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The Design Of Self-Evolving Artificial Immune System Ii For Permutation Flow-Shop Problem

Meng-Hui Chen, Pei-Chann Chang, Wei-Hsiu Huang
2012 Zenodo  
In this paper, we continue the previous research to develop a Self-evolving Artificial Immune System II via coordinating the T and B cell in Immune System and built a block-based artificial chromosome  ...  Nevertheless, many of these applications took advantage of the benefit for applications but seldom proposed approaches for enhancing the efficiency.  ...  Affinity Affinity chromatography is a method of separating biochemical mixtures and based on a highly specific interaction such as that between antigen and antibody, enzyme and substrate, or receptor and  ... 
doi:10.5281/zenodo.1062951 fatcat:kstmmmlfqjh7dbmm7le3bo6dyq

Evolving Consensus Sequence for Multiple Sequence Alignment with a Genetic Algorithm [chapter]

Conrad Shyu, James A. Foster
2003 Lecture Notes in Computer Science  
In this paper we present an approach that evolves the consensus sequence [25] for multiple sequence alignment (MSA) with genetic algorithm (GA).  ...  We have developed a schema such that the number of generations needed to find the optimal solution is approximately the same regardless the number of sequences.  ...  Acknowledgements Shyu was partially funded by a grant from Proctor and Gamble and Foster was partially funded for this research by NIH NCRR 1P20 RR16448.  ... 
doi:10.1007/3-540-45110-2_124 fatcat:bhz3zqaxkzh2bogl4m265kngeq

Multiple Sequence Alignment with Evolutionary Computation

Conrad Shyu, Luke Sheneman, James A. Foster
2004 Genetic Programming and Evolvable Machines  
The second novel approach facilitates the optimization of a consensus sequence with a GA using a vertically scalable encoding scheme in which the number of iterations needed to find the optimal solution  ...  Our first novel approach utilizes a GA to evolve an optimal guide tree in a progressive alignment algorithm and serves as an alternative to the more traditional heuristic techniques such as neighbor-joining  ...  Shyu was partially funded by a grant from Proctor and Gamble and Sheneman was partially funded by NIH NCRR 1P20 RR16448. Foster was partially funded for this research by NIH NCRR 1P20 RR16448.  ... 
doi:10.1023/b:genp.0000023684.05565.78 fatcat:x4lqgrbmbbb5xot23xee427csi

Fast dual selection using genetic algorithms for large data sets

Frederic Ros, Rachid Harba, Marco Pintore
2012 2012 12th International Conference on Intelligent Systems Design and Applications (ISDA)  
We propose a GA encoded by binary chromosomes having the same size as the feature space for selecting features in which each evaluated chromosome delivers a set of instances.  ...  This paper is devoted to feature and instance selection managed by genetic algorithms (GA) in the context of supervised classification.  ...  using a selection mechanism and specific genetic operators such as crossover and mutation.  ... 
doi:10.1109/isda.2012.6416642 dblp:conf/isda/RosHP12 fatcat:dhojalvrpjembfg35gziuyayvm

A Survey on Multi Objective Optimization Challenges in Swarm Intelligence

Rich Caruana, Yin Lou
2021 Journal of Computing and Natural Science  
The main purpose of this contribution is to present a basis of understanding on MOO challenges.  ...  ., alter concurrent optimization). This implies that a single objective is optimized based on another's cost.  ...  In order to enhance MOO, the researchers created Non-dominated Sorting Particle Swarm Optimizer (NSPSO).  ... 
doi:10.53759/181x/jcns202101018 fatcat:akpp2yudgbc5lew4v74h3ud2mm

Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module

M.R. Maurya, S.J. Bornheimer, V. Venkatasubramanian, S. Subramaniam
2005 IEE Proceedings - Systems Biology  
Coarse-grained biochemical models, called reduced-order models (ROMs), consisting of essential biochemical mechanisms are more useful for computational analysis and for studying important features of a  ...  Biochemical systems embed complex networks and hence development and analysis of their detailed models pose a challenge for computation.  ...  We also thank the reviewers of this manuscript for elaborate review and numerous suggestions.  ... 
doi:10.1049/ip-syb:20050014 pmid:16986265 pmcid:PMC3417759 fatcat:55ridnjgvndprddensjhi7fsdy

