Distance-based Approach Research Articles

Focusing on variation: methods and applications of the concept of beta diversity in aquatic ecosystems

Ecologists usually estimate means, but devote much less attention to variation. The study of variation is a key aspect to understand natural systems and to make predictions regarding them. In community ecology, most studies focus on local species diversity (alpha diversity), but only in recent decades have ecologists devoted proper attention to variation in community composition among sites (beta diversity). This is in spite of the fact that the first attempts to estimate beta diversity date back to the pioneering work by Koch and Whittaker in the 1950s. Progress in the last decade has been made in the development both of methods and of hypotheses about the origin and maintenance of variation in community composition. For instance, methods are available to partition total diversity in a region (gamma diversity), in a local component (alpha), and several beta diversities, each corresponding to one scale in a hierarchy. The popularization of the so-called raw-data approach (based on partial constrained ordination techniques) and the distance-based approach (based on correlation of dissimilarity/distance matrices) have allowed many ecologists to address current hypotheses about beta diversity patterns. Overall, these hypotheses are based on niche and neutral theory, accounting for the relative roles of environmental and spatial processes (or a combination of them) in shaping metacommunities. Recent studies have addressed these issues on a variety of spatial and temporal scales, habitats and taxonomic groups. Moreover, life history and functional traits of species such as dispersal abilities and rarity have begun to be considered in studies of beta diversity. In this article we briefly review some of these new tools and approaches developed in recent years, and illustrate them by using case studies in aquatic ecosystems.

Measuring consensus in a preference-approval context

We consider measuring the degree of homogeneity for preference-approval profiles which include the approval information for the alternatives as well as the rankings of them. A distance-based approach is followed to measure the disagreement for any given two preference-approvals. Under the condition that a proper metric is used, we propose a measure of consensus which is robust to some extensions of the ordinal framework. This paper also shows that there exists a limit for increasing the homogeneity level in a group of individuals by simply replicating their preference-approvals.

Security risk assessment: toward a comprehensive practical risk management

This paper introduces a unique approach to a more integrated security risk assessment SRA. This is formalised based on the proven mathematical methods described in various articles in the literature and combined with the work developed by the author. Whilst the widely used qualitative frameworks were introduced by existing international standards, the approach presented in this paper provides a novel way of better managing security risks in organisations. It uses a combination of qualitative and ranking methods based on a distance-based approach. The successful implementation of this approach in one of the world's largest financial institutions provided an alternative and unconventional means of performing more practical integrated security risk management, in a manner consistent with the current set of standards and practices. The method used in this paper is more effective than the existing single-faceted methods available. It gauges the significance of each risk by ranking them and providing preferences based on users' perspectives. These are qualified and quantified to achieve more comprehensive and effective risk assessment results.

Relative Value of Managed Wetlands and Tidal Marshlands for Wintering Northern Pintails

Abstract Northern pintail Anas acuta (hereafter pintail) populations have declined substantially throughout the western United States since the 1970s, largely as a result of converting wetlands to cropland. Managed wetlands have been developed throughout the San Francisco Bay estuaries to provide wildlife habitat, particularly for waterfowl. Many of these areas were historically tidal baylands, and plans are underway to remove dikes and restore tidal action. The relationship between tidal baylands and waterfowl populations is poorly understood. Our objective was to provide information on selection and avoidance of managed and tidal marshland by pintails. During 1991–1993 and 1998–2000, we radiomarked and relocated 330 female pintails (relocations, n = 11,574) at Suisun Marsh, California, the largest brackish water estuary within San Francisco Bay, to estimate resource selection functions during the nonbreeding months (winter). Using a distance-based modeling approach, we calculated selection functions for different ecological communities (e.g., tidal baylands) and investigated variation explained by time of day (day or night hours) to account for differences in pintail behavior (i.e., foraging vs. roosting). We found strong evidence for selection of managed wetlands. Pintails also avoided tidal marshes and bays and channels. We did not detect differences in selection function between day and night hours for managed wetlands, but the degree of avoidance of other habitats varied by time of day. We also found that areas subjected to tidal action did not influence the selection of immediately adjacent managed wetlands. In areas where tidal marsh is restored, improving habitat conditions in adjacent wetlands would likely increase local carrying capacities and offset the loss of wetland area.

