Relevant bibliographies by topics / Polymerase chain reaction (PCR)

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Polymerase chain reaction (PCR)'

Author: Grafiati
Published: 4 June 2021
Last updated: 7 September 2023

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Journal articles on the topic "Polymerase chain reaction (PCR)"

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INABA, Hiroshi. "Polymerase chain reaction (PCR)." Blood & Vessel 20, no. 4 (1989): 365–67. http://dx.doi.org/10.2491/jjsth1970.20.365.

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YAMADA, Akira, Jiro IMANISHI, and Etsuro NAKAJIMA. "Detection of Influenza Virus with PCR (Polymerase Chain Reaction)." Journal of the Japanese Association for Infectious Diseases 65, no. 6 (1991): 759–60. http://dx.doi.org/10.11150/kansenshogakuzasshi1970.65.759.

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Prosser, Jane. "PCR The polymerase chain reaction." Trends in Biotechnology 12, no. 12 (December 1994): 521–22. http://dx.doi.org/10.1016/0167-7799(94)90063-9.

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McCorquodale, D. James. "PCR: the polymerase chain reaction." Trends in Endocrinology & Metabolism 6, no. 3 (April 1995): 107. http://dx.doi.org/10.1016/1043-2760(95)90019-5.

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Green, Michael R., and Joseph Sambrook. "Touchdown Polymerase Chain Reaction (PCR)." Cold Spring Harbor Protocols 2018, no. 5 (May 2018): pdb.prot095133. http://dx.doi.org/10.1101/pdb.prot095133.

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Green, Michael R., and Joseph Sambrook. "Inverse Polymerase Chain Reaction (PCR)." Cold Spring Harbor Protocols 2019, no. 2 (February 2019): pdb.prot095166. http://dx.doi.org/10.1101/pdb.prot095166.

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Green, Michael R., and Joseph Sambrook. "Nested Polymerase Chain Reaction (PCR)." Cold Spring Harbor Protocols 2019, no. 2 (February 2019): pdb.prot095182. http://dx.doi.org/10.1101/pdb.prot095182.

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Danilova, V. M., O. P. Matyshevska, and S. V. Komisarenko. "Nobel Prize laureate Kary Mullis and the polymerase chain reaction (PCR)." Ukrainian Biochemical Journal 93, no. 5 (November 3, 2021): 122–31. http://dx.doi.org/10.15407/ubj93.05.122.

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McInerney, Peter, Paul Adams, and Masood Z. Hadi. "Error Rate Comparison during Polymerase Chain Reaction by DNA Polymerase." Molecular Biology International 2014 (August 17, 2014): 1–8. http://dx.doi.org/10.1155/2014/287430.

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As larger-scale cloning projects become more prevalent, there is an increasing need for comparisons among high fidelity DNA polymerases used for PCR amplification. All polymerases marketed for PCR applications are tested for fidelity properties (i.e., error rate determination) by vendors, and numerous literature reports have addressed PCR enzyme fidelity. Nonetheless, it is often difficult to make direct comparisons among different enzymes due to numerous methodological and analytical differences from study to study. We have measured the error rates for 6 DNA polymerases commonly used in PCR applications, including 3 polymerases typically used for cloning applications requiring high fidelity. Error rate measurement values reported here were obtained by direct sequencing of cloned PCR products. The strategy employed here allows interrogation of error rate across a very large DNA sequence space, since 94 unique DNA targets were used as templates for PCR cloning. The six enzymes included in the study, Taq polymerase, AccuPrime-Taq High Fidelity, KOD Hot Start, cloned Pfu polymerase, Phusion Hot Start, and Pwo polymerase, we find the lowest error rates with Pfu, Phusion, and Pwo polymerases. Error rates are comparable for these 3 enzymes and are >10x lower than the error rate observed with Taq polymerase. Mutation spectra are reported, with the 3 high fidelity enzymes displaying broadly similar types of mutations. For these enzymes, transition mutations predominate, with little bias observed for type of transition.
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Kumari, S., K. Kundu J, and J. Polák. "Identification of Xiphinema vuittenezi by polymerase chain reaction." Plant Protection Science 40, No. 1 (March 7, 2010): 1–4. http://dx.doi.org/10.17221/3120-pps.

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So far, the identification of the nematode species <I>Xiphinema vuittenezi</I> relied mainly on time-consuming morphological and morphometrical studies. Therefore, a polymerase chain reaction (PCR) protocol was optimised that both reliably and rapidly identifies <I>X. vuittenezi</I>. The internal transcribed spacer (ITS) species-specific primer of ribosomal DNA gene of <I>X. vuittenezi </I>was used. Nine populations of this species from Central Bohemia were investigated by means of PCR.
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Dissertations / Theses on the topic "Polymerase chain reaction (PCR)"

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Feugeas, Olivier. "Pcr (polymerase chain reaction) et vih." Lille 2, 1990. http://www.theses.fr/1990LIL2M264.

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Lantz, Pär-G. "PCR-based detection of microorganisms in complex biological samples." Lund : Dept. of Applied Microbiology, Lund University, 1998. http://catalog.hathitrust.org/api/volumes/oclc/39178906.html.

