platoon to react quickly to unexpected events. In this scope, having a predictable and highly effective medium access control (MAC method is of utmost importance. However, the currently available IEEE 802.11p technology is unable to adequately address these challenges. In this paper, we propose a MAC method especially adapted to platoons, able to transmit beacons within the required time constraints, but with a higher reliability level than IEEE 802.11p, while concurrently enabling efficient dissemination of event-driven messages. The protocol circulates the token within the platoon not in a round-robin fashion, but based on beacon data age, i.e., the time that has passed since the previous collection of status information, thereby automatically offering repeated beacon transmission opportunities for increased reliability. In addition, we propose three different methods for supporting event-driven messages co-existing with beacons. Analysis and simulation results in single and multi-hop scenarios showed that, by providing non-competitive channel access and frequent retransmission opportunities, our protocol can offer beacon delivery within one beacon generation interval while fulfilling the requirements on low-delay dissemination of event-driven messages for traffic safety applications.

  9. Accelerated Adoption of Advanced Health Information Technology in Beacon Community Health Centers.

    Science.gov (United States)

    Jones, Emily; Wittie, Michael

    2015-01-01

    To complement national and state-level HITECH Act programs, 17 Beacon communities were funded to fuel community-wide use of health information technology to improve quality. Health centers in Beacon communities received supplemental funding. This article explores the association between participation in the Beacon program and the adoption of electronic health records. Using the 2010-2012 Uniform Data System, trends in health information technology adoption among health centers located within and outside of Beacon communities were explored using differences in mean t tests and multivariate logistic regression. Electronic health record adoption was widespread and rapidly growing in all health centers, especially quality improvement functionalities: structured data capture, order and results management, and clinical decision support. Adoption lagged for functionalities supporting patient engagement, performance measurement, care coordination, and public health. The use of advanced functionalities such as care coordination grew faster in Beacon health centers, and Beacon health centers had 1.7 times higher odds of adopting health records with basic safety and quality functionalities in 2010-2012. Three factors likely underlie these findings: technical assistance, community-wide activation supporting health information exchange, and the layering of financial incentives. Additional technical assistance and community-wide activation is needed to support the use of functionalities that are currently lagging. © Copyright 2015 by the American Board of Family Medicine.

  10. Recent research in flaxseed (oil seed) on molecular structure and metabolic characteristics of protein, heat processing-induced effect and nutrition with advanced synchrotron-based molecular techniques.

    Science.gov (United States)

    Doiron, Kevin J; Yu, Peiqiang

    2017-01-02

    Advanced synchrotron radiation-based infrared microspectroscopy is able to reveal feed and food structure feature at cellular and molecular levels and simultaneously provides composition, structure, environment, and chemistry within intact tissue. However, to date, this advanced synchrotron-based technique is still seldom known to food and feed scientists. This article aims to provide detailed background for flaxseed (oil seed) protein research and then review recent progress and development in flaxseed research in ruminant nutrition in the areas of (1) dietary inclusion of flaxseed in rations; (2) heat processing effect; (3) assessing dietary protein; (4) synchrotron-based Fourier transform infrared microspectroscopy as a tool of nutritive evaluation within cellular and subcellular dimensions; (5) recent synchrotron applications in flaxseed research on a molecular basis. The information described in this paper gives better insight in flaxseed research progress and update.

  11. Application of radiation grafting techniques to prepare the high molecular weight water-soluble polymer

    International Nuclear Information System (INIS)

    Le Hai; Nguyen Quoc Hien; Nguyen Tan Man; Truong Thi Hanh; Le Huu Tu; Tran Thi Tam; Pham Thi Sam; Pham Anh Tuan; Le Dinh Lang

    2003-01-01

    The results of the study on the preparation of the high molecular weight water-soluble polymers by radiation grafting and their properties is presented as follows: 1/ by radiation grafting, the molecular weight of PVA was increased 20 times and PAM was increased only 3 times; 2/ the thermal and medium stability of poly(vinyl alcohol) grafted with acrylamide was obviously improved. (LH)

  12. 15th Anniversary of the Molecular Techniques Unit at the Department of Forensic Medicine at Wroclaw Medical University.

    Science.gov (United States)

    Pluta, Dominika; Tokarski, Miron; Karpiewska, Anna; Dobosz, Tadeusz

    2017-01-01

    Molecular Techniques Unit at the Department of Forensic Medicine, Wroclaw Medical University has been operating since December 2003. Soon it will be 15 years since its establishment. This anniversary become an inspiration to write down the story of this institution whose origins illustrate the immense changes that have taken place in forensic genetics. The aim of our work was also to consolidate the professional achievements of Professor Tadeusz Dobosz, chief of the Unit, one of the pioneers of introducing DNA testing technology into Polish forensic medicine. The most important achievements of the Unit include participation in two EU research projects, the development of a non-destructive method of extraction of genetic material, research in field of gene therapy and certification of the Laboratory of the Molecular Techniques Unit by the Polish Accreditation Center (PCA) confirming compliance with the requirements of the PN-EN ISO/IEC 17025:2005 standard.

  13. Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Agarwal, Animesh, E-mail: animesh@zedat.fu-berlin.de; Delle Site, Luigi, E-mail: dellesite@fu-berlin.de [Institute for Mathematics, Freie Universität Berlin, Berlin (Germany)

    2015-09-07

    Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however, computationally this technique is very demanding. The above mentioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One of the possible solutions to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper, we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in the literature. The comparison of our results with those reported in the literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement.

  14. Current applications of molecular imaging and luminescence-based techniques in traditional Chinese medicine.

    Science.gov (United States)

    Li, Jinhui; Wan, Haitong; Zhang, Hong; Tian, Mei

    2011-09-01

    Traditional Chinese medicine (TCM), which is fundamentally different from Western medicine, has been widely investigated using various approaches. Cellular- or molecular-based imaging has been used to investigate and illuminate the various challenges identified and progress made using therapeutic methods in TCM. Insight into the processes of TCM at the cellular and molecular changes and the ability to image these processes will enhance our understanding of various diseases of TCM and will provide new tools to diagnose and treat patients. Various TCM therapies including herbs and formulations, acupuncture and moxibustion, massage, Gua Sha, and diet therapy have been analyzed using positron emission tomography, single photon emission computed tomography, functional magnetic resonance imaging and ultrasound and optical imaging. These imaging tools have kept pace with developments in molecular biology, nuclear medicine, and computer technology. We provide an overview of recent developments in demystifying ancient knowledge - like the power of energy flow and blood flow meridians, and serial naturopathies - which are essential to visually and vividly recognize the body using modern technology. In TCM, treatment can be individualized in a holistic or systematic view that is consistent with molecular imaging technologies. Future studies might include using molecular imaging in conjunction with TCM to easily diagnose or monitor patients naturally and noninvasively. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  15. On the computation of molecular surface correlations for protein docking using fourier techniques.

    Science.gov (United States)

    Sakk, Eric

    2007-08-01

    The computation of surface correlations using a variety of molecular models has been applied to the unbound protein docking problem. Because of the computational complexity involved in examining all possible molecular orientations, the fast Fourier transform (FFT) (a fast numerical implementation of the discrete Fourier transform (DFT)) is generally applied to minimize the number of calculations. This approach is rooted in the convolution theorem which allows one to inverse transform the product of two DFTs in order to perform the correlation calculation. However, such a DFT calculation results in a cyclic or "circular" correlation which, in general, does not lead to the same result as the linear correlation desired for the docking problem. In this work, we provide computational bounds for constructing molecular models used in the molecular surface correlation problem. The derived bounds are then shown to be consistent with various intuitive guidelines previously reported in the protein docking literature. Finally, these bounds are applied to different molecular models in order to investigate their effect on the correlation calculation.

  16. Refinement of homology-based protein structures by molecular dynamics simulation techniques

    NARCIS (Netherlands)

    Fan, H; Mark, AE

    The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to

  17. Heterogeneous chemical kinetics by modulated molecular beam mass spectrometry: limitations of technique

    International Nuclear Information System (INIS)

    Olander, D.R.

    1977-01-01

    The advantages and limitations of modulated molecular beam, mass spectrometry as applied to the study of heterogeneous chemical kinetics are reviewed. The process of deducing a model of the surface reaction from experimental data is illustrated by analysis of the hydrogen reduction of uranium dioxide

  18. Management of insect pests: Nuclear and related molecular and genetic techniques

    International Nuclear Information System (INIS)

    1993-01-01

    The conference was organized in eight sessions: opening, genetic engineering and molecular biology, genetics, operational programmes, F 1 sterility and insect behaviour, biocontrol, research and development on the tsetse fly, and quarantine. The 64 individual contributions have been indexed separately for INIS. Refs, figs and tabs

  19. Detection of microbial diversity in endocarditis using cultivation-independent molecular techniques

    DEFF Research Database (Denmark)

    Wolff, Tine Y; Moser, Claus Ernst; Bundgaard, Henning

    2011-01-01

    Background: The aim of this study was to investigate whether the diagnosis of infective endocarditis (IE) could be improved using molecular tools in addition to standard microscopy and cultivation methods. Methods: Cultivation was performed on blood or tissue samples as recommended in the modified...

  20. Molecular confocal laser endomicroscopy: a novel technique for in vivo cellular characterization of gastrointestinal lesions.

    Science.gov (United States)

    Karstensen, John Gásdal; Klausen, Pia Helene; Saftoiu, Adrian; Vilmann, Peter

    2014-06-28

    While flexible endoscopy is essential for macroscopic evaluation, confocal laser endomicroscopy (CLE) has recently emerged as an endoscopic method enabling visualization at a cellular level. Two systems are currently available, one based on miniprobes that can be inserted via a conventional endoscope or via a needle guided by endoscopic ultrasound. The second system has a confocal microscope integrated into the distal part of an endoscope. By adding molecular probes like fluorescein conjugated antibodies or fluorescent peptides to this procedure (either topically or systemically administered during on-going endoscopy), a novel world of molecular evaluation opens up. The method of molecular CLE could potentially be used for estimating the expression of important receptors in carcinomas, subsequently resulting in immediate individualization of treatment regimens, but also for improving the diagnostic accuracy of endoscopic procedures by identifying otherwise invisible mucosal lesions. Furthermore, studies have shown that fluorescein labelled drugs can be used to estimate the affinity of the drug to a target organ, which probably can be correlated to the efficacy of the drug. However, several of the studies in this research field have been conducted in animal facilities or in vitro, while only a limited number of trials have actually been carried out in vivo. Therefore, safety issues still needs further evaluations. This review will present an overview of the implications and pitfalls, as well as future challenges of molecular CLE in gastrointestinal diseases.

  1. Accurate beacon positioning method for satellite-to-ground optical communication.

    Science.gov (United States)

    Wang, Qiang; Tong, Ling; Yu, Siyuan; Tan, Liying; Ma, Jing

    2017-12-11

    In satellite laser communication systems, accurate positioning of the beacon is essential for establishing a steady laser communication link. For satellite-to-ground optical communication, the main influencing factors on the acquisition of the beacon are background noise and atmospheric turbulence. In this paper, we consider the influence of background noise and atmospheric turbulence on the beacon in satellite-to-ground optical communication, and propose a new locating algorithm for the beacon, which takes the correlation coefficient obtained by curve fitting for image data as weights. By performing a long distance laser communication experiment (11.16 km), we verified the feasibility of this method. Both simulation and experiment showed that the new algorithm can accurately obtain the position of the centroid of beacon. Furthermore, for the distortion of the light spot through atmospheric turbulence, the locating accuracy of the new algorithm was 50% higher than that of the conventional gray centroid algorithm. This new approach will be beneficial for the design of satellite-to ground optical communication systems.

  2. A spiral wave front beacon for underwater navigation: transducer prototypes and testing.

    Science.gov (United States)

    Dzikowicz, Benjamin R; Hefner, Brian T

    2012-05-01

    Transducers for acoustic beacons which can produce outgoing signals with wave fronts whose horizontal cross sections are circular or spiral are studied experimentally. A remote hydrophone is used to determine its aspect relative to the transducers by comparing the phase of the circular signal to the phase of the spiral signal. The transducers for a "physical-spiral" beacon are made by forming a strip of 1-3 piezocomposite transducer material around either a circular or spiral backing. A "phased-spiral" beacon is made from an array of transducer elements which can be driven either in phase or staggered out of phase so as to produce signals with either a circular or spiral wave front. Measurements are made to study outgoing signals and their usefulness in determining aspect angle. Vertical beam width is also examined and phase corrections applied when the hydrophone is out of the horizontal plane of the beacon. While numerical simulations indicate that the discontinuity in the physical-spiral beacon introduces errors into the measured phase, damping observed at the ends of the piezocomposite material is a more significant source of error. This damping is also reflected in laser Doppler vibrometer measurements of the transducer's surface velocity.

  3. Adaptive Beaconing in Mobility Aware Clustering Based MAC Protocol for Safety Message Dissemination in VANET

    Directory of Open Access Journals (Sweden)

    Nishu Gupta

    2017-01-01

    Full Text Available Majority of research contributions in wireless access in vehicular environment (WAVE/IEEE 802.11p standard focus on life critical safety-related applications. These applications require regular status update of vehicle’s position referred to as beaconing. Periodic beaconing in vehicle to vehicle communication leads to severe network congestion in the communication channel. The condition worsens under high vehicular density where it impacts reliability and upper bound latency of safety messages. In this paper, WAVE compliant enhancement to the existing IEEE 802.11p protocol is presented which targets prioritized delivery of safety messages while simultaneously provisioning the dissemination of nonsafety messages. Proposed scheme relies on dynamic generation of beacons to mitigate channel congestion and inefficient bandwidth utilization by reducing transmission frequency of beacons. Through the use of clustering mechanism, different beaconing frequencies and different data transmission rates are assigned to prioritize vehicular mobility. Through extensive simulation results, the performance of the proposed approach is evaluated in terms of a wide range of quality of service (QoS parameters for two different transmission ranges. Results show that the proposed protocol provides significant enhancement and stability of the clustered topology in vehicular ad hoc network over existing standard and other protocols with similar applications.

  4. Evaluation of molecular typing techniques to assign genetic diversity among Saccharomyces cerevisiae strains

    NARCIS (Netherlands)

    Baleiras Couto, M.M.; Eijsma, B.; Hofstra, H.; Huis in 't Veld, J.H.J.; Vossen, J.M.B.M. van der

    1996-01-01

    Discrimination of strains within the species Saccharomyces cerevisiae was demonstrated by the use of four different techniques to type 15 strains isolated from spoiled wine and beer. Random amplified polymorphic DNA with specific oligonucleotides and PCR fingerprinting with the microsatellite

  5. The molecular imaging approach to image infections and inflammation by nuclear medicine techniques

    NARCIS (Netherlands)

    Signore, Alberto; Glaudemans, Andor W. J. M.

    2011-01-01

    Inflammatory and infectious diseases are a heterogeneous class of diseases that may be divided into infections, acute inflammation and chronic inflammation. Radiological imaging techniques have, with the exception of functional MRI, high sensitivity but lack in specificity. Nuclear medicine

  6. Exploring Surface Analysis Techniques for the Detection of Molecular Contaminants on Spacecraft

    Science.gov (United States)

    Rutherford, Gugu N.; Seasly, Elaine; Thornblom, Mark; Baughman, James

    2016-01-01

    Molecular contamination is a known area of concern for spacecraft. To mitigate this risk, projects involving space flight hardware set requirements in a contamination control plan that establishes an allocation budget for the exposure of non-volatile residues (NVR) onto critical surfaces. The purpose of this work will focus on non-contact surface analysis and in situ monitoring to mitigate molecular contamination on space flight hardware. By using Scanning Electron Microscopy and Energy Dispersive Spectroscopy (SEM-EDS) with Raman Spectroscopy, an unlikely contaminant was identified on space flight hardware. Using traditional and surface analysis methods provided the broader view of the contamination sources allowing for best fit solutions to prevent any future exposure.

  7. Molecular techniques for detection and identification of pathogens in food: advantages and limitations

    OpenAIRE

    Palomino-Camargo, Carolina; Instituto de Ciencia y Tecnología de Alimentos, Facultad de Ciencias, Universidad Central de Venezuela. Caracas, Venezuela. Magíster en Ciencia y Tecnología de los Alimentos licenciada en Biología; González-Muñoz, Yuniesky; Instituto de Ciencia y Tecnología de Alimentos, Facultad de Ciencias, Universidad Central de Venezuela. Caracas, Venezuela. Ministerio del Poder Popular para la Alimentación. Caracas, Venezuela. licenciado en Ciencias de los Alimentos.

    2014-01-01

    Foodborne diseases, caused by pathogenic microorganisms, are a major public health problem worldwide. Microbiological methods commonly used in the detection of these foodborne pathogens are laborious and time consuming. This situation, coupled with the demand for immediate results and with technological advances, has led to the development of a wide range of rapid methods in recent decades. On this basis, this review describes the advantages and limitations of the main molecular methods used ...

  8. Direct assignment of molecular vibrations via normal mode analysis of the neutron dynamic pair distribution function technique

    International Nuclear Information System (INIS)

    Fry-Petit, A. M.; Sheckelton, J. P.; McQueen, T. M.; Rebola, A. F.; Fennie, C. J.; Mourigal, M.; Valentine, M.; Drichko, N.

    2015-01-01

    For over a century, vibrational spectroscopy has enhanced the study of materials. Yet, assignment of particular molecular motions to vibrational excitations has relied on indirect methods. Here, we demonstrate that applying group theoretical methods to the dynamic pair distribution function analysis of neutron scattering data provides direct access to the individual atomic displacements responsible for these excitations. Applied to the molecule-based frustrated magnet with a potential magnetic valence-bond state, LiZn 2 Mo 3 O 8 , this approach allows direct assignment of the constrained rotational mode of Mo 3 O 13 clusters and internal modes of MoO 6 polyhedra. We anticipate that coupling this well known data analysis technique with dynamic pair distribution function analysis will have broad application in connecting structural dynamics to physical properties in a wide range of molecular and solid state systems

  9. Accuracy of molecular biology techniques for the diagnosis of Strongyloides stercoralis infection-A systematic review and meta-analysis.

    Science.gov (United States)

    Buonfrate, Dora; Requena-Mendez, Ana; Angheben, Andrea; Cinquini, Michela; Cruciani, Mario; Fittipaldo, Andrea; Giorli, Giovanni; Gobbi, Federico; Piubelli, Chiara; Bisoffi, Zeno

    2018-02-01

    Strongyloides stercoralis infection is a neglected tropical disease which can lead to severe symptoms and even death in immunosuppressed people. Unfortunately, its diagnosis is hampered by the lack of a gold standard, as the sensitivity of traditional parasitological tests (including microscopic examination of stool samples and coproculture) is low. Hence, alternative diagnostic methods, such as molecular biology techniques (mostly polymerase chain reaction, PCR) have been implemented. However, there are discrepancies in the reported accuracy of PCR. A systematic review with meta-analysis was conducted in order to evaluate the accuracy of PCR for the diagnosis of S. stercoralis infection. The protocol was registered with PROSPERO International Prospective Register of Systematic Reviews (record: CRD42016054298). Fourteen studies, 12 of which evaluating real-time PCR, were included in the analysis. The specificity of the techniques resulted high (ranging from 93 to 95%, according to the reference test(s) used). When all molecular techniques were compared to parasitological methods, the sensitivity of PCR was assessed at 71.8% (95% CI 52.2-85.5), that decreased to 61.8% (95% CI 42.0-78.4) when serology was added among the reference tests. Similarly, sensitivity of real-time PCR resulted 64.4% (95% CI 46.2-77.7) when compared to parasitological methods only, 56.5% (95% CI 39.2-72.4) including serology. PCR might not be suitable for screening purpose, whereas it might have a role as a confirmatory test.

  10. Efficient Beacon Collision Resolution Procedure for IEEE 802.15.4 /Zigbee Wireless Personal Area Networks

    Directory of Open Access Journals (Sweden)

    Bassam A. Zafar

    2017-04-01

    Full Text Available While IEEE 802.15.4/Zigbee is a promising technology for Wireless Personal Area Networks, several transmission problems are not yet resolved. In particular, the problem of beacon transmission interferences is causing the device connection loss to the network. In order to resolve this problem, we present a new distributed and reactive procedure for beacon collision resolution. It is an extension of the alignment procedure to reorganize randomly the beacon transmission time when a collision has occurred. The detail of the proposed procedure will be fully described and analyzed. The performance of our approach is performed by simulations. The results show that our approach reduces the collision probability and the device disconnections consequently.

  11. A beacon interval shifting scheme for interference mitigation in body area networks.

    Science.gov (United States)

    Kim, Seungku; Kim, Seokhwan; Kim, Jin-Woo; Eom, Doo-Seop

    2012-01-01

    This paper investigates the issue of interference avoidance in body area networks (BANs). IEEE 802.15 Task Group 6 presented several schemes to reduce such interference, but these schemes are still not proper solutions for BANs. We present a novel distributed TDMA-based beacon interval shifting scheme that reduces interference in the BANs. A design goal of the scheme is to avoid the wakeup period of each BAN coinciding with other networks by employing carrier sensing before a beacon transmission. We analyze the beacon interval shifting scheme and investigate the proper back-off length when the channel is busy. We compare the performance of the proposed scheme with the schemes presented in IEEE 802.15 Task Group 6 using an OMNeT++ simulation. The simulation results show that the proposed scheme has a lower packet loss, energy consumption, and delivery-latency than the schemes of IEEE 802.15 Task Group 6.

  12. Development of satellite position location system for aircraft and boat distress beacons

    Science.gov (United States)

    Kahle, D. R.

    1982-01-01

    An international satellite system for the detection and location of distress beacons carried on aircraft and vessels is in its technical checkout phase. User demonstration and evaluation (D&E) will start in early 1983 and continue for two years. The D&E phase and a subsequent transition period will form the basis for improved search and rescue operations for the 1980's and beyond. The system, called COSPAS/SARSAT, has international participation involving the U.S., Canada, and France as SARSAT members and joint participation with the Soviet Union's COSPAS Project. Norway and the U.K. have recently joined as investigators. Average position location error of the satellite aided processing is expected to be from 10-20KM for the existing 121.5/243 MHz distress beacons and from 2-5KM for experimental beacons transmitting in the 406 MHz band.

  13. Hepatozoon canis infection in a domestic dog in Southern Brazil confirmed by molecular techniques

    OpenAIRE

    Lasta, Camila Serina; Santos, Andrea Pires dos; Mello, Fabíola Peixoto da Silva; Lacerda, Luciana de Almeida; Messick, Joanne Belle; Díaz González, Félix Hilário

    2009-01-01

    Hepatozoonose canina é uma doença transmitida por carrapatos e causada pelo protozoário Hepatozoon spp. No Brasil, existem poucos relatos da infecção e dados sobre sua epidemiologia, patogenicidade, seus vetores e sua caracterização genética. No presente estudo, são utilizadas técnicas moleculares para o diagnóstico e a caracterização do parasita. Foi estudado um canino que apresentava emagrecimento progressivo, anemia regenerativa, neutropenia e hiperglobulinemia. Gamontes de Hepatozoon spp....

  14. Development of an aptamer beacon for detection of interferon-gamma.

    Science.gov (United States)

    Tuleuova, Nazgul; Jones, Caroline N; Yan, Jun; Ramanculov, Erlan; Yokobayashi, Yohei; Revzin, Alexander

    2010-03-01

    Traditional antibody-based affinity sensing strategies employ multiple reagents and washing steps and are unsuitable for real-time detection of analyte binding. Aptamers, on the other hand, may be designed to monitor binding events directly, in real-time, without the need for secondary labels. The goal of the present study was to design an aptamer beacon for fluorescence resonance energy transfer (FRET)-based detection of interferon-gamma (IFN-gamma)--an important inflammatory cytokine. Variants of DNA aptamer modified with biotin moieties and spacers were immobilized on avidin-coated surfaces and characterized by surface plasmon resonance (SPR). The SPR studies showed that immobilization of aptamer via the 3' end resulted in the best binding IFN-gamma (K(d) = 3.44 nM). This optimal aptamer variant was then used to construct a beacon by hybridizing fluorophore-labeled aptamer with an antisense oligonucleotide strand carrying a quencher. SPR studies revealed that IFN-gamma binding with an aptamer beacon occurred within 15 min of analyte introduction--suggesting dynamic replacement of the quencher-complementary strand by IFN-gamma molecules. To further highlight biosensing applications, aptamer beacon molecules were immobilized inside microfluidic channels and challenged with varying concentration of analyte. Fluorescence microscopy revealed low fluorescence in the absence of analyte and high fluorescence after introduction of IFN-gamma. Importantly, unlike traditional antibody-based immunoassays, the signal was observed directly upon binding of analyte without the need for multiple washing steps. The surface immobilized aptamer beacon had a linear range from 5 to 100 nM and a lower limit of detection of 5 nM IFN-gamma. In conclusion, we designed a FRET-based aptamer beacon for monitoring of an inflammatory cytokine-IFN-gamma. In the future, this biosensing strategy will be employed to monitor dynamics of cytokine production by the immune cells.

  15. Building and strengthening infrastructure for data exchange: lessons from the beacon communities.

    Science.gov (United States)

    Torres, Gretchen W; Swietek, Karen; Ubri, Petry S; Singer, Rachel F; Lowell, Kristina H; Miller, Wilhelmine

    2014-01-01

    The Beacon Community Cooperative Agreement Program supports interventions, including care-delivery innovations, provider performance measurement and feedback initiatives, and tools for providers and consumers to enhance care. Using a learning health system framework, we examine the Beacon Communities' processes in building and strengthening health IT (HIT) infrastructures, specifically successes and challenges in sharing patient information to improve clinical care. In 2010, the Office of the National Coordinator for Health Information Technology (ONC) launched the three-year program, which provided $250 million to 17 Beacon Communities to invest in HIT and health information exchange (HIE) infrastructure. Beacon Communities used this funding to develop and disseminate HIT-enabled quality improvement practices found effective in particular community and practice environments. NORC conducted 7 site visits, November 2012-March 2013, selecting Communities to represent diverse program features. From August-October 2013, NORC held discussions with the remaining 10 Communities. Following each visit or discussion, NORC summarized the information gathered, including transcripts, team observations, and other documents the Community provided, to facilitate a within-Community analysis of context and stakeholders, intervention strategies, enabling factors, and challenges. Although each Community designed and implemented data-sharing strategies in a unique environment, similar challenges and enabling factors emerged across the Beacons. From a learning health system perspective, their strategies to build and strengthen data-sharing infrastructures address the following crosscutting priorities: promoting technical advances and innovations by helping providers adapt EHRs for data exchange and performance measurement with customizable IT and offering technical support to smaller, independent providers; engaging key stakeholders; and fostering transparent governance and stewardship

  16. Results from the northern New Mexico satellite-beacon radio interferometer

    International Nuclear Information System (INIS)

    Carlos, R.; Jacobson, A.; Massey, R.; Wu, G.

    1994-01-01

    An interferometer described in the Boston, 1992, meeting of the Beacon Satellite Symposium has been in full operation for over a year now. It consists of four autonomous stations; three are in a triangle 70 km on a side and one is in the center. The stations receive the VHF beacons from two geosynchronous satellites, GOES-2 and ATS-3. The phases of the beacons are tracked at each station by referring them to an extremely stable rubidium oscillator. The studies of the two satellites are virtually separate experiments. The received phase of the beacon is retarded by the increased Total-Electron-Content of the dense regions of waves in the ionosphere. By comparing the phase history at four spatially separated stations, the authors can determine the two-dimensional propagation vector of the waves. This array is optimal for wavelengths of 70--300 km (periods of 300--3,000 seconds). Since the measurement is of the phase of the signal rather than the difference between the O-mode and X-mode phases, and since the beacons are in the VHF rather than in the L-band of GPS beacons, the array is very sensitive. It has a noise level of 10 13 electrons/m 2 , or 10 -4 of the normal daytime TEC. This has been verified by operating two stations in the same location, so that they saw the same ionosphere. The first interesting results from a year's study is that the authors do not see the same TID's when looking at the two satellites. One conclusion they draw is that they do not see evidence of ionospheric winds

  17. Time-Resolved Nucleic Acid Hybridization Beacons Utilizing Unimolecular and Toehold-Mediated Strand Displacement Designs.

