Maximum Dissimilarity Research Articles

Assessment of Genetic Diversity of Local and Exotic Brassica napus Germplasm

Estimation of genetic diversity of Brassica germplasm provides the basis for rapeseed/mustard genetic improvement. Studies were undertaken to estimate the genetic diversity of 30 lines of Brassica napus using Randomly Amplified Polymorphic DNA (RAPD) primers. A total of 30 B. napus genotypes of local and exotic origin were characterized using molecular markers. Four RAPD primers were used to estimate the genetic distances among the genotypes in all the possible combinations. The genetic diversity study revealed different levels of genetic polymorphism for RAPD primers GLA05, GLA07, GLA09 and GLA 10, resulting in amplification of 5.7, 3.5, 3.1 and 5.4 scorable bands (loci) per genotype, respectively. Individual genetic distances observed among B. napus genotypes ranged from 6.5 to 51%. Bivariate data matrix was generated and genetic distances were calculated using Unweighted Pair Group of Arithmetic Mean (UPGMA) procedure. The UPGMA cluster analyses revealed maximum genetic dissimilarity for 8966-1 and 8969-1 genotypes, closely followed by Ganyou-5, 89127-1, 89111-2 and Mlep-048. It is recommended that among the thirty B. napus genotypes, genetically distinct lines pointed out in the present study, should be used in future breeding programs for improvement of Brassica napus.

Bicriterion methods for partitioning dissimilarity matrices

Partitioning indices associated with the within-cluster sums of pairwise dissimilarities often exhibit a systematic bias towards clusters of a particular size, whereas minimization of the partition diameter (i.e. the maximum dissimilarity element across all pairs of objects within the same cluster) does not typically have this problem. However, when the partition-diameter criterion is used, there is often a myriad of alternative optimal solutions that can vary significantly with respect to their substantive interpretation. We propose a bicriterion partitioning approach that considers both diameter and within-cluster sums in the optimization problem and facilitates selection from among the alternative optima. We developed several MATLAB-based exchange algorithms that rapidly provide excellent solutions to bicriterion partitioning problems. These algorithms were evaluated using synthetic data sets, as well as an empirical dissimilarity matrix.

Middle Permian Brachiopods from Greece and their palaeobiogeographical significance: New evidence for a Gondwanan affinity of the Chios Island upper unit

Synopsis Wordian (Middle Permian) brachiopods from the allochthonous Upper Unit of Chios (Greece) are described and used to perform a palaeobiogeographical analysis to establish the pa‐laeogeographicalaffinities of the unit. Species of the genera Stenoscisma Conrad, 1839, Cleiothyridina Buckman, 1906, Martinia McCoy, 1844 and Dielasma King, 1859 are reported for the first time from Chios and their systematic descriptions are given. In addition, the revision and discussion of the genus Kotlaia Grant, 1993 and its comparison with Orthotichia Hall & Clarke, 1892 are provided in the systematic section. A matrix of presence/absence data of Wordian (Middle Permian) brachiopod genera from Crimea, Sosio, Oman, Chios, the Salt Range and Timor was analysed using multivariate methods. Cluster analysis, principal coordinate analysis, non‐metric multidimensional scaling, minimum spanning trees and bond analyses indicate a similarity between Chios and the Gondwanan data sets of Oman and the Salt Range. However, maximum dissimilarity is recorded when comparing Chios to the Crimean brachiopod faunas. This indicates a clear Gondwanan affinity of the Wordian brachiopods of the Upper Unit of Chios.