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Ballagi-Pordány, András. "Application of polymerase chain reaction (PCR) in veterinary virology /." Uppsala : Sveriges lantbruksuniv, 1995. http://epsilon.slu.se/avh/1995/91-576-4997-9.gif.

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Erill, Sagalés Ivan. "High-speed Polymerase chain reaction in CMOS-compatible chips." Doctoral thesis, Universitat Autònoma de Barcelona, 2002. http://hdl.handle.net/10803/3031.

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En la última década del siglo XX, el campo de los microsistemas para análisis total (µ-TAS) y, más concretamente, el de los DNA-chips ha adquirido una importancia preponderante en el ámbito de los microsistemas. En gran parte, el creciente interés por estos dispositivos se debe a las substanciales mejoras que prometen: análisis más rápidos, baratos y automatizados, pero también es debido a la posibilidad de implementar técnicas analíticas antes impensables (e.g. chips de hibridación). En el caso particular de los DNA-chips, se han desarrollado prototipos funcionales para PCR, LCR, electroforesis en gel, di-electroforesis, hibridación y varias combinaciones de estas técnicas, al tiempo que los chips de hibridación masiva (mayoritariamente basados en arrayers) han llegado a convertirse en un éxito comercial. Aun así, y aunque se ha llevado a cabo mucho trabajo en estos años, es necesaria todavía mucha investigación para afrontar algunos de los principales retos de los DNA-chips.
En el transcurso de esta tesis doctoral, se ha llevado a cabo el desarrollo un proceso tecnológico común para la fabricación de DNA-chips multifunción (i.e. sistemas versátiles basados en PCR y electroforesis), poniendo un especial énfasis en la compatibilidad con los procesos CMOS estándar, a fin de conseguir desarrollar prototipos proto-industriales. Como demostrador de esta puesta a punto tecnológica, se han diseñado, fabricado y testado chips de PCR, y la PCR en chips ha sido optimizada con respecto a materiales de fabricación, metodologías de inserción/extracción, composición bioquímica de la mix de PCR, diferentes configuraciones de calentadores/sensores (Peltier/termopares vs. resistencias integradas) y la cinética de la reacción.
In the last decade of the twentieth century, the fields of µ-TAS and, more specifically, DNA-chips have acquired increasing importance in the microsystems arena. The main reason for this surge of interest lies in the advantages these new devices seek to bring forth: faster, cheaper and completely automated analyses, and also in the outbreak of novel analytical techniques (e.g. hybridization chips). In the particular case of DNA-chips, functional prototypes have been demonstrated for PCR, LCR, gel electrophoresis, di-electrophoresis, hybridization and various combinations of these techniques, whilst hybridization chips (mainly arrayer chips) have become a successful market application. But, even though a considerable amount of work has been carried out in these few years, much research is still required to address fundamental problems of DNA-chips.
In this doctoral work, a common-ground technological setup for the production of multifunction DNA-chips (i.e. PCR plus electrophoresis systems) has been laid down, placing strong emphasis in its compatibility with standard CMOS processes in order to produce proto-industrial prototypes. As a demonstrator of this technological setup, PCR-chips have been designed, manufactured and tested, and the chip PCR reaction has been optimized with respect to surface materials, insertion and extraction methods, biochemical mix composition, heater/sensor setups (Peltier/thermocouple vs. thin-film driven systems) and reaction kinetics.
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Aydin, Gamze. "Detection Of Genetically Modified Maize Via Polymerase Chain Reaction." Master's thesis, METU, 2004. http://etd.lib.metu.edu.tr/upload/3/12605495/index.pdf.

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In recent years, foods produced by genetic engineering technology have been on the world food market. The biosafety aspects, regulations, and labelling of these foods are still contentious issues in most countries. It is necessary to have approval for the use of GMOs in the production of food. Thus, detection and quantification of GMOs play crucial role for developing regulations on GM foods. In this study, raw and processed maize samples were analysed for genetic modification using a DNA based detection method, the Polymerase Chain Reaction. Ten raw food and 18 processed maize food including maize flour, starch, corn flakes, maize chips were collected from different markets located in different places in Turkey. The samples were examined for the presence of genetic elements located in the majority of transgenic crops such as NOS terminator, CaMV 35S promoter, kanamycin resistance (KanR) gene, using conventional PCR with oligonucleotide sets targeting to novel genes. Furthermore screening was conducted via Real-Time PCR assay for NOS terminator and 35S promoter. For confirming the presence of Bt11 maize lines event specific primers were utilised. Quantification of Bt11 maize lines were performed via Real-Time PCR. The result indicates that foreign genetic elements were found in all analysed raw material. In six out of 10 raw material, presence of Bt11 gene were identified. GMO detection was also possible for maize flour and starch, however in processed material as corn starch, corn flakes, corn chips and pop corn, transgenes were not detected.
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Allmann, Michael. "Applications of the polymerase chain reaction (PCR) in food chemistry /." [S.l.] : [s.n.], 1994. http://www.ub.unibe.ch/content/bibliotheken_sammlungen/sondersammlungen/dissen_bestellformular/index_ger.html.

