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1
Burke, Donald S., Kenneth A. De Jong, John J. Grefenstette, Connie Loggia Ramsey, and Annie S. Wu. "Putting More Genetics into Genetic Algorithms." Evolutionary Computation 6, no. 4 (December 1998): 387–410. http://dx.doi.org/10.1162/evco.1998.6.4.387.
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The majority of current genetic algorithms (GAs), while inspired by natural evolutionary systems, are seldom viewed as biologically plausible models. This is not a criticism of GAs, but rather a reflection of choices made regarding the level of abstraction at which biological mechanisms are modeled, and a reflection of the more engineering-oriented goals of the evolutionary computation community. Understanding better and reducing this gap between GAs and genetics has been a central issue in an interdisciplinary project whose goal is to build GA-based computational models of viral evolution. The result is a system called Virtual Virus (VIV). VIV incorporates a number of more biologically plausible mechanisms, including a more flexible genotype-to-phenotype mapping. In VIV the genes are independent of position, and genomes can vary in length and may contain noncoding regions, as well as duplicative or competing genes. Initial computational studies with VIV have already revealed several emergent phenomena of both biological and computational interest. In the absence of any penalty based on genome length, VIV develops individuals with long genomes and also performs more poorly (from a problem-solving viewpoint) than when a length penalty is used. With a fixed linear length penalty, genome length tends to increase dramatically in the early phases of evolution and then decrease to a level based on the mutation rate. The plateau genome length (i.e., the average length of individuals in the final population) generally increases in response to an increase in the base mutation rate. When VIV converges, there tend to be many copies of good alternative genes within the individuals. We observed many instances of switching between active and inactive genes during the entire evolutionary process. These observations support the conclusion that noncoding regions serve as scratch space in which VIV can explore alternative gene values. These results represent a positive step in understanding how GAs might exploit more of the power and flexibility of biological evolution while simultaneously providing better tools for understanding evolving biological systems.
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Meester, Luc De, Lawrence J. Weider, and Ralph Tollrian. "Alternative antipredator defences and genetic polymorphism in a pelagic predator–prey system." Nature 378, no. 6556 (November 1995): 483–85. http://dx.doi.org/10.1038/378483a0.
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Chen, Jesse J., Xin Cai, and Jack W. Szostak. "N2′→P3′ Phosphoramidate Glycerol Nucleic Acid as a Potential Alternative Genetic System." Journal of the American Chemical Society 131, no. 6 (February 18, 2009): 2119–21. http://dx.doi.org/10.1021/ja809069b.
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Tkatek, Said, Saadia Bahti, Otman Abdoun, and Jaafar Abouchabaka. "Intelligent system for recruitment decision making using an alternative parallel-sequential genetic algorithm." Indonesian Journal of Electrical Engineering and Computer Science 22, no. 1 (April 1, 2021): 385. http://dx.doi.org/10.11591/ijeecs.v22.i1.pp385-395.
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<p>The human resources (HR) manager needs effective tools to be able to move away from traditional recruitment processes to make the good decision to select the good candidates for the good posts. To do this, we deliver an intelligent recruitment decision-making method for HR, incorporating a recruitment model based on the multipack model known as the NP-hard model. The system, which is a decision support tool, often integrates a genetic approach that operates alternately in parallel and sequentially. This approach will provide the best recruiting solution to allow HR managers to make the right decision to ensure the best possible compatibility with the desired objectives. Operationally, this system can also predict the altered choice of parallel genetic algorithm (PGA) or sequential genetic algorithm (SeqGA) depending on the size of the instance and constraints of the recruiting posts to produce the quality solution in a reduced CPU time for recruiting decision-making. The results obtained in various tests confirm the performance of this intelligent system which can be used as a decision support tool for intelligently optimized recruitment.</p>
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Likhoshvai, Vitaly A., Vladislav V. Kogai, Stanislav I. Fadeev, and Tamara M. Khlebodarova. "Alternative splicing can lead to chaos." Journal of Bioinformatics and Computational Biology 13, no. 01 (February 2015): 1540003. http://dx.doi.org/10.1142/s021972001540003x.
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Alternative splicing is a widespread phenomenon in higher eukaryotes, where it serves as a mechanism to increase the functional diversity of proteins. This phenomenon has been described for different classes of proteins, including transcription regulatory proteins. We demonstrated that in the simplest genetic system model the formation of the alternatively spliced isoforms with opposite functions (activators and repressors) could be a cause of transition to chaotic dynamics. Under the simplest genetic system we understand a system consisting of a single gene encoding the structure of a transcription regulatory protein whose expression is regulated by a feedback mechanism. As demonstrated by numerical analysis of the models, if the synthesized isoforms regulate the expression of their own gene acting through different sites and independently of each other, for the generation of chaotic dynamics it is sufficient that the regulatory proteins have a dimeric structure. If regulatory proteins act through one site, the chaotic dynamics is generated in the system only when the repressor protein is either a tetrameric or a higher-dimensional multimer. In this case the activator can be a dimer. It was also demonstrated that if the transcription factor isoforms exhibit either activating or inhibiting activity and are lower-dimensional multimers (< 4), independently of the regulation type the model demonstrates either cyclic or stationary trajectories.
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Doronina, J. V. "Improving the Design Efficiency of Complex Systems Based on Reducing the Power of Many Generated Alternatives." Quality and life 27, no. 3 (September 23, 2020): 27–32. http://dx.doi.org/10.34214/2312-5209-2020-27-3-27-32.
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The article proposes an approach to the structural synthesis of elements of a system-technical complex, which consists in using a modified genetic algorithm and a method for narrowing the cardinality of the sets of alternatives. The modification of the genetic algorithm is implemented as part of a directed mutation operation for three types of the initial elemental composition of the alternative and is used for objects with a given (limited) duration of their life cycle. Application of the proposed approach made it possible to both reduce efforts in obtaining alternatives at the stage of designing elements of a system-technical complex, and to reduce labor intensity in the formation of the appearance of the system.
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Boland, M. A., P. V. Preckel, and A. P. Schinckel. "Optimal Hog Slaughter Weights Under Alternative Pricing Systems." Journal of Agricultural and Applied Economics 25, no. 2 (December 1993): 148–63. http://dx.doi.org/10.1017/s1074070800019039.
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AbstractThree hog genotypes are simulated to determine how producer profits, economically optimal slaughter weights, and carcass component weights change under three pricing models. Live weight pricing pays more for the fatter barrows whereas a three component (separate payments for fat, lean, and byproducts) and six component (separate payments for major primal cuts, other lean, fat, and byproducts) pricing system pay more for the leaner gilts. Implications for selection of genetic stock and pricing system are presented.
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Kim, Sangyong, and Jae Heon Shim. "Combining case-based reasoning with genetic algorithm optimization for preliminary cost estimation in construction industry." Canadian Journal of Civil Engineering 41, no. 1 (January 2014): 65–73. http://dx.doi.org/10.1139/cjce-2013-0223.