Non-sequential multiscale content-based video decomposition

In this paper, a multiscale content-based video decomposition scheme is presented for efficient non-linear (non-sequential) organization of the video visual content. In particular, each video file is analyzed in a multiscale structure of different “content resolution levels”, creating a hierarchy from the lowest (coarse) to the highest (fine) resolution. The scheme resembles the progressive transmission of still images, where instead of transmitting the image sequentially at a full resolution, by scanning it line by line, a lower image resolution is first delivered and then, the image quality gradually enhances so that the user is able at any time to see a preview of the image content. The proposed video decomposition is represented as a graph structure, each level of which corresponds to a particular content resolution, while the graph-nodes the respective regions that the content is analyzed at this level. Transitions among nodes of the same level are also permitted. The number of nodes at a given level expresses the degree of detail that the content at this level is analyzed. This number is estimated by minimizing the average transmitted information, required for localizing a video segment of interest and also takes into account the content complexity. Quality criteria are introduced to evaluate the efficiency of the proposed scheme. The efficiency of the organization is maximized if multiscale content decomposition is performed using content representatives and constructing content classes. Content representatives are estimated in our approach as the ones of the maximum dissimilarity, expressed by a distance metric. The optimization is conducted by incorporating a stochastic algorithm of logarithmically reduced searching area (stochastic logarithmic). Experimental results on real-life video sequences show that the proposed multiscale video organization enables users to detect content of interest much faster, compared to the conventional sequential video scanning or other video decomposition/summarization methods, resulting in a better organization efficiency as measured by the quality criteria.

Is Twelve-Tone Music Artistically Defective?

abstracting from the music. If they do not learn the specific order ofthe prime form of a row, how are they recognizing permutations (inversion, ret-rograde, etc.) of the prime form as such? Here one wonders whether the fact thatonly two rows were used in this study made the various tasks artificially easy.I want to mention also some experiments designed to test Allen Forte’s well-known theory of the pitch structure of atonal (not necessarily twelve-tone) music.While the structures Forte discusses differ from those specified by Schoenberg,they equally avoid any implication of tonal center. Hence as far as the psychol-ogy of perception is concerned, the results of these experiments are likely to beinformative.Gibson (1985) tested 198 subjects, of whom 173 were university music stu-dents or faculty; 63 of the latter group were experienced with the atonal idiom.Each trial consisted of the presentation of two pairs of chords, in which themembers of one pair were highly similar in pitch content according to Forte’sanalysis, while the members of the other pair were highly different (indeed, com-plementary). The subjects’ task on each trial was to say “which pair sounds moredifferent.”Gibson discovered that even his expert listeners were unable to performthis task. (Also, contrary to what Krumhansl and her colleagues found, Gibson’ssubjects did less well when stimuli were presented in a musical context than whenthey were presented neutrally.) He concludes:“[these] results...strongly suggestthat the relationships presented in this experiment do not present the aural cor-relate of their theoretical associations to listeners” (1985, p. 21). In a subsequentpaper reporting similar results from another experiment (1993), Gibson writes that the “overall evidence suggested that neither maximum pc similarity (pc setidentity) nor maximum pc dissimilarity (literal complementation) was capable of projecting its aural correlate to auditors....[I]t seems clear that theoreticalspeculation is not always reflected in aural experience” (1993, p. 23).

Assessing reference sites and ecological quality of river plant assemblages from an Iberian basin using a multivariate approach

This study attempts to develop and discuss the applicability of a method for using river plant assemblages as indicators of ecological quality in a southern Iberian basin, located in Portugal. Several relevant aspects contribute to make this purpose scientifically challenging. Two thirds of the basin are located in Spanish territory, a large part of the river system is intermittent, the historical reference data on river plants in the basin are non-existent and the distribution patterns of Iberian river plants are scarcely known. A survey of 40 sites was conducted in late spring 1999, covering all the basin. Vegetation data were treated by hierarchical classification and by canonical correspondence analysis, using both environmental (19) and anthropogenic (9) variables. Three plant ecotypes were identified, having different geological and geographical backgrounds. For the selection of reference sites of each ecotype, the environmental variables significantly explaining within-ecotype species distribution were determined by a forward selection procedure and latterly used as co-variables. A partial canonical correspondence analysis was then performed for each ecotype, using a unique variable for the anthropogenic influence, henceforth, leading to a sequence of less human disturbed sites being opposed to the more disturbed ones along the first canonical axis. A cluster analysis for the group of sites of each ecotype contributed to the final distinction of the reference sites, still presenting some intrinsic natural floral variability. The Bray-Curtis dissimilarity within the group of sites from each ecotype ranged between a natural similarity variation and a maximum dissimilarity (a community within the same ecotype but with a plant composition completely different from the floral reference). This range was partitioned into four classes of floristic quality corresponding to an increasing deviation from the pro-natural floristic state. The use of river plants as indicators of river integrity and the method used are discussed, considering the particular features of the river system studied and its plant assemblages.

Design and quantitative structure-activity relationship of 3-amidinobenzyl-1H-indole-2-carboxamides as potent, nonchiral, and selective inhibitors of blood coagulation factor Xa.