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Duman, Zeynep. "Polymerase Chain Reaction (pcr) For Detection Of Borrelia Burgdorferi Sensu Lato." Master's thesis, METU, 2008. http://etd.lib.metu.edu.tr/upload/2/12609199/index.pdf.

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The present study aimed detection of a human pathogen B. bugdorferi sensu lato species in suspected Lyme borreliosis (LB) patients in Turkey by PCR analysis and supportive serologic tests. The 152 clinical samples (140 serum and blood, 10 cerebrospinal fluid (CSF), 1 synovial fluid, 1 skin biopsy specimens) from 140 patients sent from 22 different cities of Turkey to The Spirochetal Diseases Diagnosis Laboratory of Central Veterinary Control and Research Institute were analysed. Serum samples were subjected to ELISA with a commercial kit and all of the blood, CSF, synovial fluid and skin biopsy samples were examined by PCR. In PCR analysis two primer sets targeting the ospA gene located on the plasmid and ribosomal 23S rRNA gene of B. burgdorferi sensu lato were used. The results indicated that 32,1% (45 of 140) seropositivity was detectable by ELISA. Our results support that there is a risk of acquiring LB in different regions of Turkey. Although considerable positive detections were recorded using serologic tests,none of the specimens were positive in PCR analysis. Further studies on PCR based methods for detection of B. burgdorferi sensu lato in patients with a high clinical probability of LB apparently may require that the specimen should be taken in the early phases and before the administration of any therapeutic agent.
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Ros, Bascuñana Carlos. "Diagnostic application of the polymerase chain reaction (PCR) in veterinary microbiology /." Uppsala : Swedish Univ. of Agricultural Sciences (Sveriges lantbruksuniv.), 1997. http://epsilon.slu.se/avh/1997/91-576-5247-3.gif.

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Liao, Yu-Hua. "Polymerase chain reaction based cloning of acetate kinase in propionibacterium acidipropionici." The Ohio State University, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=osu1072778140.

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Burns, Nigel. "Towards the absolute quantification of DNA by PCR." Thesis, Open University, 1999. http://oro.open.ac.uk/57922/.

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Amplification techniques such as the Polymerase Chain Reaction (PCR) are held to be largely qualitative procedures and are widely used as such. Since the efficiency of amplification is less than perfect, small changes in efficiency can yield dramatic differences in the final amount of product generated. Despite this unpredictability the exquisite sensitivity of PCR makes the demanding goal of absolute quantification highly desirable. Consequently, the use of this technique for the quantification of nucleic acids has increased at an exponential rate. However, the ability of PCR to accurately quantify absolute levels of DNA is still not universally accepted. The overall aim of this investigation was to determine the critical factors affecting the quantification of DNA using PCR and to use these findings to develop an assay for the absolute quantification of DNA in a model system. The novel work presented here illustrates the need for careful examination of sequencesfo r GC-rich domains which could give rise to stable secondary structures and reduce the efficiency of amplification by serving as termination sites. To determine the accuracy of competitive PCR, CE and IP-RP-HPLC were employed to quantify PCR- products. These two techniques provided valuable information on the identification and elimination of sources of error which led to improvements in speed, accuracy and precision, as well as ease of quantification by PCR. They also yielded information on the process of heteroduplex formation whilst simultaneously revealing assay limitations. Consequently, the on-line fluorescence monitoring of PCR was used as an alternative method for the quantification of Legionella pneumophila. This technique was highly reproducible however, mispriming and the subsequent amplification of non-specific PCR products limited the level of detection. The Y-end labelling of degraded DNA with DIG prevented short DNA fragments from mispriming (and consequently extending) allowing the amplification of DNA targets. Therefore, to reduce mispriming and hence improve assay sensitivity, this approach was adapted for the first time to produce 5'-degenerate, 3'- DIG-terminated competitive primer analogues. These analogues, coupled with the use of the LightcyclerTm, allowed the detection and absolute quantification of a single cell of Legionella pneumophila. This is the first time that this level of sensitivity has been achieved using this type of assay. This technique should provide a very rapid and sensitive alternative for quantification comparedt o the other,m oree xpensivete chnologiesa vailablea t present.
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Books on the topic "Polymerase chain reaction (PCR)"

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Tevfik, Dorak M., ed. Real-time PCR. New York: Taylor & Francis, 2006.

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W, Larrick James, ed. The PCR technique: Quantitative PCR. [Natick, Mass.]: BioTechniques Books, 1997.

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Sarkar, Gobinda. PCR in Neuroscience: PCR in Neuroscience. Burlington: Elsevier, 1995.

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Ralph, Rapley, ed. PCR sequencing protocols. Totowa, N.J: Humana Press, 1996.

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Oswald, Nick, and Suzanne Kennedy. PCR troubleshooting and optimization: The essential guide. Norfolk, UK: Caister Academic Press, 2011.

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missing], [name. PCR protocols. 2nd ed. Totowa, NJ: Humana Press, 2003.

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Julie, Logan, Edwards Kirstin, and Saunders Nick, eds. Real-time PCR: Current technology and applications. Norfolk, UK: Caister Academic Press, 2009.