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In this paper, we propose a hybrid case-based reasoning (CBR) system for predicting the construction cost of high-rise buildings at the preliminary design stage. First, the extracted cost factors (CFs) of a high-rise building were shown to significantly improve the cost estimation system’s performance. For developing a CBR system, a hybrid approach that combines CBR with genetic algorithms (GAs) for cost estimation was adopted. Genetic algorithms were used for optimized weight generation and applied to real project cases. Additionally, this paper proposes the identification of an alternative similarity score measurement formula. The proposed formula evaluates the contrast between the alternative case matching approach and the classical formula in a scenario involving the use of cost factors describing a case. The results indicate that the proposed GA-based CBR system can consistently reduce errors and potentially be useful to owners and contractors in the early financial planning stage. Accordingly, it is expected that the developed CBR system would provide decision-makers with accurate cost information to assess and compare multiple alternatives for obtaining the optimal solution and controlling the cost.
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Diwo, Christian, and Nediljko Budisa. "Alternative Biochemistries for Alien Life: Basic Concepts and Requirements for the Design of a Robust Biocontainment System in Genetic Isolation." Genes 10, no. 1 (December 28, 2018): 17. http://dx.doi.org/10.3390/genes10010017.
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The universal genetic code, which is the foundation of cellular organization for almost all organisms, has fostered the exchange of genetic information from very different paths of evolution. The result of this communication network of potentially beneficial traits can be observed as modern biodiversity. Today, the genetic modification techniques of synthetic biology allow for the design of specialized organisms and their employment as tools, creating an artificial biodiversity based on the same universal genetic code. As there is no natural barrier towards the proliferation of genetic information which confers an advantage for a certain species, the naturally evolved genetic pool could be irreversibly altered if modified genetic information is exchanged. We argue that an alien genetic code which is incompatible with nature is likely to assure the inhibition of all mechanisms of genetic information transfer in an open environment. The two conceivable routes to synthetic life are either de novo cellular design or the successive alienation of a complex biological organism through laboratory evolution. Here, we present the strategies that have been utilized to fundamentally alter the genetic code in its decoding rules or its molecular representation and anticipate future avenues in the pursuit of robust biocontainment.
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Dormatey, Richard, Chao Sun, Kazim Ali, Sajid Fiaz, Derong Xu, Alejandro Calderón-Urrea, Zhenzhen Bi, Junlian Zhang, and Jiangping Bai. "ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review." PeerJ 9 (July 27, 2021): e11809. http://dx.doi.org/10.7717/peerj.11809.
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Antibiotic and herbicide resistance genes are the most common marker genes for plant transformation to improve crop yield and food quality. However, there is public concern about the use of resistance marker genes in food crops due to the risk of potential gene flow from transgenic plants to compatible weedy relatives, leading to the possible development of “superweeds” and antibiotic resistance. Several selectable marker genes such as aph, nptII, aaC3, aadA, pat, bar, epsp and gat, which have been synthesized to generate transgenic plants by genetic transformation, have shown some limitations. These marker genes, which confer antibiotic or herbicide resistance and are introduced into crops along with economically valuable genes, have three main problems: selective agents have negative effects on plant cell proliferation and differentiation, uncertainty about the environmental effects of many selectable marker genes, and difficulty in performing recurrent transformations with the same selectable marker to pyramid desired genes. Recently, a simple, novel, and affordable method was presented for plant cells to convert non-metabolizable phosphite (Phi) to an important phosphate (Pi) for developing cells by gene expression encoding a phosphite oxidoreductase (PTXD) enzyme. The ptxD gene, in combination with a selection medium containing Phi as the sole phosphorus (P) source, can serve as an effective and efficient system for selecting transformed cells. The selection system adds nutrients to transgenic plants without potential risks to the environment. The ptxD/Phi system has been shown to be a promising transgenic selection system with several advantages in cost and safety compared to other antibiotic-based selection systems. In this review, we have summarized the development of selection markers for genetic transformation and the potential use of the ptxD/Phi scheme as an alternative selection marker system to minimize the future use of antibiotic and herbicide marker genes.
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Marchetti, Francesco, and Edmondo Minisci. "Genetic Programming Guidance Control System for a Reentry Vehicle under Uncertainties." Mathematics 9, no. 16 (August 6, 2021): 1868. http://dx.doi.org/10.3390/math9161868.
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As technology improves, the complexity of controlled systems increases as well. Alongside it, these systems need to face new challenges, which are made available by this technology advancement. To overcome these challenges, the incorporation of AI into control systems is changing its status, from being just an experiment made in academia, towards a necessity. Several methods to perform this integration of AI into control systems have been considered in the past. In this work, an approach involving GP to produce, offline, a control law for a reentry vehicle in the presence of uncertainties on the environment and plant models is studied, implemented and tested. The results show the robustness of the proposed approach, which is capable of producing a control law of a complex nonlinear system in the presence of big uncertainties. This research aims to describe and analyze the effectiveness of a control approach to generate a nonlinear control law for a highly nonlinear system in an automated way. Such an approach would benefit the control practitioners by providing an alternative to classical control approaches, without having to rely on linearization techniques.
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Yu, Hanyang, Su Zhang, and John C. Chaput. "Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor." Nature Chemistry 4, no. 3 (January 10, 2012): 183–87. http://dx.doi.org/10.1038/nchem.1241.
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Yang, Zunyi, Daniel Hutter, Pinpin Sheng, A. Michael Sismour, and Steven A. Benner. "Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern." Nucleic Acids Research 34, no. 21 (October 29, 2006): 6095–101. http://dx.doi.org/10.1093/nar/gkl633.
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Groisman, Irina, and Hanna Engelberg-Kulka. "Translational bypassing: a new reading alternative of the genetic code." Biochemistry and Cell Biology 73, no. 11-12 (December 1, 1995): 1055–59. http://dx.doi.org/10.1139/o95-113.
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The translation of the genetic code, once thought to be rigid, has been found to be quite flexible, and several alternatives in its reading have been described. An unusual alternative is translational bypassing, a frameshift event where the transition from frame 0 to another frame occurs by translational bypassing of an extended region of the mRNA sequence rather than by slippage past a single nucleotide, as has been described for most examples of frameshifting. Translational bypassing has been characterized in two cases, T4 gene 60 coding for a topoisomerase subunit and in a trpR–lac′Z fusion. The latter was discovered in our laboratory, and the unique bypass mechanism is investigated further in this study. Using a trpR+1–lac′Z fusion system, we show that the Gln codon at the beginning of lacZ end at the 3′ side of the gap is required for bypassing to occur. The Gln codon is part of an mRNA segment that can (potentially) base pair with a segment at the 5′ and of Escherichia coli 16S rRNA. A model of trpR+1–lac′Z bypassing is suggested in which the untranslated region of the mRNA is looped out through base pairing between a segment in the 5′ end of the 16S rRNA and two sites in the mRNA. Translational bypassing is a newly discovered mechanism of gene expression, and trpR is the first cellular gene identified in which such a mechanism could operate. The understanding of this mechanism and its associated signals may be considered a paradigm for the expression of other genes by this alternative reading of the genetic code.Key words: genetic code, translation, frameshifting, trpR.
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Hellerich, Gert. "Nonpsychiatry: An Alternative to Contemporary Mental Health Work." Ethical Human Psychology and Psychiatry 7, no. 2 (June 2005): 149–58. http://dx.doi.org/10.1891/1559-4343.7.2.149.
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The central theme of this article is nonpsychiatry. The implication of this term is illustrated in the mental health system and its significance is shown as an alternative to the established psychiatry. The article differentiates between genetic and social psychiatry on the one hand and antipsychiatry on the other when dealing with nonpsychiatry. An example of a psychosocial self-help group in Germany illustrates the nonpsychiatric services and strategies.