Process designing for laser forming of circular sheet metal

Laser forming is a new type of flexible manufacturing process that has become viable for the shaping of metallic components. Process designing of laser forming involves finding a set of process parameters, including laser power, laser scanning paths, and scanning speed, given a prescribed shape. To date, research has focused on process designing for rectangular plates, and only a few studies are presented for axis-symmetric geometries like circular plates. In the present study, process designing for axis-symmetric geometries—with focus on class of shapes—is handled using a formerly proposed distance-based approach. A prescribed shape is achieved for geometries such as quarter-circular and half-circular ring plates. Experimental results verify the applicability of the proposed method for a class of shapes.

Weighted Euclidean distance-based approach as a multiple attribute decision making method for manufacturing situations

The selection of appropriate alternative in the manufacturing environment is a very important but at the same time a complex and difficult problem because of the availability of wide range of alternatives and similarity among them. So, there is a need for simple, systematic, and logical methods or mathematical tools to guide decision makers in considering a number of selection attributes and their interrelations. In this paper, a new multi-attribute decision making (MADM) method, ‘weighted Euclidean distance-based approach (WEDBA)’ is developed and applied to various decision making situations of the manufacturing environment. The method considers the objective weights of importance of the attributes as well as the subjective preferences of the decision maker to decide the integrated weights of importance of the attributes. Furthermore, the method uses fuzzy logic to convert the qualitative attributes into the quantitative attributes. Four examples are presented to illustrate the potential of the proposed WEDBA method and the results are compared with the results obtained by using other decision making methods.

Stability of gp41 hairpin and helix bundle assembly probed by combined stacking and circular dichroic approaches

The envelope glycoprotein gp41 of HIV-1 undergoes structural rearrangement to form a helix hairpin during the virus-mediated fusion. Previous studies to investigate the folding and stability of hairpin did not monitor the end-to-end distance of the molecule. To directly probe the distance change, rhodamine dye was conjugated to the gp41 recombinant near the N- and C-terminal regions to detect the UV absorption and fluorescence intensity changes induced by the chemical denaturant guanidinium chloride (GdmCl). Using the singly- and doubly-labeled constructs allowed us to distinguish between the hairpin formation and protein oligomerization. A biphasic transition of helical structure for the wild type protein was revealed by circular dichroism measurements while unfolding of the hairpin occurred at 6M GdmCl. The relevance of our study to the fusion inhibitor for HIV-1 was borne out by results on the mutants at the positions within the N-terminal heptad repeat (NHR) and the C-terminal heptad repeat (CHR) regions. A monophasic transition at lower denaturant concentration was detected for the NHR mutant supporting the concept of differential stability of NHR and CHR helical structure. The conclusion that the observed unstacking of doubly-labeled variant arises principally from the intra-molecular dimers was drawn from the unstacking of the protein labeled in the loop. Remarkably, it is deduced that the hairpin is more stable than the CHR helical structure. A model for denaturation of the helix hairpin bundle was proposed from these results. The biological implications of the findings and further applications of the distance-based approach were discussed.

Distance-based tractography in high angular resolution diffusion MRI

High angular resolution diffusion imaging (HARDI) is a magnetic resonance imaging (MRI) technique, determining the diffusion of water molecules in tissue in vivo. HARDI is advantageous over the well-known diffusion tensor imaging (DTI), since it is able to extract more than one fiber orientation within a voxel and can therefore resolve crossing, kissing or fanning fiber tracts. However, multiple orientations per voxel require more sophisticated tractography approaches. In this paper we introduce a new deterministic fiber tracking method using the complete orientation distribution function (ODF) reconstructed from Q-ball imaging to enable tractography in challenging regions. Anisotropy classifiers are used to differentiate intra-voxel fiber populations and adjust a curvature threshold for one and multiple fiber configurations, respectively. In addition, we determine the most appropriate propagation direction in complex white matter regions, using the course of the current tract. To ensure tractography running within fiber bundles, a distance-based approach is integrated, which aims to maintain the initial distance of the seed point to the white matter boundary through the whole tracking. We evaluated our method using a phantom dataset featuring crossing, kissing and fanning fiber configurations and a human brain dataset, reconstructing the fanning of the corpus callosum and considering the region of the centrum semiovale.

