581 research outputs found
Homoplasy corrected estimation of genetic similarity from AFLP bands, and the effect of the number of bands on the precision of estimation
No full textAFLP is a DNA fingerprinting technique, resulting in binary band presence–absence patterns, called profiles, with known or unknown band positions. We model AFLP as a sampling procedure of fragments, with lengths sampled from a distribution. Bands represent fragments of specific lengths. We focus on estimation of pairwise genetic similarity, defined as average fraction of common fragments, by AFLP. Usual estimators are Dice (D) or Jaccard coefficients. D overestimates genetic similarity, since identical bands in profile pairs may correspond to different fragments (homoplasy). Another complicating factor is the occurrence of different fragments of equal length within a profile, appearing as a single band, which we call collision. The bias of D increases with larger numbers of bands, and lower genetic similarity. We propose two homoplasy- and collision-corrected estimators of genetic similarity. The first is a modification of D, replacing band counts by estimated fragment counts. The second is a maximum likelihood estimator, only applicable if band positions are available. Properties of the estimators are studied by simulation. Standard errors and confidence intervals for the first are obtained by bootstrapping, and for the second by likelihood theory. The estimators are nearly unbiased, and have for most practical cases smaller standard error than D. The likelihood-based estimator generally gives the highest precision. The relationship between fragment counts and precision is studied using simulation. The usual range of band counts (50–100) appears nearly optimal. The methodology is illustrated using data from a phylogenetic study on lettuc
Course System Architecting for Management
No full textThis article describes the condensed version the course System Architecture by the Center for Technical Training CTT. Trainer is the author of this article Gerrit Muller. At this moment this course is only accessible for Philips Employees
Drivers of female power in bonobos
No full textAbstract In mammals, female dominance over males is a rare phenomenon. However, recent findings indicate that even in species with sexual dimorphism biased towards males, females sometimes occupy high status. Here we test three main hypotheses explaining intersexual power relationships, namely the self-reinforcing effects of winning and losing conflicts, the strength of mate competition, and female coalition formation. We test these for bonobos ( Pan paniscus ), one of our closest living relatives, where females have high status relative to males despite male-biased size dimorphism. We compiled demographic and behavioral data of 30 years and 6 wild living communities. Our results only support predictions of the female coalition hypothesis. We found that females target males in 85% of their coalitions and that females occupy higher ranks compared to males when they form more frequent coalitions. This result indicates that female coalition formation is a behavioral tool for females to gain power over males
An extraordinary photograph: Gerrit Rietveld, Mart Stam and El Lissitzky at the Schröder House, 1926
No full textThe Schröder House, designed in 1924 by Gerrit Th. Rietveld (1888-1964) in closecollaboration with the client Truus Schröder-Schräder (1889-1985), has beenphotographed countless times.1 Most of the photographs of this well-knownmonument are architectural photographs, of its exterior or interior. Only a fewof them include one or both of the designers. One such photograph, from 1926,appears in many publications concerning Rietveld or the Schröder House. It is anintriguing shot; but what exactly does it tell us?Heritage & Value
Gerrit Rietveld 's shop designs in the Netherlands from 1922 to 1962
No full textThis essay investigates the shops as well as commercial buildings designed by Gerrit Rietveld in the Netherlands from 1922 to 1962, focusing on the relation between the interior and the exterior in each project. Gaining insight into his contribution to the history of shop designs. This research has been conducted through a combination of literature study, and the archive of Gerrit Rietveld in the Het Nieuwe Instituut in Rotterdam, and provides elaboration on themes as the designs of the shop front, the interior, and the connection between them. These themes are addressed through observation of the images, and drawings in the archive and other resources. The essay also provides a critical view for the role of those shops in history, and their influences on subsequent shop designs after that. AR2A011Architecture, Urbanism and Building Science
The sense of God’s presence in prayer
No full textThe awareness of God’s presence and the experience of his works – key notions in practices of prayer – find reasonable doubt in our secular age. Meanwhile, there are, worldwide, many communities of faith where people enthusiastically pray and hold that they hear the voice of God. How can we understand this sense of God’s presence?