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Dennis, Lo Y. M., ed. Clinical applications of PCR. Totowa, N.J: Humana Press, 1998.

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Dennis, Lo Y. M., Chiu Rossa W. K, and Chan K. C. Allen, eds. Clinical applications of PCR. 2nd ed. Totowa, N.J: Humana Press, 2006.

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PCR protocols. 3rd ed. New York, N.Y: Humana Press, 2011.

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Book chapters on the topic "Polymerase chain reaction (PCR)"

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Ochman, Howard, James W. Ajioka, Dan Garza, and Daniel L. Hartl. "Inverse Polymerase Chain Reaction." In PCR Technology, 105–11. London: Palgrave Macmillan UK, 1989. http://dx.doi.org/10.1007/978-1-349-20235-5_10.

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Frank, J. Howard, J. Howard Frank, Michael C. Thomas, Allan A. Yousten, F. William Howard, Robin M. Giblin-davis, John B. Heppner, et al. "Polymerase Chain Reaction (PCR)." In Encyclopedia of Entomology, 2991–92. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6359-6_3049.

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Nahler, Gerhard. "polymerase chain reaction (PCR)." In Dictionary of Pharmaceutical Medicine, 141–42. Vienna: Springer Vienna, 2009. http://dx.doi.org/10.1007/978-3-211-89836-9_1075.

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Yamada, Takahiro. "Polymerase Chain Reaction (PCR)." In Fetal Morph Functional Diagnosis, 331–34. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-8171-7_25.

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Gooch, Jan W. "Polymerase Chain Reaction (PCR)." In Encyclopedic Dictionary of Polymers, 916. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-6247-8_14534.

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Gautam, Akash. "Polymerase Chain Reaction (PCR)." In DNA and RNA Isolation Techniques for Non-Experts, 157–63. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-94230-4_20.

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Frohman, Michael A. "Cloning PCR Products." In The Polymerase Chain Reaction, 14–37. Boston, MA: Birkhäuser Boston, 1994. http://dx.doi.org/10.1007/978-1-4612-0257-8_2.

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Garner, H. R. "Automating the PCR Process." In The Polymerase Chain Reaction, 182–98. Boston, MA: Birkhäuser Boston, 1994. http://dx.doi.org/10.1007/978-1-4612-0257-8_16.

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Andersson, Bjorn, and Richard A. Gibbs. "PCR and DNA Sequencing." In The Polymerase Chain Reaction, 201–13. Boston, MA: Birkhäuser Boston, 1994. http://dx.doi.org/10.1007/978-1-4612-0257-8_17.

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Daniell, Ellen. "PCR in the Marketplace." In The Polymerase Chain Reaction, 421–26. Boston, MA: Birkhäuser Boston, 1994. http://dx.doi.org/10.1007/978-1-4612-0257-8_34.

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Conference papers on the topic "Polymerase chain reaction (PCR)"

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Lin, Yu-Cheng, and Hua-Lin Wu. "Nanoparticle-Assisted High Efficient Polymerase Chain Reaction." In 2008 Second International Conference on Integration and Commercialization of Micro and Nanosystems. ASMEDC, 2008. http://dx.doi.org/10.1115/micronano2008-70214.

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This paper reports that the Au nanoparticles could dramatically enhance efficiency of polymer chain reaction (PCR) and shorten reaction time. The excellent energy transfer property of the nanoparticles should be the major factor in improving the PCR efficiency. With the addition of 0.7 nM of 13 nm Au nanoparticles into the PCR reagent, the PCR efficiency was increased. The results demonstrated that Au nanoparticles increase the sensitivity of PCR detection 5–10 fold in a slower PCR system (i.e. conventional PCR) and at least 104 fold in a quicker PCR system (i.e. real-time PCR). This innovation could improve the PCR efficiency using non-expensive polymerases, and general PCR reagent.
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Foong, Chow Ming, and Norrakiah Abdullah Sani. "Identifying of meat species using polymerase chain reaction (PCR)." In THE 2013 UKM FST POSTGRADUATE COLLOQUIUM: Proceedings of the Universiti Kebangsaan Malaysia, Faculty of Science and Technology 2013 Postgraduate Colloquium. AIP Publishing LLC, 2013. http://dx.doi.org/10.1063/1.4858733.

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Persat, Alexandre, Tomoyuki Morita, and Juan G. Santiago. "On-Chip Isothermal Polymerase Chain Reaction." In ASME 2007 International Mechanical Engineering Congress and Exposition. ASMEDC, 2007. http://dx.doi.org/10.1115/imece2007-43070.

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We present a novel technique for on-chip PCR where temperature is held constant and uniform in the reactor. Specific chemicals, known as denaturants, have the ability to melt DNA. A flow control scheme establishes spatio-temporal fluctuations in the concentration of denaturants along a microchannel, while electromigration drives DNA through this spatially varying denaturant concentration field. Preliminary results show denaturation and extension of a 200 base pairs (bp) DNA template.
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Chong, K. S., and K. B. Gan. "Portable Polymerase Chain Reaction (PCR): Thermal ramping rate performance evaluation." In 2016 IEEE EMBS Conference on Biomedical Engineering and Sciences (IECBES). IEEE, 2016. http://dx.doi.org/10.1109/iecbes.2016.7843490.