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Roden, J. A. "A simulation study of open nucleus and closed nucleus breeding systems in a sheep population." Animal Science 60, no. 1 (February 1995): 117–24. http://dx.doi.org/10.1017/s1357729800008213.
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AbstractStochastic simulation was used to compare the results of alternative breeding systems in a sheep population divided into 10 flocks of 120 ewes. The breeding systems compared were selection within closed flocks (CF), a closed nucleus system (CNS), an open nucleus system (ONS) and open nucleus systems with the selection of nucleus replacements being restricted to either nucleus born males (ONSRm) or nucleus born females (ONSRf). Selection was for a best linear unbiased prediction of breeding value for lamb live weight which had a heritability of 0·17. The open nucleus breeding systems (ONS, ONSRm, ONSRf) resulted in higher rates of genetic gain, more predictable selection responses and lower rates of inbreeding than either the closed nucleus system (CNS) or selection within closed flocks (CF). Initial genetic differences between flocks resulted in higher rates of genetic gain in the nucleus breeding systems due to the use of between flock genetic variance. In the ONS system up to 25% of nucleus sires and approximately 50% of nucleus dams were born in base flocks. Nevertheless if selection of either nucleus sires or dams was restricted to nucleus born animals there was very little change in genetic gain or rate of inbreeding.
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Gallese, Vittorio, and Corrado Sinigaglia. "Understanding action with the motor system." Behavioral and Brain Sciences 37, no. 2 (April 2014): 199–200. http://dx.doi.org/10.1017/s0140525x13002288.
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AbstractWe challenge Cook et al.'s claim about the vagueness of the notion of action understanding in relation with mirror neurons. We show the multidimensional nature of action understanding and provide a definition of motor-based action understanding, shedding new light on the various components of action understanding and on their relationship. Finally, we propose an alternative perspective on the origin of mirror neurons, stressing the necessity to abandon the dichotomy between genetic and associative hypotheses.
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Mate, Toth, Szabo Zoltan, and Toth Zoltan. "Alternative method for the transformation of Capsicum species." Journal of Plant Science and Phytopathology 5, no. 1 (February 1, 2021): 001–3. http://dx.doi.org/10.29328/journal.jpsp.1001053.
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Capsicum (pepper) species have high economic values as vegetable crops and medicinal plants. Most of the Capsicum is known to be recalcitrant to plant regeneration in vitro, and to genetic transformation with Agrobacterium tumefaciens. However, genetic improvement against pathogens requires discovering new pest resistance genes and revealing their functions and mechanism in vitro. The development of improved transformation methods serves this purpose, which needs a binary vector technology carrying the gene of interest to be transferred into the host plants. Agrobacterium rhizogenes mediated transformation serves as a useful alternative way for the Capsicum transformation. The A. rhizogenes transformation compared to the A. tumefaciens transformation has the advantage that the method needs no regeneration step in vitro. Our goal is to obtain a highly efficient transformation system that can be used to study the functions of different genes in Capsicum annuum varieties. Our study’s further goal is to validate and describe the candidate gene (Me1) involved in resistance against root-knot nematode species.
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Kolesnikov, A. V., and O. P. Fedorov. "SYSTEM OF THE COMPLICATED PRACTICAL PROBLEMS ANALYSIS." Mathematical Modelling and Analysis 7, no. 1 (June 30, 2002): 83–92. http://dx.doi.org/10.3846/13926292.2002.9637181.
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The original methodology of the system analysis of the inhomogeneous problem is offered, including stages of its reducing to homogeneous parts and selecting for them appropriate toolkits: methods and models. This system applies the accumulated knowledge and the experts skills to refer of each homogeneous problem to one or several alternative classes of modelling methods: analytical methods, statistical methods, artificial neuronets, knowledge based systems, fuzzy systems, genetic algorithms. The knowledge base testing has shown sufficiency and consistency of knowledge for realization of the inhomogeneous problems analysis even in conditions with a low and average distortion in the problem descriptions.
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Dziurzanski, Piotr, Shuai Zhao, Sebastian Scholze, Albert Zilverberg, Karl Krone, and Leandro Soares Indrusiak. "Process planning and scheduling optimisation with alternative recipes." at - Automatisierungstechnik 68, no. 2 (February 25, 2020): 140–47. http://dx.doi.org/10.1515/auto-2019-0104.
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AbstractThis paper considers an application of a new variant of a multi-objective flexible job-shop scheduling problem, featuring multisubset selection of manufactured recipes, to a real-world chemical plant. The problem is optimised using a multi-objective genetic algorithm with customised mutation and elitism operators that minimises both the total production time and the produced commodity surplus. The algorithm evaluation is performed with both random and historic manufacturing orders. The latter demonstrated that the proposed system can lead to more than 10 % makespan improvements in comparison with human operators.
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GIANOLA, DANIEL, and GUSTAVO de los CAMPOS. "Inferring genetic values for quantitative traits non-parametrically." Genetics Research 90, no. 6 (December 2008): 525–40. http://dx.doi.org/10.1017/s0016672308009890.
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SummaryInferences about genetic values and prediction of phenotypes for a quantitative trait in the presence of complex forms of gene action, issues of importance in animal and plant breeding, and in evolutionary quantitative genetics, are discussed. Current methods for dealing with epistatic variability via variance component models are reviewed. Problems posed by cryptic, non-linear, forms of epistasis are identified and discussed. Alternative statistical procedures are suggested. Non-parametric definitions of additive effects (breeding values), with and without employing molecular information, are proposed, and it is shown how these can be inferred using reproducing kernel Hilbert spaces regression. Two stylized examples are presented to demonstrate the methods numerically. The first example falls in the domain of the infinitesimal model of quantitative genetics, with additive and dominance effects inferred both parametrically and non-parametrically. The second example tackles a non-linear genetic system with two loci, and the predictive ability of several models is evaluated.
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Li, Lu, and Zhong Fu Tan. "Optimization Design of Wind/Photovoltaic Hybrid Power Systems Based on Genetic Algorithms." Applied Mechanics and Materials 278-280 (January 2013): 1692–95. http://dx.doi.org/10.4028/www.scientific.net/amm.278-280.1692.
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Wind power and solar energy power are clean, abundant and renewable. Wind power and photovoltaic power are important alternative energy in the world, which will contribute to adjusting energy structures and protecting environments. The genetic algorithm has the characteristics of automatic optimization and approaches the simulate stuff illimitably. Also, there has no use for accurate model on questions, which is very suitable in the non-linear system. The wind/photovoltaic hybrid systems consist with wind power generation units, photovoltaic matrix, storage battery, diesel engine and data collection and control. This paper optimized the wind/photovoltaic hybrid system using genetic algorithm. The result showed the efficiency of this algorithm in the design of this kind of non-linear system. On the other hand, this hybrid system is strongly non-linear when is running. Finally, abundant operating expenses and maintains expenses will be saved by using genetic algorithm in its dynamic management according to the change of load, wind power and irradiation.
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Roden, J. A. "A comparison of alternative nucleus breeding systems and a sire referencing scheme for sheep improvement." Animal Science 62, no. 2 (April 1996): 265–70. http://dx.doi.org/10.1017/s1357729800014569.
