Journal articles: 'Primer designs'

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Ahern, Kevin, and Primer Premier. "Premier Primer Designs." Science 286, no. 5439 (October 15, 1999): 433.1–433. http://dx.doi.org/10.1126/science.286.5439.433a.

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SINGH, KAVITA, PRITI GUPTA, and ROOPA SHIVASHANKAR. "Primer of Epidemiology IV. Study designs II: Interventional or experimental designs." National Medical Journal of India 34 (January 29, 2022): 228–31. http://dx.doi.org/10.25259/nmji_373_19.

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In this article, we describe experimental study designs and focus on randomized controlled trials. Experimental studies are intervention studies in which the investigator tests a new treatment on a selected group of patients. In a controlled design, the effects of an intervention (new treatment) are measured by comparing the outcome in the experimental group with that in a control group. Experimental studies are similar to cohort studies except that the exposure is a deliberate change (intervention) made by the researcher in one group of participants and it overcomes confounding because the treatment is assigned randomly. Further, we discuss various types of randomization (random sequence allocation) and importance of allocation concealment and blinding for proper assessment of outcomes in randomized trials.

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Bauman, Sheri. "Using Comparison Groups in School Counseling Research: A Primer." Professional School Counseling 9, no. 4 (January 2006): 2156759X0500900. http://dx.doi.org/10.1177/2156759x0500900419.

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This article describes comparison group research designs and discusses how such designs can be used in school counseling research to demonstrate the effectiveness of school counselors and school counseling interventions. The article includes a review of internal and external validity constructs as they relate to this approach to research. Examples of relevant research using this design are presented.

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Baker, Timothy B., Stevens S. Smith, Daniel M. Bolt, Wei-Yin Loh, Robin Mermelstein, Michael C. Fiore, Megan E. Piper, and Linda M. Collins. "Implementing Clinical Research Using Factorial Designs: A Primer." Behavior Therapy 48, no. 4 (July 2017): 567–80. http://dx.doi.org/10.1016/j.beth.2016.12.005.

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Ledford, Jennifer R., Erin E. Barton, Katherine E. Severini, and Kathleen N. Zimmerman. "A Primer on Single-Case Research Designs: Contemporary Use and Analysis." American Journal on Intellectual and Developmental Disabilities 124, no. 1 (January 1, 2019): 35–56. http://dx.doi.org/10.1352/1944-7558-124.1.35.

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Abstract The overarching purpose of this article is to provide an introduction to the use of rigorous single-case research designs (SCRDs) in special education and related fields. Authors first discuss basic design types and research questions that can be answered with SCRDs, examine threats to internal validity and potential ways to control for and detect common threats, and provide guidelines for selection of specific designs. Following, contemporary standards regarding rigor, measurement, description, and outcomes are presented. Then, authors discuss data analytic techniques, differentiating rigor, positive outcomes, functional relations, and magnitude of effects.

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Havstad, Suzanne L., and George W. Divine. "Biostatistical Analysis: A Primer for Clinical Exercise Physiology, Part 1." Journal of Clinical Exercise Physiology 7, no. 3 (September 1, 2018): 63–69. http://dx.doi.org/10.31189/2165-6193-7.3.63.

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ABSTRACT In this first of a two-part series on introductory biostatistics, we briefly describe common designs. The advantages and disadvantages of six design types are highlighted. The randomized clinical trial is the gold standard to which other designs are compared. We present the benefits of randomization and discuss the importance of power and sample size. Sample size and power calculations for any design need to be based on meaningful effects of interest. We give examples of how the effect of interest and the sample size interrelate. We also define concepts helpful to the statistical inference process. When drawing conclusions from a completed study, P values, point estimates, and confidence intervals will all assist the researcher. Finally, the issue of multiple comparisons is briefly explored. The second paper in this series will describe basic analytical techniques and discuss some common mistakes in the interpretation of data.

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Prabhakaran, Poornima, and Roopa Shivashankar. "Primer of Epidemiology 3: An overview and observational study designs." National Medical Journal of India 33, no. 5 (2020): 291. http://dx.doi.org/10.4103/0970-258x.317472.

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O'Brien, Ralph G., and Mary K. Kaiser. "MANOVA method for analyzing repeated measures designs: An extensive primer." Psychological Bulletin 97, no. 2 (1985): 316–33. http://dx.doi.org/10.1037/0033-2909.97.2.316.

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Nuryady, Moh Mirza, H. Husamah, Fuad Jaya Miharja, Iin Hindun, and P. Patmawati. "Desain dan Optimasi Primer Gen Pengkode MRPA Trypanosoma evansi dan Penerapan pada Pembelajaran Biologi Molekuler." Jurnal Penelitian dan Pengkajian Ilmu Pendidikan: e-Saintika 4, no. 2 (July 2, 2020): 211. http://dx.doi.org/10.36312/e-saintika.v4i2.217.

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Penelitian molekuler untuk menemukan gen pengkode resistensi Multidrug Resistance Prtotein A (MRPA) T. evansi dan perbanyakan gen secara Polimeration Chain Reaction (PCR) masih sedikit dilakukan dan sangat penting untuk dipahami oleh mahasiswa calon guru biologi. Kajian ini bertujuan untuk menganalisis proses desain dan optimasi primer untuk gen target MRPA T. evansi yang dapat digunakan sebagai sumber belajar mahasiswa pendidikan biologi. Penelitian ini merupakan penelitian deskriptif mengenai tahapan mendesain primer secara online, optimasi primer secara laboratorium serta kajian mengenai pentingnya penerapan hasil studi ini dalam pembelajaran. Hasil penelitian menunjukkan terdapat tiga desain primer yang memenuhi syarat, selanjutnya dari tiga primer tersebut hasil optimasi di laboratorium menunjukkan hanya terdapat dua primer yang menunjukkan hasil yang baik dan dapat digunakan untuk penelitian amplifikasi gen MRPA T. evansi, yaitu primer pertama (F1’, R1’) dan primer kedua (F2’, R2’). Hasil kajian desain dan optimasi primer ini menunjukkan bahwa mahasiswa pendidikan biologi sangatlah penting untuk memahami konsep terkait dengan pekerjaan molekuler seperti mendesain dan optimasi primer, dikarenakan mereka memiliki tuntutan untuk menjadi seorang calon pendidik atau sebagai calon peneliti dimasa depan.Design and Optimization of Trypanosoma evansi MRPA Primer Coding Genes and Application to Molecular Biology LearningAbstractMolecular research to find Multidrug Resistance Prtotein A (MRPA) resistance coding genes and gene propagation by Polimeration Chain Reaction (PCR) is still little done and is very important to be understood by prospective biology teacher students. This study aims to analyze the design and primary optimization process for the T. evansi MRPA target gene that can be used as a learning resource for biology education students. This research was a descriptive study to described the step of primer design and optimization due to the importance of this steps to be applied as learning source. The results showed that there were 3 primer designs that qualified, then after the optimizing step there were only two primers that showed a good result, the first primer (F1, R1) and second primer (F2', R2). The results of this study showed the importance of biology education students to understand the concepts related to molecular work because in the future they are not only become prospective educators, they also have demands as prospective researchers.

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Joseph, Anjali, Matthew H. E. M. Browning, and Shan Jiang. "Using Immersive Virtual Environments (IVEs) to Conduct Environmental Design Research: A Primer and Decision Framework." HERD: Health Environments Research & Design Journal 13, no. 3 (May 21, 2020): 11–25. http://dx.doi.org/10.1177/1937586720924787.