    Science.gov (United States)

    Massey, Melissa; Ancona, Mario G; Medintz, Igor L; Algar, W Russ

    2015-12-01

    Nucleic acid hybridization probes are sought after for numerous assay and imaging applications. These probes are often limited by the properties of fluorescent dyes, prompting the development of new probes where dyes are paired with novel or nontraditional luminescent materials. Luminescent terbium complexes are an example of such a material, and these complexes offer several unique spectroscopic advantages. Here, we demonstrate two nonstem-loop designs for light-up nucleic acid hybridization beacons that utilize time-resolved Förster resonance energy transfer (TR-FRET) between a luminescent Lumi4-Tb cryptate (Tb) donor and a fluorescent reporter dye, where time-resolved emission from the dye provides an analytical signal. Both designs are based on probe oligonucleotides that are labeled at their opposite termini with Tb and a fluorescent reporter dye. In one design, a probe is partially blocked with a quencher dye-labeled oligonucleotide, and target hybridization is signaled through toehold-mediated strand displacement and loss of a competitive FRET pathway. In the other design, the intrinsic folding properties of an unblocked probe are utilized in combination with a temporal mechanism for signaling target hybridization. This temporal mechanism is based on a recently elucidated "sweet spot" for TR-FRET measurements and exploits distance control over FRET efficiencies to shift the Tb lifetime within or outside the time-gated detection window for measurements. Both the blocked and unblocked beacons offer nanomolar (femtomole) detection limits, response times on the order of minutes, multiplexing through the use of different reporter dyes, and detection in complex matrices such as serum and blood. The blocked beacons offer better mismatch selectivity, whereas the unblocked beacons are simpler in design. The temporal mechanism of signaling utilized with the unblocked beacons also plays a significant role with the blocked beacons and represents a new and effective

  18. Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes

    NARCIS (Netherlands)

    Justé, A.; Thomma, B.P.H.J.; Lievens, B.

    2008-01-01

    In the last two decades major changes have occurred in how microbial ecologists study microbial communities. Limitations associated with traditional culture-based methods have pushed for the development of culture-independent techniques, which are primarily based on the analysis of nucleic acids.

  19. Approaches for the analysis of low molecular weight compounds with laser desorption/ionization techniques and mass spectrometry.

    Science.gov (United States)

    Bergman, Nina; Shevchenko, Denys; Bergquist, Jonas

    2014-01-01

    This review summarizes various approaches for the analysis of low molecular weight (LMW) compounds by different laser desorption/ionization mass spectrometry techniques (LDI-MS). It is common to use an agent to assist the ionization, and small molecules are normally difficult to analyze by, e.g., matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) using the common matrices available today, because the latter are generally small organic compounds themselves. This often results in severe suppression of analyte peaks, or interference of the matrix and analyte signals in the low mass region. However, intrinsic properties of several LDI techniques such as high sensitivity, low sample consumption, high tolerance towards salts and solid particles, and rapid analysis have stimulated scientists to develop methods to circumvent matrix-related issues in the analysis of LMW molecules. Recent developments within this field as well as historical considerations and future prospects are presented in this review.

  20. Growth of CdTe on Si(100) surface by ionized cluster beam technique: Experimental and molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Araghi, Houshang, E-mail: araghi@aut.ac.ir [Department of Physics, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of); Zabihi, Zabiholah [Department of Physics, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of); Nayebi, Payman [Department of Physics, College of Technical and Engineering, Saveh Branch, Islamic Azad University, Saveh (Iran, Islamic Republic of); Ehsani, Mohammad Mahdi [Department of Physics, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of)

    2016-10-15

    II–VI semiconductor CdTe was grown on the Si(100) substrate surface by the ionized cluster beam (ICB) technique. In the ICB method, when vapors of solid materials such as CdTe were ejected through a nozzle of a heated crucible into a vacuum region, nanoclusters were created by an adiabatic expansion phenomenon. The clusters thus obtained were partially ionized by electron bombardment and then accelerated onto the silicon substrate at 473 K by high potentials. The cluster size was determined using a retarding field energy analyzer. The results of X-ray diffraction measurements indicate the cubic zinc blende (ZB) crystalline structure of the CdTe thin film on the silicon substrate. The CdTe thin film prepared by the ICB method had high crystalline quality. The microscopic processes involved in the ICB deposition technique, such as impact and coalescence processes, have been studied in detail by molecular dynamics (MD) simulation.

  1. In vitro DNA binding studies of lenalidomide using spectroscopic in combination with molecular docking techniques

    Science.gov (United States)

    Xu, Liang; Hu, Yan-Xi; Li, Yan-Cheng; Zhang, Li; Ai, Hai-Xin; Liu, Yu-Feng; Liu, Hong-Sheng

    2018-02-01

    In the present work, the binding interaction between lenalidomide (LEN) and calf thymus DNA (ct-DNA) was systematically studied by using fluorescence, ultraviolet-visible (UV-vis) absorption, circular dichroism (CD) spectroscopies under imitated physiological conditions (pH = 7.4) coupled with molecular docking. It was found that LEN was bound to ct-DNA with high binding affinity (Ka = 2.308 × 105 M-1 at 283 K) through groove binding as evidenced by a slight decrease in the absorption intensity in combination with CD spectra. Thermodynamic parameters (ΔG 0 and ΔS interaction. Furthermore, competitive binding experiments with ethidium bromide and 4‧, 6-dia-midino-2-phenylindoleas probes showed that LEN could preferentially bind in the minor groove of double-stranded DNA. The average lifetime of LEN was calculated to be 7.645 ns. The φ of LEN was measured as 0.09 and non-radiation energy transfer between LEN and DNA had occurred. The results of the molecular docking were consistent with the experimental results. This study explored the potential applicability of the spectroscopic properties of LEN and also investigated its interactions with relevant biological targets. In addition, it will provide some theoretical references for the deep research of simultaneous administration of LEN with other drugs.

  2. Molecular characterisation of a germplasm bank for Theobroma genus using the RAPD technique

    Directory of Open Access Journals (Sweden)

    Yovany Moreno

    2004-07-01

    Full Text Available RAPD markers (Random Amplified Polymorphic DNA were used for analysing 145 individuals (128 T. grandiflorum and 17 T. bicolor from the ex situ Theobroma genus germplasm bank at Instituto Sinchi, located at San José del Guaviare. 5 primers able to generated polymorphism were selected from an initial set of 20, generating 114 bands that enable to us to distinguish between more than 99% of individuals analysed: 57 bands for T. grandiflorum (84.2% polymorphic, 45 bands for T. bicolor (26.7% polymorphic and 12 bands shared between the two species (58.3% polymorphic. A high degree of intra-specific similarity particularly in T. bicolor was established from the similarity matrix obtained by using the Dice index and represented in a UPGMA dendrogram and the principal components analysis (PCA. The comparison of this analysis with a previous morpho-agronomic evaluation of some T. grandiflorum individuals revealed that the groups generated on the basis of its agronomic and morphological traits were heterogeneous at molecular level. The obtained information will be used as a tool in strategies regarding maintenance, enrichment and use of the germplasm bank. Key words: Theobroma grandiflorum, Theobroma bicolour, RAPD, molecular characterisation.

  3. Experience and evaluation of advanced on-line core monitoring system 'BEACON' at IKATA site

    International Nuclear Information System (INIS)

    Fujitsuka, Nobumichi; Tanouchi, Hideyuki; Imamura, Yasuhiro; Mizobuchil, Daisuke

    1997-01-01

    Shikoku Electric Power Company installed BEACON core monitoring system into IKATA unit 3 in May 1994. During its first cycle of core operation, various operational data were obtained including data of some anomalous reactor conditions introduced for the test objective of the plant start-up. This paper presents the evaluation of the BEACON system capability based on this experience. The system functions such as core monitoring and anomaly detection, prediction of future reactor conditions and increased efficiency of core management activities are discussed. Our future plan to utilize the system is also presented. (authors)

  4. Code Development and Analysis Program: developmental checkout of the BEACON/MOD2A code

    International Nuclear Information System (INIS)

    Ramsthaler, J.A.; Lime, J.F.; Sahota, M.S.

    1978-12-01

    A best-estimate transient containment code, BEACON, is being developed by EG and G Idaho, Inc. for the Nuclear Regulatory Commission's reactor safety research program. This is an advanced, two-dimensional fluid flow code designed to predict temperatures and pressures in a dry PWR containment during a hypothetical loss-of-coolant accident. The most recent version of the code, MOD2A, is presently in the final stages of production prior to being released to the National Energy Software Center. As part of the final code checkout, seven sample problems were selected to be run with BEACON/MOD2A

  5. Optimal placement of range-only beacons for mobile robot localisation

    CSIR Research Space (South Africa)

    Burke, Michael G

    2011-11-01

    Full Text Available of the Euclidean distance between the position estimate (x; y; z) and the largest orthogo- nal standard deviations in 3D space, and is an improvement on the GDOP metric as it considers both off-diagonal covariance terms and individual beacon noise. The beacon... is the Euclidean distance between an accessed node and a goal. This results in the shortest route to a goal being determined. The cost of traversing to a node is typically the distance between nodes. However, by replacing this cost with the uncertainty metric...

  6. Biological, serological and molecular techniques to xanthomonas axonopodis pv. Ci tri Asymptomatic detection

    International Nuclear Information System (INIS)

    Peyrou, M.; Del Campo, R.; Russi, P.; Mara, H.; Rigamonti, N.; Larrechart, L.; Perez, E.

    2012-01-01

    Xanthomonas axonopodis pv. ci tri (X ac) produces citrus canker disease in all citrus commercial species. The bacteria can be disseminated through vegetative propagation material in asymptomatic form. To optimize bacteria detection techniques applicable to asymptomatic citrus plant tissue routine analysis, ELISA, Immunofluorescence, Pcr, qRT P CR and host plant inoculation (bioassay) diagnostic techniques were compared. Tests were made from decimal dilutions between 108 uf6.ml-1 and 102 ufc.mL-1 using a pure culture of 49b strain.The detection level obtained was 1.8 x 102 ufc.mL-1 using Inmunofluorescence; 1.8x104 ufc.mL-1 with indirect ELISA, 1.8 x 103 ufc.mL-1 by means of PCR; 10 ufc.mL-1 through of qRT P CR and 230 ufc.mL-1 in sour orange inoculated plants. The experiment was repeated at least three times for each technique. Considering this result, and taking into account that sensitivity, practicity and cost, are important when a great number of plants need to be tested, the PCR and inoculation in host plants were those that met the best characteristics to be evaluated in asymptomatic plant material

  7. Random sampling technique for ultra-fast computations of molecular opacities for exoplanet atmospheres

    Science.gov (United States)

    Min, M.

    2017-10-01

    Context. Opacities of molecules in exoplanet atmospheres rely on increasingly detailed line-lists for these molecules. The line lists available today contain for many species up to several billions of lines. Computation of the spectral line profile created by pressure and temperature broadening, the Voigt profile, of all of these lines is becoming a computational challenge. Aims: We aim to create a method to compute the Voigt profile in a way that automatically focusses the computation time into the strongest lines, while still maintaining the continuum contribution of the high number of weaker lines. Methods: Here, we outline a statistical line sampling technique that samples the Voigt profile quickly and with high accuracy. The number of samples is adjusted to the strength of the line and the local spectral line density. This automatically provides high accuracy line shapes for strong lines or lines that are spectrally isolated. The line sampling technique automatically preserves the integrated line opacity for all lines, thereby also providing the continuum opacity created by the large number of weak lines at very low computational cost. Results: The line sampling technique is tested for accuracy when computing line spectra and correlated-k tables. Extremely fast computations ( 3.5 × 105 lines per second per core on a standard current day desktop computer) with high accuracy (≤1% almost everywhere) are obtained. A detailed recipe on how to perform the computations is given.

  8. Chemical intermediate detection following corona discharge on volatile organic compounds: general method using molecular beam techniques

    International Nuclear Information System (INIS)

    He Luning; Sulkes, Mark

    2011-01-01

    Nonthermal plasma (NTP)-based treatments of volatile organic compounds (VOCs) have potential for effective environmental remediation. Theory and experiment that consider the basic science pertaining to discharge events have helped improve NTP remediation outcomes. If direct information on early post-discharge chemical intermediates were also available, it would likely lead to additional improvement in NTP remediation outcomes. To this point, however, experiments yielding direct information on post-NTP VOC intermediates have been limited. An approach using supersonic expansion molecular beam methods offers general promise for detection of post-discharge VOC intermediates. To illustrate the potential utility of these methods, we present mass spectra showing the growth of early products formed when pulsed corona discharges were carried out on toluene in He and then in He with added O 2 . Good general detection of neutral post-discharge species was obtained using 800 nm 150 fs photoionization pulses.

  9. BEACON/MOD3, 1-D and 2-D 2 Phase Flow and Heat Transfer in Containment, LWR LOCA

    International Nuclear Information System (INIS)

    Broadus, C.R.; Doyle, R.J.; James, S.W.; Lime, J.F.; Mings, W.J.; Ramsthaler, J.A.; Sahota, M.S.

    1982-01-01

    1 - Description of problem or function: The BEACON series of programs is designed to perform a best-estimate analysis of the flow of a mixture of air, water, and steam in a nuclear reactor containment system under loss-of-coolant accident conditions. The code can simulate two-component, two-phase fluid flow in complex geometries using a combination of two-dimensional, one-dimensional, and lumped- parameter representations for the various parts of the system. BEACON/MOD3 contains mass and heat transfer models for wall film and for wall conduction, and is suitable for the evaluation of short- term transients in PWR dry containment systems. The capability to examine the details of a two-components, two-phase flow field in one or two dimensions under nonhomogeneous, nonequilibrium conditions (unequal velocities, unequal temperatures between the two phases) allows analysis of such problems as the calculation of jet impact forces of a fluid leaving a pipe break, the motion of a large pressure wave across a compartment, the variation in flow properties as air is displaced from a compartment by steam and water, the water entrainment or de-entrainment by a high-speed vapor flow, the flow of a flashing liquid, and many other complex nonequilibrium problems of containment system analyses. 2 - Method of solution: The basic Eulerian flow solution procedure is based on the K-FIX two-dimensional two-phase numerical method. Each phase is described by its own density, velocity, and temperature as determined by separate sets of mass, momentum, and energy equations. The two phases are coupled by exchange parameters which model the exchange of mass, momentum, and energy between the two phases. The two sets of field equations are solved with a Eulerian finite- difference technique that implicitly treats the phase transitions and inter-phasic heat transfer in the pressure iteration. The implicit solution is accomplished iteratively without linearization and allows both phases to be

  10. Interaction of the minocycline with extracelluar protein and intracellular protein by multi-spectral techniques and molecular docking

    Science.gov (United States)

    Fang, Qing; Wang, Yirun; Hu, Taoying; Liu, Ying

    2017-02-01

    The interaction of minocyeline (MNC) with extracelluar protein (lysozyme, LYSO) or intracellular protein (bovine hemoglobin, BHb) was investigated using multi-spectral techniques and molecular docking in vitro. Fluorescence studies suggested that MNC quenched LYSO/BHb fluorescence in a static mode with binding constants of 2.01 and 0.26 × 104 L•mol-1 at 298 K, respectively. The LYZO-MNC system was more easily influenced by temperature (298 and 310 K) than the BHb-MNC system. The thermodynamic parameters demonstrated that hydrogen bonds and van der Waals forces played the major role in the binding process. Based on the Förster theory of nonradiative energy transfer, the binding distances between MNC and the inner tryptophan residues of LYSO and BHb were calculated to be 4.34 and 3.49 nm, respectively. Furthermore, circular dichroism spectra (CD), Fourier transforms infrared (FTIR), UV-vis, and three-dimensional fluorescence spectra results indicated the secondary structures of LYSO and BHb were partially destroyed by MNC with the α-helix percentage of LYZO-MNC increased (17.8-28.6%) while that of BHb-MNC was decreased (41.6-39.6%). UV-vis spectral results showed these binding interactions could cause conformational and some micro-environmental changes of LYSO and BHb. In accordance with the results of molecular docking, In LYZO-MNC system, MNC was mainly bound in the active site hinge region where Trp-62 and Trp-63 are located, and in MNC-BHb system, MNC was close to the subunit α 1 of BHb, molecular docking analysis supported the thermodynamic results well. The work contributes to clarify the mechanism of MNC with two proteins at molecular level.

  11. Withania somnifera: Advances and Implementation of Molecular and Tissue Culture Techniques to Enhance Its Application

    Directory of Open Access Journals (Sweden)

    Vibha Pandey

    2017-08-01

    Full Text Available Withania somnifera, commonly known as Ashwagandha an important medicinal plant largely used in Ayurvedic and indigenous medicine for over 3,000 years. Being a medicinal plant, dried powder, crude extract as well as purified metabolies of the plant has shown promising therapeutic properties. Withanolides are the principal metabolites, responsible for the medicinal properties of the plant. Availability and amount of particular withanolides differ with tissue type and chemotype and its importance leads to identification characterization of several genes/ enzymes related to withanolide biosynthetic pathway. The modulation in withanolides can be achieved by controlling the environmental conditions like, different tissue culture techniques, altered media compositions, use of elicitors, etc. Among all the in vitro techniques, hairy root culture proved its importance at industrial scale, which also gets benefits due to more accumulation (amount and number of withanolides in roots tissues of W. somnifera. Use of media compostion and elicitors further enhances the amount of withanolides in hairy roots. Another important modern day technique used for accumulation of desired secondary metabolites is modulating the gene expression by altering environmental conditions (use of different media composition, elicitors, etc. or through genetic enginnering. Knowing the significance of the gene and the key enzymatic step of the pathway, modulation in withanolide contents can be achieved upto required amount in therapeutic industry. To accomplish maximum productivity through genetic enginnering different means of Withania transformation methods have been developed to obtain maximum transformation efficiency. These standardized transformation procedues have been used to overexpress/silence desired gene in W. somnifera to understand the outcome and succeed with enhanced metabolic production for the ultimate benefit of human race.

  12. The FADE mass-stat: A technique for inserting or deleting particles in molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Borg, Matthew K., E-mail: matthew.borg@strath.ac.uk [Department of Mechanical and Aerospace Engineering, University of Strathclyde, Glasgow G1 1XJ (United Kingdom); Lockerby, Duncan A., E-mail: duncan.lockerby@warwick.ac.uk [School of Engineering, University of Warwick, Coventry CV4 7AL (United Kingdom); Reese, Jason M., E-mail: jason.reese@ed.ac.uk [School of Engineering, University of Edinburgh, Edinburgh EH9 3JL (United Kingdom)

    2014-02-21

    The emergence of new applications of molecular dynamics (MD) simulation calls for the development of mass-statting procedures that insert or delete particles on-the-fly. In this paper we present a new mass-stat which we term FADE, because it gradually “fades-in” (inserts) or “fades-out” (deletes) molecules over a short relaxation period within a MD simulation. FADE applies a time-weighted relaxation to the intermolecular pair forces between the inserting/deleting molecule and any neighbouring molecules. The weighting function we propose in this paper is a piece-wise polynomial that can be described entirely by two parameters: the relaxation time scale and the order of the polynomial. FADE inherently conserves overall system momentum independent of the form of the weighting function. We demonstrate various simulations of insertions of atomic argon, polyatomic TIP4P water, polymer strands, and C{sub 60} Buckminsterfullerene molecules. We propose FADE parameters and a maximum density variation per insertion-instance that restricts spurious potential energy changes entering the system within desired tolerances. We also demonstrate in this paper that FADE compares very well to an existing insertion algorithm called USHER, in terms of accuracy, insertion rate (in dense fluids), and computational efficiency. The USHER algorithm is applicable to monatomic and water molecules only, but we demonstrate that FADE can be generally applied to various forms and sizes of molecules, such as polymeric molecules of long aspect ratio, and spherical carbon fullerenes with hollow interiors.

  13. The FADE mass-stat: A technique for inserting or deleting particles in molecular dynamics simulations

    International Nuclear Information System (INIS)

    Borg, Matthew K.; Lockerby, Duncan A.; Reese, Jason M.

    2014-01-01

    The emergence of new applications of molecular dynamics (MD) simulation calls for the development of mass-statting procedures that insert or delete particles on-the-fly. In this paper we present a new mass-stat which we term FADE, because it gradually “fades-in” (inserts) or “fades-out” (deletes) molecules over a short relaxation period within a MD simulation. FADE applies a time-weighted relaxation to the intermolecular pair forces between the inserting/deleting molecule and any neighbouring molecules. The weighting function we propose in this paper is a piece-wise polynomial that can be described entirely by two parameters: the relaxation time scale and the order of the polynomial. FADE inherently conserves overall system momentum independent of the form of the weighting function. We demonstrate various simulations of insertions of atomic argon, polyatomic TIP4P water, polymer strands, and C 60 Buckminsterfullerene molecules. We propose FADE parameters and a maximum density variation per insertion-instance that restricts spurious potential energy changes entering the system within desired tolerances. We also demonstrate in this paper that FADE compares very well to an existing insertion algorithm called USHER, in terms of accuracy, insertion rate (in dense fluids), and computational efficiency. The USHER algorithm is applicable to monatomic and water molecules only, but we demonstrate that FADE can be generally applied to various forms and sizes of molecules, such as polymeric molecules of long aspect ratio, and spherical carbon fullerenes with hollow interiors

  14. Risk organ preservation technique in reirradiation. Injection of native type high molecular weight hyaluronate

    International Nuclear Information System (INIS)

    Kishi, Kazushi; Noda, Yasutaka; Tanaka, Kayo

    2012-01-01

    We developed a practical method of brachytherapy effective for reirradiation, using hyaluronate gel injection to separate the target to be intensively. We intended curative reirradiation with preserving organs at risk. Native-type high molecular weight hyaluronate that has an ideal biologic property to reduce inflammation via inhibitory activity to CD44 and other inflammation receptors was injected to create space during radiotherapy. Rectum, small intestines, skin, and various normal organs are effectively separated and thus eradicative re-irradiation was carried out in safe. We reviewed 55 patients who required the method. There were no complications related to the procedure. Prescribed dose to 100% of the planning target volume (PTV) was 77.93 Gy (range 54-92) equivalent at alpha/beta ratio of 3, with much higher subvolume effect, and the saving effects were enhanced at 3.35 times in the average of those without gel injection. In conclusion, the interventional brachytherapy with hyaluronate gel injection provided 3.35 times safer dose-escalated and eradicative treatment in reirradiation. (author)

  15. Molecular structure and spectroscopic characterization of Carbamazepine with experimental techniques and DFT quantum chemical calculations

    Science.gov (United States)

    Suhasini, M.; Sailatha, E.; Gunasekaran, S.; Ramkumaar, G. R.

    2015-04-01

    A systematic vibrational spectroscopic assignment and analysis of Carbamazepine has been carried out by using FT-IR, FT-Raman and UV spectral data. The vibrational analysis were aided by electronic structure calculations - ab initio (RHF) and hybrid density functional methods (B3LYP) performed with standard basis set 6-31G(d,p). Molecular equilibrium geometries, electronic energies, natural bond order analysis, harmonic vibrational frequencies and IR intensities have been computed. A detailed interpretation of the vibrational spectra of the molecule has been made on the basis of the calculated Potential Energy Distribution (PED) by VEDA program. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λmax were determined by HF/6-311++G(d,p) Time-Dependent method. The thermodynamic functions of the title molecule were also performed using the RHF and DFT methods. The restricted Hartree-Fock and density functional theory-based nuclear magnetic resonance (NMR) calculation procedure was also performed, and it was used for assigning the 13C and 1H NMR chemical shifts of Carbamazepine.

  16. Geologic map of the Beacon Rock quadrangle, Skamania County, Washington

    Science.gov (United States)

    Evarts, Russell C.; Fleck, Robert J.

    2017-06-06

    The Beacon Rock 7.5′ quadrangle is located approximately 50 km east of Portland, Oregon, on the north side of the Columbia River Gorge, a scenic canyon carved through the axis of the Cascade Range by the Columbia River. Although approximately 75,000 people live within the gorge, much of the region remains little developed and is encompassed by the 292,500-acre Columbia River Gorge National Scenic Area, managed by a consortium of government agencies “to pro­tect and provide for the enhancement of the scenic, cultural, recreational and natural resources of the Gorge and to protect and support the economy of the Columbia River Gorge area.” As the only low-elevation corridor through the Cascade Range, the gorge is a critical regional transportation and utilities corridor (Wang and Chaker, 2004). Major state and national highways and rail lines run along both shores of the Columbia River, which also provides important water access to ports in the agricultural interior of the Pacific Northwest. Transmission lines carry power from hydroelectric facilities in the gorge and farther east to the growing urban areas of western Oregon and Washington, and natural-gas pipelines transect the corridor (Wang and Chaker, 2004). These lifelines are highly vulnerable to disruption by earthquakes, landslides, and floods. A major purpose of the work described here is to identify and map geologic hazards, such as faults and landslide-prone areas, to provide more accurate assessments of the risks associated with these features.The steep canyon walls of the map area reveal exten­sive outcrops of Miocene flood-basalt flows of the Columbia River Basalt Group capped by fluvial deposits of the ances­tral Columbia River, Pliocene lavas erupted from the axis of the Cascade arc to the east, and volcanic rocks erupted from numerous local vents. The Columbia River Basalt Group unconformably rests on a sequence of late Oligocene and early Miocene rocks of the ancestral Cascade volcanic arc

  17. Molecular techniques for the personalised management of patients with chronic myeloid leukaemia.

    Science.gov (United States)

    Alikian, Mary; Gale, Robert Peter; Apperley, Jane F; Foroni, Letizia

    2017-03-01

    Chronic myeloid leukemia (CML) is the paradigm for targeted cancer therapy. RT-qPCR is the gold standard for monitoring response to tyrosine kinase-inhibitor (TKI) therapy based on the reduction of blood or bone marrow BCR-ABL1 . Some patients with CML and very low or undetectable levels of BCR-ABL1 transcripts can stop TKI-therapy without CML recurrence. However, about 60 percent of patients discontinuing TKI-therapy have rapid leukaemia recurrence. This has increased the need for more sensitive and specific techniques to measure residual CML cells. The clinical challenge is to determine when it is safe to stop TKI-therapy. In this review we describe and critically evaluate the current state of CML clinical management, different technologies used to monitor measurable residual disease (MRD) focus on comparingRT-qPCR and new methods entering clinical practice. We discuss advantages and disadvantages of new methods.

  18. ClassBeacons: designing distributed visualization of teachers’ physical proximity in the classroom.

    NARCIS (Netherlands)

    An, P.; Bakker, S.; Ordanovski, S.; Taconis, R.; Eggen, J.H.

    2018-01-01

    Pengcheng An, Saskia Bakker, Sara Ordanovski, Ruurd Taconis, Berry Eggen. 2018 (accepted at Oct 2017). ClassBeacons: designing distributed visualization of teachers’ physical proximity in the classroom. In Proceedings of Tangible and Embodied Interaction, TEI 2018, Mar 18-21, 2018,

  19. Pedestrian hybrid beacon crosswalk system (PHB) or high-intensity activated crosswalk (HAWK).

    Science.gov (United States)

    2014-11-01

    The Pedestrian Hybrid Beacon Crosswalk (PHB) is a type of traffic control system, used to aid : pedestrians safely crossing the street and to regulate traffic flow. This study examines the : success of the first PHB installed in the state of Vermont....

  20. Beacon satellite studies and modelling of total electron contents of the ionosphere

    International Nuclear Information System (INIS)

    Tyagi, T.R.

    1990-01-01

    An attempt is made to highlight some of the beacon satellite studies, particularly those relating to total electron content (TEC) and scintillations, with special attention to Indian subcontinent observations. The modelling of TEC is described. The scope of new experiments for specific problem is indicated. (author). 78 refs., 12 figs

  1. Improved fixation quality provided by a Bessel beacon in an adaptive optics system.

    Science.gov (United States)

    Lambert, Andrew J; Daly, Elizabeth M; Dainty, Christopher J

    2013-07-01

    We investigate whether a structured probe beam that creates the beacon for use in a retinal imaging adaptive optics system can provide useful side effects. In particular we investigate whether a Bessel beam that is seen by the subject as a set of concentric rings has a dampening effect on fixation variations of the subject under observation. This calming effect would allow longer periods of observation, particularly for patients with abnormal fixation. An experimental adaptive optics system developed for retinal imaging is used to monitor the fluctuations in aberrations for artificial and human subjects. The probe beam is alternated between a traditional beacon and one provided by a Bessel beam created by SLM. Time-frequency analysis is used to indicate the differences in power and time variation during fixation depending on whether the Bessel beam or the traditional beacon is employed. Comparison is made with the response for an artificial eye to discount systemic variations. Significant evidence is accrued to indicate the reduced fluctuations in fixation when the Bessel beam is employed to create the beacon. © 2013 The Authors Ophthalmic & Physiological Optics © 2013 The College of Optometrists.

