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.
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Akhmetzianova, L. U., T. M. Davletkulov, R. R. Garafutdinov, and I. M. Gubaydullin. "Application of the Aho-Korasik Algorithm for the Selection of Primers for Loop Isothermal Amplification." Mathematical Biology and Bioinformatics 17, no. 2 (November 14, 2022): 250–65. http://dx.doi.org/10.17537/2022.17.250.
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This paper presents a program which allows user to do primer design for identifying DNA target site or a whole genome with a goal of performing loopmediated isothermal amplification. The review of the most popular existing primer design programs for LAMP is carried out. Recommended conditions are presented in the paper. They are required to be taken in consideration during the process of primer design for loop-mediated isothermal amplification. These are the conditions: primer’s length, GC-content, amplicon average size, annealing temperature and distance between primers. A search for primer positions in genome is needed since loop-mediated isothermal amplification requires primer kits that consist of 6 primers in order for primer design to be done. The Aho–Corasick algorithm was proposed for a search implementation. This algorithm is capable of simultaneous search for a number of sample (primer) entries in a longer sequence (a fragment or a whole genome). This software allows the search for primers in genomes of various length and it groups primers by kits, which in turn could be applied in laboratory experiments. These kits are formed according both to the recommended conditions of primer selection for performing loop-mediated isothermal amplification and to the initial conditions, which are determined by the user before the process. After that, the user may choose the best option for their case from a list of primer kits that are being created as a result of performed computer analysis. The test run of the program was done during the search for a specific primer kit that is meant to be used for performing loop-mediated isothermal amplification of genome with a goal of detection of novel coronavirus infection SARS-CoV-2, a virus that triggers a dangerous disease, COVID-19. The software was developed using Python with BioPython and Pyahocorasick libraries and available at the link: https://cloud.mail.ru/public/C7av/QCkSiUomz.
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Zerilli, Francesco, Cinzia Bonanno, Erlet Shehi, Giulia Amicarelli, Daniel Adlerstein, and G. Mike Makrigiorgos. "Methylation-Specific Loop-Mediated Isothermal Amplification for Detecting Hypermethylated DNA in Simplex and Multiplex Formats." Clinical Chemistry 56, no. 8 (August 1, 2010): 1287–96. http://dx.doi.org/10.1373/clinchem.2010.143545.
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BACKGROUND Aberrant DNA methylation of gene promoters and the associated silencing of tumor suppressor genes are recognized as mechanisms contributing to tumor development. Therefore, detection of promoter hypermethylation is becoming important for diagnosis, prognosis, and aiding the design of cancer therapies. We describe a novel isothermal method for the detection of DNA hypermethylation. METHODS Methylation-specific loop-mediated isothermal amplification (MS-LAMP) is a novel adaptation of LAMP. MS-LAMP was used for the highly specific detection of hypermethylated CpGs in the promoters of the CDKN2A [cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)], GATA5 (GATA binding protein 5), and DAPK1 (death-associated protein kinase 1) genes. The reactions occurred under isothermal conditions with 3 primer sets specific for methylated promoters. Both turbidimetry and fluorescence were used for detection. The MS-LAMP assay was validated with bisulfite-treated plasmid and genomic DNA controls of known methylation status and was applied to detect hypermethylation in 18 clinical tumor samples. A multiplex MS-LAMP for CDKN2A, GATA5, and DAPK1 was also validated with the aid of synthetic positive and negative controls. RESULTS The MS-LAMP assay showed high specificity with plasmid and genomic DNA targets in reactions carried out in <1 h. The assay had a detection limit of approximately 30 copies of methylated target sequence and a selectivity of 0.5% methylated DNA in a mixture with unmethylated DNA. Compared with methylation-specific PCR, the MS-LAMP assay detected lower rates of methylation in lung adenocarcinoma samples. Simultaneous multiplex detection of hypermethylation in the 3 targets (CDKN2A, GATA5, and DAPK1) was readily achieved with the MS-LAMP assay in both the turbidimetric and fluorescence detection formats. CONCLUSIONS MS-LAMP provides a highly specific isothermal method for methylation detection and is well suited for multiplex approaches.
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Yusuf, Muhammad Yusuf, and Winarso Winarso. "Evaluasi Tingkat Kualitas Pencahayaan Pada Gedung Fakultas Keguruan Dan Ilmu Pendidikan Universitas Muhammadiyah Purwokerto." Jurnal Riset Rekayasa Elektro 4, no. 2 (January 3, 2023): 51. http://dx.doi.org/10.30595/jrre.v4i2.12790.
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Good lighting intensity can affect the quality of performance in activity, improper lighting can also cause mental stress on room users, eye disorders, and disorders of the body. This research was created to analyze the needs and suitability of light quality by performing calculations of lamp types, luxmeter measurements and visualization using Dialux. Dialux is software for simulating, visualizing, and analyzing the performance of lighting systems in geographic locations and environments of specific objects, with optimal lighting situation results. When researching the intensity of lighting in the room in the Building of the Faculty of Teacher Training and Education, one of them in the development laboratory room obtained the results of calculations of 86.66 lux, measurement of luxmeter 83.44 lux, and the results of 109 lux dialux analysis, this is due to shrinkage in the installed lamp, as well as the lack of armature, and lamp point so that the intensity of lighting has not met the Indonesian National Standard of laboratory space of 500 lux. So the solution was made a design recommendation that refers to the Indonesian National Standard. One of the design recommendations made in the development laboratory room obtained results of 561 lux using a type of Meval LED Tube lamp 22 Watts. Because the index in each room is different, when determining the light point must be rounded according to the needs of the room. Keywords :Dialux Visualization, Evaluation of lighting levels, Design recommendations, Indonesian National Standard
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Lin, Jian Yi, Ting Zhao, and Gong Quan Liu. "The Design of Active Power Filter Based on Power Line Carrier Communication." Advanced Materials Research 614-615 (December 2012): 1587–90. http://dx.doi.org/10.4028/www.scientific.net/amr.614-615.1587.
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The development of street lamp control system has set a higher demand of more energy-saving and more effective which urges us to research the data transmission method based on Power Line Carrier between lamps and control center.By analyzing the influences on power line channel and signals burdened which produced by high harmonics and pulse interference from power supplies,we designed the active power filter fitted our demands.Besides, object oriented design method has been taken,combined software calculation and emulation,having effectively avoided complex computations in analogue filter design.
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Yang, Lina, Liang Zhang, Jun Cao, Lingyun Wang, Hengsong Shi, Feng Zhu, and Zhaolin Ji. "Rapid Detection of Peach Shoot Blight Caused by Phomopsis amygdali Utilizing a New Target Gene Identified from Genome Sequences Within Loop-Mediated Isothermal Amplification." Plant Disease 106, no. 2 (February 1, 2022): 669–75. http://dx.doi.org/10.1094/pdis-08-21-1645-re.
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Peach shoot blight (PSB), caused by Phomopsis amygdali, is a serious threat to the healthy development of the peach industry and leads to 30 to 50% damage to peach production in southern China. In this study, loop-mediated isothermal amplification (LAMP) technology was used to detect the P. amygdali target of a gene of GME6801 that was unique in the whole genome of the pathogen compared with that of Diaporthe (Phomopsis) longicolla TWH P74, Fusarium graminearum PH-1, Colletotrichum gloeosporioides SMCG1 and Magnaporthe oryzae 70-15. Blast comparison of this gene sequence in NCBI database showed that no homologous sequences were found. Therefore, the gene sequence of GME6801 was used to design two pairs of LAMP primers and one pair of PCR primers. The results showed that both primer sets were specific to the 15 strains of P. amygdali, and the other 15 fungal strains presented negative reactions, similar to the control. In addition, 50 pg of genomic DNA of P. amygdali in a 25-μl reaction system could be detected by LAMP assay, which was 100 times more sensitive than PCR. Furthermore, the GME6801 LAMP assay was used to detect artificially inoculated twigs of the pathogen, disease twigs within significantly symptomatic PSB in the fields, and healthy twigs in the same orchard, with detection rates of 100, 75, and 20.8%, respectively. However, detection rates of conventional PCR were separately 100, 62.5, and 16.7%. The results indicated that GME6801-based LAMP could be used for P. amygdali detection as its specificity, sensitivity, and simplicity. This study provides a rapid experimental basis for the identification and prediction of P. amygdali that causes PSB and is beneficial for precise prevention and control of the disease.
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Shirshikov, Fedor V., Yuri A. Pekov, and Konstantin A. Miroshnikov. "MorphoCatcher: a multiple-alignment based web tool for target selection and designing taxon-specific primers in the loop-mediated isothermal amplification method." PeerJ 7 (April 26, 2019): e6801. http://dx.doi.org/10.7717/peerj.6801.
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Background Advantages of loop-mediated isothermal amplification in molecular diagnostics allow to consider the method as a promising technology of nucleic acid detection in agriculture and medicine. A bioinformatics tool that provides rapid screening and selection of target nucleotide sequences with subsequent taxon-specific primer design toward polymorphic orthologous genes, not only unique or conserved common regions of genome, would contribute to the development of more specific and sensitive diagnostic assays. However, considering features of the original software for primer selection, also known as the PrimerExplorer (Eiken Chemical Co. LTD, Tokyo, Japan), the taxon-specific primer design using multiple sequence alignments of orthologs or even viral genomes with conservative architecture is still complicated. Findings Here, MorphoCatcher is introduced as a fast and simple web plugin for PrimerExplorer with a clear interface. It enables an execution of multiple-alignment based search of taxon-specific mutations, visual screening and selection of target sequences, and easy-to-start specific primer design using the PrimerExplorer software. The combination of MorphoCatcher and PrimerExplorer allows to perform processing of the multiple alignments of orthologs for informative sliding-window plot analysis, which is used to identify the sequence regions with a high density of taxon-specific mutations and cover them by the primer ends for better specificity of amplification. Conclusions We hope that this new bioinformatics tool developed for target selection and taxon-specific primer design, called the MorphoCatcher, will gain more popularity of the loop-mediated isothermal amplification method for molecular diagnostics community. MorphoCatcher is a simple web plugin tool for the PrimerExplorer software which is freely available only for non-commercial and academic users at http://morphocatcher.ru.
