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Genetic algorithm

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https://www.readbyqxmd.com/read/29781496/a-universal-platform-for-selection-and-high-resolution-phenotypic-screening-of-bacterial-mutants-using-the-nanowell-slide
#1
H Antypas, M Veses-Garcia, E Weibull, H Andersson-Svahn, A Richter-Dahlfors
The Petri dish and microtiter plate are the golden standard for selection and screening of bacteria in microbiological research. To improve on the limited resolution and throughput of these methods, we developed a universal, user-friendly platform for selection and high-resolution phenotypic screening based on the nanowell slide. This miniaturized platform has an optimal ratio between throughput and assay complexity, holding 672 nanowells of 500 nl each. As monoclonality is essential in bacterial genetics, we used FACS to inoculate each nanowell with a single bacterium in 15 min...
May 21, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29780632/management-pathways-for-solitary-pulmonary-nodules
#2
REVIEW
Masaoki Ito, Yoshihiro Miyata, Morihito Okada
Pulmonary nodules are often detected during the clinical course of several diseases or through routine screening. Various guidelines have proposed management algorithms for suspicious solitary nodules in lung cancer. Generally, solitary pulmonary nodules are managed according to nodule appearance and risk of lung cancer using low-dose, thin section computed tomography (CT). Liquid biopsy is promising for diagnosis, therapeutic-monitoring and follow-up in lung cancer; however, diagnosis and management pathways based on genetic examination alone have not been established...
April 2018: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29779772/dissecting-whole-genome-sequencing-based-online-tools-for-predicting-resistance-in-mycobacterium-tuberculosis-can-we-use-them-for-clinical-decision-guidance
#3
Rita Macedo, Alexandra Nunes, Isabel Portugal, Sílvia Duarte, Luís Vieira, João Paulo Gomes
Whole-genome sequencing (WGS)-based bioinformatics platforms for the rapid prediction of resistance will soon be implemented in the Tuberculosis (TB) laboratory, but their accuracy assessment still needs to be strengthened. Here, we fully-sequenced a total of 54 multidrug-resistant (MDR) and five susceptible TB strains and performed, for the first time, a simultaneous evaluation of the major four free online platforms (TB Profiler, PhyResSE, Mykrobe Predictor and TGS-TB). Overall, the sensitivity of resistance prediction ranged from 84...
May 2018: Tuberculosis
https://www.readbyqxmd.com/read/29778764/a-method-to-optimize-the-shield-compact-and-lightweight-combining-the-structure-with-components-together-by-genetic-algorithm-and-mcnp-code
#4
Yao Cai, Huasi Hu, Ziheng Pan, Guang Hu, Tao Zhang
To optimize the shield for neutrons and gamma rays compact and lightweight, a method combining the structure and components together was established employing genetic algorithms and MCNP code. As a typical case, the fission energy spectrum of 235 U which mixed neutrons and gamma rays was adopted in this study. Six types of materials were presented and optimized by the method. Spherical geometry was adopted in the optimization after checking the geometry effect. Simulations have made to verify the reliability of the optimization method and the efficiency of the optimized materials...
May 17, 2018: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/29778033/weight-and-the-vitamin-k-expoxide-reductase-1-genotype-primarily-contribute-to-the-warfarin-dosing-in-pediatric-patients-with-kawasaki-disease
#5
Zhouping Wang, Li Zhang, Ping Huang, Xiaoqiong Gu, Xiaofei Xie, Yanfei Wang, Wei Li, Qiyi Zeng
INTRODUCTION: Warfarin therapy is recommended in children with giant coronary artery aneurysms (GCAAs) after Kawasaki disease (KD). Large individual variability makes it difficult to predict the warfarin dose. Polymorphisms in the vitamin K expoxide reductase 1 (VKORC1) and cytochrome P4502C9 (CYP2C9) genes have been reported to influence the warfarin dose. We investigated the effects of the VKORC1 and CYP2C9 genotypes on the warfarin dose in pediatric patients with giant CAAs after KD...
