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Genetic algorithms in medicine

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https://www.readbyqxmd.com/read/28444439/back-to-the-future-part-2-post-mortem-assessment-and-evolutionary-role-of-the-bio-medicolegal-sciences
#1
REVIEW
Santo Davide Ferrara, Giovanni Cecchetto, Rossana Cecchi, Donata Favretto, Silke Grabherr, Takaki Ishikawa, Toshikazu Kondo, Massimo Montisci, Heidi Pfeiffer, Maurizio Rippa Bonati, Dina Shokry, Marielle Vennemann, Thomas Bajanowski
Part 2 of the review "Back to the Future" is dedicated to the evolutionary role of the bio-medicolegal sciences, reporting the historical profiles, the state of the art, and prospects for future development of the main related techniques and methods of the ancillary disciplines that have risen to the role of "autonomous" sciences, namely, Genetics and Genomics, Toxicology, Radiology, and Imaging, involved in historic synergy in the "post-mortem assessment," together with the mother discipline Legal Medicine, by way of its primary fundament, universally denominated as Forensic Pathology...
April 25, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28439010/cyclops-reveals-human-transcriptional-rhythms-in-health-and-disease
#2
Ron C Anafi, Lauren J Francey, John B Hogenesch, Junhyong Kim
Circadian rhythms modulate many aspects of physiology. Knowledge of the molecular basis of these rhythms has exploded in the last 20 years. However, most of these data are from model organisms, and translation to clinical practice has been limited. Here, we present an approach to identify molecular rhythms in humans from thousands of unordered expression measurements. Our algorithm, cyclic ordering by periodic structure (CYCLOPS), uses evolutionary conservation and machine learning to identify elliptical structure in high-dimensional data...
April 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28431171/heritability-of-heart-rate-response-to-arousals-in-twins
#3
Xiaoling Gao, Ali Azarbarzin, Brendan T Keenan, Michele Ostrowski, Frances M Pack, Bethany Staley, Greg Maislin, Allan I Pack, Magdy Younes, Samuel T Kuna
Objectives: To determine if the large and highly reproducible inter-individual differences in arousal intensity and heart rate response to arousal (ΔHR) during non-REM sleep are heritable. Methods: Polysomnograms of 55 monozygotic (14 male and 41 female pairs) and 36 dizygotic (15 male and 21 female pairs) same-sex twin pairs were analyzed. Arousals were scored using the 2012 American Academy of Sleep Medicine criteria. Arousal intensity was scaled (between 0 and 9) using an automatic algorithm based on the change in EEG time and frequency characteristics...
April 18, 2017: Sleep
https://www.readbyqxmd.com/read/28399500/on-line-monitoring-of-extraction-process-of-flos-lonicerae-japonicae-using-near-infrared-spectroscopy-combined-with-synergy-interval-pls-and-genetic-algorithm
#4
Yue Yang, Lei Wang, Yongjiang Wu, Xuesong Liu, Yuan Bi, Wei Xiao, Yong Chen
There is a growing need for the effective on-line process monitoring during the manufacture of traditional Chinese medicine to ensure quality consistency. In this study, the potential of near infrared (NIR) spectroscopy technique to monitor the extraction process of Flos Lonicerae Japonicae was investigated. A new algorithm of synergy interval PLS with genetic algorithm (Si-GA-PLS) was proposed for modeling. Four different PLS models, namely Full-PLS, Si-PLS, GA-PLS, and Si-GA-PLS, were established, and their performances in predicting two quality parameters (viz...
April 6, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28357616/prenatal-screening-for-chromosomal-abnormalities-in-ivf-patients-that-opted-for-preimplantation-genetic-screening-diagnosis-pgs-d-a-need-for-revised-algorithms-in-the-era-of-personalized-medicine
#5
Afua Takyi, Joaquin Santolaya-Forgas
Obstetricians offer prenatal screening for most common chromosomal abnormalities to all pregnant women including those that had in vitro fertilization (IVF) and preimplantation genetic screening/diagnosis (PGS/D). We propose that free fetal DNA in maternal circulation together with the second trimester maternal serum alfa feto protein (MSAFP) and ultrasound imaging is the best prenatal screening test for chromosomal abnormalities and congenital anomalies in IVF-PGD/S patients because risk estimations from all other prenatal screening algorithms for chromosomal abnormalities depend heavily on maternal age which is irrelevant in PGS/D patients...
March 29, 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/28333918/21-gene-recurrence-score-testing-among-medicare-beneficiaries-with-breast-cancer-in-2010-2013
#6
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/28327571/insights-from-early-experience-of-a-rare-disease-genomic-medicine-multidisciplinary-team-a-qualitative-study
#7
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
https://www.readbyqxmd.com/read/28293716/-diagnostics-in-human-genetics-integration-of-phenotypic-and-genomic-data
#8
Sebastian Köhler, Peter N Robinson
The development of reliable methods for annotation of clinical phenotypes and algorithms to calculate similarity values for clinical phenotype profiles will be a major challenge for genomic personalized medicine, since combined analysis of phenotypic features and genetic variants can increase diagnostic yield, especially with exome or genome sequencing. The Human Phenotype Ontology project (HPO; www.human-phenotype-ontology.org ) provides an ontology for capturing phenotypic abnormalities in human disease in a precise and comprehensive fashion...
