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https://www.readbyqxmd.com/read/28637337/matrix-completion-with-side-information-and-its-applications-in-predicting-the-antigenicity-of-influenza-viruses
#1
Li Huang, Xianhong Li, Pengfei Guo, Yuhua Yao, Bo Liao, Weiwei Zhang, Fayou Wang, Jiasheng Yang, Yulong Zhao, Hailiang Sun, Pingan He, Jialiang Yang
Motivation: Low-rank matrix completion has been demonstrated to be powerful in predicting antigenic distances among influenza viruses and vaccines from partially revealed hemagglutination inhibition (HI) table. Meanwhile, influenza hemagglutinin (HA) protein sequences are also effective in inferring antigenic distances. Thus, it is natural to integrate HA protein sequence information into low-rank matrix completion model to help infer influenza antigenicity, which is critical to influenza vaccine development...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28633685/cross-validation-analysis-for-genetic-evaluation-models-for-ranking-in-endurance-horses
#2
S García-Ballesteros, L Varona, M Valera, J P Gutiérrez, I Cervantes
Ranking trait was used as a selection criterion for competition horses to estimate racing performance. In the literature the most common approaches to estimate breeding values are the linear or threshold statistical models. However, recent studies have shown that a Thurstonian approach was able to fix the race effect (competitive level of the horses that participate in the same race), thus suggesting a better prediction accuracy of breeding values for ranking trait. The aim of this study was to compare the predictability of linear, threshold and Thurstonian approaches for genetic evaluation of ranking in endurance horses...
June 21, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28625422/online-version-of-the-self-administered-food-frequency-questionnaire-for-the-japan-public-health-center-based-prospective-study-for-the-next-generation-jphc-next-protocol-relative-validity-usability-and-comparison-with-a-printed-questionnaire
#3
Erika Kato, Ribeka Takachi, Junko Ishihara, Yuri Ishii, Shizuka Sasazuki, Norie Sawada, Motoki Iwasaki, Yurie Shinozawa, Jun Umezawa, Junta Tanaka, Yuta Yokoyama, Kaori Kitamura, Kazutoshi Nakamura, Shoichiro Tsugane
BACKGROUND: Online dietary assessment tools offer advantages over printed questionnaires, such as the automatic and direct data storage of answers, and have the potential to become valuable research methods. We developed an online survey system (web-FFQ) for the existing printed FFQ used in the JPHC-NEXT protocol, the platform of a large-scale genetic cohort study. Here, we examined the validity of ranking individuals according to dietary intake using this web-FFQ and its usability compared with the printed questionnaire (print-FFQ) for combined usage...
June 15, 2017: Journal of Epidemiology
https://www.readbyqxmd.com/read/28623477/use-of-the-boadicea-web-application-in-clinical-practice-appraisals-by-clinicians-from-various-countries
#4
Anne Brédart, Jean-Luc Kop, Antonis C Antoniou, Alex P Cunningham, Antoine De Pauw, Marc Tischkowitz, Hans Ehrencrona, Sylvie Dolbeault, Léonore Robieux, Kerstin Rhiem, Douglas F Easton, Peter Devilee, Dominique Stoppa-Lyonnet, Rita Schmutlzer
The 'BOADICEA' Web Application (BWA) used to assess breast cancer risk, is currently being further developed, to integrate additional genetic and non-genetic factors. We surveyed clinicians' perceived acceptability of the existing BWA v3. An online survey was conducted through the BOADICEA website, and the British, Dutch, French and Swedish genetics societies. Cross-sectional data from 443 participants who provided at least 50% responses were analysed. Respondents varied in age and, clinical seniority, but mainly comprised women (77%) and genetics professionals (82%)...
June 16, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28619006/tag-snp-selection-for-prediction-of-tick-resistance-in-brazilian-braford-and-hereford-cattle-breeds-using-bayesian-methods
#5
Bruna P Sollero, Vinícius S Junqueira, Cláudia C G Gomes, Alexandre R Caetano, Fernando F Cardoso
BACKGROUND: Cattle resistance to ticks is known to be under genetic control with a complex biological mechanism within and among breeds. Our aim was to identify genomic segments and tag single nucleotide polymorphisms (SNPs) associated with tick-resistance in Hereford and Braford cattle. The predictive performance of a very low-density tag SNP panel was estimated and compared with results obtained with a 50 K SNP dataset. RESULTS: BayesB (π = 0.99) was initially applied in a genome-wide association study (GWAS) for this complex trait by using deregressed estimated breeding values for tick counts and 41,045 SNP genotypes from 3455 animals raised in southern Brazil...