  2. The Effects of a Rectangular Rapid-Flashing Beacon on Vehicle Speed

    Science.gov (United States)

    VanWagner, Michelle; Van Houten, Ron; Betts, Brian

    2011-01-01

    In 2008, nearly 31% of vehicle fatalities were related to failure to adhere to safe vehicle speeds (National Highway Traffic Safety Administration [NHTSA], 2009). The current study evaluated the effect of a rectangular rapid-flashing beacon (RRFB) triggered by excessive speed on vehicle speed using a combined alternating treatments and reversal…

  3. Beacon-Based Service Publishing Framework in Multiservice Wi-Fi Hotspots

    Directory of Open Access Journals (Sweden)

    Di Sorte Dario

    2007-01-01

    Full Text Available In an expected future multiaccess and multiservice IEEE 802.11 environment, the problem of providing users with useful service-related information to support a correct rapid network selection is expected to become a very important issue. A feasible short-term 802.11-tailored working solution, compliant with existing equipment, is to publish service information encoded within the SSID information element within beacon frames. This makes it possible for an operator to implement service publishing in 802.11 networks while waiting for a standardized mechanism. Also, this straightforward approach has allowed us to evaluate experimentally the performance of a beacon-based service publishing solution. In fact, the main focus of the paper is indeed to present a quantitative comparison of service discovery times between the legacy scenario, where the user is forced to associate and authenticate with a network point of access to check its service offer, and the enhanced scenario where the set of service-related information is broadcasted within beacons. These discovery times are obtained by processing the results of a measurement campaign performed in a multiaccess/service 802.11 environment. This analysis confirms the effectiveness of the beacon-based approach. We also show that the cost in terms of wireless bandwidth consumption of such solution is low.

  4. Application of the BEACON-TSM system to the operation of PWR reactors

    International Nuclear Information System (INIS)

    Lozano, J. A.; Mildrum, C.; Serrano, J. F.

    2011-01-01

    BEACON-TSM is an advanced system of the operation support of PWR reactors that combines the capabilities of an advanced nodal neutronic model and the measures of the instrumentation available in plant to determine, accurately and continuously, the distribution of power in the core and the available margins to the limits of the beak factors.

  5. Beacon signal in transcranial color coded ultrasound: A sign for brain death

    Directory of Open Access Journals (Sweden)

    Mehmet Akif Topçuoğlu

    2014-04-01

    Full Text Available A widely under-recognized brain-death confirming transcranial ultrasonography pattern resembling the red-blue beacon signal was demonstrated. Familiarity to this distinct and characteristic ultrasonic pattern seems to be important in the perspective of point-of-care neurological ultrasound use and knobology.

  6. Sequential strand displacement beacon for detection of DNA coverage on functionalized gold nanoparticles.

    Science.gov (United States)

    Paliwoda, Rebecca E; Li, Feng; Reid, Michael S; Lin, Yanwen; Le, X Chris

    2014-06-17

    Functionalizing nanomaterials for diverse analytical, biomedical, and therapeutic applications requires determination of surface coverage (or density) of DNA on nanomaterials. We describe a sequential strand displacement beacon assay that is able to quantify specific DNA sequences conjugated or coconjugated onto gold nanoparticles (AuNPs). Unlike the conventional fluorescence assay that requires the target DNA to be fluorescently labeled, the sequential strand displacement beacon method is able to quantify multiple unlabeled DNA oligonucleotides using a single (universal) strand displacement beacon. This unique feature is achieved by introducing two short unlabeled DNA probes for each specific DNA sequence and by performing sequential DNA strand displacement reactions. Varying the relative amounts of the specific DNA sequences and spacing DNA sequences during their coconjugation onto AuNPs results in different densities of the specific DNA on AuNP, ranging from 90 to 230 DNA molecules per AuNP. Results obtained from our sequential strand displacement beacon assay are consistent with those obtained from the conventional fluorescence assays. However, labeling of DNA with some fluorescent dyes, e.g., tetramethylrhodamine, alters DNA density on AuNP. The strand displacement strategy overcomes this problem by obviating direct labeling of the target DNA. This method has broad potential to facilitate more efficient design and characterization of novel multifunctional materials for diverse applications.

  7. A Beacon Transmission Power Control Algorithm Based on Wireless Channel Load Forecasting in VANETs.

    Science.gov (United States)

    Mo, Yuanfu; Yu, Dexin; Song, Jun; Zheng, Kun; Guo, Yajuan

    2015-01-01

    In a vehicular ad hoc network (VANET), the periodic exchange of single-hop status information broadcasts (beacon frames) produces channel loading, which causes channel congestion and induces information conflict problems. To guarantee fairness in beacon transmissions from each node and maximum network connectivity, adjustment of the beacon transmission power is an effective method for reducing and preventing channel congestion. In this study, the primary factors that influence wireless channel loading are selected to construct the KF-BCLF, which is a channel load forecasting algorithm based on a recursive Kalman filter and employs multiple regression equation. By pre-adjusting the transmission power based on the forecasted channel load, the channel load was kept within a predefined range; therefore, channel congestion was prevented. Based on this method, the CLF-BTPC, which is a transmission power control algorithm, is proposed. To verify KF-BCLF algorithm, a traffic survey method that involved the collection of floating car data along a major traffic road in Changchun City is employed. By comparing this forecast with the measured channel loads, the proposed KF-BCLF algorithm was proven to be effective. In addition, the CLF-BTPC algorithm is verified by simulating a section of eight-lane highway and a signal-controlled urban intersection. The results of the two verification process indicate that this distributed CLF-BTPC algorithm can effectively control channel load, prevent channel congestion, and enhance the stability and robustness of wireless beacon transmission in a vehicular network.

  8. Some measurements of total electron content made with the ATS-6 radio beacon

    International Nuclear Information System (INIS)

    Davies, K.; Degenhardt, W.; Hartmann, G.K.

    1978-01-01

    The paper deals with some measurements made with the radio beacon on board the ATS-6 satellite in the American and European sectors. Measurements of the slant electron content, the Faraday content, and the plasmaspheric (or residual) content, made under different geographic and geomagnetic conditions, are discussed and compared

  9. A Beacon Transmission Power Control Algorithm Based on Wireless Channel Load Forecasting in VANETs.

    Directory of Open Access Journals (Sweden)

    Yuanfu Mo

    Full Text Available In a vehicular ad hoc network (VANET, the periodic exchange of single-hop status information broadcasts (beacon frames produces channel loading, which causes channel congestion and induces information conflict problems. To guarantee fairness in beacon transmissions from each node and maximum network connectivity, adjustment of the beacon transmission power is an effective method for reducing and preventing channel congestion. In this study, the primary factors that influence wireless channel loading are selected to construct the KF-BCLF, which is a channel load forecasting algorithm based on a recursive Kalman filter and employs multiple regression equation. By pre-adjusting the transmission power based on the forecasted channel load, the channel load was kept within a predefined range; therefore, channel congestion was prevented. Based on this method, the CLF-BTPC, which is a transmission power control algorithm, is proposed. To verify KF-BCLF algorithm, a traffic survey method that involved the collection of floating car data along a major traffic road in Changchun City is employed. By comparing this forecast with the measured channel loads, the proposed KF-BCLF algorithm was proven to be effective. In addition, the CLF-BTPC algorithm is verified by simulating a section of eight-lane highway and a signal-controlled urban intersection. The results of the two verification process indicate that this distributed CLF-BTPC algorithm can effectively control channel load, prevent channel congestion, and enhance the stability and robustness of wireless beacon transmission in a vehicular network.

  10. Analysis and Enhancement of IEEE 802.15.4e DSME Beacon Scheduling Model

    Directory of Open Access Journals (Sweden)

    Kwang-il Hwang

    2014-01-01

    Full Text Available In order to construct a successful Internet of things (IoT, reliable network construction and maintenance in a sensor domain should be supported. However, IEEE 802.15.4, which is the most representative wireless standard for IoT, still has problems in constructing a large-scale sensor network, such as beacon collision. To overcome some problems in IEEE 802.15.4, the 15.4e task group proposed various different modes of operation. Particularly, the IEEE 802.15.4e deterministic and synchronous multichannel extension (DSME mode presents a novel scheduling model to solve beacon collision problems. However, the DSME model specified in the 15.4e draft does not present a concrete design model but a conceptual abstract model. Therefore, in this paper we introduce a DSME beacon scheduling model and present a concrete design model. Furthermore, validity and performance of DSME are evaluated through experiments. Based on experiment results, we analyze the problems and limitations of DSME, present solutions step by step, and finally propose an enhanced DSME beacon scheduling model. Through additional experiments, we prove the performance superiority of enhanced DSME.

  11. Scheduled MAC in Beacon Overlay Networks for Underwater Localization and Time-Synchronization

    NARCIS (Netherlands)

    van Kleunen, W.A.P.; Meratnia, Nirvana; Havinga, Paul J.M.

    2011-01-01

    In this article we introduce a MAC protocol designed for underwater localization and time-synchronisation. The MAC protocol assumes a network of static reference nodes and allows blind nodes to be localized by listening-only to the beacon messages. Such a system is known to be very scalable. We show

  12. Molecular detection and variability of Strawberry vein banding virus

    Czech Academy of Sciences Publication Activity Database

    Hanzlíková-Vašková, Dana; Špak, Josef

    2004-01-01

    Roč. 656, - (2004), 33-38 ISSN 0567-7572 Grant - others:EU EU QLR5-1999-1553 Institutional research plan: CEZ:AV0Z5051902 Keywords : AmpliDet RNA * caulimovirus * molecular beacon * nucleic acid sequence based amplification * PCR, SVBV * CaM Subject RIV: EE - Microbiology, Virology

  13. Visual detection of STAT5B gene expression in living cell using the hairpin DNA modified gold nanoparticle beacon.

    Science.gov (United States)

    Xue, Jianpeng; Shan, Lingling; Chen, Haiyan; Li, Yang; Zhu, Hongyan; Deng, Dawei; Qian, Zhiyu; Achilefu, Samuel; Gu, Yueqing

    2013-03-15

    Signal transducer and activator of transcription 5B (STAT5B) is an important protein in JAK-STAT signaling pathway that is responsible for the metastasis and proliferation of tumor cells. Determination of the STAT5B messenger Ribonucleic Acid (mRNA) relating to the STAT5B expression provides insight into the mechanism of tumor progression. In this study, we designed and used a special hairpin deoxyribonucleic acid (DNA) for human STAT5B mRNA to functionalize gold nanoparticles, which served as a beacon for detecting human STAT5B expression. Up to 90% quenching efficiency was achieved. Upon hybridizing with the target mRNA, the hairpin DNA modified gold nanoparticle beacons (hDAuNP beacons) release the fluorophores attached at 5' end of the oligonucleotide sequence. The fluorescence properties of the beacon before and after the hybridization with the complementary DNA were confirmed in vitro. The stability of hDAuNP beacons against degradation by DNase I and GSH indicated that the prepared beacon is stable inside cells. The detected fluorescence in MCF-7 cancer cells correlates with the specific STAT5B mRNA expression, which is consistent with the result from PCR measurement. Fluorescence microscopy showed that the hDAuNP beacons internalized in cells without using transfection agents, with intracellular distribution in the cytoplasm rather than the nucleus. The results demonstrated that this beacon could directly provide quantitative measurement of the intracellular STAT5B mRNA in living cells. Compared to the previous approaches, this beacon has advantages of higher target to background ratio of detection and an increased resistance to nuclease degradation. The strategy reported in this study is a promising approach for the intracellular measurement of RNA or protein expression in living cells, and has great potential in the study of drug screening and discovery. Copyright © 2012 Elsevier B.V. All rights reserved.

  14. Diagnostic reproducibility of hydatidiform moles: ancillary techniques (p57 immunohistochemistry and molecular genotyping) improve morphologic diagnosis.

    Science.gov (United States)

    Vang, Russell; Gupta, Mamta; Wu, Lee-Shu-Fune; Yemelyanova, Anna V; Kurman, Robert J; Murphy, Kathleen M; Descipio, Cheryl; Ronnett, Brigitte M

    2012-03-01

    Distinction of hydatidiform moles (HMs) from nonmolar specimens (NMs) and subclassification of HMs as complete hydatidiform moles (CHMs) and partial hydatidiform moles (PHMs) are important for clinical practice and investigational studies; yet, diagnosis based solely on morphology is affected by interobserver variability. Molecular genotyping can distinguish these entities by discerning androgenetic diploidy, diandric triploidy, and biparental diploidy to diagnose CHMs, PHMs, and NMs, respectively. Eighty genotyped cases (27 CHMs, 27 PHMs, and 26 NMs) were selected from a series of 200 potentially molar specimens previously diagnosed using p57 immunostaining and genotyping. Cases were classified by 3 gynecologic pathologists on the basis of H&E slides (masked to p57 immunostaining and genotyping results) into 1 of 3 categories (CHM, PHM, or NM) during 2 diagnostic rounds; a third round incorporating p57 immunostaining results was also conducted. Consensus diagnoses (those rendered by 2 of 3 pathologists) were determined. Genotyping results were used as the gold standard for assessing diagnostic performance. Sensitivity of a diagnosis of CHM ranged from 59% to 100% for individual pathologists and from 70% to 81% by consensus; specificity ranged from 91% to 96% for individuals and from 94% to 98% by consensus. Sensitivity of a diagnosis of PHM ranged from 56% to 93% for individual pathologists and from 70% to 78% by consensus; specificity ranged from 58% to 92% for individuals and from 74% to 85% by consensus. The percentage of correct classification of all cases by morphology ranged from 55% to 75% for individual pathologists and from 70% to 75% by consensus. The κ values for interobserver agreement ranged from 0.59 to 0.73 (moderate to good) for a diagnosis of CHM, from 0.15 to 0.43 (poor to moderate) for PHM, and from 0.13 to 0.42 (poor to moderate) for NM. The κ values for intraobserver agreement ranged from 0.44 to 0.67 (moderate to good). Addition of the p57

  15. High throughput techniques to reveal the molecular physiology and evolution of digestion in spiders.

    Science.gov (United States)

    Fuzita, Felipe J; Pinkse, Martijn W H; Patane, José S L; Verhaert, Peter D E M; Lopes, Adriana R

    2016-09-07

    Spiders are known for their predatory efficiency and for their high capacity of digesting relatively large prey. They do this by combining both extracorporeal and intracellular digestion. Whereas many high throughput ("-omics") techniques focus on biomolecules in spider venom, so far this approach has not yet been applied to investigate the protein composition of spider midgut diverticula (MD) and digestive fluid (DF). We here report on our investigations of both MD and DF of the spider Nephilingis (Nephilengys) cruentata through the use of next generation sequencing and shotgun proteomics. This shows that the DF is composed of a variety of hydrolases including peptidases, carbohydrases, lipases and nuclease, as well as of toxins and regulatory proteins. We detect 25 astacins in the DF. Phylogenetic analysis of the corresponding transcript(s) in Arachnida suggests that astacins have acquired an unprecedented role for extracorporeal digestion in Araneae, with different orthologs used by each family. The results of a comparative study of spiders in distinct physiological conditions allow us to propose some digestion mechanisms in this interesting animal taxon. All the high throughput data allowed the demonstration that DF is a secretion originating from the MD. We identified enzymes involved in the extracellular and intracellular phases of digestion. Besides that, data analyses show a large gene duplication event in Araneae digestive process evolution, mainly of astacin genes. We were also able to identify proteins expressed and translated in the digestive system, which until now had been exclusively associated to venom glands.

  16. Supplementary Material for: BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal M.; Alam, Intikhab; Bajic, Vladimir B.

    2015-01-01

    Abstract Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACONâ s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/ .

  17. Investigation of three flavonoids binding to bovine serum albumin using molecular fluorescence technique

    International Nuclear Information System (INIS)

    Bi Shuyun; Yan Lili; Pang Bo; Wang Yu

    2012-01-01

    The three flavonoids including naringenin, hesperetin and apigenin binding to bovine serum albumin (BSA) at pH 7.4 was studied by fluorescence quenching, synchronous fluorescence and UV-vis absorption spectroscopic techniques. The results obtained revealed that naringenin, hesperetin and apigenin strongly quenched the intrinsic fluorescence of BSA. The Stern-Volmer curves suggested that these quenching processes were all static quenching processes. At 291 K, the value and the order of the binding constant were K A n aringenin) =4.08x10 4 A(hesperetin) =5.40x10 4 ∼K A(apigenin) =5.32x10 4 L mol -1 . The main binding force between the flavonoid and BSA was hydrophobic and electrostatic force. According to the Foerster theory of non-radiation energy transfer, the binding distances (r 0 ) were obtained as 3.36, 3.47 and 3.30 nm for naringenin-BSA, hesperetin-BSA and apigenin-BSA, respectively. The effect of some common ions such as Fe 3+ , Cu 2+ , Mg 2+ , Mn 2+ , Zn 2+ and Ca 2+ on the binding was also studied in detail. The competition binding was also performed. The apparent binding constant (K' A ) obtained suggested that one flavonoid had an obvious effect on the binding of another flavonoid to protein when they coexisted in BSA solution. - Highlights: → Quenchings of BSA fluorescence by the flavonoids was all static quenchings. → Synchronous fluorescence was applied to study the structural change of BSA. → Binding constant, binding site and binding force were determined. → Competition binding experiments were performed. → One flavonoid had an obvious effect on the binding of another one to BSA.

  18. Novel technique for spatially resolved imaging of molecular bond orientations using x-ray birefringence

    Energy Technology Data Exchange (ETDEWEB)

    Sutter, John P., E-mail: john.sutter@diamond.ac.uk; Dolbnya, Igor P.; Collins, Stephen P. [Diamond Light Source Ltd, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE (United Kingdom); Harris, Kenneth D. M., E-mail: HarrisKDM@cardiff.ac.uk; Edwards-Gau, Gregory R.; Kariuki, Benson M. [School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT (United Kingdom); Palmer, Benjamin A. [Department of Structural Biology, Weizmann Institute of Science, 234 Herzl St., Rehovot 7610001 (Israel)

    2016-07-27

    Birefringence has been observed in anisotropic materials transmitting linearly polarized X-ray beams tuned close to an absorption edge of a specific element in the material. Synchrotron bending magnets provide X-ray beams of sufficiently high brightness and cross section for spatially resolved measurements of birefringence. The recently developed X-ray Birefringence Imaging (XBI) technique has been successfully applied for the first time using the versatile test beamline B16 at Diamond Light Source. Orientational distributions of the C–Br bonds of brominated “guest” molecules within crystalline “host” tunnel structures (in thiourea or urea inclusion compounds) have been studied using linearly polarized incident X-rays near the Br K-edge. Imaging of domain structures, changes in C–Br bond orientations associated with order-disorder phase transitions, and the effects of dynamic averaging of C–Br bond orientations have been demonstrated. The XBI setup uses a vertically deflecting high-resolution double-crystal monochromator upstream from the sample and a horizontally deflecting single-crystal polarization analyzer downstream, with a Bragg angle as close as possible to 45°. In this way, the ellipticity and rotation angle of the polarization of the beam transmitted through the sample is measured as in polarizing optical microscopy. The theoretical instrumental background calculated from the elliptical polarization of the bending-magnet X-rays, the imperfect polarization discrimination of the analyzer, and the correlation between vertical position and photon energy introduced by the monochromator agrees well with experimental observations. The background is calculated analytically because the region of X-ray phase space selected by this setup is sampled inefficiently by standard methods.

  19. Interaction of an antiepileptic drug, lamotrigine with human serum albumin (HSA): Application of spectroscopic techniques and molecular modeling methods.

    Science.gov (United States)

    Poureshghi, Fatemeh; Ghandforoushan, Parisa; Safarnejad, Azam; Soltani, Somaieh

    2017-01-01

    Lamotrigine (an epileptic drug) interaction with human serum albumin (HSA) was investigated by fluorescence, UV-Vis, FTIR, CD spectroscopic techniques, and molecular modeling methods. Binding constant (K b ) of 5.74×10 3 and number of binding site of 0.97 showed that there is a slight interaction between lamotrigine and HSA. Thermodynamic studies was constructed using the flourimetric titrations in three different temperatures and the resulted data used to calculate the parameters using Vant Hoff equation. Decreased Stern Volmer quenching constant by enhanced temperature revealed the static quenching mechanism. Negative standard enthalpy (ΔH) and standard entropy (ΔS) changes indicated that van der Waals interactions and hydrogen bonds were dominant forces which facilitate the binding of Lamotrigine to HSA, the results were confirmed by molecular docking studies which showed no hydrogen binding. The FRET studies showed that there is a possibility of energy transfer between Trp214 and lamotrigine. Also the binding of lamotrigine to HSA in the studied concentrations was not as much as many other drugs, but the secondary structure of the HSA was significantly changed following the interaction in a way that α-helix percentage was reduced from 67% to 57% after the addition of lamotrigine in the molar ratio of 4:1 to HSA. According to the docking studies, lamotrigine binds to IB site preferably. Copyright © 2016. Published by Elsevier B.V.

  20. First prokaryotic biodiversity assessment using molecular techniques of an acidic river in Neuquén, Argentina.

    Science.gov (United States)

    Urbieta, M Sofía; González Toril, E; Aguilera, A; Giaveno, M Alejandra; Donati, E

    2012-07-01

    Two acidic hot springs close to the crater of Copahue Volcano (Neuquén, Argentina) are the source of the Río Agrio. The river runs several kilometres before flowing into Caviahue Lake. Along the river, temperature, iron, other metal and proton concentrations decrease gradually with distance downstream. From the source to the lake and depending on the season, pH can rise from 1.0 (or even less) to about 4.0, while temperature values decrease from 70°C to 15°C. Water samples were taken from different stations on the river selected according to their physicochemical parameters. In order to assess prokaryotic biodiversity throughout the water column, different and complementary molecular biology techniques were used, mainly in situ hybridisation and 16S rRNA gene cloning and sequencing. All microorganisms found are typical of acidic environments. Sulphur-oxidizing bacteria like Acidithiobacillus thiooxidans and Acidithiobacillus albertensis were detected in every station. Moderately thermophile iron- and sulphur-oxidizing bacteria like members of Alicyclobacillus and Sulfobacillus genera were also ubiquitous. Strict iron-oxidizing bacteria like Leptospirillum and Ferrimicrobium were present at the source of the river, but disappeared downstream where iron concentrations were much lower. Iron-oxidizing, mesophilic Ferroplasma spp. were the main archaea found. The data presented in this work represent the first molecular assessment of this rare natural acidic environment.

  1. Size-exclusion chromatography (HPLC-SEC) technique optimization by simplex method to estimate molecular weight distribution of agave fructans.

    Science.gov (United States)

    Moreno-Vilet, Lorena; Bostyn, Stéphane; Flores-Montaño, Jose-Luis; Camacho-Ruiz, Rosa-María

    2017-12-15

    Agave fructans are increasingly important in food industry and nutrition sciences as a potential ingredient of functional food, thus practical analysis tools to characterize them are needed. In view of the importance of the molecular weight on the functional properties of agave fructans, this study has the purpose to optimize a method to determine their molecular weight distribution by HPLC-SEC for industrial application. The optimization was carried out using a simplex method. The optimum conditions obtained were at column temperature of 61.7°C using tri-distilled water without salt, adjusted pH of 5.4 and a flow rate of 0.36mL/min. The exclusion range is from 1 to 49 of polymerization degree (180-7966Da). This proposed method represents an accurate and fast alternative to standard methods involving multiple-detection or hydrolysis of fructans. The industrial applications of this technique might be for quality control, study of fractionation processes and determination of purity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. The use of a molecular technique for the detection of porcine ingredients in the Malaysian food market.

    Science.gov (United States)

    Farouk, Abd-ElAziem; Batcha, Mohamed F; Greiner, Ralf; Salleh, Hamzah M; Salleh, Mohamad R; Sirajudin, Abdur R

    2006-09-01

    To develop a molecular technique that is fast and reliable in detecting porcine contamination or ingredients in foods. The method applied involved DNA amplification using polymerase chain reaction (PCR) technology. Thus, the sequence of a certain gene found uniquely in pork was identified and its sequence was used to design specific primers for the PCR. The extraction of DNA was optimized in respect to PCR and detection limits were established. The optimized method was then used to identify pork in food products obtained from various local hypermarkets. The latest results were confirmed in triplicates on the 20th April 2006 at the Molecular Biology Laboratory, International Islamic University, Malaysia. The method was shown to be robust and reliable. Out of 30 food samples not expected to contain pork material, 3 samples were shown to be contaminated with pork material; 2 chocolates and one chicken nugget. We observed that 2 food products that were labeled as halal showed positive for porcine ingredients, while another that did not have any halal logo but originated from outside Malaysia and exported to many Middle Eastern nations also showed positive.

  3. Study on the interaction of tussilagone with human serum albumin (HSA) by spectroscopic and molecular docking techniques

    Science.gov (United States)

    Xu, Liang; Hu, Yan-Xi; Li, Yan-Cheng; Zhang, Li; Ai, Hai-Xin; Liu, Hong-Sheng; Liu, Yu-Feng; Sang, Yu-Li

    2017-12-01

    Tussilagone is a sesquiterpenoid which exhibits a variety of pharmacological activities. The interaction of tussilagone with human serum albumin (HSA) was investigated using fluorescence spectroscopy, UV-vis absorption, fluorescence probe experiments, synchronous fluorescence, circular dichroism (CD) spectra, three-dimensional spectra and molecular docking techniques under simulative physiological conditions. The results clarified that the fluorescence quenching of HSA by tussilagone was a static quenching process as a result of HSA-tussilagone (1:1) complex. Tussilagone spontaneously bound to HSA in site I (subdomain IIA), which was primarily driven by hydrophobic forces and hydrogen bonds (ΔH° = -13.89 kJ mol-1, ΔS° = 16.39 J mol-1 K-1). The binding constant was calculated to be 2.182 × 103 L mol-1 and the binding distance was estimated to be 2.07 nm at 291 K, showing the occurrence of fluorescence energy transfer. The results of CD, synchronous and three-dimensional fluorescence spectra all revealed that tussilagone induced the conformational changes of HSA. Meanwhile, the study of molecular docking also indicated that tussilagone could bind to the site I of HSA mainly by hydrophobic and hydrogen bond interactions.

  4. Recent research on inherent molecular structure, physiochemical properties, and bio-functions of food and feed-type Avena sativa oats and processing-induced changes revealed with molecular microspectroscopic techniques

    Energy Technology Data Exchange (ETDEWEB)

    Prates, Luciana Louzada [Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Yu, Peiqiang [Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

    2017-05-16

    Avena sativa oat is a cereal widely used as human food and livestock feed. However, the low metabolized energy and the rapid rumen degradations of protein and starch have limited the use of A. sativa oat grains. To overcome this disadvantage, new A. sativa oat varieties have been developed. Additionally, heat-related processing has been performed to decrease the degradation rate and improve the absorption of amino acids in the small intestine. The nutritive value is reflected by both chemical composition and inherent molecular structure conformation. However, the traditional wet chemical analysis is not able to detect the inherent molecular structures within an intact tissue. The advanced synchrotron-radiation and globar-based molecular microspectroscopy have been developed recently and applied to study internal molecular structures and the processing induced structure changes in A. sativa oats and reveal how molecular structure changes in relation to nutrient availability. This review aimed to obtain the recent information regarding physiochemical properties, molecular structures, metabolic characteristics of protein, and the heat-induced changes in new A. sativa oat varieties. The use of the advanced vibrational molecular spectroscopy was emphasized, synchrotron- and globar-based (micro)spectroscopy, to reveal the inherent structure of A. sativa oats at cellular and molecular levels and to reveal the heat processing effect on the degradation characteristics and the protein molecular structure in A. sativa oats. The relationship between nutrient availability and protein molecular inherent structure was also presented. Information described in this review gives better insight in the physiochemical properties, molecular structure, and the heat-induced changes in A. sativa oat detected with advanced molecular spectroscopic techniques in combinination with conventional nutrition study techniques.

  5. Ex vivo irradiation of human blood to determine DNA damage using molecular techniques; Irradiacion ex vivo de sangre humana para determinar dano genomico utilizando tecnicas moleculares

    Energy Technology Data Exchange (ETDEWEB)

    Montes, Angel; Agapito, Juan [Laboratorio de Biologia Molecular, Instituto Peruano de Energia Nuclear, Lima (Peru)

    2014-07-01

    Biological dosimetry is the assessment of absorbed dose in individuals exposed to ionizing radiation from blood samples based on the radiation induced damage in cellular DNA. The aim of this study was to determine the damage in the DNA through the assessment of an experimental ex vivo assay using irradiated samples of human blood cells. For this purpose, blood samples were irradiated at low doses (<100 mGy) considering the following parameters: blood volume (3mL), temperature (37 °C) and incubation time (0.5, 2, 4, 8 and 24 h). Dose values were: 0, 12.5, 25 and 50 mGy using Cesium -137 gamma rays at 662 keV and a dose rate of 38.46 mGy/h. The qualitative damage in the genomic DNA was determined using agarose gel electrophoresis and polymerase chain reaction (PCR) for the p53 gene in a sequence of 133 pb of exon 7, related to the protein that acts in the cell repair process. The results of the qualitative analysis showed no degradation of genomic DNA; also an increase in the DNA concentration was observed up to the fourth hour of incubation, finding maximum values for all doses in the two samples. As a conclusion, the effects of ionizing radiation at doses used in this experiment do not generate a detectable damage, by means of molecular techniques such as those used in the present study. (authors).

