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Genetic algorithms in medicine

Lukmaan A Bawazer, Ciara S McNally, Christopher J Empson, William J Marchant, Tim P Comyn, Xize Niu, Soongwon Cho, Michael J McPherson, Bernard P Binks, Andrew deMello, Fiona C Meldrum
Although droplet-based systems are used in a wide range of technologies, opportunities for systematically customizing their interface chemistries remain relatively unexplored. This article describes a new microfluidic strategy for rapidly tailoring emulsion droplet compositions and properties. The approach uses a simple platform for screening arrays of droplet-based microfluidic devices and couples this with combinatorial selection of the droplet compositions. Through the application of genetic algorithms over multiple screening rounds, droplets with target properties can be rapidly generated...
October 2016: Science Advances
Cagin Kandemir-Cavas, Levent Cavas, Hakan Alyuruk
There is a great need for development of educational materials on the transfer of current bioinformatics knowledge to undergraduate students in bioscience departments. In this study, it is aimed to prepare an example in silico laboratory tutorial on the topology prediction of membrane proteins by bioinformatics tools. This laboratory tutorial is prepared for biochemistry lessons at bioscience departments (biology, chemistry, biochemistry, molecular biology and genetics, and faculty of medicine). The tutorial is intended for students who have not taken a bioinformatics course yet or already have taken a course as an introduction to bioinformatics...
October 7, 2016: Interdisciplinary Sciences, Computational Life Sciences
Adeyemi Ojutalayo Adeeyo, Agbaje Lateef, Evariste Bosco Gueguim-Kana
Exopolysaccharide (EPS) production by a strain of Lentinus edodes was studied via the effects of treatments with ultraviolet (UV) irradiation and acridine orange. Furthermore, optimization of EPS production was studied using a genetic algorithm coupled with an artificial neural network in submerged fermentation. Exposure to irradiation and acridine orange resulted in improved EPS production (2.783 and 5.548 g/L, respectively) when compared with the wild strain (1.044 g/L), whereas optimization led to improved productivity (23...
2016: International Journal of Medicinal Mushrooms
Zhongwei Li, Beibei Sun, Yuezhen Xin, Xun Wang, Hu Zhu
Flavones, the secondary metabolites of Phellinus igniarius fungus, have the properties of antioxidation and anticancer. Because of the great medicinal value, there are large demands on flavones for medical use and research. Flavones abstracted from natural Phellinus can not meet the medical and research need, since Phellinus in the natural environment is very rare and is hard to be cultivated artificially. The production of flavones is mainly related to the fermentation culture of Phellinus, which made the optimization of culture conditions an important problem...
2016: BioMed Research International
Ying-Wooi Wan, Genevera I Allen, Yulia Baker, Eunho Yang, Pradeep Ravikumar, Matthew Anderson, Zhandong Liu
BACKGROUND: Technological advances in medicine have led to a rapid proliferation of high-throughput "omics" data. Tools to mine this data and discover disrupted disease networks are needed as they hold the key to understanding complicated interactions between genes, mutations and aberrations, and epi-genetic markers. RESULTS: We developed an R software package, XMRF, that can be used to fit Markov Networks to various types of high-throughput genomics data. Encoding the models and estimation techniques of the recently proposed exponential family Markov Random Fields (Yang et al...
2016: BMC Systems Biology
M Sandeva, E Uchikova
Premature birth (PB) remains an unresolved problem, despite progress in prenatal medicine and the introduction of new methods and techniques of prolonged respiratory resuscitation in recent decades. Premature birth is the cause of 70% of neonatal mortality and 50% of long-term neurological complications in newborns, many of whom debilitating. Notwithstanding the significant progress prenatal care in the last twenty years in developed countries is a trend towards a gradual and continuous increase in premature births...
2016: Akusherstvo i Ginekologii︠a︡
Ying Wang, Ce Shi, Jin-Yan Liu, Wen-Jing Li, Yue Zhao, Ming-Jie Xiang
To explore the putative correlation between the multilocus sequence types (MLST) and antifungal susceptibility of clinical Candida tropicalis isolates in Mainland China. Eighty-two clinical C. tropicalis isolates were collected from sixty-nine patients at Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, from July 2012 to February 2015, and antifungal susceptibility tests were performed. Genetic profiles of those 82 isolates (30 azole-resistant and 52 azole-susceptible) were characterised by multilocus sequence typing...