June 15, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28612220/individual-outcome-prediction-for-myelodysplastic-syndrome-mds-and-secondary-acute-myeloid-leukemia-from-mds-after-allogeneic-hematopoietic-cell-transplantation
#6
Michael Heuser, Razif Gabdoulline, Patrick Löffeld, Vera Dobbernack, Henriette Kreimeyer, Mira Pankratz, Madita Flintrop, Alessandro Liebich, Sabrina Klesse, Victoria Panagiota, Michael Stadler, Martin Wichmann, Rabia Shahswar, Uwe Platzbecker, Christian Thiede, Thomas Schroeder, Guido Kobbe, Robert Geffers, Brigitte Schlegelberger, Gudrun Göhring, Hans-Heinrich Kreipe, Ulrich Germing, Arnold Ganser, Nicolaus Kröger, Christian Koenecke, Felicitas Thol
We integrated molecular data with available prognostic factors in patients undergoing allogeneic hematopoietic cell transplantation (alloHCT) for myelodysplastic syndrome (MDS) or secondary acute myeloid leukemia (sAML) from MDS to evaluate their impact on prognosis. Three hundred four patients were sequenced for mutations in 54 genes. We used a Cox multivariate model and competing risk analysis with internal and cross validation to identify factors prognostic of overall survival (OS), cumulative incidence of relapse (CIR), and non-relapse mortality (NRM)...
June 13, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/28601624/age-at-menarche-and-cardiovascular-risk-factors-using-mendelian-randomization-in-the-guangzhou-biobank-cohort-study
#7
Shiu Lun Au Yeung, Chaoqiang Jiang, Kar Keung Cheng, Lin Xu, Weisen Zhang, Tai Hing Lam, Gabriel Matthew Leung, C Mary Schooling
Observational studies show earlier age at menarche associated with higher risk of cardiovascular disease although these studies could be confounded by childhood obesity or childhood socioeconomic position. We hypothesized that earlier age at menarche is associated with poorer cardiovascular risk factors using a Mendelian randomization design. We conducted a Mendelian randomization study in a large Southern Chinese cohort, the Guangzhou Biobank Cohort Study (n=12,279), to clarify the causal role of menarche in cardiovascular disease risk factors including blood pressure, lipids, fasting glucose, adiposity and type 2 diabetes...
June 7, 2017: Preventive Medicine
https://www.readbyqxmd.com/read/28600346/genetic-control-of-plasticity-in-root-morphology-and-anatomy-of-rice-in-response-to-water-deficit
#8
Niteen Kadam, Anandhan Tamilselvan, Lovely Mae F Lawas, Cherryl Quinones, Rajeev Bahuguna, Michael J Thomson, Michael Dingkuhn, Raveendran Muthurajan, Paul Struik, Xinyou Yin, Krishna Jagadish
Elucidating the genetic control of rooting behaviour under water-deficit stress is essential to breed climate-robust rice cultivars. Using a diverse panel of 274 indica genotypes grown under control and water-deficit conditions during vegetative growth, we phenotyped 35 traits, mostly related to root morphology and anatomy, involving ~45,000 root scanning images and nearly ~25,000 cross-sections from the root-shoot junction. Phenotypic plasticity of these traits was quantified as the relative change in trait value under water-deficit compared to control conditions...
June 9, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28598989/leveraging-genomic-prediction-to-scan-germplasm-collection-for-crop-improvement
#9
Leonardo de Azevedo Peixoto, Tara C Moellers, Jiaoping Zhang, Aaron J Lorenz, Leonardo L Bhering, William D Beavis, Asheesh K Singh
The objective of this study was to explore the potential of genomic prediction (GP) for soybean resistance against Sclerotinia sclerotiorum (Lib.) de Bary, the causal agent of white mold (WM). A diverse panel of 465 soybean plant introduction accessions was phenotyped for WM resistance in replicated field and greenhouse tests. All plant accessions were previously genotyped using the SoySNP50K BeadChip. The predictive ability of six GP models were compared, and the impact of marker density and training population size on the predictive ability was investigated...
2017: PloS One
https://www.readbyqxmd.com/read/28592647/the-beavis-effect-in-next-generation-mapping-panels-in-drosophila-melanogaster
#10
Elizabeth G King, Anthony D Long
A major goal in the analysis of complex traits is to partition the observed genetic variation in a trait into components due to individual loci and perhaps variants within those loci. However, in both QTL mapping and genetic association studies, the estimated percent variation attributable to a QTL is upwardly biased conditional on it being discovered. This bias was first described in two-way QTL mapping experiments by William Beavis, and has been referred to extensively as "the Beavis effect." The Beavis effect is likely to occur in multiparent population (MPP) panels as well as collections of sequenced lines used for genome-wide association studies (GWAS)...