  6. Surfactant sodium lauryl sulfate enhances skin vaccination: molecular characterization via a novel technique using ultrafiltration capillaries and mass spectrometric proteomics.

    Science.gov (United States)

    Huang, Chun-Ming; Wang, Chao-Cheng; Kawai, Mikako; Barnes, Stephen; Elmets, Craig A

    2006-03-01

    The skin is a highly accessible organ and thus provides an attractive immune environment for cost-effective, simple, and needle-free delivery of vaccines and immunomodulators. In this study, we pretreated mouse skin with an anionic surfactant, sodium lauryl sulfate (SLS), for a short period of time (10 min) followed by epicutaneous vaccination with hen egg lysozyme antigen. We demonstrated for the first time that pretreatment of skin with surfactant SLS significantly enhances the production of antibody to hen egg lysozyme. Short term pretreatment with SLS disorganized the stratum corneum, extracted partial lamellar lipids, induced the maturation of Langerhans cells, and did not result in epidermis thickening. To reveal the mechanism underlying these changes, particularly at the molecular level, we used a novel proteomic technique using ultrafiltration capillaries and mass spectrometry to identify in vivo proteins/peptides secreted in the SLS-pretreated skin. Two secretory proteins, named as calcium-binding protein S100A9 and thymosin beta4, were identified by this novel technique. These two proteins thus may provide new insight into the enhancing effect of surfactants on skin vaccination.

  7. Use of multiple molecular subtyping techniques to investigate a Legionnaires' disease outbreak due to identical strains at two tourist lodges.

    Science.gov (United States)

    Mamolen, M; Breiman, R F; Barbaree, J M; Gunn, R A; Stone, K M; Spika, J S; Dennis, D T; Mao, S H; Vogt, R L

    1993-10-01

    A multistate outbreak of Legionnaires' disease occurred among nine tour groups of senior citizens returning from stays at one of two lodges in a Vermont resort in October 1987. Interviews and serologic studies of 383 (85%) of the tour members revealed 17 individuals (attack rate, 4.4%) with radiologically documented pneumonia and laboratory evidence of legionellosis. A survey of tour groups staying at four nearby lodges and of Vermont-area medical facilities revealed no additional cases. Environmental investigation of common tour stops revealed no likely aerosol source of Legionella infection outside the lodges. Legionella pneumophila serogroup 1 was isolated from water sources at both implicated lodges, and the monoclonal antibody subtype matched those of the isolates from six patients from whom clinical isolates were obtained. The cultures reacted with monoclonal antibodies MAB1, MAB2, 33G2, and 144C2 to yield a 1,2,5,7 or a Benidorm 030E pattern. The strains were also identical by alloenzyme electrophoresis and DNA ribotyping techniques. The epidemiologic and laboratory data suggest that concurrent outbreaks occurred following exposures to the same L. pneumophila serogroup 1 strain at two separate lodges. Multiple molecular subtyping techniques can provide essential information for epidemiologic investigations of Legionnaires' disease.

  8. Diphtheria in the Republic of Georgia: Use of Molecular Typing Techniques for Characterization of Corynebacterium diphtheriae Strains

    Science.gov (United States)

    Sulakvelidze, Alexander; Kekelidze, Merab; Gomelauri, Tsaro; Deng, Yingkang; Khetsuriani, Nino; Kobaidze, Ketino; De Zoysa, Aruni; Efstratiou, Androulla; Morris, J. Glenn; Imnadze, Paata

    1999-01-01

    Sixty-six Corynebacterium diphtheriae strains (62 of the gravis biotype and 4 of the mitis biotype) isolated during the Georgian diphtheria epidemic of 1993 to 1998 and 13 non-Georgian C. diphtheriae strains (10 Russian and 3 reference isolates) were characterized by (i) biotyping, (ii) toxigenicity testing with the Elek assay and PCR, (iii) the randomly amplified polymorphic DNA (RAPD) technique, and (iv) pulsed-field gel electrophoresis (PFGE). Fifteen selected strains were ribotyped. Six RAPD types and 15 PFGE patterns were identified among all strains examined, and 12 ribotypes were found among the 15 strains that were ribotyped. The Georgian epidemic apparently was caused by one major clonal group of C. diphtheriae (PFGE type A, ribotype R1), which was identical to the predominant epidemic strain(s) isolated during the concurrent diphtheria epidemic in Russia. A dendrogram based on the PFGE patterns revealed profound differences between the minor (nonpredominant) epidemic strains found in Georgia and Russia. The methodologies for RAPD typing, ribotyping, and PFGE typing of C. diphtheriae strains were improved to enable rapid and convenient molecular typing of the strains. The RAPD technique was adequate for biotype differentiation; however, PFGE and ribotyping were better (and equal to each other) at discriminating between epidemiologically related and unrelated isolates. PMID:10488190

  9. Utilization of Cell-Transfer Technique for Molecular Testing on Hematoxylin-Eosin-Stained Sections: A Viable Option for Small Biopsies That Lack Tumor Tissues in Paraffin Block.

    Science.gov (United States)

    Wu, Howard H; Jovonovich, Stephen M; Randolph, Melissa; Post, Kristin M; Sen, Joyashree D; Curless, Kendra; Cheng, Liang

    2016-12-01

    - In some instances the standard method of doing molecular testing from formalin-fixed, paraffin-embedded block is not possible because of limited tissue. Tumor cell-enriched cell-transfer technique has been proven useful for performing immunocytochemistry and molecular testing on cytologic smears. - To establish the cell-transfer technique as a viable option for isolating tumor cells from hematoxylin-eosin (H&E)-stained slides. - Molecular testing was performed by using the cell-transfer technique on 97 archived H&E-stained slides from a variety of different tumors. Results were compared to the conventional method of molecular testing. - Polymerase chain reaction-based molecular testing via the cell-transfer technique was successfully performed on 82 of 97 samples (85%). This included 39 of 47 cases for EGFR, 10 of 11 cases for BRAF, and 33 of 39 cases for KRAS mutations. Eighty-one of 82 cell-transfer technique samples (99%) showed agreement with previous standard method results, including 4 mutations and 35 wild-type alleles for EGFR, 4 mutations and 6 wild-type alleles for BRAF, and 11 mutations and 21 wild-type alleles for KRAS. There was only 1 discrepancy: a cell-transfer technique with a false-negative >KRAS result (wild type versus G12C). - Molecular testing performed on H&E-stained sections via cell-transfer technique is useful when tissue from cell blocks and small surgical biopsy samples is exhausted and the only available material for testing is on H&E-stained slides.

  10. BEACON/MOD: a computer program for thermal-hydraulic analysis of nuclear reactor containments - user's manual

    International Nuclear Information System (INIS)

    Broadus, C.R.; Doyle, R.J.; James, S.W.; Lime, J.F.; Mings, W.J.

    1980-04-01

    The BEACON code is a best-estimate, advanced containment code designed to perform a best-estimate analysis of the flow of a mixture of air, water, and steam in a nuclear reactor containment system under loss-of-coolant accident conditions. The code can simulate two-component, two-phase fluid flow in complex geometries using a combination of two-dimensional, one-dimensional, and lumped-parameter representations for the various parts of the system. The current version of BEACON, which is designated BEACON/MOD3, contains mass and heat transfer models for wall film and wall conduction. It is suitable for the evaluation of short-term transients in dry-containment systems. This manual describes the models employed in BEACON/MOD3 and specifies code implementation requirements. It provides application information for input data preparation and for output data interpretation

  11. BEACON/MOD2A analysis of the Arkansas-1 reactor cavity during a hypothetical hot leg break

    International Nuclear Information System (INIS)

    Ramsthaler, J.A.

    1979-01-01

    As part of the evaluation of the new MOD2A version of the BEACON code, the Arkansas-1 reactor cavity was modeled during a hypothetical loss-of-coolant accident. Results of the BEACON analysis were compared with results obtained previously with the COMPARE containment code. Studies were also made investigating some of the BEACON interphasic, timestep control, and wall heat transfer options to assure that these models were working properly and to observe their effects on the results. Descriptions of the Arkansas-1 reactor cavity, initial assumptions during the hypothetical LOCA, and methods of modeling with BEACON are presented. Some of the problems encountered in accurately modeling the penetrations surrounding the hot and cold leg pipes are also discussed

  12. Traveling-Wave Tube Amplifier Second Harmonic as Millimeter-Wave Beacon Source for Atmospheric Propagation Studies

    Science.gov (United States)

    Simons, Rainee N.; Wintucky, Edwin G.

    2014-01-01

    This paper presents the design and test results of a CW millimeter-wave satellite beacon source, based on the second harmonic from a traveling-wave tube amplifier and utilizes a novel waveguide multimode directional coupler. A potential application of the beacon source is for investigating the atmospheric effects on Q-band (37-42 GHz) and V/W-band (71- 76 GHz) satellite-to-ground signals.

  13. The value of molecular techniques to diagnose Ureaplasma urealyticum and Nocardia farcinica pleuropneumonia in a patient with diffuse large B-cell lymphoma

    Directory of Open Access Journals (Sweden)

    Etienne Canouï

    2017-11-01

    Full Text Available An unusual case of pleural empyema related to Nocardia farcinica and Ureaplasma urealyticum, occurring after autologous haematopoietic stem cell transplantation in a 30-year-old patient with lymphoma, is reported. This case illustrates the role of repeated and comprehensive microbiological investigations and the contribution of molecular techniques in reaching the aetiological diagnosis. Keywords: Nocardia farcinica, Ureaplasma urealyticum, Pleuropneumonia, Immunocompromised patient, Molecular microbiological diagnosis

  14. Eutectic-based wafer-level-packaging technique for piezoresistive MEMS accelerometers and bond characterization using molecular dynamics simulations

    Science.gov (United States)

    Aono, T.; Kazama, A.; Okada, R.; Iwasaki, T.; Isono, Y.

    2018-03-01

    We developed a eutectic-based wafer-level-packaging (WLP) technique for piezoresistive micro-electromechanical systems (MEMS) accelerometers on the basis of molecular dynamics analyses and shear tests of WLP accelerometers. The bonding conditions were experimentally and analytically determined to realize a high shear strength without solder material atoms diffusing to adhesion layers. Molecular dynamics (MD) simulations and energy dispersive x-ray (EDX) spectrometry done after the shear tests clarified the eutectic reaction of the solder materials used in this research. Energy relaxation calculations in MD showed that the diffusion of solder material atoms into the adhesive layer was promoted at a higher temperature. Tensile creep MD simulations also suggested that the local potential energy in a solder material model determined the fracture points of the model. These numerical results were supported by the shear tests and EDX analyses for WLP accelerometers. Consequently, a bonding load of 9.8 kN and temperature of 300 °C were found to be rational conditions because the shear strength was sufficient to endure the polishing process after the WLP process and there was little diffusion of solder material atoms to the adhesion layer. Also, eutectic-bonding-based WLP was effective for controlling the attenuation of the accelerometers by determining the thickness of electroplated solder materials that played the role of a cavity between the accelerometers and lids. If the gap distance between the two was less than 6.2 µm, the signal gains for x- and z-axis acceleration were less than 20 dB even at the resonance frequency due to air-damping.

  15. Probing the interactions of bromchlorbuterol-HCl and phenylethanolamine A with HSA by multi-spectroscopic and molecular docking technique

    International Nuclear Information System (INIS)

    Bi, Shuyun; Zhao, Tingting; Zhou, Huifeng; Wang, Yu; Li, Zhihong

    2016-01-01

    Highlights: • Molecular docking showed that BCB/PEA was bound at sub-domain IIA of HSA. • Fluorescence lifetimes indicated that the quenching was a static quenching. • CD spectra showed that BCB/PEA changed the conformation of HSA. • The competitive binding between site markers and BCB/PEA was studied. • The mutual influence on the two drugs binding HSA was studied. - Abstract: Using fluorescence quenching, fluorescence lifetime, (UV + vis) absorption, circular dichroism (CD) and molecular docking technique, the interactions of human serum albumin (HSA) with bromchlorbuterol-HCl (BCB) and phenylethanolamine A (PEA) were investigated. The quenching rate constants and binding constants for BCB/PEA with HSA were determined at T = (292.15, 302.15 and 312.15) K respectively, which were all decreased with the increase of the temperature, showing not a dynamic quenching. The fluorescence lifetime of HSA with BCB/PEA had changed little compared to that of HSA alone (τ_0), further confirming that BCB/PEA quenching of intrinsic fluorescence of HSA is a static quenching. The effects of K"+, Ca"2"+, Cu"2"+, Zn"2"+ and Fe"3"+ on the binding were studied. The analysis of the thermodynamic parameters for BCB/(PEA + HSA) showed that BCB/PEA could bind to HSA via hydrophobic force. The binding distances were determined as 2.90 and 4.11 nm for (BCB + HSA) and (PEA + HSA) based on the Förster’s non-radiative energy transfer theory (FRET). Synchronous fluorescence and CD spectra indicated that the conformation of HSA was changed by BCB/PEA. The competitive studies for the drug with site marker suggested that both BCB and PEA were bound at Sudlow’s sites I (sub-domain IIA, also known as indometacin binding site) in HSA, and the results of the study of molecular docking also leads to the same conclusion. The competitive binding experiments for the two drugs were also performed, which further indicates that PEA and BCB could share the same binding site, and PEA has a much

  16. Assessment of beta-emitter radionuclides in biological samples using liquid scintillation counting. Application to the study of internal doses in molecular and cellular biology techniques

    International Nuclear Information System (INIS)

    Sierra, I.; Delgado, A.; Navarro, T.; Macias, M. T.

    2007-01-01

    The radioisotopic techniques used in Molecular and Cellular Biology involve external and internal irradiation risk. It is necessary to control the possible internal contamination associated to the development of these techniques. The internal contamination risk can be due to physical and chemical properties of the labelled compounds, aerosols generated during the performance technique. The aim of this work was to estimate the possible intake of specific beta emitters during the technique development and to propose the required criterions to perform Individual Monitoring. The most representative radioisotopic techniques were selected attending their potential risk of internal contamination. Techniques were analysed applying IAEA methodology according to the used activity in each technique. It was necessary to identify the worker groups that would require individual monitoring on the base of their specific risk. Different measurement procedures were applied to study the possible intake in group risk and more than 160 persons were measured by in vitro bioassay. (Author) 96 refs

  17. Molecular techniques in fisheries

    Digital Repository Service at National Institute of Oceanography (India)

    Goswami, U.

    stream_size 2 stream_content_type text/plain stream_name Genetic_Biotechnol_Tool_Aquacult_Fish_1998_60.pdf.txt stream_source_info Genetic_Biotechnol_Tool_Aquacult_Fish_1998_60.pdf.txt Content-Encoding ISO-8859-1 Content-Type text...

  18. Simultaneous visualization of the subfemtomolar expression of microRNA and microRNA target gene using HILO microscopy† †Electronic supplementary information (ESI) available: The LED device for the sample photobleaching, a schematic presentation of HILO microscopy, fluorescence spectra and hybridization curves of the molecular beacons, the linear correlation between the miRNA fluorescence intensity and the miRNA copy number, a validation of the miRNA adsorption and miRNA target gene expression via RT-qPCR, a validation of RT-qPCR using capillary electrophoresis, the reproducibility of RT-qPCR and Poisson distribution of the miRNA pipetting as well as a complete list of the oligonucleotides used in this study. See DOI: 10.1039/c7sc02701j Click here for additional data file.

    Science.gov (United States)

    Lin, Yi-Zhen; Ou, Da-Liang; Chang, Hsin-Yuan; Lin, Wei-Yu; Hsu, Chiun

    2017-01-01

    The family of microRNAs (miRNAs) not only plays an important role in gene regulation but is also useful for the diagnosis of diseases. A reliable method with high sensitivity may allow researchers to detect slight fluctuations in ultra-trace amounts of miRNA. In this study, we propose a sensitive imaging method for the direct probing of miR-10b (miR-10b-3p, also called miR-10b*) and its target (HOXD10 mRNA) in fixed cells based on the specific recognition of molecular beacons combined with highly inclined and laminated optical sheet (HILO) fluorescence microscopy. The designed dye-quencher-labelled molecular beacons offer excellent efficiencies of fluorescence resonance energy transfer that allow us to detect miRNA and the target mRNA simultaneously in hepatocellular carcinoma cells using HILO fluorescence microscopy. Not only can the basal trace amount of miRNA be observed in each individual cell, but the obtained images also indicate that this method is useful for monitoring the fluctuations in ultra-trace amounts of miRNA when the cells are transfected with a miRNA precursor or a miRNA inhibitor (anti-miR). Furthermore, a reasonable causal relation between the miR-10b and HOXD10 expression levels was observed in miR-10b* precursor-transfected cells and miR-10b* inhibitor-transfected cells. The trends of the miRNA alterations obtained using HILO microscopy completely matched the RT-qPCR data and showed remarkable reproducibility (the coefficient of variation [CV] = 0.86%) and sensitivity (<1.0 fM). This proposed imaging method appears to be useful for the simultaneous visualisation of ultra-trace amounts of miRNA and target mRNA and excludes the procedures for RNA extraction and amplification. Therefore, the visualisation of miRNA and the target mRNA should facilitate the exploration of the functions of ultra-trace amounts of miRNA in fixed cells in biological studies and may serve as a powerful tool for diagnoses based on circulating cancer cells. PMID:28989695

  19. Visually Detecting the Variation of miR-301a Expression Using Gold Nanoparticle Beacon.

    Science.gov (United States)

    Zhang, Ying; Li, Kai; Li, Dandan; Li, Changfeng; Zhang, Bin

    2018-02-01

    It is well known that microRNA-301a plays an important role in many diseases, as well as is overexpressed in human colon cancer and affects the process of tumorigenesis. Determination of the miR-301a expression provides insight into the mechanism of tumor progression. In this study, we designed a special hairpin deoxyribonucleic acid (DNA) for miR-301a to functionalize gold nanoparticles, which served as a beacon for detecting miR-301a expression. A-quenching efficiency up to 90% was achieved. The beacon we designed in this study can monitor the precise variation of miR-301a expression in vivo. The strategy reported in this study is a promising approach for the measurement of miRNA in living cells. Moreover, it has a great potential in the study of drug screening and discovery.

  20. Multi-Band Multi-Tone Tunable Millimeter-Wave Frequency Synthesizer For Satellite Beacon Transmitter

    Science.gov (United States)

    Simons, Rainee N.; Wintucky, Edwin G.

    2016-01-01

    This paper presents the design and test results of a multi-band multi-tone tunable millimeter-wave frequency synthesizer, based on a solid-state frequency comb generator. The intended application of the synthesizer is in a satellite beacon transmitter for radio wave propagation studies at K-band (18 to 26.5 GHz), Q-band (37 to 42 GHz), and E-band (71 to 76 GHz). In addition, the architecture for a compact beacon transmitter, which includes the multi-tone synthesizer, polarizer, horn antenna, and power/control electronics, has been investigated for a notional space-to-ground radio wave propagation experiment payload on a small satellite. The above studies would enable the design of robust high throughput multi-Gbps data rate future space-to-ground satellite communication links.

  1. Design of a K/Q-Band Beacon Receiver for the Alphasat TDP#5 Experiment

    Science.gov (United States)

    Morse, Jacquelynne R.

    2014-01-01

    This paper describes the design and performance of a coherent KQ-band (2040 GHz) beacon receiver developed at NASA Glenn Research Center (GRC) that will be installed at the Politecnico di Milano (POLIMI) for use in the Alphasat Technology Demonstration Payload 5 (TDP5) beacon experiment. The goal of this experiment is to characterize rain fade attenuation at 40 GHz to improve the performance of existing statistical rain attenuation models in the Q-band. The ground terminal developed by NASA GRC utilizes an FFT-based frequency estimation receiver capable of characterizing total path attenuation effects due to gaseous absorption, clouds, rain, and scintillation. The receiver system has been characterized in the lab and demonstrates a system dynamic range performance of better than 58 dB at 1 Hz and better than 48 dB at 10 Hz rates.

  2. Nanosecond-level time synchronization of AERA using a beacon reference transmitter and commercial airplanes

    Directory of Open Access Journals (Sweden)

    Huege Tim

    2017-01-01

    Full Text Available Radio detection of cosmic-ray air showers requires time synchronization of detectors on a nanosecond level, especially for advanced reconstruction algorithms based on the wavefront curvature and for interferometric analysis approaches. At the Auger Engineering Radio Array, the distributed, autonomous detector stations are time-synchronized via the Global Positioning System which, however, does not provide sufficient timing accuracy. We thus employ a dedicated beacon reference transmitter to correct for eventby-event clock drifts in our offline data analysis. In an independent cross-check of this “beacon correction” using radio pulses emitted by commercial airplanes, we have shown that the combined timing accuracy of the two methods is better than 2 nanoseconds.

  3. Nanosecond-level time synchronization of AERA using a beacon reference transmitter and commercial airplanes

    Science.gov (United States)

    Huege, Tim

    2017-03-01

    Radio detection of cosmic-ray air showers requires time synchronization of detectors on a nanosecond level, especially for advanced reconstruction algorithms based on the wavefront curvature and for interferometric analysis approaches. At the Auger Engineering Radio Array, the distributed, autonomous detector stations are time-synchronized via the Global Positioning System which, however, does not provide sufficient timing accuracy. We thus employ a dedicated beacon reference transmitter to correct for eventby-event clock drifts in our offline data analysis. In an independent cross-check of this "beacon correction" using radio pulses emitted by commercial airplanes, we have shown that the combined timing accuracy of the two methods is better than 2 nanoseconds.

  4. Beaconing Performance in IEEE 802.11p Vehicular Networks: the Effect of Radio Channel Congestion

    OpenAIRE

    Librino, Francesco; Renda, Maria Elena; Santi, Paolo

    2013-01-01

    In this paper, we study the performance of the beaconing mechanism underlying active safety vehicular applications in presence of different levels of channel congestion. The importance of this study lies in the fact that channel congestion is considered a major factor influencing communication performance in vehicular networks, and that ours is the first investigation of the effects of congestion based on extensive, real-world measurements. The results of our study reveal that congestion has ...

  5. Molecular imaging techniques in magnetic resonance imaging and nuclear imaging; Molekulare Bildgebung in der Magnetresonanztomographie und der Nuklearmedizin

    Energy Technology Data Exchange (ETDEWEB)

    Hoegemann, D.; Basilion, J.P.; Weissleder, R. [Center for Molecular Imaging Research, Massachusetts General Hospital, Charleston, MA (United States)

    2001-02-01

    The identification of genetic and biochemical changes allows a more conclusive characterization and classification of disease. Up to now this information is mostly obtained through in vitro analysis after resection or biopsy by immunohistopathology and molecular biology. There is a definite need for non-invasive detection and repeated monitoring of such changes in experimental research as well as in clinical trials. Therefore, it is necessary to develop radiological imaging techniques that not only visualize morphologic and physiologic alterations, but track genetic and biochemical processes. This short review reports some of the various ongoing research projects that address this problem and provide some very promising approaches. (orig.) [German] Die Bestimmung genetischer und biochemischer Veraenderungen erlaubt in zunehmendem Masse die eindeutige Charakterisierung und Klassifikation von Erkrankungen. Bisher ist hierzu in der Regel eine gezielte immunohistopathologische oder molekularbiologische In-vitro-Analyse nach Resektion oder Entnahme einer Biopsie erforderlich. In der experimentellen Forschung wie auch in der klinischen Anwendung sind bildgebende Verfahren wuenschenswert, die eine nichtinvasive Detektion und ein wiederholt durchfuehrbares Monitoring gewaehrleisten. Aus diesem Grunde ist die Entwicklung radiologischer Untersuchungsmethoden erforderlich, die ueber die morphologischen und physiologischen Veraenderungen hinaus eine Beurteilung der genetischen und biochemischen Vorgaenge ermoeglichen. In diesem kurzen Uebersichtsartikel werden einige der zahlreichen aktuellen Forschungsprojekte zusammengefasst, die sich mit diesem Problem beschaeftigen und inzwischen aussichtsreiche Techniken zur Verfuegung stellen. (orig.)

  6. Combined spectroscopic and molecular docking techniques to study interaction of Zn (II) DiAmsar with serum albumins

    Energy Technology Data Exchange (ETDEWEB)

    Bardajee, Ghasem Rezanejade, E-mail: rezanejad@pnu.ac.ir; Hooshyar, Zari; Shafagh, Pegah; Ghiasvand, Samira; Kakavand, Nahaleh

    2014-12-15

    Zinc (II) diamine-sarcophagine (Zn (II) DiAmsar) as a water soluble hexadentate ligand was synthesized and characterized by nuclear magnetic resonance (NMR), Fourier transform infrared (FT-IR) and UV–visible (UV–vis) spectroscopy. The bindings of Zn (II) DiAmsar with human serum albumin (HSA) and bovine serum albumin (BSA) were investigated under the simulative physiological conditions. To study this binding, the fluorescence spectra in combination with FT-IR, UV–vis, cyclic voltammetry (CV), and molecular docking techniques were used in the present work. The results indicate that Zn (II) DiAmsar quenched effectively the intrinsic fluorescence of HSA and BSA via a static quenching process. The fluorescence quenching data was also used to determine binding sites and binding constants at different temperatures. The calculated thermodynamic parameters (∆G°, ∆H°, and ∆S°) suggest that the binding process occurs spontaneously by involving hydrogen bond and van der Waals interactions. The distance between HSA (or BSA) as a donor and Zn (II) DiAmsar as an acceptor was obtained according to fluorescence resonance energy transfer (FRET). In addition, the docking results revealed the possible binding sites and assess the microenvironment around the bounded Zn (II) DiAmsar.

  7. Study On Application Of Molecular Techniques (RAPD-PCR And RAMP-PCR) To Detect Mutation In Rice Breeding

    International Nuclear Information System (INIS)

    Hoang Thi My Linh; Phan, D. T. Son; Nguyen Thi Vang; Nguyen, T. T. Hien; Le XuanTham

    2007-01-01

    The project was carried out in 2007 with the purpose of consideration for using the two simple and inexpensive molecular techniques to estimate changes in DNA of rice mutant after gamma irradiation. Three rice cultivars: Basmati370, Tam Thom (TT1), IR64 and three gamma irradiated mutants BDS, TDS and VND 95-20 respectively, were used. Suitable DNA extraction procedure was obtained. PCR optimization was conducted on three important factors including: amount of MgCl 2 , DNA concentration and annealing temperature. 2.5 mM of MgCl 2 for RAPD-PCR and 3.75 mM for RAMP-PCR were found the best. 40 ng DNA provided a good amplification for RAMP-PCR; this figure was 50 ng for RAPD-PCR. Annealing temperatures were determined at 36 o C for RAPD primer and at 55±3 o C for Microsatellite primer. Final results showed that, both RAPD-PCR and RAMP-PCR could detect changes in DNA of rice mutants after gamma irradiation compared to their parents. Percentage of DNA changes determined by RAPD-PCR and RAMP-PCR on Basmati370 and its mutant BDS were 11.49% and 21.2% respectively; These on TT1 and TDS were 8.98% and 15.4%; and on IR64 and VND 95-20 were 3.45% and 4.95%. (author)

  8. Beacon: A three-dimensional structural analysis code for bowing history of fast breeder reactor cores

    International Nuclear Information System (INIS)

    Miki, K.

    1979-01-01

    The core elements of an LMFBR are bowed due to radial gradients of both temperature and neutron flux in the core. Since all hexagonal elements are multiply supported by adjacent elements or the restraint system, restraint forces and bending stresses are induced. In turn, these forces and stresses are relaxed by irradiation enhanced creep of the material. The analysis of the core bowing behavior requires a three-dimensional consideration of the mechanical interactions among the core elements, because the core consists of different kinds of elements and of fuel assemblies with various burnup histories. A new computational code BEACON has been developed for analyzing the bowing behavior of an LMFBR's core in three dimensions. To evaluate mechanical interactions among core elements, the code uses the analytical method of the earlier SHADOW code. BEACON analyzes the mechanical interactions in three directions, which form angles of 60 0 with one another. BEACON is applied to the 60 0 sector of a typical LMFBR's core for analyzing the bowing history during one equilibrium cycle. 120 core elements are treated, assuming the boundary condition of rotational symmetry. The application confirms that the code can be an effective tool for parametric studies as well as for detailed structural analysis of LMFBR's core. (orig.)