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Karim, Shaista, R. Ryan McNally, Afnan S. Nasaruddin, Alexis DeReeper, Ramil P. Mauleon, Amy O. Charkowski, Jan E. Leach, Asa Ben-Hur, and Lindsay R. Triplett. "Development of the Automated Primer Design Workflow Uniqprimer and Diagnostic Primers for the Broad-Host-Range Plant Pathogen Dickeya dianthicola." Plant Disease 103, no. 11 (November 2019): 2893–902. http://dx.doi.org/10.1094/pdis-10-18-1819-re.
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Uniqprimer, a software pipeline developed in Python, was deployed as a user-friendly internet tool in Rice Galaxy for comparative genome analyses to design primer sets for PCRassays capable of detecting target bacterial taxa. The pipeline was trialed with Dickeya dianthicola, a destructive broad-host-range bacterial pathogen found in most potato-growing regions. Dickeya is a highly variable genus, and some primers available to detect this genus and species exhibit common diagnostic failures. Upon uploading a selection of target and nontarget genomes, six primer sets were rapidly identified with Uniqprimer, of which two were specific and sensitive when tested with D. dianthicola. The remaining four amplified a minority of the nontarget strains tested. The two promising candidate primer sets were trialed with DNA isolated from 116 field samples from across the United States that were previously submitted for testing. D. dianthicola was detected in 41 samples, demonstrating the applicability of our detection primers and suggesting widespread occurrence of D. dianthicola in North America.
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Zhao, Zhong Li, Bao Jun Zhou, Jian Zhuang, Da Ming Wu, Ya Jun Zhang, Xiu Ting Zheng, and Kai Fang Dang. "Design and Simulation Analysis of a New Type of Micro Metal-Plastic Heat Radiator." Key Engineering Materials 562-565 (July 2013): 1127–31. http://dx.doi.org/10.4028/www.scientific.net/kem.562-565.1127.
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With the development of micro-nanomachining technology (MNMT), micro heat radiator is getting attention. In this paper, the heat dissipation mechanism of light emitting diode (LED) ball lamp is introduced. And the LED heat radiator is simplified. On the basis of that, a new type of micro metal-plastic heat radiator of LED is put forward. And the LED heat radiator is simplified. A series of numerical simulations are carried out to compare the heat dissipation performance of micro heat radiator respectively made by metal, plastic, metal-plastic composite by the FloEFD software. Micro metal-plastic heat radiator structures, including fin spacing, fin thickness, fin height and substrate thickness, are carry out to be simulated.
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Ziolek, Scott A., and Pieter C. Kruithof. "Human Modeling & Simulation: A Primer for Practitioners." Proceedings of the Human Factors and Ergonomics Society Annual Meeting 44, no. 38 (July 2000): 825–27. http://dx.doi.org/10.1177/154193120004403839.
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More and more, digital human modeling and simulation is being used in conjunction with CAD systems to address ergonomic issues early within the development and manufacturing process. However, purchasing a human modeling software package does not guarantee a user-centered design anymore than purchasing a word processor makes someone an author. This paper addresses some of the practical issues that confront human modeling and simulation users, including the collection of geometry, posturing the manikin, and selection of an analysis. For the purposes of discussion, human simulation will be divided into three broad areas: the environment, manikin selection, and analysis.
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Iqbal, M. J., L. J. Grauke, A. S. Reddy, and T. E. Thompson. "066 Development of Simple Sequence Repeat DNA Markers for Use in Pecan Genetic Studies." HortScience 34, no. 3 (June 1999): 452D—452. http://dx.doi.org/10.21273/hortsci.34.3.452d.
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A microsatellite library has been developed from `Halbert', a native pecan selection from Coleman County, Texas, using methods developed at the Texas A&M Univ. Crop Biotechnology Center. A total of 6144 DNA fragment clones were archived in 384 well plates for screening. Four-hundred-thirty-nine clones were positive after Southern hybridization using di- and tri-nucleotide repeats as probes. One-hundred-twenty-five positive clones were sequenced on an ABI 377 automated DNA sequencer. Of these, 24 repeats had enough sequences at the two ends to design primers. Primers were designed using Primer Express software, and were synthesized by Genosys, USA. The simple sequence repeats (SSRs) chosen for primer analysis include di- (CA and GA) and tri-nucleotide repeats (CTT, GAA and GAT). The SSRs were amplified under high stringency conditions with temperatures based on length and GC content. Reproducibility was verified using `Halbert' DNA isolated from different inventories. Of the 24 primer pairs tested, 20 successfully amplified microsatellites from `Halbert'. DNA was isolated from 48 pecan and hickory accessions selected to strategically represent the genetic diversity of the NCGR Carya collections (a core collection). The accessions included parent-progeny combinations, individuals from geographically distant native populations, species, and interspecific hybrids. The 20 SSR primers that produced good amplification products in `Halbert' were used to evaluate the collection, with 11 revealing multiple sizes of the repeat. The number of bands amplified with different primer combinations ranged from 4 to 32 in the 48 genotypes tested. We used RFLPscan software to aid in gel scoring (sizing amplified fragments, and comparing amplification profiles), and NTSYSpc software to evaluate genetic similarities. Evaluation of the data confirms the utility of the primers in delimiting known relationships.
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Maulana, Ilham Tri, and Fadil Firdian. "DESIGN MULTIMEDIA INTERACTIVE FOR MEDIA LEARNING ON SOFTWARE APPLICATION COURSES." Jurnal Sains dan Informatika 3, no. 2 (November 30, 2017): 89. http://dx.doi.org/10.22216/jsi.v3i2.2350.
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<p>Penelitian ini bertujuan untuk merancang sebuah media pembelajaran berupa Multimedia Interaktif pada mata kuliah aplikasi software. Multimedia Interaktif ini dirancang sebagai salah satu media pembelajaran bagi dosen di perkuliahan. Penelitian ini menggunakan metode SDLC (System Development Life Cycle), adapun prosedur metode SDLC yaitu: Definisi Kebutuhan, Analisis Kebutuhan, Pengumpulan Data, Desain Aplikasi, Coding, Pengujian Sistem. Jenis data yaitu data primer dimana data yang diberikan oleh dosen pengampu mata kuliah. Teknik analisis data yang digunakan adalah teknik analisis data deskriptif yaitu dengan mendeskripsikan rancangan Multimedia Interaktif. Perancangan multimedia interaktif diharapkan bisa memfasilitasi kebutuhan mahasiswa dan dosen untuk mempelajari materi tersebut setiap saat tanpa ada batasan waktu dan tempat. Software yang digunakan adalah Macromedia Flash CS .3</p><p> </p><p><em>This research aimed to design a learning media in the form of Interactive Multimedia course on software applications. Interactive Multimedia is designed as a media of learning for lecturer in the Class. This study uses SDLC (System Development Life Cycle), while the procedure SDLC methods are: Definition of Requirements, Needs Analysis, Data Collection, Application Design, Coding, Testing System. Types of data are primary data where the data provided by the lecturer of the course. Data analysis technique used is the technique of descriptive data analysis is to describe the design of Interactive Multimedia. The design of interactive multimedia is expected to facilitate the needs of students and faculty to learn the material at any time without any limitation of time and place. Software used is Macromedia Flash CS 3.</em></p><p><em> </em></p>
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Slamet Winardi, Didik Dwi Suharso, Hendra Purnomo, and Arief Budijanto. "Battery Power Control and Monitoring System with Internet of Things Technology." IJCONSIST JOURNALS 3, no. 1 (December 28, 2021): 07–12. http://dx.doi.org/10.33005/ijconsist.v3i1.56.
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Along with the development of battery/ACCU technology, the ACCU charging and loading system has also developed manually or automatically. In this paper, the results of research on the manufacture of tools that function to monitor and control the charging and loading of electrical power will be explained from batteries that are burdened with lights and DC motors through a control panel or android smart phone with IoT technology. This tool is designed to monitor 2 ACCUs, namely ACCU1 and ACCU2. ACCU1 is loaded with lamp and parallel with DC motor load while ACCU2 is loaded with DC motor and parallel with lamp load. If ACCU1 and ACCU2 are full, ACCU1 is loaded with only one lamp and ACCU2 is only loaded with DC motor. For example, ACCU1's electrical power is still within the limits that can be loaded with lights and DC motors while ACCU2 can't be loaded because electric power is not capable of being loaded with DC motors, the DC motor's load will be transferred to ACCU1. So that ACCU1 is loaded with DC lamps and motors and ACCU2 is charging the electricity, as well as for the opposite condition. The design of this tool uses the main component of the ESP32 microcontroller, where this component has been integrated with the wifi module and other supporting circuit modules, namely the current sensor circuit, voltage sensor and OLED display. The software design consists of a program code designer for hardware using C++ and an android smart phone application design using MIT App Inventor. The results of this study are in accordance with the design specifications, namely the device can be used to control charging and loading as well as monitor ACCU1 and ACCU2 electrical power on OLED screens and on Android smart phones screens
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Li, Xueyi, Shuhui Ding, Junying Wei, and Quanwei Wang. "Research on Teaching Method of Mold Course Based on CAD/CAE/CAM Technology." International Journal of Emerging Technologies in Learning (iJET) 12, no. 07 (July 12, 2017): 136. http://dx.doi.org/10.3991/ijet.v12i07.7224.
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The teaching of the traditional mold courses focus on the illustration of theoretical knowledge. Therefore, associating the design, evaluation, and manufacture links as a whole is difficult. Students cannot shape system knowledge, thereby making the study difficult. In addition, traditional teaching cannot meet the current enterprise needs of talents who have mold CAD/CAE/CAM technology. This study presents a teaching method that applies CAD/CAE/CAM technology to mold teaching. First, the positive effects of these technologies on the mold design and manufacturing process are introduced. Thereafter, lamp cover is used as an example to establish a series of computer-aided teaching development processes using existing software for mold design, mold flow analysis, and machining simulation. Lastly, survey results demonstrate that the effects of the proposed teaching method are better than the traditional method. Moreover, students and enterprises are substantially recognized in this teaching method.
