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Genetics cross validation

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https://www.readbyqxmd.com/read/28813480/paleogenetic-study-on-the-17th-century-korean-mummy-with-atherosclerotic-cardiovascular-disease
#1
Dong Hoon Shin, Chang Seok Oh, Jong Ha Hong, Yusu Kim, Soong Deok Lee, Eunju Lee
While atherosclerotic cardiovascular disease (ASCVD) is known to be common among modern people exposed to various risk factors, recent paleopathological studies have shown that it affected ancient populations much more frequently than expected. In 2010, we investigated a 17th century Korean female mummy with presumptive ASCVD signs. Although the resulting report was a rare and invaluable conjecture on the disease status of an ancient East Asian population, the diagnosis had been based only on anatomical and radiological techniques, and so could not confirm the existence of ASCVD in the mummy...
2017: PloS One
https://www.readbyqxmd.com/read/28809947/high-density-genetic-linkage-map-construction-by-f2-populations-and-qtl-analysis-of-early-maturity-traits-in-upland-cotton-gossypium-hirsutum-l
#2
Libei Li, Shuqi Zhao, Junji Su, Shuli Fan, Chaoyou Pang, Hengling Wei, Hantao Wang, Lijiao Gu, Chi Zhang, Guoyuan Liu, Dingwei Yu, Qibao Liu, Xianlong Zhang, Shuxun Yu
Due to China's rapidly increasing population, the total arable land area has dramatically decreased; as a consequence, the competition for farming land allocated for grain and cotton production has become fierce. Therefore, to overcome the existing contradiction between cotton grain and fiber production and the limited farming land, development of early-maturing cultivars is necessary. In this research, a high-density linkage map of upland cotton was constructed using genotyping by sequencing (GBS) to discover single nucleotide polymorphism (SNP) markers associated with early maturity in 170 F2 individuals derived from a cross between LU28 and ZHONG213...
2017: PloS One
https://www.readbyqxmd.com/read/28808041/inclusion-of-a-genetic-risk-score-into-a-validated-risk-prediction-model-for-colorectal-cancer-in-japanese-men-improves-performance
#3
Motoki Iwasaki, Sachiko Tanaka-Mizuno, Aya Kuchiba, Taiki Yamaji, Norie Sawada, Atsushi Goto, Taichi Shimazu, Shizuka Sasazuki, Hansong Wang, Loïc Le Marchand, Shoichiro Tsugane
We previously developed and validated a risk prediction model for colorectal cancer in Japanese men using modifiable risk factors. To further improve risk prediction, we evaluated the degree of improvement obtained by adding a genetic risk score (GRS) using genome-wide association study (GWAS)-identified risk variants to our validated model. We examined the association between 36 risk variants identified by GWAS and colorectal cancer risk using a weighted Cox proportional hazards model in a nested case-control study within the Japan Public Health Center-based Prospective Study...
July 20, 2017: Cancer Prevention Research
https://www.readbyqxmd.com/read/28805929/the-impact-of-training-strategies-on-the-accuracy-of-genomic-predictors-in-united-states-red-angus-cattle
#4
J Lee, S D Kachman, M L Spangler
Genomic selection (GS) has become an integral part of genetic evaluation methodology and has been applied to all major livestock species, including beef and dairy cattle, pigs, and chickens. Significant contributions in increased accuracy of selection decisions have been clearly illustrated in dairy cattle after practical application of GS. In the majority of U.S. beef cattle breeds, similar efforts have also been made to increase the accuracy of genetic merit estimates through the inclusion of genomic information into routine genetic evaluations using a variety of methods...
August 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28804937/breast-tumor-classification-based-on-a-computerized-breast-imaging-reporting-and-data-system-feature-system
#5
Mengyun Qiao, Yuzhou Hu, Yi Guo, Yuanyuan Wang, Jinhua Yu
OBJECTIVES: This work focused on extracting novel and validated digital high-throughput features to present a detailed and comprehensive description of the American College of Radiology Breast Imaging Reporting and Data System (BI-RADS) with the goal of improving the accuracy of ultrasound breast cancer diagnosis. METHODS: First, the phase congruency approach was used to segment the tumors automatically. Second, high-throughput features were designed and extracted on the basis of each BI-RADS category...