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AbstractStochastic simulation was used to compare selection response and rate of inbreeding in four nucleus breeding systems and a sire referencing scheme for sheep: an open nucleus system (ONS), an open nucleus system with sequential selection of the nucleus (ONS-S), a sire referencing scheme (SRS) and a dispersed open nucleus system (DONS). Selection was based on best linear unbiased prediction of breeding values for a single trait measurable on all individuals prior to selection. Selection in a population of 1200 ewes equally divided into 10 flocks was simulated over a 15-year period. The mean rate of genetic gain was proportionately about 0-15 higher in ONS-S and DONS compared with ONS and SRS. The rate of inbreeding in SRS was considerably lower and in ONS-S, considerably higher, than in the other systems. The level of prolificacy in the population did not influence the relative ranking of the breeding systems but may have implications for their optimal structure.
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Gee, Peter, Huaigeng Xu, and Akitsu Hotta. "Cellular Reprogramming, Genome Editing, and Alternative CRISPR Cas9 Technologies for Precise Gene Therapy of Duchenne Muscular Dystrophy." Stem Cells International 2017 (2017): 1–11. http://dx.doi.org/10.1155/2017/8765154.
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In the past decade, the development of two innovative technologies, namely, induced pluripotent stem cells (iPSCs) and the CRISPR Cas9 system, has enabled researchers to model diseases derived from patient cells and precisely edit DNA sequences of interest, respectively. In particular, Duchenne muscular dystrophy (DMD) has been an exemplary monogenic disease model for combining these technologies to demonstrate that genome editing can correct genetic mutations in DMD patient-derived iPSCs. DMD is an X-linked genetic disorder caused by mutations that disrupt the open reading frame of the dystrophin gene, which plays a critical role in stabilizing muscle cells during contraction and relaxation. The CRISPR Cas9 system has been shown to be capable of targeting the dystrophin gene and rescuing its expression in in vitro patient-derived iPSCs and in vivo DMD mouse models. In this review, we highlight recent advances made using the CRISPR Cas9 system to correct genetic mutations and discuss how emerging CRISPR technologies and iPSCs in a combined platform can play a role in bringing a therapy for DMD closer to the clinic.
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De Luca, V., R. De Souza, E. Viggiano, J. Volavka, J. Lieberman, S. G. Potkin, H. Meltzer, A. Wong, and J. L. Kennedy. "Genomics, Transcriptomics and Methylomics: Alternative Approaches for the Analysis of Serotonin System and Antipsychotic Response." European Psychiatry 24, S1 (January 2009): 1. http://dx.doi.org/10.1016/s0924-9338(09)71236-2.
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Serotonin receptors blockade is the major basis for the action of atypical antipsychotic drugs. Genetic factors affecting the density and/or function of serotonergic receptors, transporters and enzymes may therefore affect antipsychotic response. This exploratory study investigates the effect of ten polymorphisms from HTR1A, HTR1D, HTR2A, HTR3A, HTR3B, HTR4, HTR6, SLC6A4, TPH1, TPH2 genes on antipsychotic response in a sample of 289 patients with DSM-diagnosis of schizophrenia. Clinical Response was assessed using Brief Psychiatric Rating Scale (BPRS). Response was determined as 20% reduction improvement of BPRS compared to baseline. Selection of the biological relevant interactions, regardless the phenotype was performed using different statistics strategies regardless the phenotype to investigate epistasis within the serotonin system. the test for relevant interaction selection showed that 5HT4 and 5HT6 can be in epistatic relationship. the single locus analysis of these two receptor polymorphisms showed no significant results and the logistic regression model incorporating both genes, the clinical and demographic variables was not significant. Even this result is not significant, this strategy aimed to investigate the epistatic effect among genes could be useful for finding relevant biological interaction among genetic variants. Furthermore we are currently analyzing the methylation level of HTR2A in responders and non-responders, this epigenetic analysis will be very valuable in adding more information to the classic pharmacogenetic studies.
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Dou, Jiajia, Chunlin Chen, and Pei Yang. "Genetic Scheduling and Reinforcement Learning in Multirobot Systems for Intelligent Warehouses." Mathematical Problems in Engineering 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/597956.
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A new hybrid solution is presented to improve the efficiency of intelligent warehouses with multirobot systems, where the genetic algorithm (GA) based task scheduling is combined with reinforcement learning (RL) based path planning for mobile robots. Reinforcement learning is an effective approach to search for a collision-free path in unknown dynamic environments. Genetic algorithm is a simple but splendid evolutionary search method that provides very good solutions for task allocation. In order to achieve higher efficiency of the intelligent warehouse system, we design a new solution by combining these two techniques and provide an effective and alternative way compared with other state-of-the-art methods. Simulation results demonstrate the effectiveness of the proposed approach regarding the optimization of travel time and overall efficiency of the intelligent warehouse system.
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Dutta, Pijush, and Asok Kumar. "Modelling of Liquid Flow control system Using Optimized Genetic Algorithm." Statistics, Optimization & Information Computing 8, no. 2 (February 20, 2020): 565–82. http://dx.doi.org/10.19139/soic-2310-5070-618.
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Estimation of a highly accurate model for liquid flow process industry and control of the liquid flow rate from experimental data is an important task for engineers due to its non linear characteristics. Efficient optimization techniques are essential to accomplish this task.In most of the process control industry flowrate depends upon a multiple number of parameters like sensor output,pipe diameter, liquid conductivity ,liquid viscosity & liquid density etc.In traditional optimization technique its very time consuming for manually control the parameters to obtain the optimial flowrate from the process.Hence the alternative approach , computational optimization process is utilized by using the different computational intelligence technique.In this paper three different selection of Genetic Algorithm is proposed & tested against the present liquid flow process.The proposed algorithm is developed based on the mimic genetic evolution of species that allow the consecutive generations in population to adopt their environment.Equations for Response Surface Methodology (RSM) and Analysis of Variance (ANOVA) are being used as non-linear models and these models are optimized using the proposed different selection of Genetic optimization techniques. It can be observed that the among these three different selection of Genetic Algorithm ,Rank selected GA is better than the other two selection (Tournament & Roulette wheel) in terms of the accuracy of final solutions, success rate, convergence speed, and stability.
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Michael, Michael, and Winarno Winarno. "Design and Development of Computer Specification Recommendation System Based on User Budget With Genetic Algorithm." International Journal of New Media Technology 5, no. 1 (July 5, 2018): 25–29. http://dx.doi.org/10.31937/ijnmt.v5i1.814.
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There are a lot of things that must be considered when determining specifications of computer components to make sure those components chose are working compatible. According to a survey conducted to 78 respondents, about 72.5% of the respondents prefer to buy a built-up computer. The reason is because of a lack of knowledge of computer components and how to assemble computer properly. This research aimed to develop a recommendation system that able to give recommendation of buying computer based on compatible components to be assembled, with the available budget, so that people who do not know computer components can also buy a assembled computer. The Genetic Algorithm was chosen for making this recommendation system because this Algorithm gives more alternative solutions through the process of crossover and mutation compared to the Greedy Algorithm which doesn’t produce a solution by trying all alternative solution nor Exhaustive Search on Brute Force Algorithm which takes a long time to find optimum solution. The recommendation system of computer components specifications based on the budget available has been successfully developed using Genetic Algorithm and achieved 75.75% user satisfaction.
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Carpintero, D. D., and M. Melita. "An alternative stable solution for the Kepler-419 system, obtained with the use of a genetic algorithm." Astronomy & Astrophysics 620 (November 30, 2018): A88. http://dx.doi.org/10.1051/0004-6361/201731997.
