Academic literature on the topic 'LAMP, Primer Design, Software Development'
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Journal articles on the topic "LAMP, Primer Design, Software Development"
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Wekesa, Francis, Mark Wamalwa, Richard Oduor, Yatinder Binepal, Leonard Ateya, Noah Okumu, Angela M’kwenda, Christopher Masaba, and Eugine Mukhaye. "Development and Validation of Rapid Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification for Detection of Rift Valley Fever Virus." Advances in Virology 2023 (January 30, 2023): 1–14. http://dx.doi.org/10.1155/2023/1863980.
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Rift Valley fever virus (RVFV) is a high-priority zoonotic pathogen with the ability to cause massive loss during its outbreak within a very short period of time. Lack of a highly sensitive, instant reading diagnostic method for RVFV, which is more suitable for on-site testing, is a big gap that needs to be addressed. The aim of this study was to develop a novel one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for the rapid detection of RVFV. To achieve this, the selected RVFV M segment nucleotide sequences were aligned using Multiple Sequence Comparison by Log-Expectation (MUSCLE) software in MEGA11 version 11.0.11 program to identify conserved regions. A 211 pb sequence was identified and six different primers to amplify it were designed using NEB LAMP Primer design tool version 1.1.0. The specificity of the designed primers was tested using primer BLAST, and a primer set, specific to RVFV and able to form a loop, was selected. In this study, we developed a single-tube test based on calorimetric RT-LAMP that enabled the visual detection of RVFV within 30 minutes at 65°C. Diagnostic sensitivity and specificity of the newly developed kit were compared with RVFV qRT-PCR, using total RNA samples extracted from 118 blood samples. The colorimetric RT-LAMP assay had a sensitivity of 98.36% and a specificity of 96.49%. The developed RT-LAMP was found to be tenfold more sensitive compared to the RVFV qRT-PCR assay commonly used in the confirmatory diagnosis of RVFV.
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Shiraho, Esther A., Agola L. Eric, Ibrahim N. Mwangi, Geoffrey M. Maina, Joseph M. Kinuthia, Martin W. Mutuku, Robert M. Mugambi, Jackson M. Mwandi, and Gerald M. Mkoji. "Development of a Loop Mediated Isothermal Amplification for Diagnosis ofAscaris lumbricoidesin Fecal Samples." Journal of Parasitology Research 2016 (2016): 1–7. http://dx.doi.org/10.1155/2016/7376207.
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Ascaris lumbricoidesis a nematode parasite that causes the common tropical infection ascariasis in humans. It is also considered among the neglected tropical diseases. Diagnosis relies mainly on microscopy-based methods which are laborious, are limited by low sensitivity, and require high expertise. We have developed a loop mediated isothermal amplification (LAMP) for diagnosis of ascariasis in fecal samples, based on the first internal transcribed (ITS-1) spacer region of the ribosomal DNA. We used Primer Explorer V4 software to design primers.Ascarisadult and ova were obtained from naturally infected school children, whose parents/guardians gave consent for their participation in the study. Genomic DNA was extracted using alkaline lysis method and amplified by LAMP at 63°C for 45 minutes. LAMP products were visualized by naked eyes after adding SYBR Green dye and also on agarose gel. LAMP successfully and reliably detectedAscarisDNA from a single egg and in fecal samples. The assay specifically detectedAscarisDNA without amplifying DNA from ova of other parasites which commonly coexist withA. lumbricoidesin feces. The developed LAMP assay has great potential for use in ascariasis diagnosis at the point of care and in low infection intensity situation that characterize control and elimination campaigns.
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Sun, Miaomiao, Hao Liu, Junbin Huang, Jinbo Peng, Fuhua Fei, Ya Zhang, Tom Hsiang, and Lu Zheng. "A Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Pectobacterium aroidearum that Causes Soft Rot in Konjac." International Journal of Molecular Sciences 20, no. 8 (April 19, 2019): 1937. http://dx.doi.org/10.3390/ijms20081937.