  9. Magnetic resonance beacon to detect intracellular microRNA during neurogenesis.

    Science.gov (United States)

    Lee, Jonghwan; Jin, Yeon A; Ko, Hae Young; Lee, Yong Seung; Heo, Hyejung; Cho, Sujeong; Kim, Soonhag

    2015-02-01

    Magnetic resonance imaging (MRI) offers great spatial resolution for viewing deep tissues and anatomy. We developed a self-assembling signal-on magnetic fluorescence nanoparticle to visualize intracellular microRNAs (miRNAs or miRs) during neurogenesis using MRI. The self-assembling nanoparticle (miR124a MR beacon) was aggregated by the incubation of three different oligonucleotides: a 3' adaptor, a 5' adaptor, and a linker containing miR124a-binding sequences. The T2-weighted magnetic resonance (MR) signal of the self-assembled nanoparticle was quenched when miR124a was absent from test tubes or was minimally expressed in cells and tissues. When miR124a was present in test tubes or highly expressed in vitro and in vivo during P19 cell neurogenesis, it hybridized with the miR124a MR beacon, causing the linker to detach, resulting in increased signal-on MRI intensity. This MR beacon can be used as a new imaging probe to monitor the miRNA-mediated regulation of cellular processes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. A Microfluidic Love-Wave Biosensing Device for PSA Detection Based on an Aptamer Beacon Probe.

    Science.gov (United States)

    Zhang, Feng; Li, Shuangming; Cao, Kang; Wang, Pengjuan; Su, Yan; Zhu, Xinhua; Wan, Ying

    2015-06-11

    A label-free and selective aptamer beacon-based Love-wave biosensing device was developed for prostate specific antigen (PSA) detection. The device consists of the following parts: LiTaO3 substrate with SiO2 film as wave guide layer, two set of inter-digital transducers (IDT), gold film for immobilization of the biorecongniton layer and a polydimethylsiloxane (PDMS) microfluidic channels. DNA aptamer, or "artificial antibody", was used as the specific biorecognition probe for PSA capture. Some nucleotides were added to the 3'-end of the aptamer to form a duplex with the 3'-end, turning the aptamer into an aptamer-beacon. Taking advantage of the selective target-induced assembly changes arising from the "aptamer beacon", highly selective and specific detection of PSA was achieved. Furthermore, PDMS microfluidic channels were designed and fabricated to realize automated quantitative sample injection. After optimization of the experimental conditions, the established device showed good performance for PSA detection between 10 ng/mL to 1 μg/mL, with a detection limit of 10 ng/mL. The proposed sensor might be a promising alternative for point of care diagnostics.

  11. Sparse Localization with a Mobile Beacon Based on LU Decomposition in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Chunhui Zhao

    2015-09-01

    Full Text Available Node localization is the core in wireless sensor network. It can be solved by powerful beacons, which are equipped with global positioning system devices to know their location information. In this article, we present a novel sparse localization approach with a mobile beacon based on LU decomposition. Our scheme firstly translates node localization problem into a 1-sparse vector recovery problem by establishing sparse localization model. Then, LU decomposition pre-processing is adopted to solve the problem that measurement matrix does not meet the re¬stricted isometry property. Later, the 1-sparse vector can be exactly recovered by compressive sensing. Finally, as the 1-sparse vector is approximate sparse, weighted Cen¬troid scheme is introduced to accurately locate the node. Simulation and analysis show that our scheme has better localization performance and lower requirement for the mobile beacon than MAP+GC, MAP-M, and MAP-MN schemes. In addition, the obstacles and DOI have little effect on the novel scheme, and it has great localization performance under low SNR, thus, the scheme proposed is robust.

  12. Use of Faraday-rotation data from beacon satellites to determine ionospheric corrections for interplanetary spacecraft navigation

    Science.gov (United States)

    Royden, H. N.; Green, D. W.; Walson, G. R.

    1981-01-01

    Faraday-rotation data from the linearly polarized 137-MHz beacons of the ATS-1, SIRIO, and Kiku-2 geosynchronous satellites are used to determine the ionospheric corrections to the range and Doppler data for interplanetary spacecraft navigation. The JPL operates the Deep Space Network of tracking stations for NASA; these stations monitor Faraday rotation with dual orthogonal, linearly polarized antennas, Teledyne polarization tracking receivers, analog-to-digital converter/scanners, and other support equipment. Computer software examines the Faraday data, resolves the pi ambiguities, constructs a continuous Faraday-rotation profile and converts the profile to columnar zenith total electron content at the ionospheric reference point; a second program computes the line-of-sight ionospheric correction for each pass of the spacecraft over each tracking complex. Line-of-sight ionospheric electron content using mapped Faraday-rotation data is compared with that using dispersive Doppler data from the Voyager spacecraft; a difference of about 0.4 meters, or 5 x 10 to the 16th electrons/sq m is obtained. The technique of determining the electron content of interplanetary plasma by subtraction of the ionospheric contribution is demonstrated on the plasma torus surrounding the orbit of Io.

  13. Comparison of mapped and measured total ionospheric electron content using global positioning system and beacon satellite observations

    International Nuclear Information System (INIS)

    Lanyi, G.E.; Roth, T.

    1988-01-01

    Total ionospheric electron contents (TEC) were measured by global positioning system (GPS) dual-frequency receivers developed by the Jet Propulsion Laboratory. The measurements included P-code (precise ranging code) and carrier phase data for six GPS satellites during multiple five-hour observing sessions. A set of these GPS TEC measurements were mapped from the GPS lines of sight to the line of sight of a Faraday beacon satellite by statistically fitting the TEC data to a simple model of the ionosphere. The mapped GPS TEC values were compared with the Faraday rotation measurements. Because GPS transmitter offsets are different for each satellite and because some GPS receiver offsets were uncalibrated, the sums of the satellite and receiver offsets were estimated simultaneously with the TEC in a least squares procedure. The accuracy of this estimation procedure is evaluated indicating that the error of the GPS-determined line of sight TEC can be at or below 1 x 10 to the 16th el/sq cm. Consequently, the current level of accuracy is comparable to the Faraday rotation technique; however, GPS provides superior sky coverage. 15 references

  14. Iris colour as an indicator of age feature in female Brazilian tanagers (Passeriformes: Emberizidae confirmed by a molecular sexing technique

    Directory of Open Access Journals (Sweden)

    Denise Monnerat Nogueira

    2008-12-01

    Full Text Available The Brazilian tanager, Ramphocelus bresilius is an endemic species from Brazil that is sexually dimorphic in adult plumage. Young males are similar to adult and young females until their second year. Adults and young females are not distinguishable in plumage. We tested whether iris colour can be used to separate adult females from immature females. We used for the first time the molecular sexing technique based on CHD-genes to confirm the sex of the individuals classified as "female plumage with red iris", and to identify the sex of individuals classified as "female plumage and brown iris". The adult males were used as a positive control. DNA samples from 190 individuals were analysed. The sizes of the PCR products were identified as 350 base pairs (bp for CHD-Z and 388 bp for CHD-W. We confirmed that adult females have a red iris and the young females a brown iris. We could also separate young males and females which present the same iris colour and plumage. Although there are indications that the iris colour can be used by birds to identify the adults in co-operative breeding species such as the Brazilian tanager, more behavioural data are required to understand the role of iris coloration in this species. Rev. Biol. Trop. 56 (4: 1629-1633. Epub 2008 December 12.El ave Ramphocelus bresilius es una especie endémica de Brasil con dimorfismo sexual en el plumaje del adulto. Los machos jóvenes son similares a las hembras adultas y jóvenes hasta el segundo año de vida. Adultos y hembras jóvenes son indistinguibles por el plumaje. Evaluamos si el color del iris puede ser utilizado para distinguir hembras adultas de hembras inmaduras. Utilizamos por primera vez la técnica molecular de identificación de sexos basada en los genes CHD para confirmar el género de individuos clasificados como plumaje femenino con iris rojo, y para identificar el sexo de los individuos clasificados como plumaje femenino e iris marrón. Usamos machos adultos como

  15. Studying the interaction between three synthesized heterocyclic sulfonamide compounds with hemoglobin by spectroscopy and molecular modeling techniques.

    Science.gov (United States)

    Naeeminejad, Samane; Assaran Darban, Reza; Beigoli, Sima; Saberi, Mohammad Reza; Chamani, Jamshidkhan

    2017-11-01

    The interaction between synthesized heterocyclic benzene sulfonamide compounds, N-(7-benzyl-56-biphenyl-2m-tolyl-7H-pyrrolo[23-d]pyrimidine-4-yl)-benzene sulfonamide (HBS 1 ), N-(7-benzyl-56-biphenyl-2-m-tolyl-7H-pyrrolo[23-d] pyrimidine-4-yl)-4-methyl- benzene sulfonamide (HBS 2 ), and N-(7-benzyl-56-biphenyl-2-m-tolyl-7H-pyrrolo[23-d]pyrimidine-4-yl)-4-chloro-benzene sulfonamide (HBS 3 ) with Hb was studied by fluorescence quenching, zeta potentional, circular dichroism, and molecular modeling techniques. The fluorescence spectroscopy experiments were performed in order to study the conformational changes, possibly due to a discrete reorganization of Trp residues during binding between HBS derivatives and Hb. The variation of the K SV value suggested that hydrophobic and electrostatic interactions were the predominant intermolecular forces stabilizing the complex. The K SV1 ans K SV2 values of HBS derivatives with Hb are .6 × 10 13 and 3 × 10 13  M -1 for Hb-HBS 1 , 1 × 10 13 and 4 × 10 13  M -1 for Hb-HBS 2 , .9 × 10 13 , and 6 × 10 13  M -1 for Hb-HBS 3 , respectively. The molecular distances between Hb and HBS derivatives in binary and ternary systems were estimated according to Förster's theory of dipole-dipole non-radiation energy transfer. The quantitative analysis data of circular dichroism spectra demonstrated that the binding of the three HBS derivatives to Hb induced conformational changes in Hb. Changes in the zeta potential of the Hb-HBS derivatives complexes demonstrated a hydrophobic adsorption of the anionic ligand onto the surface of Hb as well as both electrostatic and hydrophobic adsorption in the case of the complex. The modeling data thus confirmed the experimental results. This study is expected to provide important insight into the interaction of Hb with three HBS derivatives to use in various toxicological and therapeutic processes.

  16. ENVIROSUITE: USING STATE-OF-THE-ART SYNCHROTRON TECHNIQUES TO UNDERSTAND ENVIRONMENTAL REMEDIATION SCIENCE ISSUES AT THE MOLECULAR LEVEL.

    Energy Technology Data Exchange (ETDEWEB)

    FITTS,J.P.; KALB,P.D.; FRANCIS,A.J.; FUHRMANN,M.; DODGE,C.J.; GILLOW,J.B.

    2004-03-01

    Although DOE's Environmental Management program has made steady progress in cleaning up environmental legacies throughout the DOE complex, there are still significant remediation issues that remain to be solved. For example, DOE faces difficult challenges related to potential mobilization of radionuclides (e.g., actinides) and other hazardous contaminants in soils, removal and final treatment of high-level waste and residuals from leaking tanks, and the long-term stewardship of remediated sites and engineered disposal facilities, to name just a few. In some cases, new technologies and technology applications will be required based on current engineering expertise. In others, however, basic scientific research is needed to understand the mechanisms of how contaminants behave under specific conditions and how they interact with the environment, from which new engineering solutions can emerge. At Brookhaven National Laboratory (BNL) and Stony Brook University, scientists have teamed to use state-of-the-art synchrotron techniques to help understand the basic interactions of contaminants in the environment. Much of this work is conducted at the BNL National Synchrotron Light Source (NSLS), which is a user facility that provides high energy X-ray and ultraviolet photon beams to facilitate the examination of contaminants and materials at the molecular level. These studies allow us to determine how chemical speciation and structure control important parameters such as solubility, which in turn drive critical performance characteristics such as leaching. In one study for example, we are examining the effects of microbial activity on actinide contaminants under conditions anticipated at the Waste Isolation Pilot Plant. One possible outcome of this research is the identification of specific microbes that can trap uranium or other contaminants within the intracellular structure and help mitigate mobility. In another study, we are exploring the interaction of contaminants

  17. ENVIROSUITE: USING STATE-OF-THE-ART SYNCHROTRON TECHNIQUES TO UNDERSTAND ENVIRONMENTAL REMEDIATION SCIENCE ISSUES AT THE MOLECULAR LEVEL

    International Nuclear Information System (INIS)

    FITTS, J.P.; KALB, P.D.; FRANCIS, A.J.; FUHRMANN, M.; DODGE, C.J.; GILLOW, J.B.

    2004-01-01

    Although DOE's Environmental Management program has made steady progress in cleaning up environmental legacies throughout the DOE complex, there are still significant remediation issues that remain to be solved. For example, DOE faces difficult challenges related to potential mobilization of radionuclides (e.g., actinides) and other hazardous contaminants in soils, removal and final treatment of high-level waste and residuals from leaking tanks, and the long-term stewardship of remediated sites and engineered disposal facilities, to name just a few. In some cases, new technologies and technology applications will be required based on current engineering expertise. In others, however, basic scientific research is needed to understand the mechanisms of how contaminants behave under specific conditions and how they interact with the environment, from which new engineering solutions can emerge. At Brookhaven National Laboratory (BNL) and Stony Brook University, scientists have teamed to use state-of-the-art synchrotron techniques to help understand the basic interactions of contaminants in the environment. Much of this work is conducted at the BNL National Synchrotron Light Source (NSLS), which is a user facility that provides high energy X-ray and ultraviolet photon beams to facilitate the examination of contaminants and materials at the molecular level. These studies allow us to determine how chemical speciation and structure control important parameters such as solubility, which in turn drive critical performance characteristics such as leaching. In one study for example, we are examining the effects of microbial activity on actinide contaminants under conditions anticipated at the Waste Isolation Pilot Plant. One possible outcome of this research is the identification of specific microbes that can trap uranium or other contaminants within the intracellular structure and help mitigate mobility. In another study, we are exploring the interaction of contaminants with

  18. Identification of microorganisms involved in nitrogen removal from wastewater treatment systems by means of molecular biology techniques; Identificacion de microorganismos implicados en la eliminacion de nitrogeno en sistemas de tratamiento de aguas residuales mediante tecnicas de biologia molecular

    Energy Technology Data Exchange (ETDEWEB)

    Figueroa, M.; Alonso-Gutierrez, J.; Campos, J. L.; Mendez, R.; Mosquera-Corral, A.

    2010-07-01

    The identification of the main bacteria populations present in the granular biomass from a biological reactor treating wastewater has been performed by applying two different molecular biology techniques. By means of the DGGE technique five different genera of heterotrophic bacteria (Thiothrix, Thauera, Cloroflexi, Comamanas y Zoogloea) and one of ammonia oxidizing bacteria (Nitrosomanas) were identified. The FISH technique, based on microscopy, allowed the in situ visualization and quantification of those microorganisms. Special attention was paid to filamentous bacteria distribution (Thiothrix and Cloroflexi) which could exert a structural function in aerobic granular sludge. (Author) 26 refs.

  19. Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins.

    Science.gov (United States)

    Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

    2016-03-05

    The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm(-1) and 1545 cm(-1), respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Multifluorophore DNA Origami Beacon as a Biosensing Platform

    DEFF Research Database (Denmark)

    Selnihhin, Denis; Sparvath, Steffen Møller; Preus, Søren

    2018-01-01

    -based sensors are limited by cumbersome and time-consuming readouts involving advanced experimental techniques. Here we describe design, construction, and characterization of an optical DNA origami nanobiosensor device exploiting arrays of precisely positioned organic fluorophores. Two arrays of donor...

  1. Tracking neuronal marker expression inside living differentiating cells using molecular beacons

    DEFF Research Database (Denmark)

    Ilieva, Mirolyuba; Della Vedova, Paolo; Hansen, Ole

    2013-01-01

    and tyrosine hydroxylase mRNAs were expressed 2 and 3 days post induction of differentiation, respectively. Oct 4 was not detected with MB in these cells and signal was not increased over time suggesting that MB are generally stable inside the cells. The gene expression changes measured using MBs were...... confirmed using qRT-PCR. These results suggest that MBs are simple to use sensors inside living cell, and particularly useful for studying dynamic gene expression in heterogeneous cell populations....

  2. Next Generation Sensors for Contaminants in Water: Catalytic DNA as a Molecular Beacon

    Science.gov (United States)

    2006-11-01

    Bohn, P. W., 1998: Electric Field Induced Permeability Modulation in Pure and Mixed Langmuir - Blodgett Multilayers of Hemicyanine Dyes and...c) the magnitude of κa. Because κ is controlled by solution ionic strength, control of flow in these nanometer channels is exceptionally versatile...added. Finally, the sensor can be extremely rugged -- in particular, it is insensitive to episodic loss of liquid analyte stream, so it can survive

  3. Molecular beacon nanosensors for live cell detection and tracking differentiation and reprogramming

    DEFF Research Database (Denmark)

    Ilieva, Mirolyuba

    2013-01-01

    open to closed state within living cells. Using MBs targeting pluripotent stem cell markers we demonstrated reverse into a more immature state of LUHMES induced by neurosphere-like growth conditions. Moreover, we have been able to trace localisation of this particular population during differentiation...... in separation of fluorophore from quencher and thereby emission of a fluorescent signal that can be detected. In this project the usability and applicability of MBs for live cell detection and tracing of gene expression was demonstrated. MBs library targeting gene markers for pluripotent stem cells as well...... and thus demonstrate the usability of MBs for monitoring cell behaviour within 3D clusters. Finally, MBs detection of expression of human pluripotent markers after reprograming of adult somatic cells with plasmid codding for mouse transcription factors was demonstrated. In conclusion, the method of using...

  4. RAPID DETECTION OF MICROORGANISMS USING 5S RRNA SPECIFIC MOLECULAR BEACONS. (R825354)

    Science.gov (United States)

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  5. Photodynamic Molecular Beacons: An Image-Guided Therapeutic Approach to Breast Cancer Vertebral Metastases

    Science.gov (United States)

    2012-03-01

    uptake. Prog Clin Biol Res. 1984;; 170: 629-­36. 14. Wilson BC, Firnau G, Jeeves WP, Brown KL, Burns-­McCormick DM . Chromatographic analysis and...Photosensitizer-­conjugated human serum albumin nanoparticles for effective photodynamic therapy. Theranostics. 2011;; 1: 230-­9. 24. Ferreira CL, Yapp DT, Crisp

  6. Highly sensitive and selective hyphenated technique (molecularly imprinted polymer solid-phase microextraction-molecularly imprinted polymer sensor) for ultra trace analysis of aspartic acid enantiomers.

    Science.gov (United States)

    Prasad, Bhim Bali; Srivastava, Amrita; Tiwari, Mahavir Prasad

    2013-03-29

    The present work is related to combination of molecularly imprinted solid-phase microextraction and complementary molecularly imprinted polymer-sensor. The molecularly imprinted polymer grafted on titanium dioxide modified silica fiber was used for microextraction, while the same polymer immobilized on multiwalled carbon nanotubes/titanium dioxide modified pencil graphite electrode served as a detection tool. In both cases, the surface initiated polymerization was found to be advantageous to obtain a nanometer thin imprinted film. The modified silica fiber exhibited high adsorption capacity and enantioselective diffusion of aspartic acid isomers into respective molecular cavities. This combination enabled double preconcentrations of d- and l-aspartic acid that helped sensing both isomers in real samples, without any cross-selectivity and matrix complications. Taking into account 6×10(4)-fold dilution of serum and 2×10(3)-fold dilution of cerebrospinal fluid required by the proposed method, the limit of detection for l-aspartic acid is 0.031ngmL(-1). Also, taking into account 50-fold dilution required by the proposed method, the limit of detection for d-aspartic acid is 0.031ngmL(-1) in cerebrospinal fluid. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. Creating a Connected Community: Lessons Learned from the Western New York Beacon Community

    Science.gov (United States)

    Maloney, Nancy; Heider, Arvela R.; Rockwood, Amy; Singh, Ranjit

    2014-01-01

    Introduction: Secure exchange of clinical data among providers has the potential to improve quality, safety, efficiency, and reduce duplication. Many communities are experiencing challenges in building effective health information exchanges (HIEs). Previous studies have focused on financial and technical issues regarding HIE development. This paper describes the Western New York (WNY) HIE growth and lessons learned about accelerating progress to become a highly connected community. Methods: HEALTHeLINK, with funding from the Office of the National Coordinator for Health Information Technology (ONC) under the Beacon Community Program, expanded HIE usage in eight counties. The communitywide transformation process used three main drivers: (1) a communitywide Electronic Health Record (EHR) adoption program; (2) clinical transformation partners; and (3) HIE outreach and infrastructure development. Results: ONC Beacon Community funding allowed WNY to achieve a new level in the use of interoperable HIE. Electronic delivery of results into the EHR expanded from 23 practices in 2010 to 222 practices in 2013, a tenfold increase. There were more than 12.5 million results delivered electronically (HL7 messages) to 222 practices’ EHRs via the HIE in 2013. Use of a secure portal and Virtual Health Record (VHR) to access reports (those not delivered directly to the EHR) also increased significantly, from 13,344 report views in 2010 to over 600,000 in 2013. Discussion and Conclusion: The WNY Beacon successfully expanded the sharing of clinical information among different sources of data and providers, creating a highly connected community to improve the quality and continuity of care. Technical, organizational, and community lessons described in this paper should prove beneficial to others as they pursue efforts to create connected communities. PMID:25848618

  8. Making it local: Beacon Communities use health information technology to optimize care management.

    Science.gov (United States)

    Allen, Amy; Des Jardins, Terrisca R; Heider, Arvela; Kanger, Chatrian R; Lobach, David F; McWilliams, Lee; Polello, Jennifer M; Rein, Alison L; Schachter, Abigail A; Singh, Ranjit; Sorondo, Barbara; Tulikangas, Megan C; Turske, Scott A

    2014-06-01

    Care management aims to provide cost-effective, coordinated, non-duplicative care to improve care quality, population health, and reduce costs. The 17 communities receiving funding from the Office of the National Coordinator for Health Information Technology through the Beacon Community Cooperative Agreement Program are leaders in building and strengthening their health information technology (health IT) infrastructure to provide more effective and efficient care management. This article profiles 6 Beacon Communities' health IT-enabled care management programs, highlighting the influence of local context on program strategy and design, and describing challenges, lessons learned, and policy implications for care delivery and payment reform. The unique needs (eg, disease burden, demographics), community partnerships, and existing resources and infrastructure all exerted significant influence on the overall priorities and design of each community's care management program. Though each Beacon Community needed to engage in a similar set of care management tasks--including patient identification, stratification, and prioritization; intervention; patient engagement; and evaluation--the contextual factors helped shape the specific strategies and tools used to carry out these tasks and achieve their objectives. Although providers across the country are striving to deliver standardized, high-quality care, the diverse contexts in which this care is delivered significantly influence the priorities, strategies, and design of community-based care management interventions. Gaps and challenges in implementing effective community-based care management programs include: optimizing allocation of care management services; lack of available technology tailored to care management needs; lack of standards and interoperability; integrating care management into care settings; evaluating impact; and funding and sustainability.

  9. The use of low frequency HF beacons to derive layer shape

    International Nuclear Information System (INIS)

    Heron, M.L.; Davies, K.

    1978-01-01

    The ATS-6 with its coherent multifrequency channels and various calibrations has brought the technology of beacon experiments to the point where the experimental accuracy exceeds that of some of the approximations used to derive total electron content. For example, the magnetic field term in the Faraday rotation experiment used to be given a mean value corresponding to about 50 km above the F layer peak. Another quantity that depends on profile shape is also available with present experiment, namely the refraction or second order term for carrier phase, modulation phase, or Faraday rotation. Some theoretical and experimental results are presented on these problems

  10. Developing children’s palliative care in Africa through beacon centres: lessons learnt

    Science.gov (United States)

    2013-01-01

    Much progress has been made in the provision of palliative care across sub-Saharan Africa, however much still remains to be done, particularly in the area of children’s palliative care (CPC). The Beacon Centres programme was set up in 2009, aimed at improving access to CPC in South Africa, Uganda and Tanzania through more and better-trained health professionals and CPC clinical services of a high standard. Having identified sites in each country to develop into CPC Beacon Centres, Navigators were identified who would be the ‘champions’ for CPC in those sites and lead a programme of training, mentorship and support. Five navigators (2 in Uganda and Tanzania and 1 in South Africa) were trained between September and December 2009. Following this they undertook CPC needs assessments at the 3 centres and set up and delivered a six-month CPC training programme, providing mentorship and support to students to enable them to integrate CPC into their workplaces. To date, 188 participants have commenced the six-month course, with 80 having completed it. CPC has been integrated into the activities of the centres and a CPC virtual resource centre set up in South Africa. The achievements from the Beacon project have been great and the work of the navigators immense, but as in all projects it has not been without its challenges. Lessons learnt include issues around: the focus of the project; the length and nature of the training; assessment; accreditation; the choice of navigators; mentoring; administrative support; co-ordination; the choice of project sites; and the integration of CPC into services. The need for CPC is not going to go away and it is therefore important that models of scaling-up are found that are not only practical, feasible, affordable and sustainable, but that focus on the outcome of improved CPC for all those who need it. It is hoped that the lessons shared from the Beacon Project will help in developing and implementing such models. PMID:23419095

  11. Controlling the signal: Practical privacy protection of genomic data sharing through Beacon services.

    Science.gov (United States)

    Wan, Zhiyu; Vorobeychik, Yevgeniy; Kantarcioglu, Murat; Malin, Bradley

    2017-07-26

    Genomic data is increasingly collected by a wide array of organizations. As such, there is a growing demand to make summary information about such collections available more widely. However, over the past decade, a series of investigations have shown that attacks, rooted in statistical inference methods, can be applied to discern the presence of a known individual's DNA sequence in the pool of subjects. Recently, it was shown that the Beacon Project of the Global Alliance for Genomics and Health, a web service for querying about the presence (or absence) of a specific allele, was vulnerable. The Integrating Data for Analysis, Anonymization, and Sharing (iDASH) Center modeled a track in their third Privacy Protection Challenge on how to mitigate the Beacon vulnerability. We developed the winning solution for this track. This paper describes our computational method to optimize the tradeoff between the utility and the privacy of the Beacon service. We generalize the genomic data sharing problem beyond that which was introduced in the iDASH Challenge to be more representative of real world scenarios to allow for a more comprehensive evaluation. We then conduct a sensitivity analysis of our method with respect to several state-of-the-art methods using a dataset of 400,000 positions in Chromosome 10 for 500 individuals from Phase 3 of the 1000 Genomes Project. All methods are evaluated for utility, privacy and efficiency. Our method achieves better performance than all state-of-the-art methods, irrespective of how key factors (e.g., the allele frequency in the population, the size of the pool and utility weights) change from the original parameters of the problem. We further illustrate that it is possible for our method to exhibit subpar performance under special cases of allele query sequences. However, we show our method can be extended to address this issue when the query sequence is fixed and known a priori to the data custodian, so that they may plan stage their

  12. The Southeastern Minnesota Beacon Project for Community-driven Health Information Technology: Origins, Achievements, and Legacy.

    Science.gov (United States)

    Chute, Christopher G; Hart, Lacey A; Alexander, Alex K; Jensen, Daniel W

    2014-01-01

    The Southeastern (SE) Minnesota Beacon organized all the health care providers, county public health organizations, and school districts in the deployment and integration of health information exchange (HIE) and targeted health communication around childhood asthma and diabetes. The community cooperated to establish a clinical data repository for all residents in the 11-county region. Through this community of practice approach that involved traditional and nontraditional providers, the SE Minnesota Beacon was able to realize unique applications of this technology. This manuscript overviews the associated organization and infrastructure of this community collaboration. The Office of the National Coordinator for Health Information Technology (ONC), as part of the American Recovery and Reinvestment Act of 2009 (ARRA) stimulus, established 17 projects throughout the United States targeting the introduction and meaningful use of health information technology (HIT). These 17 communities were intended to serve as an example of what could be accomplished. The SE Minnesota Beacon is one of these communities. The community ultimately opted for peer-to-peer HIE, using Nationwide Health Information Network (NwHIN) Connect software. The clinical data repository was established using the infrastructure developed by the Regenstrief Institute, which operated as a trusted third party. As an extension to HIE, the consortium of county public health departments created a patient data portal for use by school nurses and parents. Childhood asthma was addressed by creating, exchanging, and maintaining an "asthma action plan" for each affected child, shared throughout the community, including through the patient portal. Diabetes management introduced patient treatment decision tools and patient quality of life measures, facilitating care. Influenza vaccination was enhanced by large-scale community reporting in partnership with the state vaccination registry. The methodology and

  13. In situ exposure to non-directional beacons for air traffic control.

    Science.gov (United States)

    Joseph, Wout; Goeminne, Francis; Vermeeren, Günter; Verloock, Leen; Martens, Luc

    2012-04-01

    In situ electromagnetic field exposure of workers and the general public due to non-directional beacons (NDB) for air traffic control is assessed and characterized. For occupational exposure, the maximal measured electric field value is 881.6 V/m and the maximal magnetic field value is 9.1 A/m. The maximum electric fields exceed the International Commission on Non-Ionizing Radiation Protection (ICNIRP) reference levels at all seven NDB sites, and the magnetic fields at two of the seven NDB sites (occupational exposure). Recommendations and compliance distances for workers and the general public are provided. © 2012 Wiley Periodicals, Inc.