August 14, 2017: Journal of Ultrasound in Medicine: Official Journal of the American Institute of Ultrasound in Medicine
https://www.readbyqxmd.com/read/28799976/effect-of-gene-gene-and-gene-environment-interactions-associated-with-antituberculosis-drug-induced-hepatotoxicity
#6
Julián G Chamorro, Jorge P Castagnino, Omar Aidar, Rosa M Musella, Ana Frías, Mabel Visca, Mabel Nogueras, Lucas Costa, Alessandro Perez, Fabio Caradonna, Gabriela F de Larrañaga
OBJECTIVES: This study evaluated the association between environmental factors and genetic variations in enzymes that metabolize antituberculosis (anti-TB) drugs [arylamine N-acetyltransferase 2, cytochrome P450 2E1 (CYP2E1), glutathione S-transferase theta 1 (GSTT1), and glutathione S-transferase mu 1] with antituberculosis drug-induced hepatotoxicity (ATDH). We also investigated the potential gene-gene and gene-environment interactions as well as their association with ATDH development in a population of hospitalized TB patients from Buenos Aires...
August 9, 2017: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/28791985/knowledge-of-medical-students-about-epilepsy-need-for-a-change
#7
B A Ezeala-Adikaibe, T Okpara, O S Ekenze, O Onodugo, N P Ezeala-Adikaibe, T Nnaji, G Onyebueke
PURPOSE: Though most doctors in their professional life will provide care for people with epilepsy, many will not get further training in their professional life. There may be other barriers, perceived or not, to providing care to people living with epilepsy by doctors which need to be approached in the medical undergraduate curriculum and medical continuing education. The aim of this study was to determine the knowledge gaps of medical students on basic issues regarding epilepsy that could be useful in preparing training material for the students and continuous medical education for doctors working in the community...
July 2017: Nigerian Journal of Clinical Practice
https://www.readbyqxmd.com/read/28790336/identifying-the-mirna-signature-associated-with-survival-time-in-patients-with-lung-adenocarcinoma-using-mirna-expression-profiles
#8
Srinivasulu Yerukala Sathipati, Shinn-Ying Ho
Lung adenocarcinoma is a multifactorial disease. MicroRNA (miRNA) expression profiles are extensively used for discovering potential theranostic biomarkers of lung cancer. This work proposes an optimized support vector regression (SVR) method called SVR-LUAD to simultaneously identify a set of miRNAs referred to the miRNA signature for estimating the survival time of lung adenocarcinoma patients using their miRNA expression profiles. SVR-LUAD uses an inheritable bi-objective combinatorial genetic algorithm to identify a small set of informative miRNAs cooperating with SVR by maximizing estimation accuracy...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28789690/first-year-medical-students-learning-style-preferences-and-their-correlation-with-performance-in-different-subjects-within-the-medical-course
#9
Daniel Hernández-Torrano, Syed Ali, Chee-Kai Chan
BACKGROUND: Students commencing their medical training arrive with different educational backgrounds and a diverse range of learning experiences. Consequently, students would have developed preferred approaches to acquiring and processing information or learning style preferences. Understanding first-year students' learning style preferences is important to success in learning. However, little is understood about how learning styles impact learning and performance across different subjects within the medical curriculum...