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Punch, Jeff, Bryan Rodgers, David Newport, and Mark Davies. "Thermal Analysis of a Micro-Polymerase Chain Reaction Device." In ASME 2004 International Mechanical Engineering Congress and Exposition. ASMEDC, 2004. http://dx.doi.org/10.1115/imece2004-59161.

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Micro-scale polymerase chain reaction (micro-PCR) systems offer substantial advantages over macro-scale systems. Smaller sample volumes are required, and faster process times are feasible. Thermal control of micro-PCR systems is a substantial technical challenge, however. The PCR process requires the fluid sample to be cycled through three temperature ranges — typically 90–95°C, 50–65°C and 72–77°C for denaturation, hybridisation and replication respectively. Durations of the three steps are required to be in the ratio of 4:4:9. In this paper, the thermal analysis of a continuous flow micro-PCR device is reported. The objective of the analysis is to optimize the thermal performance of the device for fast amplification cycles with high efficiency - an efficient PCR features rapid heating and cooling between steps, and good temperature uniformity within each step. The device comprises an array of parallel microchannels formed within a polypropylene substrate to carry fluid, with the base of the substrate mounted on an aluminium carrier. Substrate depth is 500 micron, and each channel is 60 micron wide by 40 micron deep. Thermoelectric cells (TECs) are bonded to the carrier, and powered by a thermoelectric controller with feedback from sensors embedded in the carrier. A Pyrex Glass slide is bonded to the substrate to form closed channels. Arrays of film heaters mounted on the slide adjacent to the channel are used to establish the required temperature regions along the channel. By pumping the fluid at a fixed flow rate, temperature cycling of specific period is achieved. Thermal analysis of the substrate is performed using an approximate closed-form solution, in conjunction with Finite Element (FE) and Computational Fluid Dynamics (CFD) simulations. The analysis is used to conduct a parametric study in order to determine the optimum configurations of substrate materials, cooling conditions, heaters and flow rates required to impose specific temperature cycles. The use of thermoelectric cells is shown to increase the rate of change of temperature between the various regions, improving the efficiency and decreasing the cycle time of the PCR process. Cycle times of 6s or less are shown to be feasible, yielding benefits in time saved for multiple amplifications. Finally, the analysis is also used to identify the dimensionless parameters which govern the thermal characteristics of the device, illustrating the importance of the Biot number.
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Wrightson, JM, NM Rahman, T. Novak, JF Huggett, RF Miller, and RJ Davies. "Polymerase Chain Reaction (PCR) Demonstrates No Evidence ofPneumocystis jiroveciiin Pleural Infection." In American Thoracic Society 2009 International Conference, May 15-20, 2009 • San Diego, California. American Thoracic Society, 2009. http://dx.doi.org/10.1164/ajrccm-conference.2009.179.1_meetingabstracts.a4469.

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Chung, Kwang Hyo, Yo Han Choi, Hong Kyw Choi, Jin Tae Kim, Young-Jun Yu, Jin Sik Choi, Doo-Hyeb Youn, and Choon-Gi Choi. "Convection-based realtime polymerase chain reaction (PCR) utilizing transparent graphene heaters." In 2014 IEEE Sensors. IEEE, 2014. http://dx.doi.org/10.1109/icsens.2014.6985173.

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Sirr, Noel, Doina Ciobanu, Ronan Grimes, and Mark Davies. "A Continuous Flow Polymerase Chain Reactor for DNA Expression Analysis." In ASME 4th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2006. http://dx.doi.org/10.1115/icnmm2006-96180.

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The polymerase chain reaction (PCR) has revolutionised molecular biology, and is at the forefront of many current efforts to document and understand human genetic diversity. Recent years has seen a move towards incorporating the PCR technique into a micro Total Analysis System (μTAS) thus exploiting its full potential. Micro scale PCR design offers the opportunity to integrate all functional steps of DNA expression analysis into a miniaturised device allowing for high throughput and reduced analysis times, reduced sample volume requirements and cost efficiency. Consequently, it is desirable to replace the traditional stationary or well based thermal cyclers with continuous flow designs. A continuous flow polymerase chain reaction device consisting of a cylindrical heating core, which is segmented axially into three symmetric heating zones providing the denaturating, annealing and extension phases of the polymerase chain reaction, and a flow through capillary tube which is wound helically around the core has been fabricated and shown to consistently amplify target plasmid DNA samples. At the inlet to the device, PCR samples are segmented into droplets and entrained in an immiscible carrier fluid to eliminate cross contamination between PCR samples. This approach also prevents degradation of the micro-reactor droplets from inhibitory effects posed by the high surface to volume ratios associated with the device. The droplet train is then cycled through the capillary tube with each complete revolution constituting one cycle of the PCR reaction. The results reported in this paper include, initial validation of the spiral cycler design in comparison to an existing commercial PCR platform, and subsequent optimisation of the reaction time and its effects on the devices performance. The spiral thermal cycler has demonstrated successful PCR amplification at the nano scale with stable trains of 30–35nl droplet volumes being processed in an amplification time of 32 minutes. At this level the device offers the potential to process approximately 3500 such droplets in of order one hour.
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Suwa, Tohru, Hamid Hadim, and Yong Shi. "Multidisciplinary Design and Optimization for Oscillating Flow Polymerase Chain Reaction Microfluidics Device." In ASME 2009 International Mechanical Engineering Congress and Exposition. ASMEDC, 2009. http://dx.doi.org/10.1115/imece2009-11820.