  14. Observability analysis of 2D single-beacon navigation in the presence of constant currents for two classes of maneuvers

    Digital Repository Service at National Institute of Oceanography (India)

    Crasta, N.; Bayat, M.; Aguiar, A.P.; Pascoal, A.M.

    . In particular, xc = 0 represents a circular motion about the beacon with radius v ω−1. The following result characterizes set of indistinguishable states for the system (5.1)-(5.2) subject to input class Ucir. Proposition 5.6. Consider the system (5...) = npi + 0.5 (−1)n pi, n ∈ Z. Notice also that under this condition the motion is a circular motion around the beacon. The following corollary follows from propositions 5.3 and 5.6. Corollary 5.8. Consider x0 ∈ M. Then (4.1)-(4.2) is observable...

  15. Preliminary Statistics from the NASA Alphasat Beacon Receiver in Milan, Italy

    Science.gov (United States)

    Nessel, James; Zemba, Michael; Morse, Jacquelynne; Luini, Lorenzo; Riva, Carlo

    2015-01-01

    NASA Glenn Research Center (GRC) and the Politecnico di Milano (POLIMI) have initiated a joint propagation campaign within the framework of the Alphasat propagation experiment to characterize rain attenuation, scintillation, and gaseous absorption effects of the atmosphere in the 40 gigahertz band. NASA GRC has developed and installed a K/Q-band (20/40 gigahertz) beacon receiver at the POLIMI campus in Milan, Italy, which receives the 20/40 gigahertz signals broadcast from the Alphasat Aldo Paraboni TDP no. 5 beacon payload. The primary goal of these measurements is to develop a physical model to improve predictions of communications systems performance within the Q-band. Herein, we provide an overview of the design and data calibration procedure, and present 6 months of preliminary statistics of the NASA propagation terminal, which has been installed and operating in Milan since May 2014. The Q-band receiver has demonstrated a dynamic range of 40 decibels at an 8-hertz sampling rate. A weather station with an optical disdrometer is also installed to characterize rain drop size distribution for correlation with physical based models.

  16. Performance Evaluation of Beacon-Enabled Mode for IEEE 802.15.4 Wireless Sensor Network

    Directory of Open Access Journals (Sweden)

    M. Udin Harun Al Rasyid

    2013-12-01

    Full Text Available IEEE 802.15.5 standard support structure of star and peer-to-peer network formation. Strating from these, the cluster tree network can be built as a special case of peer-to-peer network to increse coverage area. In this paper, we provide an performance evaluation of beacon- enabled mode for IEEE 802.15.4 wireless sensor network on star and cluster topology in order to get the maximum result to apply the appropriate topology model as needed. We conduct analysis on each topology model by using the numbers of nodes from 10 nodes to 100 nodes to analyze throughput, delay, energy consumption, and probability success packet by using NS2 simulator. The simulation results show that the throughput and the probability of success packet of cluster topology are higher than that of star topology, and the energy consumption of cluster topology is lesser than that of star topology. However, cluster topology increases the delay more than star topology. Keywords: IEEE 802.15.4, wireless sensor network, beacon-enabled mode, topology, csma/ca

  17. Secure Utilization of Beacons and UAVs in Emergency Response Systems for Building Fire Hazard.

    Science.gov (United States)

    Seo, Seung-Hyun; Choi, Jung-In; Song, Jinseok

    2017-09-25

    An intelligent emergency system for hazard monitoring and building evacuation is a very important application area in Internet of Things (IoT) technology. Through the use of smart sensors, such a system can provide more vital and reliable information to first-responders and also reduce the incidents of false alarms. Several smart monitoring and warning systems do already exist, though they exhibit key weaknesses such as a limited monitoring coverage and security, which have not yet been sufficiently addressed. In this paper, we propose a monitoring and emergency response method for buildings by utilizing beacons and Unmanned Aerial Vehicles (UAVs) on an IoT security platform. In order to demonstrate the practicability of our method, we also implement a proof of concept prototype, which we call the UAV-EMOR (UAV-assisted Emergency Monitoring and Response) system. Our UAV-EMOR system provides the following novel features: (1) secure communications between UAVs, smart sensors, the control server and a smartphone app for security managers; (2) enhanced coordination between smart sensors and indoor/outdoor UAVs to expand real-time monitoring coverage; and (3) beacon-aided rescue and building evacuation.

  18. A Two-Layer Method for Sedentary Behaviors Classification Using Smartphone and Bluetooth Beacons.

    Science.gov (United States)

    Cerón, Jesús D; López, Diego M; Hofmann, Christian

    2017-01-01

    Among the factors that outline the health of populations, person's lifestyle is the more important one. This work focuses on the caracterization and prevention of sedentary lifestyles. A sedentary behavior is defined as "any waking behavior characterized by an energy expenditure of 1.5 METs (Metabolic Equivalent) or less while in a sitting or reclining posture". To propose a method for sedentary behaviors classification using a smartphone and Bluetooth beacons considering different types of classification models: personal, hybrid or impersonal. Following the CRISP-DM methodology, a method based on a two-layer approach for the classification of sedentary behaviors is proposed. Using data collected from a smartphones' accelerometer, gyroscope and barometer; the first layer classifies between performing a sedentary behavior and not. The second layer of the method classifies the specific sedentary activity performed using only the smartphone's accelerometer and barometer data, but adding indoor location data, using Bluetooth Low Energy (BLE) beacons. To improve the precision of the classification, both layers implemented the Random Forest algorithm and the personal model. This study presents the first available method for the automatic classification of specific sedentary behaviors. The layered classification approach has the potential to improve processing, memory and energy consumption of mobile devices and wearables used.

  19. Temporal change of EIA asymmetry revealed by a beacon receiver network in Southeast Asia

    Science.gov (United States)

    Watthanasangmechai, Kornyanat; Yamamoto, Mamoru; Saito, Akinori; Maruyama, Takashi; Yokoyama, Tatsuhiro; Nishioka, Michi; Ishii, Mamoru

    2015-05-01

    To reveal the temporal change of the equatorial ionization anomaly (EIA) asymmetry, a multipoint satellite-ground beacon experiment was conducted along the meridional plane of the Thailand-Indonesia sector. The observation includes one station near the magnetic equator and four stations at off-equator latitudes. This is the first EIA asymmetry study with high spatial resolution using GNU Radio Beacon Receiver (GRBR) observations in Southeast Asia. GRBR-total electron contents (TECs) from 97 polar-orbit satellite passes in March 2012 were analyzed in this study. Successive passes captured rapid evolution of EIA asymmetry, especially during geomagnetic disturbances. The penetrating electric fields that occur during geomagnetic disturbed days are not the cause of the asymmetry. Instead, high background TEC associated with an intense electric field empowers the neutral wind to produce severe asymmetry of the EIA. Such rapid evolution of EIA asymmetry was not seen during nighttime, when meridional wind mainly controlled the asymmetric structures. Additional data are necessary to identify the source of the variations, i.e., atmospheric waves. Precisely capturing the locations of the crests and the evolution of the asymmetry enhances understanding of the temporal change of EIA asymmetry at the local scale and leads to a future local modeling for TEC prediction in Southeast Asia.

  20. Perancangan Prototipe Receiver Beacon Black Box Locator Acoustic 37,5 kHz Pingers

    Directory of Open Access Journals (Sweden)

    RUSTAMAJI RUSTAMAJI

    2016-01-01

    When an aircraft caught in an accident and crashes into the water, its location can be detected using a device called a receiver beacon black box locator acoustic (pingers receiver. The pingers receiver functioned as a reciever signal with 37,5 kHz ± 1 kHz frequency from trnasmitter pingers or Underwater Locator Beacon (ULB which is on air plane black blox. In this research made design pingers receiver composed of a series of  Band Pass Filter (BPF, envelope detector, audio amplifier, and loud speaker. The signal of 37,5 kHz ± 1 kHz  frequency sent by pingers transmitter will bereceived by pingers receiver, after which the signal will be processed by the Band Pass Filter (BPF circuit before being detected by envelope detector for take back the signal information which like pulse signal with 10ms width and 1 second interval as pingers signal tha can  be to  be heard by human ear. Based on the  design that  was made, the signal ouput generated by the prototype has a 14 ms width with 1 second interval. Keywords: pingers receiver, band pass filter (BPF, envelope detector, loud speaker.

  1. HIGHLY SELECTIVE SENSORS FOR CHEMICAL AND BIOLOGICAL WARFARE AGENTS, INSECTICIDES AND VOCS BASED ON A MOLECULAR SURFACE IMPRINTING TECHNIQUE

    Science.gov (United States)

    Abstract was given as an oral platform presentation at the Pittsburgh Conference, Orlando FL (March 5-9, 2006). Research described is the development of sensors based on molecular surface imprinting. Applications include the monitoring of chemical and biological agents and inse...

  2. 75 FR 20364 - Public Buildings Service; Key Largo Beacon Annex Site; Key Largo, FL; Transfer of Property

    Science.gov (United States)

    2010-04-19

    ... GENERAL SERVICES ADMINISTRATION [Wildlife Order 187; 4-D-FL-1218] Public Buildings Service; Key Largo Beacon Annex Site; Key Largo, FL; Transfer of Property Pursuant to section 2 of Public Law 537, 80th Congress, approved May 19, 1948 (16 U.S.C. 667c), notice is hereby given that: 1. The General...

  3. Guiding Math Students to Campus Services: An Impact Evaluation of the Beacon Program at South Texas College

    Science.gov (United States)

    Visher, Mary; Butcher, Kristin F.; Cerna, Oscar S.

    2011-01-01

    This research rigorously evaluates whether a low-cost intervention can improve students' performance in developmental math. The "Beacon Mentoring Program" was developed at South Texas College by professors, administrators, and staff at the college. Surveys of students revealed that many did not have someone on campus whom they felt they…

  4. Beacon Charter School Needs a School: A Case of Capital Outlay of Charters in a Public District

    Science.gov (United States)

    Wronowski, Meredith L.

    2017-01-01

    The case study presented below is a representation of a real-world, ongoing situation involving a public school district's capital outlay for charter schools within its boundaries. One particular charter, Beacon Charter School, was promised a permanent building by the public school district that also acts as its authorizer. However, recent events…

  5. BEACON/MOD2A: a computer program for subcompartment analysis of nuclear reactor containment. A user's manual

    International Nuclear Information System (INIS)

    Wells, R.A.

    1979-03-01

    The BEACON code is a Best Estimate Advanced Containment code which being developed by EG and G, Idaho, Inc., at the Idaho National Engineering Laboratory. The program is designed to perform a best estimate analysis of the flow of a mixture of air, water, and steam in a nuclear reactor containment system under loss-of-coolant accident conditions. The code can simulate two-component, two-phase fluid flow in complex geometries using a combination of two-dimensional, one-dimensional, and lumped-parameter representations for the various parts of the system. The current version of BEACON, which is designated BEACON/MOD2A, contains mass and heat transfer models for wall film and for wall conduction. It is suitable for the evaluation of short term transients in PWR dry containment systems. This manual describes the models employed in BEACON/MOD2A and specifies code implementation requirements. It provides application information for input data preparation and for output data interpretation

  6. Design and Practical Evaluation of a Family of Lightweight Protocols for Heterogeneous Sensing through BLE Beacons in IoT Telemetry Applications.

    Science.gov (United States)

    Hernández-Rojas, Dixys L; Fernández-Caramés, Tiago M; Fraga-Lamas, Paula; Escudero, Carlos J

    2017-12-27

    The Internet of Things (IoT) involves a wide variety of heterogeneous technologies and resource-constrained devices that interact with each other. Due to such constraints, IoT devices usually require lightweight protocols that optimize the use of resources and energy consumption. Among the different commercial IoT devices, Bluetooth and Bluetooth Low Energy (BLE)-based beacons, which broadcast periodically certain data packets to notify their presence, have experienced a remarkable growth, specially due to their application in indoor positioning systems. This article proposes a family of protocols named Lightweight Protocol for Sensors (LP4S) that provides fast responses and enables plug-and-play mechanisms that allow IoT telemetry systems to discover new nodes and to describe and auto-register the sensors and actuators connected to a beacon. Thus, three protocols are defined depending on the beacon hardware characteristics: LP4S-6 (for resource-constraint beacons), LP4S-X (for more powerful beacons) and LP4S-J (for beacons able to run complex firmware). In order to demonstrate the capabilities of the designed protocols, the most restrictive (LP4S-6) is tested after implementing it for a telemetry application in a beacon based on Eddystone (Google's open beacon format). Thus, the beacon specification is extended in order to increase its ability to manage unlimited sensors in a telemetry system without interfering in its normal operation with Eddystone frames. The performed experiments show the feasibility of the proposed solution and its superiority, in terms of latency and energy consumption, with respect to approaches based on Generic Attribute Profile (GATT) when multiple users connect to a mote or in scenarios where latency is not a restriction, but where low-energy consumption is essential.

  7. Design and Practical Evaluation of a Family of Lightweight Protocols for Heterogeneous Sensing through BLE Beacons in IoT Telemetry Applications

    Science.gov (United States)

    2017-01-01

    The Internet of Things (IoT) involves a wide variety of heterogeneous technologies and resource-constrained devices that interact with each other. Due to such constraints, IoT devices usually require lightweight protocols that optimize the use of resources and energy consumption. Among the different commercial IoT devices, Bluetooth and Bluetooth Low Energy (BLE)-based beacons, which broadcast periodically certain data packets to notify their presence, have experienced a remarkable growth, specially due to their application in indoor positioning systems. This article proposes a family of protocols named Lightweight Protocol for Sensors (LP4S) that provides fast responses and enables plug-and-play mechanisms that allow IoT telemetry systems to discover new nodes and to describe and auto-register the sensors and actuators connected to a beacon. Thus, three protocols are defined depending on the beacon hardware characteristics: LP4S-6 (for resource-constraint beacons), LP4S-X (for more powerful beacons) and LP4S-J (for beacons able to run complex firmware). In order to demonstrate the capabilities of the designed protocols, the most restrictive (LP4S-6) is tested after implementing it for a telemetry application in a beacon based on Eddystone (Google’s open beacon format). Thus, the beacon specification is extended in order to increase its ability to manage unlimited sensors in a telemetry system without interfering in its normal operation with Eddystone frames. The performed experiments show the feasibility of the proposed solution and its superiority, in terms of latency and energy consumption, with respect to approaches based on Generic Attribute Profile (GATT) when multiple users connect to a mote or in scenarios where latency is not a restriction, but where low-energy consumption is essential. PMID:29280975

  8. Design and Practical Evaluation of a Family of Lightweight Protocols for Heterogeneous Sensing through BLE Beacons in IoT Telemetry Applications

    Directory of Open Access Journals (Sweden)

    Dixys L. Hernández-Rojas

    2017-12-01

    Full Text Available The Internet of Things (IoT involves a wide variety of heterogeneous technologies and resource-constrained devices that interact with each other. Due to such constraints, IoT devices usually require lightweight protocols that optimize the use of resources and energy consumption. Among the different commercial IoT devices, Bluetooth and Bluetooth Low Energy (BLE-based beacons, which broadcast periodically certain data packets to notify their presence, have experienced a remarkable growth, specially due to their application in indoor positioning systems. This article proposes a family of protocols named Lightweight Protocol for Sensors (LP4S that provides fast responses and enables plug-and-play mechanisms that allow IoT telemetry systems to discover new nodes and to describe and auto-register the sensors and actuators connected to a beacon. Thus, three protocols are defined depending on the beacon hardware characteristics: LP4S-6 (for resource-constraint beacons, LP4S-X (for more powerful beacons and LP4S-J (for beacons able to run complex firmware. In order to demonstrate the capabilities of the designed protocols, the most restrictive (LP4S-6 is tested after implementing it for a telemetry application in a beacon based on Eddystone (Google’s open beacon format. Thus, the beacon specification is extended in order to increase its ability to manage unlimited sensors in a telemetry system without interfering in its normal operation with Eddystone frames. The performed experiments show the feasibility of the proposed solution and its superiority, in terms of latency and energy consumption, with respect to approaches based on Generic Attribute Profile (GATT when multiple users connect to a mote or in scenarios where latency is not a restriction, but where low-energy consumption is essential.

  9. Towards mosquito sterile insect technique programmes: Exploring genetic, molecular, mechanical and behavioural methods of sex separation in mosquitoes

    Czech Academy of Sciences Publication Activity Database

    Gilles, J. R. L.; Schetelig, M. F.; Scolari, F.; Marec, František; Capurro, M.L.; Franz, G.; Bourtzis, K.

    132S, č. 1 (2014), S178-S187 ISSN 0001-706X R&D Projects: GA ČR GA523/09/2106 Grant - others:Deutsche Forschungsgemeinschalft(DE) SCHE 1833/1 Institutional support: RVO:60077344 Keywords : female elimination * vector control * genetic sexing strains (GSS) Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.270, year: 2014 http://www.sciencedirect.com/science/article/pii/S0001706X13002209?via=ihub

  10. Complex polarimetric and spectral techniques in diagnostics of blood plasma of patients with ovarian cancer as a preliminary stage molecular genetic screening

    Science.gov (United States)

    Grzegorzewski, B.; Peresunko, O. P.; Yermolenko, S. B.

    2018-01-01

    This work is devoted to the substantiation and selection of patients with ovarian cancer (OC) for the purpose of conducting expensive molecular genetic studies on genotyping. As diagnostic methods have been used ultraviolet spectrometry samples of blood plasma in the liquid state, infrared spectroscopy middle range (2,5 - 25 microns) dry residue of plasma polarization and laser diagnostic technique of thin histological sections of biological tissues. Obtained results showed that the use of spectrophotometry in the range of 1000-3000 cm-1 allowed to establish quantitative parameters of the plasma absorption rate of blood of patients in the third group in different ranges, which would allow in the future to conduct an express analysis of the patient's condition (procedure screening) for further molecular-genetic typing on BRCA I and II.

  11. Data governance and data sharing agreements for community-wide health information exchange: lessons from the beacon communities.

    Science.gov (United States)

    Allen, Claudia; Des Jardins, Terrisca R; Heider, Arvela; Lyman, Kristin A; McWilliams, Lee; Rein, Alison L; Schachter, Abigail A; Singh, Ranjit; Sorondo, Barbara; Topper, Joan; Turske, Scott A

    2014-01-01

    Unprecedented efforts are underway across the United States to electronically capture and exchange health information to improve health care and population health, and reduce costs. This increased collection and sharing of electronic patient data raises several governance issues, including privacy, security, liability, and market competition. Those engaged in such efforts have had to develop data sharing agreements (DSAs) among entities involved in information exchange, many of whom are "nontraditional" health care entities and/or new partners. This paper shares lessons learned based on the experiences of six federally funded communities participating in the Beacon Community Cooperative Agreement Program, and offers guidance for navigating data governance issues and developing DSAs to facilitate community-wide health information exchange. While all entities involved in electronic data sharing must address governance issues and create DSAs accordingly, until recently little formal guidance existed for doing so - particularly for community-based initiatives. Despite this lack of guidance, together the Beacon Communities' experiences highlight promising strategies for navigating complex governance issues, which may be useful to other entities or communities initiating information exchange efforts to support delivery system transformation. For the past three years, AcademyHealth has provided technical assistance to most of the 17 Beacon Communities, 6 of whom contributed to this collaborative writing effort. Though these communities varied widely in terms of their demographics, resources, and Beacon-driven priorities, common themes emerged as they described their approaches to data governance and DSA development. The 6 Beacon Communities confirmed that DSAs are necessary to satisfy legal and market-based concerns, and they identified several specific issues, many of which have been noted by others involved in network data sharing initiatives. More importantly, these

  12. Beacon of Hope? Lessons Learned from Efforts to Reduce Civilian Deaths from Police Shootings in an Australian State.

    Science.gov (United States)

    Saligari, Jessica; Evans, Richard

    2016-04-01

    In the 1990s, the police service in Victoria, Australia, faced a crisis of community confidence due to a spate of civilian deaths from police shootings. In that decade, twice as many civilians died at the hands of the police in Victoria than in every other Australian state combined. Most of those killed were mentally ill and affected by drugs and alcohol, and were rarely a serious threat except to themselves. The problem was also almost entirely an urban phenomenon. Shootings in rural communities, where mentally ill people were more likely to be personally known to local police, were (and remain) almost unknown. The large number of fatalities was recognised as a serious threat to public confidence, and Victoria Police introduced a ground-breaking training programme, Operation Beacon. Operating procedures and weapons training were fundamentally changed, to focus on de-escalation of conflict and avoiding or minimising police use of force. In the short term, Operation Beacon was successful. Shooting incidents were dramatically reduced. However, during the first decade of the new century, the number of civilians being killed again increased. This article examines Operation Beacon, both as a successful model for reducing civilian deaths at the hand of police and as a cautionary tale for police reform. We argue that the lessons of Operation Beacon have been gradually forgotten and that old habits and attitudes resurfaced. Fatal shootings of mentally ill civilians can be prevented, but if success is to be other than temporary, the Beacon philosophy must be continually reemphasised by police management.

  13. Nanomechanical molecular devices made of DNA origami.

    Science.gov (United States)

    Kuzuya, Akinori; Ohya, Yuichi

    2014-06-17

    CONSPECTUS: Eight years have passed since the striking debut of the DNA origami technique ( Rothemund, P. W. K. Nature 2006 , 440 , 297 - 302 ), in which long single-stranded DNA is folded into a designed nanostructure, in either 2D or 3D, with the aid of many short staple strands. The number of proposals for new design principles for DNA origami structures seems to have already reached a peak. It is apparent that DNA origami study is now entering the second phase of creating practical applications. The development of functional nanomechanical molecular devices using the DNA origami technique is one such application attracting significant interest from researchers in the field. Nanomechanical DNA origami devices, which maintain the characteristics of DNA origami structures, have various advantages over conventional DNA nanomachines. Comparatively high assembly yield, relatively large size visible via atomic force microscopy (AFM) or transmission electron microscopy (TEM), and the capability to assemble multiple functional groups with precision using multiple staple strands are some of the advantages of the DNA origami technique for constructing sophisticated molecular devices. This Account describes the recent developments of such nanomechanical DNA origami devices and reviews the emerging target of DNA origami studies. First, simple "dynamic" DNA origami structures with transformation capability, such as DNA origami boxes and a DNA origami hatch with structure control, are briefly summarized. More elaborate nanomechanical DNA origami devices are then reviewed. The first example describes DNA origami pinching devices that can be used as "single-molecule" beacons to detect a variety of biorelated molecules, from metal ions at the size of a few tens of atomic mass number units to relatively gigantic proteins with a molecular mass greater than a hundred kilodaltons, all on a single platform. Clamshell-like DNA nanorobots equipped with logic gates can discriminate

  14. Even an old technique is suitable in the molecular world of science: the everted sac preparation turns 60 years old.

    Science.gov (United States)

    Hamilton, Kirk L

    2014-04-15

    An old proverb states "necessity is the mother of invention." This certainly holds true in science as one pursues research questions. Experimental techniques have evolved as scientists have asked more specific research questions. Indeed, techniques such as the Ussing chamber, the perfused renal tubule preparation, patch-clamp, polymerase chain reaction, and site-directed mutagenesis have been developed over the past 60 years. However, sometimes, simple techniques may be useful and still very informative, and this certainly applies to intestinal physiology. Indeed, Gerald Wiseman and Thomas Hastings Wilson described the intestinal everted sac preparation some 60 years ago. Since then, this technique has been used for numerous research purposes including determining ion, amino acid, water and solute transport across the intestinal epithelium; and drug metabolism, absorption, and interactions in pharmaceutical/pharmacological research and even in education. This article provides a historical review of the development of the in vitro intestinal preparation that led to the everted sac preparation and its use in science.

  15. Extensive Evaluation of a Diffusion Denuder Technique for the Quantification of Atmospheric Stable and Radioactive Molecular Iodine

    DEFF Research Database (Denmark)

    Huang, Ru-Jin; Hou, Xiaolin; Hoffmann, Thorsten

    2010-01-01

    In this paper we present the evaluation and optimization of a new approach for the quantification of gaseous molecular iodine (I2) for laboratory- and field-based studies and its novel application for the measurement of radioactive molecular iodine. α-Cyclodextrin (α-CD) in combination with 129I......, and condition of release and derivatization of iodine, is extensively evaluated and optimized. The collection efficiency is larger than 98% and the limit of detection (LOD) obtained is 0.17 parts-per-trillion-by-volume (pptv) for a sampling duration of 30 min at 500 mL min−1. Furthermore, the potential use...... of this protocol for the determination of radioactive I2 at ultra trace level is also demonstrated when 129I− used in the coating is replaced by 127I− and a multiple denuder system is used. Using the present method we observed 25.7−108.6 pptv 127I2 at Mweenish Bay, Ireland and 108 molecule m−3 129I2 at Mainz...

  16. Interaction of Flavonoids from Woodwardia unigemmata with Bovine Serum Albumin (BSA): Application of Spectroscopic Techniques and Molecular Modeling Methods.

    Science.gov (United States)

    Ma, Rui; Pan, Hong; Shen, Tao; Li, Peng; Chen, Yanan; Li, Zhenyu; Di, Xiaxia; Wang, Shuqi

    2017-08-09

    Phytochemical investigation on the methanol extract of Woodwardia unigemmata resulted in the isolation of seven flavonoids, including one new flavonol acylglycoside ( 1 ). The structures of these compounds were elucidated on the basis of extensive spectroscopic analysis and comparison of literature data. The multidrug resistance (MDR) reversing activity was evaluated for the isolated compounds using doxorubicin-resistant K562/A02 cells model. Compound 6 showed comparable MDR reversing effect to verapamil. Furthermore, the interaction between compounds and bovine serum albumin (BSA) was investigated by spectroscopic methods, including steady-state fluorescence, synchronous fluorescence, circular dichroism (CD) spectroscopies, and molecular docking approach. The experimental results indicated that the seven flavonoids bind to BSA by static quenching mechanisms. The negative ΔH and ΔS values indicated that van der Waals interactions and hydrogen bonds contributed in the binding of compounds 2 - 6 to BSA. In the case of compounds 1 and 7 systems, the hydrophobic interactions play a major role. The binding of compounds to BSA causes slight changes in the secondary structure of BSA. There are two binding sites of compound 6 on BSA and site I is the main site according to the molecular docking studies and the site marker competitive binding assay.

  17. An overview of techniques for linking high-dimensional molecular data to time-to-event endpoints by risk prediction models.

    Science.gov (United States)

    Binder, Harald; Porzelius, Christine; Schumacher, Martin

    2011-03-01

    Analysis of molecular data promises identification of biomarkers for improving prognostic models, thus potentially enabling better patient management. For identifying such biomarkers, risk prediction models can be employed that link high-dimensional molecular covariate data to a clinical endpoint. In low-dimensional settings, a multitude of statistical techniques already exists for building such models, e.g. allowing for variable selection or for quantifying the added value of a new biomarker. We provide an overview of techniques for regularized estimation that transfer this toward high-dimensional settings, with a focus on models for time-to-event endpoints. Techniques for incorporating specific covariate structure are discussed, as well as techniques for dealing with more complex endpoints. Employing gene expression data from patients with diffuse large B-cell lymphoma, some typical modeling issues from low-dimensional settings are illustrated in a high-dimensional application. First, the performance of classical stepwise regression is compared to stage-wise regression, as implemented by a component-wise likelihood-based boosting approach. A second issues arises, when artificially transforming the response into a binary variable. The effects of the resulting loss of efficiency and potential bias in a high-dimensional setting are illustrated, and a link to competing risks models is provided. Finally, we discuss conditions for adequately quantifying the added value of high-dimensional gene expression measurements, both at the stage of model fitting and when performing evaluation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Considerations for Community-Based mHealth Initiatives: Insights From Three Beacon Communities

    Science.gov (United States)

    2013-01-01

    Mobile health (mHealth) is gaining widespread attention for its potential to engage patients in their health and health care in their daily lives. Emerging evidence suggests that mHealth interventions can be used effectively to support behavior change, but numerous challenges remain when implementing these programs at the community level. This paper provides an overview of considerations when implementing community-based mHealth initiatives, based on the experiences of three Beacon Communities across the United States that have launched text messaging (short message service, SMS) pilot programs aimed at diabetes risk reduction and disease management. The paper addresses lessons learned and suggests strategies to overcome challenges related to developing text message content, conducting marketing and outreach, enrolling participants, engaging providers, evaluating program effectiveness, and sustaining and scaling the programs. PMID:24128406

  19. ATS-6 radio beacon electron content measurements at Ootacamund, India, October 1975-July 1976

    International Nuclear Information System (INIS)

    Bouwer, S.D.; Davies, K.; Donnelly, R.F.; Grubb, R.N.; Jones, J.E.

