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Genetic algorithm

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https://www.readbyqxmd.com/read/28931033/artificial-intelligence-in-peer-review-how-can-evolutionary-computation-support-journal-editors
#1
Maciej J Mrowinski, Piotr Fronczak, Agata Fronczak, Marcel Ausloos, Olgica Nedic
With the volume of manuscripts submitted for publication growing every year, the deficiencies of peer review (e.g. long review times) are becoming more apparent. Editorial strategies, sets of guidelines designed to speed up the process and reduce editors' workloads, are treated as trade secrets by publishing houses and are not shared publicly. To improve the effectiveness of their strategies, editors in small publishing groups are faced with undertaking an iterative trial-and-error approach. We show that Cartesian Genetic Programming, a nature-inspired evolutionary algorithm, can dramatically improve editorial strategies...
2017: PloS One
https://www.readbyqxmd.com/read/28931004/the-logic-of-the-floral-transition-reverse-engineering-the-switch-controlling-the-identity-of-lateral-organs
#2
Jean-Louis Dinh, Etienne Farcot, Charlie Hodgman
Much laboratory work has been carried out to determine the gene regulatory network (GRN) that results in plant cells becoming flowers instead of leaves. However, this also involves the spatial distribution of different cell types, and poses the question of whether alternative networks could produce the same set of observed results. This issue has been addressed here through a survey of the published intercellular distribution of expressed regulatory genes and techniques both developed and applied to Boolean network models...
September 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28930911/an-enrichment-strategy-yields-seven-novel-single-nucleotide-polymorphisms-associated-with-mortality-and-altered-th17-responses-following-blunt-trauma
#3
Lukas Schimunek, Rami A Namas, Jinling Yin, Dongmei Liu, Derek Barclay, Fayten El-Dehaibi, Andrew Abboud, Haley Lindberg, Ruben Zamora, R Billiar Timothy, Yoram Vodovotz
Trauma is the leading cause of death worldwide for individuals under the age of 55. Interpatient genomic differences, in the form of candidate single nucleotide polymorphisms (SNPs), have been associated previously with adverse outcomes after trauma. However, the utility of these SNPs to predict outcomes based on a meaningful endpoint such as survival is as yet undefined. We hypothesized that specific SNP haplotypes could segregate trauma survivors from non-survivors. Genomic DNA samples were obtained from 453 blunt trauma patients, for whom complete daily clinical and biomarker data were available for 397...
September 19, 2017: Shock
https://www.readbyqxmd.com/read/28929417/a-metaheuristically-tuned-interval-type-2-fuzzy-system-to-reduce-segmentation-uncertainty-in-brain-mri-images
#4
Abolfazl Taghribi, Saeed Sharifian
Precise segmentation of magnetic resonance image (MRI) seems challenging because of the complex structure of the brain, non-uniform field in images, and noise. As a result, decision-making is associated with uncertainty. Fuzzy based approaches have been developed to overcome this problem, though most of them use fuzzy type 1 method, and sometimes contain a pre-processing step. This paper "modified type 2 fuzzy system" (MT2FS) declares a state-of-the-art method to segment MRI images using interval fuzzy type-2...
September 19, 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28925994/chimeric-antigen-receptor-t-cell-therapy-assessment-and-management-of-toxicities
#5
REVIEW
Sattva S Neelapu, Sudhakar Tummala, Partow Kebriaei, William Wierda, Cristina Gutierrez, Frederick L Locke, Krishna V Komanduri, Yi Lin, Nitin Jain, Naval Daver, Jason Westin, Alison M Gulbis, Monica E Loghin, John F de Groot, Sherry Adkins, Suzanne E Davis, Katayoun Rezvani, Patrick Hwu, Elizabeth J Shpall
Immunotherapy using T cells genetically engineered to express a chimeric antigen receptor (CAR) is rapidly emerging as a promising new treatment for haematological and non-haematological malignancies. CAR-T-cell therapy can induce rapid and durable clinical responses, but is associated with unique acute toxicities, which can be severe or even fatal. Cytokine-release syndrome (CRS), the most commonly observed toxicity, can range in severity from low-grade constitutional symptoms to a high-grade syndrome associated with life-threatening multiorgan dysfunction; rarely, severe CRS can evolve into fulminant haemophagocytic lymphohistiocytosis (HLH)...