March 14, 2017: Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz
https://www.readbyqxmd.com/read/28257413/uncovering-precision-phenotype-biomarker-associations-in-traumatic-brain-injury-using-topological-data-analysis
#9
Jessica L Nielson, Shelly R Cooper, John K Yue, Marco D Sorani, Tomoo Inoue, Esther L Yuh, Pratik Mukherjee, Tanya C Petrossian, Jesse Paquette, Pek Y Lum, Gunnar E Carlsson, Mary J Vassar, Hester F Lingsma, Wayne A Gordon, Alex B Valadka, David O Okonkwo, Geoffrey T Manley, Adam R Ferguson
BACKGROUND: Traumatic brain injury (TBI) is a complex disorder that is traditionally stratified based on clinical signs and symptoms. Recent imaging and molecular biomarker innovations provide unprecedented opportunities for improved TBI precision medicine, incorporating patho-anatomical and molecular mechanisms. Complete integration of these diverse data for TBI diagnosis and patient stratification remains an unmet challenge. METHODS AND FINDINGS: The Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Pilot multicenter study enrolled 586 acute TBI patients and collected diverse common data elements (TBI-CDEs) across the study population, including imaging, genetics, and clinical outcomes...
2017: PloS One
https://www.readbyqxmd.com/read/28257315/personalized-medicine-and-chronic-obstructive-pulmonary-disease
#10
E F M Wouters, B B R A F Wouters, I M L Augustin, F M E Franssen
PURPOSE OF REVIEW: The current review summarizes ongoing developments in personalized medicine and precision medicine in chronic obstructive pulmonary disease (COPD). Our current approach is far away of personalized management algorithms as current recommendations for COPD are largely based on a reductionist disease description, operationally defined by results of spirometry. RECENT FINDINGS: Besides precision medicine developments, a personalized medicine approach in COPD is described based on a holistic approach of the patient and considering illness as the consequence of dynamic interactions within and between multiple interacting and self-adjusting systems...
May 2017: Current Opinion in Pulmonary Medicine
https://www.readbyqxmd.com/read/28198728/personalized-medicine-in-interstitial-lung-diseases
#11
Paolo Spagnolo, Justin M Oldham, Mark G Jones, Joyce S Lee
PURPOSE OF REVIEW: A number of recent studies have explored the possibility to apply personalized medicine to interstitial lung diseases (ILDs), particularly idiopathic pulmonary fibrosis (IPF), the most common and deadly of the idiopathic interstitial pneumonias. In our review, we summarize and discuss the most recent literature on personalized medicine in IPF as well as hypersensitivity pneumonitis and sarcoidosis, with emphasis on patient subgroups for which a personalized approach to disease prognostication and management may become a reality in the near future...
May 2017: Current Opinion in Pulmonary Medicine
https://www.readbyqxmd.com/read/28198666/design-connecting-gene-expression-with-therapeutics-for-drug-repurposing-and-development
#12
Bernard Kok Bang Lee, Kai Hung Tiong, Jit Kang Chang, Chee Sun Liew, Zainal Ariff Abdul Rahman, Aik Choon Tan, Tsung Fei Khang, Sok Ching Cheong
BACKGROUND: The drug discovery and development pipeline is a long and arduous process that inevitably hampers rapid drug development. Therefore, strategies to improve the efficiency of drug development are urgently needed to enable effective drugs to enter the clinic. Precision medicine has demonstrated that genetic features of cancer cells can be used for predicting drug response, and emerging evidence suggest that gene-drug connections could be predicted more accurately by exploring the cumulative effects of many genes simultaneously...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28197794/therapeutic-options-in-refractory-diabetic-macular-oedema
#13
Sanket U Shah, Raj K Maturi
Diabetic macular oedema (DMO) results from alterations of several biochemical pathways in diabetic eyes. Centre-involving DMO is an important cause of visual loss in diabetes. Anti-vascular endothelial growth factor agents are now the mainstay of centre-involving DMO treatment. Oedema that does not achieve optimal response to these agents occurs in a sizeable proportion of eyes and is called refractory or persistent DMO. Management of refractory DMO is challenging. In this paper, the pathophysiology of DMO, and the definitions used in various studies are summarised...
February 15, 2017: Drugs
https://www.readbyqxmd.com/read/28133611/diagnostic-method-of-diabetes-based-on-support-vector-machine-and-tongue-images
#14
Jianfeng Zhang, Jiatuo Xu, Xiaojuan Hu, Qingguang Chen, Liping Tu, Jingbin Huang, Ji Cui
Objective. The purpose of this research is to develop a diagnostic method of diabetes based on standardized tongue image using support vector machine (SVM). Methods. Tongue images of 296 diabetic subjects and 531 nondiabetic subjects were collected by the TDA-1 digital tongue instrument. Tongue body and tongue coating were separated by the division-merging method and chrominance-threshold method. With extracted color and texture features of the tongue image as input variables, the diagnostic model of diabetes with SVM was trained...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28121178/classification-of-sphingosine-kinase-inhibitors-using-counter-propagation-artificial-neural-networks-a-systematic-route-for-designing-selective-sphk-inhibitors
#15
M S Neiband, A Mani-Varnosfaderani, A Benvidi
Accurate and robust classification models for describing and predicting the activity of 330 chemicals that are sphingosine kinase 1 (SphK1) and/or sphingosine kinase 2 (SphK2) inhibitors were derived. The classification models developed in this work assist in finding selective subspaces in chemical space occupied by particular groups of SphK inhibitors. A combination of a genetic algorithm (GA) and a counter propagation artificial neural network (CPANN) was utilized to select the most efficient subsets of the molecular descriptors...