In prayer, people express their hope and fear, and they do so with heart and mind. This subjective involvement is characteristic for prayer. At the same time, supplicants address God in the conviction that God is present and active. Critics of religion, however, criticise this ‘external’ realm of the divine and consider prayer a superstitious delusion. Passages of William James and John Calvin help us to get some insight in the ‘object’ of our religious consciousness. Furthermore, William Alston defends a non-sensory mystical perception of the divine. Using these insights, the author explores prayer as a conversation with God and reflects on the notion: hearing the voice of God
Nawoord: Over veldwerk en antropologie als wetenschap
No full textSince the 1970s anthropologists write in a more reflexive way about their fieldwork. Anthropologist and travel author Gerrit Jan Zwier wrote a book about the rise of this genre. He asked the historian and anthropologist Yme Kuiper to add an epilogue to a new edition of his classic (first published in 1980)
Codominant scoring of AFLP in association panels
No full textA study on the codominant scoring of AFLP markers in association panels without prior knowledge on genotype probabilities is described. Bands are scored codominantly by fitting normal mixture models to band intensities, illustrating and optimizing existing methodology, which employs the EM-algorithm. We study features that improve the performance of the algorithm, and the unmixing in general, like parameter initialization, restrictions on parameters, data transformation, and outlier removal. Parameter restrictions include equal component variances, equal or nearly equal distances between component means, and mixing probabilities according to Hardy–Weinberg Equilibrium. Histogram visualization of band intensities with superimposed normal densities, and optional classification scores and other grouping information, assists further in the codominant scoring. We find empirical evidence favoring the square root transformation of the band intensity, as was found in segregating populations. Our approach provides posterior genotype probabilities for marker loci. These probabilities can form the basis for association mapping and are more useful than the standard scoring categories A, H, B, C, D. They can also be used to calculate predictors for additive and dominance effects. Diagnostics for data quality of AFLP markers are described: preference for three-component mixture model, good separation between component means, and lack of singletons for the component with highest mean. Software has been developed in R, containing the models for normal mixtures with facilitating features, and visualizations. The methods are applied to an association panel in tomato, comprising 1,175 polymorphic markers on 94 tomato hybrids, as part of a larger study within the Dutch Centre for BioSystems Genomics
Genotype calling in tetraploid species from bi-allelic marker data using mixture models
No full textAbstract Background Automated genotype calling in tetraploid species was until recently not possible, which hampered genetic analysis. Modern genotyping assays often produce two signals, one for each allele of a bi-allelic marker. While ample software is available to obtain genotypes (homozygous for either allele, or heterozygous) for diploid species from these signals, such software is not available for tetraploid species which may be scored as five alternative genotypes (aaaa, baaa, bbaa, bbba and bbbb; nulliplex to quadruplex). Results We present a novel algorithm, implemented in the R package fitTetra, to assign genotypes for bi-allelic markers to tetraploid samples from genotyping assays that produce intensity signals for both alleles. The algorithm is based on the fitting of several mixture models with five components, one for each of the five possible genotypes. The models have different numbers of parameters specifying the relation between the five component means, and some of them impose a constraint on the mixing proportions to conform to Hardy-Weinberg equilibrium (HWE) ratios. The software rejects markers that do not allow a reliable genotyping for the majority of the samples, and it assigns a missing score to samples that cannot be scored into one of the five possible genotypes with sufficient confidence. Conclusions We have validated the software with data of a collection of 224 potato varieties assayed with an Illumina GoldenGate™ 384 SNP array and shown that all SNPs with informative ratio distributions are fitted. Almost all fitted models appear to be correct based on visual inspection and comparison with diploid samples. When the collection of potato varieties is analyzed as if it were a population, almost all markers seem to be in Hardy-Weinberg equilibrium. The R package fitTetra is freely available under the GNU Public License from http://www.plantbreeding.wur.nl/UK/software_fitTetra.html and as Additional files with this article.</p
Public Management and Disaster Risk Reduction: potential interdisciplinary contributions
No full textThis article investigates the interdisciplinary nature of Disaster Risk Reduction as an emerging field of study. The development of this field of study is interpreted within the context of the evolution of Public Management as an academic discipline. The author argues that the philosophical and theoretical underpinnings of both Public Management and Disaster Risk Reduction share commonalities. Thus, the foundational and functional aspects of Public Management did, and should continue to, inform and enrich the study of Disaster Risk Reduction
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