September 19, 2017: Nature Reviews. Clinical Oncology
https://www.readbyqxmd.com/read/28923545/computational-model-for-vitamin-d-deficiency-using-hair-mineral-analysis
#6
Aboul Ella Hassanien, Alaa Tharwat, Hala S Own
Vitamin D deficiency is prevalent in the Arabian Gulf region, especially among women. Recent studies show that the vitamin D deficiency is associated with a mineral status of a patient. Therefore, it is important to assess the mineral status of the patient to reveal the hidden mineral imbalance associated with vitamin D deficiency. A well-known test such as the red blood cells is fairly expensive, invasive, and less informative. On the other hand, a hair mineral analysis can be considered an accurate, excellent, highly informative tool to measure mineral imbalance associated with vitamin D deficiency...
August 30, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28922645/spectrophotometric-determination-of-fluoxetine-by-molecularly-imprinted-polypyrrole-and-optimization-by-experimental-design-artificial-neural-network-and-genetic-algorithm
#7
Azizollah Nezhadali, Maryam Omidvar Motlagh, Samira Sadeghzadeh
A selective method based on molecularly imprinted polymer (MIP) solid-phase extraction (SPE) using UV-Vis spectrophotometry as a detection technique was developed for the determination of fluoxetine (FLU) in pharmaceutical and human serum samples. The MIPs were synthesized using pyrrole as a functional monomer in the presence of FLU as a template molecule. The factors that affecting the preparation and extraction ability of MIP such as amount of sorbent, initiator concentration, the amount of monomer to template ratio, uptake shaking rate, uptake time, washing buffer pH, take shaking rate, Taking time and polymerization time were considered for optimization...
September 13, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28920893/a-functional-genetic-scheme-for-seizure-forecasting-in-canine-epilepsy
#8
E Bou Assi, D K Nguyen, S Rihana, M Sawan
OBJECTIVE: The objective of this work is the development of an accurate seizure forecasting algorithm that considers brain's functional connectivity for electrode selection. METHODS: We start by proposing Kmeans-directed transfer function, an adaptive functional connectivity method intended for seizure onset zone localization in bilateral intracranial EEG recordings. Electrodes identified as seizure activity sources and sinks are then used to implement a seizure-forecasting algorithm on long-term continuous recordings in dogs with naturallyoccurring epilepsy...
September 13, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28920614/molecular-weight-prediction-in-polystyrene-blends-unprecedented-use-of-a-genetic-algorithm-in-pulse-field-gradient-spin-echo-pgse-nmr
#9
Francisco M Arrabal-Campos, José D Álvarez, Amador García-Sancho, Ignacio Fernández
A genetic algorithm that uses boxcar functions (diffGA) has been applied for the first time in PGSE NMR. It reconstructs accurate diffusion coefficients for all the components of the mixture, and therefore predicts correct weight-average molecular weights for all of them. The results reported herein complement those obtained with established methods such as ITAMeD, CONTIN and TRAIn algorithms, and provide a detailed solution picture. Its robustness and limits have been stretched in order to ascertain the minimum separation within diffusion coefficients or relative proportion between components...
September 18, 2017: Soft Matter
https://www.readbyqxmd.com/read/28918301/mathematical-fundamentals-for-the-noise-immunity-of-the-genetic-code
#10
Elena Fimmel, Lutz Strüngmann
Symmetry is one of the essential and most visible patterns that can be seen in nature. Starting from the left-right symmetry of the human body, all types of symmetry can be found in crystals, plants, animals and nature as a whole. Similarly, principals of symmetry are also some of the fundamental and most useful tools in modern mathematical natural science that play a major role in theory and applications. As a consequence, it is not surprising that the desire to understand the origin of life, based on the genetic code, forces us to involve symmetry as a mathematical concept...
September 13, 2017: Bio Systems
https://www.readbyqxmd.com/read/28918098/identifying-novel-factor-xiia-inhibitors-with-pca-ga-svm-developed-vhts-models
#11
Jonathan Jun Feng Chen, Donald P Visco
There currently is renewed interest in blood clotting Factor XII as a potential target for thrombosis inhibition. Historically untargeted, there is little drug information with which to start drug candidate searches. Typical high-throughput screening can identify potential drug candidates, but is inefficient. Virtual high-throughput screening can be used to raise efficiency by focusing experimental efforts on compounds predicted to be active and is applied here to identify new Factor XIIa inhibitors. We combine principal component analysis, genetic algorithm and support vector machine to create the models used in the virtual high-throughput screening...