February 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28117080/genomic-and-clinical-profiling-of-a-national-nephrotic-syndrome-cohort-advocates-a-precision-medicine-approach-to-disease-management
#16
Agnieszka Bierzynska, Hugh J McCarthy, Katrina Soderquest, Ethan S Sen, Elizabeth Colby, Wen Y Ding, Marwa M Nabhan, Larissa Kerecuk, Shivram Hegde, David Hughes, Stephen Marks, Sally Feather, Caroline Jones, Nicholas J A Webb, Milos Ognjanovic, Martin Christian, Rodney D Gilbert, Manish D Sinha, Graham M Lord, Michael Simpson, Ania B Koziell, Gavin I Welsh, Moin A Saleem
Steroid Resistant Nephrotic Syndrome (SRNS) in children and young adults has differing etiologies with monogenic disease accounting for 2.9-30% in selected series. Using whole exome sequencing we sought to stratify a national population of children with SRNS into monogenic and non-monogenic forms, and further define those groups by detailed phenotypic analysis. Pediatric patients with SRNS were identified via a national United Kingdom Renal Registry. Whole exome sequencing was performed on 187 patients, of which 12% have a positive family history with a focus on the 53 genes currently known to be associated with nephrotic syndrome...
April 2017: Kidney International
https://www.readbyqxmd.com/read/28104618/hysa-a-hybrid-structural-variant-assembly-approach-using-next-generation-and-single-molecule-sequencing-technologies
#17
Xian Fan, Mark Chaisson, Luay Nakhleh, Ken Chen
Achieving complete, accurate and cost-effective assembly of human genomes is of great importance for realizing the promise of precision medicine. The abundance of repeats and genetic variations in human genomes and the limitations of existing sequencing technologies call for the development of novel assembly methods that can leverage the complementary strengths of multiple technologies. We propose a hybrid structural variant assembly (HySA) approach that integrates sequencing reads from next-generation sequencing and single-molecule sequencing technologies to accurately assemble and detect structural variations in human genomes...
January 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28056037/accurate-promoter-and-enhancer-identification-in-127-encode-and-roadmap-epigenomics-cell-types-and-tissues-by-genostan
#18
Benedikt Zacher, Margaux Michel, Björn Schwalb, Patrick Cramer, Achim Tresch, Julien Gagneur
Accurate maps of promoters and enhancers are required for understanding transcriptional regulation. Promoters and enhancers are usually mapped by integration of chromatin assays charting histone modifications, DNA accessibility, and transcription factor binding. However, current algorithms are limited by unrealistic data distribution assumptions. Here we propose GenoSTAN (Genomic STate ANnotation), a hidden Markov model overcoming these limitations. We map promoters and enhancers for 127 cell types and tissues from the ENCODE and Roadmap Epigenomics projects, today's largest compendium of chromatin assays...
2017: PloS One
https://www.readbyqxmd.com/read/28031973/life-as-an-early-career-researcher-interview-with-heloisa-helena-milioli
#19
Heloisa Helena Milioli
Heloisa Helena Milioli speaks to Francesca Lake, Managing Editor: Heloisa received a BSc degree in Biological Sciences (2008) from the Universidade Federal de Santa Catarina (Brazil) and obtained a MSc degree in Genetics (2011) from Universidade Federal do Paraná (Brazil). In 2011 and 2012, she worked as a lecturer and tutor in the Department of Cell Biology, Embryology and Genetics (Universidade Federal de Santa Catarina). She moved to Australia in 2012 to obtain her PhD in Biological Sciences, with emphasis on Bioinformatics, from The University of Newcastle...
June 2016: Future Science OA
https://www.readbyqxmd.com/read/27897013/harnessing-big-data-for-precision-medicine-infrastructures-and-applications
#20
Kun-Hsing Yu, Steven N Hart, Rachel Goldfeder, Qiangfeng Cliff Zhang, Stephen C J Parker, Michael Snyder
Precision medicine is a health management approach that accounts for individual differences in genetic backgrounds and environmental exposures. With the recent advancements in high-throughput omics profiling technologies, collections of large study cohorts, and the developments of data mining algorithms, big data in biomedicine is expected to provide novel insights into health and disease states, which can be translated into personalized disease prevention and treatment plans. However, petabytes of biomedical data generated by multiple measurement modalities poses a significant challenge for data analysis, integration, storage, and result interpretation...
2016: Pacific Symposium on Biocomputing
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