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Valiente Moro, Claire, Olivier Crouzet, S�r�na Rasconi, Antoine Thouvenot, G�rard Coffe, Isabelle Batisson, and Jacques Bohatier. "New Design Strategy for Development of Specific Primer Sets for PCR-Based Detection of Chlorophyceae and Bacillariophyceae in Environmental Samples." Applied and Environmental Microbiology 75, no. 17 (July 10, 2009): 5729–33. http://dx.doi.org/10.1128/aem.00509-09.
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ABSTRACT Studying aquatic microalgae is essential for monitoring biodiversity and water quality. We designed new sets of 18S rRNA PCR primers for Chlorophyceae and Bacillariophyceae by using the ARB software and implementing a virtual PCR program. The results of specificity analysis showed that most of the targeted algal families were identified and nontargeted organisms, such as fungi or ciliates, were excluded. These newly developed PCR primer sets were also able to amplify microalgal rRNA genes from environmental samples with accurate specificity. These tools could be of great interest for studying freshwater microalgal ecology and for developing bioindicators of the health status of aquatic environments.
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Ilamsyah, Ilamsyah, Feizal Hazriel Maulana, and Roy Denni Simanjuntak. "PROTOTYPE PENGONTROLAN SISTEM HIDROLIK PADA GUDANG BERBASIS ARDUINO." Journal CERITA 3, no. 1 (February 1, 2017): 18–26. http://dx.doi.org/10.33050/cerita.v3i1.614.
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Along with the development of the automatic control the world of technology at this present time, making the control system automatically helps a person to ease his work. A lot out there who already using a wide variety of automatically working systems. Automatic control system now can make various kinds of variety such as controlling hydraulic system automatically to avoid flooding. This control is done using an Arduino microcontroller and ultrasonic sensors, which the microcontroller as input media program that will be in the process and ultrasonic sensors to measure the distance of the water level. The method used to design the hydraulic system uses a flowchart, The hardware used includes Arduino Uno, Ultrasonic Sensors, Motor-drive (DC), Lamp LED, buzzer and several other electronic devices. The design of the hardware using the Arduino Uno as a medium to instill the program and software design were performed using of Arduino . Automatic control is intended to avoid damage to the goods caused by flooding.
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Gagliardi, Gianfranco, Marco Lupia, Gianni Cario, Francesco Tedesco, Francesco Cicchello Gaccio, Fabrizio Lo Scudo, and Alessandro Casavola. "Advanced Adaptive Street Lighting Systems for Smart Cities." Smart Cities 3, no. 4 (December 7, 2020): 1495–512. http://dx.doi.org/10.3390/smartcities3040071.
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This paper reports the results of a recently concluded R&D project, SCALS (Smart Cities Adaptive Lighting System), which aimed at the development of all hardware/software components of an adaptive urban smart lighting architecture allowing municipalities to manage and control public street lighting lamps. The system is capable to autonomously adjust street lamps’ brightness on the basis of the presence of vehicles (busses/trucks, cars, motorcycles and bikes) and/or pedestrians in specific areas or segments of the streets/roads of interest to reduce the energy consumption. The main contribution of this work is to design a low cost smart lighting system and, at same time, to define an IoT infrastructure where each lighting pole is an element of a network that can increase their amplitude. More generally, the proposed smart infrastructure can be viewed as the basis of a wider technological architecture aimed at offering value-added services for sustainable cities. The smart architecture combines various sub-systems (local controllers, motion sensors, video-cameras, weather sensors) and electronic devices, each of them in charge of performing specific operations: remote street segments lamp management, single street lamp brightness control, video processing for vehicles motion detection and classification, wireless and wired data exchanges, power consumptions analysis and traffic evaluation. Two pilot sites have been built up in the project where the smart architecture has been tested and validated in real scenarios. Experimental results show that energy savings of up to 80% are possible compared to a traditional street lamp system.
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Jagesar, Raj R., Jacob A. Vorstman, and Martien J. Kas. "Requirements and Operational Guidelines for Secure and Sustainable Digital Phenotyping: Design and Development Study." Journal of Medical Internet Research 23, no. 4 (April 7, 2021): e20996. http://dx.doi.org/10.2196/20996.
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Background Digital phenotyping, the measurement of human behavioral phenotypes using personal devices, is rapidly gaining popularity. Novel initiatives, ranging from software prototypes to user-ready research platforms, are innovating the field of biomedical research and health care apps. One example is the BEHAPP project, which offers a fully managed digital phenotyping platform as a service. The innovative potential of digital phenotyping strategies resides among others in their capacity to objectively capture measurable and quantitative components of human behavior, such as diurnal rhythm, movement patterns, and communication, in a real-world setting. The rapid development of this field underscores the importance of reliability and safety of the platforms on which these novel tools are operated. Large-scale studies and regulated research spaces (eg, the pharmaceutical industry) have strict requirements for the software-based solutions they use. Security and sustainability are key to ensuring continuity and trust. However, the majority of behavioral monitoring initiatives have not originated primarily in these regulated research spaces, which may be why these components have been somewhat overlooked, impeding the further development and implementation of such platforms in a secure and sustainable way. Objective This study aims to provide a primer on the requirements and operational guidelines for the development and operation of a secure behavioral monitoring platform. Methods We draw from disciplines such as privacy law, information, and computer science to identify a set of requirements and operational guidelines focused on security and sustainability. Taken together, the requirements and guidelines form the foundation of the design and implementation of the BEHAPP behavioral monitoring platform. Results We present the base BEHAPP data collection and analysis flow and explain how the various concepts from security and sustainability are addressed in the design. Conclusions Digital phenotyping initiatives are steadily maturing. This study helps the field and surrounding stakeholders to reflect upon and progress toward secure and sustainable operation of digital phenotyping–driven research.
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Badran, Samir, Ming Chen, and John E. Coia. "Multiplex Droplet Digital Polymerase Chain Reaction Assay for Rapid Molecular Detection of Pathogens in Patients With Sepsis: Protocol for an Assay Development Study." JMIR Research Protocols 10, no. 12 (December 13, 2021): e33746. http://dx.doi.org/10.2196/33746.
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Background Blood cultures are the cornerstone of diagnosis for detecting the presence of bacteria or fungi in the blood, with an average detection time of 48 hours and failure to detect a pathogen occurring in approximately 50% of patients with sepsis. Rapid diagnosis would facilitate earlier treatment and/or an earlier switch to narrow-spectrum antibiotics. Objective The aim of this study is to develop and implement a multiplex droplet digital polymerase chain reaction (ddPCR) assay as a routine diagnostic tool in the detection and identification of pathogens from whole blood and/or blood culture after 3 hours of incubation. Methods The study consists of three phases: (1) design of primer-probe pairs for accurate and reliable quantification of the most common sepsis-causing microorganisms using a multiplex reaction, (2) determination of the analytical sensitivity and specificity of the multiplex ddPCR assay, and (3) a clinical study in patients with sepsis using the assay. The QX200 Droplet Digital PCR System will be used for the detection of the following species-specific genes in blood from patients with sepsis: coa (staphylocoagulase) in Staphylococcus aureus, cpsA (capsular polysaccharide) in Streptococcus pneumoniae, uidA (beta-D-glucuronidase) in Escherichia coli, oprL (peptidoglycan-associated lipoprotein) in Pseudomonas aeruginosa, and the highly conserved regions of the 16S rRNA gene for Gram-positive and Gram-negative bacteria. All data will be analyzed using QuantaSoft Analysis Pro Software. Results In phase 1, to determine the optimal annealing temperature for the designed primer-probe pairs, results from a gradient temperature experiment will be collected and the limit of detection (LOD) of the assay will be determined. In phase 2, results for the analytical sensitivity and specificity of the assay will be obtained after an optimization of the extraction and purification method in spiked blood. In phase 3, clinical sensitivity and specificity as compared to the standard blood culture technique will be determined using 301 clinical samples. Conclusions Successful design of primer-probe pairs in the first phase and subsequent optimization and determination of the LOD will allow progression to phase 3 to compare the novel method with existing blood culture methods. International Registered Report Identifier (IRRID) PRR1-10.2196/33746
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Handayani, Indah Nursyamsi, Wike Kristianti, Mamurotun Mamurotun, and Andy Sambiono. "RANCANG BANGUN SISTEM PEMUTUS ARUS SEBAGAI PENGAMAN TEMPERATUR BERLEBIH PADA INKUBATOR BAYI." Jurnal Sehat Mandiri 16, no. 1 (June 30, 2021): 162–71. http://dx.doi.org/10.33761/jsm.v16i1.331.
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Several countries in the world, including Indonesia, have reported baby-care accidents in the baby incubator due to the failure of the temperature control system to maintain a stable temperature. Therefore, this study reports the design of an circuit breaker system as an over-temperature safety in a baby incubator. Experimentally, the prototype consists of hardware design, software design, and testing system design. The hardware design has four main part, sensing layer using PT1000 as a temperature sensor, data processing layer using an ESP32 microcontroller, a circuit breaker system using a solid-state relay as an electronic switching, and LCD as a display. System testing has been done by evaluating the temperature readings on a prototype against the HTC-02 digital thermometer instrument and carried out in the electromedical engineering laboratory. The results show the accuracy of the temperature parameter is 99% and the circuit breaker system is able to cut the current from the power supply to the appliance when the temperature is more than 39°C which is indicated by an incandescent lamp "off" where this is equivalent to a heater at the baby incubator is in the "off" condition. From the results of this test, it can be concluded that the circuit breaker system as a safety over temperature in the baby incubator has functioned according to the design.Recommended the development of this prototype needs to be followed up by testing on low-tech baby incubators available at basic health care facilities so as to improve technology readiness to be effective in the community.
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Denning, Stephen. "New lessons for leaders about continuous innovation." Strategy & Leadership 43, no. 1 (January 19, 2015): 11–15. http://dx.doi.org/10.1108/sl-11-2014-0083.
