keyword
MENU ▼
Read by QxMD icon Read
search

Genetic algorithm

keyword
https://www.readbyqxmd.com/read/27913608/the-clinical-utility-of-circulating-neuroendocrine-gene-transcript-analysis-in-well-differentiated-paragangliomas-and-pheochromocytomas
#1
M Pęczkowska, J Cwikla, M Kidd, A Lewczuk, A Kolasinska-Ćwikła, D Niec, I Michałowska, A Prejbisz, A Januszewicz, J Chiarelli, L Bodei, I Modlin
CONTEXT: Paragangliomas and pheochromocytomas (PPGLs) exhibit variable malignancy, which is difficult to determine by histopathology, amine measurements or tissue genetic analyses. OBJECTIVE: To evaluate whether a 51-neuroendocrine gene blood analysis has clinical utility as a diagnostic and prognostic marker. DESIGN: Prospective cohort study. Well-differentiated PPGLs (n = 32), metastatic (n = 4); SDHx mutation (n = 25); 12 biochemically active, Lanreotide treated (n = 4)...
February 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/27913546/diagnosing-von-willebrand-disease-genetic-analysis
#2
Anne Goodeve
Investigation of a patient with possible von Willebrand disease (VWD) includes a range of phenotypic analyses. Often, this is sufficient to discern disease type, and this will suggest relevant treatment. However, for some patients, phenotypic analysis does not sufficiently explain the patient's disorder, and for this group, genetic analysis can aid diagnosis of disease type. Polymerase chain reaction and Sanger sequencing have been mainstays of genetic analysis for several years. More recently, next-generation sequencing has become available, with the advantage that several genes can be simultaneously analyzed where necessary, eg, for discrimination of possible type 2N VWD or mild hemophilia A...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27912835/second-line-chemotherapy-and-beyond-for-non-small-cell-lung-cancer
#3
REVIEW
Greg Durm, Nasser Hanna
The landscape for the second- and third-line treatment of advanced non-small cell lung cancer has changed dramatically over the last two decades. Immunotherapeutic agents have become a preferred choice following progression on platinum-based first-line chemotherapy. However, there remains a role for cytotoxic chemotherapy and pemetrexed and docetaxel (with or without ramucirumab) are approved for single-agent use in the second-line setting. With the discovery of new genetic alterations and the development of novel targeted drugs, the treatment of advanced non-small cell lung cancer following progression on first-line therapy continues to become more complicated as new treatment algorithms evolve...
February 2017: Hematology/oncology Clinics of North America
https://www.readbyqxmd.com/read/27911939/a-new-model-for-solving-time-cost-quality-trade-off-problems-in-construction
#4
Fang Fu, Tao Zhang
A poor quality affects project makespan and its total costs negatively, but it can be recovered by repair works during construction. We construct a new non-linear programming model based on the classic multi-mode resource constrained project scheduling problem considering repair works. In order to obtain satisfactory quality without a high increase of project cost, the objective is to minimize total quality cost which consists of the prevention cost and failure cost according to Quality-Cost Analysis. A binary dependent normal distribution function is adopted to describe the activity quality; Cumulative quality is defined to determine whether to initiate repair works, according to the different relationships among activity qualities, namely, the coordinative and precedence relationship...
2016: PloS One
https://www.readbyqxmd.com/read/27911912/comprehensive-genetic-analysis-of-japanese-autosomal-dominant-sensorineural-hearing-loss-patients
#5
Yoh-Ichiro Iwasa, Shin-Ya Nishio, Shin-Ichi Usami
BACKGROUND: In general, autosomal dominant inherited hearing loss does not have a founder mutation, with the causative mutation different in each family. For this reason, there has been a strong need for efficient diagnosis methods for autosomal dominant sensorineural hearing loss (ADSNHL) patients. This study sought to verify the effectiveness of our analysis algorithm for the screening of ADSNHL patients as well as the usefulness of the massively parallel DNA sequencing (MPS). SUBJECTS AND METHODS: Seventy-five Japanese ADSNHL patients from 53 ENT departments nationwide participated in this study...
2016: PloS One
https://www.readbyqxmd.com/read/27909940/enhancement-of-rapamycin-production-by-metabolic-engineering-in-streptomyces-hygroscopicus-based-on-genome-scale-metabolic-model
#6
Lanqing Dang, Jiao Liu, Cheng Wang, Huanhuan Liu, Jianping Wen
Rapamycin, as a macrocyclic polyketide with immunosuppressive, antifungal, and anti-tumor activity produced by Streptomyces hygroscopicus, is receiving considerable attention for its significant contribution in medical field. However, the production capacity of the wild strain is very low. Hereby, a computational guided engineering approach was proposed to improve the capability of rapamycin production. First, a genome-scale metabolic model of Streptomyces hygroscopicus ATCC 29253 was constructed based on its annotated genome and biochemical information...
