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Genetic algorithm

Haoyuan Hong, Paraskevas Tsangaratos, Ioanna Ilia, Junzhi Liu, A-Xing Zhu, Chong Xu
The main objective of the present study was to utilize Genetic Algorithms (GA) in order to obtain the optimal combination of forest fire related variables and apply data mining methods for constructing a forest fire susceptibility map. In the proposed approach, a Random Forest (RF) and a Support Vector Machine (SVM) was used to produce a forest fire susceptibility map for the Dayu County which is located in southwest of Jiangxi Province, China. For this purpose, historic forest fires and thirteen forest fire related variables were analyzed, namely: elevation, slope angle, aspect, curvature, land use, soil cover, heat load index, normalized difference vegetation index, mean annual temperature, mean annual wind speed, mean annual rainfall, distance to river network and distance to road network...
March 1, 2018: Science of the Total Environment
Mohammad Kalantar, Mohammad Mahdi Mardanpour, Soheila Yaghmaei
Bacterial transport parameters play a fundamental role in microbial population dynamics, biofilm formation and bacteria dispersion. In this study, the novel model was extended based on the capability of microsized microbial fuel cells (MFCs) as amperometric biosensors to predict the cells' chemotactic and bioelectrochemical properties. The model prediction results coincide with the experimental data of Shewanella oneidensis and chemotaxis mutant of P. aeruginosa bdlA and pilT strains, indicating the complementary role of numerical predictions for bioscreening applications of microsized MFCs...
March 12, 2018: Bioelectrochemistry
Rainer Malik, Martin Dichgans
Stroke, ischemic stroke and subtypes of ischemic stroke display substantial heritability. Compared to related vascular conditions, the number of established risk loci reaching genome-wide significance for association with stroke is still in the lower range, particularly for etiological stroke subtypes such as large artery atherosclerotic stroke or small vessel stroke. Nevertheless, for individual loci substantial progress has been made in determining the specific mechanisms mediating stroke risk. In this review, we present a roadmap for functional follow-up of common risk variants associated with stroke...
March 15, 2018: Cardiovascular Research
Alberto Lleó, David J Irwin, Ignacio Illán-Gala, Corey T McMillan, David A Wolk, Edward B Lee, Vivianna M Van Deerlin, Leslie M Shaw, John Q Trojanowski, Murray Grossman
Importance: Cerebrospinal fluid (CSF) core Alzheimer disease (AD) biomarkers have shown an excellent capacity for the in vivo detection of AD. Previous studies have shown that CSF levels of phosphorylated tau (p-tau) also correlate with tau pathology in frontotemporal lobar degeneration (FTLD) after accounting for AD copathology. Objective: To develop an algorithm based on core AD CSF measures to exclude cases with AD pathology and then differentiate between FTLD-tau and FTLD transactive response DNA-binding protein of approximately 43kDa (FTLD-TDP)...
March 19, 2018: JAMA Neurology
Najat Dzaki, Ghows Azzam
Members of the Aedes genus of mosquitoes are widely recognized as vectors of viral diseases. Ae.albopictus is its most invasive species, and are known to carry viruses such as Dengue, Chikugunya and Zika. Its emerging importance puts Ae.albopictus on the forefront of genetic interaction and evolution studies. However, a panel of suitable reference genes specific for this insect is as of now undescribed. Nine reference genes, namely ACT, eEF1-γ, eIF2α, PP2A, RPL32, RPS17, PGK1, ILK and STK were evaluated. Expression patterns of the candidate reference genes were observed in a total of seventeen sample types, separated by stage of development and age...
2018: PloS One
Yuhong Li, Guanghong Gong, Ni Li
In this paper, we propose a novel algorithm-parallel adaptive quantum genetic algorithm-which can rapidly determine the minimum control nodes of arbitrary networks with both control nodes and state nodes. The corresponding network can be fully controlled with the obtained control scheme. We transformed the network controllability issue into a combinational optimization problem based on the Popov-Belevitch-Hautus rank condition. A set of canonical networks and a list of real-world networks were experimented...
2018: PloS One
Xiao Zhang, Guigao Lin, Liming Tan, Jinming Li
Tacrolimus is effective for the prevention of acute rejection, but is also highly toxic and has great intra- and inter-individual variability in transplant patients. Genetic variation and other factors influence the response of an individual to tacrolimus treatment. Therefore, even if therapeutic drug monitoring is universally applied, rejection and toxicity still occur. Although the appropriate action on pharmacogenomic variability provides a cornerstone for the precise tacrolimus prescription, at present there are many obstacles to translating it into clinical practice...