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Purpose – After firms have made a technological breakthrough they need to practice continuous innovation to delight their customers so they will be able to keep dominating those markets in an enduring fashion. This masterclass aims to address the question, “So what’s involved in this rapid innovation?” Design/methodology/approach – To answer the question, the author looks first at a primer, What is DevOps? by Mike Loukides. It describes the continuing acceleration in innovation in software development. To illustrate best practice the author looks at the case of Software developer Etsy. Findings – In leading firms, instead of management approval being required for all changes, now all improvements that have been fully tested are deployed immediately – Within the broad strategic framework, the staff is authorized to proceed with continuous improvement. Practical implications – The reality is that most firms today, whether they know it or not, are already software companies and will steadily become more so. Their competence in dealing with software will be a key part of their competitive edge – or lack thereof. Originality/value – For leaders in all markets the lesson is – networked organizations using agile management practices and continuous deployment with a culture of trust, delegation and collaboration are able to move and innovate much more rapidly than traditional managements that are saddled with legacy cultures of hierarchical bureaucracy.
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Kulikov, Dmitriy, Viktor Moiseev, and Alexandra Artemeva. "COMPUTATIONAL AND EXPERIMENTAL STUDY OF THE EFFECT OF AN INFRARED EMITTER WITH A CORNER REFLECTOR ON A PLATE UNDER CONDITIONS OF NATURAL CONVECTION." Perm National Research Polytechnic University Aerospace Engineering Bulletin, no. 68 (2022): 38–48. http://dx.doi.org/10.15593/2224-9982/2022.68.05.
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The paper presents the results of work on the creation and development of a numerical thermal infrared radiator based on a tubular halogen lamp KGT-220-1300, used during thermal vacuum tests of spacecraft. To develop a model and solve the problem of radiant-conductive-convective heat transfer, the Thermal Model Generator software was used. The analysis of temperature fields was carried out using a thermal imaging camera. Variants of calculations for the functioning of the radiator at different values of the supply voltage are performed. The results of mathematical modeling using band approximation of the properties of the system elements together with the Monte Carlo method in solving the problem of heat exchange by radiation of the incandescent body-quartz bulb-reflector system have shown high efficiency. The reliability of the developed model is considered in the context of an experiment conducted to measure temperature fields on a plate, which acts as an object of control interacting with radiation, and a thermal imaging camera is an instrument of thermal control. The availability of such a model at the disposal of developers of spacecraft thermal regime systems is an important step in a comprehensive work aimed at conducting end-to-end mathematical modeling of spacecraft thermal regimes, and will also allow it to be used for design calculations of radiation simulators.
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Fitri, Irza Guari Syah, and Tri Handoyo. "IDENTIFIKASI KARAKTERISTIK MORFOLOGI DAN MOLEKULER 21 VARIETAS PADI AROMATIK (Oryza sativa L.) BERDASARKAN PENANDA RAPD (Random Amplified Polymorphic DNA)." Berkala Ilmiah Pertanian 2, no. 2 (May 2, 2019): 72. http://dx.doi.org/10.19184/bip.v2i2.16174.
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ABSTRACT Aromatic rice (Oryza sativa L.) is one type of rice that has aroma and high selling price than non-aromatic rice. The variety development is needed to form superior aromatic rice. The variety development requires information about kinship and diversity between varieties. Kinship analysis with identification of morphological characteristics is an observation based on taxonomic approach. This research aims to determine the morphological characteristics and kinship of 21 aromatic rice varieties. The research was conducted from March to September 2018 with a randomized block design (RBD) of 3 replications. Observation variables used plant height (cm), number of productive tillers (tiller), age of flowering and harvesting (days), weight of 100 grain (gram), shape of grain, color of grain, color of rice and DNA band pattern as molecular data. Morphological data were analyzed by variance (ANOVA) and cluster analysis with UPGMA program (Unweight Pair Group Method with Arithmetic Mean) using DIST Coefficient on NTSYS 2.02 software. Molecular data showed in visualisation of DNA band using Primer OPB-07 based on RAPD marker. The research results showed the differences in morphological characters and kinship levels. Cluster analysis forms 2 clusters and 2 sub-clusters. Keywords: Aromatic Rice, Mophological Diversity, RAPD, Dendrogram ABSTRAK Padi aromatik (Oryza sativa L.) merupakan salah satu jenis padi yang memiliki aroma wangi dan memiliki harga jual yang lebih tinggi dibanding padi biasa. Pengembangan varietas diperlukan untuk membentuk padi aromatik yang lebih unggul. Pengembangan varietas membutuhkan informasi tentang kekerabatan dan keanekaragaman antar varietas. Analisis kekerabatan dengan identifikasi karakteristik morfologi merupakan suatu observasi berdasarkan pendekatan taksonomi. Percobaan ini bertujuan untuk mengetahui karakteristik morfologi dan molekuler 21 varietas padi aromatik. Percobaan dilakukan di mulai Maret - September 2018 dengan Rancangan Acak Kelompok (RAK) 3 ulangan. Variabel pengamatan menggunakan tinggi tanaman (cm), jumlah anakan produktif (batang), umur berbunga dan panen (HSS), bobot 100 gabah, bentuk gabah, warna gabah, dan warna beras serta pola pita DNA sebagai data molekuler. Data morfologi dianalisis dengan ragam (ANOVA) serta dianalisis gerombol dengan program UPGMA (Unweight Pair Group Method with Arithmetic Mean) menggunakan DIST Koefisien pada software NTSYS 2.02. Data molekuler ditunjukkan dalam bentuk visualisasi DNA menggunakan primer OPB-07 berdasarkan penanda RAPD. Hasil percobaan menunjukkan perbedaan karakter morfologi dan tingkat kekerabatan yang berbeda. Analisis gerombol membentuk 2 cluster dan 2 sub-cluster. Kata kunci: Padi Aromatik, Kekerabatan Morfologi, RAPD, Dendrogram
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Suyono, Bambang, and Eddy Prianto. "KAJIAN SENSASI KENYAMANAN TERMAL DAN KONSUMSI ENERGI DI TAMAN SRIGUNTING KOTA LAMA SEMARANG." MODUL 18, no. 1 (May 23, 2018): 18. http://dx.doi.org/10.14710/mdl.18.1.2018.18-25.
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An active park is indicated by the people activities and supported by the elements of street furniture. Hardware and software elements are the inside parts which play an important role in creating the comfort, wherein supported by the sustainability of the exterior gardens (outside the building) in the tropics play a very important role in the microclimate environment. The phenomenon of the relationship between conservation of ancient areas in the tropics such as Semarang city and the national energy crisis in the last decade is very interesting to be explored. As the development of instructional subject matter of Advance Landscape, Architecture Design and Building Physics in the basic of this research, our research question is: How far is the relationship between the energy profile consumption (lamp lighting) to comfort in the park?Two methods used in the field observation, the measurement of climate aspect to find out the micro climate profile and the distribution of questionnaire in the park to discover the user comfort sensation. The results found Taman Srigunting in the old city of Semarang is categorized both as a passive and active park, used for prominent activity in photography. These parks also influence the surrounding nature by decreasing the microclimate such as air temperature and humidity in the evening in the amount of 76% and 57% in the day. The air temperature went down from 34.8 C to 28.7 C. The micro climatic conditions and characteristics of energy consumption level was significant with the visitors comfort sensations, where in 56% visitors felt comfortable and only 4% felt the sensation of heat.
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Xu, Zhengwang, Wei Mei, Jiaqi Yu, Jiarui Zhang, Yuchun Yi, and Zhou Huang. "Contradiction Analysis and Solution in the R&D of High-Power Solar LED Street Lamp Controller." Recent Advances in Electrical & Electronic Engineering (Formerly Recent Patents on Electrical & Electronic Engineering) 12, no. 1 (January 10, 2019): 12–19. http://dx.doi.org/10.2174/2352096511666180314141920.
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As being restricted by factors such as cost, efficiency and size, the development of high-power solar LED street light controller is faced with plenty of difficulties. In case that a structure of two independent DC/DC is applied as the main circuit, it has to face problems such as large size and high cost; in case of applying the bidirectional BUCK/BOOST circuit, it requires change-over switches to control the solar panel and LED light. As being restricted by withstanding voltage, on-resistance and cost, a PMOS device cannot be used as the change-over switch of solar panel and LED light. However, when being used as a change-over switch, an NMOS device must apply the low-side mode under which the negative ends of the mentioned three parts are cut off. In the condition of applying the low-side mode, a differential circuit must be used to detect the voltage of the solar panel. Furthermore, in order to make sure batteries can still be regularly charged after wearing out in daylight, the controller must be supplied with power through a dual power supply circuit that can obtain power from both the solar panel and the battery. The demander has a requirement on extremely low standby power consumption of the product, and thus it is necessary to minimize the circuit that is live while working in standby mode. Methods: The bidirectional BUCK/BOOST circuit structure is applied to the main circuit to realize a higher change-over efficiency while giving considerations to both cost and size. The NMOS device, model IRFB4410ZPBF, with a price of about three yuan, is used as the switching device, and the low-side mode is applied, that is the switches inserted in between negative end of the solar panel or LED light and that of the DC/DC circuit. The low-cost rail-to-rail operational amplifier LM358 is used to form a differential amplification circuit for detecting the voltage of the solar panel. A XL1509-12E1 chip that only costs 0.88 yuan/pc is selected as the main change-over chip for the power supply, which has realized the highly-efficient and low-cost change-over of the power supply. A dual power supply circuit and a step-down protective circuit are designed for the XL1509-12E1 change-over chip. By comparing solar panel voltage with battery voltage, the solar panel booting circuit is realized. Only when solar panel voltage is higher than battery voltage, does the system program start to power it up for running, so that the outage of most of the circuits of the system under standby mode does not consume energy. Furthermore, the solar panel voltage detecting circuit, the solar panel booting circuit and several return difference functions are corrected during system debugging. Results: The circuit board of the entire controller features small size, low cost and high efficiency. It measures about 100*62*18mm in size, costs about 60 yuan, and the charge/discharge change-over efficiency reaches up to over 95%. The controller has many functions: it is capable of operating within a large scope, in which, solar panel voltage is subject to 15~50V, LED light voltage is subject to 15~60V, battery voltage is subject to 10~35V and battery-end charge/discharge current is 10A; it is capable of adapting to monocrystalline silicon/multicrystalline silicon/thin-film and many other kinds of solar panels, as well as lithium/lead-acid and many other kinds of batteries; it is capable of detecting the conversion of day and night, automatically controlling charging and discharging and automatically making adaptive adjustment according to seasonal variations; the current to be consumed during standby will be maintained below 3mA, and thus the power consumption is extremely low. Conclusion: By selecting the bidirectional BUCK/BOOST circuit structure, applying low-side mode for switching of solar panel and LED light, using a differential circuit to detect solar panel voltage, using a low-cost DC/DC chip to realize power supply change-over, designing a dual power supply circuit, introducing solar panel booting circuit and other hardware design, as well as MPPT algorithm, state recognition and control, return difference control and other software design, a solar LED street light control product featuring small size, low cost, high efficiency and multiple functions is successfully developed.