May 8, 2018: Thrombosis Research
https://www.readbyqxmd.com/read/29777302/emerging-strategies-in-brca-positive-pancreatic-cancer
#6
REVIEW
Adam Kowalewski, Łukasz Szylberg, Michał Saganek, Wojciech Napiontek, Paulina Antosik, Dariusz Grzanka
PURPOSE: We propose a treatment algorithm for PDAC with particular emphasis on BRCA1 or 2 mutation-positive patients. Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest diseases in the United States and Europe. BRCA1 and BRCA2 are among the most common of the known genetic mutations involved in familial PDAC. The optimal chemotherapy regimen to use for BRCA1 or 2 mutation carriers with PDAC is not yet established. As new treatment options emerge, algorithms must balance the need to give the best drugs first with ensuring that there are still beneficial options available for later...
May 18, 2018: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/29775073/diffuse-gliomas-for-nonneuropathologists-the-new-integrated-molecular-diagnostics
#7
Sunhee C Lee
Diffuse gliomas comprise the bulk of "brain cancer" in adults. The recent update to the 4th edition of the World Health Organization's classification of tumors of the central nervous system reflects an unprecedented change in the landscape of the diagnosis and management of diffuse gliomas that will affect all those involved in the management and care of patients. Of the recently discovered gene alterations, mutations in the Krebs cycle enzymes isocitrate dehydrogenases (IDHs) 1 and 2 have fundamentally changed the way the gliomas are understood and classified...
May 18, 2018: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/29774539/clinical-and-molecular-characterization-of-indian-patients-with-fructose-1-6-bisphosphatase-deficiency-identification-of-a-frequent-variant-e281k
#8
Pratibha Bhai, Sunita Bijarnia-Mahay, Ratna D Puri, Renu Saxena, Deepti Gupta, Udhaya Kotecha, Anil Sachdev, Dhiren Gupta, Vyomesh Vyas, Divya Agarwal, Vivek Jain, Rajeev K Bansal, Tapisha G Kumar, Ishwar Chander Verma
Fructose-1, 6-bisphosphatase deficiency is an autosomal recessive disorder of gluconeogenesis caused by genetic defect in the FBP1 gene. It is characterized by episodic, often life-threatening metabolic acidosis, liver dysfunction, and hyperlactatemia. Without a high index of suspicion, it may remain undiagnosed with devastating consequences. Accurate diagnosis can be achieved either by enzyme assay or gene studies. Enzyme assay requires a liver biopsy and is tedious, invasive, expensive, and not easily available...
May 18, 2018: Annals of Human Genetics
https://www.readbyqxmd.com/read/29772801/ogt-o-glcnac-transferase-selectively-modifies-multiple-residues-unique-to-lamin-a
#9
Dan N Simon, Amanda Wriston, Qiong Fan, Jeffrey Shabanowitz, Alyssa Florwick, Tejas Dharmaraj, Sherket B Peterson, Yosef Gruenbaum, Cathrine R Carlson, Line M Grønning-Wang, Donald F Hunt, Katherine L Wilson
The LMNA gene encodes lamins A and C with key roles in nuclear structure, signaling, gene regulation, and genome integrity. Mutations in LMNA cause over 12 diseases ('laminopathies'). Lamins A and C are identical for their first 566 residues. However, they form separate filaments in vivo, with apparently distinct roles. We report that lamin A is β- O -linked N -acetylglucosamine- (O -GlcNAc)-modified in human hepatoma (Huh7) cells and in mouse liver. In vitro assays with purified O -GlcNAc transferase (OGT) enzyme showed robust O -GlcNAcylation of recombinant mature lamin A tails (residues 385⁻646), with no detectable modification of lamin B1, lamin C, or 'progerin' (Δ50) tails...
May 17, 2018: Cells
https://www.readbyqxmd.com/read/29772713/genetic-optimization-algorithm-for-metabolic-engineering-revisited
#10
Tobias B Alter, Lars M Blank, Birgitta E Ebert
To date, several independent methods and algorithms exist for exploiting constraint-based stoichiometric models to find metabolic engineering strategies that optimize microbial production performance. Optimization procedures based on metaheuristics facilitate a straightforward adaption and expansion of engineering objectives, as well as fitness functions, while being particularly suited for solving problems of high complexity. With the increasing interest in multi-scale models and a need for solving advanced engineering problems, we strive to advance genetic algorithms, which stand out due to their intuitive optimization principles and the proven usefulness in this field of research...