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Purpose: We propose a methodological framework to use immersive virtual environments (IVEs) in head-mounted displays for environmental design research. Background: IVEs offer researchers with experimental control and realistic representations of environments with high levels of ecological validity. IVEs are also increasingly being used to visualize proposed designs. Despite these tremendous benefits, IVEs are underutilized in environmental design research. We are unaware of preexisting frameworks that synthesize the methodological decisions related to the use of IVEs to conduct environmental design research. Methods/Results: We define the concepts necessary to conduct IVE research (virtual reality [VR], IVEs, ecological validity, visual realism, behavioral realism, and contextual realism). We also summarize the available study designs (correlational studies, experimental studies, and performance evaluations) and software systems used to create IVEs. We conclude with a conceptual framework that describes how research questions and study designs inform IVE selection and ecological validity. This framework is accompanied by a workflow that operationalizes the creation and use of IVEs in research. Conclusions: VR provides a robust and innovative research strategy for environmental design research because of its high degree of experimental control, rich data collection options, and opportunities for systematic evaluation of alternative design configurations.

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Lau, Chi-Chuen, and Francis Kuk. "Enough is enough: A primer on power analysis in study designs." Hearing Journal 64, no. 4 (April 2011): 30. http://dx.doi.org/10.1097/01.hj.0000396585.52118.6b.

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Farley, Nicole J., Adrian A. Vasquez, Richard Kik, Solomon R. David, Arjun S. Katailiha, Xavier N. Walker, and Jeffrey L. Ram. "Primer Designs for Identification and Environmental DNA (eDNA) Detection of Gars." Transactions of the American Fisheries Society 147, no. 4 (June 7, 2018): 687–95. http://dx.doi.org/10.1002/tafs.10043.

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Kechin, Andrey, Viktoria Borobova, Ulyana Boyarskikh, Evgeniy Khrapov, Sergey Subbotin, and Maxim Filipenko. "NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions." PLOS Computational Biology 16, no. 12 (December 30, 2020): e1008468. http://dx.doi.org/10.1371/journal.pcbi.1008468.

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Multiplex polymerase chain reaction (PCR) has multiple applications in molecular biology, including developing new targeted next-generation sequencing (NGS) panels. We present NGS-PrimerPlex, an efficient and versatile command-line application that designs primers for different refined types of amplicon-based genome target enrichment. It supports nested and anchored multiplex PCR, redistribution among multiplex reactions of primers constructed earlier, and extension of existing NGS-panels. The primer design process takes into consideration the formation of secondary structures, non-target amplicons between all primers of a pool, primers and high-frequent genome single-nucleotide polymorphisms (SNPs) overlapping. Moreover, users of NGS-PrimerPlex are free from manually defining input genome regions, because it can be done automatically from a list of genes or their parts like exon or codon numbers. Using the program, the NGS-panel for sequencing the LRRK2 gene coding regions was created, and 354 DNA samples were studied successfully with a median coverage of 97.4% of target regions by at least 30 reads. To show that NGS-PrimerPlex can also be applied for bacterial genomes, we designed primers to detect foodborne pathogens Salmonella enterica, Escherichia coli O157:H7, Listeria monocytogenes, and Staphylococcus aureus considering variable positions of the genomes.

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Liu, Ruhui, Jiaxu Ning, Yueqiu Jiang, Xianghe Wang, and Jiaxuan Wu. "A Method for Degenerate Primer Design Based on Artificial Bee Colony Algorithm." Applied Sciences 12, no. 10 (May 15, 2022): 4992. http://dx.doi.org/10.3390/app12104992.

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Aiming to address the complex degenerate primer design problem in the biological field, in this paper, we design a degenerate primer optimization model considering primer coverage and degeneracy that allows a small number of base mismatches, and propose a global optimization method based on the artificial bee colony algorithm. The proposed algorithm combines the idea of the ant colony algorithm with the optimization process of the artificial bee colony algorithm, overcomes the disadvantage of the uncertain candidate solution length of the artificial bee colony algorithm in solving discrete optimization problems, designs the search space model according to the construction process of candidate solution in ant colony optimization algorithm, and redesigns various bee foraging strategies according to the optimization process information. In the comparative experiments on DNA template sequences of different scales, the degenerate primer designed by the proposed algorithm is superior to the existing methods in terms of stability, specificity, coverage and degeneracy.

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Gottlieb, Michael, Teresa Chan, Jenna Fredette, Anne Messman, Daniel Robinson, Robert Cooney, Megan Boysen-Osborn, and Jonathan Sherbino. "Academic Primer Series: Five Key Papers about Study Designs in Medical Education." Western Journal of Emergency Medicine 18, no. 4 (June 1, 2017): 705–12. http://dx.doi.org/10.5811/westjem.2017.4.33906.

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Gauthier, Jordan, Ying Yuan, and Peter Thall. "Bayesian Phase 1/2 trial designs and cellular immunotherapies: a practical primer." Cell and Gene Therapy Insights 5, no. 11 (November 18, 2019): 1483–94. http://dx.doi.org/10.18609/cgti.2019.152.

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Liao, Yu-Chieh, Feng-Jui Chen, Min-Chieh Chuang, Han-Chieh Wu, Wan-Chen Ji, Guann-Yi Yu, and Tsi-Shu Huang. "High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination." International Journal of Molecular Sciences 23, no. 6 (March 17, 2022): 3257. http://dx.doi.org/10.3390/ijms23063257.

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For tiling of the SARS-CoV-2 genome, the ARTIC Network provided a V4 protocol using 99 pairs of primers for amplicon production and is currently the widely used amplicon-based approach. However, this technique has regions of low sequence coverage and is labour-, time-, and cost-intensive. Moreover, it requires 14 pairs of primers in two separate PCRs to obtain spike gene sequences. To overcome these disadvantages, we proposed a single PCR to efficiently detect spike gene mutations. We proposed a bioinformatic protocol that can process FASTQ reads into spike gene consensus sequences to accurately call spike protein variants from sequenced samples or to fairly express the cases of missing amplicons. We evaluated the in silico detection rate of primer sets that yield amplicon sizes of 400, 1200, and 2500 bp for spike gene sequencing of SARS-CoV-2 to be 59.49, 76.19, and 92.20%, respectively. The in silico detection rate of our proposed single PCR primers was 97.07%. We demonstrated the robustness of our analytical protocol against 3000 Oxford Nanopore sequencing runs of distinct datasets, thus ensuring high-integrity sequencing of spike genes for variant SARS-CoV-2 determination. Our protocol works well with the data yielded from versatile primer designs, making it easy to determine spike protein variants.

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Batnyam, Nomin, Jimin Lee, Jungnam Lee, Seung Bok Hong, Sejong Oh, and Kyudong Han. "UniPrimer: A Web-Based Primer Design Tool for Comparative Analyses of Primate Genomes." Comparative and Functional Genomics 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/520732.

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Whole genome sequences of various primates have been released due to advanced DNA-sequencing technology. A combination of computational data mining and the polymerase chain reaction (PCR) assay to validate the data is an excellent method for conducting comparative genomics. Thus, designing primers for PCR is an essential procedure for a comparative analysis of primate genomes. Here, we developed and introduced UniPrimer for use in those studies. UniPrimer is a web-based tool that designs PCR- and DNA-sequencing primers. It compares the sequences from six different primates (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque) and designs primers on the conserved region across species. UniPrimer is linked to RepeatMasker, Primer3Plus, and OligoCalc softwares to produce primers with high accuracy and UCSCIn-SilicoPCR to confirm whether the designed primers work. To test the performance of UniPrimer, we designed primers on sample sequences using UniPrimer and manually designed primers for the same sequences. The comparison of the two processes showed that UniPrimer was more effective than manual work in terms of saving time and reducing errors.