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Bacterial soft rot caused by Pectobacterium species is a serious disease in konjac (Amorphophallus konjac), a healthy source of starch particularly in East Asia. An effective diagnostic method is crucial to control the disease and reduce losses in konjac production. In this study, we evaluated a loop-mediated isothermal amplification (LAMP) assay with a specific primer set for the rapid and accurate detection of P. aroidearum. A comparative genomics approach was used to identify the specific genes suitable for the design of LAMP primers. The candidate target genes were determined through a first-round comparison with a 50-genome nucleotide database, and subjected to a second-round screening with the GenBank NR database. As a result, nine specific genes of P. aroidearum were selected for LAMP primer design. After screening of the primers, the primer set 1675-1 was chosen for LAMP detection owing to its high specificity and sensitivity. The LAMP assay could detect the presence of P. aroidearum genomic DNA at a concentration as low as 50 fg and 1.2 × 104 CFU/g artificially infected soil within 40 min at 65 °C. Subsequently, this primer set was successfully used to specifically detect P. aroidearum in naturally infected and non-symptomatic plant samples or soil samples from the field. This study indicates that a comparative genomic approach may facilitate the development of highly specific primers for LAMP assays, and a LAMP diagnostic assay with the specific primer set 1675-1 should contribute to the rapid and accurate detection of soft-rot disease in konjac at an early stage.
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Chen, Ze Zhong, Kai Fan, and Zhen Liang Lou. "Key Technology and Development on Side Pattern CAD/CAM on Mould for Auto Lamp." Advanced Materials Research 97-101 (March 2010): 370–73. http://dx.doi.org/10.4028/www.scientific.net/amr.97-101.370.
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A model of side pattern CAD/CAM on mould for auto lamp integrated with CATIA V5 is built. After analyzing the properties of design and the manufacture of side pattern on mould for auto lamp, key technology, such as grouping, sorting, determination of continuity, fairing and fitting of side pattern curves, generating of NC files and G codes, are presented. Using out-process redeveloping tools of CATIA V5, a CATIA V5 integrated side pattern CAD/CAM system for mould of auto lamp is developed. At last, a practical example shows that the technology and the software satisfy the design and manufacture of side pattern on mould for auto lamp. The technology and the software have been used in related enterprise successfully.
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Lee, Szu-Yuan, Chun-Nan Lee, Holl Mark, Deirdre R. Meldrum, Chih-Kung Lee, and Chii-Wann Lin. "OPTIMAL HEPATITIS B VIRUS PRIMER SEQUENCE DESIGN FOR ISOTHERMAL AMPLIFICATION." Biomedical Engineering: Applications, Basis and Communications 19, no. 03 (June 2007): 137–44. http://dx.doi.org/10.4015/s1016237207000215.
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We have reported the successful use of the Loop Mediated Isothermal Amplification (LAMP) reaction for Hepatitis B Virus (HBV) DNA in a 25 μl micro-reactor for the development of a rapid diagnostic device recently. This method shows the successful amplification of HBV DNA with high specificity and sensitivity efficiently within one hour. Such a powerful method can be used for many other fast diagnostic applications with the help of optimal primer design and miniaturization of reactor. In this report, we will first summarize the general design rules for primer design from literature reviews and our experimental results. We will discuss the effects of HBV primers and concentrations of working buffers for optimal performance.
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Gill, Pooria, and Arash Hadian Amree. "Allele-Specific Loop-Mediated Isothermal Amplification for the Detection of IVSII-I G>A Mutation On β-Globin Gene." Open Access Macedonian Journal of Medical Sciences 7, no. 10 (May 28, 2019): 1582–87. http://dx.doi.org/10.3889/oamjms.2019.285.