August 8, 2017: BMC Medical Education
https://www.readbyqxmd.com/read/28770015/maternal-blood-contamination-of-collected-cord-blood-can-be-identified-using-dna-methylation-at-three-cpgs
#10
Alexander M Morin, Evan Gatev, Lisa M McEwen, Julia L MacIsaac, David T S Lin, Nastassja Koen, Darina Czamara, Katri Räikkönen, Heather J Zar, Karestan Koenen, Dan J Stein, Michael S Kobor, Meaghan J Jones
BACKGROUND: Cord blood is a commonly used tissue in environmental, genetic, and epigenetic population studies due to its ready availability and potential to inform on a sensitive period of human development. However, the introduction of maternal blood during labor or cross-contamination during sample collection may complicate downstream analyses. After discovering maternal contamination of cord blood in a cohort study of 150 neonates using Illumina 450K DNA methylation (DNAm) data, we used a combination of linear regression and random forest machine learning to create a DNAm-based screening method...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28757654/predicting-triple-negative-breast-cancer-subtype-using-multiple-single-nucleotide-polymorphisms-for-breast-cancer-risk-and-several-variable-selection-methods
#11
Lothar Häberle, Alexander Hein, Matthias Rübner, Michael Schneider, Arif B Ekici, Paul Gass, Arndt Hartmann, Rüdiger Schulz-Wendtland, Matthias W Beckmann, Wing-Yee Lo, Werner Schroth, Hiltrud Brauch, Peter A Fasching, Marius Wunderle
INTRODUCTION: Studies of triple-negative breast cancer have recently been extending the inclusion criteria and incorporating additional molecular markers into the selection criteria, opening up scope for targeted therapies. The screening phases required for studies of this type are often prolonged, since the process of determining the molecular subtype and carrying out additional biomarker assessment is time-consuming. Parameters such as germline genotypes capable of predicting the molecular subtype before it becomes available from pathology might be helpful for treatment planning and optimizing the timing and cost of screening phases...
June 2017: Geburtshilfe und Frauenheilkunde
https://www.readbyqxmd.com/read/28756587/phenotyping-first-generation-genome-editing-mutants-a-new-standard
#12
Lydia Teboul, Stephen A Murray, Patrick M Nolan
The unprecedented efficiency of the CRISPR/Cas9 system in genome engineering has opened the prospect of employing mutant founders for phenotyping cohorts, thus accelerating research projects by circumventing the requirement to generate cohorts using conventional two- or three-generation crosses. However, these first-generation mutants are often genetic mosaics, with a complex and difficult to define genetic make-up. Here, we discuss the potential benefits, challenges and scientific validity of such models.
July 29, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28753641/uv-vis-and-atr-ftir-spectroscopic-investigations-of-postmortem-interval-based-on-the-changes-in-rabbit-plasma
#13
Qi Wang, Haijun He, Bing Li, Hancheng Lin, Yinming Zhang, Ji Zhang, Zhenyuan Wang
Estimating PMI is of great importance in forensic investigations. Although many methods are used to estimate the PMI, a few investigations focus on the postmortem redistribution. In this study, ultraviolet-visible (UV-Vis) measurement combined with visual inspection indicated a regular diffusion of hemoglobin into plasma after death showing the redistribution of postmortem components in blood. Thereafter, attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy was used to confirm the variations caused by this phenomenon...
2017: PloS One
https://www.readbyqxmd.com/read/28751801/drought-tolerant-brassica-rapa-shows-rapid-expression-of-gene-networks-for-general-stress-responses-and-programmed-cell-death-under-simulated-drought-stress
#14
Yi Ming Guo, Birgit Samans, Sheng Chen, Kidist B Kibret, Sarah Hatzig, Neil C Turner, Matthew N Nelson, Wallace A Cowling, Rod J Snowdon
Production of oilseed rape/canola (Brassica napus) is increasingly threatened by dry conditions while the demand for vegetable oil is increasing. Brassica rapa is a genetically diverse ancestor of B. napus, and is readily crossed with B. napus. Recently, we reported promising levels of drought tolerance in a wild type of B. rapa which could be a source of drought tolerance for B. napus. We analysed global gene expression by messenger RNA sequencing in seedlings of the drought-tolerant and a drought-sensitive genotype of B...