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Wu, Yelena P., Janet A. Deatrick, Elizabeth L. McQuaid, and Deborah Thompson. "A Primer on Mixed Methods for Pediatric Researchers." Journal of Pediatric Psychology 44, no. 8 (July 1, 2019): 905–13. http://dx.doi.org/10.1093/jpepsy/jsz052.

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Abstract Objective To provide a primer on conducting and analyzing mixed methods research studies, and to provide guidance on the write-up of mixed methods research. Methods A question and answer format is used to provide an overview of mixed methods research study designs, tasks and considerations related to conducting and analyzing mixed methods studies, and recommendations for the write-up of results for mixed methods studies. Results Individuals who conduct mixed methods research are encouraged to delineate the quantitative, qualitative, and mixed methods features of the research and how these features fit with the overall study questions. Research teams will benefit from including individuals with expertise in qualitative, quantitative, and mixed methods research. Data integration should be a central component to the analysis and write-up of mixed methods research. Conclusions Increasing the use of mixed methods research in the field of pediatric psychology will contribute to advances in observational studies with children and families, intervention development and evaluation, and creation of new tools and assessments that aim to optimize child and family health outcomes.

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Heath, Gregory W., and Nicholas Boer. "Epidemiologic Research: A Primer for the Clinical Exercise Physiologist." Journal of Clinical Exercise Physiology 9, no. 1 (March 1, 2020): 29–39. http://dx.doi.org/10.31189/2165-6193-9.1.29.

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ABSTRACT An understanding of epidemiologic methods is important for the clinical exercise physiologist to assess the complex relationships between physical activity and health and disease. It is essential to the practice of preventive and rehabilitative care to understand the web of causation and complex interactions among agent (exercise), host (individual), and environment (affects transmission of agent source to host) in relationship to disease/injury and clinical outcomes. Application of the epidemiologic measures of disease/injury occurrence, variations in occurrence, and statistical measures of attributable risk and population attributable risk contribute to the clinician's skill level in assessing potential cause-effect relationships reported in the literature about exercise medicine, physical activity, and public health. By becoming familiar with the study methods used in epidemiology, the clinical exercise physiologist will be better positioned to assess criteria for a cause-effect relationship as well as to critically evaluate the assessment efforts used across a variety of study designs and applications of epidemiology in clinical research and practice.

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Purnawinadi, I. Gede, and Ranti Jesiy Pontoh. "DETERMINAN HIPERTENSI PRIMER PADA MASYARAKAT NON-ADVENT." Nutrix Journal 5, no. 1 (April 27, 2021): 39. http://dx.doi.org/10.37771/nj.vol5.iss1.538.

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Secara global hipertensi merupakan penyebab kematian utama dari total semua kematian. Hipertensi belum diketahui penyebab pastinya, tapi hal yang dapat dilakukan adalah dengan menghindari faktor-faktor pencetus. Penelitian ini bertujuan untuk mengetahui faktor risiko yang berhubungan dengan kejadian hipertensi pada masyarakat Non-Advent. Jenis penelitian ini adalah kuantitatif dengan desain survei analitik melalui pendekatan cross sectional dan uji statistik yang digunakan Chi-Square. Jumlah sampel yang digunakan untuk mewakili populasi adalah 252 orang dengan menggunakan rumus slovin yang dipilih dengan teknik purposive sampling. Hasil uji statistik menunjukkan variabel usia (p value = 0,000; OR=7,590), riwayat keluarga (p value = 0,001; OR= 2,401), dan obesitas (p value = 0,000 dan nilai OR= 4,418) memiliki hubungan yang signifikan dengan kejadian hipertensi dimana nilai p value<0,05, sedangkan jenis kelamin (p value = 0,272; OR= 1,371), konsumsi kopi (p value = 0,503; OR= 1,236), merokok (p value = 0,844; OR= 1,109), konsumsi alkohol (p value = 0,986; OR= 1,058) tidak memiliki hubungan yang signifikan. Direkomendasikan untuk masyarakat agar memanfaatkan sebaik-baiknya ketersediaan tenaga atau pelayanan kesehatan, dengan tujuan melakukan pencegahan ataupun dalam hal menanggulangi masalah kesehatan dan untuk peneliti selanjutnya dapat menggunakan rancangan penelitian yang lebih lanjut seperti studi kasus kontrol dan studi kohort. Kata Kunci: determinan, hipertensi primer, non-advent Globally hypertension is the leading cause of death of all deaths. Hypertension is not yet known the exact cause, but what can be done is to avoid trigger factors. This study aims to determine the risk factors associated with the incidence of hypertension in the Non-Adventist community. This type of research is quantitative with analytic survey design through cross sectional approach and statistical tests used Chi- Square. The number of samples used to represent the population is 252 people using the Slovin formula selected by purposive sampling technique. The results of statistical tests showed that the variable age (p value = 0.000; OR = 7.590), family history (p value = 0.001; OR = 2.401), and obesity (p value = 0.000 and OR value = 4.418) had a significant relationship with the incidence of hypertension. where the p value <0.05, while gender (p value = 0.272; OR = 1.371), coffee consumption (p value = 0.503; OR = 1.236), smoking (p value = 0.844; OR = 1.109), alcohol consumption (p value = 0.986; OR = 1.058) did not have a significant relationship. It is recommended for the public to make the best use of the availability of health personnel or services, with the aim of doing prevention or in terms of overcoming health problems and for further researchers to use further research designs such as case control studies and cohort studies. Keywords: determinant, non-adventist, primary hypertension.

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Agostini, Tina, Dina Berchanskiy, Joel Shi, and David Dinauer. "139-P: Sequencing of HLA-DRB1 Exons 2 and 3 With Intron Based Primer Designs." Human Immunology 71 (September 2010): S105. http://dx.doi.org/10.1016/j.humimm.2010.06.193.

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Premkrishnan, Balakrishnan Vasanthakumari, and Vadivel Arunachalam. "In Silico RAPD Priming Sites in Expressed Sequences and iSCAR Markers for Oil Palm." Comparative and Functional Genomics 2012 (2012): 1–5. http://dx.doi.org/10.1155/2012/913709.

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RAPD is a simple dominant marker system widely used in biology. Effectiveness of RAPD can be improved by selecting and redesigning primers whose priming sites occur in target sequence(s) of gene or organism at optimum distance. We developed software that uses sequences of random decamer primers and nucleotide sequence(s) as two input files. It locates the priming sites in input sequences and generates output files listing frequency and distance between priming sites. When the priming sites of a single primer occur more than once in a sequence with a distance of 200 to 2000 bp, the software also designs pairs of iSCAR primers. An input of 387 RAPD primers and 42,432 expressed sequences of oil palm are used as test. Wet-lab PCR results from a publication that used the same set of primers were compared with software output on priming sites. In the test sequences of oil palm covering 1.4% of genome, we found that at least 60% the primers chosen using software are sure of giving PCR amplification. We designed 641 iSCAR primers suitable for amplification of oil palm DNA. The software successfully predicted 92% (67 out of 73) of published polymorphic RAPD primers in oil palm.

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Hegde, G. S., and G. M. Madhu. "Primer interfaced algorithm for non-linear optimization of engineering systems." Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science 221, no. 8 (August 1, 2007): 955–60. http://dx.doi.org/10.1243/09544062jmes656.

