A Comparison of Some Measures for the Determination of Inter-Molecular Structural Similarity Measures of Inter-Molecular Structural Similarity

1986 ◽  
Vol 5 (1) ◽  
pp. 18-25 ◽  
Author(s):  
Peter Willett ◽  
Vivienne Winterman
Keyword(s):  
Similarity Measures ◽  
Structural Similarity

Determination of the Number of Conserved Chromosomal Segments Between Species

Genetics ◽  
2001 ◽  
Vol 157 (3) ◽  
pp. 1387-1395 ◽  
Author(s):  
Sudhir Kumar ◽  
Sudhindra R Gadagkar ◽  
Alan Filipski ◽  
Xun Gu
Keyword(s):  
Statistical Approach ◽  
Common Ancestor ◽  
Chromosomal Rearrangements ◽  
Structural Similarity ◽  
The Other ◽  
Segment Length ◽  
Human Genomes ◽  
Genomic Divergence ◽  
Human And Mouse

AbstractGenomic divergence between species can be quantified in terms of the number of chromosomal rearrangements that have occurred in the respective genomes following their divergence from a common ancestor. These rearrangements disrupt the structural similarity between genomes, with each rearrangement producing additional, albeit shorter, conserved segments. Here we propose a simple statistical approach on the basis of the distribution of the number of markers in contiguous sets of autosomal markers (CSAMs) to estimate the number of conserved segments. CSAM identification requires information on the relative locations of orthologous markers in one genome and only the chromosome number on which each marker resides in the other genome. We propose a simple mathematical model that can account for the effect of the nonuniformity of the breakpoints and markers on the observed distribution of the number of markers in different conserved segments. Computer simulations show that the number of CSAMs increases linearly with the number of chromosomal rearrangements under a variety of conditions. Using the CSAM approach, the estimate of the number of conserved segments between human and mouse genomes is 529 ± 84, with a mean conserved segment length of 2.8 cM. This length is <40% of that currently accepted for human and mouse genomes. This means that the mouse and human genomes have diverged at a rate of ∼1.15 rearrangements per million years. By contrast, mouse and rat are diverging at a rate of only ∼0.74 rearrangements per million years.

WE-C-I-609-02: Investigation of Various Methods for Determination of Similarity Measures for Pairs of Clustered Microcalcifications On Mammograms

2005 ◽  
Vol 32 (6Part18) ◽  
pp. 2120-2120
Author(s):  
C Muramatsu ◽  
Q Li ◽  
RA Schmidt ◽  
K Suzuki ◽  
J Shiraishi ◽  
...  
Keyword(s):  
Similarity Measures

Determination of Similarity Measures for Pairs of Mass Lesions on Mammograms by Use of BI-RADS Lesion Descriptors and Image Features

2009 ◽  
Vol 16 (4) ◽  
pp. 443-449 ◽  
Author(s):  
Chisako Muramatsu ◽  
Qiang Li ◽  
Robert A. Schmidt ◽  
Junji Shiraishi ◽  
Kunio Doi
Keyword(s):  
Similarity Measures ◽  
Image Features ◽  
Mass Lesions

scholarly journals Using Local Alignments for Relation Recognition

2010 ◽  
Vol 38 ◽  
pp. 1-48 ◽  
Author(s):  
S. Katrenko ◽  
P. W. Adriaans ◽  
M. Van Someren
Keyword(s):  
Sequence Similarity ◽  
General Relation ◽  
Similarity Measures ◽  
Semantic Relatedness ◽  
Structural Similarity ◽  
Learning Task ◽  
Semantic Knowledge ◽  
Local Alignment ◽  
Data Sets ◽  
Definition Of

This paper discusses the problem of marrying structural similarity with semantic relatedness for Information Extraction from text. Aiming at accurate recognition of relations, we introduce local alignment kernels and explore various possibilities of using them for this task. We give a definition of a local alignment (LA) kernel based on the Smith-Waterman score as a sequence similarity measure and proceed with a range of possibilities for computing similarity between elements of sequences. We show how distributional similarity measures obtained from unlabeled data can be incorporated into the learning task as semantic knowledge. Our experiments suggest that the LA kernel yields promising results on various biomedical corpora outperforming two baselines by a large margin. Additional series of experiments have been conducted on the data sets of seven general relation types, where the performance of the LA kernel is comparable to the current state-of-the-art results.