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Ivanova, Olga Nikolaevna, Sergey Alexandrovich Prokof'ev, and Tatiana Prokop'evna Bardymova. "Association of HLA-DQ trans-heterodimers with prevalence of type 1 diabetes mellitus in Buryat ethnic group." Diabetes mellitus 15, no. 3 (September 15, 2012): 11–18. http://dx.doi.org/10.14341/2072-0351-6080.
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Aims. Search for the most pronounced HLA II markers of type 1 diabetes mellitus (T1DM) in Buryat ethnic group and analysis ofHLA-DQ trans-heterodimers. Materials and methods. Case control design was applied for assessment of 74 patients with T1DM and 61 healthy individuals. Alleleidentification was performed with multi-primer allele-specific PCR technique. Association of genetic markers with pathology wasevaluated according to odds ratio (OR) index. All calculations were performed with StatSoft and STATISTICA 6 software applications. Results. We show that regarding race-specific highly diabetogenic HLA class II haplotypes Buryat ethnic group holds intermediateposition between Mongoloids and Caucasians and none of those haplotypes are associated with T1DM. We revealed a statisticallysignificant association of T1DM with DQA1*0301+DQB1*0201+ phenotype represented by trans-coding alleles in 77% of cases. Onpopulation level DQA1*0301+DQB1*0302+ or *0201+ phenotype is found to be the most sensitive marker. It was registered in 43%of patients with T1DM against 11.5% of controls (OR 5.9; рс=0.0094). DQA1*0301+/DQВ1*0201 and DQВ1*0302 phenotype is themost specific marker, registered in 16% of patients, but not found in controls (OR 11.8; рс=0.047).Conclusions. HLA-mediated risk for development of T1DM in Buryat ethnic group is determined by HLA-DQ trans-heterodimers.
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Nusyirwan, Deny, Muhammad Fahrudin, and Prasetya Perwira Putra Perdana. "Perancangan Purwarupa Pengatur Suhu Otomatis pada Inkubator Penetasan Telur Ayam Menggunakan Arduino Uno dan Sensor Suhu IC LM 35." JAST : Jurnal Aplikasi Sains dan Teknologi 3, no. 1 (June 11, 2019): 60. http://dx.doi.org/10.33366/jast.v3i1.1315.
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The development of electronic technology has created an ease in doing work especially those that require a long time as an example is the chicken egg incubator technology. If carried out manually, the chicken farmer must manually transfer the eggs, monitor the temperature set by the hour or set the expected temperature by experimenting many times. By using an automatic temperature controller, the farmer only needs one time to put the egg and put the sensor in the egg incubator. This study will discuss hardware and software which includes how to design a control device on a manually-controlled egg incubator for automatic control which consists of Arduino uno, a lamp as a heat source, a heat sensor, an LCD screen as an actual temperature sensor reader and fan as a room temperature stabilizer. From the results of testing the tool can function properly, ie the temperature is set to 38oC, if it exceeds the heat> 38oC, the fan will turn on to stabilize the temperature to 38oC.ABSTRAKPerkembangan teknologi elektronika telah menciptakan suatu kemudahan dalam melakukan pekerjaan terutama yang membutuhkan waktu yang lama sebagai contoh adalah teknologi penetas telur ayam. Jika dilaksanakan secara manual maka peternak ayam harus melakukan pemindahan telur secara manual, memantau keadaan suhu yang ditetapkan per jam atau mengatur suhu yang diharapkan dengan melakukan percobaan berkali-kali. Dengan menggunakan alat pengatur suhu otomatis maka peternak hanya memerlukan waktu sekali saja yaitu meletakkan telur dan meletakkan sensor dalam inkubator telur. Penelitian ini akan membahas tentang perangkat keras dan perangkat lunak yang meliputi Bagaimana merancang alat kontrol pada inkubator penetas telur yang terbuat secara manual kontrolnya menjadi kontrol otomatis yang terdiri dari Arduino uno, lampu sebagai sumber panas, sensor panas, layar LCD sebagai pembaca sensor suhu aktual dan kipas sebagai penstabil suhu ruangan. Dari hasil pengujian alat dapat berfungsi dengan baik yaitu suhu dibuat set point 38oC, jika melebihi panasnya > 38oC maka kipas akan hidup untuk menstabilkan suhu menjadi 38oC. Kata Kunci : perancangan; sensor suhu; arduino; penetas telur ayam
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Sandoval Delgado, MC Norma Angélica, MC María E. Loeza Corichi, MVZ Francisco Javier Gómez Ordóñez, and MC Salvador Jiménez Vallejo. "Creatividad y ambientes virtuales en el proceso de enseñanza-aprendizaje." CPU-e, Revista de Investigación Educativa, no. 12 (November 6, 2012): 115–29. http://dx.doi.org/10.25009/cpue.v0i12.53.
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Frente al requerimiento hacia las escuelas para que hagan uso de medios educativos que apoyen la enseñanza-aprendizaje, se realizó un material didáctico que ayudó a los alumnos de Primer Nivel de la Licenciatura de Médico Veterinario y Zootecnista, mediante el uso de ambientes virtuales. Se pretende aportar un instrumento que automatice y facilite el acceso y la utilización eficaz en el proceso de enseñanza-aprendizaje. El instrumento en cuestión es un tutorial de fácil manejo que simplifica la administración de la asignatura. Este trabajo toma como base los fundamentos de la investigación y desarrollo para diseñar, crear y aplicar un programa de software educativo. El programa informático utilizado para la preparación del tutorial es el Hot Potatoes. Esta elección se debe a que este programa permite la preparación de material interactivo autoejecutable y de autoaprendizaje. El proyecto también se plantea como un tutorial que sea útil a los profesores y que a través del CD puedan orientarse sobre cómo actualizarse y disponer de un medio que les permita sacar el máximo partido de la didáctica que utilizan.AbstractFaced with schools’ requirement of making use of educational media to support teaching and learning, a new form of teaching material was made in order to help freshman students in the Bachelors’ of Veterinary Medicine and Animal Science, through the use of virtual environments. It aims to provide a tool that systematises and facilitates access and effective use in the teaching-learning process. The instrument is an easy-to-use tutorial that simplifies the management of the course. This work builds on the fundamentals of research and development to design, create and implement an educational software program. The software needed for this tutorial is ‘Hot Potatoes’, due to this program allowing for the preparation of an interactive self-learning and self-executing material. This project is also intended as a useful tutorial for teachers who, through the CD, can be orientated in how to bring themselves up to date and provides a way that allows them to take advantage of their methodology to the maximum capacity.Recibido: 3 de febrero de 2010Aceptado: 27 de agosto de 2010
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Wroclawska, E., J. O. Brant, T. P. Yang, and K. Moore. "100 ASSESSMENT OF LOCUS-SPECIFIC DNA METHYLATION: OPTIMIZATION FOR BOVINE EMBRYOS." Reproduction, Fertility and Development 21, no. 1 (2009): 150. http://dx.doi.org/10.1071/rdv21n1ab100.
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Assessment of chromatin remodeling in early embryos is a major focus of studies today, and evaluation of DNA methylation at specific loci is one approach to study these epigenetic modifications. Our objective was to optimize the bisulfite sequencing methodology for use with very small cell numbers originating from pre-implantation embryos, making the process more time- and cost-efficient. The optimized steps include bisulfite conversion of small samples, bisulfite primer design, high-throughput plasmid DNA amplification, and preparation for sequencing. Methylation at 2 loci, Satellite I and Oct4, was investigated in bovine in vitro-produced (IVP) embryos collected at the 2-cell, 8-cell, and blastocyst stages. Bovine skin fibroblasts were first used to optimize the particular steps of the process. All reactions were run in duplicate and no-template negative and somatic cell-positive controls were treated alongside samples. Incorporating the use of Methyl Primer Express (Applied Biosystems, Foster City, CA), MacVector (Oxford Molecular Ltd., Campbell, CA), and Mfold software (Mathews DH et al. 1999 J. Mol. Biol. 288, 911–940; Zuker M 2003 Nucleic Acids Res. 31, 3406–3415) improved the specificity of bisulfite primers by exclusion of secondary or tertiary structures. The DNA from bisulfite treatment for 15 to 16 h was of better quality than DNA treated for 18 h. After initial PCR optimization, different cell concentrations were used to establish that detectable PCR products and subsequent methylation data could be obtained from DNA isolated from as few as 8 cells. Treating single blastocysts and pools of ten 8-cell and forty 2-cell embryos was sufficient for the entire scope of the experiment, allowing use of the same samples across all loci. After molecular cloning, plasmid DNA was amplified by 3 different methods and evaluated for efficiency: miniprep, TempliPhi (GE Healthcare, Piscataway, NJ), or 96-well glycerol stocks and automated TempliPhi format. Although TempliPhi alone was better than miniprep for small-scale experiments, it was the 96-well format that saved weeks of time and was most cost-effective. Sequencing was performed on a minimum of 8 clones/sample using ABI Prism sequencers (Applied Biosystems), and results were analyzed using Chromas Pro software (Technelysium Pty. Ltd., Helensvale, Australia). Percentage methylation of bovine IVP 2-cell, 8-cell, and blastocyst stage embryos for Satellite I was 25, 10, and 22%, respectively, and for Oct4 was 88, 88, and 79%, respectively. However, somatic cell methylation was 74% for Satellite I and 88% for Oct4, implying that Satellite I is demethylated during early embryo development, whereas Oct4 remains hypermethylated. In conclusion, these improved methods will benefit further studies of chromatin remodeling in early bovine pre-implantation embryos. This project was supported by National Research Initiative Competitive Grant no. 2006-35203-16620 from the USDA Cooperative State Research, Education, and Extension Service.
