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Journal articles on the topic 'Fragments optimization'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Škerlová, Jana, Vlastimil Král, Milan Fábry, Juraj Sedláček, Václav Veverka, and Pavlína Řezáčová. "Optimization of the crystallizability of a single-chain antibody fragment." Acta Crystallographica Section F Structural Biology Communications 70, no. 12 (2014): 1701–6. http://dx.doi.org/10.1107/s2053230x1402247x.

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Single-chain variable antibody fragments (scFvs) are molecules with immense therapeutic and diagnostic potential. Knowledge of their three-dimensional structure is important for understanding their antigen-binding mode as well as for protein-engineering approaches such as antibody humanization. A major obstacle to the crystallization of single-chain variable antibody fragments is their relatively poor homogeneity caused by spontaneous oligomerization. A new approach to optimization of the crystallizability of single-chain variable antibody fragments is demonstrated using a representative singl

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Rathee, Manisha, and T. V. Vijay Kumar. "DNA Fragment Assembly Using Multi-Objective Genetic Algorithms." International Journal of Applied Evolutionary Computation 5, no. 3 (2014): 84–108. http://dx.doi.org/10.4018/ijaec.2014070105.

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DNA Fragment Assembly Problem (FAP) is concerned with the reconstruction of the target DNA, using the several hundreds (or thousands) of sequenced fragments, by identifying the right order and orientation of each fragment in the layout. Several algorithms have been proposed for solving FAP. Most of these have solely dwelt on the single objective of maximizing the sum of the overlaps between adjacent fragments in order to optimize the fragment layout. This paper aims to formulate this FAP as a bi-objective optimization problem, with the two objectives being the maximization of the overlap betwe

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Recht, Michael I., Vandana Sridhar, John Badger, et al. "Identification and Optimization of PDE10A Inhibitors Using Fragment-Based Screening by Nanocalorimetry and X-ray Crystallography." Journal of Biomolecular Screening 19, no. 4 (2013): 497–507. http://dx.doi.org/10.1177/1087057113516493.

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Fragment-based lead discovery (FBLD) is a technique in which small, low-complexity chemical fragments of 6 to 15 heavy atoms are screened for binding to or inhibiting activity of the target. Hits are then linked and/or elaborated into tightly binding ligands, ideally yielding early lead compounds for drug discovery. Calorimetry provides a label-free method to assay binding and enzymatic activity that is unaffected by the spectroscopic properties of the sample. Conventional microcalorimetry is hampered by requiring large quantities of reagents and long measurement times. Nanocalorimeters can ov

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Ulasov, A. V., Y. V. Khramtsov, T. N. Lupanova, et al. "MNT Optimization for Intracellular Delivery of Antibody Fragments." Doklady Biochemistry and Biophysics 479, no. 1 (2018): 62–65. http://dx.doi.org/10.1134/s1607672918020023.

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Seong, Jae-Dong, and Hae-Dong Kim. "Optimization of collision avoidance maneuver planning for cluster satellites in space debris explosion situation." Proceedings of the Institution of Mechanical Engineers, Part G: Journal of Aerospace Engineering 232, no. 3 (2016): 407–22. http://dx.doi.org/10.1177/0954410016682270.

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In this study, the conjunction situation when a number of explosion fragments approach four cluster satellites was simulated, and an optimum avoidance maneuver plan that mitigates this risk was established. The orbits of four deputy satellites around a virtual chief satellite were defined using the Hill–Clohessy–Wiltshire equation, and NASA’s breakup model was applied to similar altitude rocket body to simulate explosions situation. The distribution of 230 explosion fragments after an explosion was simulated, and the size and direction of the Delta-V were applied to each fragment. In this situ

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Haab, Brian B., and Richard A. Mathies. "Optimization of Single-Molecule Fluorescence Burst Detection of ds-DNA: Application to Capillary Electrophoresis Separations of 100–1000 Basepair Fragments." Applied Spectroscopy 51, no. 10 (1997): 1579–84. http://dx.doi.org/10.1366/0003702971939136.

