RAMP based fingerprinting and assessment of relationships among Australian narrow-leafed lupin (Lupinus angustifolius L.) cultivars

2005 ◽  
Vol 56 (12) ◽  
pp. 1339 ◽  
Author(s):  
H. Yuan ◽  
G. Yan ◽  
K. H. M. Siddique ◽  
H. Yang
Keyword(s):  
Cluster Analysis ◽  
Molecular Identification ◽  
Distance Matrix ◽  
Farming System ◽  
Pairwise Distance ◽  
Grain Legume ◽  
Dna Variation ◽  
Legume Crop ◽  
Commercial Cultivars ◽  
Pairwise Distance Matrix

Narrow-leafed lupin is a major winter grain legume crop in the Australian farming system and a number of commercial cultivars are currently available to growers. A significant level of polymorphism was detected in narrow-leafed lupin cultivars by the randomly amplified microsatellite polymorphism (RAMP) approach, suggesting that cultivars harbour considerable DNA variation. Seventy-seven cultivar-specific markers were found among the 23 lupin cultivars examined and a dichotomous fingerprinting key was developed for the molecular identification of lupin cultivars. Cluster analysis of pairwise distance matrix computed from RAMP profiles grouped the 23 cultivars into 4–5 clusters, which generally agreed with their pedigree relationships.

scholarly journals Cluster Analysis Stopping Rules in Stata

2016 ◽  
Author(s):  
Brendan Halpin
Keyword(s):  
Cluster Analysis ◽  
Distance Matrix ◽  
Stopping Rules ◽  
Pairwise Distance ◽  
Optimum Number ◽  
Pairwise Similarity ◽  
Number Of Clusters ◽  
Euclidean Distances ◽  
New Applications ◽  
Pairwise Distance Matrix

AbstractAnalysts doing cluster analysis sometimes want the data to tell them the optimum number of clusters. Common "stopping rules" use the Calinski-Harabasz pseudo-F statistic and Duda-Hart indices, which are based on squared Euclidean distances between cases. Cluster analysis operates on a pairwise matrix of distances between the objects clusters, which are usually created from the observed variables. However, approaches such as expert judgement or algorithmic pattern-recognition (as used for instance in sequence analysis) often output matrices of pairwise similarity or difference whose relationship to the observed variables is much less direct. Built-in Stata utilities allow calculation of the CH and DH indices when cluster analysis starts from variables, but not with cluster analysis that starts from a pairwise distance matrix (unless the distances are squared Euclidean distances defined on variables which are still available). In this note I present two small Stata utilities that will calculate the CH and DH statistics from the distance matrix, if the distances are squared Euclidean. If the distances have another metric, these utilities can be seen as calculating a pseudo-CH pseudo-F or pseudo-DH statistic, potentially extending their use to new applications.-- Brendan Halpin, Head, Department of Sociology, University of Limerick, IrelandTel: w +353-61-213147 f +353-61-202569 h +353-61-338562; Room F1-002 x 3147mailto:[email protected] ULSociology on Facebook: http://on.fb.me/fjIK9thttp://teaching.sociology.ul.ie/bhalpin/wordpress twitter:@ULSociology

scholarly journals Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling

2020 ◽  
Vol 21 (3) ◽  
pp. 944 ◽  
Author(s):  
Valery V. Panyukov ◽  
Sergey S. Kiselev ◽  
Olga N. Ozoline
Keyword(s):  
Distance Matrix ◽  
Pairwise Distance ◽  
Clinical Samples ◽  
E Coli ◽  
Taxonomic Profiling ◽  
New Methods ◽  
Natural Microflora ◽  
Microbiome Profiling ◽  
Pairwise Distance Matrix

The need for a comparative analysis of natural metagenomes stimulated the development of new methods for their taxonomic profiling. Alignment-free approaches based on the search for marker k-mers turned out to be capable of identifying not only species, but also strains of microorganisms with known genomes. Here, we evaluated the ability of genus-specific k-mers to distinguish eight phylogroups of Escherichia coli (A, B1, C, E, D, F, G, B2) and assessed the presence of their unique 22-mers in clinical samples from microbiomes of four healthy people and four patients with Crohn’s disease. We found that a phylogenetic tree inferred from the pairwise distance matrix for unique 18-mers and 22-mers of 124 genomes was fully consistent with the topology of the tree, obtained with concatenated aligned sequences of orthologous genes. Therefore, we propose strain-specific “barcodes” for rapid phylotyping. Using unique 22-mers for taxonomic analysis, we detected microbes of all groups in human microbiomes; however, their presence in the five samples was significantly different. Pointing to the intraspecies heterogeneity of E. coli in the natural microflora, this also indicates the feasibility of further studies of the role of this heterogeneity in maintaining population homeostasis.