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A Polymerase Chain Reaction (PCR) process is almost always required prior to DNA (deoxyribonucleic acid) analysis to create multiple copies of DNA fragments. Using microfluidics technology, the PCR process requires much shorter process time and much less DNA samples than conventional PCR systems. Among existing microfluidics-based techniques, the oscillating flow PCR has advantages including faster analysis time than cavity PCR microfluidics, and smaller contact area between the sample and polymer channel wall compared to flow-through PCR. The smaller contact area reduces DNA adsorption and enhances DNA detection accuracy. In the proposed study, new design features of the oscillating flow PCR concept are evaluated including: (1) PDMS (polydimethylsiloxane) and glass are selected as the microfluidics chip material for realizing a disposable chip, (2) water impingement cooling is applied to effectively isolate the temperature zones, and (3) a copper layer is attached outside of the chip to enhance uniform temperature distribution within the temperature zones. When PDMS is used for PCR microfluidics devices, lower efficiency has been a disadvantage. The efficiency is lowered because the DNA fragments are trapped at the PDMS surface. This trapping can be reduced by minimizing the contact area between the sample and the PDMS surface. When the sample contact area is reduced, which can be achieved by increasing the flow channel cross-sectional area, thermal response is degraded. Optimal channel dimensions are determined by considering the trade-off between thermal response and sample contact area with PDMS channel wall. The resulting thermal response of the sample in the temperature zone is comparable to existing studies, which use silicon as the chip material. A transient FEM heat transfer analysis for the temperature zone is performed for more effective thermal design and optimization.
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Muddu, Radha, Victor M. Ugaz, and Yassin A. Hassan. "Three Dimensional Simulation of Rayleigh-Be´nard Convection for Rapid Microscale Polymerase Chain Reaction." In ASME 2009 Fluids Engineering Division Summer Meeting. ASMEDC, 2009. http://dx.doi.org/10.1115/fedsm2009-78119.

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A variety of biochemical reactions involve cycling reagents through different temperature regimes in a specific order as dictated by chemical kinetics. One such reaction is the polymerase chain reaction (PCR), a fundamental process used to selectively amplify specific regions of interest within a larger DNA strand to very high concentration levels. Natural convection has recently been explored as a novel way to perform PCR by providing a passive approach to circulate reactants through the correct temperature zones. Optimal reactor design requires the spatial velocity and temperature distributions to be precisely controlled to ensure that the reactants sequentially occupy the correct temperature zones for a sufficient period of time. Rayleigh-Be´nard convection in vertical cylindrical reaction chambers maintained at fixed upper and lower surface temperatures provides a convenient model system to study these phenomena. In this work, we present results of three dimensional numerical simulations of the flow and temperature distributions in cylindrical reactors of different aspect ratios (height (h) / diameter (d)). These results helped identify different flow profiles that are possible in each of the geometries and led to an optimized redesign of the Rayleigh-Be´nard PCR convection system for rapid DNA replication.
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Reports on the topic "Polymerase chain reaction (PCR)"

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Osburn, Bennie, Marius Ianconescu, Geoffrey Akita, and Rozalia Kaufman. Rapid, Sensitive Bluetongue Virus Serogroup and Serotype Detection Using Polymerase Chain Reaction. United States Department of Agriculture, September 1995. http://dx.doi.org/10.32747/1995.7612836.bard.

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The objectives of this proposal were to enhance animal health by 1) development of a BTV serogroup diagnostic assay using polymerase chain reaction (PCR) and 2) development of a BTV serotype specific diagnostic PCR assay. A PCR assay for diagnosis of bluetongue virus (BTV) serogroup from clinical samples meeting the criteria of objective 1 was developed. This PCR assay is more sensitive than virus isolation and has been adopted by both the U.S. and Israeli collaborating laboratories of this project, as well as at least one other U.S. laboratory for routine diagnosis of BTV infection in ruminants. The basic BTV PCR protocol has also become an essential tool in BTV molecular research in both collaborating laboratories. During development of the BTV serotype specific PCR we had the opportunity to investigate a nationwide outbreak of abortions and fatal disease in dogs in the U.S. purportedly due to BTV infection via a BTV contaminated canine vaccine. The BTV serogroup PCR was integral in confirming BTV in tissues from affected dogs and in lots of the suspect vaccine. This led to the first published report of BTV infection in dogs. We discovered that BTV can produce silent persistent infection in canine cell culture. This indicated a need for more stringent screening of biologics for occult BTV infection. A novel mixed cell culture method was developed to identify occult BTV and other occult viral infection cell cultures. Serotype specific primers for PCR detection of all U.S. BTV serotypes and two Israel serotypes (BTV-2 and 10) have been evaluated and are available. A subsequent collaboration would logically include sequencing of the L2 genes of Israel BTV-4, 6 and 16, allowing incorporation of these Israel BTV serotypes into a multiplex PCR assay.
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Arnett, Clint M., Giselle Rodriguez, and Stephen W. Maloney. Polymerase Chain Reaction (PCR) Analysis of Microbial Consortia on Wastewater Treatment Processes for High Explosives. Fort Belvoir, VA: Defense Technical Information Center, September 2009. http://dx.doi.org/10.21236/ada544671.

