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https://www.readbyqxmd.com/read/28340391/optimization-of-the-marinelli-beaker-dimensions-using-genetic-algorithm
#1
Seyed Mehrdad Zamzamian, Seyed Abolfazl Hosseini, Mohammad Samadfam
A computational code, based on the genetic algorithm and MCNPX version 2.6 code was developed and used to investigate the effects of some important parameters of HPGe detector (such as Al cap thickness, dead-layer thickness and Ge hole size) on optimum dimensions of marinelli beaker. In addition, the effects of detector material on optimal beaker dimensions were also investigated. Finally, the optimized beaker dimensions at various beaker volumes (300, 500, 700, 1000 and 1500 cm(3)) were determined for some conventional Ge detectors with different crystal sizes (16 sizes)...
March 21, 2017: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/28340243/finite-time-parametric-identification-for-the-model-representing-the-metabolic-and-genetic-regulatory-effects-of-sequential-aerobic-respiration-and-anaerobic-fermentation-processes-in-escherichia-coli
#2
Alfonso Sepúlveda-Gálvez, Jesús Agustín Badillo-Corona, Isaac Chairez
Mathematical modelling applied to biological systems allows for the inferring of changes in the dynamic behaviour of organisms associated with variations in the environment. Models based on ordinary differential equations are most commonly used because of their ability to describe the mechanisms of biological systems such as transcription. The disadvantage of using this approach is that there is a large number of parameters involved and that it is difficult to obtain them experimentally. This study presents an algorithm to obtain a finite-time parameter characterization of the model used to describe changes in the metabolic behaviour of Escherichia coli associated with environmental changes...
March 17, 2017: Mathematical Medicine and Biology: a Journal of the IMA
https://www.readbyqxmd.com/read/28339169/gesp-a-computer-program-for-modeling-genetic-effective-population-size-inbreeding-and-divergence-in-substructured-populations
#3
Fredrik Olsson, Linda Laikre, Ola Hössjer, Nils Ryman
The genetically effective population size (Ne) is of key importance for quantifying rates of inbreeding and genetic drift, and is often used in conservation management to set targets for genetic viability. The concept was developed for single, isolated populations and the mathematical means for analyzing the expected Ne in complex, subdivided populations have previously not been available. We recently developed such analytical theory and central parts of that work have now been incorporated into a freely available software tool presented here...
March 24, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28336339/optimal-feature-selection-from-fnirs-signals-using-genetic-algorithms-for-bci
#4
Farzan Majeed Noori, Noman Naseer, Nauman Khalid Qureshi, Hammad Nazeer, Rayyan Azam Khan
In this paper, a novel technique for determination of the optimal feature combinations and, thereby, acquisition of the maximum classification performance for a functional near-infrared spectroscopy (fNIRS)-based brain-computer interface (BCI), is proposed. After obtaining motor-imagery and rest signals from the motor cortex, filtering is applied to remove the physiological noises. Six features (signal slope, signal mean, signal variance, signal peak, signal kurtosis and signal skewness) are then extracted from the oxygenated hemoglobin (HbO)...
March 20, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28335480/weighted-kernel-entropy-component-analysis-for-fault-diagnosis-of-rolling-bearings
#5
Hongdi Zhou, Tielin Shi, Guanglan Liao, Jianping Xuan, Jie Duan, Lei Su, Zhenzhi He, Wuxing Lai
This paper presents a supervised feature extraction method called weighted kernel entropy component analysis (WKECA) for fault diagnosis of rolling bearings. The method is developed based on kernel entropy component analysis (KECA) which attempts to preserve the Renyi entropy of the data set after dimension reduction. It makes full use of the labeled information and introduces a weight strategy in the feature extraction. The class-related weights are introduced to denote differences among the samples from different patterns, and genetic algorithm (GA) is implemented to seek out appropriate weights for optimizing the classification results...