October 2016: Infection, Genetics and Evolution
S Bek, J V Nielsen, A B Bojesen, A Franke, S Bank, U Vogel, V Andersen
BACKGROUND: Personalised medicine, including biomarkers for treatment selection, may provide new algorithms for more effective treatment of patients. Genetic variation may impact drug response and genetic markers could help selecting the best treatment strategy for the individual patient. AIM: To identify polymorphisms and candidate genes from the literature that are associated with anti-tumour necrosis factor (TNF) treatment response in patients with inflammatory bowel diseases (IBD), Crohn's disease (CD) and ulcerative colitis...
September 2016: Alimentary Pharmacology & Therapeutics
Mihai V Putz, Corina Duda-Seiman, Daniel Duda-Seiman, Ana-Maria Putz, Iulia Alexandrescu, Maria Mernea, Speranta Avram
Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners' (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions...
2016: International Journal of Molecular Sciences
Ruifang Sun, L Jeffrey Medeiros, Ken H Young
Lymphomas are a group of hematological malignancies derived from lymphocytes. Lymphomas are clinically and biologically heterogeneous and have overlapping diagnostic features. With the advance of new technologies and the application of efficient and feasible detection platforms, an unprecedented number of novel biomarkers have been discovered or are under investigation at the genetic, epigenetic, and protein level as well as the tumor microenvironment. These biomarkers have enabled new clinical and pathological insights into the mechanisms underlying lymphomagenesis and also have facilitated improvements in the diagnostic workup, sub-classification, outcome stratification, and personalized therapy for lymphoma patients...
October 2016: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
Yulan Liang, Arpad Kelemen
Construction of gene-gene interaction networks and potential pathways is a challenging and important problem in genomic research for complex diseases while estimating the dynamic changes of the temporal correlations and non-stationarity are the keys in this process. In this paper, we develop dynamic state space models with hierarchical Bayesian settings to tackle this challenge for inferring the dynamic profiles and genetic networks associated with disease treatments. We treat both the stochastic transition matrix and the observation matrix time-variant and include temporal correlation structures in the covariance matrix estimations in the multivariate Bayesian state space models...
August 1, 2016: Statistical Applications in Genetics and Molecular Biology
M Kotze
BACKGROUND: Genetic testing has evolved from a niche speciality for diagnosis of rare disorders and carrier screening to subtyping of complex medical conditions for targeted treatment. Genes causing monogenic disorders are well characterised, but risk management of multifactorial and polygenic disorders guided from the genetic background remains a challenge. Objective. This study describes the use of a pathology-supported genetic testing (PSGT) strategy designed to facilitate the move from single- to multi-gene testing and next-generation sequencing (NGS)...
June 2016: South African Medical Journal, Suid-Afrikaanse Tydskrif Vir Geneeskunde
Yuan-zhong Wang, Yan-li Zhao, Ji Zhang, Hang Jin
Medicinal and edible plant Maca is rich in various nutrients and owns great medicinal value. Based on near infrared diffuse reflectance spectra, 139 Maca samples collected from Peru and Yunnan were used to identify their geographical origins. Multiplication signal correction (MSC) coupled with second derivative (SD) and Norris derivative filter (ND) was employed in spectral pretreatment. Spectrum range (7,500-4,061 cm⁻¹) was chosen by spectrum standard deviation. Combined with principal component analysis-mahalanobis distance (PCA-MD), the appropriate number of principal components was selected as 5...
February 2016: Guang Pu Xue Yu Guang Pu Fen Xi, Guang Pu
Hongyan Li, Bingjian Feng, Alexander Miron, Xiaoqing Chen, Jonathan Beesley, Emmanuella Bimeh, Daniel Barrowdale, Esther M John, Mary B Daly, Irene L Andrulis, Saundra S Buys, Peter Kraft, Heather Thorne, Georgia Chenevix-Trench, Melissa C Southey, Antonis C Antoniou, Paul A James, Mary Beth Terry, Kelly-Anne Phillips, John L Hopper, Gillian Mitchell, David E Goldgar
PURPOSE: This study examined the utility of sets of single-nucleotide polymorphisms (SNPs) in familial but non-BRCA-associated breast cancer (BC). METHODS: We derived a polygenic risk score (PRS) based on 24 known BC risk SNPs for 4,365 women from the Breast Cancer Family Registry and Kathleen Cuningham Consortium Foundation for Research into Familial Breast Cancer familial BC cohorts. We compared scores for women based on cancer status at baseline; 2,599 women unaffected at enrollment were followed-up for an average of 7...