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Majority of engineering system designs are deemed to be optimization problems with unknown multiple variables that are more than the known information and data. Several numerical algorithms have been evolved in the past half a decade in an attempt to improve the accuracy of results. The aim of this paper is to provide a perfect solver for the non-linear, single objective, and multi-variable optimization problems. The algorithm termed primer interfaced algorithm for non-linear optimization (PIANO) is a resolved solution methodology based on Hegde's primer value theorem. The methodology is formulated and developed by computing a primer adapter, which is interfaced with coefficient of the terms of constraints and objective functions to arrive at the decision vector. To demonstrate the procedure, two problems from the mechanics of structure are considered as exercises. The results are compared with the results recently published in the literature. The chosen examples for the optimization are a four bar truss and a simply supported beam with uniformly distributed load. The results of PIANO are compared with the results of fuzzy dynamic programming, and crisp optimal solutions are reported in the literature. The authors are sure of absolute contained perfection in the application of PIANO. To the authors' understanding, PIANO is original, new, and different.

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Scribante, Andrea, Maria Francesca Sfondrini, Danilo Fraticelli, Paola Daina, Alessandra Tamagnone, and Paola Gandini. "The Influence of No-Primer Adhesives and Anchor Pylons Bracket Bases on Shear Bond Strength of Orthodontic Brackets." BioMed Research International 2013 (2013): 1–6. http://dx.doi.org/10.1155/2013/315023.

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Objective. The aim of this study was to compare the shear bond strength (SBS) and adhesive remnant index (ARI) scores of no-primer adhesives tested with two different bracket bases.Materials and Methods. 120 bovine permanent mandibular incisors were divided into 6 groups of 20 specimens. Two brackets (ODP) with different bracket bases (anchor pylons and 80-gauge mesh) were bonded to the teeth using a conventional adhesive (Transbond XT) and two different no-primer adhesive (Ortho Cem; Heliosit) systems. Groups were tested using an instron universal testing machine. SBS values were recorded. ARI scores were measured. SEM microphotographs were taken to evaluate the pattern of bracket bases. Statistical analysis was performed. ANOVA and Tukey tests were carried out for SBS values, whereas a chi-squared test was applied for ARI scores.Results. Highest bond strength values were reported with Transbond XT (with both pad designs), Ortho Cem bonded on anchor pylons and Heliosit on 80-gauge mesh. A higher frequency of ARI score of “3” was reported for Transbond XT groups. Other groups showed a higher frequency of ARI score “2” and “1.”Conclusion. Transbond XT showed the highest shear bond strength values with both pad designs.

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Collins, Andrew, and Xiayi Ke. "Primer1: Primer Design Web Service for Tetra-Primer ARMS-PCR." Open Bioinformatics Journal 6, no. 1 (November 30, 2012): 55–58. http://dx.doi.org/10.2174/1875036201206010055.

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Levin, Joel R. "Overcoming feelings of powerlessness in "aging" researchers: A primer on statistical power in analysis of variance designs." Psychology and Aging 12, no. 1 (1997): 84–106. http://dx.doi.org/10.1037/0882-7974.12.1.84.

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Shadish, William R., Larry V. Hedges, and James E. Pustejovsky. "Analysis and meta-analysis of single-case designs with a standardized mean difference statistic: A primer and applications." Journal of School Psychology 52, no. 2 (April 2014): 123–47. http://dx.doi.org/10.1016/j.jsp.2013.11.005.

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Macko, Peter, and Jason Hennessey. "Survey of Distributed File System Design Choices." ACM Transactions on Storage 18, no. 1 (February 28, 2022): 1–34. http://dx.doi.org/10.1145/3465405.

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Decades of research on distributed file systems and storage systems exists. New researchers and engineers have a lot of literature to study, but only a comparatively small number of high-level design choices are available when creating a distributed file system. And within each aspect of the system, typically several common approaches are used. So, rather than surveying distributed file systems, this article presents a survey of important design decisions and, within those decisions, the most commonly used options. It also presents a qualitative exploration of their tradeoffs. We include several relatively recent designs and their variations that illustrate other tradeoff choices in the design space, despite being underexplored. In doing so, we provide a primer on distributed file systems, and we also show areas that are overexplored and underexplored, in the hopes of inspiring new research.

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Hashish, Amro, Avanti Sinha, Yuko Sato, Nubia R. Macedo, and Mohamed El-Gazzar. "Development and Validation of a New TaqMan Real-Time PCR for the Detection of Ornithobacterium rhinotracheale." Microorganisms 10, no. 2 (February 1, 2022): 341. http://dx.doi.org/10.3390/microorganisms10020341.

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Ornithobacterium rhinotracheale (ORT) has been associated with poultry respiratory disease worldwide. The organism is fastidious and isolation is challenging. One TaqMan real-time PCR (qPCR) assay has been developed for the detection of ORT. However, during validating the ORT qPCR, the assay performance was suboptimal. During the in silico evaluation, deviations from the basic parameters for primers and probes designs (e.g., presence of stable undesirable primer-dimers) were observed. The suboptimal design led to low efficiency and low sensitivity of the assay. Initially, modification on the probe was carried out to improve the performance of the assay. However, the assay’s performance (efficiency and sensitivity) was still suboptimal. In this manuscript, we describe the development of a new qPCR assay and the comparison of its performance with the currently available assay. A highly efficient, sensitive, and specific qPCR assay was developed with approximately 1000-folds reduction in the limit of detection (from 3 × 106 plasmid DNA copies/mL to 1 × 103 plasmid DNA copies/mL). Additionally, the efficiency of the new assay (E = 98.70%) was significantly better than the current assay (E = 73.18%). The newly developed assay is an improved diagnostic tool for the sensitive and efficient diagnosis of ORT from clinical samples.

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James, Delano, and Chris Upton. "Single primer pair designs that facilitate simultaneous detection and differentiation of peach mosaic virus and cherry mottle leaf virus." Journal of Virological Methods 83, no. 1-2 (December 1999): 103–11. http://dx.doi.org/10.1016/s0166-0934(99)00112-3.

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Koressaar, T., and M. Remm. "Enhancements and modifications of primer design program Primer3." Bioinformatics 23, no. 10 (March 22, 2007): 1289–91. http://dx.doi.org/10.1093/bioinformatics/btm091.

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Mida, Alhamida Salnaf Ituga, Yusrah, and Tutik Agustini. "Pengaruh Pemberian Terapi Musik Klasik Terhadap Penurunan Dismenore Primer Pada Remaja Putri Di SMA Negeri 1 Buton." Window of Nursing Journal 1, no. 2 (January 21, 2021): 61–72. http://dx.doi.org/10.33096/won.v1i2.310.

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Menorrhea during menstruation, unpleasant experiences of sensations and emotions, circumstances that exhibit subjective/individual discomfort, hurt the body, and whenever individuals say it is real. If the dismenmenore is not handled it can affect the activities and attitudes of the students. One of the non- pharmacological measures in dealing with pain is the technique of distraction with music therapy that can safely reduce pain. Listening to music can produce zatendorphins (a substance similar to morphine supplied by the body that can reduce pain that can inhibit the transmission of pain impulses in the central nervous system, so that the sensation of menstrual pain can be reduced. The purpose of this study was to find out the effect of classical music therapy on the reduction of primary dismenorrhea pain in young women of SMAN 1 Buton. This research uses experimental methods, using pre-experimental designs with pretest-postest designs. In this study using non probability sampling with consecutive sampling method, the population in this study was all girls who experienced primary dismenorrhea in xli ipa1, IPA2 and IPA3 classes of 35 people. The data analysis used is univariate and bivariate, where bivariate uses Wilcoxon test analysis. Instruments used numeric rating scale (NRS). Samples were given classical music therapy 10-20 minutes for 3 consecutive days. The results showed a value of ρ = 0.000, where the ρ value is smaller than α=0.05 then Ha is accepted and H0 is rejected. Thus, it can be concluded that there are different results before and after the administration of classical music therapy, so there is an effect of effective classical music therapy on disminore. While the advice from this study is to address menorrhea pain not directly taking pharmacological drugs but rather using musical therapies such as classical music therapy, then this study can also be an additional reference related classical music therapy to menstrual pain.