Quaternary range dynamics of ecologically divergent species (Edraianthus serpyllifolius and E. tenuifolius, Campanulaceae) within the Balkan refugium

Aim We investigated Quaternary range dynamics of two closely related but ecologically divergent species (cold-tolerant Edraianthus serpyllifolius and thermophilic Edraianthus tenuifolius) with overlapping distribution ranges endemic to the western Balkan Peninsula, an important yet understudied Pleistocene refugium. Our aims were: to test predictions of the ‘refugia-withinrefugia’ model of strong genetic subdivisions due to population isolation in separate refugia; to explore whether two ecologically divergent species reacted differently to Pleistocene climatic fluctuations; and to test predictions of the displacement refugia model of stronger differentiation among populations in the thermophilic E. tenuifolius compared with the cold-tolerant E. serpyllifolius. Location The western Balkan Peninsula. Methods We gathered amplified fragment-length polymorphism (AFLP) data and plastid DNA sequences from two to five individuals from 10 populations of E. serpyllifolius and 22 populations of E. tenuifolius, spanning their entire respective distribution areas. AFLP data were analysed using a Bayesian clustering approach and a distance-based network approach. Plastid sequences were used to depict relationships among haplotypes in a statistical parsimony network, and to obtain age estimates in a Bayesian framework. Results In E. serpyllifolius, both AFLP and plastid sequence data showed clear geographic structure. Western populations showed high AFLP diversity and a high number of rare fragments. In E. tenuifolius, both markers congruently identified a majorphylogeographicsplitalongthelowerNeretvavalleyincentralDalmatia.The most distinct and earliest diverging chloroplast DNA (cpDNA) haplotypes were found further south in the south-easternmost populations. North-western populations, identified as a separate cluster by Bayesian clustering, were characterized by low genetic diversity and a low number of rare AFLP markers. Main conclusions Clear evidence for multiple Pleistocene refugia is found not only in the high-elevation E. serpyllifolius, but also in the lowland E. tenuifolius, despite the lack of obvious dispersal barriers, in line with the refugia-withinrefugia model. Genealogical relationships and genetic diversity patterns support the hypothesis that cold-adapted E. serpyllifolius responded to climatic oscillations mostly by elevational range shifts, whereas thermophilic E. tenuifolius did so mainly by latitudinal range shifts, with different phases (and probably extents) of range expansion. In contrast to the displacement refugia hypothesis, the two elevationally differentiated species do not differ in their genetic diversity.

Evaluating flexible manufacturing systems using Euclidean distance-based integrated approach

A flexible manufacturing system (FMS) is designed to combine the efficiency of a mass-production line and the flexibility of a job shop to produce a variety of products on a group of machines. Even though a number of studies were proposed in the past to address the issue of evaluation and selection of FMSs, there is a need for a simple and systematic method to guide user organisations in taking a proper decision. In this paper, a new multiple attribute decision making (MADM) method, named as ‘Euclidean distance-based approach (EDBA)’, is presented for the selection of an FMS from a set of mutually exclusive alternatives. The results are compared with the results obtained by using other decision making methods. The method considers the objective weights of importance of the attributes as well as the subjective preferences of the decision maker to decide the integrated weights of importance of the attributes. Furthermore, the method uses fuzzy logic to convert the qualitative attributes into the quantitative attributes. Three examples are presented to illustrate the potential of the proposed approach.

Loop-closing: A typicality approach

Loop-closing has long been identified as a critical issue when building maps from local observations. Topological mapping methods abstract the problem of how loops are closed from the problem of how to determine the metrical layout of places in the map and how to deal with noisy sensors. The typicality problem refers to the identification of new classes in a general classification context. This typicality concept is used in this paper to help a robot acquire a topological representation of the environment during its exploration phase. The problem is addressed using the INCA statistic which follows a distance-based approach. In this paper we describe a place recognition approach based on match testing by means of the INCA test. We describe the theoretical basis of the approach and present extensive experimental results performed in both a simulated and a real robot-environment system; Behaviour Based philosophy is used to construct the whole control architecture. Obtained results show the validity of the approach.

