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Genetic algorithms in medicine

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https://www.readbyqxmd.com/read/29764369/vareporter-variant-reporter-for-cancer-research-of-massive-parallel-sequencing
#1
Po-Jung Huang, Chi-Ching Lee, Ling-Ya Chiu, Kuo-Yang Huang, Yuan-Ming Yeh, Chia-Yu Yang, Cheng-Hsun Chiu, Petrus Tang
BACKGROUND: High throughput sequencing technologies have been an increasingly critical aspect of precision medicine owing to a better identification of disease targets, which contributes to improved health care cost and clinical outcomes. In particular, disease-oriented targeted enrichment sequencing is becoming a widely-accepted application for diagnostic purposes, which can interrogate known diagnostic variants as well as identify novel biomarkers from panels of entire human coding exome or disease-associated genes...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29757393/snpnexus-assessing-the-functional-relevance-of-genetic-variation-to-facilitate-the-promise-of-precision-medicine
#2
Abu Z Dayem Ullah, Jorge Oscanoa, Jun Wang, Ai Nagano, Nicholas R Lemoine, Claude Chelala
Broader functional annotation of genetic variation is a valuable means for prioritising phenotypically-important variants in further disease studies and large-scale genotyping projects. We developed SNPnexus to meet this need by assessing the potential significance of known and novel SNPs on the major transcriptome, proteome, regulatory and structural variation models. Since its previous release in 2012, we have made significant improvements to the annotation categories and updated the query and data viewing systems...
May 11, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29662297/graphics-processing-unit-enhanced-genetic-algorithms-for-solving-the-temporal-dynamics-of-gene-regulatory-networks
#3
REVIEW
Raúl García-Calvo, J L Guisado, Fernando Diaz-Del-Rio, Antonio Córdoba, Francisco Jiménez-Morales
Understanding the regulation of gene expression is one of the key problems in current biology. A promising method for that purpose is the determination of the temporal dynamics between known initial and ending network states, by using simple acting rules. The huge amount of rule combinations and the nonlinear inherent nature of the problem make genetic algorithms an excellent candidate for finding optimal solutions. As this is a computationally intensive problem that needs long runtimes in conventional architectures for realistic network sizes, it is fundamental to accelerate this task...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29662055/in-silico-optimization-of-a-guava-antimicrobial-peptide-enables-combinatorial-exploration-for-peptide-design
#4
William F Porto, Luz Irazazabal, Eliane S F Alves, Suzana M Ribeiro, Carolina O Matos, Állan S Pires, Isabel C M Fensterseifer, Vivian J Miranda, Evan F Haney, Vincent Humblot, Marcelo D T Torres, Robert E W Hancock, Luciano M Liao, Ali Ladram, Timothy K Lu, Cesar de la Fuente-Nunez, Octavio L Franco
Plants are extensively used in traditional medicine, and several plant antimicrobial peptides have been described as potential alternatives to conventional antibiotics. However, after more than four decades of research no plant antimicrobial peptide is currently used for treating bacterial infections, due to their length, post-translational modifications or  high dose requirement for a therapeutic effect . Here we report the design of antimicrobial peptides derived from a guava glycine-rich peptide using a genetic algorithm...
April 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29658407/c-mix-a-high-dimensional-mixture-model-for-censored-durations-with-applications-to-genetic-data
#5
Simon Bussy, Agathe Guilloux, Stéphane Gaïffas, Anne-Sophie Jannot
We introduce a supervised learning mixture model for censored durations (C-mix) to simultaneously detect subgroups of patients with different prognosis and order them based on their risk. Our method is applicable in a high-dimensional setting, i.e. with a large number of biomedical covariates. Indeed, we penalize the negative log-likelihood by the Elastic-Net, which leads to a sparse parameterization of the model and automatically pinpoints the relevant covariates for the survival prediction. Inference is achieved using an efficient Quasi-Newton Expectation Maximization algorithm, for which we provide convergence properties...
January 1, 2018: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/29649981/in-silico-cancer-research-towards-3r
#6
Claire Jean-Quartier, Fleur Jeanquartier, Igor Jurisica, Andreas Holzinger
BACKGROUND: Improving our understanding of cancer and other complex diseases requires integrating diverse data sets and algorithms. Intertwining in vivo and in vitro data and in silico models are paramount to overcome intrinsic difficulties given by data complexity. Importantly, this approach also helps to uncover underlying molecular mechanisms. Over the years, research has introduced multiple biochemical and computational methods to study the disease, many of which require animal experiments...
April 12, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29621253/a-correlation-comparison-between-altmetric-attention-scores-and-citations-for-six-plos-journals
#7
Wenya Huang, Peiling Wang, Qiang Wu
This study considered all articles published in six Public Library of Science (PLOS) journals in 2012 and Web of Science citations for these articles as of May 2015. A total of 2,406 articles were analyzed to examine the relationships between Altmetric Attention Scores (AAS) and Web of Science citations. The AAS for an article, provided by Altmetric aggregates activities surrounding research outputs in social media (news outlet mentions, tweets, blogs, Wikipedia, etc.). Spearman correlation testing was done on all articles and articles with AAS...