2017: Plant Molecular Biology Reporter
https://www.readbyqxmd.com/read/28750087/risk-prediction-of-developing-venous-thrombosis-in-combined-oral-contraceptive-users
#15
Aaron McDaid, Emmanuelle Logette, Valérie Buchillier, Maude Muriset, Pierre Suchon, Thierry Daniel Pache, Goranka Tanackovic, Zoltán Kutalik, Joëlle Michaud
BACKGROUND: Venous thromboembolism (VTE) is a complex multifactorial disease influenced by genetic and environmental risk factors. An example for the latter is the regular use of combined oral contraceptives (CC), which increases the risk to develop VTE by 3 to 7 fold, depending on estrogen dosage and the type of progestin present in the pill. One out of 1'000 women using CC develops thrombosis, often with life-long consequences; a risk assessment is therefore necessary prior to such treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28743254/association-between-serotonin-transporter-gene-polymorphisms-and-increased-suicidal-risk-among-hiv-positive-patients-in-uganda
#16
Allan Kalungi, Soraya Seedat, Sian M J Hemmings, Lize van der Merwe, Moses L Joloba, Ann Nanteza, Noeline Nakassujja, Harriet Birabwa, Jennifer Serwanga, Pontiano Kaleebu, Eugene Kinyanda
BACKGROUND: Persons living with HIV/AIDS (PLWHA) are at an increased risk of suicide. Increased suicidal risk is a predictor of future attempted and completed suicides and has been associated with poor quality of life and poor adherence with antiretroviral therapy. Clinical risk factors have low predictive value for suicide, hence the interest in potential neurobiological correlates and specific heritable markers of suicide vulnerability. The serotonin transporter gene has previously been implicated in the aetiology of increased suicidal risk in non-HIV infected study populations and its variations may provide a platform for identifying genetic risk for suicidality among PLWHA...
July 25, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28742459/identification-of-clusters-that-condition-resistance-to-anthracnose-in-the-common-bean-differential-cultivars-ab136-and-mdrk
#17
Ana Campa, Noemi Trabanco, Juan Jose Ferreira
The correct identification of the anthracnose resistance systems present in the common bean cultivars AB136 and MDRK is important because both are included in the set of 12 differential cultivars proposed for use in classifying the races of the anthracnose causal agent, Colletrotrichum lindemuthianum. In this work, the responses against seven C. lindemuthianum races were analyzed in a recombinant inbred line population derived from the cross AB136 x MDRK. A genetic linkage map of 100 molecular markers distributed across the 11 bean chromosomes was developed in this population to locate the gene or genes conferring resistance against each race, based on linkage analyses and chi-square tests of independence...
July 25, 2017: Phytopathology
https://www.readbyqxmd.com/read/28738459/-gene-gene-interaction-on-central-obesity-in-school-aged-children-in-china
#18
L W Fu, M X Zhang, L J Wu, L W Gao, J Mi
Objective: To investigate possible effect of 6 obesity-associated SNPs in contribution to central obesity and examine whether there is an interaction in the 6 SNPs in the cause of central obesity in school-aged children in China. Methods: A total of 3 502 school-aged children who were included in Beijing Child and Adolescent Metabolic Syndrome (BCAMS) Study were selected, and based on the age and sex specific waist circumference (WC) standards in the BCAMS study, 1 196 central obese cases and 2 306 controls were identified...
July 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28737713/quality-assessment-of-gentiana-rigescens-from-different-geographical-origins-using-ft-ir-spectroscopy-combined-with-hplc
#19
Zhe Wu, Yanli Zhao, Ji Zhang, Yuanzhong Wang
Gentiana rigescens is a precious herbal medicine in China because of its liver-protective and choleretic effects. A method for the qualitative identification and quantitative evaluation of G. rigescens from Yunnan Province, China, has been developed employing Fourier transform infrared (FT-IR) spectroscopy and high performance liquid chromatography (HPLC) with the aid of chemometrics such as partial least squares discriminant analysis (PLS-DA) and support vector machines (SVM) regression. Our results indicated that PLS-DA model could efficiently discriminate G...
July 24, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28736445/dietary-fat-and-total-energy-intake-modifies-the-association-of-genetic-profile-risk-score-on-obesity-evidence-from-48%C3%A2-170-uk-biobank-participants
#20
C A Celis-Morales, D M Lyall, S R Gray, L Steell, J Anderson, S Iliodromiti, P Welsh, Y Guo, F Petermann, D F Mackay, M E S Bailey, J P Pell, J M R Gill, N Sattar
BACKGROUND: Obesity is a multifactorial condition influenced by both genetics and lifestyle. The aim of this study was to investigate whether the association between a validated genetic profile risk score for obesity (GPRS-obesity) and body mass index (BMI) or waist circumference (WC) was modified by macronutrient intake in a large general population study. METHODS: This study included cross-sectional data from 48 170 white European adults, aged 37-73 years, participating in the UK Biobank...
July 24, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
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