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Genetics cross validation

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https://www.readbyqxmd.com/read/29152841/adjusting-for-heterogeneity-of-experimental-data-in-genetic-evaluation-of-dry-matter-intake-in-dairy-cattle
#1
M E Uddin, T Meuwissen, R F Veerkamp
The objectives of the present study were (i) to find the best fitted model for repeatedly measured daily dry matter intake (DMI) data obtained from different herds and experiments across lactations and (ii) to get better estimates of the genetic parameters and better genetic evaluations. After editing, there were 572,512 daily DMI records of 3,495 animals (Holstein cows) from 11 different herds across 13 lactations and the animals were under 110 different nutritional experiments. The fitted model for this data set was a univariate repeated-measure animal model (called model 1) in which additive genetic and permanent environmental (within and across lactations) effects were fitted as random...
November 20, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/29152235/serum-25-hydroxyvitamin-d3-and-24r-25-dihydroxyvitamin-d3-concentrations-in-adult-dogs-are-more-substantially-increased-by-oral-supplementation-of-25-hydroxyvitamin-d3-than-by-vitamin-d3
#2
Lauren R Young, Robert C Backus
We previously found a weak response in serum 25-hydroxyvitamin D3 (25(OH)D3) concentrations when dogs were supplemented with oral vitamin D3 (D3). In the present study, we determined the relative potency of oral 25(OH)D3 compared with D3 for increasing vitamin D status in dogs with low serum 25(OH)D concentrations. Four male and three female, 4-year-old, intact, lean, genetically related, Chinese-crested/beagle dogs were studied in a randomised, single cross-over trial. After feeding a low-vitamin D diet (<4 IU/100 g) for 30 d, four dogs received daily D3 supplementation at 2·3 µg/kg body weight(0·75), while three dogs received a molar equivalency as 25(OH)D3...
2017: Journal of Nutritional Science
https://www.readbyqxmd.com/read/29150722/cross-lagged-analysis-of-interplay-between-differential-traits-in-sibling-pairs-validation-and-application-to-parenting-behavior-and-adhd-symptomatology
#3
Arden Moscati, Brad Verhulst, Kevin McKee, Judy Silberg, Lindon Eaves
Understanding the factors that contribute to behavioral traits is a complex task, and partitioning variance into latent genetic and environmental components is a useful beginning, but it should not also be the end. Many constructs are influenced by their contextual milieu, and accounting for background effects (such as gene-environment correlation) is necessary to avoid bias. This study introduces a method for examining the interplay between traits, in a longitudinal design using differential items in sibling pairs...
November 17, 2017: Behavior Genetics
https://www.readbyqxmd.com/read/29146399/label-free-discrimination-analysis-of-de-differentiated-vascular-smooth-muscle-cells-mesenchymal-stem-cells-and-their-vascular-and-osteogenic-progeny-using-vibrational-spectroscopy
#4
Claire Molony, Jennifer McIntyre, Adrian Maguire, Roya Hakimjavadi, Denise Burtenshaw, Gillian Casey, Mariana Di Luca, Bryan Hennelly, Hugh J Byrne, Paul A Cahill
The accumulation of vascular smooth muscle (SMC)-like cells and stem cell-derived myogenic and osteogenic progeny contributes significantly to arteriosclerotic disease. This study established whether label-free vibrational spectroscopy can discriminate de-differentiated 'synthetic' SMCs from undifferentiated stem cells and their myogenic and osteogenic progeny in vitro, compared with conventional immunocytochemical and genetic analyses. TGF-β1- and Jagged1-induced myogenic differentiation of CD44(+)mesenchymal stem cells was confirmed in vitro by immunocytochemical analysis of specific SMC differentiation marker expression (α-actin, calponin and myosin heavy chain 11), an epigenetic histone mark (H3K4me2) at the myosin heavy chain 11 locus, promoter transactivation and mRNA transcript levels...