December 1, 2016: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/27908705/a-novel-method-for-in-silico-identification-of-regulatory-snps-in-human-genome
#7
Rong Li, Dexing Zhong, Ruiling Liu, Hongqiang Lv, Xinman Zhang, Jun Liu, Jiuqiang Han
Regulatory single nucleotide polymorphisms (rSNPs), kind of functional noncoding genetic variants, can affect gene expression in a regulatory way, and they are thought to be associated with increased susceptibilities to complex diseases. Here a novel computational approach to identify potential rSNPs is presented. Different from most other rSNPs finding methods which based on hypothesis that SNPs causing large allele-specific changes in transcription factor binding affinities are more likely to play regulatory functions, we use a set of documented experimentally verified rSNPs and nonfunctional background SNPs to train classifiers, so the discriminating features are found...
November 28, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27908164/comparison-of-low-contrast-detectability-between-two-ct-reconstruction-algorithms-using-voxel-based-3d-printed-textured-phantoms
#8
Justin Solomon, Alexandre Ba, François Bochud, Ehsan Samei
PURPOSE: To use novel voxel-based 3D printed textured phantoms in order to compare low-contrast detectability between two reconstruction algorithms, FBP (filtered-backprojection) and SAFIRE (sinogram affirmed iterative reconstruction) and determine what impact background texture (i.e., anatomical noise) has on estimating the dose reduction potential of SAFIRE. METHODS: Liver volumes were segmented from 23 abdominal CT cases. The volumes were characterized in terms of texture features from gray-level co-occurrence and run-length matrices...
December 2016: Medical Physics
https://www.readbyqxmd.com/read/27907163/bi-objective-flexible-job-shop-scheduling-problem-considering-energy-consumption-under-stochastic-processing-times
#9
Xin Yang, Zhenxiang Zeng, Ruidong Wang, Xueshan Sun
This paper presents a novel method on the optimization of bi-objective Flexible Job-shop Scheduling Problem (FJSP) under stochastic processing times. The robust counterpart model and the Non-dominated Sorting Genetic Algorithm II (NSGA-II) are used to solve the bi-objective FJSP with consideration of the completion time and the total energy consumption under stochastic processing times. The case study on GM Corporation verifies that the NSGA-II used in this paper is effective and has advantages to solve the proposed model comparing with HPSO and PSO+SA...
2016: PloS One
https://www.readbyqxmd.com/read/27906637/prevalence-of-urat1-allelic-variants-in-the-roma-population
#10
Blanka Stiburkova, Dana Gabrikova, Pavel Čepek, Pavel Šimek, Pavol Kristian, Elizabeth Cordoba-Lanus, Felix Claverie-Martin
The Roma represents a transnational ethnic group, with a current European population of 8-10 million. The evolutionary process that had the greatest impact on the gene pool of the Roma population is called the founder effect. Renal hypouricemia (RHUC) is a rare heterogenous inherited disorder characterized by impaired renal urate reabsorption. The affected individuals are predisposed to recurrent episodes of exercise-induced nonmyoglobinuric acute kidney injury and nephrolithiasis. To date, more than 150 patients with a loss-of-function mutation for the SLC22A12 (URAT1) gene have been found, most of whom are Asians...
December 2016: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/27903825/synthetic-biology-routes-to-bio-artificial-intelligence
#11
REVIEW
Darren N Nesbeth, Alexey Zaikin, Yasushi Saka, M Carmen Romano, Claudiu V Giuraniuc, Oleg Kanakov, Tetyana Laptyeva
The design of synthetic gene networks (SGNs) has advanced to the extent that novel genetic circuits are now being tested for their ability to recapitulate archetypal learning behaviours first defined in the fields of machine and animal learning. Here, we discuss the biological implementation of a perceptron algorithm for linear classification of input data. An expansion of this biological design that encompasses cellular 'teachers' and 'students' is also examined. We also discuss implementation of Pavlovian associative learning using SGNs and present an example of such a scheme and in silico simulation of its performance...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903644/a-reference-data-set-of-5-4-million-phased-human-variants-validated-by-genetic-inheritance-from-sequencing-a-three-generation-17-member-pedigree
#12
Michael A Eberle, Epameinondas Fritzilas, Peter Krusche, Morten Källberg, Benjamin L Moore, Mitchell A Bekritsky, Zamin Iqbal, Han-Yu Chuang, Sean J Humphray, Aaron L Halpern, Semyon Kruglyak, Elliott H Margulies, Gil McVean, David R Bentley
Improvement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalog of high-confidence variants called in a set of genomes for use as a benchmark. We generated deep, whole-genome sequence data of 17 individuals in a three-generation pedigree and called variants in each genome using a range of currently available algorithms. We used haplotype transmission information to create a phased "Platinum" variant catalog of 4.7 million single-nucleotide variants (SNVs) plus 0...