A series of 138 nonchiral 3-amidinobenzyl-1H-indole-2-carboxamides and analogues as inhibitors of the blood coagulation enzyme factor Xa (fXa) were designed, synthesized, and investigated by X-ray structure analysis and 3D quantitative structure-activity relationship (QSAR) studies (CoMFA, CoMSIA) in order to identify important protein-ligand interactions responsible for biological affinity and selectivity. Several compounds from this series are highly potent and selective inhibitors of this important enzyme linking extrinsic and intrinsic coagulation pathways. To rationalize biological affinity and to provide guidelines for further design, all compounds were docked into the factor Xa binding site. Those docking studies were based on X-ray structures of factor Xa in complex with literature-known inhibitors. It was possible to validate those binding modes by four X-ray crystal structures of representative ligands in factor Xa, while one ligand was additionally crystallized in trypsin to rationalize requirements for selective factor Xa inhibition. The 3D-QSAR models based on a superposition rule derived from these docking studies were validated using conventional and cross-validated r(2) values using the leave-one-out method and repeated analyses using two randomly chosen cross-validation groups plus randomization of biological activities. This led to consistent and highly predictive 3D-QSAR models with good correlation coefficients for both CoMFA and CoMSIA, which were found to correspond to experimentally determined factor Xa binding site topology in terms of steric, electrostatic, and hydrophobic complementarity. Subsets selected as smaller training sets using 2D fingerprints and maximum dissimilarity methods resulted in 3D-QSAR models with remarkable correlation coefficients and a high predictive power. The final quantitative SAR information agrees with all experimental data for the binding topology and thus provides reasonable activity predictions for novel factor Xa inhibitors.

Optimised soundprint selection for identification in audio streams

An improved iterative method for selection of reference soundprints from a set of sound records to be identified is presented. The soundprints applied for reliable streaming audio identification should have maximum dissimilarity to each other. As the first trial of the iteration, a set of soundprints is randomly selected according to a grid placed on the records. To the accepted set, a further local refinement process is applied using the quadratic local approximations of the Euclidean distance between the soundprints. A large number of measurements have shown that the method significantly improves the reliability of real-time monitoring.

Comparing 3D Pharmacophore Triplets and 2D Fingerprints for Selecting Diverse Compound Subsets

The performance of two important 2D and 3D molecular descriptors for rational design to maximize the structural diversity of databases is investigated in this publication. Those methods are based either on a 2D description using a binary fingerprint, which accounts for the absence or presence of molecular fragments, or a 3D description based on the geometry of pharmacophoric features encoded in a fingerprint (pharmacophoric definition triplets, PDTs). Both descriptors in combination with maximum dissimilarity selections, complete linkage hierarchical cluster analysis, or sequential dissimilarity selections were compared to random subsets as reference. This comparison is based on their ability to cover representative biological classes from parent databases (coverage analysis) and the degree of separation between active and inactive compounds for a biological target from hierarchical clustering (cluster separation analysis). While the similarity coefficients (Tanimoto, cosine) show only a minor influence, the number of conformations to generate the 3D PDT fingerprint lead to remarkably different results. PDT fingerprints derived from a lower number of conformers perform significantly better, but they are not comparable to a 2D fingerprint-based design. When 2D and 3D descriptors are combined with weighting factors > 0.5 for 2D fingerprints, a significant improvement of coverage and cluster separation results is observed for a small number of PDT conformers and medium sized subsets. Some combined descriptors outperform 2D fingerprints, but not for all subset populations. Applying sequential dissimilarity selection to PDT descriptors reveals that its performance is dependent on the initial ordering of compounds, while presorting according to 2D fingerprint diversity does not improve results. Finally the relationship between biological activity and similarity was investigated, showing that PDTs quantify smaller structural differences due to the large number of bits in the fingerprint.