May 12, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Ruowang Li, Scott M Dudek, Dokyoon Kim, Molly A Hall, Yuki Bradford, Peggy L Peissig, Murray H Brilliant, James G Linneman, Catherine A McCarty, Le Bao, Marylyn D Ritchie
BACKGROUND: The future of medicine is moving towards the phase of precision medicine, with the goal to prevent and treat diseases by taking inter-individual variability into account. A large part of the variability lies in our genetic makeup. With the fast paced improvement of high-throughput methods for genome sequencing, a tremendous amount of genetics data have already been generated. The next hurdle for precision medicine is to have sufficient computational tools for analyzing large sets of data...
2016: BioData Mining
Lynn Pique, Steve Graham, Michelle Pearl, Martin Kharrazi, Iris Schrijver
PURPOSE: Cystic fibrosis newborn screening (CFNBS) has been offered across the United States since 2010. However, as compared with white patients with CF, CFTR variant identification in nonwhite populations remains inequitable. Utilizing the recent characterization of the nonwhite CF variant spectrum, we examined the effectiveness of current CFNBS molecular panels in identifying affected nonwhite newborns. METHODS: Based on a cross-sectional evaluation of genotyping data from the CF Foundation Patient Registry that compared 3,496 nonwhite with 22,206 white CF patients, the current CFNBS algorithms used in the 50 states and the District of Columbia were analyzed...
May 5, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Chen-An Tsai, Kuan-Ting Lee, Jen-Pei Liu
A key feature of precision medicine is that it takes individual variability at the genetic or molecular level into account in determining the best treatment for patients diagnosed with diseases detected by recently developed novel biotechnologies. The enrichment design is an efficient design that enrolls only the patients testing positive for specific molecular targets and randomly assigns them for the targeted treatment or the concurrent control. However there is no diagnostic device with perfect accuracy and precision for detecting molecular targets...
2016: PloS One
Donato Rigante, Bruno Frediani, Luca Cantarini
Innate immunity is a critical partner in the regulation of inflammation and some mutations in genes implied in innate immunity pathways can cause genetic disorders characterized by seemingly unprovoked self-limited inflammatory attacks. These rare conditions are collectively named "hereditary periodic fever syndromes" (HPFS), and protean pathogenetic mechanisms combined with several clinical phenotypes characterize at least four distinct conditions: (1) familial Mediterranean fever, which is the prototype and the most widely recognized among HPFS, inherited as an autosomal recessive disorder showing recurrent dysregulated inflammatory processes, caused by an abnormal interaction between cytoskeleton and inflammasome, a key-signaling platform that releases interleukin-1β (IL-1β); (2) the group of cryopyrin-associated periodic syndrome, which upsets directly the production of IL-1β, with a dominant pattern of inheritance; (3) tumor necrosis factor receptor-associated periodic syndrome, which is an autosomal dominant disorder subverting the functions and traffic of a cell membrane protein; and (4) mevalonate kinase deficiency, which is an autosomal recessive metabolic disorder halting the biosynthesis of cholesterol...
April 11, 2016: Clinical Reviews in Allergy & Immunology
Smaranda Belciug, Florin Gorunescu
PURPOSE: Explore how efficient intelligent decision support systems, both easily understandable and straightforwardly implemented, can help modern hospital managers to optimize both bed occupancy and utilization costs. METHODS AND MATERIALS: This paper proposes a hybrid genetic algorithm-queuing multi-compartment model for the patient flow in hospitals. A finite capacity queuing model with phase-type service distribution is combined with a compartmental model, and an associated cost model is set up...
March 2016: Artificial Intelligence in Medicine
Peng Hu, Ming-Hua Hsieh, Ming-Jie Lei, Bin Cui, Sung-Kay Chiu, Chi-Meng Tzeng
A single-nucleotide polymorphism (SNP) is a variation in the DNA sequence that occurs when a single nucleotide in the genome differs across members of the same species. Variations in the DNA sequences of humans are associated with human diseases. This makes SNPs as a key to open up the door of personalized medicine. SNP(s) can also be used for human identification and forensic applications. Compared to short tandem repeat (STR) loci, SNPs have much lower statistical testing power for individual recognition due to the fact that there are only 3 possible genotypes for each SNP marker, but it may provide sufficient information to identify the population to which a certain samples may belong...
2016: Scientific Reports
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