May 16, 2018: Metabolites
https://www.readbyqxmd.com/read/29770368/multi-label-inductive-matrix-completion-for-joint-mgmt-and-idh1-status-prediction-for-glioma-patients
#11
Lei Chen, Han Zhang, Kim-Han Thung, Luyan Liu, Junfeng Lu, Jinsong Wu, Qian Wang, Dinggang Shen
MGMT promoter methylation and IDH1 mutation in high-grade gliomas (HGG) have proven to be the two important molecular indicators associated with better prognosis. Traditionally, the statuses of MGMT and IDH1 are obtained via surgical biopsy, which is laborious, invasive and time-consuming. Accurate presurgical prediction of their statuses based on preoperative imaging data is of great clinical value towards better treatment plan. In this paper, we propose a novel Multi-label Inductive Matrix Completion (MIMC) model, highlighted by the online inductive learning strategy, to jointly predict both MGMT and IDH1 statuses...
September 2017: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
https://www.readbyqxmd.com/read/29770255/a-method-for-the-interpretation-of-flow-cytometry-data-using-genetic-algorithms
#12
Cesar Angeletti
Background: Flow cytometry analysis is the method of choice for the differential diagnosis of hematologic disorders. It is typically performed by a trained hematopathologist through visual examination of bidimensional plots, making the analysis time-consuming and sometimes too subjective. Here, a pilot study applying genetic algorithms to flow cytometry data from normal and acute myeloid leukemia subjects is described. Subjects and Methods: Initially, Flow Cytometry Standard files from 316 normal and 43 acute myeloid leukemia subjects were transformed into multidimensional FITS image metafiles...
2018: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/29769698/mutation-screening-using-formalin-fixed-paraffin-embedded-tissues-a-stratified-approach-according-to-dna-quality
#13
Francesco Cucco, Alexandra Clipson, Hannah Kennedy, Joe Sneath Thompson, Ming Wang, Sharon Barrans, Moniek van Hoppe, Eguzkine Ochoa Ruiz, Josh Caddy, Debbie Hamid, Thomas Cummin, Cathy Burton, Andrew J Davies, Peter Johnson, Ming-Qing Du
DNA samples from formalin-fixed paraffin-embedded tissues are highly degraded with variable quality, and this imposes a big challenge for targeted sequencing due to false positives, largely caused by PCR errors and cytosine deamination. To eliminate false positives, a common practice is to validate the detected variants by Sanger sequencing or perform targeted sequencing in duplicate. Technically, PCR errors could be removed by molecular barcoding of template DNA prior to amplification as in the HaloPlexHS design...
May 16, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29769556/optimal-design-of-miniaturized-reflecting-metasurfaces-for-ultra-wideband-and-angularly-stable-polarization-conversion
#14
Michele Borgese, Filippo Costa, Simone Genovesi, Agostino Monorchio, Giuliano Manara
An ultra-wideband linear polarization converter based on a reflecting metasurface is presented. The polarizer is composed by a periodic arrangement of miniaturized metallic elements printed on a grounded dielectric substrate. In order to achieve broadband polarization converting properties, the metasurface is optimized by employing a genetic algorithm (GA) which imposes the minimization of the amplitude of the co-polar reflection coefficient over a wide frequency band. The enhanced angular stability of the polarization converter is due to the miniaturized unit cell which is obtained by imposing the maximum periodicity of the metasurface in the GA optimization process...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29768684/practical-approach-to-the-gastrointestinal-manifestations-of-cystic-fibrosis
#15
REVIEW
Rishi Bolia, Chee Y Ooi, Peter Lewindon, Jonathan Bishop, Sarath Ranganathan, Jo Harrison, Kristyn Ford, Natalie van der Haak, Mark R Oliver
Cystic fibrosis (CF) is the most common, life-shortening, genetic illness affecting children in Australia and New Zealand. The genetic abnormality results in abnormal anion transport across the apical membrane of epithelial cells in a number of organs, including the lungs, gastrointestinal tract, liver and genito-urinary tract. Thus, CF is a multi-system disorder that requires a multi-disciplinary approach. Respiratory disease is the predominant cause of both morbidity and mortality in patients with CF. However, there are significant and clinically relevant gastrointestinal, liver, pancreatic and nutritional manifestations that must be detected and managed in a timely and structured manner...