March 15, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Chun-Fu Hong, Ying-Chen Chen, Wei-Chun Chen, Keng-Chang Tu, Meng-Hsiun Tsai, Yung-Kuan Chan, Shyr Shen Yu
A microarray analysis generally contains expression data of thousands of genes, but most of them are irrelevant to the disease of interest, making analyzing the genes concerning specific diseases complicated. Therefore, filtering out a few essential genes as well as their regulatory networks is critical, and a disease can be easily diagnosed just depending on the expression profiles of a few critical genes. In this study, a target gene screening (TGS) system, which is a microarray-based information system that integrates F-statistics, pattern recognition matching, a two-layer K-means classifier, a Parameter Detection Genetic Algorithm (PDGA), a genetic-based gene selector (GBG selector) and the association rule, was developed to screen out a small subset of genes that can discriminate malignant stages of cancers...
March 14, 2018: Journal of Biomedical Informatics
Zhao-Lian Lu, Ying-Jian Chen, Xin-Yan Jing, Na-Na Wang, Ting Zhang, Cheng-Jin Hu
BACKGROUND Papillary thyroid cancer (PTC) is currently the most commonly diagnosed endocrine malignancy. In addition, the sex- and age-adjusted incidence of PTC has exhibited a greater increase over the last 2 decades than in many other malignancies. Thus, discovering noninvasive specific serum biomarker to distinguish PTC from cancer-free controls in its early stages remains an important goal. MATERIAL AND METHODS Serum samples from 88 PTC patients and 80 cancer-free controls were randomly allocated into training or validation sets...
March 17, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Carolina Sheng Whei Miaw, Camila Assis, Alessandro Rangel Carolino Sales Silva, Maria Luísa Cunha, Marcelo Martins Sena, Scheilla Vitorino Carvalho de Souza
Grape, orange, peach and passion fruit nectars were formulated and adulterated by dilution with syrup, apple and cashew juices at 10 levels for each adulterant. Attenuated total reflectance Fourier transform mid infrared (ATR-FTIR) spectra were obtained. Partial least squares (PLS) multivariate calibration models allied to different variable selection methods, such as interval partial least squares (iPLS), ordered predictors selection (OPS) and genetic algorithm (GA), were used to quantify the main fruits. PLS improved by iPLS-OPS variable selection showed the highest predictive capacity to quantify the main fruit contents...
July 15, 2018: Food Chemistry
Cliff C Kerr, Salvador Dura-Bernal, Tomasz G Smolinski, George L Chadderdon, David P Wilson
When standard optimization methods fail to find a satisfactory solution for a parameter fitting problem, a tempting recourse is to adjust parameters manually. While tedious, this approach can be surprisingly powerful in terms of achieving optimal or near-optimal solutions. This paper outlines an optimization algorithm, Adaptive Stochastic Descent (ASD), that has been designed to replicate the essential aspects of manual parameter fitting in an automated way. Specifically, ASD uses simple principles to form probabilistic assumptions about (a) which parameters have the greatest effect on the objective function, and (b) optimal step sizes for each parameter...
2018: PloS One
Ruili Shi, Pengju Wang, Lingli Tang, Xiaoming Huang, Yonggang Chen, Yan Su, Jijun Zhao
Using a genetic algorithm incorporated in density functional theory, we explore the ground state structures of fluoride anion-water clusters F-(H2O)n with n = 1-10. The F-(H2O)n clusters prefer structures in which the F- anion remains at the surface of the structure and coordinates with four water molecules, as the F-(H2O)n clusters have strong F--H2O interactions as well as strong hydrogen bonds between H2O molecules. The strong interaction between the F- anion and adjacent H2O molecule leads to a longer O-H distance in the adjacent molecule than in an individual water molecule...
March 16, 2018: Journal of Physical Chemistry. A
Runyu Jing, Yu Liang, Yi Ran, Shengzhong Feng, Yanjie Wei, Li He
In genetic data modeling, the use of a limited number of samples for modeling and predicting, especially well below the attribute number, is difficult due to the enormous number of genes detected by a sequencing platform. In addition, many studies commonly use machine learning methods to evaluate genetic datasets to identify potential disease-related genes and drug targets, but to the best of our knowledge, the information associated with the selected gene set was not thoroughly elucidated in previous studies...
