Multidimensional Scaling with Regional Restrictions for Facet Theory: An Application to Levi's Political Protest Data

Multidimensional scaling (MDS) is often used for the analysis of correlation matrices of items generated by a facet theory design. The emphasis of the analysis is on regional hypotheses on the location of the items in the MDS solution. An important regional hypothesis is the axial constraint where the items from different levels of a facet are assumed to be located in different parallel slices. The simplest approach is to do an MDS and draw the parallel lines separating the slices as good as possible by hand. Alternatively, Borg and Shye (1995) propose to automate the second step. Borg and Groenen (1997, 2005) proposed a simultaneous approach for ordered facets when the number of MDS dimensions equals the number of facets. In this paper, we propose a new algorithm that estimates an MDS solution subject to axial constraints without the restriction that the number of facets equals the number of dimensions. The algorithm is based on constrained iterative majorization of De Leeuw and Heiser (1980) with special constraints. This algorithm is applied to Levi’s (1983) data on political protests.Axial Partitioning;Constrained Estimation;Facet Theory;Iterative Majorization;Multidimensional Scaling;Regional Restrictions

Synthesis of monoalkylated calix[4]arenes via direct alkylation

A new one-step procedure for the synthesis of monoalkylated calix[4]arenes is presented. Reaction of calix[4]arene 1a or 1b with 1.2 equivalent of a weak base (K2CO3 in MeCN or CsF in DMF) and excess of alkylating agent affords the monoalkylated calix[4]arenes in moderate to good yield

Buitenzorg Ayrshire Farm Breeding Diagram

A diagram of a family tree of the Ayrshire cows on Ralph LeCocq\u27s farm, with photos and descriptions.https://nwcommons.nwciowa.edu/lecocqfarm/1000/thumbnail.jp

Multidimensional Scaling with Regional Restrictions for Facet Theory: An Application to Levi's Political Protest Data

Multidimensional scaling (MDS) is often used for the analysis of correlation matrices of items generated by a facet theory design. The emphasis of the analysis is on regional hypotheses on the location of the items in the MDS solution. An important regional hypothesis is the axial constraint where the items from different levels of a facet are assumed to be located in different parallel slices. The simplest approach is to do an MDS and draw the parallel lines separating the slices as good as possible by hand. Alternatively, Borg and Shye (1995) propose to automate the second step. Borg and Groenen (1997, 2005) proposed a simultaneous approach for ordered facets when the number of MDS dimensions equals the number of facets. In this paper, we propose a new algorithm that estimates an MDS solution subject to axial constraints without the restriction that the number of facets equals the number of dimensions. The algorithm is based on constrained iterative majorization of De Leeuw and Heiser (1980) with special constraints. This algorithm is applied to Levi’s (1983) data on political protests

Participatory plant breeding: a way to arrive at better-adapted onion varieties

The search for varieties that are better adapted to organic farming is a current topic in the organic sector. Breeding programmes specific for organic agriculture should solve this problem. Collaborating with organic farmers in such programmes, particularly in the selection process, can potentially result in varieties better adapted to their needs. Here, we assume that organic farmers' perceptive of plant health is broader than that of conventional breeders. Two organic onion farmers and one conventional onion breeder were monitored in their selection activities in 2004 and 2005 in order to verify whether and in which way this broader view on plant health contributes to improvement of organic varieties. They made selections by positive mass selection in three segregating populations under organic conditions. The monitoring showed that the organic farmers selected in the field for earliness and downy mildew and after storage for bulb characteristics. The conventional breeder selected only after storage. Farmers and breeder applied identical selection directions for bulb traits as a round shape, better hardness and skin firmness. This resulted in smaller bulbs in the breeders’ populations, while the bulbs in the farmer populations were bigger than in the original population. In 2006 and 2007 the new onion populations will be compared with each other and the original populations to determine the selection response

Multidimensional scaling with regional restrictions for facet theory: an application to Levy's political protest data