September 1, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28918066/enzymatic-testing-sensitivity-variability-and-practical-diagnostic-algorithm-for-pyruvate-dehydrogenase-complex-pdc-deficiency
#12
Ha Kyung Shin, George Grahame, Shawn E McCandless, Douglas S Kerr, Jirair K Bedoyan
Pyruvate dehydrogenase complex (PDC) deficiency is a major cause of primary lactic acidemia in children. Prompt and correct diagnosis of PDC deficiency and differentiating between specific vs generalized, or secondary deficiencies has important implications for clinical management and therapeutic interventions. Both genetic and enzymatic testing approaches are being used in the diagnosis of PDC deficiency. However, the diagnostic efficacy of such testing approaches for individuals affected with PDC deficiency has not been systematically investigated in this disorder...
September 8, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/28917984/multi-objective-optimization-of-asymmetric-acoustic-transmission-with-periodical-structure
#13
Jiu-Jiu Chen, Jian-Cheng Zhang, Shao-Yong Huo
Asymmetric acoustic wave propagation is important for control and manipulation of the acoustic wave signals in various devices. However, previous approach to find optimal asymmetric acoustic transmission (AAT) is through repeatedly adjusting the geometrical parameters, thus causing time-consuming. Here we propose a study on the multi-objective optimization of the AAT, aiming to achieve the widest working frequency range (fr) and the highest transmittance peak (η) with regard to the design variables. For this purpose, the Radial Basis Function (RBF) neural work and finite element (FE) method are applied to obtain the valuable data in the procedure...
September 8, 2017: Ultrasonics
https://www.readbyqxmd.com/read/28916311/lenalidomide-maintenance-after-first-line-therapy-for-high-risk-chronic-lymphocytic-leukaemia-cllm1-final-results-from-a-randomised-double-blind-phase-3-study
#14
Anna Maria Fink, Jasmin Bahlo, Sandra Robrecht, Othman Al-Sawaf, Ali Aldaoud, Holger Hebart, Kathleen Jentsch-Ullrich, Steffen Dörfel, Kirsten Fischer, Clemens-Martin Wendtner, Thomas Nösslinger, Paolo Ghia, Francesc Bosch, Arnon P Kater, Hartmut Döhner, Michael Kneba, Karl-Anton Kreuzer, Eugen Tausch, Stephan Stilgenbauer, Matthias Ritgen, Sebastian Böttcher, Barbara Eichhorst, Michael Hallek
BACKGROUND: The combined use of genetic markers and detectable minimal residual disease identifies patients with chronic lymphocytic leukaemia with poor outcome after first-line chemoimmunotherapy. We aimed to assess lenalidomide maintenance therapy in these high-risk patients. METHODS: In this randomised, double-blind, phase 3 study (CLLM1; CLL Maintenance 1 of the German CLL Study Group), patients older than 18 years and diagnosed with immunophenotypically confirmed chronic lymphocytic leukaemia with active disease, who responded to chemoimmunotherapy 2-5 months after completion of first-line therapy and who were assessed as having a high risk for an early progression with at least a partial response after four or more cycles of first-line chemoimmunotherapy, were eligible if they had high minimal residual disease levels or intermediate levels combined with an unmutated IGHV gene status or TP53 alterations...
September 12, 2017: Lancet Haematology
https://www.readbyqxmd.com/read/28915756/a-thermally-driven-differential-mutation-approach-for-the-structural-optimization-of-large-atomic-systems
#15
Katja Biswas
A computational method is presented which is capable to obtain low lying energy structures of topological amorphous systems. The method merges a differential mutation genetic algorithm with simulated annealing. This is done by incorporating a thermal selection criterion, which makes it possible to reliably obtain low lying minima with just a small population size and is suitable for multimodal structural optimization. The method is tested on the structural optimization of amorphous graphene from unbiased atomic starting configurations...