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Methods for optimizing the dye labeling, laser excitation, and data analysis for single-molecule fluorescence burst detection of ds-DNA have been developed and then validated through capillary electrophoresis (CE) separations of 100–1000 basepair (bp) DNA. Confocal microscopy is used to observe fluorescence bursts from individual DNA fragments labeled with the intercalation dye TO6 as they pass through the ∼ 2-μm-diameter focused laser beam. The dye concentration and laser power were optimized by studying fluorescence burst intensities from pBluescript DNA fragments. The optimal TO6 concentrat

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Zahra, Sana Ali, Ayesha Imran, Faiza Khalid, and Mubashir Rehman. "Fragment-Based Approach towards the Design of Potent and Versatile Anti-Cancer Agents." Global Drug Design & Development Review V, no. I (2020): 1–14. http://dx.doi.org/10.31703/gdddr.2020(v-i).01.

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Despite years of clinical research and trials of encouraging new therapies, cancer remains a leading cause of morbidity and mortality. The fragment-based drug discovery has evolved formerly as an efficient approach for identification, optimization, and generation of lead. After identifying the fragments having binding affinity with the target using computational method for fragment screening, they are optimized into more active compounds. This review elaborates the application of methodology of fragment-based drug design in designing potent and versatile anti-cancer drug candidates. It compris

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8

Suresh, Blessy M., Weichao Li, Peiyuan Zhang, et al. "A general fragment-based approach to identify and optimize bioactive ligands targeting RNA." Proceedings of the National Academy of Sciences 117, no. 52 (2020): 33197–203. http://dx.doi.org/10.1073/pnas.2012217117.

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RNAs have important functions that are dictated by their structure. Indeed, small molecules that interact with RNA structures can perturb function, serving as chemical probes and lead medicines. Here we describe the development of a fragment-based approach to discover and optimize bioactive small molecules targeting RNA. We extended the target validation method chemical cross-linking and isolation by pull-down (Chem-CLIP) to identify and map the binding sites of low molecular weight fragments that engage RNA or Chem-CLIP fragment mapping (Chem-CLIP-Frag-Map). Using Chem-CLIP-Frag-Map, we ident

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Zhao, Minrui, Hongni Gao, Qi Han, Jiaang Ge, Wei Wang, and Jue Qu. "Development of a Driving Cycle for Fuzhou Using K-Means and AMPSO." Journal of Advanced Transportation 2021 (February 24, 2021): 1–15. http://dx.doi.org/10.1155/2021/5430137.

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The driving cycle is a speed-to-time curve, a fundamental technique in the automotive industry, and also a basis to set standards for fuel consumption and emissions of vehicles. A driving cycle is developed based on firsthand driving data collected from fieldwork. First, bad data in the original dataset are preprocessed, the time-series standard smoothing algorithm is used to smoothen the data, and Lagrange’s interpolation is used to realize data interpolation. Next, the rules for kinematic fragment extraction are set to divide the data into kinematic fragments. Last, an evaluation system of k

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Kurniawati, Siti, and Sri Hartati. "Optimization Of The Annealing Temperature With Degenerate Primer For Amplification Of Arginine Decarboxylase (ADC) Fragment Gene From Genomic DNA of Maluku Tenggara Local Cassava." Jurnal ILMU DASAR 19, no. 2 (2018): 135. http://dx.doi.org/10.19184/jid.v19i2.6261.

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Arginine decarboxylase (ADC) is a key enzyme responsible for polyamines biosynthesis and has been shown to increase resistance to biotic and abiotic stress. Cassava (Manihot esculenta Crantz.) is able to grow and produce storage roots well on marginal land. The purpose of this study was to optimize annealing temperature of primers in PCR reaction to amplify candidate cassava ADC gene fragments. Annealing temperature is a crucial factor in PCR reaction affecting product (gene fragments) specificity. Four pairs of primers; MeADC1, MeADC2, MeADC3, andMeADC4, were designed using degenerate method

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Kashyap, Aanchal, Pankaj Kumar Singh, and Om Silakari. "Counting on Fragment Based Drug Design Approach for Drug Discovery." Current Topics in Medicinal Chemistry 18, no. 27 (2019): 2284–93. http://dx.doi.org/10.2174/1568026619666181130134250.