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BACKGROUND: Thalassemia is one of the most common genetic health problems in the world. More than 200 different mutations have been identified in the beta-globin gene and among the 24 β-globin gene mutations in β-thalassemia carriers in the north of Iran IVSII-I G>A mutation has the highest frequency. Using fast, inexpensive, simple and reliable methods for the detection of the mutations in β-thal carriers is very important in prenatal diagnosis, and introduction of alternative methods to the existing ones can help to simplify the detection of mutations. Since its introduction, different methods derived from LAMP have been widely used for SNPs detection.
AIM: This study was aimed to design a new method for the detection of IVSII-I G>A mutation on β-globin gene based on AS - LAMP technique.
METHODS: Primer explorer V5 software was used for the design of LAMP primers. Three sets of primers were designed. In the first set, the BIP primers were exactly complementary to the normal and mutant alleles. In the second set, 1 nucleotide (T) was inserted at the 5’ end of BIP primers, and in the last set, one nucleotide at the 5’ end of BIP primer was changed. The other required primers for the LAMP reaction (FIP, B3, and F3) were the same for all 3 sets of primers. The LAMP reaction was applied on three DNA samples (Wild type, Heterozygote and Homozygote for IVSII-I G>A mutation) and synthetic DNA.
RESULTS: The results of the present study showed that LAMP reaction using three sets of primers could not successfully detect the IVSII-I G > A mutation among subjects DNA sample and synthetic DNA.
CONCLUSION: Although several studies have successfully used ARMS-LAMP method to detect the SNPs, and other studies use a variety of methods to identify IVSII-I G>A mutation, the present study was unable to differentiate between a normal allele and IVSII-I G>A mutation. Hence further studies are recommended to consider redesigning of primer set, DNA concentration and using commercial LAMP Master Mix to detect the mutation.
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Su, Daizhong, Jose L. Casamayor, and Xuemin Xu. "An Integrated Approach for Eco-Design and Its Application in LED Lighting Product Development." Sustainability 13, no. 2 (January 6, 2021): 488. http://dx.doi.org/10.3390/su13020488.
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Lighting products are essential for our modern life nowadays, but they also produce high negative impacts on the environment. Although there are tools and methods available for reducing the environmental impact of lighting products, it is a challenging task to integrate them throughout the product development process. To overcome the challenge, this research developed an approach to integrate tools/methods relevant for the eco-design through product development process to reduce the environmental impact of lighting products. Six types of methods, such module design, and 30 tools, such as lifecycle assessment software packages, are considered in the integrated approach. The product specification with eco-constrains is established for implementation at each design stage to ensure the product eco-features. The approach was applied in the development of an LED table lamp which was then assessed in comparison with a benchmark LED lamp regarding environmental lifecycle impact and lighting performance. The comparative assessment results indicate that the LED lamp developed with this approach is much better than the benchmark lamp.
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Kit, M., J. Schwarz, and A. Gerilovych. "Development of a loop-mediated isothermal amplification (LAMP) assay based on the C962R gene for african swine fever virus detection." Agricultural Science and Practice 8, no. 3 (December 20, 2021): 3–12. http://dx.doi.org/10.15407/agrisp8.03.003.