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Valentine, Jeffrey C., Emily E. Tanner‐Smith, James E. Pustejovsky, and T. S. Lau. "Between‐case standardized mean difference effect sizes for single‐case designs: a primer and tutorial using the scdhlm web application." Campbell Systematic Reviews 12, no. 1 (January 2016): 1–31. http://dx.doi.org/10.4073/cmdp.2016.1.

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Zaini, Syasya Azra, Siti Hajar Yusoff, Amira Aziera Abdullah, Sheroz Khan, Faridah Abd Rahman, and Nadia Nazieha Nanda. "INVESTIGATION OF MAGNETIC PROPERTIES FOR DIFFERENT COIL SIZES OF DYNAMIC WIRELESS CHARGING PADS FOR ELECTRIC VEHICLES (EV)." IIUM Engineering Journal 21, no. 1 (January 20, 2020): 23–32. http://dx.doi.org/10.31436/iiumej.v21i1.1108.

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Electric vehicles (EV) have been introduced in the recent years due to public awareness of the effect of gas emission from traditional cars and the extinction of petroleum natural resources. For charging EV, dynamic wireless charging is considered in this paper. This is because it is more convenient and saves charging time since it charges the electric vehicle while moving. The main challenge of this process is to maintain a high amount of power transfer from primary to secondary coil. One of the factors contributing to a good power transfer is the size of the coil [1]. There are various designs of coil for wireless charging of electric vehicles (EV). Among the most common designs are circular pad (CP), rectangular pad (RP), double-D pad (DDP), and double-D quadrature pad (DDQP). In this paper, circular pad (CP) is chosen for use, due to its simplicity in design and good electrical and magnetic properties. Three different coil pair sizes are tested to find the most suitable coil pair for the primary and secondary pads that has the maximum power transfer and is least sensitive to misalignment. The magnetic properties have been investigated to obtain the highest value of magnetic flux. The geometry design of the pads and simulation was done using COMSOL Multiphysics software. From the simulation, it was found that the unsymmetrical coil pair gives high magnetic strength when the outer diameters of the primary and secondary coils have the same value. ABSTRAK: Kenderaan Elektrik (EV) telah diperkenalkan sejak beberapa tahun ini hasil kesedaran awam tentang kesan pembebasan gas dari kenderaan lama dan pengurangan sumber asli petroleum. Kajian ini berkaitan pengecas dinamik tanpa wayar bagi mengecas EV. Ini kerana pengecas ini lebih sesuai dan jimat masa mengecas kerana kenderaan elektrik dicas ketika bergerak. Cabaran utama proses ini adalah mengekalkan pemindahan tenaga yang tinggi daripada gegelung primer kepada gegelung sekunder. Salah satu faktor bagi mendapatkan pemindahan tenaga yang tinggi adalah saiz gegelung wayar [1]. Terdapat pelbagai bentuk gegelung bagi mengecas kenderaan elektrik (EV) tanpa wayar. Antaranya adalah pad membulat (CP), pad segiempat tepat (RP), pad berganda-D (DDP), dan pad kuadratur berganda-D (DDQP). Kajian ini telah menggunakan pad membulat (CP) kerana reka bentuknya yang ringkas dan ia mempunyai sifat elektrikal dan magnatik yang baik. Tiga pasang gegelung berbeza telah diuji bagi mendapatkan pasangan gegelung pad primer dan sekunder yang paling sesuai di mana ianya mempunyai pemindahan tenaga maksima dan paling kurang sensitif pada ketidakjajaran. Sifat magnet telah diuji bagi mendapatkan nilai fluks magnet tertinggi. Rekabentuk geometri pad dan simulasi telah dijalankan menggunakan perisian Multifizik COMSOL. Hasil simulasi mendapati pasangan gegelung yang tidak simetri telah menghasilkan kekuatan magnetik tertinggi apabila diameter luaran gegelung primer dan sekunder mempunyai nilai sama.

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Inagaki, Takayuki, Shoki Asahi, Kenji Ogawa, Taku Nakagawa, Toshiaki Nikai, Kiyofumi Yamada, Tetsuya Yagi, and Kei-ichi Uchiya. "1654. Evaluation of a rapid detection method of clarithromycin resistance genes in Mycobacterium avium using the Amplification Refractory Mutation System-Loop-Mediated Isothermal Amplification method." Open Forum Infectious Diseases 7, Supplement_1 (October 1, 2020): S815—S816. http://dx.doi.org/10.1093/ofid/ofaa439.1832.

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Abstract Background Clarithromycin (CLR) is the key drug in multidrug therapy for Mycobacterium avium complex (MAC) diseases and the only drug for which drug susceptibility is correlated with a clinical response in these diseases. In the case of CLR-resistant MAC, a point mutation is present at either position 2058 or 2059 of the peptidyl transferase active center in the domain V region of 23S rRNA at the macrolide binding site. Using conventional investigation, we clarified the correlation between drug susceptibility testing and mutation of drug resistance genes. In this study, we adapted a rapid detection method using the amplification refractory mutation system (ARMS)-loop-mediated isothermal amplification (LAMP) to identify a mutation in the 23S rRNA gene in M. avium isolates (Figure 1). Furthermore, we evaluated the usefulness as point-of-care testing (POCT) technology using clinical isolates. Figure 1. The designs of CLR resistance A2058G mutant-type mismatch primers used for the ARMS-LAMP assay. a) A strand-displacing DNA polymerase extends the DNA from FIP while separating from the DNA chain. The primer F3 binds to its complementary region on the DNA to displace the newly synthesized DNA. An analogous reaction is performed by BIP and B3. α (α = A, wild type; G, A2058G) and β (β = A, wild type; C, A2058G) are indicated by the point mutation at position 2058 of the 23S rRNA gene. The bold area indicates the mismatched base C (cytosine). b) The synthesized DNA self-anneals because of the complementary region at both ends and forms ‘dumbbell’ structures. c) After repeated rounds, a complementary region on the same chain is amplified. Methods Primers for ARMS-LAMP were designed using PrimerExplorerV5 software based on the nucleotide sequence data for 23S rRNA in M. avium strain 104 (Figure 2). Using the minimum inhibitory concentration of CLR, drug susceptibility was determined for 18 clinical M. avium isolates. Of these, eight CLR-susceptible and 10 CLR-resistant strains were analyzed by sequencing the 23S rRNA gene and ARMS-LAMP. Figure 2. Alignment of the nucleotide sequences including the domain V region of 23S rRNA at the macrolide binding site. The constructed LAMP primer sets are shown in solid boxes (forward primers, F1-3) and dashed boxes (backward primers, B1-3). The bold area indicates the point mutation at position 2058 or 2059 of the 23S rRNA gene. Results Sequence analysis revealed that all eight CLR-sensitive strains tested were wild type, whereas all 10 CLR-resistant strains were mutants. Using ARMS-LAMP, no amplification with the mutant-type mismatch primer sets (MTPS) was observed in the eight wild-type strains, but amplification was observed with MTPS in the 10 mutant strains (Table 1). Table 1. MICs of CLR and results of ARMS–LAMP using Mycobacterium avium isolates. Conclusion The developed rapid detection method for the CLR resistance gene using ARMS-LAMP can determine drug resistance in a few hours without the need for special equipment. ARMS-LAMP may be a new clinically beneficial POCT technology for examination that is novel and extremely practical. Disclosures All Authors: No reported disclosures

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Ria Santi, Yumira, Yhona Paratmanitya, and Pratiwi Pratiwi. "Terapi Bekam dan Akupunktur Terhadap Penurunan Tekanan Darah pada Penderita Hipertensi Primer (Esensial) di Klinik Herbal El Zahra Kota Tarakan." Jurnal Ners dan Kebidanan Indonesia 2, no. 3 (May 9, 2016): 147. http://dx.doi.org/10.21927/jnki.2014.2(3).147-154.