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Denaro, Tracy R., Sarah K. Chelgren, Jara N. Lang, Ellen M. Strobel, Lori M. T. Balster, and Marlin D. Vangsness. DNA Isolation of Microbial Contaminants in Aviation Turbine Fuel via Traditional Polymerase Chain Reaction (PCR) and Direct PCR. Preliminary Results. Fort Belvoir, VA: Defense Technical Information Center, November 2005. http://dx.doi.org/10.21236/ada446701.

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López-Valverde, Nansi, Antonio López-Valverde, Ana Suarez, Bruno Macedo de Sousa, and Juan Manuel Aragoneses. Association of gastric infection and periodontal disease through Helicobacter pylori as a common denominator: A systematic review and meta-analysi. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, October 2021. http://dx.doi.org/10.37766/inplasy2021.10.0097.

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Review question / Objective: Is gastric helicobacter pylori infection related to periodontal diseases? Condition being studied: Therefore, the aim of this systematic review and meta-analysis was to identify and analyze clinical studies to determine the direct correlation between Helicobacter Pylori gastric infection andPeriodontal Disease. Study designs to be included: Clinical studies that provided data on Helicobacter Pylori infection in both the stomach and oral cavity, confirmed by polymerase chain reaction (PCR), rapid urease test (RUT) or enzyme-linked immunosorbent assay (ELISA). Clinical studies that associated PD with Helicobacter Pylori. The diagnosis of PD was confirmed ac-cording to the diagnostic criteria in periodontology.
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Strachan, Anna Louise. The Impact of Covid-19 on Research Methods and Approaches. Institute of Development Studies (IDS), January 2021. http://dx.doi.org/10.19088/cc.2021.002.

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The Covid-19 pandemic, and measures to contain the spread of the virus, such as border closures, quarantine requirements, mandatory PCR (Polymerase Chain Reaction) tests, curfews, and social distancing requirements, have had a significant impact on research methods and approaches. Most of the available literature assumes that remote data collection is the only viable means of collecting primary data during the pandemic, so that is the focus of this report. While there is an extensive discussion of challenges associated with undertaking primary data collection during this time, there are also several commentaries and opinion pieces that highlight the opportunities and positive aspects of remote data collection.
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Zhelev, Doncho V., Christopher Dupuis, Suelynn Ren, Anna Le, Mia Hunt, and Henry Gibbons. Single Nucleotide Polymorphisms (SNP)-specific Quantitative Real Time Polymerase Chain Reaction (PCR) Assay for Analyzing Competition and Emergence of the Military Hypersporulating Strains of Bacillus Atrophaeous var. Globigii. Fort Belvoir, VA: Defense Technical Information Center, September 2012. http://dx.doi.org/10.21236/ada570597.

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GUI, ZHEN, Yue-Ying WANG, Jia-Xin Li, and Tao XIANG. Prevalence of poor sleep quality in COVID-19 patients: a systematic review and meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, February 2023. http://dx.doi.org/10.37766/inplasy2023.2.0121.

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Review question / Objective: The inclusion criteria for this study are based on the PICOS acronym: Participants (P): COVID-19 patients based on positive Coronavirus RT-PCR (reverse transcription-polymerase chain reaction) of nasopharyngeal and oropharyngeal swabs or a history of COVID-19 infection. Following previous research, the COVID-19 patients in this study will include the period of COVID-19 infection, symptom onset, recovery, and the onset of post-acute COVID-19 symptoms. Interventions (I): not applicable; Comparisons (C): healthy controls in comparative studies, or not applicable to epidemiological surveys; Outcome (O): the prevalence of poor sleep quality (PSQ) or available data could yield the prevalence of PSQ in COVID-19 patients. Sleep quality in COVID-19 patients will be assessed using standardized scales such as the Pittsburgh Sleep Quality Index (PSQI); Study design (S): epidemiological and comparative studies (only the baseline data of cohort study will be extracted).
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Lance, Richard, and Xin Guan. Variation in inhibitor effects on qPCR assays and implications for eDNA surveys. Engineer Research and Development Center (U.S.), August 2021. http://dx.doi.org/10.21079/11681/41740.