2018: PloS One
https://www.readbyqxmd.com/read/29569149/-aortic-diseases-modern-diagnostic-and-therapeutic-strategies
#8
R Erbel
Aortic diseases include not only the thoracic but also the abdominal part of the aorta. In the etiology cardiovascular risk factors, such as hypertension, smoking and hyperlipoproteinemia play a major role, but more and more genetic diseases with familiar predisposition are being identified. Even large aneurysms remain asymptomatic as long as other organs in the neighborhood are not damaged and no acute aortic event occurs including aortic dissection, intramural hematoma, penetrating aortic ulcer, and traumatic aortic injury...
March 22, 2018: Herz
https://www.readbyqxmd.com/read/29543224/laboratory-analysis-of-organic-acids-2018-update-a-technical-standard-of-the-american-college-of-medical-genetics-and-genomics-acmg
#9
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
https://www.readbyqxmd.com/read/29516562/automatic-artefact-detection-in-single-channel-sleep-eeg-recordings
#10
Alexander Malafeev, Ximena Omlin, Aleksandra Wierzbicka, Adam Wichniak, Wojciech Jernajczyk, Robert Riener, Peter Achermann
Quantitative electroencephalogram analysis (e.g. spectral analysis) has become an important tool in sleep research and sleep medicine. However, reliable results are only obtained if artefacts are removed or excluded. Artefact detection is often performed manually during sleep stage scoring, which is time consuming and prevents application to large datasets. We aimed to test the performance of mostly simple algorithms of artefact detection in polysomnographic recordings, derive optimal parameters and test their generalization capacity...
March 8, 2018: Journal of Sleep Research
https://www.readbyqxmd.com/read/29512050/clinical-pharmacokinetic-and-pharmacodynamic-considerations-in-the-treatment-of-inflammatory-bowel-disease
#11
REVIEW
Luc J J Derijks, Dennis R Wong, Daniel W Hommes, Adriaan A van Bodegraven
According to recent clinical consensus, pharmacotherapy of inflammatory bowel disease (IBD) is, or should be, personalized medicine. IBD treatment is complex, with highly different treatment classes and relatively few data on treatment strategy. Although thorough evidence-based international IBD guidelines currently exist, appropriate drug and dose choice remains challenging as many disease (disease type, location of disease, disease activity and course, extraintestinal manifestations, complications) and patient characteristics [(pharmaco-)genetic predisposition, response to previous medications, side-effect profile, necessary onset of response, convenience, concurrent therapy, adherence to (maintenance) therapy] are involved...
March 6, 2018: Clinical Pharmacokinetics
https://www.readbyqxmd.com/read/29499103/precision-medicine-in-diabetes-prevention-classification-and-management
#12
REVIEW
Fangying Xie, Juliana Cn Chan, Ronald Cw Ma
Diabetes has become a major burden of healthcare expenditure. Diabetes management following a uniform treatment algorithm is often associated with progressive treatment failure and development of diabetic complications. Recent advances in our understanding of the genomic architecture of diabetes and its complications have provided the framework for development of precision medicine to personalize diabetes prevention and management. In the present review, we summarized recent advances in the understanding of the genetic basis of diabetes and its complications...
March 2, 2018: Journal of Diabetes Investigation
https://www.readbyqxmd.com/read/29495892/intensification-of-the-convective-drying-process-of-salvia-officinalis-modeling-and-optimization
#13
Monia Jebri, José Tarrazó, José Bon, Hélène Desmorieux, Mehrez Romdhane
The current study deals with an innovation in the hot air convective drying process consisting of the application of two consecutive drying steps. Temperatures ranging between 60 and 80 ℃ for times between 200 and 600 s were applied for the first stage, and from 40 to 80 ℃ for the second stage. Salvia officinalis, an aromatic, medicinal Mediterranean plant with remarkable antioxidant properties, was selected for this study. A management of the process regarding the antioxidant capacity of S. officinalis extracts and energy consumption was carried out: (i) artificial neural networks were applied to model the evolution of the antioxidant capacity and moisture content of the product in the drying process; (ii) a genetic algorithm and a multiobjective genetic algorithm were selected to optimize the drying process, considering the antioxidant capacity and/or the energy consumption in the objective function...