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Fragment based drug design (FBDD) is a structure guided ligand design approach used in the process of drug discovery. It involves identification of low molecular weight fragments as hits followed by determination of their binding mode using X-ray crystallography and/or NMR spectroscopy. X-ray protein crystallography is one of the most sensitive biophysical methods used for screening and is least prone to false positives. It also provides detailed structural information of the protein–fragment complex at the atomic level. The retrieved binding information facilitates the optimization of fragmen

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Singh, Arjan, Karanjeet Singh Kahlon, and Rajinder Singh Virk. "Nonreplicated Static Data Allocation in Distributed Databases Using Biogeography-Based Optimization." Chinese Journal of Engineering 2014 (February 23, 2014): 1–9. http://dx.doi.org/10.1155/2014/785321.

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Allocation of data is one of the key design issues of distributed database. A major cost of query execution in a distributed database system is the data transfer cost from one site to another site. The allocation of fragments among the different sites over the network plays an important role in performance of the distributed database system. The main objective of a data allocation in distributed database is to place the data fragments at different sites in such a way, so that the total data transfer cost can be minimized while executing a set of queries. In this paper, a new biogeography-based

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Narum, David L., Sanjai Kumar, William O. Rogers, et al. "Codon Optimization of Gene Fragments EncodingPlasmodium falciparum Merzoite Proteins Enhances DNA Vaccine Protein Expression and Immunogenicity in Mice." Infection and Immunity 69, no. 12 (2001): 7250–53. http://dx.doi.org/10.1128/iai.69.12.7250-7253.2001.

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ABSTRACT In contrast to conventional vaccines, DNA and other subunit vaccines exclusively utilize host cell molecules for transcription and translation of proteins. The adenine plus thymine content of Plasmodium falciparum gene sequences (∼80%) is much greater than that of Homo sapiens(∼59%); consequently, codon usage is markedly different. We hypothesized that modifying codon usage of P. falciparumgenes encoded by DNA vaccines from that used by the parasite to those resembling mammalian codon usage would lead to increased P. falciparum protein expression in vitro in mouse cells and increased

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Sun, Jia Ze, Guo Hua Geng, and Xiao Ying Pan. "D-S Algorithm Based on SCO for Matching Fragments." Applied Mechanics and Materials 411-414 (September 2013): 1876–79. http://dx.doi.org/10.4028/www.scientific.net/amm.411-414.1876.

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The Dempster-Shafer (D-S) evidence theory is an effective method for uncertain information fusion. Because multiple evidences from different sources of different importance or reliability in the reassembling fractured 3D objects are not equally important when they are combined. This paper presents a social cognitive optimization algorithm (SCO) to generate optimal evidence weight values based on historical training data. In the algorithm, a constrained nonlinear optimized model is established, which is solved by SCO. Compared with the two methods, optimization weight D-S proves more effective

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Almiñana, Nuria, Dolores Polo, M. Asuncion Alsina, and Francesca Reig. "OPTIMIZATION STUDY OF DOXORUBICIN LIPOSOMAL PREPARATIONS COATED WITH LAMININ FRAGMENTS." Preparative Biochemistry and Biotechnology 32, no. 1 (2002): 1–16. http://dx.doi.org/10.1081/pb-120013157.

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16

Kuruba, Balaganesh, Dmitri Tolkatchev, Alla S. Kostyukova, et al. "Design and Optimization of Tropomyosin Fragments for Tropomodulin Interaction Studies." Biophysical Journal 118, no. 3 (2020): 123a—124a. http://dx.doi.org/10.1016/j.bpj.2019.11.811.

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17

Budin, N., N. Majeux, and A. Caflisch. "Fragment-Based Flexible Ligand Docking by Evolutionary Optimization." Biological Chemistry 382, no. 9 (2001): 1365–72. http://dx.doi.org/10.1515/bc.2001.168.