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<p>Hypertension is health problems are often happens in society, both of urban and rural community. Prevalence in Indonesia reached was 75.8% quite high, the long term medical treatment make it more difficult to handled properly. Alternative treatment like cupping and acupuncture are patients hypertension efforts to be free from side effects inflicted by chemical medicines. The purpose of this study was to determine the effect of cupping and acupuncture therapy effectiveness in blood pressure reduction among patients with primary hypertension. Study design used in this study was pre experimental designs with pretest–posttest, used statistics of paired t-test and independent t-test. The Results of paired test showed that value of p were 0.003 for systole blood pressure of cupping and 0.000 for systole blood pressure of acupuncture while diastole blood pressure of cupping obtained by value of p were 0.065 and 0.775 for diastole blood pressure of acupuncture, it means that cupping and acupuncture only had an affect on systole blood pressure reduction. Analysis results of independent t-test showed that value of p were 0.051 for systole blood pressure and 0.511 for diastole blood pressure, it means that there was no differences between cupping and acupuncture therapy. Based on average of blood pleasure reduction, acupuncture can reduce of 17 mmHg of systole blood pressure while cupping only 10 mmHg, in acupuncture also reduce of 16 mmHg diastole blood pressure while cupping canl 19 mmHg.</p>

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Nomoto, Mika, and Yasuomi Tada. "Cloning-free template DNA preparation for cell-free protein synthesis via two-step PCR using versatile primer designs with short 3′-UTR." Genes to Cells 23, no. 1 (December 13, 2017): 46–53. http://dx.doi.org/10.1111/gtc.12547.

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Tsai, M. F., Y. J. Lin, Y. C. Cheng, K. H. Lee, C. C. Huang, Y. T. Chen, and A. Yao. "PrimerZ: streamlined primer design for promoters, exons and human SNPs." Nucleic Acids Research 35, Web Server (May 8, 2007): W63—W65. http://dx.doi.org/10.1093/nar/gkm383.

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Hardin, S. H., L. B. Jones, R. Homayouni, and J. C. McCollum. "Octamer-primed cycle sequencing: design of an optimized primer library." Genome Research 6, no. 6 (June 1, 1996): 545–50. http://dx.doi.org/10.1101/gr.6.6.545.

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Mignolo, Walter. "Reconstitución epistémica/estética: la aesthesis decolonial una década después." Calle 14 revista de investigación en el campo del arte 14, no. 25 (January 9, 2019): 14–33. http://dx.doi.org/10.14483/21450706.14132.

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Mi argumento conjuga dos instancias decoloniales. La primera es la re-orientación decolonial introducida por Aníbal Quijano (en 1990) en el mero cierre de la Guerra Fría. En los 80s era ya evidente que los objetivos de la descolonización no podrían lograrse por medio de la fundación de Estados nacionales. Quijano intuyó que la colonialidad del poder era un estructura invisible y subyacente de la civilización occidental, oculta bajo las promesas vertidas en nombre de la modernidad. Para Quijano la tarea decolonial era, en primer lugar, desprendernos de la colonialidad del poder y, en segundo lugar, engancharnos en la reconstitución epistemológica. La segunda instancia, 20 años después, fue la introducción de reflexiones decoloniales en el marco de la colonialidad del poder de la restitución estética. En los procesos de avanzar en la reconstitución epistemológica y estética, rescatamos el concepto de aestésis (aiesthésis) del olvido al que la relegó la hegemonía de la estética. Aunque el vocablo proviene de Grecia, nos apropiamos de ella en el marco del pensamiento decolonial. En este ensayo reintroduzco el concepto de gnosis, ya incorporado en Local Histories/Global Designs (2000), para re-organizar los sentidos y la política de la reconstitución epistémica/estética (dos conceptos moderno/coloniales) mediante la introducción de gnosis y aestésica, dos conceptos decoloniales apropiados y expropiados del Griego antiguo y sepultados en el vocabulario moderno/colonial.

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Rianti, P., A. L. Hutapea, D. A. Rahman, and Y. Santosa. "Primer design of D-loop region for wild population genetics of Rusa timorensis in Indonesia." IOP Conference Series: Earth and Environmental Science 948, no. 1 (December 1, 2021): 012017. http://dx.doi.org/10.1088/1755-1315/948/1/012017.

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Abstract Rusa timorensis (Javan deer) is endemic wildlife in Indonesia and is estimated at less than 10.000 individuals with continuously declining populations due to habitat loss and illegal hunting in the wild. This declining low population indicates a greater risk of extinction. Unfortunately, the genetic information of the wild Javan deer population for conservation management strategies still lacks data due to challenging sampling in the wild. Most recent studies were analysing the breeding populations outside Indonesia. Here, we propose the primer design of the D-loop genetic marker to determine the genetic population of wild Javan deer. We used metadata analysis of genetic sequences and new samples from five wild populations to design the specific primer of the D-loop region of the wild Javan deer in Indonesia. We used software, i.e.., Primer3 to design the primers, BLAST for specificity and Oligo Analyzer™ Tool for efficiency of the primer. The Annealing temperature optimisation started with pre-denaturation at 94 °C followed by 35 cycles of denaturation at 95°C; 51-56°C annealing for each one degree’s different per PCR treatment; and 72°C extensions. We successfully designed a specific primer (RL-3.1a) to amplify 235 bp of the D-loop region at 52°C annealing’s temperature.

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Yang, Xiaohan, Brian E. Scheffler, and Leslie A. Weston. "Recent Developments in Primer Design for DNA Markers in Higher Plants." HortScience 41, no. 4 (July 2006): 1006C—1006. http://dx.doi.org/10.21273/hortsci.41.4.1006c.

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Primer design is a critical step in the application of PCR-based technologies in genetic diversity analysis of horticultural plants. As more plant genomes have been sequenced in recent years, the emphasis of primer design strategy has shifted to genome-wide and high-throughput direction. This poster summarizes recent advances in primer design for profiling of DNA polymorphism in higher plants, including new primers for the classical plant DNA marker system such as simple sequence repeat (SSR) and single-nucleotide polymorphism (SNPs), as well as newly developed DNA marker systems such as sequence-related amplified polymorphism (SRAP), sequence-specific amplification polymorphism (SSAP), target region amplification polymorphism (TRAP), and universal rice primer (URP). Although most of these primers were designed for agronomical crops, they could be applied to horticultural plants because plant genomes are evolutionarily related. Also, these new primer design strategies could help horticultural researchers develop better primers specifically for profiling of polymorphism in a variety of horticultural crops, invasive weeds, or medicinal plants. We will present examples of their utilization in these diverse systems.

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Sutriono, Bantot, Aditya Rizkiardi, and Moh Khafidz Amrulloh Ramdani. "PERENCANAAN ULANG GEDUNG UNIVERSITAS KATOLIK DARMA CENDIKA (UKDC) SURABAYA." EXTRAPOLASI 18, no. 1 (May 27, 2021): 1–9. http://dx.doi.org/10.30996/exp.v18i1.5208.