Exploring Evolution of Public Opinions on Tianya Club Using Dynamic Topic Models

2020 ◽  
Vol 8 (4) ◽  
pp. 309-324
Author(s):  
Zhihua Yan ◽  
Xijin Tang
Keyword(s):  
Family Life ◽  
Topic Model ◽  
Distance Matrix ◽  
Pairwise Distance ◽  
Online Media ◽  
Traditional Media ◽  
Public Opinions ◽  
Government Administration ◽  
Media Data ◽  
Pairwise Distance Matrix

AbstractOnline media have brought tremendous changes to civic life, public opinions, and government administration. Compared with traditional media, online media not only allow individuals to browse news and express their views more freely, but also accelerate the transmission of opinions and expand influence. As public opinions may arouse societal unrest, it is worth detecting the primary topics and uncovering the evolution trends of public opinions for societal administration. Various algorithms are developed to deal with the huge volume of unstructured online media data. In this study, dynamic topic model is employed to explore topic content evolution and prevalence evolution using the original posts published from 2013 to 2017 on the Tianya Zatan Board of Tianya Club, which is one of the most popular BBS in China. Based on semantic similarities, topics are grouped into three themes: Family life, societal affairs, and government administration. The evolution of topic prevalence and content are affected by emergent incidents. Topics on family life become popular, while themes “societal affairs” and “government administration” with bigger standard deviations are more likely to be influenced by emergent hot events. Content evolution represented by monthly pairwise distance matrix is very easy to find change points of topic content.

scholarly journals Chatbot to improve learning punctuation in Spanish and to enhance open and flexible learning environments

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Esteban Vázquez-Cano ◽  
Santiago Mengual-Andrés ◽  
Eloy López-Meneses
Keyword(s):  
Learning Process ◽  
Latent Dirichlet Allocation ◽  
Distance Matrix ◽  
Ease Of Use ◽  
Three Dimensions ◽  
Pairwise Distance ◽  
Control Group ◽  
Quantitative Methodology ◽  
Quasi Experimental ◽  
Experimental Group

AbstractThe objective of this article is to analyze the didactic functionality of a chatbot to improve the results of the students of the National University of Distance Education (UNED / Spain) in accessing the university in the subject of Spanish Language. For this, a quasi-experimental experiment was designed, and a quantitative methodology was used through pretest and posttest in a control and experimental group in which the effectiveness of two teaching models was compared, one more traditional based on exercises written on paper and another based on interaction with a chatbot. Subsequently, the perception of the experimental group in an academic forum about the educational use of the chatbot was analyzed through text mining with tests of Latent Dirichlet Allocation (LDA), pairwise distance matrix and bigrams. The quantitative results showed that the students in the experimental group substantially improved the results compared to the students with a more traditional methodology (experimental group / mean: 32.1346 / control group / mean: 28.4706). Punctuation correctness has been improved mainly in the usage of comma, colon and periods in different syntactic patterns. Furthermore, the perception of the students in the experimental group showed that they positively value chatbots in their teaching–learning process in three dimensions: greater “support” and companionship in the learning process, as they perceive greater interactivity due to their conversational nature; greater “feedback” and interaction compared to the more traditional methodology and, lastly, they especially value the ease of use and the possibility of interacting and learning anywhere and anytime.

scholarly journals Typology, Structural Characterization and Sustainability of Integrated Broiler Farming System in Epirus, Greece

2021 ◽  
Vol 13 (23) ◽  
pp. 13084
Author(s):  
Vassilios Dotas ◽  
Dimitrios Gourdouvelis ◽  
Lampros Hatzizisis ◽  
Ioannis Kaimakamis ◽  
Ioannis Mitsopoulos ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Structural Characterization ◽  
Hierarchical Cluster Analysis ◽  
Financial Management ◽  
Hierarchical Cluster ◽  
Farming System ◽  
Poultry Farms ◽  
Large Farms ◽  
Farm Types

The aim of this study was the detailed characterization of the existing zootechnical and financial management applied in broiler poultry farms in the Region of Epirus, Greece. The current situation was captured through the formation of a typology on the structural characterization of broiler farming system. The variables were recorded based on data from a stratified random sample according to Neyman’s methodology of 110 poultry farms. In the typology, hierarchical cluster analysis was applied to identify differences between farms and to support most of this differentiation. Chebyshev distance was used to maximize the effect of the cluster elements distance, as well as Ward’s clustering method, which aims to achieve greater homogeneity within the clusters. Bonferroni multiple comparison tests were used to evaluate the differences. Four clusters of different farm types were identified from the hierarchical cluster analysis. In conclusion, the production system of broiler farms in Epirus is intensive, especially in large farms that have made significant investments in fixed capital and implement successful management. However, the poultry sector in Epirus has further margin for improvement in both its productivity and profitability.