November 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29145754/cortical-and-subcortical-brain-morphometry-differences-between-patients-with-autism-spectrum-disorder-and-healthy-individuals-across-the-lifespan-results-from-the-enigma-asd-working-group
#5
Daan van Rooij, Evdokia Anagnostou, Celso Arango, Guillaume Auzias, Marlene Behrmann, Geraldo F Busatto, Sara Calderoni, Eileen Daly, Christine Deruelle, Adriana Di Martino, Ilan Dinstein, Fabio Luis Souza Duran, Sarah Durston, Christine Ecker, Damien Fair, Jennifer Fedor, Jackie Fitzgerald, Christine M Freitag, Louise Gallagher, Ilaria Gori, Shlomi Haar, Liesbeth Hoekstra, Neda Jahanshad, Maria Jalbrzikowski, Joost Janssen, Jason Lerch, Beatriz Luna, Mauricio Moller Martinho, Jane McGrath, Filippo Muratori, Clodagh M Murphy, Declan G M Murphy, Kirsten O'Hearn, Bob Oranje, Mara Parellada, Alessandra Retico, Pedro Rossa, Katya Rubia, Devon Shook, Margot Taylor, Paul M Thompson, Michela Tosetti, Gregory L Wallace, Fengfeng Zhou, Jan K Buitelaar
OBJECTIVE: Neuroimaging studies show structural differences in both cortical and subcortical brain regions in children and adults with autism spectrum disorder (ASD) compared with healthy subjects. Findings are inconsistent, however, and it is unclear how differences develop across the lifespan. The authors investigated brain morphometry differences between individuals with ASD and healthy subjects, cross-sectionally across the lifespan, in a large multinational sample from the Enhancing Neuroimaging Genetics Through Meta-Analysis (ENIGMA) ASD working group...
November 17, 2017: American Journal of Psychiatry
https://www.readbyqxmd.com/read/29145412/mapping-and-verification-of-grain-shape-qtls-based-on-an-advanced-backcross-population-in-rice
#6
Duo Xia, Hao Zhou, Lei Qiu, Haichao Jiang, Qinglu Zhang, Guanjun Gao, Yuqing He
Grain shape is a key factor that influences both the appearance quality and grain yield of rice. To clarify the genetic basis of grain shape, an advanced backcross population was developed from the cross of a slender indica variety Jin23B and a round japonica variety QingGuAi, and a total of 10 quantitative trait loci (QTLs) for grain shape were detected over 2 years. Three QTLs, qGW1, qGS3 and qGS7 have large effects on grain shape and were detected in both years. To further validate their effects, the BC4F2 populations of the three QTLs were constructed...
2017: PloS One
https://www.readbyqxmd.com/read/29129749/quantitative-proteomic-analysis-of-deciduous-molars-during-cap-to-bell-transition-in-miniature-pig
#7
Yang Li, Yiyi Gong, Xiaoshan Wu, Fu Wang, Yilin Xie, Zhao Zhu, Yingying Su, Jinsong Wang, Chunmei Zhang, Junqi He, Haiteng Deng, Songlin Wang
Taking advantage of genetic manipulation tools and accessibility, almost all molecular knowledge on vertebrate tooth development was obtained from rodent models that only have one dentition in their entire lives. Whether the tooth development in other vertebrates such as swine or human follows the same rules remains elusive. Rodent dentitions differ considerably from human dentitions, therefore limiting the application of knowledge from rodent tooth to human tooth. Signal-mediated communication between cells and complex gene and protein regulatory networks are key components of tooth development...
November 10, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29116006/analysis-of-near-infrared-spectra-for-age-grading-of-wild-populations-of-anopheles-gambiae
#8
Benjamin J Krajacich, Jacob I Meyers, Haoues Alout, Roch K Dabiré, Floyd E Dowell, Brian D Foy
BACKGROUND: Understanding the age-structure of mosquito populations, especially malaria vectors such as Anopheles gambiae, is important for assessing the risk of infectious mosquitoes, and how vector control interventions may impact this risk. The use of near-infrared spectroscopy (NIRS) for age-grading has been demonstrated previously on laboratory and semi-field mosquitoes, but to date has not been utilized on wild-caught mosquitoes whose age is externally validated via parity status or parasite infection stage...
November 7, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/29111440/a-method-for-single-pair-mating-in-an-obligate-parasitic-nematode
#9
Neil D Sargison, Elizabeth Redman, Alison A Morrison, David J Bartley, Frank Jackson, Hardeep Naghra-van Gijzel, Nancy Holroyd, Matthew Berriman, James A Cotton, John S Gilleard
Parasitic nematode species have extremely high levels of genetic diversity, presenting a number of experimental challenges for genomic and genetic work. Consequently, there is a need to develop inbred laboratory strains with reduced levels of polymorphism. The most efficient approach to inbred line development is single pair mating, but this is challenging for obligate parasites where the adult sexual reproductive stages are inside the host, and thus difficult to experimentally manipulate. This paper describes a successful approach to single pair mating of a parasitic nematode, Haemonchus contortus...