January 1, 2018: Food Science and Technology International, Ciencia y Tecnología de Los Alimentos Internacional
https://www.readbyqxmd.com/read/29493577/mosaic-maternal-10qter-deletions-are-associated-with-fra10b-expansions-and-may-cause-false-positive-noninvasive-prenatal-screening-results
#14
Karin Huijsdens-van Amsterdam, Roy Straver, Merel C van Maarle, Alida C Knegt, Diane Van Opstal, Frank Sleutels, Dominique Smeets, Erik A Sistermans
PurposeUsing genome-wide noninvasive prenatal screening (NIPS), we detected a 20-megabase specific deletion starting at 10q25 in eight pregnancies. The deletion could not be confirmed by invasive testing. Since all 10(q25→︀qter) deletions started close to the FRA10B fragile site in 10q25, we investigated whether the pregnant women were indeed carriers of FRA10B.MethodsWe performed NIPS analysis for all autosomes using single-read sequencing. Analysis was done with the WISECONDOR algorithm. Culture of blood lymphocytes with bromodeoxyuridine was used to detect FRA10B expansions...
March 1, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29488709/-medical-imaging-in-tumor-precision-medicine-opportunities-and-challenges
#15
Jingjing Xu, Yanbin Tan, Minming Zhang
Tumor precision medicine is an emerging approach for tumor diagnosis, treatment and prevention, which takes account of individual variability of environment, lifestyle and genetic information. Tumor precision medicine is built up on the medical imaging innovations developed during the past decades, including the new hardware, new imaging agents, standardized protocols, image analysis and multimodal imaging fusion technology. Also the development of automated and reproducible analysis algorithm has extracted large amount of information from image-based features...
May 25, 2017: Zhejiang da Xue Xue Bao. Yi Xue Ban, Journal of Zhejiang University. Medical Sciences
https://www.readbyqxmd.com/read/29447154/examining-the-controllability-of-sepsis-using-genetic-algorithms-on-an-agent-based-model-of-systemic-inflammation
#16
Robert Chase Cockrell, Gary An
Sepsis, a manifestation of the body's inflammatory response to injury and infection, has a mortality rate of between 28%-50% and affects approximately 1 million patients annually in the United States. Currently, there are no therapies targeting the cellular/molecular processes driving sepsis that have demonstrated the ability to control this disease process in the clinical setting. We propose that this is in great part due to the considerable heterogeneity of the clinical trajectories that constitute clinical "sepsis," and that determining how this system can be controlled back into a state of health requires the application of concepts drawn from the field of dynamical systems...
February 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29438494/artificial-intelligence-in-drug-combination-therapy
#17
Igor F Tsigelny
Currently, the development of medicines for complex diseases requires the development of combination drug therapies. It is necessary because in many cases, one drug cannot target all necessary points of intervention. For example, in cancer therapy, a physician often meets a patient having a genomic profile including more than five molecular aberrations. Drug combination therapy has been an area of interest for a while, for example the classical work of Loewe devoted to the synergism of drugs was published in 1928-and it is still used in calculations for optimal drug combinations...
February 9, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29397661/the-present-and-future-of-precision-medicine-in-psychiatry-focus-on-clinical-psychopharmacology-of-antidepressants
#18
REVIEW
Alessandro Serretti
Precision medicine is a concept which is recently gaining momentum in all branches of medicine. In particular in psychiatry it is greatly needed given the huge societal costs of psychiatric disorders and given the long time needed to observe benefit from treatments and the response variability. The future will be based on biological determinants, however until such an interesting but still futuristic aim will be reached, at present we may only rely on clinical features to guide our individualized prescription which is currently still frequently based on personal opinion and subjective previous experiences...
February 28, 2018: Clinical Psychopharmacology and Neuroscience: the Official Scientific Journal of the Korean College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/29388949/a-literature-review-at-genome-scale-improving-clinical-variant-assessment
#19
Christopher A Cassa, Daniel M Jordan, Ivan Adzhubei, Shamil Sunyaev
PurposeOver 150,000 variants have been reported to cause Mendelian disease in the medical literature. It is still difficult to leverage this knowledge base in clinical practice, as many reports lack strong statistical evidence or may include false associations. Clinical laboratories assess whether these variants (along with newly observed variants that are adjacent to these published ones) underlie clinical disorders.MethodsWe investigated whether citation data-including journal impact factor and the number of cited variants (NCV) in each gene with published disease associations-can be used to improve variant assessment...
February 1, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29379313/a-prospective-longitudinal-study-to-evaluate-the-clinical-utility-of-a-predictive-algorithm-that-detects-risk-of-opioid-use-disorder
#20
Ashley Brenton, Chee Lee, Katrina Lewis, Maneesh Sharma, Svetlana Kantorovich, Gregory A Smith, Brian Meshkin
Purpose: The purpose of this study was to determine the clinical utility of an algorithm-based decision tool designed to assess risk associated with opioid use. Specifically, we sought to assess how physicians were using the profile in patient care and how its use affected patient outcomes. Patients and methods: A prospective, longitudinal study was conducted to assess the utility of precision medicine testing in 5,397 patients across 100 clinics in the USA. Using a patent-protected, validated algorithm combining specific genetic risk factors with phenotypic traits, patients were categorized into low-, moderate-, and high-risk patients for opioid abuse...
2018: Journal of Pain Research
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