March 18, 2017: Sensors
https://www.readbyqxmd.com/read/28334861/defective-signaling-through-plexin-a1-compromises-the-development-of-the-peripheral-olfactory-system-and-neuroendocrine-reproductive-axis-in-mice
#6
Séverine Marcos, Carine Monnier, Xavier Rovira Algans, Corinne Fouveaut, Nelly Pitteloud, Fabrice Ango, Catherine Dodé, Jean-Pierre Hardelin
The olfacto-genital syndrome (Kallmann syndrome) associates congenital hypogonadism due to gonadotropin-releasing hormone (GnRH) deficiency and anosmia. This is a genetically heterogeneous developmental disease with various modes of transmission, including oligogenic inheritance. Previous reports have involved defective cell signaling by semaphorin-3A in the disease pathogenesis. Here, we report that the embryonic phenotype of Plxna1-/- mutant mice lacking plexin-A1 (a major receptor of class 3 semaphorins), though not fully penetrant, resembles that of Kallmann syndrome fetuses...
March 2, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334355/a-zoom-focus-algorithm-zfa-to-locate-the-optimal-testing-region-for-rare-variant-association-tests
#7
Maggie Haitian Wang, Haoyi Weng, Rui Sun, Jack Lee, William Ka Kei Wu, Ka Chun Chong, Benny Chung-Ying Zee
Motivation: Increasing amounts of whole exome or genome sequencing data present the challenge of analysing rare variants with extremely small minor allele frequencies. Various statistical tests have been proposed, which are specifically configured to increase power for rare variants by conducting the test within a certain bin, such as a gene or a pathway. However, a gene may contain from several to thousands of markers, and not all of them are related to the phenotype. Combining functional and non-functional variants in an arbitrary genomic region could impair the testing power...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334108/fast-admixture-analysis-and-population-tree-estimation-for-snp-and-ngs-data
#8
Yu Jade Cheng, Thomas Mailund, Rasmus Nielsen
Structure methods are highly used population genetic methods for classifying individuals in a sample fractionally into discrete ancestry components. We introduce a new optimization algorithm for the classical STRUCTURE model in a maximum likelihood framework. Using analyses of real data we show that the new method finds solutions with higher likelihoods than the state-of-the-art method inthe same computational time. The optimization algorithm is also applicable to models based on genotype likelihoods, that can account for the uncertainty in genotype-calling associated with Next Generation Sequencing (NGS) data...
February 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333918/21-gene-recurrence-score-testing-among-medicare-beneficiaries-with-breast-cancer-in-2010-2013
#9
Julie A Lynch, Brygida Berse, Nicole Coomer, John Kautter
PURPOSE: We evaluated national patient-level utilization of the 21-gene recurrence score (21-gene RS) test among Medicare beneficiaries with breast cancer. We analyzed clinical, demographic, and regional factors that predict testing. METHODS: Using 2010-2013 Medicare claims, we conducted a retrospective study of breast cancer patients. The outcome variable was whether the patient underwent testing. Independent variables expected to predict testing were age, gender, race, Medicaid status, clinical characteristics, and hospital referral region (HRR)...
March 23, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28333652/survivability-modeling-and-resource-planning-for-self-repairing-reconfigurable-device-fabrics
#10
Rashad S Oreifej, Rawad Al-Haddad, Ramtin Zand, Rizwan A Ashraf, Ronald F DeMara
A resilient system design problem is formulated as the quantification of uncommitted reconfigurable resources required for a system of components to survive its lifetime within mission availability specifications. We show that this survivability metric can be calculated according to the residual functionality obtained from pools of dynamically configurable elements constituting the amorphous resource pool (ARP). The ARP is depleted based on the failure rate to replenish the functionality lost in a reconfigurable fabric due to the occurrence of permanent faults during the mission lifetime...