June 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28592497/increased-power-to-dissect-adaptive-traits-in-global-sorghum-diversity-using-a-nested-association-mapping-population
#11
Sophie Bouchet, Marcus O Olatoye, Sandeep R Marla, Ramasamy Perumal, Tesfaye Tesso, Jianming Yu, Mitch Tuinstra, Geoffrey P Morris
Adaptation of domesticated species to diverse agroclimatic regions has led to abundant trait diversity. However, the resulting population structure and genetic heterogeneity confounds association mapping of adaptive traits. To address this challenge in sorghum [Sorghum bicolor (L.) Moench]-a widely adapted cereal crop-we developed a nested association mapping (NAM) population using 10 diverse global lines crossed with an elite reference line RTx430. We characterized the population of 2214 recombinant inbred lines at 90,000 SNPs using genotyping-by-sequencing...
June 2017: Genetics
https://www.readbyqxmd.com/read/28592496/male-infertility-is-responsible-for-nearly-half-of-the-extinction-observed-in-the-mouse-collaborative-cross
#12
John R Shorter, Fanny Odet, David L Aylor, Wenqi Pan, Chia-Yu Kao, Chen-Ping Fu, Andrew P Morgan, Seth Greenstein, Timothy A Bell, Alicia M Stevans, Ryan W Feathers, Sunny Patel, Sarah E Cates, Ginger D Shaw, Darla R Miller, Elissa J Chesler, Leonard McMillian, Deborah A O'Brien, Fernando Pardo-Manuel de Villena
The goal of the Collaborative Cross (CC) project was to generate and distribute over 1000 independent mouse recombinant inbred strains derived from eight inbred founders. With inbreeding nearly complete, we estimated the extinction rate among CC lines at a remarkable 95%, which is substantially higher than in the derivation of other mouse recombinant inbred populations. Here, we report genome-wide allele frequencies in 347 extinct CC lines. Contrary to expectations, autosomes had equal allelic contributions from the eight founders, but chromosome X had significantly lower allelic contributions from the two inbred founders with underrepresented subspecific origins (PWK/PhJ and CAST/EiJ)...
June 2017: Genetics
https://www.readbyqxmd.com/read/28587194/cross-kingdom-regulation-of-putative-mirnas-derived-from-happy-tree-in-cancer-pathway-a-systems-biology-approach
#13
Dinesh Kumar, Swapnil Kumar, Garima Ayachit, Shivarudrappa B Bhairappanavar, Afzal Ansari, Priyanka Sharma, Subhash Soni, Jayashankar Das
MicroRNAs (miRNAs) are well-known key regulators of gene expression primarily at the post-transcriptional level. Plant-derived miRNAs may pass through the gastrointestinal tract, entering into the body fluid and regulate the expression of endogenous mRNAs. Camptotheca acuminata, a highly important medicinal plant known for its anti-cancer potential was selected to investigate cross-kingdom regulatory mechanism and involvement of miRNAs derived from this plant in cancer-associated pathways through in silico systems biology approach...
June 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28571989/an-attempt-at-predicting-blood-%C3%AE-hydroxybutyrate-from-fourier-transform-mid-infrared-spectra-of-milk-using-multivariate-mixed-models-in-polish-dairy-cattle
#14
T K Belay, B S Dagnachew, Z M Kowalski, T Ådnøy
Fourier transform mid-infrared (FT-MIR) spectra of milk are commonly used for phenotyping of traits of interest through links developed between the traits and milk FT-MIR spectra. Predicted traits are then used in genetic analysis for ultimate phenotypic prediction using a single-trait mixed model that account for cows' circumstances at a given test day. Here, this approach is referred to as indirect prediction (IP). Alternatively, FT-MIR spectral variable can be kept multivariate in the form of factor scores in REML and BLUP analyses...