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Context. The mid-transit times of an exoplanet may be nonperiodic. The variations in the timing of the transits with respect to a single period, that is, the transit timing variations (TTVs), can sometimes be attributed to perturbations by other exoplanets present in the system, which may or may not transit the star. Aims. Our aim is to compute the mass and the six orbital elements of an nontransiting exoplanet, given only the central times of transit of the transiting body. We also aim to recover the mass of the star and the mass and orbital elements of the transiting exoplanet, suitably modified in order to decrease the deviation between the observed and the computed transit times by as much as possible. Methods. We have applied our method, based on a genetic algorithm, to the Kepler-419 system. Results. We were able to compute all 14 free parameters of the system, which, when integrated in time, give transits within the observational errors. We also studied the dynamics and the long-term orbital evolution of the Kepler-419 planetary system as defined by the orbital elements computed by us, in order to determine its stability.
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Armento, Angela, Marius Ueffing, and Simon J. Clark. "The complement system in age-related macular degeneration." Cellular and Molecular Life Sciences 78, no. 10 (March 9, 2021): 4487–505. http://dx.doi.org/10.1007/s00018-021-03796-9.
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AbstractAge-related macular degeneration (AMD) is a chronic and progressive degenerative disease of the retina, which culminates in blindness and affects mainly the elderly population. AMD pathogenesis and pathophysiology are incredibly complex due to the structural and cellular complexity of the retina, and the variety of risk factors and molecular mechanisms that contribute to disease onset and progression. AMD is driven by a combination of genetic predisposition, natural ageing changes and lifestyle factors, such as smoking or nutritional intake. The mechanism by which these risk factors interact and converge towards AMD are not fully understood and therefore drug discovery is challenging, where no therapeutic attempt has been fully effective thus far. Genetic and molecular studies have identified the complement system as an important player in AMD. Indeed, many of the genetic risk variants cluster in genes of the alternative pathway of the complement system and complement activation products are elevated in AMD patients. Nevertheless, attempts in treating AMD via complement regulators have not yet been successful, suggesting a level of complexity that could not be predicted only from a genetic point of view. In this review, we will explore the role of complement system in AMD development and in the main molecular and cellular features of AMD, including complement activation itself, inflammation, ECM stability, energy metabolism and oxidative stress.
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Newfeld, S. J., and N. T. Takaesu. "An Analysis Using the hobo Genetic System Reveals That Combinatorial Signaling by the Dpp and Wg Pathways Regulates dpp Expression in Leading Edge Cells of the Dorsal Ectoderm in Drosophila melanogaster." Genetics 161, no. 2 (June 1, 2002): 685–92. http://dx.doi.org/10.1093/genetics/161.2.685.
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Abstract Our laboratory has contributed to the development of a genetic system based upon the hobo transposable element in Drosophila melanogaster. We recently reported that hobo, like the better-known P element, is capable of local transposition. In that study, we mobilized a hobo enhancer trap vector and generated two unique alleles of decapentaplegic (dpp), a transforming growth factor-β family member with numerous roles during development. Here we report a detailed study of one of those alleles (dppF11). To our knowledge, this is the first application of the hobo genetic system to understanding developmental processes. First, we demonstrate that lacZ expression from the dppF11 enhancer trap accurately reflects dpp mRNA accumulation in leading edge cells of the dorsal ectoderm. Then we show that combinatorial signaling by the Wingless (Wg) pathway, the Dpp pathway, and the transcriptional coactivator Nejire (CBP/p300) regulates dppF11 expression in these cells. Our analysis of dppF11 suggests a model for the integration of Wg and Dpp signals that may be applicable to other developmental systems. Our analysis also illustrates several new features of the hobo genetic system and highlights the value of hobo, as an alternative to P, in addressing developmental questions.
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Anand, Diksha, and Kamal Gupta. "Face Spoof Detection System Based on Genetic Algorithm and Artificial Intelligence Technique: A Review." International Journal of Advanced Research in Computer Science and Software Engineering 8, no. 6 (June 30, 2018): 51. http://dx.doi.org/10.23956/ijarcsse.v8i6.722.
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Face recognition is an alternative means to authenticate a person in different applications for access control. Instead of many improvements, this method is prone to various attacks like photos, 3D masks and video replay attack. Due to these attacks, system should require a face spoof detection system. A face spoof detection systems have an ability to identify whether a face is from a real person or a fake image. Face spoofing effect the image by adding deformation in it and also degrades the image pattern quality. Face spoofing detection system automatically identifies the human face is a true face or a fake face. In today's era, face recognition method is widely used to authenticate the face (like for unlocking mobile phones etc.) and providing access to the services or facilities but some intruders use various trick to crack the authentication system by presenting the false face in front of the authentication system, so it become necessity to prevent our face authentication system from face spoofing attack. So the choice of the technique to detect the face spoofing attack should be accurate and highly efficient.
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De, Shankha Suvra, Abhik Hazra, and Mousumi Basu. "Artificial Immune System for Multi-Area Economic Dispatch." International Journal of Emerging Electric Power Systems 14, no. 6 (September 28, 2013): 581–90. http://dx.doi.org/10.1515/ijeeps-2013-0087.
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Abstract This article presents artificial immune system for solving multi-area economic dispatch (MAED) problem with tie line constraints considering transmission losses, multiple fuels, valve-point loading and prohibited operating zones. Artificial immune system is based on the clonal selection principle which implements adaptive cloning, hyper mutation, aging operator and tournament selection. The effectiveness of the proposed algorithm has been verified on three different test systems, both small and large, involving varying degree of complexity. Compared with differential evolution, evolutionary programming and real-coded genetic algorithm, considering the quality of the solution obtained, the proposed algorithm seems to be a promising alternative approach for solving the MAED problems in practical power system.
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Cha, Seongwon, Imhoi Koo, Byung L. Park, Sangkyun Jeong, Sun M. Choi, Kil S. Kim, Hyoung D. Shin, and Jong Y. Kim. "Genetic Effects ofFTOandMC4RPolymorphisms on Body Mass in Constitutional Types." Evidence-Based Complementary and Alternative Medicine 2011 (2011): 1–7. http://dx.doi.org/10.1093/ecam/nep162.
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Sasang constitutional medicine (SCM), a Korean tailored medicine, categorizes human beings into four types through states of physiological imbalances and responsiveness to herbal medicine. One SCM type susceptible to obesity seems sensitive to energy intake due to an imbalance toward preserving energy. Common variants of fat mass and obesity associated (FTO) and melanocortin 4 receptor (MC4R) genes have been associated with increased body mass index (BMI) by affecting energy intake. Here, we statistically examined the association ofFTOandMC4Rpolymorphisms with BMI in two populations with 1370 Koreans before and after SCM typing, and with the lowering of BMI in 538 individuals who underwent a 1-month lifestyle intervention. The increased BMI replicated the association withFTOhaplotypes (effect size ≃ 1.1 kg/m2) andMC4Rvariants (effect size ≃ 0.64 kg/m2). After the lifestyle intervention, the carriers of the haplotype represented by the minor allele of rs1075440 had a tendency to lose more waist-to-hip ratio (0.76%) than non-carriers. The constitutional discrepancy for the accumulation of body mass by the effects ofFTOand/orMC4Rvariants seemed to reflect the physique differences shown in each group of SCM constitutional types. In conclusion,FTOandMC4Rpolymorphisms appear to play an important role in weight gain, while onlyFTOvariants play a role in weight loss after lifestyle intervention. Different trends were observed among individuals of SCM types, especially for weight gain. Therefore, classification of individuals based on physiological imbalance would offer a good genetic stratification system in assessing the effects of obesity genes.