Nature inspired genetic algorithms for hard packing problems

Philipp Rohlfshagen, John A. Bullinaria
2008 Annals of Operations Research  
The algorithm for the BPP, the exon shuffling GA (ESGA), is a steady-state GA with a sophisticated crossover operator that makes maximum use of the principle of natural selection to evolve feasible solutions  ...  Three different variants of this algorithm are presented and compared, which evolve a partial ordering of items using a segmented encoding that is utilised in the repair of infeasible solutions.  ...  GAs maintain a population of potential solutions to the problem of interest and evolve solutions of increasing quality by means of selection, crossover and mutation.  ... 
doi:10.1007/s10479-008-0464-5 fatcat:6bfnjupgrfdqfllq3wq33nrszm

Harnessing the Power of Mutagenesis and Adaptive Laboratory Evolution for High Lipid Production by Oleaginous Microalgae and Yeasts

Neha Arora, Hong-Wei Yen, George P. Philippidis
2020 Sustainability  
Oleaginous microalgae and yeasts represent promising candidates for large-scale production of lipids, which can be utilized for production of drop-in biofuels, nutraceuticals, pigments, and cosmetics.  ...  to metabolic pathways, which could subsequently serve as the basis for further targeted genetic engineering.  ...  The mutated cells, sorted at a rate of 10,000 cells/sec, showing maximum fluorescence, as a result of high lipid content, are sorted out by the FACS machine [54] .  ... 
doi:10.3390/su12125125 fatcat:z6lixym4rzcblepxiqho4hipwy

G Protein Activation without a GEF in the Plant Kingdom

Daisuke Urano, Janice C. Jones, Hao Wang, Melissa Matthews, William Bradford, Jeffrey L. Bennetzen, Alan M. Jones, Harmit S. Malik
2012 PLoS Genetics  
However, unlike grasses, one representative non-vascular plant Ga showed rapid GTP hydrolysis, likely compensating for the loss of the RGS gene.  ...  Despite the absence of a Ga-inactivating protein in grasses, all vascular plant Ga proteins examined rapidly released GDP without a receptor and slowly hydrolyzed GTP, indicating that these Ga are self-activating  ...  Brenda Temple for making a model structure of OsRGA1, Jing Yang for making DNA constructs, and Ariko Urano for inspecting accession numbers in Table S1 . Author Contributions  ... 
doi:10.1371/journal.pgen.1002756 pmid:22761582 pmcid:PMC3386157 fatcat:bv25zzxvwzbtld5bhusxe7jsiy

Estimating local atmosphere-surface fluxes using eddy covariance and numerical Ogive optimization

J. Sievers, T. Papakyriakou, S. Larsen, M. M. Jammet, S. Rysgaard, M. K. Sejr, L. L. Sørensen
2014 Atmospheric Chemistry and Physics Discussions  
a lower detection limit with this particular instrument setup, as well as a superiority of open path gas analyzers, in low-flux environments.  ...  The presented method is shown to allow for flux estimation during severe signal disruption and to yield fewer estimates for an enclosed gas analyzer during low-flux conditions suggesting the presence of  ...  Inspired by Darwinian evolutionary theory it optimizes a problem by iteratively improving a population of NP candidate solutions (agents) based on random candidate mutation (motion) 21413 Introduction  ... 
doi:10.5194/acpd-14-21387-2014 fatcat:4vtr2bsdhrb3tot4wgawsd3qru

Proteomic profiling of pathological and aged skeletal muscle fibres by peptide mass fingerprinting (Review)