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Aim. The aim of this study was to develop a loop-mediated isothermal amplification (LAMP) assay for African swine fever virus (ASFV) detection. Methods. Primer design was performed using publicly available full genome sequences of ASFV. A panel of heterologous DNA samples and reference ASFV DNA samples were used for the assay specificity testing. The limit of detection (LOD) was assessed using purified and quantified serial dilution of the amplified target sequence. LAMP product detection was performed via gel-electrophoresis and via ethidium bromide fluorescence under UV after adding the ethidium bromide directly to the tube with the LAMP product. Results. Three primer sets amplifying different regions of ASFV gene C962R were developed, of which the set № 2 providing the most intense product synthesis with the most vivid and clear pattern was selected for further studies. The optimal concentration of reaction mix components for the most effective primer set was established. In the final protocol the LAMP reaction was carried out at 60 °C for 40 min. The limit of detection (LOD) of the assay was 50 copies of the target sequence per reaction. In a preliminary testing the assay proved specific, using 10 reference and 4 heterologous viral and two bacterial DNA samples. Our LAMP assay detected ASFV genotypes I and II that are currently spread in Europe, Asia, and the Pacific and IX, occurring in Africa. Conclusion. A LAMP assay was developed based on the C962R gene that proved in preliminary validation to be specific and sensitive and was able to detect down to 50 copies per reaction of purified target gene within 40 minutes. Classical gel electrophoresis and direct staining using ethidium bromide were used for product visualisation in this study. Colorimetric approaches or the use of lateral flow devices in the visuali- sation step could make the assay less equipment dependent. Further validation of the assay, determining analytical specificity, selectivity and reproducibility performance characteristics also using clinical samples under field condi- tions and inclusion of an internal control would possibly enable its use as a test of choice at point-of-care and at low resource laboratories.
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Yang, Xiaolong, Hao Yang, Tuo Li, Xiaodan Ma, and Fei Chen. "Design of Single-lamp Monitoring System for Airfield Lighting Based on Broadband Power Line Carrier Communication." Journal of Physics: Conference Series 2078, no. 1 (November 1, 2021): 012061. http://dx.doi.org/10.1088/1742-6596/2078/1/012061.
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Abstract Considering the problems of low communication rate and large communication delay of the traditional single-lamp monitoring system for airfield lighting based on narrow-band power line carrier communication technology, a solution of single-lamp monitoring system for airfield lighting based on broadband power carrier communication technology is proposed. Firstly, this paper has made a comparison of advantages and disadvantages between narrow-band power line carrier communication technology and broadband power line carrier communication technology, and briefed the problems faced by traditional single-lamp monitoring system based on narrow-band power line carrier communication. Taking technical characteristics into consideration, broadband power line carrier communication technology is selected for the development of a new single-lamp monitoring system for airfield lighting. Secondly, this paper articulated the design and development process of new airfield lighting single-lamp monitoring system based on broadband power line carrier communication technology, from the formulation of the overall architecture scheme of the system to the realization of local convergent equipment, and focused on the analysis of hardware and software development process of single-lamp monitoring module. Finally, this paper set up a test environment, and verified the performance index by experiments. The test results show that the system meets the design index requirements, can improve the performance of the single-lamp monitoring system for airfield lighting, effectively solves the problems faced by the traditional system, and can further meet the needs of the airport for airfield lighting monitoring and control.
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Ash, Gavin J., Jillian M. Lang, Lindsay R. Triplett, Benjamin J. Stodart, Valérie Verdier, Casiana Vera Cruz, Philippe Rott, and Jan E. Leach. "Development of a Genomics-Based LAMP (Loop-Mediated Isothermal Amplification) Assay for Detection of Pseudomonas fuscovaginae from Rice." Plant Disease 98, no. 7 (July 2014): 909–15. http://dx.doi.org/10.1094/pdis-09-13-0957-re.
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The vast amount of data available through next-generation sequencing technology is facilitating the design of diagnostic marker systems. This study reports the use of draft genome sequences from the bacterial plant pathogen Pseudomonas fuscovaginae, the cause of sheath brown rot of rice, to describe the genetic diversity within a worldwide collection of strains representing the species. Based on a comparative analysis with the draft sequences, primers for a loop-mediated isothermal amplification (LAMP) assay were developed to identify P. fuscovaginae. The assay reported here reliably differentiated strains of P. fuscovaginae isolated from rice from a range of other bacteria that are commonly isolated from rice and other plants using a primer combination designated Pf8. The LAMP assay identified P. fuscovaginae purified DNA, live or heat-killed cells from pure cultures, and detected the bacterium in extracts or exudates from infected host plant material. The P. fuscovaginae LAMP assay is a suitable diagnostic tool for the glasshouse and laboratory and could be further developed for in-field surveys.