October 27, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/29111409/mulan-evaluation-and-ensemble-statistical-inference-for-functional-connectivity
#10
Huifang E Wang, Karl J Friston, Christian G Bénar, Marmaduke M Woodman, Patrick Chauvel, Viktor Jirsa, Christophe Bernard
Many analysis methods exist to extract graphs of functional connectivity from neuronal networks. Confidence in the results is limited because, (i) different methods give different results, (ii) parameter setting directly influences the final result, and (iii) systematic evaluation of the results is not always performed. Here, we introduce MULAN (MULtiple method ANalysis), which assumes an ensemble based approach combining multiple analysis methods and fuzzy logic to extract graphs with the most probable structure...
October 27, 2017: NeuroImage
https://www.readbyqxmd.com/read/29100114/wall-based-measurement-features-provides-an-improved-ivus-coronary-artery-risk-assessment-when-fused-with-plaque-texture-based-features-during-machine-learning-paradigm
#11
Sumit K Banchhor, Narendra D Londhe, Tadashi Araki, Luca Saba, Petia Radeva, John R Laird, Jasjit S Suri
BACKGROUND: Planning of percutaneous interventional procedures involves a pre-screening and risk stratification of the coronary artery disease. Current screening tools use stand-alone plaque texture-based features and therefore lack the ability to stratify the risk. METHOD: This IRB approved study presents a novel strategy for coronary artery disease risk stratification using an amalgamation of IVUS plaque texture-based and wall-based measurement features. Due to common genetic plaque makeup, carotid plaque burden was chosen as a gold standard for risk labels during training-phase of machine learning (ML) paradigm...
October 23, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29096603/genomic-preselection-with-genotyping-by-sequencing-increases-performance-of-commercial-oil-palm-hybrid-crosses
#12
David Cros, Stéphanie Bocs, Virginie Riou, Enrique Ortega-Abboud, Sébastien Tisné, Xavier Argout, Virginie Pomiès, Leifi Nodichao, Zulkifli Lubis, Benoit Cochard, Tristan Durand-Gasselin
BACKGROUND: There is great potential for the genetic improvement of oil palm yield. Traditional progeny tests allow accurate selection but limit the number of individuals evaluated. Genomic selection (GS) could overcome this constraint. We estimated the accuracy of GS prediction of seven oil yield components using A × B hybrid progeny tests with almost 500 crosses for training and 200 crosses for independent validation. Genotyping-by-sequencing (GBS) yielded +5000 single nucleotide polymorphisms (SNPs) on the parents of the crosses...
November 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29089957/development-and-evaluation-of-a-barley-50k-iselect-snp-array
#13
Micha M Bayer, Paulo Rapazote-Flores, Martin Ganal, Pete E Hedley, Malcolm Macaulay, Jörg Plieske, Luke Ramsay, Joanne Russell, Paul D Shaw, William Thomas, Robbie Waugh
High-throughput genotyping arrays continue to be an attractive, cost-effective alternative to sequencing based approaches. We have developed a new 50k Illumina Infinium iSelect genotyping array for barley, a cereal crop species of major international importance. The majority of SNPs on the array have been extracted from variants called in exome capture data of a wide range of European barley germplasm. We used the recently published barley pseudomolecule assembly to map the exome capture data, which allowed us to generate markers with accurate physical positions and detailed gene annotation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29089022/genetic-basis-of-the-very-short-life-cycle-of-apogee-wheat
#14
Genqiao Li, Rungravee Boontung, Carol Powers, Vikas Belamkar, Tianrong Huang, Fang Miao, P Stephen Baenziger, Liuling Yan
BACKGROUND: 'Apogee' has a very short life cycle among wheat cultivars (flowering 25 days after planting under a long day and without vernalization), and it is a unique genetic material that can be used to accelerate cycling breeding lines. However, little is known about the genetic basis of the super-short life of Apogee wheat. RESULTS: In this study, Apogee was crossed with a strong winter wheat cultivar 'Overland', and 858 F2 plants were generated and tested in a greenhouse under constant warm temperature and long days...