May 29, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28560159/williams-syndrome-specific-neuroanatomical-profile-and-its-associations-with-behavioral-features
#15
Chun Chieh Fan, Timothy T Brown, Hauke Bartsch, Joshua M Kuperman, Donald J Hagler, Andrew Schork, Yvonne Searcy, Ursula Bellugi, Eric Halgren, Anders M Dale
Williams Syndrome (WS) is a rare genetic disorder with unique behavioral features. Yet the rareness of WS has limited the number and type of studies that can be conducted in which inferences are made about how neuroanatomical abnormalities mediate behaviors. In this study, we extracted a WS-specific neuroanatomical profile from structural magnetic resonance imaging (MRI) measurements and tested its association with behavioral features of WS. Using a WS adult cohort (22 WS, 16 healthy controls), we modeled a sparse representation of a WS-specific neuroanatomical profile...
2017: NeuroImage: Clinical
https://www.readbyqxmd.com/read/28554668/anti-tumor-effects-of-a-human-mouse-cross-reactive-anti-adam17-antibody-in-a-pancreatic-cancer-model-in-vivo
#16
Jie Ye, Shun Ming Yuen, Gillian Murphy, Ruiyu Xie, Hang Fai Kwok
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal types of tumor amongst all human cancers due to late diagnosis and resistant to treatment with chemotherapy and radiation. Preclinical and clinical studies have revealed that ErbB family for example epidermal growth factor receptor (EGFR) is a validated molecular target for pancreatic cancer prevention and therapy. The ErbB signaling cascade is regulated by a member of the ADAM (a disintegrin and metalloprotease) family, namely ADAM17, by enzymatic cleavage of precursor ligands into soluble cytokines and growth factors...
May 26, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28554315/pharmacophore-modelling-and-4d-qsar-study-of-ruthenium-ii-arene-complexes-as-anticancer-agents-inhibitors-by-electron-conformational-genetic-algorithm-method
#17
Sevtap Çağlar Yavuz, Nazmiye Sabancı, Emin Sarıpınar
OBJECTIVE: The EC-GA method was employed in this study as a 4D-QSAR method, for the identification of the pharmacophore (Pha) of ruthenium(II) arene complex derivatives and quantitative prediction of activity. METHOD: The arrangement of the computed geometric and electronic parameters for atoms and bonds of each compound occurring in a matrix is known as the electron-conformational matrix of congruity (ECMC). It contains the data from HF/3-21G level calculations...
May 28, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28547012/how-do-the-type-of-qtl-effect-and-the-form-of-the-residual-term-influence-qtl-detection-in-multi-parent-populations-a-case-study-in-the-maize-eu-nam-population
#18
Vincent Garin, Valentin Wimmer, Sofiane Mezmouk, Marcos Malosetti, Fred van Eeuwijk
In the QTL analysis of multi-parent populations, the inclusion of QTLs with various types of effects can lead to a better description of the phenotypic variation and increased power. For the type of QTL effect in QTL models for multi-parent populations (MPPs), various options exist to define them with respect to their origin. They can be modelled as referring to close parental lines or to further away ancestral founder lines. QTL models for MPPs can also be characterized by the homo- or heterogeneity of variance for polygenic effects...
May 25, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28545854/transcriptome-wide-identification-of-host-genes-targeted-by-tomato-spotted-wilt-virus-derived-small-interfering-rnas
#19
Shunmugiah V Ramesh, Sarah Williams, Madhu Kappagantu, Neena Mitter, Hanu R Pappu
RNA silencing mechanism functions as a major defense against invading viruses. The caveat in the RNA silencing mechanism is that the effector small interfering RNAs (siRNAs) act on any RNA transcripts with sequence complementarity irrespective of target's origin. A subset of highly expressed viral small interfering RNAs (vsiRNAs) derived from the tomato spotted wilt virus (TSWV; Tospovirus: Bunyaviridae) genome was analyzed for their propensity to downregulate the tomato transcriptome. A total of 11898 putative target sites on tomato transcripts were found to exhibit a propensity for down regulation by TSWV-derived vsiRNAs...
May 22, 2017: Virus Research
https://www.readbyqxmd.com/read/28540572/characterization-and-mapping-of-dt1-locus-which-co-segregates-with-cctfl1-for-growth-habit-in-pigeonpea
#20
Rachit K Saxena, Jimmy Obala, Andrey Sinjushin, C V Sameer Kumar, K B Saxena, Rajeev K Varshney
We report growth habit profiling following SEM, genetic mapping and QTL analysis. Highlighted CcTFL1 , a candidate for determinacy in pigeonpea, since an Indel marker derived from this gene co-segregated with Dt1 locus. Pigeonpea (Cajanus cajan) is one of the most important legume crops grown in arid and semi-arid regions of the world. It is characterized with few unique features compared with other legume species, such as Lotus, Medicago, and Glycine. One of them is growth habit, an important agronomic trait...
May 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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