Discovering Local Outliers using Dynamic Minimum Spanning Tree with Self-Detection of Best Number of Clusters

Detecting outliers in database (as unusual objects) using Clustering and Distance-based approach is a big desire. Minimum spanning tree based clustering algorithm is capable of detecting clusters with irregular boundaries. In this paper we propose a new algorithm to detect outliers based on minimum spanning tree clustering and distance-based approach. Outlier detection is an extremely important task in a wide variety of application. The algorithm partition the dataset into optimal number of clusters. Small clusters are then determined and considered as outliers. The rest of the outliers (if any) are then detected in the clusters using Distance-based method. The algorithm uses a new cluster validation criterion based on the geometric property of data partition of the dataset in order to find the proper number of clusters. The algorithm works in two phases. The first phase of the algorithm creates optimal number of clusters, where as the second phase of the algorithm detect outliers in the clusters. The key feature of our approach is it combines the best features of Distance-based and Clustering-based outlier detection to find noise-free/error-free clusters for a given dataset without using any input parameters. General Terms: Graph Based Algorithm; Information retrieval;

Genetic differentiation of Sorbus torminalis in Eastern Europe as determined by microsatellite markers

AbstractThe genetic variation in fourteen Sorbus torminalis (L.) Crantz. populations distributed over the eastern and south-eastern part of its range was studied using seven nuclear microsatellite loci. The differentiation level was relatively high (F ST = 0.228), as expected for a species with a fragmented range. The distance-based approach to the analysis of differentiation patterns (neighbour-joining tree based on pairwise coefficients of differentiation) did not reveal a clear geographical structure. On the other hand, model-based Bayesian methods (BAPS and STRUCTURE) gave geographically continuous clusters of populations. The occurrence of populations deviating strongly from the general pattern is attributed to founder effect. In spite of a generally high differentiation, a significant isolation-by-distance pattern was found, which might be a consequence of postglacial migration and gene flow among descendants of different refugia.

Space and habitat use of moose in southwestern Sweden

Increasingly, wildlife managers and land managers are challenged to maintain the viability of large mammal populations. Although the moose (Alces alces) is an ecologically, economically, and culturally important ungulate species found throughout most of Sweden, little is known about its ecology throughout the southern part of the country. We collected baseline ecological data on spatial and habitat use patterns in urbanized southwestern Sweden by fitting 22 adult moose (13 F, nine M) with global positioning system (GPS) radio collars. Home range size of cows did not differ among seasons (P > 0.10); however, bulls had larger home ranges during fall than all other seasons (P < 0.010). Mean home range size of males during fall and spring was larger than females during any season (P < 0.010). We used a Euclidean distance-based approach to analyze multi-scale habitat selection by moose. Moose of both sexes and during all seasons selected boreal forest and mires when establishing a home range (P < 0.10). Moose had seasonal differences in habitat selection within their home range (P 0.001), and generally selected clear-cuts and early successional forests, mature coniferous forests, and glades, but avoided agricultural areas and open water. Habitat and space use characteristics of moose in our urbanizing study area were similar to characteristics reported for moose in forest-dominated landscapes of Fennoscandia.

Population structure and linkage disequilibrium unravelled in tetraploid potato

Association mapping is considered to be an important alternative strategy for the identification of quantitative trait loci (QTL) as compared to traditional QTL mapping. A necessary prerequisite for association analysis to succeed is detailed information regarding hidden population structure and the extent of linkage disequilibrium. A collection of 430 tetraploid potato cultivars, comprising two association panels, has been analysed with 41 AFLP® and 53 SSR primer combinations yielding 3364 AFLP fragments and 653 microsatellite alleles, respectively. Polymorphism information content values and detected number of alleles for the SSRs studied illustrate that commercial potato germplasm seems to be equally diverse as Latin American landrace material. Genome-wide linkage disequilibrium (LD)—reported for the first time for tetraploid potato—was observed up to approximately 5 cM using r 2 higher than 0.1 as a criterion for significant LD. Within-group LD, however, stretched on average twice as far when compared to overall LD. A Bayesian approach, a distance-based hierarchical clustering approach as well as principal coordinate analysis were adopted to enquire into population structure. Groups differing in year of market release and market segment (starch, processing industry and fresh consumption) were repeatedly detected. The observation of LD up to 5 cM is promising because the required marker density is not likely to disable the possibilities for association mapping research in tetraploid potato. Population structure appeared to be weak, but strong enough to demand careful modelling of genetic relationships in subsequent marker-trait association analyses. There seems to be a good chance that linkage-based marker-trait associations can be identified at moderate marker densities.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-010-1379-5) contains supplementary material, which is available to authorized users.