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Aquatic environmental DNA (eDNA) surveys are sometimes impacted by polymerase chain reaction (PCR) inhibitors. We tested varying concentrations of different inhibitors (humic, phytic, and tannic acids; crude leaf extracts) for impacts on quantitative PCR (qPCR) assays designed for eDNA surveys of bighead and silver carp (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix). We also tested for inhibition by high concentrations of exogenous DNA, hypothesizing that DNA from increasingly closely related species would be increasingly inhibitory. All tested inhibitors impacted qPCR, though only at very high concentrations — likely a function, in part, of having used an inhibitor-resistant qPCR solution. Closer phylogenetic relatedness resulted in inhibition at lower exogenous DNA concentrations, but not at relatively close phylogenetic scales. Inhibition was also influenced by the qPCR reporter dye used. Importantly, different qPCR assays responded differently to the same inhibitor concentrations. Implications of these results are that the inclusion of more than one assay for the same target taxa in an eDNA survey may be an important countermeasure against false negatives and that internal positive controls may not, in the absence of efforts to maximize inhibition compatibility, provide useful information about the inhibition of an eDNA assay.
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O'Leary, Timothy J., Melanie Cushion, Cynthia Wright, Thomas Fanning, and Mark Tsai. Polymerase Chain Reaction Based Diagnostic Assays for Pneumocystis Carinii. Fort Belvoir, VA: Defense Technical Information Center, March 1992. http://dx.doi.org/10.21236/ada248259.

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Gelb, Jr., Jack, Yoram Weisman, Brian Ladman, and Rosie Meir. Identification of Avian Infectious Brochitis Virus Variant Serotypes and Subtypes by PCR Product Cycle Sequencing for the Rational Selection of Effective Vaccines. United States Department of Agriculture, December 2003. http://dx.doi.org/10.32747/2003.7586470.bard.

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Objectives 1. Determine the serotypic identities of 40 recent IBV isolates from commercial chickens raised in the USA and Israel. 2. Sequence all IBV field isolates using PCR product cycle sequencing and analyze their S 1 sequence to detennine their homology to other strains in the Genbank and EMBL databases. 3. Select vaccinal strains with the highest S 1 sequence homology to the field isolates and perform challenge of immunity studies in chickens in laboratory trials to detennine level of protection afforded by the vaccines. Background Infectious bronchitis (IB) is a common, economically important disease of the chicken. IB occurs as a respiratory form, associated with airsacculitis, condemnation, and mortality of meat-type broilers, a reproductive form responsible for egg production losses in layers and breeders, and a renal form causing high mortality in broilers and pullets. The causative agent is avian coronavirus infectious bronchitis virus (IBV). Replication of the virus' RNA genome is error-prone and mutations commonly result. A major target for mutation is the gene encoding the spike (S) envelope protein used by the virus to attach and infect the host cell. Mutations in the S gene result in antigenic changes that can lead to the emergence of variant serotypes. The S gene is able to tolerate numerous mutations without compromising the virus' ability to replicate and cause disease. An end result of the virus' "flexibility" is that many strains of IBV are capable of existing in nature. Once formed, new mutant strains, often referred to as variants, are soon subjected to immunological selection so that only the most antigenically novel variants survive in poultry populations. Many novel antigenic variant serotypes and genotypes have been isolated from commercial poultry flocks. Identification of the field isolates of IBV responsible for outbreaks is critical for selecting the appropriate strain(s) for vaccination. Reverse transcriptase polymerase chain reaction (RT-PCR) of the Sl subunit of the envelope spike glycoprotein gene has been a common method used to identify field strains, replacing other time-consuming or less precise tests. Two PCR approaches have been used for identification, restriction fragment length polymorphism (RFLP) and direct automated cycle sequence analysis of a diagnostically relevant hypervariab1e region were compared in our BARD research. Vaccination for IB, although practiced routinely in commercial flocks, is often not protective. Field isolates responsible for outbreaks may be unrelated to the strain(s) used in the vaccination program. However, vaccines may provide varying degrees of cross- protection vs. unrelated field strains so vaccination studies should be performed. Conclusions RFLP and S1 sequence analysis methods were successfully performed using the field isolates from the USA and Israel. Importantly, the S1 sequence analysis method enabled a direct comparison of the genotypes of the field strains by aligning them to sequences in public databases e.g. GenBank. Novel S1 gene sequences were identified in both USA and Israel IBVs but greater diversity was observed in the field isolates from the USA. One novel genotype, characterized in this project, Israel/720/99, is currently being considered for development as an inactivated vaccine. Vaccination with IBV strains in the US (Massachusetts, Arkansas, Delaware 072) or in Israel (Massachusetts, Holland strain) provided higher degrees of cross-protection vs. homologous than heterologous strain challenge. In many cases however, vaccination with two strains (only studies with US strains) produced reasonable cross-protection against heterologous field isolate challenge. Implications S1 sequence analysis provides numerical similarity values and phylogenetic information that can be useful, although by no means conclusive, in developing vaccine control strategies. Identification of many novel S1 genotypes of IBV in the USA is evidence that commercial flocks will be challenged today and in the future with strains unrelated to vaccines. In Israel, monitoring flocks for novel IBV field isolates should continue given the identification of Israel/720/99, and perhaps others in the future. Strains selected for vaccination of commercial flocks should induce cross- protection against unrelated genotypes. Using diverse genotypes for vaccination may result in immunity against unrelated field strains.
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