"Multidimensional scaling (MDS) is often used for the analysis of correlation matrices of items generated by a facet-theory design. The emphasis of the analysis is on regional hypotheses on the location of the items in the MDS solution. An important regional hypothesis is the axial constraint, where the items from different levels of a facet are assumed to be located in different parallel slices. The simplest approach is to do an MDS and draw the parallel lines separating the slices as good as possible by hand. Alternatively, Borg & Shye (1995) proposed to automate the second step. Borg & Groenen (1997, 2005) proposed a simultaneous approach for ordered facets, when the number of MDS dimensions equals the number of facets. In this paper, we propose a new algorithm that estimates an MDS solution subject to axial constraints without the restriction that the number of facets equals the number of dimensions. The algorithm is based on constrained iterative majorization of De Leeuw & Heiser (1980) with special constraints. This algorithm is applied to Levy's (1983) data on political protests." (author's abstract

POSA: Perl Objects for DNA Sequencing Data Analysis

BACKGROUND: Capillary DNA sequencing machines allow the generation of vast amounts of data with little hands-on time. With this expansion of data generation, there is a growing need for automated data processing. Most available software solutions, however, still require user intervention or provide modules that need advanced informatics skills to allow implementation in pipelines. RESULTS: Here we present POSA, a pair of new perl objects that describe DNA sequence traces and Phrap contig assemblies in detail. Methods included in POSA include basecalling with quality scores (by Phred), contig assembly (by Phrap), generation of primer3 input and automated SNP annotation (by PolyPhred). Although easily implemented by users with only limited programming experience, these objects considerabily reduce hands-on analysis time compared to using the Staden package for extracting sequence information from raw sequencing files and for SNP discovery. CONCLUSIONS: The POSA objects allow a flexible and easy design, implementation and usage of perl-based pipelines to handle and analyze DNA sequencing data, while requiring only minor programming skills

Effect of wetting layers on the strain and electronic structure of InAs self-assembled quantum dots

The effect of wetting layers on the strain and electronic structure of InAs self-assembled quantum dots grown on GaAs is investigated with an atomistic valence-force-field model and an empirical tight-binding model. By comparing a dot with and without a wetting layer, we find that the inclusion of the wetting layer weakens the strain inside the dot by only 1% relative change, while it reduces the energy gap between a confined electron and hole level by as much as 10%. The small change in the strain distribution indicates that strain relaxes only little through the thin wetting layer. The large reduction of the energy gap is attributed to the increase of the confining-potential width rather than the change of the potential height. First-order perturbation calculations or, alternatively, the addition of an InAs disk below the quantum dot confirm this conclusion. The effect of the wetting layer on the wave function is qualitatively different for the weakly confined electron state and the strongly confined hole state. The electron wave function shifts from the buffer to the wetting layer, while the hole shifts from the dot to the wetting layer.Comment: 14 pages, 3 figures, and 3 table

Benchmarking ortholog identification methods using functional genomics data

BACKGROUND: The transfer of functional annotations from model organism proteins to human proteins is one of the main applications of comparative genomics. Various methods are used to analyze cross-species orthologous relationships according to an operational definition of orthology. Often the definition of orthology is incorrectly interpreted as a prediction of proteins that are functionally equivalent across species, while in fact it only defines the existence of a common ancestor for a gene in different species. However, it has been demonstrated that orthologs often reveal significant functional similarity. Therefore, the quality of the orthology prediction is an important factor in the transfer of functional annotations (and other related information). To identify protein pairs with the highest possible functional similarity, it is important to qualify ortholog identification methods. RESULTS: To measure the similarity in function of proteins from different species we used functional genomics data, such as expression data and protein interaction data. We tested several of the most popular ortholog identification methods. In general, we observed a sensitivity/selectivity trade-off: the functional similarity scores per orthologous pair of sequences become higher when the number of proteins included in the ortholog groups decreases. CONCLUSION: By combining the sensitivity and the selectivity into an overall score, we show that the InParanoid program is the best ortholog identification method in terms of identifying functionally equivalent proteins