November 30, 2016: Genome Research
https://www.readbyqxmd.com/read/27902751/exploration-of-a-polygenic-risk-score-for-alcohol-consumption-a-longitudinal-analysis-from-the-alspac-cohort
#13
Michelle Taylor, Andrew J Simpkin, Philip C Haycock, Frank Dudbridge, Luisa Zuccolo
BACKGROUND: Uncertainty remains about the true extent by which alcohol consumption causes a number of health outcomes. Genetic variants, or combinations of variants built into a polygenic risk score (PGRS), can be used in an instrumental variable framework to assess causality between a phenotype and disease outcome of interest, a method known as Mendelian randomisation (MR). We aimed to identify genetic variants involved in the aetiology of alcohol consumption, and develop a PGRS for alcohol...
2016: PloS One
https://www.readbyqxmd.com/read/27901606/protein-folding-prediction-in-a-cubic-lattice-in-hydrophobic-polar-model
#14
Nicola Yanev, Metodi Traykov, Peter Milanov, Borislav Yurukov
The tertiary structure of the proteins determines their functions. Therefore, the predicting of protein's tertiary structure, based on the primary amino acid sequence from long time, is the most important and challenging subject in biochemistry, molecular biology, and biophysics. One of the most popular protein structure prediction methods, called Hydrophobic-Polar (HP) model, is based on the observation that in polar environment hydrophobic amino acids are in the core of the molecule-in contact between them and more polar amino acids are in contact with the polar environment...
November 30, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27899693/performance-testing-of-rreb1-myb-and-ccnd1-fluorescence-in-situ-hybridization-in-spindle-cell-and-desmoplastic-melanoma-argues-for-a-two-step-test-algorithm
#15
Stephanie E Weissinger, Manfred Frick, Peter Möller, Basil A Horst, Jochen K Lennerz
Background Diagnostic confirmation of spindle-cell melanoma (SM) or desmoplastic melanoma (DM) as a melanoma can be challenging. In conventional melanoma (CM), a recently established fluorescence in situ hybridization (FISH) assay for RREB1, MYB, CCND1 can be helpful. Here, we determined the presence of RREB1, MYB, and CCND1 abnormalities in an SM/DM/mixed cohort. Methods We assembled 49 cases and performed 3 separate hybridizations for RREB1/MYB/CCND1 We assessed clinical utility in diagnostically challenging cases and performed a cost and turnaround time analysis...
November 29, 2016: International Journal of Surgical Pathology
https://www.readbyqxmd.com/read/27899610/malacards-an-amalgamated-human-disease-compendium-with-diverse-clinical-and-genetic-annotation-and-structured-search
#16
Noa Rappaport, Michal Twik, Inbar Plaschkes, Ron Nudel, Tsippi Iny Stein, Jacob Levitt, Moran Gershoni, C Paul Morrey, Marilyn Safran, Doron Lancet
The MalaCards human disease database (http://www.malacards.org/) is an integrated compendium of annotated diseases mined from 68 data sources. MalaCards has a web card for each of ∼20 000 disease entries, in six global categories. It portrays a broad array of annotation topics in 15 sections, including Summaries, Symptoms, Anatomical Context, Drugs, Genetic Tests, Variations and Publications. The Aliases and Classifications section reflects an algorithm for disease name integration across often-conflicting sources, providing effective annotation consolidation...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899595/panther-version-11-expanded-annotation-data-from-gene-ontology-and-reactome-pathways-and-data-analysis-tool-enhancements
#17
Huaiyu Mi, Xiaosong Huang, Anushya Muruganujan, Haiming Tang, Caitlin Mills, Diane Kang, Paul D Thomas
The PANTHER database (Protein ANalysis THrough Evolutionary Relationships, http://pantherdb.org) contains comprehensive information on the evolution and function of protein-coding genes from 104 completely sequenced genomes. PANTHER software tools allow users to classify new protein sequences, and to analyze gene lists obtained from large-scale genomics experiments. In the past year, major improvements include a large expansion of classification information available in PANTHER, as well as significant enhancements to the analysis tools...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898940/technical-note-a-successive-over-relaxation-preconditioner-to-solve-mixed-model-equations-for-genetic-evaluation
#18
K Meyer
A computationally efficient preconditioned conjugate gradient algorithm with a symmetric successive over-relaxation (SSOR) preconditioner for the iterative solution of set mixed model equations is described. The potential computational savings of this approach are examined for an example of single-step genomic evaluation of Australian sheep. Results show that the SSOR preconditioner can substantially reduce the number of iterates required for solutions to converge compared with simpler preconditioners with marked reductions in overall computing time...
November 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27898842/inferring-phenotypic-causal-structures-among-meat-quality-traits-and-the-application-of-a-structural-equation-model-in-japanese-black-cattle
#19
K Inoue, B D Valente, N Shoji, T Honda, K Oyama, G J M Rosa
Meat quality is one of the most important traits determining carcass price in the Japanese beef market. Optimized breeding goals and management practices for the improvement of meat quality traits requires knowledge regarding any potential functional relationships between them. In this context, the objective of this research was to infer phenotypic causal networks involving beef marbling score (BMS), beef color score (BCL), firmness of beef (FIR), texture of beef (TEX), beef fat color score (BFS), and the ratio of MUFA to SFA (MUS) from 11,855 Japanese Black cattle...
October 2016: Journal of Animal Science
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
keyword
keyword
88549
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"