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Rodrigo Moriche, Mª Pilar, Margarita Vasco González, David Gil Pareja, and Javier Pericacho Gómez. "Mejora de los programas de formación inicial docente a partir de la trayectoria personal, académica y profesional del alumnado." Revista Electrónica Interuniversitaria de Formación del Profesorado 25, no. 2 (April 30, 2022): 1–14. http://dx.doi.org/10.6018/reifop.512851.
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To improve initial teacher training programs and favora positive encounter between students and those who design and implement them, it is necessary to have up-to-date information on entry profiles. This article describes the students according to their life experiences, previous knowledge, professional development and learning goals to know opportunities, needs and improvement trends. From a qualitative orientation, 62 initial evaluation tasks were selected for first-year students of the General Didactics subject of the Master's degree in Primary Education at Universidad XXX from the 2014-15 to 2019-20 academic year. The documentary analysis was supported by the computer software Atlas ti 9 from which emerged, through the articulation of the grounded theory, a set of categories whose relationships and interpretations, results were obtained that evidenced, among others: high teaching vocation and ideas preconceived in training and professional interests oriented to educational change. As main conclusions, it is proposed to connect with training and professionalexperiences related to the educational field as precursory teaching elements; promote innovative, participatory and teamwork methodologies; and guide the theory to educational practice and teaching organization. Para mejorar los programas de formación inicial docente y favorecer un encuentro positivo entre el alumnado y quienes los diseñan e implementan, es necesario disponer de información actualizada sobre los perfiles de entrada. Este artículo describe al alumnado según sus experiencias de vida, conocimientos previos, desarrollo profesional y metas de aprendizaje para conocer oportunidades, necesidades y tendencias de mejora. Desde una orientación cualitativa se seleccionaron 62 tareas de evaluación inicial del estudiantado de primer curso de la asignatura Didáctica General del grado de Maestro/a en Educación Primaria de la Universidad XXX desde el curso 2014-15 hasta 2019-20. El análisis documental fue apoyado por el software informático Atlas ti 9 del que emergieron, por medio de la articulación de la teoría fundamentada, un conjunto de categorías de cuyas relaciones e interpretaciones, se obtuvieron resultados que evidenciaban, entre otros: alta vocación docente e ideas preconcebidas en la formación e intereses profesionales orientados al cambio educativo. Como principales conclusiones se plantea conectar con la formación y experiencias profesionales afines al ámbito educativo como elementos precursores docentes; potenciar metodologías innovadoras, participativas y de trabajo en equipo; y orientar la teoría a la práctica educativa y a la organización docente.
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Paulus Sihombing, Nur Hanifah Yuninda, and Massus Subekti. "MODIFIKASI PANEL KONTROL SISTEM PENYEDIA AIR DINGIN PADA SISTEM VENTILASI ZONA RADIASI MENENGAH." Journal of Electrical Vocational Education and Technology 2, no. 1 (March 21, 2020): 6–12. http://dx.doi.org/10.21009/jevet.0021.02.
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This research aims to design and make modifications to the control panel of cold water supply system in the
ventilation system into the radiation zone semi-automatic medium so as to increase the value of the effectiveness and efficiency of the operation pattern 3 cold water supply system.
This study uses research and development and implemented in PRSG GAS BATAN, PUSPIPTEK SERPONG in november 2015 until June 2016. Modification of the control panel is used, CDAQ NI 9132, NI 9205, and 14.0
Labview software which will display chiller work in real time in graphs and nominal. Hardware input consists of, selector to choose the working water supply system cold, RTD PT100 as readers temperature of water entering the inlet pipe and the temperature of the water that comes out of the chiller, and sensor current transformer as a reader of electric current in the circulation pump, the output device is composed of pilot
working as an indication lamp chiller and a thermostat to control the chiller via the inlet pipe. The steps to create the control panel modification of the draft, the control panel wiring, wiring input NI 9205, a program in
Labview, then perform tests on the device.
Based on the results of testing known that the thermostat is able to control the chiller in accordance with the limits of the temperature setting on the thermostat. In the test results of pembacan incoming water temperature at the inlet pipe through the display labview program has a percentage error of 0.52%, while data readings out of the water temperature chiller 1 has a percentage of the reading error of 0.57%, the second chiller is 0 , 41% and chiller 3 is 0.45% and the data of electric current readings on the circulation pump shown in labv iew program has a percentage of error of 1.24% in chiller 1, and 1.62% in the chiller 2, and 1.27% the chiller 3. Once the system has been tested as a whole, so that it can be concluded that the modification of the control panel of the cold water supply system can work properly according to the principles of work that has been made
Abstrak
Sistem penyedia air dingin yang berjumlah 3 unit pada PRSG GAS BATAN sebagai penghasil air dingin
memiliki pola pengoperasian secara manual yang kurang efektif dan efesisen sehingga kurang optimal. Penelitian ini bertujuan untuk merancang dan membuat modifikasi panel kontrol sistem penyedia air dingin pada sistem ventilasi zona radiasi menengah menjadi semi otomatis sehingga dapat meningkatkan nilai efektifitas dan efesiensi dari pola pengoperasian 3 sistem penyedia air dingin.
Penelitian ini menggunakan metode penelitian dan pengembangan dan dilaksanakan di PRSG GAS BATAN, PUSPIPTEK SERPONG pada bulan november 2015 sampai juni 2016. Modifikasi panel kontrol ini menggunakan, CDAQ NI 9132, NI 9205, dan software Labview 14.0 yang akan menampilkan kerja chiller secara real time dalam bentuk grafik dan nominal. Peralatan input terdiri dari, selektor untuk memilih kerja sistem penyedia air dingin, RTD PT100 sebagai pembaca suhu air yang masuk pada pipa inlet dan suhu air yang keluar dari chiller, dan sensor current trafo sebagai pembaca listrik pada pompa sirkulasi, peralatan output terdiri dari pilot lamp sebagai indikasi kerja chiller dan thermostat untuk mengontrol chiller melalui pipa inlet. Langkah-langkah pembuatan modifikasi panel kontrol dari membuat rancangan, wiring panel kontrol, wiring input NI 9205, program pada Labview, kemudian melakukan uji coba pada alat.
Berdasarkan hasil dari pengujian diketahui bahwa thermostat mampu mengontrol chiller sesuai dengan batas setting suhu pada thermostat. Pada hasil pengujian dari pembacan suhu air yang masuk pada pipa inlet melalui tampilan program labview memiliki presentase kesalahan sebesar 0,52%, sedangkan data hasil pembacaan suhu air keluar dari chiller 1 memiliki presentase kesalahan pembacaan sebesar 0,57%, pada chiller 2 ialah 0,41% dan chiller 3 ialah 0,45% dan data hasil pembacaan listrik pada pompa sirkulasi yang ditampilkan dalam program labview memiliki presentase kesalahan 1,24% pada chiller 1, dan 1,62% pada chiller 2, dan 1,27% pada chiller 3. Setelah sistem diuji secara keseluruhan, sehingga dapat disimpulkan bahwa modifikasi panel kontrol sistem penyedia air dingin dapat bekerja dengan baik sesuai prinsip kerja yang telah dibuat
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Caballero, Juan Carlos, Mercedes Sánchez-Barba, Mónica Del Rey, Kamila Janusz, Eva Lumbreras, María Abáigar, Robledo Cristina, et al. "Could Chronic Gvhd Overcome the Poor Prognosis of Patients with MDS and TP53 Undergoing Allogeneic HSCT?" Blood 126, no. 23 (December 3, 2015): 2890. http://dx.doi.org/10.1182/blood.v126.23.2890.2890.