2018: International Journal of Genomics
Rensheng Cao, Mingyi Fan, Jiwei Hu, Wenqian Ruan, Xianliang Wu, Xionghui Wei
Highly promising artificial intelligence tools, including neural network (ANN), genetic algorithm (GA) and particle swarm optimization (PSO), were applied in the present study to develop an approach for the evaluation of Se(IV) removal from aqueous solutions by reduced graphene oxide-supported nanoscale zero-valent iron (nZVI/rGO) composites. Both GA and PSO were used to optimize the parameters of ANN. The effect of operational parameters (i.e., initial pH, temperature, contact time and initial Se(IV) concentration) on the removal efficiency was examined using response surface methodology (RSM), which was also utilized to obtain a dataset for the ANN training...
March 15, 2018: Materials
Renata C Gallagher, Laura Pollard, Anna I Scott, Suzette Huguenin, Stephen Goodman, Qin Sun
Disclaimer: These ACMG Standards are intended as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these Standards is voluntary and does not necessarily assure a successful medical outcome. These Standards should not be considered inclusive of all proper procedures and tests, or exclusive of others that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, clinical laboratory geneticists should apply their professional judgment to the specific circumstances presented by the patient or specimen...
March 15, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Shengfeng Yang, Naixie Zhou, Hui Zheng, Shyue Ping Ong, Jian Luo
First-order interfacial phaselike transformations that break the mirror symmetry of the symmetric ∑5 (210) tilt grain boundary (GB) are discovered by combining a modified genetic algorithm with hybrid Monte Carlo and molecular dynamics simulations. Density functional theory calculations confirm this prediction. This first-order coupled structural and adsorption transformation, which produces two variants of asymmetric bilayers, vanishes at an interfacial critical point. A GB complexion (phase) diagram is constructed via semigrand canonical ensemble atomistic simulations for the first time...
February 23, 2018: Physical Review Letters
Brian D Segal, Thomas Braun, Michael R Elliott, Hui Jiang
Researchers in genetics and other life sciences commonly use permutation tests to evaluate differences between groups. Permutation tests have desirable properties, including exactness if data are exchangeable, and are applicable even when the distribution of the test statistic is analytically intractable. However, permutation tests can be computationally intensive. We propose both an asymptotic approximation and a resampling algorithm for quickly estimating small permutation p-values (e.g., <10-6) for the difference and ratio of means in two-sample tests...
March 2018: Biometrics
Manijeh Beigi, Kevan Ghasemi, Parvin Mirzaghavami, Mohammadreza Khanmohammadi, Hamidreza SalighehRad
The main aim of this study was to propose a new statistical method for evaluation of spatial malignancy distribution within Magnetic Resonance Spectroscopy (MRS) grid in Glioblastoma Multiforme patients. Voxels with different malignancy probabilities were presented as a novel MRS-based Malignancy Probability Map (MPM). For this purpose, a predictive probability-based clustering approach was developed, including the two following steps: (1) Gaussian Mixture Model, (2) Quadratic Discriminate Analysis coupled with Genetic Algorithm...
March 14, 2018: Journal of Neuro-oncology
Carol Cremin, Sarah Howard, Lyly Le, Aly Karsan, David F Schaeffer, Daniel Renouf, Kasmintan A Schrader
Background: Approximately 5% to 10% of pancreatic ductal adenocarcinoma (PDAC) has a hereditary basis. In most of these defined hereditary cancer syndromes, PDAC is not the predominant cancer type. Traditional criteria for publicly funded genetic testing typically require the presence of a set combination of the predominant syndrome-associated cancer types in the family history.We report the identification of a CDKN2A pathogenic variant in a PDAC-prone family without the cutaneous features of multiple moles or melanoma that are characteristic of the Familial Atypical Multiple Mole Melanoma (FAMMM) Syndrome identified in a universal testing algorithm for inherited mutations in pancreatic cancer patients...
2018: Hereditary Cancer in Clinical Practice
Evangelia Elenis, Alkistis Skalkidou, Agneta Skoog-Svanberg, Gunilla Sydsjö, Anneli Stavreus-Evers, Helena Åkerud
BACKGROUND: Preeclampsia and gestational hypertensive disorders are thought to occur due to endothelial cell dysfunction and abnormal placentation, triggered by angiogenesis-related factors yet undetermined. The aim of this study was to investigate whether a genetic polymorphism (SNP) of Histidine-rich glycoprotein (HRG), HRG C633T SNP, is associated with gestational hypertensive disorders. METHODS: It was performed a nested case-control study from the BASIC Cohort of Uppsala University Hospital comprising 92 women diagnosed with gestational hypertensive disorders without other comorbidities and 200 women with full term uncomplicated pregnancies, all genotyped regarding HRG C633T SNP...
March 14, 2018: BMC Medical Genetics
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