March 21, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28333622/constrained-inversion-and-spectral-unmixing-in-multispectral-optoacoustic-tomography
#11
Lu Ding, Xose Luis Dean Ben, Neal C Burton, Robert W Sobol, Vasilis Ntziachristos, Daniel Razansky
Accurate extraction of physical and biochemical parameters from optoacoustic images is often impeded due to the use of unrigorous inversion schemes, incomplete tomographic detection coverage or other experimental factors that cannot be readily accounted for during the image acquisition and reconstruction process. For instance, inaccurate assumptions in the physical forward model may lead to negative optical absorption values in the reconstructed images. Any artifacts present in the single wavelength optoacoustic images can be significantly aggravated when performing a two-step reconstruction consisting in acoustic inversion and spectral unmixing aimed at rendering the distributions of spectrally-distinct absorbers...
March 22, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28333053/evaluation-of-the-information-content-of-long-term-wastewater-characteristics-data-in-relation-to-activated-sludge-model-parameters
#12
Jamal Alikhani, Imre Takacs, Ahmed Al-Omari, Sudhir Murthy, Arash Massoudieh
A parameter estimation framework was used to evaluate the ability of observed data from a full-scale nitrification-denitrification bioreactor to reduce the uncertainty associated with the bio-kinetic and stoichiometric parameters of an activated sludge model (ASM). Samples collected over a period of 150 days from the effluent as well as from the reactor tanks were used. A hybrid genetic algorithm and Bayesian inference were used to perform deterministic and parameter estimations, respectively. The main goal was to assess the ability of the data to obtain reliable parameter estimates for a modified version of the ASM...
March 2017: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/28333051/artificial-intelligence-based-model-for-optimization-of-cod-removal-efficiency-of-an-up-flow-anaerobic-sludge-blanket-reactor-in-the-saline-wastewater-treatment
#13
Alain R Picos-Benítez, Juan D López-Hincapié, Abraham U Chávez-Ramírez, Adrián Rodríguez-García
The complex non-linear behavior presented in the biological treatment of wastewater requires an accurate model to predict the system performance. This study evaluates the effectiveness of an artificial intelligence (AI) model, based on the combination of artificial neural networks (ANNs) and genetic algorithms (GAs), to find the optimum performance of an up-flow anaerobic sludge blanket reactor (UASB) for saline wastewater treatment. Chemical oxygen demand (COD) removal was predicted using conductivity, organic loading rate (OLR) and temperature as input variables...
March 2017: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/28331548/discovering-feature-relevancy-and-dependency-by-kernel-guided-probabilistic-model-building-evolution
#14
Nestor Rodriguez, Sergio Rojas-Galeano
BACKGROUND: Discovering relevant features (biomarkers) that discriminate etiologies of a disease is useful to provide biomedical researchers with candidate targets for further laboratory experimentation while saving costs; dependencies among biomarkers may suggest additional valuable information, for example, to characterize complex epistatic relationships from genetic data. The use of classifiers to guide the search for biomarkers (the so-called wrapper approach) has been widely studied...
2017: BioData Mining
https://www.readbyqxmd.com/read/28331490/ranking-of-sites-for-installation-of-hydropower-plant-using-mlp-neural-network-trained-with-ga-a-madm-approach
#15
Benjamin A Shimray, Kh Manglem Singh, Thongam Khelchandra, R K Mehta
Every energy system which we consider is an entity by itself, defined by parameters which are interrelated according to some physical laws. In recent year tremendous importance is given in research on site selection in an imprecise environment. In this context, decision making for the suitable location of power plant installation site is an issue of relevance. Environmental impact assessment is often used as a legislative requirement in site selection for decades. The purpose of this current work is to develop a model for decision makers to rank or classify various power plant projects according to multiple criteria attributes such as air quality, water quality, cost of energy delivery, ecological impact, natural hazard, and project duration...