    1980-03-01

    An atlas of total slant-path columnar electron content data measured between the ATS-6 satellite and Ootacamund, India, a site near the magnetic Equator is presented. Although these measurements were taken during a solar minimum, the general level of flare and geomagnetic activity that occurred during the observation period is summarized. These total content (N(T)) data were derived from the modulation phase (group delay) of a carrier signal transmitted from the geostationary satellite's Radio Beacon Experiment. This atlas contains two data sets: (1) N(T) as 2-min subsamples digitally recorded between 2 October 1975 and 28 January 1976 corrected for ATS-6 pitch maneuvers and (2) N(T) as 15-min subsamples chart recorded between 21 October 1975 and 22 July 1976 but uncorrected for changes in satellite orientation

  20. Considerations for community-based mHealth initiatives: insights from three Beacon Communities.

    Science.gov (United States)

    Abebe, Nebeyou A; Capozza, Korey L; Des Jardins, Terrisca R; Kulick, David A; Rein, Alison L; Schachter, Abigail A; Turske, Scott A

    2013-10-15

    Mobile health (mHealth) is gaining widespread attention for its potential to engage patients in their health and health care in their daily lives. Emerging evidence suggests that mHealth interventions can be used effectively to support behavior change, but numerous challenges remain when implementing these programs at the community level. This paper provides an overview of considerations when implementing community-based mHealth initiatives, based on the experiences of three Beacon Communities across the United States that have launched text messaging (short message service, SMS) pilot programs aimed at diabetes risk reduction and disease management. The paper addresses lessons learned and suggests strategies to overcome challenges related to developing text message content, conducting marketing and outreach, enrolling participants, engaging providers, evaluating program effectiveness, and sustaining and scaling the programs.

  1. Changing techniques in crop plant classification: molecularization at the National Institute of Agricultural Botany during the 1980s.

    Science.gov (United States)

    Holmes, Matthew

    2017-04-01

    Modern methods of analysing biological materials, including protein and DNA sequencing, are increasingly the objects of historical study. Yet twentieth-century taxonomic techniques have been overlooked in one of their most important contexts: agricultural botany. This paper addresses this omission by harnessing unexamined archival material from the National Institute of Agricultural Botany (NIAB), a British plant science organization. During the 1980s the NIAB carried out three overlapping research programmes in crop identification and analysis: electrophoresis, near infrared spectroscopy (NIRS) and machine vision systems. For each of these three programmes, contemporary economic, statutory and scientific factors behind their uptake by the NIAB are discussed. This approach reveals significant links between taxonomic practice at the NIAB and historical questions around agricultural research, intellectual property and scientific values. Such links are of further importance given that the techniques developed by researchers at the NIAB during the 1980s remain part of crop classification guidelines issued by international bodies today.

  2. Evaluation of a rectangular rapid flashing beacon system at the Belmont Ridge Road and W&OD Trail mid-block crosswalk.

    Science.gov (United States)

    2015-05-01

    On April 8, 2013, the Virginia Department of Transportation (VDOT) installed a Rectangular Rapid Flashing Beacon : (RRFB) system at Belmont Ridge Road in Loudoun County that included two units at the Washington and Old Dominion : (W&OD) Trail crossin...

  3. Energy optimization for upstream data transfer in 802.15.4 beacon-enabled star formulation

    Science.gov (United States)

    Liu, Hua; Krishnamachari, Bhaskar

    2008-08-01

    Energy saving is one of the major concerns for low rate personal area networks. This paper models energy consumption for beacon-enabled time-slotted media accessing control cooperated with sleeping scheduling in a star network formulation for IEEE 802.15.4 standard. We investigate two different upstream (data transfer from devices to a network coordinator) strategies: a) tracking strategy: the devices wake up and check status (track the beacon) in each time slot; b) non-tracking strategy: nodes only wake-up upon data arriving and stay awake till data transmitted to the coordinator. We consider the tradeoff between energy cost and average data transmission delay for both strategies. Both scenarios are formulated as optimization problems and the optimal solutions are discussed. Our results show that different data arrival rate and system parameters (such as contention access period interval, upstream speed etc.) result in different strategies in terms of energy optimization with maximum delay constraints. Hence, according to different applications and system settings, different strategies might be chosen by each node to achieve energy optimization for both self-interested view and system view. We give the relation among the tunable parameters by formulas and plots to illustrate which strategy is better under corresponding parameters. There are two main points emphasized in our results with delay constraints: on one hand, when the system setting is fixed by coordinator, nodes in the network can intelligently change their strategies according to corresponding application data arrival rate; on the other hand, when the nodes' applications are known by the coordinator, the coordinator can tune the system parameters to achieve optimal system energy consumption.

  4. Microprobing the Molecular Spatial Distribution and Structural Architecture of Feed-type Sorghum Seed Tissue (Sorghum Bicolor L.) using the Synchrotron Radiation Infrared Microspectroscopy Technique

    International Nuclear Information System (INIS)

    Yu, P.

    2011-01-01

    Sorghum seed (Sorghum bicolor L.) has unique degradation and fermentation behaviours compared with other cereal grains such as wheat, barley and corn. This may be related to its cell and cell-wall architecture. The advanced synchrotron radiation infrared microspectroscopy (SR-IMS) technique enables the study of cell or living cell biochemistry within cellular dimensions. The objective of this study was to use the SR-IMS imaging technique to microprobe molecular spatial distribution and cell architecture of the sorghum seed tissue comprehensively. High-density mapping was carried out using SR-IMS on beamline U2B at the National Synchrotron Light Source (Brookhaven National Laboratory, NY, USA). Molecular images were systematically recorded from the outside to the inside of the seed tissue under various chemical functional groups and their ratios [peaks at ∼1725 (carbonyl C=O ester), 1650 (amide I), 1657 (protein secondary structure α-helix), 1628 (protein secondary structure β-sheet), 1550 (amide II), 1515 (aromatic compounds of lignin), 1428, 1371, 1245 (cellulosic compounds in plant seed tissue), 1025 (non-structural CHO, starch granules), 1246 (cellulosic material), 1160 (CHO), 1150 (CHO), 1080 (CHO), 930 (CHO), 860 (CHO), 3350 (OH and NH stretching), 2960 (CH 3 anti-symmetric), 2929 (CH 2 anti-symmetric), 2877 (CH 3 symmetric) and 2848 cm -1 (CH 2 asymmetric)]. The relative protein secondary structure α-helix to β-sheet ratio image, protein amide I to starch granule ratio image, and anti-symmetric CH 3 to CH 2 ratio image were also investigated within the intact sorghum seed tissue. The results showed unique cell architecture, and the molecular spatial distribution and intensity in the sorghum seed tissue (which were analyzed through microprobe molecular imaging) were generated using SR-IMS. This imaging technique and methodology has high potential and could be used for scientists to develop specific cereal grain varieties with targeted food and feed

  5. Preparation and evaluation of Exendin radio conjugates for detecting insulinomas and gastrinomas by molecular nuclear medicine techniques

    International Nuclear Information System (INIS)

    Medina G, V.

    2015-01-01

    The gastro-entero-pancreatic neuroendocrine tumors (GEP-NET) are named based on the secreted hormones. Among them, the insulinomas and gastrinomas represent a diagnostic challenge because of their slow metabolic rate, small size and anatomical location that have limited their detection in some imaging procedures. About 90% of insulinomas are benign and 10% are malignant. Benign insulinomas express the glucagon-like peptide-1 receptor (GLP-1R) and low levels of somatostatin receptors (SSTR), while malignant insulinomas over express SSTR or GLP-1R in low levels. A kit for the preparation of Lys 27 ( 99m Tc-EDDA/HYNIC)-Exendin(9-39)/ 99m Tc-EDDA/HYNIC-Tyr 3 -Octreotide was developed to detect 100% of gastrinomas and insulinomas. In order to reach this aim, the peptides were radiolabeled and characterized. Stability studies will be completed and the in vitro and in vivo behavior was evaluated. The Lys 27 ( 99m Tc-EDDA/HYNIC)-Exendin(9-39)/ 99m Tc-EDDA/HYNIC-Tyr 3 -Octreotide can be labeled with 99m Tc, obtaining high radiochemical purities (>94%), high stability in human serum and affinity to GLP-1 and SST-2 receptor. This new formulation showed properties suitable for use as a target-specific agent for molecular imaging of GLP-1R/SSTR positive tumors. In vivo micro-SPECT/CT images of Lys 27 ( 99m Tc-EDDA/HYNIC)-Exendin(9-39), 99m Tc-EDDA/HYNIC-Tyr 3 -Octreotide and of the pharmaceutical formulation Lys 27 ( 99m Tc-EDDA/HYNIC)-Exendin(9-39)/ 99m Tc-EDDA/HYNIC-Tyr 3 -Octreotide showed the main elimination pathways, and tumors higher uptake compared to the background tissues. The biodistribution and imaging studies demonstrated properties suitable for its use as a target-specific agent for the simultaneous molecular imaging of GLP-1R and SSTR. (Author)

  6. MO-FG-BRA-06: Electromagnetic Beacon Insertion in Lung Cancer Patients and Resultant Surrogacy Errors for Dynamic MLC Tumour Tracking

    Energy Technology Data Exchange (ETDEWEB)

    Hardcastle, N; Booth, J; Caillet, V; Haddad, C; Crasta, C [Royal North Shore Hospital, St. Leonards, NSW (Australia); O’Brien, R; Keall, P [University of Sydney, Sydney, NSW (Australia); Szymura, K [Royal North Shore Hospital, Sydney, NSW (Australia)

    2016-06-15

    Purpose: To assess endo-bronchial electromagnetic beacon insertion and to quantify the geometric accuracy of using beacons as a surrogate for tumour motion in real-time multileaf collimator (MLC) tracking of lung tumours. Methods: The LIGHT SABR trial is a world-first clinical trial in which the MLC leaves move with lung tumours in real time on a standard linear accelerator. Tracking is performed based on implanted electromagnetic beacons (CalypsoTM, Varian Medical Systems, USA) as a surrogate for tumour motion. Five patients have been treated and have each had three beacons implanted endo-bronchially under fluoroscopic guidance. The centre of mass (C.O.M) has been used to adapt the MLC in real-time. The geometric error in using the beacon C.O.M as a surrogate for tumour motion was measured by measuring the tumour and beacon C.O.M in all phases of the respiratory cycle of a 4DCT. The surrogacy error was defined as the difference in beacon and tumour C.O.M relative to the reference phase (maximum exhale). Results: All five patients have had three beacons successfully implanted with no migration between simulation and end of treatment. Beacon placement relative to tumour C.O.M varied from 14 to 74 mm and in one patient spanned two lobes. Surrogacy error was measured in each patient on the simulation 4DCT and ranged from 0 to 3 mm. Surrogacy error as measured on 4DCT was subject to artefacts in mid-ventilation phases. Surrogacy error was a function of breathing phase and was typically larger at maximum inhale. Conclusion: Beacon placement and thus surrogacy error is a major component of geometric uncertainty in MLC tracking of lung tumours. Surrogacy error must be measured on each patient and incorporated into margin calculation. Reduction of surrogacy error is limited by airway anatomy, however should be taken into consideration when performing beacon insertion and planning. This research is funded by Varian Medical Systems via a collaborative research agreement.

  7. MO-FG-BRA-06: Electromagnetic Beacon Insertion in Lung Cancer Patients and Resultant Surrogacy Errors for Dynamic MLC Tumour Tracking

    International Nuclear Information System (INIS)

    Hardcastle, N; Booth, J; Caillet, V; Haddad, C; Crasta, C; O’Brien, R; Keall, P; Szymura, K

    2016-01-01

    Purpose: To assess endo-bronchial electromagnetic beacon insertion and to quantify the geometric accuracy of using beacons as a surrogate for tumour motion in real-time multileaf collimator (MLC) tracking of lung tumours. Methods: The LIGHT SABR trial is a world-first clinical trial in which the MLC leaves move with lung tumours in real time on a standard linear accelerator. Tracking is performed based on implanted electromagnetic beacons (CalypsoTM, Varian Medical Systems, USA) as a surrogate for tumour motion. Five patients have been treated and have each had three beacons implanted endo-bronchially under fluoroscopic guidance. The centre of mass (C.O.M) has been used to adapt the MLC in real-time. The geometric error in using the beacon C.O.M as a surrogate for tumour motion was measured by measuring the tumour and beacon C.O.M in all phases of the respiratory cycle of a 4DCT. The surrogacy error was defined as the difference in beacon and tumour C.O.M relative to the reference phase (maximum exhale). Results: All five patients have had three beacons successfully implanted with no migration between simulation and end of treatment. Beacon placement relative to tumour C.O.M varied from 14 to 74 mm and in one patient spanned two lobes. Surrogacy error was measured in each patient on the simulation 4DCT and ranged from 0 to 3 mm. Surrogacy error as measured on 4DCT was subject to artefacts in mid-ventilation phases. Surrogacy error was a function of breathing phase and was typically larger at maximum inhale. Conclusion: Beacon placement and thus surrogacy error is a major component of geometric uncertainty in MLC tracking of lung tumours. Surrogacy error must be measured on each patient and incorporated into margin calculation. Reduction of surrogacy error is limited by airway anatomy, however should be taken into consideration when performing beacon insertion and planning. This research is funded by Varian Medical Systems via a collaborative research agreement.

  8. Biomimetic polymers in analytical chemistry. Part 1: preparation and applications of MIP (Molecularly Imprinted Polymers) in extraction and separation techniques

    International Nuclear Information System (INIS)

    Tarley, Cesar Ricardo Teixeira; Sotomayor, Maria del Pilar Taboada; Kubota, Lauro Tatsuo

    2005-01-01

    MIPs are synthetic polymers that are used as biomimetic materials simulating the mechanism verified in natural entities such as antibodies and enzymes. Although MIPs have been successfully used as an outstanding tool for enhancing the selectivity or different analytical approaches, such as separation science and electrochemical and optical sensors, several parameters must be optimized during their synthesis. Therefore, the state-of-the-art of MIP production as well as the different polymerization methods are discussed. The potential selectivity of MIPs in the extraction and separation techniques focusing mainly on environmental, clinical and pharmaceutical samples as applications for analytical purposes is presented. (author)

  9. Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques

    DEFF Research Database (Denmark)

    Friis-Holm, Lotte Bjerrum; Engberg, R.M.; Leser, T.D.

    2006-01-01

    The microbial communities of the ileum and cecum of broiler chickens from a conventional and an organic farm were investigated using conventional culture techniques as well as cloning and sequencing of 16S rRNA genes. Eighty-five percent of the 557 cloned sequences were ...% of the cecal clones belonged to this cluster in conventional and organic broiler chickens, respectively. We were, however, able to recover a number of these phylotypes by cultivation, and the isolates were shown to be butyric acid producers. The investigation was a descriptive rather than a comparative study...

  10. Formation and properties of epitaxial CdSe, ZnSe quantum dots. Conventional molecular beam epitaxy and related techniques

    Energy Technology Data Exchange (ETDEWEB)

    Mahapatra, Suddhasatta

    2008-01-16

    This thesis systematically investigates three such alternative approaches, along with conventional MBE, with emphasis on the formation-mechanism of QDs, and optimization of their morphological and optical attributes. it is shown here that no distinct 3D islands are formed in MBE growth of CdSe on ZnSe. While CdSe heteroepitaxy occurs in the multilayer-mode at T{sub G}=300 C, a reentrant recovery of the layer-by-layer mode is reported in this thesis, for growth at T{sub G}<{proportional_to}240 C. In the second variant technique, formation of large and distinct islands is demonstrated by deposition of amorphous selenium (a-Se) onto a 2D CdSe epilayer at room temperature and its subsequent desorption at a higher temperature (T{sub D}=230 C). The process steps of the third variant technique, developed in course of this work, are very similar to those of the previous one-the only alteration being the substitution of selenium with tellurium as the cap-forming-material. (orig.)

  11. Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques.

    Science.gov (United States)

    Bjerrum, L; Engberg, R M; Leser, T D; Jensen, B B; Finster, K; Pedersen, K

    2006-07-01

    The microbial communities of the ileum and cecum of broiler chickens from a conventional and an organic farm were investigated using conventional culture techniques as well as cloning and sequencing of 16S rRNA genes. Eighty-five percent of the 557 cloned sequences were <97% related to known cultured species. The chicken ileum was dominated by lactobacilli, whereas the cecum harbored a more diverse microbial community. The cecum was dominated by a large group of bacteria with hitherto no close cultured relatives but most closely related to Faecalibacterium prausnitzii. Approximately 49 and 20% of the cecal clones belonged to this cluster in conventional and organic broiler chickens, respectively. We were, however, able to recover a number of these phylotypes by cultivation, and the isolates were shown to be butyric acid producers. The investigation was a descriptive rather than a comparative study of 2 different rearing systems; however, several differences were observed. For instance, Clostridium perfringens was found in significantly higher numbers in the birds from the organic farm compared with the conventional broilers, probably due to the addition of salinomycin to the conventional feed. In the ileum, the abundance of the different Lactobacillus species differed between the 2 broiler types. The culture-based and culture-independent techniques complemented each other well. Strengths and limitations of the different methods are discussed.

  12. Molecular Techniques Revealed Highly Diverse Microbial Communities in Natural Marine Biofilms on Polystyrene Dishes for Invertebrate Larval Settlement

    KAUST Repository

    Lee, On On

    2014-01-09

    Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members in the communities using traditional 16S rRNA gene-based molecular methods and in identifying the chemical signals involved. In this study, pyrosequencing was used to characterize the bacterial communities in intertidal and subtidal marine biofilms developed during two seasons. We revealed highly diverse biofilm bacterial communities that varied with season and tidal level. Over 3,000 operational taxonomic units with estimates of up to 8,000 species were recovered in a biofilm sample, which is by far the highest number recorded in subtropical marine biofilms. Nineteen phyla were found, of which Cyanobacteria and Proteobacteria were the most dominant one in the intertidal and subtidal biofilms, respectively. Apart from these, Actinobacteria, Bacteroidetes, and Planctomycetes were the major groups recovered in both intertidal and subtidal biofilms, although their relative abundance varied among samples. Full-length 16S rRNA gene clone libraries were constructed for the four biofilm samples and showed similar bacterial compositions at the phylum level to those revealed by pyrosequencing. Laboratory assays confirmed that cyrids of the barnacle Balanus amphitrite preferred to settle on the intertidal rather than subtidal biofilms. This preference was independent of the biofilm bacterial density or biomass but was probably related to the biofilm community structure, particularly, the Proteobacterial and Cyanobacterial groups. © 2014 Springer Science+Business Media New York.

  13. GaAsBi/GaAs multi-quantum well LED grown by molecular beam epitaxy using a two-substrate-temperature technique

    Science.gov (United States)

    Kisan Patil, Pallavi; Luna, Esperanza; Matsuda, Teruyoshi; Yamada, Kohki; Kamiya, Keisuke; Ishikawa, Fumitaro; Shimomura, Satoshi

    2017-03-01

    We report a GaAs0.96Bi0.04/GaAs multiple quantum well (MQW) light emitting diode (LED) grown by molecular beam epitaxy using a two-substrate-temperature (TST) technique. In particular, the QWs and the barriers in the intrinsic region were grown at the different temperatures of {T}{{GaAsBi}} = 350 °C and {T}{{GaAs}} = 550 ^\\circ {{C}}, respectively. Investigations of the microstructure using transmission electron microscopy (TEM) reveal homogeneous MQWs free of extended defects. Furthermore, the local determination of the Bi distribution profile across the MQWs region using TEM techniques confirm the uniform Bi distribution, while revealing a slightly chemically graded GaAs-on-GaAsBi interface due to Bi surface segregation. Despite this small broadening, we found that Bi segregation is significantly reduced (up to 18% reduction) compared to previous reports on Bi segregation in GaAsBi/GaAs MQWs. Hence, the TST procedure proves as a very efficient method to reduce Bi segregation and thus increase the quality of the layers and interfaces. These improvements positively reflect in the optical properties. Room temperature photoluminescence and electroluminescence (EL) at 1.23 μm emission wavelength are successfully demonstrated using TST MQWs containing less Bi content than in previous reports. Finally, LED fabricated using the present TST technique show current-voltage (I-V) curves with a forward voltage of 3.3 V at an injection current of 130 mA under 1.0 kA cm-2 current excitation. These results not only demonstrate that TST technique provides optical device quality GaAsBi/GaAs MQWs but highlight the relevance of TST-based growth techniques on the fabrication of future heterostructure devices based on dilute bismides.

  14. Electrospray ionization mass spectrometry: a technique to access the information beyond the molecular weight of the analyte.

    Science.gov (United States)

    Banerjee, Shibdas; Mazumdar, Shyamalava

    2012-01-01

    The Electrospray Ionization (ESI) is a soft ionization technique extensively used for production of gas phase ions (without fragmentation) of thermally labile large supramolecules. In the present review we have described the development of Electrospray Ionization mass spectrometry (ESI-MS) during the last 25 years in the study of various properties of different types of biological molecules. There have been extensive studies on the mechanism of formation of charged gaseous species by the ESI. Several groups have investigated the origin and implications of the multiple charge states of proteins observed in the ESI-mass spectra of the proteins. The charged analytes produced by ESI can be fragmented by activating them in the gas-phase, and thus tandem mass spectrometry has been developed, which provides very important insights on the structural properties of the molecule. The review will highlight recent developments and emerging directions in this fascinating area of research.

  15. Electrospray Ionization Mass Spectrometry: A Technique to Access the Information beyond the Molecular Weight of the Analyte

    Science.gov (United States)

    Banerjee, Shibdas; Mazumdar, Shyamalava

    2012-01-01

    The Electrospray Ionization (ESI) is a soft ionization technique extensively used for production of gas phase ions (without fragmentation) of thermally labile large supramolecules. In the present review we have described the development of Electrospray Ionization mass spectrometry (ESI-MS) during the last 25 years in the study of various properties of different types of biological molecules. There have been extensive studies on the mechanism of formation of charged gaseous species by the ESI. Several groups have investigated the origin and implications of the multiple charge states of proteins observed in the ESI-mass spectra of the proteins. The charged analytes produced by ESI can be fragmented by activating them in the gas-phase, and thus tandem mass spectrometry has been developed, which provides very important insights on the structural properties of the molecule. The review will highlight recent developments and emerging directions in this fascinating area of research. PMID:22611397

  16. Formation and properties of epitaxial CdSe, ZnSe quantum dots. Conventional molecular beam epitaxy and related techniques

    International Nuclear Information System (INIS)

    Mahapatra, Suddhasatta

    2008-01-01

    This thesis systematically investigates three such alternative approaches, along with conventional MBE, with emphasis on the formation-mechanism of QDs, and optimization of their morphological and optical attributes. it is shown here that no distinct 3D islands are formed in MBE growth of CdSe on ZnSe. While CdSe heteroepitaxy occurs in the multilayer-mode at T G =300 C, a reentrant recovery of the layer-by-layer mode is reported in this thesis, for growth at T G D =230 C). The process steps of the third variant technique, developed in course of this work, are very similar to those of the previous one-the only alteration being the substitution of selenium with tellurium as the cap-forming-material. (orig.)

  17. Design of a K/Q-Band Beacon Receiver for the Alphasat Technology Demonstration Payload (TDP) #5 Experiment

    Science.gov (United States)

    Morse, Jacquelynne R.

    2014-01-01

    This paper describes the design and performance of a coherent KQ-band (2040 GHz) beacon receiver developed at NASA Glenn Research Center (GRC) that will be installed at the Politecnico di Milano (POLIMI) for use in the Alphasat Technology Demonstration Payload 5 (TDP5) beacon experiment. The goal of this experiment is to characterize rain fade attenuation at 40 GHz to improve the performance of existing statistical rain attenuation models in the Q-band. The ground terminal developed by NASA GRC utilizes an FFT-based frequency estimation receiver capable of characterizing total path attenuation effects due to gaseous absorption, clouds, rain, and scintillation. The receiver system has been characterized in the lab and demonstrates a system dynamic range performance of better than 58 dB at 1 Hz and better than 48 dB at 10 Hz rates.

  18. Diagnosis of Familial Wolf-Hirschhorn Syndrome due to a Paternal Cryptic Chromosomal Rearrangement by Conventional and Molecular Cytogenetic Techniques

    Directory of Open Access Journals (Sweden)

    Carlos A. Venegas-Vega

    2013-01-01

    Full Text Available The use of conventional cytogenetic techniques in combination with fluorescent in situ hybridization (FISH and single-nucleotide polymorphism (SNP microarrays is necessary for the identification of cryptic rearrangements in the diagnosis of chromosomal syndromes. We report two siblings, a boy of 9 years and 9 months of age and his 7-years- and 5-month-old sister, with the classic Wolf-Hirschhorn syndrome (WHS phenotype. Using high-resolution GTG- and NOR-banding karyotypes, as well as FISH analysis, we characterized a pure 4p deletion in both sibs and a balanced rearrangement in their father, consisting in an insertion of 4p material within a nucleolar organizing region of chromosome 15. Copy number variant (CNV analysis using SNP arrays showed that both siblings have a similar size of 4p deletion (~6.5 Mb. Our results strongly support the need for conventional cytogenetic and FISH analysis, as well as high-density microarray mapping for the optimal characterization of the genetic imbalance in patients with WHS; parents must always be studied for recognizing cryptic balanced chromosomal rearrangements for an adequate genetic counseling.

  19. Diagnosis of Familial Wolf-Hirschhorn Syndrome due to a Paternal Cryptic Chromosomal Rearrangement by Conventional and Molecular Cytogenetic Techniques

    Science.gov (United States)

    Venegas-Vega, Carlos A.; Zepeda, Luis M.; Garduño-Zarazúa, Luz M.; Berumen, Jaime; Kofman, Susana; Cervantes, Alicia

    2013-01-01

    The use of conventional cytogenetic techniques in combination with fluorescent in situ hybridization (FISH) and single-nucleotide polymorphism (SNP) microarrays is necessary for the identification of cryptic rearrangements in the diagnosis of chromosomal syndromes. We report two siblings, a boy of 9 years and 9 months of age and his 7-years- and 5-month-old sister, with the classic Wolf-Hirschhorn syndrome (WHS) phenotype. Using high-resolution GTG- and NOR-banding karyotypes, as well as FISH analysis, we characterized a pure 4p deletion in both sibs and a balanced rearrangement in their father, consisting in an insertion of 4p material within a nucleolar organizing region of chromosome 15. Copy number variant (CNV) analysis using SNP arrays showed that both siblings have a similar size of 4p deletion (~6.5 Mb). Our results strongly support the need for conventional cytogenetic and FISH analysis, as well as high-density microarray mapping for the optimal characterization of the genetic imbalance in patients with WHS; parents must always be studied for recognizing cryptic balanced chromosomal rearrangements for an adequate genetic counseling. PMID:23484094

  20. Isolation of methanotrophic bacteria from a london landfill: a preliminary study using molecular and stable isotopic techniques.

    Science.gov (United States)

    Sriskantharajah, S.; Cutting, S.; Lowry, D.; Grassineau, N.; Nisbet, E.