Dissertations / Theses on the topic "LAMP, Primer Design, Software Development"
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MONTRASIO, CHIARA. "Development of a Software Application for Loop-Mediated Isothermal Amplification (LAMP) Primer Design." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2016. http://hdl.handle.net/10281/103099.
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Loop-mediated isothermal AMPlification (LAMP) is an innovative gene amplification technique alternative to PCR, whose main features consist of constant temperature (isothermal reaction), the employment of a strand-displacement polymerase and the use of a set of 6 primers, that target 8 separate regions of a nucleic acid sequence. An accurate selection of the primers, their concentrations and their melting temperatures (Tm) is essential in order that the annealing of the numerous primers on the target can be finely orchestrated at the proper reaction temperature: therefore the phase of primers’ design is crucial in order to obtain successful LAMP reactions.
Although some software applications specific for LAMP primer design exist, they often have several limitations: as a consequence, the selection of the candidate primer set is time-consuming and needs to be done by numerous trial-and-error laboratory experimentations.
The aim of this project was the development of a primer designing software application tailored to DiaSorin LAMP requisites.
As a first step, we have created a database of thermodynamic parameters that has been integrated with a hybridization algorithm: this tool has enabled us to obtain primers Tm calculation and prediction of secondary structures formation at different temperatures and salt concentrations.
Once created the engine of our prediction system, we have developed an assisted and an automatic primer design modes. In the first case, after selecting the target sequence, the experimental conditions and the design criteria, the user is helped during the manual selection of primers along the target thanks to a conditional formatting highlighting data that differ from the design criteria previously set. In the automatic design mode, the software generates a number of primer sets based on the acceptance criteria inserted into the system and identifies the best sets by assigning them a score.
In addition, the software has been implemented through the development of a tool for the evaluation of primers dimers in multiplex assays, characterized by the simultaneous amplification of more transcripts in one single reaction. This tool predicts the formation of possible intermolecular secondary structures between the numerous primers present in the solution, displays them graphically and provides information about their extensibility.
Finally, we have developed a tool for the graphical representation of dumbbells, which are the key structures of the exponential amplification characteristic of a LAMP reaction.
In the future we will assess if our primer designing software provides accurate predictions of the real experimental conditions of a LAMP reaction: at this purpose we will perform explorative studies on the software through dedicated tests. In addition we will evaluate the possibility to add further improvements to the software, based on DiaSorin experience with LAMP technique.
The creation of such a software guarantees the existence of a DiaSorin primer designing system, which ensures intellectual property, can make a significant contribution to an easier and more efficient development of LAMP assays and can be further implemented according to our needs.
Books on the topic "LAMP, Primer Design, Software Development"
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Blikle, Andrzej. MetaSoft primer: Towards a metalanguage for applied denotational semantics. Berlin: Springer-Verlag, 1987.
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MetaSoft primer: Towards a metalanguage for applied denotational semantics. Berlin: Springer-Verlag, 1987.
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Kelsey, Todd. Drupal 7 primer: Creating CMS-based websites : a guide for beginners. Boston, Mass: Cengage Learning, 2012.
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Blikle, Andrzej. Metasoft Primer: Towards a Metalanguage for Applied Denotational Semantics (Lecture Notes in Computer Science). Springer, 1988.
Find full textConference papers on the topic "LAMP, Primer Design, Software Development"
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Pakštas, Algirdas, Danuté Paketūraite, and Artūras Tamkevičius. "OCCAM-Oriented Software Tools." In Simpósio Brasileiro de Arquitetura de Computadores e Processamento de Alto Desempenho. Sociedade Brasileira de Computação, 1992. http://dx.doi.org/10.5753/sbac-pad.1992.22735.