2017: Computational Intelligence and Neuroscience
https://www.readbyqxmd.com/read/28328508/hapiso-an-accurate-method-for-the-haplotype-specific-isoforms-reconstruction-from-long-single-molecule-reads
#16
Serghei Mangul, Harry Taegyun Yang, Farhad Hormozdiari, Alex Dainis, Elizabeth Tseng, Euan A Ashley, Alex Zelikovsky, Eleazar Eskin
Sequencing of RNA provides the possibility to study an individual's transcriptome landscape and determine allelic expression ratios. Single-molecule protocols generate multi-kilobase reads longer than most transcripts allowing sequencing of complete haplotype isoforms. This allows partitioning the reads into two parental haplotypes. While the read length of the single-molecule protocols is long, the relatively high error rate limits the ability to accurately detect the genetic variants and assemble them into the haplotype-specific isoforms...
March 17, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28327993/stepwise-distributed-open-innovation-contests-for-software-development-acceleration-of-genome-wide-association-analysis
#17
Andrew Hill, Po-Ru Loh, Ragu B Bharadwaj, Pascal Pons, Jingbo Shang, Eva Guinan, Karim Lakhani, Iain Kilty, Scott A Jelinsky
BACKGROUND: The association of differing genotypes with disease related phenotypic traits offers great potential to both help identify new therapeutic targets and support stratification of patients who would gain the greatest benefit from specific drug classes. Development of low cost genotyping and sequencing has made collecting large scale genotyping data routine in population and therapeutic intervention studies. In addition, a range of new technologies are being used to capture numerous new and complex phenotypic descriptors...
February 28, 2017: GigaScience
https://www.readbyqxmd.com/read/28327978/a-dataset-of-images-and-morphological-profiles-of-30-000-small-molecule-treatments-using-the-cell-painting-assay
#18
Mark-Anthony Bray, Sigrun M Gustafsdottir, Vebjorn Ljosa, Shantanu Singh, Katherine L Sokolnicki, Joshua A Bittker, Nicole E Bodycombe, Vlado Dancík, Thomas P Hasaka, C Suk-Yee Hon, Melissa M Kemp, Kejie Li, Deepika Walpita, Mathias J Wawer, Todd R Golub, Stuart L Schreiber, Paul A Clemons, Alykhan F Shamji, Anne E Carpenter
Background: Large-scale image sets acquired by automated microscopy of perturbed samples enable a detailed comparison of cell states induced by each perturbation, such as a small molecule from a diverse library. Highly multiplexed measurements of cellular morphology can be extracted from each image and subsequently mined for a number of applications. Findings: This microscopy data set includes 919,874 five-channel fields of view representing 30,616 tested compounds, available at 'The Cell Image Library' repository...
January 7, 2017: GigaScience
https://www.readbyqxmd.com/read/28327945/enhancing-knowledge-discovery-from-cancer-genomics-data-with-galaxy
#19
Marco A Albuquerque, Bruno M Grande, Elie J Ritch, Prasath Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K Grewal, Sohrab P Shah, Paul C Boutros, Ryan D Morin
The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data...
March 9, 2017: GigaScience
https://www.readbyqxmd.com/read/28327571/insights-from-early-experience-of-a-rare-disease-genomic-medicine-multidisciplinary-team-a-qualitative-study
#20
Elizabeth Ormondroyd, Michael P Mackley, Edward Blair, Jude Craft, Julian C Knight, John Taylor, Jenny C Taylor, Andrew Om Wilkie, Hugh Watkins
Whole-exome/whole-genome sequencing (WES/WGS) has the potential to enhance genetic diagnosis of rare disease, and is increasingly becoming part of routine clinical care in mainstream medicine. Effective translation will require ongoing efforts in a number of areas including: selection of appropriate patients, provision of effective consent, pre- and post-test genetic counselling, improving variant interpretation algorithms and practices, and management of secondary findings including those found incidentally and those actively sought...
March 22, 2017: European Journal of Human Genetics: EJHG
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