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Abstract A new computational approach for the efficient docking of flexible ligands in a rigid protein is presented. It exploits the binding modes of functional groups determined by an exhaustive search with solvation. The search in ligand conformational space is performed by a genetic algorithm whose scoring function approximates steric effects and intermolecular hydrogen bonds. Ligand conformations generated by the genetic algorithm are docked in the protein binding site by optimizing the fit of their fragments to optimal positions of chemically related functional groups. We show that the us

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18

Zvereva, I. O., N. B. Savelieva, P. V. Postnikov, Yu A. Efimova, and M. A. Dikunets. "APPROACHES TO CHORIONIC GONADOTROPIN QUANTITATIVE DETERMINATION IN ANTI-DOPING CONTROL." Fine Chemical Technologies 12, no. 1 (2017): 64–75. http://dx.doi.org/10.32362/2410-6593-2017-12-1-64-75.

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The article presents the results of the first stage of development of a new quantitative method for human chorionic gonadotropin (hCG) determination by means of ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) to uncover doping abuse by athletes. The identified tryptic peptides correspond to the most abundant hCG isoforms: the α- and β-subunits, the nicked and β-core fragment of the hormone. Identification and sequencing of specific fragments were performed with the use of nanoLC-MS/MS. A high resolution / high accuracy hybrid mass-spectrometer was

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19

Yang, Ze Xiao, Gui Li Li, Yin Wang, et al. "Primary Establishment of LAMP Method for Cyprinid Herpesvirus 2 Detection." Applied Mechanics and Materials 602-605 (August 2014): 1823–28. http://dx.doi.org/10.4028/www.scientific.net/amm.602-605.1823.

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A new loop-mediated isothermal amplification (LAMP) method for the detection of Cyprinid herpesvirus 2 (CyHV-2) was developed. Following the synthesis in vitro of a 413 bp DNA fragment of CyHV2 DNA-dependent DNA polymerase gene by overlap extension PCR using 11 overlapping oligo primers designed according to the gensome sequences information of CyHV2 published in GenBank, a set of 6 LAMP primers were designed based on the synthesized DNA fragment, and the LAMP assay was primarily established after preparation of target gene fragments, optimization of reaction conditions, products identificatio

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Neydorf, Rudolf, and Orkhan Iarakhmedov. "Structural-parametric optimization of the experimental data decomposition into approximated fragments." MATEC Web of Conferences 132 (2017): 04027. http://dx.doi.org/10.1051/matecconf/201713204027.

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21

Crowley, Vincent M., Marvin Thielert, and Benjamin F. Cravatt. "Functionalized Scout Fragments for Site-Specific Covalent Ligand Discovery and Optimization." ACS Central Science 7, no. 4 (2021): 613–23. http://dx.doi.org/10.1021/acscentsci.0c01336.

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22

GADRE, SHRIDHAR R., and V. GANESH. "MOLECULAR TAILORING APPROACH: TOWARDS PC-BASED AB INITIO TREATMENT OF LARGE MOLECULES." Journal of Theoretical and Computational Chemistry 05, no. 04 (2006): 835–55. http://dx.doi.org/10.1142/s021963360600260x.

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The development of a fragmentation-based scheme, viz. molecular tailoring approach (MTA) for ab initio computation of one-electron properties and geometry optimization is described. One-electron properties such as the molecular electrostatic potential (MESP), molecular electron density (MED), and dipole moments are computed by synthesizing the density matrix (DM) of the parent molecule from DMs of its small overlapping fragments. The electron density obtained via MTA was found to be typically within 0.5% of its actual counterpart, while maximum errors of about 2% were noticed in the case of th

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Szeto, Cheuk-Chun, Christopher William McIntyre, and Philip Kam-Tao Li. "Circulating Bacterial Fragments as Cardiovascular Risk Factors in CKD." Journal of the American Society of Nephrology 29, no. 6 (2018): 1601–8. http://dx.doi.org/10.1681/asn.2018010068.

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Cardiovascular disease (CVD) is a major cause of mortality and morbidity in patients with CKD. In the past decade, intestinal dysbiosis and altered gut epithelial barrier function are increasingly recognized in CKD. Uremic patients have slow intestinal transit time, impaired protein assimilation, and decreased consumption of dietary fiber. The use of multiple medications also may contribute to the proliferation of dysbiotic bacteria, which affect the barrier function of intestinal epithelium. In addition, fluid overload and uremic toxins per se directly reduce the gut barrier function. The maj

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Zhang, Xiaowang, Jan Van den Bussche, Kewen Wang, Heng Zhang, Xuanxing Yang, and Zhiyong Feng. "On the Expressivity of ASK Queries in SPARQL." Proceedings of the AAAI Conference on Artificial Intelligence 34, no. 03 (2020): 3057–64. http://dx.doi.org/10.1609/aaai.v34i03.5700.