    2003-04-01

    Methane emissions from landfills are an important source of European greenhouse emissions, and could be reduced by a biological management program that used methanotrophs in landfill cover soils. Topsoil samples taken from a London Landfill were incubated on Nitrate Mineral Salts medium in the presence of methane. The resulting colonies were probed for methanotrophic DNA using PCR amplification. DNA from methanotroph positive colonies was cloned and sequenced for identification. Isolates belonging to the genera Methylocaldum, Methylomonas and Methylosinus were detected. Phylogenetic analysis suggests the presence of possible new species. In addition dried samples of the isolates were analysed for their stable carbon isotope (δ 13C) composition. The results were δ 13C values of -27 per mil and -25 per mil for Methylomonas isolates, -35 per mil and -44 per mil for Methylosinus isolates, -58 per mil and -60 per mil for some of the Methylocaldum isolates and -35 per mil and -45 per mil for the others. This isotopic variation is reflected in a phylogenetic tree of the isolates. The differences shown in the δ 13C analysis could be due to differing biochemical properties, and if the technique is further developed, it may be used for rapid identification of bacteria useful in landfill management for reducing methane emissions. The results suggest that useful reductions in methane emissions could be achieved by a careful design of landfill cover to culture methanotrophs.

  1. A case study of pediatric asthma alerts from the beacon community program in cincinnati: technology is just the first step.

    Science.gov (United States)

    Trudnak, Tara; Mansour, Mona; Mandel, Keith; Sauers, Hadley; Pandzik, Gerry; Donisi, Carl; Fairbrother, Gerry

    2014-01-01

    The Beacon Community in Cincinnati, Ohio was an innovative, community-wide initiative to use technology to transform care. One important feature was the development of regional alerts to notify practices when patients were hospitalized or seen in the emergency department. The purpose of this paper is to describe the way in which technology engages the improvement process, and to describe the early stages of learning how to use technology to enhance quality improvement. We interviewed key Beacon leaders as well as providers and office staff in selected practices. We also collected preliminary data from practices that reflected handling of alerts, including the number of asthma related alerts received and followed up. Regional alerts, supplied by the community-wide health information exchange, were a significant addition to the quality improvement effort in that they enabled practices to identify and follow up with additional children at risk. An important finding was the substantial effort at the practice level to integrate technology into ongoing patient care. Developing the technology for community wide alerts represented a significant endeavor in the Cincinnati Beacon Community. However, the technology was just the first step. Despite extra effort and time required on the part of individual practices, they reported that the value of having alerts was high. Hospital and ED visits represent some of the most costly aspects of care, and an efficient process for intervening with children using these costly services was seen as of significant value.

  2. Exploring pyrazolo[3,4-d]pyrimidine phosphodiesterase 1 (PDE1) inhibitors: a predictive approach combining comparative validated multiple molecular modelling techniques.

    Science.gov (United States)

    Amin, Sk Abdul; Bhargava, Sonam; Adhikari, Nilanjan; Gayen, Shovanlal; Jha, Tarun

    2018-02-01

    Phosphodiesterase 1 (PDE1) is a potential target for a number of neurodegenerative disorders such as Schizophrenia, Parkinson's and Alzheimer's diseases. A number of pyrazolo[3,4-d]pyrimidine PDE1 inhibitors were subjected to different molecular modelling techniques [such as regression-based quantitative structure-activity relationship (QSAR): multiple linear regression, support vector machine and artificial neural network; classification-based QSAR: Bayesian modelling and Recursive partitioning; Monte Carlo based QSAR; Open3DQSAR; pharmacophore mapping and molecular docking analyses] to get a detailed knowledge about the physicochemical and structural requirements for higher inhibitory activity. The planarity of the pyrimidinone ring plays an important role for PDE1 inhibition. The N-methylated function at the 5th position of the pyrazolo[3,4-d]pyrimidine core is required for interacting with the PDE1 enzyme. The cyclopentyl ring fused with the parent scaffold is necessary for PDE1 binding potency. The phenylamino substitution at 3rd position is crucial for PDE1 inhibition. The N2-substitution at the pyrazole moiety is important for PDE1 inhibition compared to the N1-substituted analogues. Moreover, the p-substituted benzyl side chain at N2-position helps to enhance the PDE1 inhibitory profile. Depending on these observations, some new molecules are predicted that may possess better PDE1 inhibition.

  3. A Semester-Long Project for Teaching Basic Techniques in Molecular Biology Such as Restriction Fragment Length Polymorphism Analysis to Undergraduate and Graduate Students

    Science.gov (United States)

    DiBartolomeis, Susan M.

    2011-01-01

    Several reports on science education suggest that students at all levels learn better if they are immersed in a project that is long term, yielding results that require analysis and interpretation. I describe a 12-wk laboratory project suitable for upper-level undergraduates and first-year graduate students, in which the students molecularly locate and map a gene from Drosophila melanogaster called dusky and one of dusky's mutant alleles. The mapping strategy uses restriction fragment length polymorphism analysis; hence, students perform most of the basic techniques of molecular biology (DNA isolation, restriction enzyme digestion and mapping, plasmid vector subcloning, agarose and polyacrylamide gel electrophoresis, DNA labeling, and Southern hybridization) toward the single goal of characterizing dusky and the mutant allele dusky73. Students work as individuals, pairs, or in groups of up to four students. Some exercises require multitasking and collaboration between groups. Finally, results from everyone in the class are required for the final analysis. Results of pre- and postquizzes and surveys indicate that student knowledge of appropriate topics and skills increased significantly, students felt more confident in the laboratory, and students found the laboratory project interesting and challenging. Former students report that the lab was useful in their careers. PMID:21364104

  4. DNA: Polymer and molecular code

    Science.gov (United States)

    Shivashankar, G. V.

    1999-10-01

    The thesis work focusses upon two aspects of DNA, the polymer and the molecular code. Our approach was to bring single molecule micromanipulation methods to the study of DNA. It included a home built optical microscope combined with an atomic force microscope and an optical tweezer. This combined approach led to a novel method to graft a single DNA molecule onto a force cantilever using the optical tweezer and local heating. With this method, a force versus extension assay of double stranded DNA was realized. The resolution was about 10 picoN. To improve on this force measurement resolution, a simple light backscattering technique was developed and used to probe the DNA polymer flexibility and its fluctuations. It combined the optical tweezer to trap a DNA tethered bead and the laser backscattering to detect the beads Brownian fluctuations. With this technique the resolution was about 0.1 picoN with a millisecond access time, and the whole entropic part of the DNA force-extension was measured. With this experimental strategy, we measured the polymerization of the protein RecA on an isolated double stranded DNA. We observed the progressive decoration of RecA on the l DNA molecule, which results in the extension of l , due to unwinding of the double helix. The dynamics of polymerization, the resulting change in the DNA entropic elasticity and the role of ATP hydrolysis were the main parts of the study. A simple model for RecA assembly on DNA was proposed. This work presents a first step in the study of genetic recombination. Recently we have started a study of equilibrium binding which utilizes fluorescence polarization methods to probe the polymerization of RecA on single stranded DNA. In addition to the study of material properties of DNA and DNA-RecA, we have developed experiments for which the code of the DNA is central. We studied one aspect of DNA as a molecular code, using different techniques. In particular the programmatic use of template specificity makes

  5. Nanosecond pulsed electric field incorporation technique to predict molecular mechanisms of teratogenicity and developmental toxicity of estradiol-17β on medaka embryos.

    Science.gov (United States)

    Yamaguchi, Akemi; Ishibashi, Hiroshi; Kono, Susumu; Iida, Midori; Uchida, Masaya; Arizono, Koji; Tominaga, Nobuaki

    2018-05-01

    Herein, we propose using a nanosecond pulsed electric field (nsPEF) technique to assess teratogenicity and embryonic developmental toxicity of estradiol-17β (E 2 ) and predict the molecular mechanisms of teratogenicity and embryonic developmental defects caused by E 2 on medaka (Oryzias latipes). The 5 hour post-fertilization embryos were exposed to co-treatment with 10 μm E 2 and nsPEF for 2 hours and then continuously cultured under non-E 2 and nsPEF conditions until hatching. Results documented that the time to hatching of embryos was significantly delayed in comparison to the control group and that typical abnormal embryo development, such as the delay of blood vessel formation, was observed. For DNA microarray analysis, 6 day post-fertilization embryos that had been continuously cultured under the non-E 2 and nsPEF condition after 2 hour co-treatments were used. DNA microarray analysis identified 542 upregulated genes and one downregulated gene in the 6 day post-fertilization embryos. Furthermore, bioinformatic analyses using differentially expressed genes revealed that E 2 exposure affected various gene ontology terms, such as response to hormone stimulus. The network analysis also documented that the estrogen receptor α in the mitogen-activated protein kinase signaling pathway may be involved in regulating several transcription factors, such as FOX, AKT1 and epidermal growth factor receptor. These results suggest that our nsPEF technique is a powerful tool for assessing teratogenicity and embryonic developmental toxicity of E 2 and predict their molecular mechanisms in medaka embryos. Copyright © 2017 John Wiley & Sons, Ltd.

  6. A quantum dot-aptamer beacon using a DNA intercalating dye as the FRET reporter: application to label-free thrombin detection.

    Science.gov (United States)

    Chi, Chun-Wei; Lao, Yeh-Hsing; Li, Yi-Shan; Chen, Lin-Chi

    2011-03-15

    A new quantum dot (QD)-aptamer (apt) beacon that acts by folding-induced dissociation of a DNA intercalating dye, BOBO-3(B), is demonstrated with label-free thrombin detection. The beacon, denoted as QD-apt:B, is constructed by (1) coupling of a single-stranded thrombin aptamer to Qdot 565 via EDC/Sulfo-NHS chemistry and (2) staining the duplex regions of the aptamer on QD with excess BOBO-3 before thrombin binding. When mixing a thrombin sample with QD-apt:B, BOBO-3 is competed away from the beacon due to target-induced aptamer folding, which then causes a decrease in QD fluorescence resonance energy transfer (FRET)-mediated BOBO-3 emission and achieves thrombin quantitation. In this work, the effects of Mg(2+), coupling time, and aptamer type on the beacon's performances are investigated and discussed thoroughly with various methods, including transmission electron microscopy (TEM), dynamic light scattering (DLS), and two-color differential gel electrophoresis. Using the best aptamer beacon (HTQ37), we attain highly specific and wide-range detection (from nM to μM) of thrombin in buffer, and the beacon can sense nM-range thrombin in 15% diluted serum. Compared to the reported QD aptamer assays, our method is advantageous from the aspect of using a simple sensory unit design without losing the detection sensitivity. Therefore, we consider the QD-apt:B beacon a potential alternative to immuno-reagents and an effective tool to study nucleic acid folding on QD as well. Copyright © 2011 Elsevier B.V. All rights reserved.

  7. Progress on molecular imaging

    International Nuclear Information System (INIS)

    Chen Quan; Zhang Yongxue

    2011-01-01

    Molecular imaging is a new era of medical imaging,which can non-invasively monitor biological processes at the cellular and molecular level in vivo, including molecular imaging of nuclear medicine, magnetic resonance molecular imaging, ultrasound molecular imaging,optical molecular imaging and molecular imaging with X-ray. Recently, with the development of multi-subjects amalgamation, multimodal molecular imaging technology has been applied in clinical imaging, such as PET-CT and PET-MRI. We believe that with development of molecular probe and multi-modal imaging, more and more molecular imaging techniques will be applied in clinical diagnosis and treatment. (authors)

  8. Application of molecular cytogenetic techniques to clarify apparently balanced complex chromosomal rearrangements in two patients with an abnormal phenotype: case report

    Directory of Open Access Journals (Sweden)

    Rongen Michel A

    2009-07-01

    Full Text Available Abstract Background Complex chromosomal rearrangements (CCR are rare cytogenetic findings that are difficult to karyotype by conventional cytogenetic analysis partially because of the relative low resolution of this technique. High resolution genotyping is necessary in order to identify cryptic imbalances, for instance near the multiple breakpoints, to explain the abnormal phenotype in these patients. We applied several molecular techniques to elucidate the complexity of the CCRs of two adult patients with abnormal phenotypes. Results Multicolour fluorescence in situ hybridization (M-FISH showed that in patient 1 the chromosomes 1, 10, 15 and 18 were involved in the rearrangement whereas for patient 2 the chromosomes 5, 9, 11 and 13 were involved. A 250 k Nsp1 SNP-array analysis uncovered a deletion in chromosome region 10p13 for patient 1, harbouring 17 genes, while patient 2 showed no pathogenic gains or losses. Additional FISH analysis with locus specific BAC-probes was performed, leading to the identification of cryptic interstitial structural rearrangements in both patients. Conclusion Application of M-FISH and SNP-array analysis to apparently balanced CCRs is useful to delineate the complex chromosomal rearrangement in detail. However, it does not always identify cryptic imbalances as an explanation for the abnormal phenotype in patients with a CCR.

  9. Introducing Thermal Wave Transport Analysis (TWTA): A Thermal Technique for Dopamine Detection by Screen-Printed Electrodes Functionalized with Molecularly Imprinted Polymer (MIP) Particles.

    Science.gov (United States)

    Peeters, Marloes M; van Grinsven, Bart; Foster, Christopher W; Cleij, Thomas J; Banks, Craig E

    2016-04-26

    A novel procedure is developed for producing bulk modified Molecularly Imprinted Polymer (MIP) screen-printed electrodes (SPEs), which involves the direct mixing of the polymer particles within the screen-printed ink. This allowed reduction of the sample preparation time from 45 min to 1 min, and resulted in higher reproducibility of the electrodes. The samples are measured with a novel detection method, namely, thermal wave transport analysis (TWTA), relying on the analysis of thermal waves through a functional interface. As a first proof-of-principle, MIPs for dopamine are developed and successfully incorporated within a bulk modified MIP SPE. The detection limits of dopamine within buffer solutions for the MIP SPEs are determined via three independent techniques. With cyclic voltammetry this was determined to be 4.7 × 10(-6) M, whereas by using the heat-transfer method (HTM) 0.35 × 10(-6) M was obtained, and with the novel TWTA concept 0.26 × 10(-6) M is possible. This TWTA technique is measured simultaneously with HTM and has the benefits of reducing measurement time to less than 5 min and increasing effect size by nearly a factor of two. The two thermal methods are able to enhance dopamine detection by one order of magnitude compared to the electrochemical method. In previous research, it was not possible to measure neurotransmitters in complex samples with HTM, but with the improved signal-to-noise of TWTA for the first time, spiked dopamine concentrations were determined in a relevant food sample. In summary, novel concepts are presented for both the sensor functionalization side by employing screen-printing technology, and on the sensing side, the novel TWTA thermal technique is reported. The developed bio-sensing platform is cost-effective and suitable for mass-production due to the nature of screen-printing technology, which makes it very interesting for neurotransmitter detection in clinical diagnostic applications.

  10. Space Weather Operation at KASI With Van Allen Probes Beacon Signals

    Science.gov (United States)

    Lee, Jongkil; Kim, Kyung-Chan; Giuseppe, Romeo; Ukhorskiy, Sasha; Sibeck, David; Kessel, Ramona; Mauk, Barry; Giles, Barbara; Gu, Bon-Jun; Lee, Hyesook; Park, Young-Deuk; Lee, Jaejin

    2018-02-01

    The Van Allen Probes (VAPs) are the only modern National Aeronautics and Space Administration (NASA) spacecraft broadcasting real-time data on the Earth's radiation belts for space weather operations. Since 2012, the Korea Astronomy and Space Science Institute (KASI) has contributed to the receipt of these data via a 7 m satellite-tracking antenna and used these beacon data for space weather operations. An approximately 15 min period is required from measurement to acquisition of Level-1 data. In this paper, we demonstrate the use of VAP data for monitoring space weather conditions at geostationary orbit (GEO) by highlighting the Saint Patrick's Day storm of 2015. During that storm, Probe-A observed a significant increase in the relativistic electron flux at 3 RE. Those electrons diffused outward resulting in a large increase of the electron flux >2 MeV at GEO, which potentially threatened satellite operations. Based on this study, we conclude that the combination of VAP data and National Oceanic and Atmospheric Administration-Geostationary Operational Environmental Satellite (NOAA-GOES) data can provide improved space environment information to geostationary satellite operators. In addition, the findings obtained indicate that more data-receiving sites would be necessary and data connections improved if this or a similar system were to be used as an operational data service.

  11. The Inversion of Ionospheric/plasmaspheric Electron Density From GPS Beacon Observations

    Science.gov (United States)

    Zou, Y. H.; Xu, J. S.; Ma, S. Y.

    It is a space-time 4-D tomography to reconstruct ionospheric/ plasmaspheric elec- tron density, Ne, from ground-based GPS beacon measurements. The mathematical foundation of such inversion is studied in this paper and some simulation results of reconstruction for GPS network observation are presented. Assuming reasonably a power law dependence of NE on time with an index number of 1-3 during one ob- servational time of GPS (60-90min.), 4-D inversion in consideration is reduced to a 3-D cone-beam tomography with incomplete projections. To see clearly the effects of the incompleteness on the quality of reconstruction for 3-D condition, we deduced theoretically the formulae of 3-D parallel-beam tomography. After establishing the mathematical basis, we adopt linear temporal dependence of NE and voxel elemental functions to perform simulation of NE reconstruction with the help of IRI90 model. Reasonable time-dependent 3-D images of ionosphere/ plasmasphere electron density distributions are obtained when taking proper layout of the GPS network and allowing variable resolutions in vertical.

  12. Learning from Health Information Exchange Technical Architecture and Implementation in Seven Beacon Communities

    Science.gov (United States)

    McCarthy, Douglas B.; Propp, Karen; Cohen, Alexander; Sabharwal, Raj; Schachter, Abigail A.; Rein, Alison L.

    2014-01-01

    As health care providers adopt and make “meaningful use” of health information technology (health IT), communities and delivery systems must set up the infrastructure to facilitate health information exchange (HIE) between providers and numerous other stakeholders who have a role in supporting health and care. By facilitating better communication and coordination between providers, HIE has the potential to improve clinical decision-making and continuity of care, while reducing unnecessary use of services. When implemented as part of a broader strategy for health care delivery system and payment reform, HIE capability also can enable the use of analytic tools needed for population health management, patient engagement in care, and continuous learning and improvement. The diverse experiences of seven communities that participated in the three-year federal Beacon Community Program offer practical insight into factors influencing the technical architecture of exchange infrastructure and its role in supporting improved care, reduced cost, and a healthier population. The case studies also document challenges faced by the communities, such as significant time and resources required to harmonize variations in the interpretation of data standards. Findings indicate that their progress developing community-based HIE strategies, while driven by local needs and objectives, is also influenced by broader legal, policy, and market conditions. PMID:25848591

  13. The Keys to Governance and Stakeholder Engagement: The Southeast Michigan Beacon Community Case Study

    Science.gov (United States)

    Des Jardins, Terrisca R.

    2014-01-01

    Community-based health information exchanges (HIEs) and efforts to consolidate and house data are growing, given the advent of Accountable Care Organizations (ACOs) under the Affordable Care Act and other similar population health focused initiatives. The Southeast Michigan Beacon Community (SEMBC) can be looked to as one case study that offers lessons learned, insights on challenges faced and accompanying workarounds related to governance and stakeholder engagement. The SEMBC case study employs an established Data Warehouse Governance Framework to identify and explain the necessary governance and stakeholder engagement components, particularly as they relate to community-wide data sharing and data warehouses or repositories. Perhaps the biggest lesson learned through the SEMBC experience is that community-based work is hard. It requires a great deal of community leadership, collaboration and resources. SEMBC found that organizational structure and guiding principles needed to be continually revisited and nurtured in order to build the relationships and trust needed among stakeholder organizations. SEMBC also found that risks and risk mitigation tactics presented challenges and opportunities at the outset and through the duration of the three year pilot period. Other communities across the country embarking on similar efforts need to consider realistic expectations about community data sharing infrastructures and the accompanying and necessary governance and stakeholder engagement fundamentals. PMID:25848612

  14. Modified beacon probe assisted dual signal amplification for visual detection of microRNA.

    Science.gov (United States)

    Sun, Xiuwei; Ying, Na; Ju, Chuanjing; Li, Zhongyi; Xu, Na; Qu, Guijuan; Liu, Wensen; Wan, Jiayu

    2018-04-21

    In a recent study, we reported a novel assay for the detection of microRNA-21 based on duplex-specific nuclease (DSN)-assisted isothermal cleavage and hybridization chain reaction (HCR) dual signal amplification. The Fam modified double-stranded DNA products were generated after the HCR, another biotin modified probe was digested by DSN and released from the magnetic beads after the addition of the target miRNA. The released sequence was then combined with HCR products to form a double-tagging dsDNA, which can be recognized by the lateral flow strips. In this study, we introduced a 2-OMethyl-RNA modified beacon probe (2-OMe-MB) to make some improvements based on the previous study. Firstly, the substitution of modified probe combined on magnetic beads avoids the fussy washing steps for the separation of un-reacted probes. Furthermore, the modification of 2-OMe on the stem of the probe avoided the unnecessary cleavage by DSN, which greatly reduce the background signal. Compared to the previous work, these improvements save us a lot of steps but possess the comparable sensitivity and selectivity. Copyright © 2018 Elsevier Inc. All rights reserved.

  15. Observations of inner plasmasphere irregularities with a satellite-beacon radio-interferometer array

    International Nuclear Information System (INIS)

    Jacobson, A.R.; Hoogeveen, G.; Carlos, R.C.; Wu, G.; Fejer, B.G.; Kelley, M.C.

    1996-01-01

    A radio-interferometer array illuminated by 136-MHz beacons of several geosynchronous satellites has been used to study small (≥10 13 m -2 ) transient disturbances in the total electron content along the lines of sight to the satellites. High-frequency (f>3 mHz) electron content oscillations are persistently observed, particularly during night and particularly during geomagnetically disturbed periods. The oscillations move across the array plane at speeds in the range 200 endash 2000 m/s, with propagation azimuths that are strongly peaked in lobes toward the western half-plane. Detailed analysis of this azimuth behavior, involving comparison between observations on various satellite positions, indicates compellingly that the phase oscillations originate in radio refraction due to geomagnetically aligned plasma density perturbations in the inner plasmasphere. The motion of the phase perturbations across the array plane is caused by EXB drift of the plasma medium in which the irregularities are embedded. We review the statistics of 2.5 years of around-the-clock data on the local time, magnetic disturbance, seasonal, and line-of-sight variations of these observed irregularities. We compare the irregularities close-quote inferred electrodynamic drifts to what is known about midlatitude plasma drift from incoherent scatter. Finally, we show in detail how the observation of these irregularities provides a unique and complementary monitor of inner plasmasphere irregularity incidence and zonal drift.copyright 1996 American Geophysical Union

  16. Outage Probability Analysis in Power-Beacon Assisted Energy Harvesting Cognitive Relay Wireless Networks

    Directory of Open Access Journals (Sweden)

    Ngoc Phuc Le

    2017-01-01

    Full Text Available We study the performance of the secondary relay system in a power-beacon (PB assisted energy harvesting cognitive relay wireless network. In our system model, a secondary source node and a relay node first harvest energy from distributed PBs. Then, the source node transmits its data to the destination node with the help of the relay node. Also, fading coefficients of the links from the PBs to the source node and relay node are assumed independent but not necessarily identically distributed (i.n.i.d Nakagami-m random variables. We derive exact expressions for the power outage probability and the channel outage probability. Based on that, we analyze the total outage probability of the secondary relay system. Asymptotic analysis is also performed, which provides insights into the system behavior. Moreover, we evaluate impacts of the primary network on the performance of the secondary network with respect to the tolerant interference threshold at the primary receiver as well as the interference introduced by the primary transmitter at the secondary source and relay nodes. Simulation results are provided to validate the analysis.

  17. Learning from health information exchange technical architecture and implementation in seven beacon communities.

    Science.gov (United States)

    McCarthy, Douglas B; Propp, Karen; Cohen, Alexander; Sabharwal, Raj; Schachter, Abigail A; Rein, Alison L

    2014-01-01

    As health care providers adopt and make "meaningful use" of health information technology (health IT), communities and delivery systems must set up the infrastructure to facilitate health information exchange (HIE) between providers and numerous other stakeholders who have a role in supporting health and care. By facilitating better communication and coordination between providers, HIE has the potential to improve clinical decision-making and continuity of care, while reducing unnecessary use of services. When implemented as part of a broader strategy for health care delivery system and payment reform, HIE capability also can enable the use of analytic tools needed for population health management, patient engagement in care, and continuous learning and improvement. The diverse experiences of seven communities that participated in the three-year federal Beacon Community Program offer practical insight into factors influencing the technical architecture of exchange infrastructure and its role in supporting improved care, reduced cost, and a healthier population. The case studies also document challenges faced by the communities, such as significant time and resources required to harmonize variations in the interpretation of data standards. Findings indicate that their progress developing community-based HIE strategies, while driven by local needs and objectives, is also influenced by broader legal, policy, and market conditions.

  18. The keys to governance and stakeholder engagement: the southeast michigan beacon community case study.

    Science.gov (United States)

    Des Jardins, Terrisca R

    2014-01-01

    Community-based health information exchanges (HIEs) and efforts to consolidate and house data are growing, given the advent of Accountable Care Organizations (ACOs) under the Affordable Care Act and other similar population health focused initiatives. The Southeast Michigan Beacon Community (SEMBC) can be looked to as one case study that offers lessons learned, insights on challenges faced and accompanying workarounds related to governance and stakeholder engagement. The SEMBC case study employs an established Data Warehouse Governance Framework to identify and explain the necessary governance and stakeholder engagement components, particularly as they relate to community-wide data sharing and data warehouses or repositories. Perhaps the biggest lesson learned through the SEMBC experience is that community-based work is hard. It requires a great deal of community leadership, collaboration and resources. SEMBC found that organizational structure and guiding principles needed to be continually revisited and nurtured in order to build the relationships and trust needed among stakeholder organizations. SEMBC also found that risks and risk mitigation tactics presented challenges and opportunities at the outset and through the duration of the three year pilot period. Other communities across the country embarking on similar efforts need to consider realistic expectations about community data sharing infrastructures and the accompanying and necessary governance and stakeholder engagement fundamentals.

  19. VLC-beacon detection with an under-sampled ambient light sensor

    Science.gov (United States)

    Green, Jacob; Pérez-Olivas, Huetzin; Martínez-Díaz, Saúl; García-Márquez, Jorge; Domínguez-González, Carlos; Santiago-Montero, Raúl; Guan, Hongyu; Rozenblat, Marc; Topsu, Suat

    2017-08-01

    LEDs will replace in a near future the current worldwide lighting mainly due to their low production-cost and energy-saving assets. Visible light communications (VLC) will turn gradually the existing lighting network into a communication network. Nowadays VLC transceivers can be found in some commercial centres in Europe; some of them broadcast continuously an identification tag that contains its coordinate position. In such a case, the transceiver acts as a geolocation beacon. Nevertheless, mobile transceivers represent a challenge in the VLC communication chain, as smartphones have not integrated yet a VLC customized detection stage. In order to make current smartphones capable to detect VLC broadcasted signals, their Ambient Light Sensor (ALS) is adapted as a VLC detector. For this to be achieved, lighting transceivers need to adapt their modulation scheme. For instance, frequencies representing start bit, 1, and 0 logic values can be set to avoid flicker from illumination and to permit detecting the under-sampled signal. Decoding the signal requires a multiple steps real-time signal processing as shown here.

  20. Implications of recent research on microstructure modifications, through heat-related processing and trait alteration to bio-functions, molecular thermal stability and mobility, metabolic characteristics and nutrition in cool-climate cereal grains and other types of seeds with advanced molecular techniques.

    Science.gov (United States)

    Ying, Yuguang; Zhang, Huihua; Yu, Peiqiang

    2018-02-16

    The cutting-edge synchrotron radiation based and globar-sourced vibrational infrared microspectroscopy have recently been developed. These novel techniques are able to reveal structure features at cellular and molecular levels with the tested tissues being intact. However, to date, the advanced techniques are unfamiliar or unknown to food and feed scientists and have not been used to study the molecular structure changes in cool-climate cereal grain seeds and other types of bio-oil and bioenergy seeds. This article aims to provide some recent research in cool-climate cereal grains and other types of seeds on molecular structures and metabolic characteristics of carbohydrate and protein, and implication of microstructure modification through heat-related processing and trait alteration to bio-functions, molecular thermal stability and mobility, and nutrition with advanced molecular techniques- synchrotron radiation based and globar-sourced vibrational infrared microspectroscopy in the areas of (1) Inherent microstructure of cereal grain seeds; (2) The nutritional values of cereal grains; (3) Impact and modification of heat-related processing to cereal grain; (4) Conventional nutrition evaluation methodology; (5) Synchrotron radiation-based and globar-sourced vibrational (micro)-spectroscopy for molecular structure study and molecular thermal stability and mobility, and (6) Recent molecular spectroscopic technique applications in research on raw, traits altered and processed cool-climate cereal grains and other types of seeds. The information described in this article gives better insights of research progress and update in cool-climate cereal grains and other seeds with advanced molecular techniques.