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AbstractIn the era of globalization various innovations are needed to meet human needs, in the civil engineering world various innovations are also needed to realize a variety of modern designs that continue to grow. The development starts from the function of the building, the shape of the building, the aesthetics of the building and the strength of the building to accept the burden to be received.This research discusses the structural planning of reinforced concrete covering plates, beams and columns with method of Special Moment Resisting Frame System (SRPMK). Planning is done based on the Procedure of Calculation of Concrete Structure for Building Building (SNI 2847-2013). Minimum load regulations for the design of buildings and other structures (SNI 1727-2013). Regulation of earthquake resistance planning procedures for building structures (SNI 1726-2012). Earthquake calculations are based on seismic map 2017 which is the basis of consideration to determine the degree of structural ductality that depends on the moment frame system bearer. The result of this research is to know the dimension of primary structure (beam, column) and secondary structure (floor plate, roof plate) and to know the dimension of steel reinforcement on primary structure (beam, column) and secondary structure (floor plate, roof plate).AbstrakDi era globalisasi berbagai inovasi dibutuhkan untuk memenuhi kebutuhan manusia, dalam dunia teknik sipil juga dibutuhkan berbagai inovasi untuk mewujudkan berbagai desain modern yang terus berkembang. Pembangunan dimulai dari fungsi bangunan, bentuk bangunan, nilai estetika bangunan dan kekuatan bangunan untuk menerima beban yang akan diterima. Penelitian ini membahas tentang perencanaan struktur beton bertulang yang meliputi pelat, balok dan kolom dengan metode Sistem Rangka Pemikul Momen Khusus (SRPMK). Perencanaan dilakukan berdasarkan Tata Cara Perhitungan Struktur Beton Bangunan Gedung (SNI 2847-2013). Peraturan beban minimum untuk desain gedung dan struktur lainnya (SNI 1727-2013). Pengaturan tata cara perencanaan ketahanan gempa untuk struktur bangunan gedung (SNI 1726-2012). Perhitungan gempa didasarkan pada peta seismik 2017 yang menjadi dasar pertimbangan untuk menentukan derajat daktalitas struktur yang bergantung pada pemikul sistem kerangka momen. Hasil dari penelitian ini adalah untuk mengetahui dimensi struktur primer (balok, kolom) dan struktur sekunder (pelat lantai, pelat atap) serta mengetahui dimensi tulangan baja pada struktur primer (balok, kolom) dan struktur sekunder (pelat lantai) dan dimensi tulangan baja pada struktur primer (balok, kolom) dan struktur sekunder (pelat lantai) , pelat atap). Kata kunci: Sistem Rangka Pemikul Momen Khusus, SNI 1726-2012, SNI 1727-2013, SNI 2847-2013, Peta Seismik 2017.

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Herrera-Mesías, Fernanda, Imen Kharrat Ep Jarboui, and Alexander M. Weigand. "A metabarcoding framework for wild bee assessment in Luxembourg." Journal of Hymenoptera Research 94 (December 20, 2022): 215–46. http://dx.doi.org/10.3897/jhr.94.84617.

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Wild bees are crucial organisms for terrestrial environments. Their ongoing decline could cause irreparable damage to ecosystem services vital to plant reproduction and human food production. The importance of taking swift action to prevent further declines is widely acknowledged, but the current deficit of reliable taxonomic information complicates the development of efficient conservation strategies targeting wild bees. DNA metabarcoding can help to improve this situation by providing rapid and standardized mass identification. This technique allows the analysis of large numbers of specimens without the need for specialized taxonomic knowledge by matching high-throughput sequencing reads against public DNA barcode reference libraries. However, the validation of this approach for wild bees requires the evaluation of potential error sources on a regional scale. Here we analyzed the effects of three potential error sources on a metabarcoding pipeline customized for the wild bee fauna of Luxembourg. In an in silico study, we checked the completeness of the BOLD reference library for 349 species found in the country, the correspondence between molecular and morphological species delimitation for these taxa, and the amplification efficiency of three commonly used metabarcoding primer pairs (mlCOlintF/HCO2198, LepF1/MLepF1-Rev and BF2/BR2). The detection power of the pipeline was evaluated based on the species recovery rates from mock communities of known composition under variable DNA concentration treatments. The reference barcode library evaluation results show that 97% of the species have at least a single barcode in BOLD Systems (minimal length 196 bp) and that 85% of species have ≥ 5 barcodes in the public domain. The mlCOlintF/HCO2198 target fragment presented the highest coverage (77.94% of the species with full barcode sequences), followed by the target fragments of LepF1/MLepF1-Rev (77.65%) and BF2/BR2 (68.48%). Only 60% of the morphospecies presented a complete coverage of the prominent Folmer region (658 bp). The in silico amplification efficiency analysis shows that the BF2/BR2 primer pair has the best-predicted amplification performance, but none of the primer combinations evaluated can be expected to efficiently amplify all local wild bee genera. Finally, all species detection rates in the mock communities, except for the sample with the most discrepant DNA concentrations, were above 97%, with no significant differences found among treatments. These results indicate that the detection capacity of the pipeline is robust enough to be used for the reliable assessment of local wild bee biodiversity, even if species from various size categories are pooled together. Primer bias has a major effect on species detection, which can be acknowledged with a preliminary assessment of primer-template mismatch and sophisticated methodological designs (e.g. mock community controls, replicates). Overall, the metabarcoding pipeline here described provides a suitable tool for quick and reliable taxonomic identification of the regional wild bee fauna to aid conservation initiatives in Luxembourg – and beyond.

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Singh, Vinay K., A. K. Mangalam, S. Dwivedi, and S. Naik. "Primer Premier: Program for Design of Degenerate Primers from a Protein Sequence." BioTechniques 24, no. 2 (February 1998): 318–19. http://dx.doi.org/10.2144/98242pf02.

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Triyani, Yani, Nurizzatun Nafsi, Lelly Yuniarti, Nanan Sekarwana, Endang Sutedja, Dida Ahmad Gurnida, Ida Parwati, and Bachti Alisjahbana. "RANCANGAN PRIMER SPESIFIK GEN MACROPHAGE MANNOSE RECEPTOR (MMR) UNTUK POLYMERASE CHAIN REACTION (PCR) DAN SEKUENSING DEOXYRIBO NUCLEIC ACID (DNA)." INDONESIAN JOURNAL OF CLINICAL PATHOLOGY AND MEDICAL LABORATORY 22, no. 2 (March 27, 2018): 158. http://dx.doi.org/10.24293/ijcpml.v22i2.1120.

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The order (sequencing) determinationof DeoxyribonucleicAcid (DNA) bases is the gene’s most basic information, using the methodof Polymerase Chain Reaction (PCR) as its stage. A key factor of successful detection by PCR is specific PCR primer design choice. Thedetection of diversity of Mycobacterium Mannose Receptor (MMR) gene, responsible for recognizing mannosylated antigen structureof Mycobacterium tuberculosis (M.tb) by DNA sequencing of exon 7 chromosome 10p12, related to susceptiblity for PulmonaryTuberculosis(TB), was first performed in China in 2012. The purpose of this study was to find specific primerfromboth design originatedfrom the research in China/primer I and my own design/primer IIby using Primer3 software. This study was based on 10 healthy subjectsand was a preliminary study of a research titled. The Relationship of Single Nucleotide Polymorphisms (SNPs) of Macrophage MannoseReceptor Gene to Pulmonary Tuberculosis Cases. The examination materials consist of 3 mL of EDTA blood and DNA extraction from itsbuffy coat. The resulting DNA was processed by PCR to amplify MMR gene with primer I and II. The primer I successfully amplified DNAfragments up to 780bp while primer II only 329 bp. The MMR gene DNA sequencing analysis was performed on the amplification resultof both kinds primers by using DNA Baser and Ensembl−BLAST software. The results were different, DNA sequencing result by using theprimer I was found in several chromosomes and also in several loci. Whereas, by using the primer II, it was only found in chromosome10 and in the same locus. Based on this study, it can be concluded that the specific primer design is one of the most important factorsin the success of DNA sequencing.