October 31, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29081953/defining-the-current-scope-and-limitations-of-dual-noncanonical-amino-acid-mutagenesis-in-mammalian-cells
#15
Yunan Zheng, Partha Sarathi Addy, Raja Mukherjee, Abhishek Chatterjee
The ability to site-specifically incorporate two distinct noncanonical amino acids (ncAAs) into the proteome of a mammalian cell with high fidelity and efficiency will have many enabling applications. It would require the use of two different engineered aminoacyl-tRNA synthetase (aaRS)/tRNA pairs, each suppressing a distinct nonsense codon, and which cross-react neither with each other, nor with their counterparts from the host cell. Three different aaRS/tRNA pairs have been developed so far to expand the genetic code of mammalian cells, which can be potentially combined in three unique ways to drive site-specific incorporation of two distinct ncAAs...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29081789/genetic-architecture-of-natural-variation-in-rice-nonphotochemical-quenching-capacity-revealed-by-genome-wide-association-study
#16
Quanxiu Wang, Hu Zhao, Junpeng Jiang, Jiuyue Xu, Weibo Xie, Xiangkui Fu, Chang Liu, Yuqing He, Gongwei Wang
The photoprotective processes conferred by nonphotochemical quenching (NPQ) serve fundamental roles in maintaining plant fitness and sustainable yield. So far, few loci have been reported to be involved in natural variation of NPQ capacity in rice (Oryza sativa), and the extents of variation explored are very limited. Here we conducted a genome-wide association study (GWAS) for NPQ capacity using a diverse worldwide collection of 529 O. sativa accessions. A total of 33 significant association loci were identified...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29073733/tracing-the-breeding-farm-of-domesticated-pig-using-feature-selection-sus-scrofa
#17
Taehyung Kwon, Joon Yoon, Jaeyoung Heo, Wonseok Lee, Heebal Kim
OBJECTIVE: Increasing food safety demands in the animal product market have created a need for a system to trace the food distribution process, from the manufacturer to the retailer, and genetic traceability is an effective method to trace the origin of animal products. In this study, we successfully achieved the farm tracing of 6,018 multi-breed pigs, using single nucleotide polymorphism (SNP) markers strictly selected through least absolute shrinkage and selection operator (LASSO) feature selection...
November 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/29065906/biological-function-integrated-prediction-of-severe-radiographic-progression-in-rheumatoid-arthritis-a-nested-case-control-study
#18
Young Bin Joo, Yul Kim, Youngho Park, Kwangwoo Kim, Jeong Ah Ryu, Seunghun Lee, So-Young Bang, Hye-Soon Lee, Gwan-Su Yi, Sang-Cheol Bae
BACKGROUND: Radiographic progression is reported to be highly heritable in rheumatoid arthritis (RA). However, previous study using genetic loci showed an insufficient accuracy of prediction for radiographic progression. The aim of this study is to identify a biologically relevant prediction model of radiographic progression in patients with RA using a genome-wide association study (GWAS) combined with bioinformatics analysis. METHODS: We obtained genome-wide single nucleotide polymorphism (SNP) data for 374 Korean patients with RA using Illumina HumanOmni2...
October 25, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/29057969/controlling-the-overfitting-of-heritability-in-genomic-selection-through-cross-validation
#19
Zhenyu Jia
In genomic selection (GS), all the markers across the entire genome are used to conduct marker-assisted selection such that each quantitative trait locus of complex trait is in linkage disequilibrium with at least one marker. Although GS improves estimated breeding values and genetic gain, in most GS models genetic variance is estimated from training samples with many trait-irrelevant markers, which leads to severe overfitting in the calculation of trait heritability. In this study, we demonstrated overfitting heritability due to the inclusion of trait-irrelevant markers using a series of simulations, and such overfitting can be effectively controlled by cross validation experiment...
October 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29054068/quantitative-determination-of-additive-chlorantraniliprole-in-abamectin-preparation-investigation-of-bootstrapping-soft-shrinkage-approach-by-mid-infrared-spectroscopy
#20
Hong Yan, Xiangzhong Song, Kuangda Tian, Yilin Chen, Yanmei Xiong, Shungeng Min
A novel method, mid-infrared (MIR) spectroscopy, which enables the determination of Chlorantraniliprole in Abamectin within minutes, is proposed. We further evaluate the prediction ability of four wavelength selection methods, including bootstrapping soft shrinkage approach (BOSS), Monte Carlo uninformative variable elimination (MCUVE), genetic algorithm partial least squares (GA-PLS) and competitive adaptive reweighted sampling (CARS) respectively. The results showed that BOSS method obtained the lowest root mean squared error of cross validation (RMSECV) (0...
September 1, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
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