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Smith, Peter W. H., and Kim Harries. "Code Growth, Explicitly Defined Introns, and Alternative Selection Schemes." Evolutionary Computation 6, no. 4 (December 1998): 339–60. http://dx.doi.org/10.1162/evco.1998.6.4.339.
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Previous work on introns and code growth in genetic programming is expanded on and tested experimentally. Explicitly defined introns are introduced to tree-based representations as an aid to measuring and evaluating intron behavior. Although it is shown that introns do create code growth, they are not its only cause. Removing introns merely decreases the growth rate; it does not eliminate it. By systematically negating various forms of intron behavior, a deeper understanding of the causes of code growth is obtained, leading to the development of a system that keeps unnecessary bloat to a minimum. Alternative selection schemes and recombination operators are examined and improvements demonstrated over the standard selection methods in terms of both performance and parsimony.
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Lai, Hsiang-Chun, Qwang-Yuen Chang, and Ching-Liang Hsieh. "Signal Transduction Pathways of Acupuncture for Treating Some Nervous System Diseases." Evidence-Based Complementary and Alternative Medicine 2019 (July 11, 2019): 1–37. http://dx.doi.org/10.1155/2019/2909632.
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In this article, we review signal transduction pathways through which acupuncture treats nervous system diseases. We electronically searched the databases, including PubMed, MEDLINE, clinical Key, the Cochrane Library, and the China National Knowledge Infrastructure from their inception to December 2018 using the following MeSH headings and keywords alone or in varied combination: acupuncture, molecular, signal transduction, genetic, cerebral ischemic injury, cerebral hemorrhagic injury, stroke, epilepsy, seizure, depression, Alzheimer’s disease, dementia, vascular dementia, and Parkinson’s disease. Acupuncture treats nervous system diseases by increasing the brain-derived neurotrophic factor level and involves multiple signal pathways, including p38 MAPKs, Raf/MAPK/ERK 1/2, TLR4/ERK, PI3K/AKT, AC/cAMP/PKA, ASK1-JNK/p38, and downstream CREB, JNK, m-TOR, NF-κB, and Bcl-2/Bax balance. Acupuncture affects synaptic plasticity, causes an increase in neurotrophic factors, and results in neuroprotection, cell proliferation, antiapoptosis, antioxidant activity, anti-inflammation, and maintenance of the blood-brain barrier.
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Elhadef, Mourad, Kaouther Abrougui, Shantanu Das, and Amiya Nayak. "A PARALLEL PROBABILISTIC SYSTEM-LEVEL FAULT DIAGNOSIS APPROACH FOR LARGE MULTIPROCESSOR SYSTEMS." Parallel Processing Letters 16, no. 01 (March 2006): 63–79. http://dx.doi.org/10.1142/s0129626406002472.
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In this paper, we present a system-level fault identification algorithm, using a parallel genetic algorithm, for diagnosing faulty nodes in large heterogeneous systems. The algorithm is based on a probabilistic model where individual node fails with an a priori probability p. The assumptions concerning test outcomes are the same as in the PMC model, that is, fault-free testers always give correct test outcomes and faulty testers are totally unpredictable. The parallel diagnosis algorithm was implemented and simulated on randomly generated large systems. The proposed parallelization is intended to speed up the performance of the evolutionary diagnosis approach, hence reducing the computation time by evolving various sub-populations in parallel. Simulation results are provided showing that the parallel diagnosis did improve the efficiency of the evolutionary diagnosis approach, in that it allowed faster diagnosis of faulty situations, making it a viable alternative to existing techniques of diagnosis. Moreover, the evolutionary approach still provide good results even when extreme non-diagnosable faulty situations are considered.
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Tanaka, Hidenori, Jason F. Kreisberg, and Trey Ideker. "Genetic dissection of complex traits using hierarchical biological knowledge." PLOS Computational Biology 17, no. 9 (September 17, 2021): e1009373. http://dx.doi.org/10.1371/journal.pcbi.1009373.
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Despite the growing constellation of genetic loci linked to common traits, these loci have yet to account for most heritable variation, and most act through poorly understood mechanisms. Recent machine learning (ML) systems have used hierarchical biological knowledge to associate genetic mutations with phenotypic outcomes, yielding substantial predictive power and mechanistic insight. Here, we use an ontology-guided ML system to map single nucleotide variants (SNVs) focusing on 6 classic phenotypic traits in natural yeast populations. The 29 identified loci are largely novel and account for ~17% of the phenotypic variance, versus <3% for standard genetic analysis. Representative results show that sensitivity to hydroxyurea is linked to SNVs in two alternative purine biosynthesis pathways, and that sensitivity to copper arises through failure to detoxify reactive oxygen species in fatty acid metabolism. This work demonstrates a knowledge-based approach to amplifying and interpreting signals in population genetic studies.
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Ruotsalainen, Seppo, and Dag Lindgren. "Stratified sublining: a new option for structuring breeding populations." Canadian Journal of Forest Research 30, no. 4 (April 1, 2000): 596–604. http://dx.doi.org/10.1139/x99-245.
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When structuring a breeding population into sublines, the conventional approach is to assign parents to sublines randomly, so that each subline has approximately the same genetic value. By using deterministic infinitesimal model we study an alternative, stratified sublining system, where sublines are initially formed by positive assortative grouping of parents according to their breeding values. Stratified and random allocation to sublines are compared by evaluating the genetic quality of the seed orchards that each approach can provide. The seed orchards were established by selecting first the best individual from each subline and then a given best proportion from them. The greater among-subline variance in stratified sublining led to higher genetic gain in resulting seed orchards than did random sublining. For the case studied, stratified sublining gave considerably more genetic gain than random sublining, over 15% more, making it an interesting alternative that deserves further consideration and study.
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Deep, Kamal, and Pardeep K. Singh. "Dynamic cellular manufacturing system design considering alternative routing and part operation tradeoff using simulated annealing based genetic algorithm." Sādhanā 41, no. 9 (September 2016): 1063–79. http://dx.doi.org/10.1007/s12046-016-0530-7.
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Simantirakis, Emmanouil, Ioannis Tsironis, and George Vassilopoulos. "FV Vectors as Alternative Gene Vehicles for Gene Transfer in HSCs." Viruses 12, no. 3 (March 19, 2020): 332. http://dx.doi.org/10.3390/v12030332.
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Hematopoietic Stem Cells (HSCs) are a unique population of cells, capable of reconstituting the blood system of an organism through orchestrated self-renewal and differentiation. They play a pivotal role in stem cell therapies, both autologous and allogeneic. In the field of gene and cell therapy, HSCs, genetically modified or otherwise, are used to alleviate or correct a genetic defect. In this concise review, we discuss the use of SFVpsc_huHSRV.13, formerly known as Prototype Foamy Viral (PFV or FV) vectors, as vehicles for gene delivery in HSCs. We present the properties of the FV vectors that make them ideal for HSC delivery vehicles, we review their record in HSC gene marking studies and their potential as therapeutic vectors for monogenic disorders in preclinical animal models. FVs are a safe and efficient tool for delivering genes in HSCs compared to other retroviral gene delivery systems. Novel technological advancements in their production and purification in closed systems, have allowed their production under cGMP compliant conditions. It may only be a matter of time before they find their way into the clinic.