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Susyadi, Susyadi. "THERMAL-HYDRAULIC ANALYSIS OF SMR WITH NATURALLY CIRCULATING PRIMARY SYSTEM DURING LOSS OF FEED WATER ACCIDENT." JURNAL TEKNOLOGI REAKTOR NUKLIR TRI DASA MEGA 18, no. 3 (September 14, 2016): 117. http://dx.doi.org/10.17146/tdm.2016.18.3.2670.

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ABSTRACT Small Modular Reactors (SMRs) have several advantages over conventional large reactors. With integral and simplified design, application of natural laws for safety system, and lower capital cost this reactor is very suitable to be deployed in Indonesia. One of SMR designs being developed implements natural driving force for its primary cooling system. With such innovative approach, it is important to understand safety implication of the design for all operating circumstances. One of conditions need to be investigated is the loss of feed-water (LoFW) accident. In this study, thermal-hydraulic performance of the SMR with naturally circulating primary system during LoFW accident is analysed. The purpose is to investigate the characteristics of flow in primary system during the accident and to clarify whether the naturally circulating coolant is adequately capable to transfer the heat from core in order to maintain safe condition under considered scenario. The method used is by representing the reactor system into RELAP5 code generic models and performing numerical simulation. Calculation result shows that following the initiating event and reactor trip, primary system flow becomes significantly fluctuated and coolant temperature decreases gradually, while in secondary side steam quality descends into saturated. The primary flow slows down from ~711 kg/s to ~263 kg/s and starts to increase up again at t= ~46 seconds. At the slowest point, fuel centerline and coolant temperatures were ~565 K and ~554 K, showing that temperatures of the fuel and coolant are still below its design limit and saturation point, respectively. This fact reveals that throughout transient the two main thermal hydraulic parameters stay in acceptable values so it could be concluded that under LoFW accident the SMR with naturally circulating primary system is in safe condition. Keywords: SMR, loss of feed water, natural circulation, reactor safety, RELAP5 ABSTRAK Reaktor daya kecil modular (SMR) memiliki beberapa keunggulan dibanding reaktor daya besar konvensional. Dengan disain yang lebih sederhana dan terintegrasi, penerapan hukum alamiah untuk sistem keselamatannya dan biaya modal yang rendah, reaktor ini sangat cocok untuk dibangun di Indonesia. Salah satunya disain SMR yang sedang dikembangkan menerapkan gaya penggerak alami untuk sistim pendingin primernya. Dengan disain seperti itu, adalah sangat penting untuk memahami implikasinya terhadap aspek keselamatan pada seluruh kondisi operasi. Salah satu yang perlu diinvestigasi adalah kecelakaan kehilangan air umpan (LoFW). Pada studi ini, dilakukan analisis kinerja thermal hidrolik SMR yang menggunakan sistim pendinginan primer sirkulasi alam saat kecelakaan LoFW. Tujuannya adalah untuk menginvestigasi karakteristik aliran sistem primer saat kecelakaan LoFW dan untuk memastikan apakah aliran sirkulasi alam cukup untuk memindahkan panas dari teras guna menjaga kondisi tetap aman selama kecelakaan tersebut. Metoda yang digunakan adalah dengan merepresentasikan sistem reaktor ke dalam model-model generik program RELAP5 dan melakukan simulasi numerik. Hasil perhitungan menunjukkan bahwa setelah kejadian pemicu dan trip reaktor, pada sisi primer laju alirnya berfluktuasi secara signifikan dan temperatur pendinginnya menurun secara bertahap sedangkan pada sisi sekunder kondisi uap berubah menjadi uap jenuh. Laju alir turun dari ~711 kg/detik menjadi ~263 kg/detik sebelum kembali naik lagi pada t=~46 detik. Saat laju alir di titik terendah, temperatur pusat bahan bakar dan fluida pendingin adalah sekitar ~565 K dan ~554 K, yang menujukkan bahwa temperatur bahan bakar masih jauh di bawah batas disain dan temperatur fluidanya juga berada di bawah titik saturasi. Keadaan ini menunjukkan bahwa saat transien kedua parameter utama termohidrolik reaktor tetap dalam kondisi yang dapat diterima sehingga dapat disimpulkan bahwa saat kecelakaan kehilangan air umpan, SMR dengan sistim primer sirkulasi alam tetap dalam kondisi aman. Kata kunci: SMR, kehilangan air umpan, sirkulasi alamiah, keselamatan reaktor, RELAP5

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Wu, Yueni, Kai Feng, Ziyan Wei, Zhujun Wang, and Ye Deng. "ARDEP, a Rapid Degenerate Primer Design Pipeline Based on k-mers for Amplicon Microbiome Studies." International Journal of Environmental Research and Public Health 17, no. 16 (August 17, 2020): 5958. http://dx.doi.org/10.3390/ijerph17165958.

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The survey of microbial diversity in various environments has relied upon the widespread use of well-evaluated amplification primers for taxonomic marker genes (e.g., prokaryotic 16S and fungal ITS). However, it is urgent to develop a fast and accurate bioinformatic program to design primers for microbial functional genes to explore more mechanisms in the microbial community. Here, we provide a rapid degenerate primer design pipeline (ARDEP) based on the k-mer algorithm, which can bypass the time-consuming step of sequence alignment to greatly reduce run times while ensuring accuracy. In addition, we developed an open-access platform for the implementation of primer design projects that could also calculate the amplification product length, GC content, Annealing Temperature (Tm), and ΔG of primer self-folding, and identify covered species and functional groups. Using this new platform, we designed primers for several functional genes in the nitrogen cycle, including napA and amoA. Our newly designed primers achieved higher coverage than the commonly used primers for all tested genes. The program and the associated platform that applied the k-mer algorithm could greatly enhance the design and evaluation of primers for environmental microbiome studies.

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Iserte, Javier Alonso, Betina Ines Stephan, Sandra Elizabeth Goñi, Cristina Silvia Borio, Pablo Daniel Ghiringhelli, and Mario Enrique Lozano. "Family-Specific Degenerate Primer Design: A Tool to Design Consensus Degenerated Oligonucleotides." Biotechnology Research International 2013 (February 21, 2013): 1–9. http://dx.doi.org/10.1155/2013/383646.

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Designing degenerate PCR primers for templates of unknown nucleotide sequence may be a very difficult task. In this paper, we present a new method to design degenerate primers, implemented in family-specific degenerate primer design (FAS-DPD) computer software, for which the starting point is a multiple alignment of related amino acids or nucleotide sequences. To assess their efficiency, four different genome collections were used, covering a wide range of genomic lengths: Arenavirus ( nucleotides), Baculovirus ( to bp), Lactobacillus sp. ( to bp), and Pseudomonas sp. ( to bp). In each case, FAS-DPD designed primers were tested computationally to measure specificity. Designed primers for Arenavirus and Baculovirus were tested experimentally. The method presented here is useful for designing degenerate primers on collections of related protein sequences, allowing detection of new family members.

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Journal articles on the topic 'Primer designs'

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