↵Genetic Diversity and Principal Component Analysis in Mungbean [Vigna radiata (L.) Wilczek] under Rainfed Condition

2021 ◽  
Author(s):  
Deepak Gupta ◽  
Suresh Muralia ◽  
N.K. Gupta ◽  
Sunita Gupta ◽  
M.L. Jakhar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Principal Component Analysis ◽  
Cluster Analysis ◽  
Seed Yield ◽  
Agricultural Research ◽  
Principal Component ◽  
Component Analysis ◽  
Grain Legume ◽  
Research Station ◽  
Rainfed Condition

Background: Mungbean is a short duration grain legume widely grown in south and Southeast Asia. The extent of variability through Principal Component Analysis (PCA) and cluster analysis in promising mungbean genotypes should be known for possible yield improvement. A study was undertaken to work out the extent of variability among twenty four mungbean genotypes through cluster analysis and Principal Component Analysis (PCA). Methods: The experiment was laid out in a randomized block design with three replications during kharif 2018 and 2019 at the experimental field of Agricultural Research Station, Navgaon (Alwar) under rainfed condition. Result: Principal component analysis revealed that the first three main PCAs amounted 78.80% of the total variation among genotypes for different traits. Out of total principal components, PC1 accounts for maximum variability in the data with respect to succeeding components. Number of branches per plant (28.62%), number of clusters per plant (23.55%) and seed yield (15.58%) showed maximum per cent contribution towards total genetic divergence on pooled basis. Cluster analysis showed that genotypes fall into seven different clusters and their inter and intra cluster distance showed genetic diversity between different genotypes. The maximum number of genotypes i.e., 8 was found in cluster II followed by cluster III comprising of 6 genotypes. Genotypes RMG-1138 and IPM-02-03 representing the mono genotypic cluster signifies that it can be the most diverse variety and it would be the appropriate genotype for hybridization with ones present in other clusters to tailor the agriculturally important traits and ultimately to boost the seed yield in mungbean under rainfed conditions.

scholarly journals Effect of salinity stress on mungbean [Vigna radiata (L.) Wilczek] during consecutive summer and spring seasons

2015 ◽  
Vol 60 (1) ◽  
pp. 23-32 ◽  
Author(s):  
Nirmala Sehrawat ◽  
Mukesh Yadav ◽  
Kangila Bhat ◽  
Raj Sairam ◽  
Pawan Jaiwal
Keyword(s):  
Salt Stress ◽  
Salinity Stress ◽  
Susceptible Variety ◽  
Grain Legume ◽  
Spring Season ◽  
Germplasm Screening ◽  
Legume Crop ◽  
Rate Of Photosynthesis ◽  
Food Grain ◽  
Resistant Genotypes

Mungbean is an ecologically important food grain legume crop. Susceptibility towards salinity stress has limited the productivity of mungbean. The effect of salt stress on two popular mungbean varieties ("Pusa vishal" and "Pusa ratna") has been compared during summer and spring seasons. The experiment was carried out at two salinity stress levels (50 mM and 75 mM NaCl). Significant variations and adaptability among stressed and non-stressed plants were observed in both varieties. The plants in early vegetative stage were found more resistant to salinity as compared to plants in late vegetative and reproductive stage. Salt stress, high temperature and salinity induced osmotic stress severely limited the plant growth, morphology, physiology and yield characteristics during summer. Measured parameters were less affected during spring season. The tolerant variety ?Pusa vishal? exhibited less reduction in plant height, total chlorophyll and carotenoid contents, plant length, leaf area, rate of photosynthesis, number of pods per plant and grain yield at high salinity level. However, the susceptible variety ?Pusa ratna? showed higher reduction for the measured parameters under salinity stress. A delay in pod ripening during spring season resulted in less pod-shattering. The present study may help to execute further research on screening of large mungbean germplasm for salt tolerance during spring season. The germplasm screening may help to identify resistant genotypes for genetic improvement of mungbean for growing in saline soil.

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