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As a major query type in SPARQL, ASK queries are boolean queries and have found applications in several domains such as semantic SPARQL optimization. This paper is a first systematic study of the relative expressive power of various fragments of ASK queries in SPARQL. Among many new results, a surprising one is that the operator UNION is redundant for ASK queries. The results in this paper as a whole paint a rich picture for the expressivity of fragments of ASK queries with the four basic operators of SPARQL 1.0 possibly together with a negation. The work in this paper provides a guideline for

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Wei, Yuanjun, and Peter E. Caines. "On Markovian Fragments of COCOLOG for Logic Control Systems." SIAM Journal on Control and Optimization 34, no. 5 (1996): 1707–33. http://dx.doi.org/10.1137/s0363012993254539.

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Boyd, Nicola Jane, and Mark R. Wilson. "Optimization of the GAFF force field to describe liquid crystal molecules: the path to a dramatic improvement in transition temperature predictions." Physical Chemistry Chemical Physics 17, no. 38 (2015): 24851–65. http://dx.doi.org/10.1039/c5cp03702f.

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27

Li, Qingxin, and CongBao Kang. "A Practical Perspective on the Roles of Solution NMR Spectroscopy in Drug Discovery." Molecules 25, no. 13 (2020): 2974. http://dx.doi.org/10.3390/molecules25132974.

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Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to study structures and dynamics of biomolecules under physiological conditions. As there are numerous NMR-derived methods applicable to probe protein–ligand interactions, NMR has been widely utilized in drug discovery, especially in such steps as hit identification and lead optimization. NMR is frequently used to locate ligand-binding sites on a target protein and to determine ligand binding modes. NMR spectroscopy is also a unique tool in fragment-based drug design (FBDD), as it is able to investigate target-ligand int

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Nielsen, R. G., and E. C. Rickard. "Method optimization in capillary zone electrophoretic analysis of hGH tryptic digest fragments." Journal of Chromatography A 516, no. 1 (1990): 99–114. http://dx.doi.org/10.1016/s0021-9673(01)90208-0.

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Wang, Hong-Liang, Bradley L. Postier, and Robert L. Burnap. "Optimization of Fusion PCR for In Vitro Construction of Gene Knockout Fragments." BioTechniques 33, no. 1 (2002): 26–32. http://dx.doi.org/10.2144/02331bm02.

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Kim, Eunhee G., Jieun Jeong, Junghyeon Lee, et al. "Rapid Evaluation of Antibody Fragment Endocytosis for Antibody Fragment–Drug Conjugates." Biomolecules 10, no. 6 (2020): 955. http://dx.doi.org/10.3390/biom10060955.

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Antibody–drug conjugates (ADCs) have emerged as the most promising strategy in targeted cancer treatment. Recent strategies for the optimization ADCs include the development of antibody fragment–drug conjugates (FDCs). The critical factor in the successful development of ADCs and FDCs is the identification of tumor antigen-specific and internalizing antibodies (Abs). However, systematic comparison or correlation studies of internalization rates with different antibody formats have not been reported previously. In this study, we generated a panel of scFv-phage Abs using phage display technology

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31

Bobyleva, T., and A. Shamaev. "Optimization Problems Arising from the Design of Pipes Made of Composite Materials." Materials Science Forum 992 (May 2020): 1024–29. http://dx.doi.org/10.4028/www.scientific.net/msf.992.1024.

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The work is devoted to the construction of analytical solutions for the stress-strain state of a cylindrical hollow elastic rod with a layered structure along the radius. Earlier, the problem of finding the stress-strain state of a rod of composite material fixed at one end with the applied forces and moments of forces at the other end was considered. An approximate representation of the solutions was given, which included auxiliary problems on one fragment of the cylinder, consisting of periodically repeating similar fragments. Such auxiliary problems in the general case do not have an analyt

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Katırcıoğlu, Şenay. "Decomposition of Ge2H6 on the Si(100)(2 × 1) Surface." Surface Review and Letters 10, no. 04 (2003): 577–83. http://dx.doi.org/10.1142/s0218625x03005335.