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Han, Zhong, Jianmin Guo, Feibiao Meng, Haifeng Liao, Yinghua Deng, Yuankeng Huang, Xialing Lei, Chun Liang, Richou Han, and Wei Yang. "Genetic Toxicology and Safety Pharmacological Evaluation of Forsythin." Evidence-Based Complementary and Alternative Medicine 2021 (June 18, 2021): 1–9. http://dx.doi.org/10.1155/2021/6610793.
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Introduction. Forsythin is the main ingredient of Forsythia suspensa and is widely used in treatment of fever, viral cold, gonorrhea, and ulcers clinically. This study aimed to evaluate the potential genetic toxicity of forsythin and its safety for human use. Methods. Based on the Good Laboratory Practice regulations and test guidelines, the genetic toxicity of forsythin was assessed by the Ames test, chromosome aberration (CA) test, and bone marrow micronucleus (MN) test in vivo. In the Ames test, five strains of Salmonella typhimurium were exposed to different concentrations of forsythin in the presence or absence of the S9 mixture, and then, the number of His + revertant colonies was counted. In the CA test, Chinese hamster lung (CHL) fibroblast cells were treated with different concentrations of forsythin, mitomycin C, or cyclophosphamide in the presence or absence of the S9 mixture, and the chromosomal aberrations were determined. In the MN test, bone marrow was isolated from the mice with different treatments, and the ratios of polychromatic erythrocytes (PCE) and erythrocytes (PCE/(PCE + NCE)) were measured. Finally, beagle dogs were divided into four groups (negative control, low dose, medium dose, and high dose groups), and then, a telemetry system was used to evaluate the safe use of forsythin. Results. Ames test results showed that the number of colonies in all test strains with different treatments showed no significantly dose-dependent increase in the presence or absence of the S9 mixture ( p > 0.05 ). In the CA test, the number of cells with aberrations in the CHL fibroblast cells treated with low, medium, and high doses of forsythin for 24/48 h in the absence of the S9 mixture was, respectively, 5.0/2.5, 4.5/1.5, and 5.0/5.0, and in the presence of the S9 mixture, the number was, respectively, 5.0, 5.0, and 4.5. These results showed that there was no significant difference compared to the negative control group either in the presence (2.0) or in the absence (4.0/2.5 for 24/48 h) of the S9 mixture ( p > 0.05 ). The MN test showed that the values of PCE/(PCE + NCE) in the negative, positive controls, and forsythin treatment groups were all more than 20%, which indicated that forsythin had no cytotoxicity. Additionally, no significant toxicological effects of forsythin on blood pressure, respiration, temperature, electrocardiogram, and other physiological indicators in the conscious beagle dogs of different groups were observed by the telemetry method. Conclusion. Our findings showed that forsythin has low probability of genetic toxicity and no significant toxicological effects, which implied that forsythin is suitable for further development and potential application.
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Jun, Hyo-Byung, and Kwee-Bo Sim. "Coevolutionary Algorithms for Realization of Intelligent Systems." Journal of Advanced Computational Intelligence and Intelligent Informatics 3, no. 5 (October 20, 1999): 418–26. http://dx.doi.org/10.20965/jaciii.1999.p0418.
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The simple genetic algorithm (SGA) proposed by J. H. Holland uses population-based optimization based on Darwinian natural selection. The theoretical foundations of GA are the Schema Theorem and Building Block Hypothesis. Although GA does well in many applications in optimization, it does not guarantee the convergence to a global optimum in some problems. In designing intelligent systems, since there is no deterministic solution, heuristic trial-and error is usually used to determine system parameters. An alternative is a coevolutionary system, where 2 populations constantly interact and coevolve. We review coevolutionary algorithms and propose coevolutionary schemes designing intelligent systems based on the relationship between system components.
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Kasarda R Mészáros, G., O. Kadlečík, E. Hazuchová, V. Šidlová, and I. Pavlík. "Influence of mating systems and selection intensity on the extent of inbreeding and genetic gain in the Slovak Pinzgau cattle." Czech Journal of Animal Science 59, No. 5 (May 19, 2014): 219–26. http://dx.doi.org/10.17221/7402-cjas.
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The aim of the present paper was to simulate the scenarios for a maximum avoidance of inbreeding (MAI) mating strategy, and compare it with a random mating alternative, with the main focus on inbreeding and development of the genetic gain. The parameters of the simulation were based on the structure of the Slovak Pinzgau active population of 2868 animals (930 purebred cows). The selection under a total merit index (TMI) was simulated, covering the milk, survival, and live weight breeding value estimation results. The heritability of TMI (h<sup>2</sup> = 0.09) was estimated using a REML single trait animal model. Alternatives assumed a closed population structure, fixed number of mating per parent, and equal use of sires in insemination. Animals in generation 0 were set as founders without pedigree information. In separate simulation runs, the number of sires of sires was set at 2, 4, 5 or 10 mated with 40 dams of sires in all cases. The sex ratio of the offspring was assumed to be 50/50 male/female. Twenty consecutive generations were simulated for both random and maximum avoidance of inbreeding mating, which resulted in a total of 8 scenarios. Significant positive differences in genetic gain were observed in the MAI mating system with 2 (0.74**), 4 (0.24**), 5 (0.13**) or 10 (0.09**) sires in comparison to random mating design. When using MAI, significantly lower inbreeding was observed with 2 (5.44**), 4 (3.18**), 5 (2.43**) or 10 (1.16**) sires. Simulation results showed that the use of a maximum avoidance of inbreeding mating strategy would lead to significantly decreased rates of inbreeding while maintaining suitable levels of genetic gain in the
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Epperson, B. K. "Spatial and space-time correlations in systems of subpopulations with genetic drift and migration." Genetics 133, no. 3 (March 1, 1993): 711–27. http://dx.doi.org/10.1093/genetics/133.3.711.
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Abstract The geographic distribution of genetic variation is an important theoretical and experimental component of population genetics. Previous characterizations of genetic structure of populations have used measures of spatial variance and spatial correlations. Yet a full understanding of the causes and consequences of spatial structure requires complete characterization of the underlying space-time system. This paper examines important interactions between processes and spatial structure in systems of subpopulations with migration and drift, by analyzing correlations of gene frequencies over space and time. We develop methods for studying important features of the complete set of space-time correlations of gene frequencies for the first time in population genetics. These methods also provide a new alternative for studying the purely spatial correlations and the variance, for models with general spatial dimensionalities and migration patterns. These results are obtained by employing theorems, previously unused in population genetics, for space-time autoregressive (STAR) stochastic spatial time series. We include results on systems with subpopulation interactions that have time delay lags (temporal orders) greater than one. We use the space-time correlation structure to develop novel estimators for migration rates that are based on space-time data (samples collected over space and time) rather than on purely spatial data, for real systems. We examine the space-time and spatial correlations for some specific stepping stone migration models. One focus is on the effects of anisotropic migration rates. Partial space-time correlation coefficients can be used for identifying migration patterns. Using STAR models, the spatial, space-time, and partial space-time correlations together provide a framework with an unprecedented level of detail for characterizing, predicting and contrasting space-time theoretical distributions of gene frequencies, and for identifying features such as the pattern of migration and estimating migration rates in experimental studies of genetic variation over space and time.