Full textAbstract:
Abstract Background and Aim Although new agents have been approved for the treatment of MDS, the only curative approach for these patients is allogeneic hematopoietic stem cell transplantation (HSCT). Nevertheless, in these patients this approach has only obtained 40-60% of overall survival. Somatic mutations in MDS have recently been analyzed in order to confirm clonally and also prognostic impact in MDS patients. In this regard, TP 53 mutated gene is present in MDS in less than 10% of patients and is associated with advanced disease and high-risk features. Recent studies confirms poor outcomes in patients with TP 53 mutated receiving allogeneic stem cell transplantation1,2. The present study try to analyze if the development of chronic graft versus host disease (cGVHD) could modify, due to graft versus leukemia effect, the adverse prognosis of these high-risk patients (TP53 mutated patients). Design and Methods <>Results of HSCT in 92 MDS patients from 5 centers in Spain were retrospectively studied. Samples were collected 1 month prior to transplant. 280ng of the genomic DNA from BM cells was screened for somatic mutations in TP53 gene. The study was done by NGS on a GS Junior Instrument (Roche) according to an amplicon sequencing design. For each sample, eight exons (4-11) were amplified with preconfigured primer plates provided within the IRON II study network. Data analysis, were carried out using the Sequence Pilot software version 3.5.2 (JSI Medical Systems) and GS Amplicon Variant Analyzer software, versions 2.7 and 2.9 (Roche Applied Science). Minimum coverage of sequenced exons was 100 reads and the sensitivity of variant detection was set to a lower limit of >2% for bidirectional reads. Only those variants that resulted in amino acid change in the protein sequence were considered. OS and RFS were calculated using the Kaplan-Meier method. The log-rank test was used for comparisons. All calculations were done using SPSS 18.0. Cumulative incidence of relapse was also calculated by xlstat version 2014 program. <>Results Median age was 54 years (17-69), 71.7% were "de novo" MDS and regarding IPSS, 53% were in the int-2/high-risk category. Other characteristics were in Table 1. In the pre-transplant evaluation, 15 patients out of 92 (16,3%) were TP 53 mutated. The mutations were located in exons 5, 6, 7, 8 and 10. These variations were present in a variable percentageof the cell population (3 to 84%). All mutations were specific nucleotide changes except for two cases. At the time of the last update, 16 patients had relapsed (17.4%) and 40 had died (43.5%). After a median follow up of 15.5 months, OS was 56.5%. Median OS for patients with mutated TP53 trend a toward to be shorter than survival for patients without mutated TP53 (median of 7 mo vs median not reached, respectively, p=0.156). Multivariate analysis for OS confirmed complex karyotype (HR 5,588, 95CI 1,794-17,407, p=0.003) and no developement of cGVHD (HR 3,531, 95IC 1,634-7,632, p=0.001) as predictors for poor outcome. Cumulative incidence of relapse was 20.3% (+/-4.3%) at 1 years. Mutational status of TP53 significantly influenced on relapse (53.3% +/-12.9% vs 13.7% +/-4% at 1 year for patients with vs without TP 53 mutation (Gray test=0.001, Figure 2). Regarding Relapse Free Survival (RFS), after a median of follow up of 17 months, RFS was 67.9% and as previously suggested, the presence of TP 53 mutation had an impact on RFS (41.7% for mutated (median RFS of 6 months) and 75% for non mutated patients (median RFS not reached), p=0.009). Multivariate analysis for RFS confirmed age (HR 1.054, 95CI 1.005-1.106, p=0.032) and TP 53 mutated (HR 3.054, 95IC 1.145-8.149, p=0.026) as predictors for lower RFS. Regarding 15 patients with mutated TP 53, 7 did relapsed and 9 had died. Developement of cGVHD showed a trend toward to improve outcome among TP 53 mutated patients, with a better OS and RFS for those developing cGVHD as compared to those who did not (OS of 55% vs 17% for patients with and without cGVHD, p=0.039, Figure 2 and RFS of 71% vs 50%, respectively, p=0.3). <>Conclusions Mutated TP53 pre-allo patients presents poor outcome as compared to not mutated, as previously described Bejar1 and Kim2. Nevertheless, the developement of cGVHD could overcome the adverse impact of this factor due to the developement of graft versus tumor efect, improving survival curves (OS and RFS) as compared to previous published results. Study supported by GRS-1033/A/14 P53. 1.-BŽjar, JCO 2014, 32(25). 2.-Kim, BBMT 2015, Epub ahead of print. Figure 2. Figure 2. Figure 3. Figure 3. Disclosures Sanz: JANSSEN CILAG: Honoraria, Research Funding, Speakers Bureau. Valcarcel:AMGEN: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; NOVARTIS: Honoraria, Membership on an entity's Board of Directors or advisory committees; GSK: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; CELGENE: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Díez-Campelo:CELGENE: Research Funding, Speakers Bureau; JANSSEN: Research Funding; NOVARTIS: Research Funding, Speakers Bureau.
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Mao, Rui, Xinyao Wu, Qing Miao, and Ting Cai. "Asymmetric stem-loop–mediated isothermal amplification of nucleic acids for DNA diagnostic assays by simple modification of canonical PCR primers." Frontiers in Bioengineering and Biotechnology 10 (July 22, 2022). http://dx.doi.org/10.3389/fbioe.2022.931770.
Full textAbstract:
Nucleic acid–based assays have been adopted as mainstream tools for clinical diagnostics, food safety, and environment monitoring with the merits of accuracy, rapidity, and sensitivity. Loop-mediated isothermal amplification (LAMP) is a well-established method to rapidly identify nucleic acids and has gained recognition and been developed for clinical applications in resource-limited areas. However, the needs for specifically designed primer sets and non-specific amplification hinder the development of LAMP-based nucleic acid tests. Here, a promoted method, termed asymmetric stem-loop–mediated isothermal amplification (ASLAMP) by simple modification of canonical PCR primers, was developed to attempt to overcome those drawbacks. The two primers in the ASLAMP reaction can be easily obtained by adding a stem-loop sequence part to one PCR primer at 5′-ends to get the folding primer (FP), then adding the same primer to the counter canonical PCR primer at 5′-ends to get the turn-back primer (TP). The ASLAMP method was demonstrated in detecting the H1N1 gene fragment with merits of simple primer design, short target sequence, and high amplification efficiency. In addition, the ASLAMP method showed similar efficacy compared with LAMP targeting at the same H1N1 gene sequence. Furthermore, Shigella detection monitored by real-time fluorescence and endpoint colorimetric approaches were taken as examples for evaluation of the practical application of the ASLAMP method, both offered 100% sensitivity and specificity. In conclusion, the novel ASLAMP method with simplicity of primer design, low requirement of equipment, efficiency, and rapidity has exhibited its great prospect for establishment of DNA isothermal amplification in point of care application.
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Wang, Yang, Junfei Dai, Yongsheng Liu, Jifei Yang, Qian Hou, Yunwen Ou, Yaozhong Ding, et al. "Development of a Potential Penside Colorimetric LAMP Assay Using Neutral Red for Detection of African Swine Fever Virus." Frontiers in Microbiology 12 (April 23, 2021). http://dx.doi.org/10.3389/fmicb.2021.609821.
Full textAbstract:
African swine fever (ASF) has caused huge economic losses to the swine industry worldwide. Since there is no commercial ASF vaccine available, an early diagnosis is extremely important to prevent and control the disease. In this study, ASF virus (ASFV) capsid protein-encoding gene (p72) was selected and used to design primers for establishing a one-step visual loop-mediated isothermal amplification (LAMP) assay with neutral red, a pH-sensitive dye, as the color shift indicator. Neutral red exhibited a sharp contrast of color change from faint orange (negative) to pink (positive) during LAMP for detection of ASFV. The designed primer set targeting highly conserved region of the p72 gene was highly specific to ASFV and showed no cross-reactivity with other swine viruses. The detection limit for the one-step visual LAMP developed was 10 copies/reaction based on the recombinant plasmid containing the p72 gene of ASFV. More importantly, the developed one-step visual LAMP showed high consistency with the results of the real-time polymerase chain reaction (qPCR) method recommended by World Organization for Animal Health (OIE). Furthermore, the results demonstrate that the colorimetric detection with this LAMP assay could be directly applied for the whole blood and serum samples without requiring genome extraction. Based on our results, the developed one-step visual LAMP assay is a promising penside diagnostic tool for development of early and cost-effective ASF monitoring program that would greatly contribute to the prevention and control of ASF.
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Ngari, M. G., I. N. Mwangi, M. P. Njoroge, J. Kinyua, F. A. Osuna, B. M. Kimeu, P. W. Okanya, and E. L. Agola. "Development and evaluation of a loop-mediated isothermal amplification (LAMP) diagnostic test for detection of whipworm, Trichuris trichiura, in faecal samples." Journal of Helminthology 94 (2020). http://dx.doi.org/10.1017/s0022149x2000022x.
Full textAbstract:
Abstract Whipworm infection or trichuriasis caused by Trichuris trichiura is of major public health concern in sub-Saharan Africa, particularly among pre-school and school-going children. It is among the neglected tropical diseases targeted for elimination through mass drug administration (MDA). One of the outcomes of MDA is a rapid decline in levels of infection intensity, making it difficult to monitor effectiveness of control measures using the conventional Kato–Katz procedure, which relies on the microscopic detection of parasite ova in faecal samples. In the present study, a loop-mediated isothermal amplification (LAMP) test was developed for the detection of T. trichiura infection in faecal samples. LAMP technology offers greater sensitivity and specificity than the microscopy-based tests. A set of four specific primers targeting the internal transcribed spacer 2 region of the ribosomal DNA were designed using Primer Explorer software. DNA was extracted from faecal samples using the alkaline lysis method (HotSHOT) and the LAMP reaction performed at 63°C for 1 h. The amplicons were visualized by both gel electrophoresis and with the naked eye following staining with SYBR green dye. Sensitivity and specificity tests were determined using the standard Kato–Katz diagnostic procedure as a reference test. The developed LAMP assay reliably detected T. trichiura DNA in faecal samples, with a specificity and sensitivity of 88% and 77%, respectively. No cross-reactivity was observed with several common helminth parasites. The developed LAMP assay is an appropriate diagnostic method for the detection of T. trichiura DNA in human faecal samples due to its simplicity, low cost, high sensitivity and specificity.
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Avila, Héctor Gabriel, Marikena Guadalupe Risso, Marta Cabrera, Paula Ruybal, Silvia Analía Repetto, Marcos Javier Butti, Marcos David Trangoni, Graciela Santillán, Verónica Mirtha Pérez, and María Victoria Periago. "Development of a New LAMP Assay for the Detection of Ancylostoma caninum DNA (Copro-LAMPAc) in Dog Fecal Samples." Frontiers in Veterinary Science 8 (November 12, 2021). http://dx.doi.org/10.3389/fvets.2021.770508.
Full textAbstract:
Ancylostoma caninum is a zoonotic nematode which is able to affect animals and humans. Diagnosis in the definitive host and environmental detection are key to prevent its dissemination and achieve control. Herein, a new coprological LAMP method for the detection of A. caninum (Copro-LAMPAc) DNA was developed. DNA extraction was performed using a low-cost method and a fragment of the cox-1 gene was used for primer design. The analytical sensitivity, evaluated with serial dilutions of genomic DNA from A. caninum adult worms, was 100 fg. A specificity of 100% was obtained using genomic DNA from the host and other pathogens. The Copro-LAMPAc was evaluated using environmental canine fecal samples. When compared with gold standard optical microscopy in epidemiological studies, it proved to be more sensitive. This new LAMP assay can provide an alternative protocol for screening and identification of A. caninum for epidemiological studies in endemic areas.