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The decomposition of Ge 2 H 6 on Si(100)(2 × 1) was investigated on different adsorption models of fragments using the density functional theory method. The most probable adsorption models of fragments for low and high surface coverage of Ge 2 H 6 have been obtained by geometry optimization and single value relative energy calculations. It has been found that, Ge 2 H 4 makes a bridge between the adjacent surface dimers, Ge 2 H 5–H is bound to the same dimer bond with an unbroken Ge–Ge bond in Ge 2 H 6, and two GeH 3 sticks to the same surface dimer bond by a broken Ge–Ge bond in Ge 2 H 6. The

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Quintaes, Bianca Ramalho, Nilma Cintra Leal, Eliane Moura Falavina Reis, and Ernesto Hofer. "Optimization of randomly amplified polymorphic DNA-polymerase chain reaction for molecular typing of Salmonella enterica serovar Typhi." Revista da Sociedade Brasileira de Medicina Tropical 37, no. 2 (2004): 143–47. http://dx.doi.org/10.1590/s0037-86822004000200006.

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Optimization of the RAPD reaction for characterizing Salmonella enterica serovar Typhi strains was studied in order to ensure the reproducibility and the discriminatory power of this technique. Eight Salmonella serovar Typhi strains isolated from various regions in Brazil were examined for the fragment patterns produced using different concentrations of DNA template, primer, MgCl2 and Taq DNA polymerase. Using two different low stringency thermal cycle profiles, the RAPD fingerprints obtained were compared. A set of sixteen primers was evaluated for their ability to produce a high number of di

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McGregor, David A., and Edward S. Yeung. "Optimization of capillary electrophoretic separation of DNA fragments based on polymer filled capillaries." Journal of Chromatography A 652, no. 1 (1993): 67–73. http://dx.doi.org/10.1016/0021-9673(93)80646-p.

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Cheng, Xu, Nijun Li, Suofei Zhang, and Zhenyang Wu. "Robust Visual Tracking with SIFT Features and Fragments Based on Particle Swarm Optimization." Circuits, Systems, and Signal Processing 33, no. 5 (2013): 1507–26. http://dx.doi.org/10.1007/s00034-013-9713-1.

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Kholodnov, Vladislav A., Denis A. Krasnoborodko, Roman Yu Kulishenko, and Sergey L. Chulin. "COMPUTER SIMULATION OF OPTIMAL OPERATIONAL MANAGEMENT OF THE START-UP AND THE OPERATION OF THE REACTOR CASCADE." Bulletin of the Saint Petersburg State Institute of Technology (Technical University) 56 (2021): 96–100. http://dx.doi.org/10.36807/1998-9849-2020-56-82-96-100.

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In the article on the example of isomerization in the cascade of reactors with countercurrent cooling the computer modeling of optimal operational control of start-up and operation of the cascade of reactors is considered. The decision of optimization tasks was performed within Mathcad using the developed original optimization procedure using Mminimize and procedures Rkadapt to solve the system of differential equations and Matlab using the fmincon optimization procedures, genetic algorithm and procedure ode15s to solve the system of differential equations. Fragments of programs and results of

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Galiullin, R. R., R. B. Jarullin, and I. R. Kafiev. "OPTIMIZATION OF THE PLANT IRRIGATION PROCESS IN PROTECTED SOIL CONSTRUCTIONS." VESTNIK OF THE BASHKIR STATE AGRARIAN UNIVERSITY 54, no. 4 (2019): 105–11. http://dx.doi.org/10.31563/1684-7628-2019-52-4-105-111.

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The paper considers a way to increase the energy efficiency of the technological process of plant irradiation by optimizing the irradiation regimes. This is achieved by fragmentation of the schedule of plant irradiation and the search for the positions of the fragments of the photoperiod in time, at which the requirement for the daily dose of radiation is satisfied and the minimum cost of the consumed electric energy is ensured.