Mating type, pathotype and RAPDs analysis inDidymella rabiei, the agent of ascochyta blight of chickpea

Eleven pathotype groups (A-K), including five not previously reported, ofDidymella rabiei (anamorphAscochyta rabiei), representing isolates of the pathogen from Ascochyta blight-affected chickpeas mainly from India, Pakistan, Spain and the USA, were characterized using 44 single-spore isolates tested against seven differential chickpea lines. Of 48 isolates tested for mating type, 58% belonged to MAT 1-1 and 42% to MAT 1-2. Thirty-nineD. rabiei isolates, as well as two isolates ofAscochyta pisi and six isolates of unrelated fungi, were analyzed using Randomly Amplified Polymorphic DNAs (RAPDs) employing five primers (P2 at 40°C, and OPA3, OPC1, OPC11 and OPC20 at 35°C). Computer cluster analysis (UPGMA / NTSYS-PC) detected a relatively low level of polymorphism among all theD. rabiei isolates, although atca 7% dissimilarity,ca 10 RAPD groups [I-X] were demarcated, as well as subclustering within the larger groups. By the same criteria, the maximum dissimilarity for the whole population ofD. rabiei isolates wasca 13%. No correlation was found between different RAPD groups, pathotype, or mating type ofD. rabiei, although some evidence of clustering based on geographic origin was detected. The use of RAPDs enabled us to identify specific DNA fragments that may have a potential use as genetic markers in sexual crosses, but none which could be used as virulence markers.

Data Structure Comparison Using Box Counting Analysis

Box counting analysis was performed to visualize complex data structures of datasets. Two datasets were used as original datasets. One included 8000 samples and the other included 53 064 samples. Nine different selection methods were used to select subsets. The selection methods were as follows: maximum dissimilarity method, maximum similarity method, group averaging hierarchical clustering method, reciprocal nearest neighbor Ward hierarchical clustering method, k-mean nonhierarchical clustering methods with two types of seed points, Genetic algorithms (GAs), Kohonen networks, and cell-based method. The data structures of selected subsets were compared to that of the original dataset by using box counting analysis.

DISSIM: a program for the analysis of chemical diversity

As interest in database searching and compound selection has grown, there has been a concomitant growth in interest in the quantification of chemical similarity. Described here is a computer program called DISSIM, which addresses the problem of selecting diverse subsets from larger collections of chemical compounds. It is a pragmatic solution combining a maximum dissimilarity search algorithm and a general multidimensional measure of chemical similarity based on the combination of different molecular descriptors. The problem of correlation between descriptors is addressed and appropriate schemes for weighting and normalisation are described. The specific application of these techniques to the comparative analysis of topological indices and their use in the area of chemical diversity analysis and compound selection are also described.

DISSIM: a program for the analysis of chemical diversity

As interest in database searching and compound selection has grown, there has been a concomitant growth in interest in the quantification of chemical similarity. Described here is a computer program called DISSIM, which addresses the problem of selecting diverse subsets from larger collections of chemical compounds. It is a pragmatic solution combining a maximum dissimilarity search algorithm and a general multidimensional measure of chemical similarity based on the combination of different molecular descriptors. The problem of correlation between descriptors is addressed and appropriate schemes for weighting and normalisation are described. The specific application of these techniques to the comparative analysis of topological indices and their use in the area of chemical diversity analysis and compound selection are also described.

Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies.

Estimation of evolutionary distances from coding sequences must take into account protein-level selection to avoid relative underestimation of longer evolutionary distances. Current modeling of selection via site-to-site rate heterogeneity generally neglects another aspect of selection, namely position-specific amino acid frequencies. These frequencies determine the maximum dissimilarity expected for highly diverged but functionally and structurally conserved sequences, and hence are crucial for estimating long distances. We introduce a codon-level model of coding sequence evolution in which position-specific amino acid frequencies are free parameters. In our implementation, these are estimated from an alignment using methods described previously. We use simulations to demonstrate the importance and feasibility of modeling such behavior; our model produces linear distance estimates over a wide range of distances, while several alternative models underestimate long distances relative to short distances. Site-to-site differences in rates, as well as synonymous/nonsynonymous and first/second/third-codon-position differences, arise as a natural consequence of the site-to-site differences in amino acid frequencies.