September 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28914994/hessian-based-quantitative-image-analysis-of-host-pathogen-confrontation-assays
#16
Zoltan Cseresnyes, Kaswara Kraibooj, Marc Thilo Figge
Host-fungus interactions have gained a lot of interest in the past few decades, mainly due to an increasing number of fungal infections that are often associated with a high mortality rate in the absence of effective therapies. These interactions can be studied at the genetic level or at the functional level via imaging. Here, we introduce a new image processing method that quantifies the interaction between host cells and fungal invaders, for example, alveolar macrophages and the conidia of Aspergillus fumigatus...
September 15, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28906493/rapid-curation-of-gene-disruption-collections-using-knockout-sudoku
#17
Isao A Anzai, Lev Shaket, Oluwakemi Adesina, Michael Baym, Buz Barstow
Knockout Sudoku is a method for the construction of whole-genome knockout collections for a wide range of microorganisms with as little as 3 weeks of dedicated labor and at a cost of ∼$10,000 for a collection for a single organism. The method uses manual 4D combinatorial pooling, next-generation sequencing, and a Bayesian inference algorithm to rapidly process and then accurately annotate the extremely large progenitor transposon insertion mutant collections needed to achieve saturating coverage of complex microbial genomes...
October 2017: Nature Protocols
https://www.readbyqxmd.com/read/28905320/genetic-algorithm-with-a-crossover-elitist-preservation-mechanism-for-protein-ligand-docking
#18
Boxin Guan, Changsheng Zhang, Jiaxu Ning
Protein-ligand docking plays an important role in computer-aided pharmaceutical development. Protein-ligand docking can be defined as a search algorithm with a scoring function, whose aim is to determine the conformation of the ligand and the receptor with the lowest energy. Hence, to improve an efficient algorithm has become a very significant challenge. In this paper, a novel search algorithm based on crossover elitist preservation mechanism (CEP) for solving protein-ligand docking problems is proposed. The proposed algorithm, namely genetic algorithm with crossover elitist preservation (CEPGA), employ the CEP to keep the elite individuals of the last generation and make the crossover more efficient and robust...
September 13, 2017: AMB Express
https://www.readbyqxmd.com/read/28904466/detection-of-dysferlin-gene-pathogenic-variants-in-the-indian-population-in-patients-predicted-to-have-a-dysferlinopathy-using-a-blood-based-monocyte-assay-and-clinical-algorithm-a-model-for-accurate-and-cost-effective-diagnosis
#19
Rashna Sam Dastur, Pradnya Satish Gaitonde, Munira Kachwala, Babi R R Nallamilli, Arunkanth Ankala, Satish V Khadilkar, Nalini Atchayaram, N Gayathri, A K Meena, Laura Rufibach, Sarah Shira, Madhuri Hegde
BACKGROUND: Limb-girdle muscular dystrophy (LGMD) is the most common adult-onset class of muscular dystrophies in India, but a majority of suspected LGMDs in India remain unclassified to the genetic subtype level. The next-generation sequencing (NGS)-based approaches have allowed molecular characterization and subtype diagnosis in a majority of these patients in India. MATERIALS AND METHODS: (I) To select probable dysferlinopathy (LGMD2B) cases from other LGMD subtypes using two screening methods (i) to determine the status of dysferlin protein expression in blood (peripheral blood mononuclear cell) by monocyte assay (ii) using a predictive algorithm called automated LGMD diagnostic assistant (ALDA) to obtain possible LGMD subtypes based on clinical symptoms...
July 2017: Annals of Indian Academy of Neurology
https://www.readbyqxmd.com/read/28903898/current-status-of-pathway-analysis-in-genome-wide-association-study
#20
Yu-Yan Wang, Zi-Xing Wang, Yao-da Hu, Lei Wang, Ning Li, Biao Zhang, Wei Han, Jing-Mei Jiang
Since the first publication in 2005, the genome-wide association study (GWAS) strategy has contributed significantly to the understanding of the mechanisms of human genetic diseases. Integrations of statistical methods and systematic biology are important means to explore the GWAS data. Pathway analysis establishes the importance of genetic variants from GWAS and provides insights into their biological significance. It is conducive in correlating the genetic variants, which have only small but interactive changes, to their importance in the biological pathways...
August 20, 2017: Yi Chuan, Hereditas
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