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Xiao, Yang Ze, Li Rui Li, Yin Wang, et al. "Development of a RT-PCR for the Detection of European Brown Hare Syndrome Virus." Advanced Materials Research 271-273 (July 2011): 410–16. http://dx.doi.org/10.4028/www.scientific.net/amr.271-273.410.

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To develop the reverse transcriptase polymerase chain reaction (RT-PCR) for the detection of European brown hare syndrome virus (EBHSV), 3 specific primers and 9 overlapping oligo primers were designed to amplify a fragment of 335 nucleotides from the genome of EBHSV according to the genome sequences published in GenBank, and a 359 bp DNA fragment of the capsid protein(VP60)gene of EBHSV was synthesized in vitro by using overlap extension PCR to construct the recombinant plasmids pGM-T-EBHSV, then the RT-PCR method was described through the optimization of reaction conditions, sensitivity and

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Trybush, Sviatlana, Steven Hanley, Kang-Hyun Cho, et al. "Getting the most out of fluorescent amplified fragment length polymorphism." Canadian Journal of Botany 84, no. 8 (2006): 1347–54. http://dx.doi.org/10.1139/b06-096.

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Amplified fragment length polymorphism (AFLP™) is one of the most widely applied molecular marker detection systems used today. Among the reasons for its popularity are its reproducibility, capacity to generate large numbers of data points in a single assay, and “off-the-shelf” universal applicability. The original AFLP protocol was developed using radioactive detection. The transfer of this technique to fluorescent detection on automated DNA fragment analysers not only removed the undesirable requirement for radioactivity but also provided the possibility for increased effectiveness and detec

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Shauqee, Mohamad Norherman, Parvathy Rajendran, and Nurulasikin Mohd Suhadis. "An Explosion Based Algorithm to Solve the Optimization Problem in Quadcopter Control." Aerospace 8, no. 5 (2021): 125. http://dx.doi.org/10.3390/aerospace8050125.

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This paper presents an optimization algorithm named Random Explosion Algorithm (REA). The fundamental idea of this algorithm is based on a simple concept of the explosion of an object. This object is commonly known as a particle: when exploded, it will randomly disperse fragments around the particle within the explosion radius. The fragment that will be considered as a search agent will fill the local space and search that particular region for the best fitness solution. The proposed algorithm was tested on 23 benchmark test functions, and the results are validated by a comparative study with

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Galkin, O. Y., Y. V. Gorshunov, and V. F. Solovjova. "Improvement of the method of obtaining human IgA Fc-fragments." Visnyk of Dnipropetrovsk University. Biology, medicine 6, no. 1 (2015): 32–35. http://dx.doi.org/10.15421/021506.

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To address a number of fundamental and applied problems in immunology, molecular and cellular biology and biotechnology it is necessary to obtain Fc-fragments of immunoglobulins. Fc-fragments may be used for studying of the effector functions of antibodies which are mediated by these areas. They are often used as an immunogen to produce anti-specie (based on so-called secondary antibody) conjugate in the development of serological tests for diagnostics (predominantly such conjugate based on monoclonal antibodies). The work is aimed to develop improved methods of obtaining and allocation of Fc-

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Alhossary, Amr, Yaw Awuni, Chee Keong Kwoh, and Yuguang Mu. "Proposing drug fragments for dengue virus NS5 protein." Journal of Bioinformatics and Computational Biology 16, no. 03 (2018): 1840017. http://dx.doi.org/10.1142/s0219720018400176.

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Dengue fever is a febrile illness caused by Dengue Virus, which belongs to the Flaviviridae family. Among its proteome, the nonstructural protein 5 (NS5) is the biggest and most conserved. It has a primer-independent RNA-dependent RNA polymerase (RdRp) domain at its C-Terminus. Zou et al. studied the biological relevance of the two conserved cavities (named A and B) within the NS5 proteins of dengue virus (DENV) and West Nile Virus (WNV) using mutagenesis and revertant analysis and found four mutations located at cavity B having effects on viral replication. They recommended Cavity B, but not

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Lu, Xiandan, and Edward S. Yeung. "Optimization of Excitation and Detection Geometry for Multiplexed Capillary Array Electrophoresis of DNA Fragments." Applied Spectroscopy 49, no. 5 (1995): 605–9. http://dx.doi.org/10.1366/0003702953963986.