A Similarity Measure Based on Extension Distance and Its Application in CBR

2008 ◽  
Author(s):  
Yanwei Zhao ◽  
Feng Zhang ◽  
Nan Su ◽  
Huijun Tang ◽  
Jian Chen
Keyword(s):  
Standard Deviation ◽  
Similar Case ◽  
Similarity Measures ◽  
Case Based Reasoning ◽  
Case Retrieval ◽  
Similarity Model ◽  
Electric Drill ◽  
Classical Distance ◽  
Case Based

Case-based reasoning (CBR) is an effective method that integrates reasoning methodology and represents related knowledge in a domain. The success of a CBR system largely depends on case retrieval, and the similarity and determination of weight for each case features have a significant influence on the efficiency and accuracy of case retrieval. The aim of the research is to improve the efficiency and accuracy of case retrieval. Analyzing the deficiency of similarity measures based on the classical distance, different similarity measures are proposed for different kinds of attribute values based on the extension distance, especially the similarity model between numerical and set considered the customer’s preference. The standard deviation related with the similarity is introduced to distribute the dynamic attribute’s weights which also considered the customer’s interest, but not the traditional methods that the weight is a constant if determined. The presented methods will enable the system to retrieve the more similar case correctly so that reducing case adaptation. In this study, an electric drill is used as a case to verify the usefulness and effectiveness of the similarity measurements and weight assignments. It is demonstrated that this method is more beneficial to case retrieval compared with other methods.

scholarly journals Phytoestrogens in bovine plasma and milk – LC-MS/MS analysis

2010 ◽  
Vol 28 (No. 4) ◽  
pp. 264-274 ◽  
Author(s):  
A. Krajčová ◽  
V. Schulzová ◽  
J. Lojza ◽  
L. Křížová ◽  
J. Hajšlová
Keyword(s):  
Biological Fluids ◽  
Structural Similarity ◽  
Biologically Active ◽  
Feeding Experiment ◽  
Plant Metabolites ◽  
Alternative Source ◽  
Biological Responses ◽  
Bovine Plasma ◽  
The Relationship

Phytoestrogens belong to a group of polyphenolic plant metabolites which induce biological responses, based on their structural similarity to 17β-estradiol. In order to investigate the relationship between the levels of these biologically active compounds and beneficial health effects, it is neccesary to quantify accurately their levels in foods and biological fluids. In this study, HPLC-MS/MS method for the determination of isoflavones genistein, daidzein, and estrogenic metabolite-equol in bovine plasma and milk was optimised and validated. The method allowed low limits of detection: 5, 2.5 and 0.5 ng/ml for genistein, daidzein and equol, respectively, thus enabling to determine the effect of phytoestrogen-rich diet on the concentration of isoflavones and the metabolite in biological fluids of cows. The feeding experiment, carried out with four dairy cows, showed that a soy-based diet significantly increased both plasma and milk contents of biologically potent equol, therefore, the latter commodity could be an alternative source of this estrogenic metabolite, namely for the consumers who are not capable to convert it from the isoflavone precursors consumed in the diet.

Comparison of the neuralized genes of Drosophila virilis and D. melanogaster

Genome ◽  
1994 ◽  
Vol 37 (5) ◽  
pp. 840-847 ◽  
Author(s):  
Lily Zhou ◽  
Gabrielle L. Boulianne
Keyword(s):  
Drosophila Melanogaster ◽  
Cell Fate ◽  
Structural Similarity ◽  
Drosophila Virilis ◽  
Interspecific Comparison ◽  
Functional Regions ◽  
Embryonic Nervous System ◽  
Localization Signal ◽  
Evolutionary Comparison

The neurogenic gene neuralized of Drosophila melanogaster is thought to play a role in the determination of cell fate in the embryonic nervous system as well as other tissues during development. To determine which sequences within the neuralized gene encode functionally important domains, we have initiated an interspecific comparison of the neuralized gene of D. virilis and D. melanogaster. In this study we show that several motifs that we have previously identified in the neuralized protein of D. melanogaster are conserved in D. virilis. These include a putative nuclear localization signal, a homeodomain similarity region, and a zinc finger motif. In contrast, a helix-turn-helix motif with structural similarity to those identified as DNA-binding regions of bacterial repressors is deleted. These results demonstrate that it is possible to identify key functional regions of the neuralized protein by an interspecific comparison.Key words: Drosophila melanogaster, Drosophila virilis, neuralized, nucleotide sequence, evolutionary comparison.

Sign in / Sign up

Export Citation Format

Share Document