Identification of zygotic and nucellar tangerine seedlings (Citrus spp.) using RAPD

The randomly amplified polymorphic DNA (RAPD) technique was used to distinguish nucellar and zygotic seedlings resulting from crosses between the ‘Montenegrina’ (Citrus deliciosa Tenore) and‘ King’ (C. nobilis Loureiro) tangerines. The aim of the present study was to develop tangerine varieties with a reduced number of seeds and organoleptic characteristics similar to the ‘Montenegrina’ tangerine. Embryos were isolated from seeds, cultivated in vitro, and acclimated in a greenhouse. Four random primers were used to identify 54 plants of sexual origin from a total of 202 individuals. The degree of polymorphism of each primer was reflected in the number of zygotic plants obtained per primer. Cluster analysis of parents and progeny separated the individuals into distinct groups with a maximum genetic dissimilarity of 20%.

OptiSim: An Extended Dissimilarity Selection Method for Finding Diverse Representative Subsets

Compound selection methods currently available to chemists are based on maximum or minimum dissimilarity selection or on hierarchical clustering. Optimizable K-Dissimilarity Selection (OptiSim) is a novel and efficient stochastic selection algorithm which includes maximum and minimum dissimilarity-based selection as special cases. By adjusting the subsample size parameter K, it is possible to adjust the balance between representativeness and diversity in the compounds selected. The OptiSim algorithm is described, along with some analytical tools for comparing it to other selection methods. Such comparisons indicate that OptiSim can mimic the representativeness of selections based on hierarchical clustering and, at least in some cases, improve upon them.

Experimental Designs for Selecting Molecules from Large Chemical Databases

Recent developments in high-throughput screening and combinatorial chemistry have generated interest in experimental design methods to select subsets of molecules from large chemical databases. In this manuscript three methods for selecting molecules from large databases are described: edge designs, spread designs, and coverage designs. Two algorithms with linear time complexity that approximate spread and coverage designs are described. These algorithms can be threaded for multiprocessor systems, are compatible with any definition of molecular distance, and may be applied to very large chemical databases. For example, ten thousand molecules were selected using the maximum dissimilarity approximation to a spread design from a sixty-dimensional simulated molecular database of one million molecules in approximately 6 h on a UNIX workstation.

Selective partition algorithm for finding regions of maximum pairwise dissimilarity among statistical class models

A technique for finding areas of maximum dissimilarity between the statistical models of two closely resembling classes is introduced. It is shown that this technique combines statistical and syntactic recognition techniques by extracting features from structurally distinctive regions of the models and is applicable in a variety of image classification and recognition tasks.

Diversity analysis and species identification in Lens using PCR generated markers

Using random amplified polymorphic DNA (RAPD) analysis we assessed the genetic relationships between 16 accessions and cultivars of lentil (Lens culinaris ssp. culinaris) in the Australian lentil breeding program. All lines exhibited polymorphism with a maximum dissimilarity value of 0.36. This indicated a limited degree of genetic variation. Polymerase chain reaction (PCR) with primers based on the flanking regions of the 5S rRNA gene from Pisum sativum amplified the non-translated spacer (NTS) region from within the 5S rRNA gene of Lens. Three distinct amplification banding patterns differentiated between restricted genomic DNA of Lens spp. L. culinaris ssp. culinaris and L. culinaris ssp. orientalis shared similar markers of two distinctly different NTS sizes. L. nigricans and L. odemensis shared the same amplification pattern of a single sized NTS region. However, L. ervoides contained two separate sizes of NTS, distinct from other Lens species. In an effort to widen the genetic base of cultivated lentil, these species-specific molecular markers may be used to follow potential introgression between species.

Bicriterion Cluster Analysis

Cluster analysis is concerned with the problem of partitioning a given set of entities into homogeneous and well-separated subsets called clusters. The concepts of homogeneity and of separation can be made precise when a measure of dissimilarity between the entities is given. Let us define the diameter of a partition of the given set of entities into clusters as the maximum dissimilarity between any pair of entities in the same cluster and the split of a partition as the minimum dissimilarity between entities in different clusters. The problems of determining a partition into a given number of clusters with minimum diameter (i.e., a partition of maximum homogeneity) or with maximum split (i.e., a partition of maximum separation) are first considered. It is shown that the latter problem can be solved by the classical single-link clustering algorithm, while the former can be solved by a graph-theoretic algorithm involving the optimal coloration of a sequence of partial graphs, described in more detail in a previous paper. A partition into a given number of clusters will be called efficient if and only if there exists no partition into at most the same number of clusters with smaller diameter and not smaller split or with larger split and not larger diameter. Two efficient partitions are called equivalent if and only if they have the same values for the split and for the diameter.