Philip Doran, Pamela Donoghue, Kathleen O'Connell, Joan Gannon, Kay Ohlendieck
2007 International Journal of Molecular Medicine  
As an alternative suggestion, the two-dimensional analysis of different protein samples separated in parallel on a single second dimension gel is introduced and the usefulness of this technique for direct  ...  This review discusses the recent progress in the biochemical analysis of skeletal muscle extracts and outlines the mass spectrometry-based proteomics approach for studying muscle tissues in normal and  ...  Introduction The availability of mass spectrometry (MS)-based proteomics for the large-scale screening of proteins has decisively enhanced the research capabilities of the modern biochemical laboratory  ... 
doi:10.3892/ijmm.19.4.547 fatcat:pw5gwxk4s5ffxnsjvjvuowhxr4

Fluorescent Protein Approaches in Alpha Herpesvirus Research

Ian Hogue, Jens Bosse, Esteban Engel, Julian Scherer, Jiun-Ruey Hu, Tony del Rio, Lynn Enquist
2015 Viruses  
of fluorescent protein-based approaches in the context of a replicating virus, and describe general strategies and best practices for creating new fluorescent fusions.  ...  In this review, we provide a compendium of reported fluorescent protein fusions to herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV) structural proteins, discuss the underappreciated challenges  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/v7112915 pmid:26610544 pmcid:PMC4664988 fatcat:kexf32hulzgzfo4ge4h232k3wu

Beyond the Signal Sequence: Protein Routing in Health and Disease

Cecilia Castro-Fernández, Guadalupe Maya-Núñez, P. Michael Conn
2005 Endocrine reviews  
Synthesis alone is insufficient for proper function, of course; for a cell to operate effectively, its components must be correctly compartmentalized.  ...  for error and resultant disease.  ...  Don Pfaff of the Rockefeller University. We thank Eliot Spindel from our Institution for commenting on a draft of the manuscript.  ... 
doi:10.1210/er.2004-0010 pmid:15536207 fatcat:7ddod6hp75hfdfaykjhn4krolm

Conservation of molecular and cellular phenotypes of invariant NKT cells between humans and non-human primates

Krystle K. Q. Yu, Damien B. Wilburn, Joshua A. Hackney, Patricia A. Darrah, Kathryn E. Foulds, Charlotte A. James, Malisa T. Smith, Lichen Jing, Robert A. Seder, Mario Roederer, David M. Koelle, Willie J. Swanson (+1 others)
2019 Immunogenetics  
These data reveal a diversity of iNKT cell phenotypes despite convergent evolution of the genes required for lipid antigen presentation and recognition in humans and non-human primates.  ...  Using an evolutionary genetic approach, we found a lack of diversifying selection in CD1 genes over 45 million years of evolution, which stands in stark contrast to the history of the MHC system for presenting  ...  Acknowledgements The authors would like to thank Erik Layton for providing technical assistance, Stephen De Rosa for assisting with the development of the intracellular cytokine staining (ICS) panel, D  ... 
doi:10.1007/s00251-019-01118-9 pmid:31123763 pmcid:PMC6647187 fatcat:udgot626wzbrhjnrqzqsiezsny

Protein stability by number: high-throughput and statistical approaches to one of protein science's most difficult problems

Thomas J Magliery, Jason J Lavinder, Brandon J Sullivan
2011 Current Opinion in Chemical Biology  
JJL was an NIH CBIP fellow and a fellow of the Great Rivers affiliate of the AHA. BJS was an NIH CBIP fellow and is a Presidential fellow of The Ohio State University.  ...  Acknowledgements The authors thank the NIH (R01 GM083114 and U54 NS058183 to TJM) and The Ohio State University for support.  ...  Ericsson UB, Hallberg BM, Detitta GT, Dekker N, Nordlund P: Thermofluor-based high-throughput stability optimization of proteins for structural studies. Anal Biochem 2006, 357:289-298.  ... 
doi:10.1016/j.cbpa.2011.03.015 pmid:21498105 pmcid:PMC3110604 fatcat:ea5gsv4igzhvbcb47ixwmdiony
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