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For many years software engineers have been providing the engineers of other fields with advanced design tools. But the tools used by software designers themselves look quite primitive in comparison. Only CASE-like systems developed during last years can provide reasonable help to software developers. Experimental software development systems ALADDIN/LAMP is oriented to creation of distributed computer control systems (DCCS). Proposed approach to development distributed software configurations (DSCs) is based on the model of virtual distributed software configuration (VDSC) with information-transport ports (ITPs) as interconnecting servers. Transputer networks and OCCAM-written software are often used for creation of DCCS. An approach to ALADDIN/LAMP tools-extention for OCCAM-written DSCs handling is discussed in this paper. Survey of tools is presented (OCCAM-oriented structure editor OSE, OCCAM structure extractor OSX, ALADDIN/OOB translator and deadlock locator and analyser DLA). A comparison with related works is given.
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Steelman, Kelly, and Holly Handley. "A Primer on the Human Readiness Level Scale (ANSI/HFES 400-2021)." In 13th International Conference on Applied Human Factors and Ergonomics (AHFE 2022). AHFE International, 2022. http://dx.doi.org/10.54941/ahfe1002448.
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The Human Readiness Level (HRL) Scale is a simple 9-level scale for evaluating, tracking, and communicating the readiness of a technology for safe and effective human use. It is modeled after the well-established Technology Readiness Level (TRL) framework that is used throughout the government and industry to communicate the maturity of a technology and to support decision making about technology acquisition. The TRL framework, however, does not consider the technology’s readiness for human use. As human error is implicated in 60-90% of incidents and accidents across a range of domains, it is critical to consider a technology’s human readiness alongside its technological maturity. The HRL scale was developed to address this need and to complement and supplement the TRL. In 2019, Drs. See (Sandia National Laboratories) and Handley (HFES Science Policy Fellow; Old Dominion University) formed a working group of practitioners across DoD, industry, and academia to mature the HRL concept; evaluate its usability, reliability, and validity; and develop a standard. The resulting ANSI/HFES 400-2021 Standard defines the HRL scale and provides guidance on how to apply them within a system development process. The standard provides questions to guide evaluation activities, with exit criteria and examples of the supporting evidence required to progress from one level to the next. The HRLs map on to three phases of the development process: Basic Research and Development (HRL 1-3), Technology Demonstrations (HRL 4-6), and Full-Scale Testing, Production, and Deployment (HRL 7-9):HRL 1: Basic principles for human characteristics, performance, and behavior observed and reportedHRL 2: Human-centered concepts, applications, and guidelines definedHRL 3: Human-centered requirements to support human performance and human-technology interactions establishedHRL 4: Modeling, part-task testing, and trade studies of human systems design concepts and applications completedHRL 5: Human-centered evaluation of prototypes in mission relevant part-task simulations completed to inform designHRL 6: Human systems design fully matured and demonstrated in a relevant high-fidelity, simulated environment or actual environmentHRL 7: Human systems design fully tested and verified in operational environment with system hardware and software and representative usersHRL 8: Human systems design fully tested, verified, and approved in mission operations, using completed system hardware and software and representative usersHRL 9: System successfully used in operations across the operational envelope with systematic monitoring of human system performance The proposed presentation is part of an HFES initiative to socialize HRLs within the government, industry, and academia. The presentation will provide concrete examples drawn from the transportation sector to illustrate how HRLs can be applied throughout a human systems integration process.ReferencesHFES/ANSI (2021). Human Readiness Level Scale in the System Development Process (ANSI/HFES 400-2021). Retrieved from https://www.hfes.org/publications/technical-standardsSalazar, G., See, J. E., Handley, H. A., & Craft, R. (2020, December). Understanding human readiness levels. In Proceedings of the Human Factors and Ergonomics Society Annual Meeting (Vol. 64, No. 1, pp. 1765-1769). Sage CA: Los Angeles, CA: SAGE Publications.See, J. E. (2021). Human Readiness Levels Explained. Ergonomics in Design, 10648046211017410.