Selection of Optimal Software Reliability Growth Models Using a Distance Based Approach

A large number of software reliability growth models (SRGMs) have been proposed during the past 30 years to estimate software reliability measures such as the number of remaining faults, software failure rate, and software reliability. Selection of an optimal SRGM for use in a particular case has been an area of interest for researchers in the field of software reliability. Tools and techniques for software reliability model selection found in the literature cannot be used with high confidence as they use a limited number of model selection criteria. For the first time, we developed a deterministic quantitative model based on a distance based approach (DBA) method, then applied it for evaluation, optimal selection, and ranking of SRGMs. DBA recognizes the need for relative importance of criteria for a given application, without which inter-criterion comparison could not be accomplished. It requires a set of model selection criteria, along with a set of SRGMs, and their level of criteria for optimal selection; and it successfully presents the results in terms of a merit value which is used to rank the SRGMs. We use two distinct, real data sets for demonstration of the DBA method. The result of this study will be a ranking of SRGMs based on the Euclidean composite distance of each alternative to the designated optimal SRGM.

Optimal selection of robots by using distance based approach method

A deterministic quantitative model based on Distance Based Approach (DBA) method has been developed for evaluation, selection and ranking of robots, which is a concept hitherto not employed in selection problem of this kind. As a significant development over and above past approaches to robot selection, it recognizes the need for, and processes the information about, relative importance of attributes for a given application, without which inter-se-attribute comparison could not be accomplished. It successfully presents the results of this information processing in terms of a merit value which is used to rank the robots. In order to demonstrate the aptness of using DBA method as a decision aid, the results so obtained have been compared with other techniques and methods available in the open literature. Sensitivity analysis test have been performed to analyze the critical and non-critical performance attributes for a robot. The model developed using DBA method is explained and illustrated with an example problem.

A distance-based rounding strategy for post-imputation ordinal data

Multiple imputation has emerged as a widely used model-based approach in dealing with incomplete data in many application areas. Gaussian and log-linear imputation models are fairly straightforward to implement for continuous and discrete data, respectively. However, in missing data settings which include a mix of continuous and discrete variables, correct specification of the imputation model could be a daunting task owing to the lack of flexible models for the joint distribution of variables of different nature. This complication, along with accessibility to software packages that are capable of carrying out multiple imputation under the assumption of joint multivariate normality, appears to encourage applied researchers for pragmatically treating the discrete variables as continuous for imputation purposes, and subsequently rounding the imputed values to the nearest observed category. In this article, I introduce a distance-based rounding approach for ordinal variables in the presence of continuous ones. The first step of the proposed rounding process is predicated upon creating indicator variables that correspond to the ordinal levels, followed by jointly imputing all variables under the assumption of multivariate normality. The imputed values are then converted to the ordinal scale based on their Euclidean distances to a set of indicators, with minimal distance corresponding to the closest match. I compare the performance of this technique to crude rounding via commonly accepted accuracy and precision measures with simulated data sets.

A Distance-Based Approach for Mining Changes in Purchase Behavior in Retail Sale

The research paper proposes the relevance of a distance-based approach for change mining and suggests a technique for distance-based change mining. Change mining gives an insight to the retailers on the changing purchase behavior of the shoppers. The research makes an attempt to account for the distance between the attribute-values within a feature of the customerprofile while measuring the similarity between two patterns.

Environmental/economic power dispatch using a hybrid multi-objective optimization algorithm

To solve the highly constrained environmental/economic dispatch problem involving conflicting objectives, this paper presents a hybrid multi-objective optimization algorithm based on particle swarm optimization (PSO) and differential evolution (DE). In this algorithm, a PSO with time variant acceleration coefficients is designed to explore the entire search space, while a local version of DE is proposed to exploit the sub-space with sparse solutions. A crowing distance-based approach is introduced to assign the particles’ leaders and to update the external archive. Moreover, a new technique for equality constraints is proposed to hurdle the unfeasible solutions directly. Finally, several optimization trials of the proposed algorithm are carried out on the IEEE 30-bus test system. Results demonstrate superiority of the proposed approach and confirm its potential to solve the multi-objective EED problem.