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Wang, Songqi, Haiyan Shen, Qijie Lin, Jun Huang, Chunhong Zhang, Zhicheng Liu, Minhua Sun, et al. "Development of a Cleaved Probe-Based Loop-Mediated Isothermal Amplification Assay for Rapid Detection of African Swine Fever Virus." Frontiers in Cellular and Infection Microbiology 12 (May 26, 2022). http://dx.doi.org/10.3389/fcimb.2022.884430.
Full textAbstract:
African Swine Fever (ASF), caused by African swine fever virus (ASFV), is a highly contagious and lethal viral disease of pigs. However, commercial vaccines are not yet available, and neither are drugs to prevent or control ASF. Therefore, rapid, accurate on-site diagnosis is urgently needed for detection during the early stages of ASFV infection. Herein, a cleaved probe-based loop-mediated isothermal amplification (CP-LAMP) detection method was established. Based on the original primer sets, we targeted the ASFV 9GL gene sequence to design a probe harboring a ribonucleotide insertion. Ribonuclease H2 (RNase H2) enzyme activity can only be activated when the probe is perfectly complementary, resulting in hydrolytic release of a quencher moiety, and consequent signal amplification. The method displayed robust sensitivity, with copy number detection as low as 13 copies/µL within 40 min at constant temperature (62°C). Visualization of the fluorescence product was employed using a self-designed 3D-printed visualization function cassette, and the CP-LAMP method achieved specific identification and visual detection of ASFV. Moreover, coupling the dual function cassette and smartphone quantitation makes the CP-LAMP assay first user-friendly, cost-effective, portable, rapid, and accurate point-of-care testing (POCT) platform for ASFV.
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Feng, Hui, Wenwu Ye, Zhuoyuan Liu, Yang Wang, Jia-Jia Chen, Yuanchao Wang, and Xiaobo Zheng. "Development of LAMP assays using a novel target gene for specific detection of Pythium terrestris, Pythium spinosum, and “Candidatus Pythium huanghuaiense”." Plant Disease, April 6, 2021. http://dx.doi.org/10.1094/pdis-01-21-0068-re.
Full textAbstract:
Pythium terrestris, Pythium spinosum, and “Candidatus Pythium huanghuaiense” are closely related species and important pathogens of soybean that cause root rot. However, the sequences of commonly-used molecular markers, such as rDNA internal transcribed spacer 2 and cytochrome oxidase 1 gene, are similar among these species, making it difficult to design species-specific primers for loop-mediated isothermal amplification (LAMP) assays. The genome sequences of these species are also currently unavailable. Based on a comparative genomic analysis and de novo RNA-seq transcript assemblies, we identified and cloned the sequences of the M90 gene, a conserved but highly polymorphic single-copy gene encoding a Puf family RNA-binding protein among oomycetes. After primer design and screening, three LAMP assays were developed that specifically amplified the targeted DNA sequences in P. terrestris and P. spinosum at 62°C for 70 min and in “Ca. Pythium huanghuaiense” at 62°C for 60 min. After adding SYBR Green I, a positive yellow–green color (under natural light) or intense green fluorescence (under ultraviolet light) was observed by the naked eye only in the presence of the target species. The minimum concentration of target DNA detected in all three LAMP assays was 100 pg·μL−1. The assays also successfully detected the target Pythium spp. with high accuracy and sensitivity from inoculated soybean seedlings and soils collected from soybean fields. This study provides a method for identification and cloning of candidate detection targets without a reference genome sequence, and identified M90 as a novel specific target for molecular detection of three Pythium species causing soybean root rot.
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Urrutia-Cabrera, Daniel, Roxanne Hsiang-Chi Liou, Jiang-Hui Wang, Jianxiong Chan, Sandy Shen-Chi Hung, Alex W. Hewitt, Keith R. Martin, Thomas L. Edwards, Patrick Kwan, and Raymond Ching-Bong Wong. "Comparative analysis of loop-mediated isothermal amplification (LAMP)-based assays for rapid detection of SARS-CoV-2 genes." Scientific Reports 11, no. 1 (November 18, 2021). http://dx.doi.org/10.1038/s41598-021-01472-3.
Full textAbstract:
AbstractThe COVID-19 pandemic caused by SARS-CoV-2 has infected millions worldwide, therefore there is an urgent need to increase our diagnostic capacity to identify infected cases. Although RT-qPCR remains the gold standard for SARS-CoV-2 detection, this method requires specialised equipment in a diagnostic laboratory and has a long turn-around time to process the samples. To address this, several groups have recently reported the development of loop-mediated isothermal amplification (LAMP) as a simple, low cost and rapid method for SARS-CoV-2 detection. Herein we present a comparative analysis of three LAMP-based assays that target different regions of the SARS-CoV-2: ORF1ab RdRP, ORF1ab nsp3 and Gene N. We perform a detailed assessment of their sensitivity, kinetics and false positive rates for SARS-CoV-2 diagnostics in LAMP or RT-LAMP reactions, using colorimetric or fluorescent detection. Our results independently validate that all three assays can detect SARS-CoV-2 in 30 min, with robust accuracy at detecting as little as 1000 RNA copies and the results can be visualised simply by color changes. Incorporation of RT-LAMP with fluorescent detection further increases the detection sensitivity to as little as 100 RNA copies. We also note the shortcomings of some LAMP-based assays, including variable results with shorter reaction time or lower load of SARS-CoV-2, and false positive results in some experimental conditions and clinical saliva samples. Overall for RT-LAMP detection, the ORF1ab RdRP and ORF1ab nsp3 assays have faster kinetics for detection but varying degrees of false positives detection, whereas the Gene N assay exhibits no false positives in 30 min reaction time, which highlights the importance of optimal primer design to minimise false-positives in RT-LAMP. This study provides validation of the performance of LAMP-based assays as a rapid, highly sensitive detection method for SARS-CoV-2, which have important implications in development of point-of-care diagnostics for SARS-CoV-2.
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Ilyichev, V. Yu, A. A. Litvinenko, and A. V. Rodionov. "Led lamp driver modelling." Science Intensive Technologies, 2021. http://dx.doi.org/10.18127/j19998465-202104-03.
Full textAbstract:
Currently, there is an increase in the use and production of energy-saving lamps of various types – fluorescent and LED ones. However, it has been found that the use of technologies that have proven themselves in the creation of luminescent sources for LED light sources is ineffective. The use of traditional secondary optics for LED luminaires makes it difficult to create an effective heat sink from LEDs, while the durability of LEDs significantly depends on the heat sink. Another important issue when designing LED luminaires is choosing the right driver. The power consumption of LEDs from the primary network depends on the efficiency of the driver used. The choice of the type of driver also determines the amount of heat that should be removed from its elements. A significant factor influencing the choice of a driver is also the possibility of its operation in conjunction with a voltage regulator – a dimmer, in order to control the illumination. It is also necessary to take into account the IEC recommendations that require manufacturers to use active power factor correctors for devices with switching power supplies and / or electronic ballast with a power of 20 watts or more. Therefore, there is a task of developing a highly efficient driver for use in LED luminaires. In the process of reviewing modern drivers, a driver based on the LT3799 microcircuit from Linear Technology was selected for further research, which is distinguished by high efficiency, working with a large number of produced LEDs, has a built-in active power factor corrector, and allows the use of dimmers. The inclusion of the driver chip recommended by the manufacturer was applied, with the addition of noise suppressing components. The galvanic isolation of the power supply circuits of the LED matrix is provided. Next, the analysis of the characteristics of the selected circuit design solution is carried out using computer simulation. LTSpice EDA was chosen as a modeling tool, which is distinguished by its versatility, ease of use and high reliability of results in comparison with similar software products. The modes of operation are analyzed depending on the requirements for the pulsation of the emitting matrix, the operation of the power factor corrector, and the suppression of interference into the industrial network from the operation of the source is estimated. Various options for the development of the circuitry implementation of the driver based on the LT3799 microcircuit and the operating modes of the most heavily loaded elements are analyzed: an inductor, a key transistor, a damper circuit, a diode in the power supply circuit of an LED matrix. Optimal values of circuit components and parameters of winding elements were selected. It is shown that due to the operation of the power factor corrector, the shape of the current consumption from a sinusoidal voltage source is also almost sinusoidal, which leads to an almost active nature of the load. The modes of operation of the LED matrix for the nominal supply voltage and for the reduced one (with a dimmer) are considered. Methods of implementation of a soft start of an LED matrix are described. Based on the results of the work, conclusions are drawn that summarize the expediency of using the developed driver for an LED device based on the LT3799 microcircuit.
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Ramdoni, Rahmat, Sugeng Supriyadi, and Nunu Nugraha. "RANCANG BANGUN SISTEM KONTROL DAN MONITORING LAMPU OTOMATIS MENGGUNAKAN ARDUINO DENGAN METODE FUZZY LOGIC BERBASIS ANDROID (Studi Kasus Koridor Lantai 1 dan 2 Fakultas Ilmu Komputer)." NUANSA INFORMATIKA 12, no. 1 (August 1, 2018). http://dx.doi.org/10.25134/nuansa.v12i1.1348.
Full textAbstract:
The rapid development of technology in various field, including the field of electronic, necessity of facility and comfort in controlling the electric devices are important, especially in controlling and monitoring the lamps. Nowdays society can control the electrical devices only with the switch connected by cabel. Then, it is needed a control system and monitoring lamps automatically. One of the systems is using micro controller. Based on the problems identified in Computer Sciences Faculty, system for controlling and monitoring lamps hasn�t� run efectivelly because it still uses manual and it has not got the lamps should be burn. Method of software development used in this research is Rational Unified Process (RUP) method by using design of Unified Modeling Language (UML) such as using case diagram, scenario, activity diagram, class diagram dan sequence diagram. Meanwhile, the problem solving method is using Fuzzy Logic method. System of controlling and monitoring the lamps built by fuzzy logic method is efective automaticallty. The system can be applied to the research object and assist in the process of controlling and monitoring the lamp automatically.Keyword : Rational Unified Proces method, Arduino, Unified Modeling Language,Fuzzy Logic, Controlling and Monitoring the Lamps