1,721,052 research outputs found
"Noisy beets": impact of phenotyping errors on genomic predictions for binary traits in Beta vulgaris
Full text linkBackground
Noise (errors) in scientific data is endemic and may have a detrimental effect on statistical analyses and experimental results. The effects of noisy data have been assessed in genome-wide association studies for case-control experiments in human medicine. Little is known, however, on the impact of noisy data on genomic predictions, a widely used statistical application in plant and animal breeding.
Results
In this study, the sensitivity to noise in the data of five classification methods (K-nearest neighbours—KNN, random forest—RF, ridge logistic regression—LR, and support vector machines with linear or radial basis function kernels) was investigated. A sugar beet population of 123 plants phenotyped for a binary trait and genotyped for 192 SNP (single nucleotide polymorphism) markers was used. Labels (0/1 phenotype) were randomly sampled to generate noise. From the base scenario without errors in the labels, increasing proportions of noisy labels—up to 50 %—were generated and introduced in the data.
Conclusions
Local classification methods—KNN and RF—showed higher tolerance to noisy labels compared to methods that leverage global data properties—LR and the two SVM models. In particular, KNN outperformed all other classifiers with AUC (area under the ROC curve) higher than 0.95 up to 20 % noisy labels. The runner-up method, RF, had an AUC of 0.941 with 20 % noise
The use of genetic markers to estimate relationships between dogs in the course of criminal investigations
Full text linkAbstract Objective: Attacks on humans by dogs in a pack, though uncommon, do happen, and result in severe, sometimes fatal, injuries. We describe the role that canine genetic markers played during the investigation of a fatal dog-pack attack involving a 50-year-old male truck driver in a parking lot in Tuscany (Italy). Using canine specific STR genetic markers, the local authorities, in the course of their investigations, reconstructed the genetic relationships between the dogs that caused the deadly aggression and other dogs belonging to the owner of the parking who, at the moment of the aggression, was located in another region of Italy. Results: From a Bayesian clustering algorithm, the most likely number of clusters was two. The average relatedness among the dogs responsible for the aggression was higher than the average relatedness among the other dogs or between the two groups. Taken together, all these results indicate that the two groups of dogs are clearly distinct. Genetic relationships showed that the two groups of dogs were not related. It was therefore unlikely that the murderous dogs belonged to the owner of the parking lot who, on grounds of this and additional evidence, was eventually acquitted
Predicting haplotype carriers from SNP genotypes in Bos taurus through linear discriminant analysis
No full textGenome-enabled predictions for binomial traits in sugar beet populations
Full text linkBackground: Genomicinformationcanbeusedtopredictnotonlycontinuousbutalsocategorical(e.g.binomial) traits. Several traits of interest in human medicine and agriculture present a discrete distribution of phenotypes (e.g. disease status). Root vigor in sugar beet (B. vulgaris) is an example of binomial trait of agronomic importance. In this paper, a panel of 192 SNPs (single nucleotide polymorphisms) was used to genotype 124 sugar beet individual plants from 18 lines, and to classify them as showing “high” or “low” root vigor.
Results: AthresholdmodelwasusedtofittherelationshipbetweenbinomialrootvigorandSNPgenotypes,through the matrix of genomic relationships between individuals in a genomic BLUP (G-BLUP) approach. From a 5-fold cross-validation scheme, 500 testing subsets were generated. The estimated average cross-validation error rate was 0.000731 (0.073%). Only 9 out of 12326 test observations (500 replicates for an average test set size of 24.65) were misclassified.
Conclusions: Theestimatedpredictionaccuracywasquitehigh.Suchaccuratepredictionsmayberelatedtothe high estimated heritability for root vigor (0.783) and to the few genes with large effect underlying the trait. Despite the sparse SNP panel, there was sufficient within-scaffold LD where SNPs with large effect on root vigor were located to allow for genome-enabled predictions to work
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds
No full textHeterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north-south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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