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Aísa-Marín, Izarbe, Rocío García-Arroyo, Serena Mirra, and Gemma Marfany. "The Alter Retina: Alternative Splicing of Retinal Genes in Health and Disease." International Journal of Molecular Sciences 22, no. 4 (February 12, 2021): 1855. http://dx.doi.org/10.3390/ijms22041855.
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Alternative splicing of mRNA is an essential mechanism to regulate and increase the diversity of the transcriptome and proteome. Alternative splicing frequently occurs in a tissue- or time-specific manner, contributing to differential gene expression between cell types during development. Neural tissues present extremely complex splicing programs and display the highest number of alternative splicing events. As an extension of the central nervous system, the retina constitutes an excellent system to illustrate the high diversity of neural transcripts. The retina expresses retinal specific splicing factors and produces a large number of alternative transcripts, including exclusive tissue-specific exons, which require an exquisite regulation. In fact, a current challenge in the genetic diagnosis of inherited retinal diseases stems from the lack of information regarding alternative splicing of retinal genes, as a considerable percentage of mutations alter splicing or the relative production of alternative transcripts. Modulation of alternative splicing in the retina is also instrumental in the design of novel therapeutic approaches for retinal dystrophies, since it enables precision medicine for specific mutations.
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Amer, P. R., T. Roughsedge, B. Lowman, and G. Simm. "Deterministic predictions of beef cow herd population dynamics with alternative replacement strategies." Animal Science 77, no. 3 (December 2003): 395–401. http://dx.doi.org/10.1017/s1357729800054345.
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AbstractA deterministic method of predicting numbers of each animal class present over time in a beef cow herd with multiple calving seasons per year is described. Breeding cow classes are defined according to the number of generations of descent from the cows in the herd prior to the introduction of a specific heifer replacement breeding policy. Cow classes are further divided into subgroups defined according to age of cow, calving interval and whether or not the cow was last mated to a terminal sire. The method is demonstrated by showing the evolution of herd breed make-up with several alternative replacement female breeding policies including grading-up, two-breed rotation and three-breed rotation breeding policies. For an example herd, the first generation of replacements peaked at approximately 0·4 of the herd at 6 years after the first matings for a new breeding system. Later generations of replacements reached equivalent proportions of the herd to the previous generation approximately 3·3 years later, with peak proportions at approximately 0·25 of the herd. Differences in the relative levels of expression of heterosis for grade up versus rotational replacement policies increased steadily from 5 years onwards with 0·17 of the heterosis expected in a herd of F1 cows remaining 20 years after the first matings of the new breeding system. The two-breed grading-up system showed less heterosis than the three-breed grading-up system only after 8 years, with the difference increasing to 0·16 of the heterosis in an F1 herd after 20 years. Results are also presented showing the difference in contributions of breeds to the herd gene pool over time with the different breeding systems. With the rotational systems, breeds lag by approximately 3 years in the timing of their contribution according to the order of their introduction to the rotation. The effects of faster heifer replacement rates on results were also discussed. It is concluded that short-to medium-term impacts of breed and replacement breeding system choices are likely to be more relevant in practical decision making by suckler herd managers than the characteristics of breeding systems once herds have reached genetic equilibrium.
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Ghamkhar, Kioumars, Janine Croser, Nader Aryamanesh, Margaret Campbell, Nina Kon’kova, and Clive Francis. "Camelina (Camelina sativa(L.) Crantz) as an alternative oilseed: molecular and ecogeographic analyses." Genome 53, no. 7 (July 2010): 558–67. http://dx.doi.org/10.1139/g10-034.
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Camelina ( Camelina sativa (L.) Crantz) is an oilseed known for its potential as a low-input biofuel feedstock and its high levels of beneficial fatty acids. We investigated the role of geographical origin in genetic variation and fatty acid content, expecting to find significant variability among 53 accessions and a link between ecogeography and both origin and key oil traits. Amplified fragment length polymorphism (AFLP) fingerprinting revealed high levels of diversity within the 53 accessions. Even though sampling was relatively biased towards the Russian–Ukrainian area, this region was identified as a genetic diversity hotspot and possible centre of origin for camelina. The accessions were categorized by principal coordinate analysis using molecular marker data, enabling identification of links between geographical distribution and these categories. The influence of geographic location on four canola oil quality measures in camelina was evaluated using a geographic information system. These measures were (1) more than 30% α-linolenic acid, (2) less than 3% erucic acid, (3) less than 10% saturated fatty acids, and (4) a ratio of α-linolenic to linoleic acid greater than 1. The results clearly confirm that camelina oil quality characteristics are strongly influenced by environmental factors. The unprecedented high genetic diversity in this group of accessions offers an excellent opportunity to investigate valuable genes for successful adaptation of camelina to specific ecogeographical conditions such as drought.
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Lekveishvili, G. A., P. G. Gogiashvili, J. T. Chogovadze, and D. G. Kbilashvili. "APPLICATION OF GENETIC ALGORITHM OF OPTIMIZATION DURING THE PROCESS OF URBAN PASSENGER TRAFFIC MANAGEMENT." Juvenis scientia, no. 11 (2018): 5–8. http://dx.doi.org/10.32415/jscientia.2018.11.01.
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The paper proposes a generalized logistic model of the urban passenger transportation system, and on its basis, there has been developed a modified model that allows for determining a set of organizational and economic indicators in each state of a system. To solve the optimization problem of the transportation process system under conditions of dynamically changing passenger traffic flows, there has been justified searching for a balance between the effectiveness and quality of solutions due to the «survival of the strongest alternative solutions» y to earn system of operational control buses on the route. There has been proven the advantage of using genetic algorithm to optimize the processes of organizing and managing the system of urban passenger transport with the aim of maximizing the profits of an enterprise at minimal cost.
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Suzuki, Shoji, and Norio Kurosawa. "Development of the Multiple Gene Knockout System with One-Step PCR in Thermoacidophilic Crenarchaeon Sulfolobus acidocaldarius." Archaea 2017 (2017): 1–12. http://dx.doi.org/10.1155/2017/7459310.
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Multiple gene knockout systems developed in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius are powerful genetic tools. However, plasmid construction typically requires several steps. Alternatively, PCR tailing for high-throughput gene disruption was also developed in S. acidocaldarius, but repeated gene knockout based on PCR tailing has been limited due to lack of a genetic marker system. In this study, we demonstrated efficient homologous recombination frequency (2.8 × 104 ± 6.9 × 103 colonies/μg DNA) by optimizing the transformation conditions. This optimized protocol allowed to develop reliable gene knockout via double crossover using short homologous arms and to establish the multiple gene knockout system with one-step PCR (MONSTER). In the MONSTER, a multiple gene knockout cassette was simply and rapidly constructed by one-step PCR without plasmid construction, and the PCR product can be immediately used for target gene deletion. As an example of the applications of this strategy, we successfully made a DNA photolyase- (phr-) and arginine decarboxylase- (argD-) deficient strain of S. acidocaldarius. In addition, an agmatine selection system consisting of an agmatine-auxotrophic strain and argD marker was also established. The MONSTER provides an alternative strategy that enables the very simple construction of multiple gene knockout cassettes for genetic studies in S. acidocaldarius.