May 16, 2018: Journal of Paediatrics and Child Health
https://www.readbyqxmd.com/read/29768326/chronic-constipation-a-review-of-literature
#16
Mojgan Forootan, Nazila Bagheri, Mohammad Darvishi
BACKGROUND: Chronic constipation is described as a common complication determined by difficult and/or rare passage of stool or both. The difference in definition of constipation has led to a wide range of reported prevalence (i.e., between 1% and 80%). Various factors are involved in the pathogenesis of the disease, including type of diet, genetic predisposition, colonic motility, absorption, social economic status, daily behaviors, and biological and pharmaceutical factors. Diagnostic and therapeutic options play a key role in the treatment of chronic constipation...
May 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29767988/experimentally-validated-structures-of-supported-metal-nanoclusters-on-mos-2
#17
Yongliang Shi, Boao Song, Reza Shahbazian-Yassar, Jin Zhao, Wissam A Saidi
In nanometer clusters (NCs) each atom counts. It is the specific arrangement of these atoms that determines the unique size-dependent functionalities of the NCs and hence their applications. Here we employ a self-consistent, combined theoretical and experimental approach to determine atom-by-atom the structures of supported Pt NCs on MoS2. The atomic structures are predicted using a genetic algorithm utilizing atomistic force fields and density functional theory, which are then validated using aberration-corrected scanning transmission electron microscopy...
May 16, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29767709/double-hits-in-schizophrenia
#18
Jacob A S Vorstman, Loes M Olde Loohuis, René S Kahn, Roel A Ophoff
The co-occurrence of a Copy Number Variant (CNV) and a functional variant on the other allele may be a relevant genetic mechanism in schizophrenia. We hypothesized that the cumulative burden of such double hits - in particular those composed of a deletion and a coding single nucleotide variation (SNV) - is increased in patients with schizophrenia.We combined CNV data with coding variants data in 795 patients with schizophrenia and 474 controls. To limit false CNV-detection, only CNVs called only by two algorithms we included...
May 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29766820/salient-aspects-of-pbp2a-inhibition-a-qsar-study
#19
Adewale J Ogunleye, Gabriel O Eniafe, Olumide K Inyang, Benjamin Adewumi, Olaposi I Omotuyi
Backgound: Inhibition of penicillin binding protein 2A (PBP2A) represents a sound drug design strategy in combatting Methicillin resistant Staphylococcus aureus (MRSA). Considering the urgent need for effective antimicrobials in combatting MRSA infections, we have developed a statistically robust ensemble of molecular descriptors (1, 2, & 3-D) from compounds targeting PBP2A in vivo. METHODS: 37 (training set: 26, test set: 11) PBP2A-inhibitors were submitted for descriptor generation after which an unsupervised, non-exhaustive genetic algorithm (GA) was deployed for fishing out the best descriptor subset...
May 15, 2018: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/29766428/modeling-and-multi-objective-optimization-for-anammox-process-under-cod-disturbance-using-hybrid-intelligent-algorithm
#20
Bin Xie, Yong-Wen Ma, Jin-Quan Wan, Yan Wang, Zhi-Cheng Yan, Lin Liu, Ze-Yu Guan
Anaerobic ammonium oxidation (ANAMMOX) has been regarded as an efficient process to treat nitrogen-containing wastewater. However, the treatment process is not fully understood in terms of reaction mechanisms, process simulation, and control. In this paper, a multi-objective control strategy mixed soft-sensing model (MCSSM) is developed to systematically design the operating variations for multi-objective control by integrating the developed model, a least square support vector machine optimized with principal component analysis (PCA-LSSVM) and non-dominated sorting genetic algorithm-II (NSGA-II)...
May 15, 2018: Environmental Science and Pollution Research International
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