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A new on-column excitation and detection geometry for multiplexed array capillary electrophoresis is evaluated. The detection limit is improved 100-fold for the same laser power because of more efficient coupling of the laser beam. The illumination is also more uniform over the entire array. Stray light and cross-talk are effectively suppressed by immersing the capillaries in water to roughly match the refractive index. A charge-coupled-device (CCD) camera combined with cutoff filters provides adequate sensitivity and speed for high-speed DNA sequencing based on sieving in a polymer-matrix sol

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Kumar, Neeraj, Damini Sood, Ravi Tomar, and Ramesh Chandra. "Antimicrobial Peptide Designing and Optimization Employing Large-Scale Flexibility Analysis of Protein-Peptide Fragments." ACS Omega 4, no. 25 (2019): 21370–80. http://dx.doi.org/10.1021/acsomega.9b03035.

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Stebbins, Michael A., Joe B. Davis, Brian K. Clark, and Michael J. Sepaniak. "Optimization of separation conditions in the size-selective capillary electrophoretic separation of DNA fragments." Journal of Microcolumn Separations 8, no. 7 (1996): 485–94. http://dx.doi.org/10.1002/(sici)1520-667x(1996)8:7<485::aid-mcs5>3.0.co;2-y.

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Harmsen, M. M., C. B. van Solt, A. M. van Zijderveld-van Bemmel, T. A. Niewold, and F. G. van Zijderveld. "Selection and optimization of proteolytically stable llama single-domain antibody fragments for oral immunotherapy." Applied Microbiology and Biotechnology 72, no. 3 (2006): 544–51. http://dx.doi.org/10.1007/s00253-005-0300-7.

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Baker, Brenda S., and Raffaele Giancarlo. "Sparse Dynamic Programming for Longest Common Subsequence from Fragments." Journal of Algorithms 42, no. 2 (2002): 231–54. http://dx.doi.org/10.1006/jagm.2002.1214.

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Palagin, Dennis, and Jonathan P. K. Doye. "DNA-stabilized Ag–Au bimetallic clusters: the effects of alloying and embedding on optical properties." Physical Chemistry Chemical Physics 18, no. 32 (2016): 22311–22. http://dx.doi.org/10.1039/c6cp04352f.

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Global geometry optimization and time-dependent density functional theory calculations have been used to study the structural evolution and optical properties of Ag<sub>n</sub>Au<sub>n</sub> (n = 2–6) nanoalloys both as individual clusters and as clusters stabilized with the fragments of DNA of different size.

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Marek, W., and C. Rauszer. "Query Optimization in the Databases Distributed by Means of Product Equivalence Relations." Fundamenta Informaticae 11, no. 3 (1988): 241–65. http://dx.doi.org/10.3233/fi-1988-11303.

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In this paper, we address the problem of query optimization in distributed databases. We show that horizontal partitions of databases, generated by products of equivalence relations, induce optimization techniques for the basic database operations (i.e., the selection, projection, and join operators). In the case of selection, our method allows for restriction of the number of blocks to be searched in the selection process and subsequent simplification of the selection formula at each block. For the natural join operation, we propose an algorithm that reduces the computation of fragments. Proo

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Ban, Bhupal, Maya Sharma, and Jagathpala Shetty. "Optimization of Methods for the Production and Refolding of Biologically Active Disulfide Bond-Rich Antibody Fragments in Microbial Hosts." Antibodies 9, no. 3 (2020): 39. http://dx.doi.org/10.3390/antib9030039.

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Antibodies have been used for basic research, clinical diagnostics, and therapeutic applications. Escherichia coli is one of the organisms of choice for the production of recombinant antibodies. Variable antibody genes have canonical and non-canonical disulfide bonds that are formed by the oxidation of a pair of cysteines. However, the high-level expression of an antibody is an inherent problem to the process of disulfide bond formation, ultimately leading to mispairing of cysteines which can cause misfolding and aggregation as inclusion bodies (IBs). This study demonstrated that fragment anti

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