scholarly journals COPLA, a taxonomic classifier of plasmids

2020 ◽  
Author(s):  
Santiago Redondo-Salvo ◽  
Roger Bartomeus ◽  
Luis Vielva ◽  
Kaitlin A. Tagg ◽  
Hattie E. Webb ◽  
...  

The Plasmid Taxonomic Unit (PTU) concept is an initial step for a natural classification of plasmids. Here we present COPLA, a software for plasmid assignation to existing PTUs. To assess its performance, we used a sample of 1,000 plasmids missing from its current database. Overall, 41% of samples could be assigned an existing PTU (63% within the most abundant order, Enterobacterales), while 4% of samples could help to define new PTUs once COPLA database was updated.

2004 ◽  
Vol 108 (1) ◽  
pp. 26-34 ◽  
Author(s):  
Andrew N. Miller ◽  
Sabine M. Huhndorf

2021 ◽  
Author(s):  
Pedro W Crous ◽  
Amy Y Rossman ◽  
Catherine Aime ◽  
Cavan Allen ◽  
Treena Burgess ◽  
...  

Names of phytopathogenic fungi and oomycetes are essential to communicate knowledge about species and their biology, control, and quarantine as well as for trade and research purposes. Many plant pathogenic fungi are pleomorphic, meaning that they produce different asexual (anamorph) and sexual (teleomorph) morphs in their lifecycles. Because of this, more than one name has been applied to different morphs of the same species, which has confused users of names. The onset of DNA technologies makes it possible to connect different morphs of the same species, resulting in a move to a more natural classification system for fungi, in which a single name for a genus as well as species can now be used. The move to a single nomenclature, as well as the advent of molecular phylogeny and the introduction of polythetic taxonomic approaches has been the main driving force for the re-classification of fungi, including pathogens. Nonetheless, finding the correct name for species remains challenging, but there is a series of steps or considerations that could greatly simplify this process, as outlined here. In addition to various online databases and resources, a list of accurate names is herewith provided of the accepted names of the most common genera and species of phytopathogenic fungi.


2010 ◽  
pp. 291-312
Author(s):  
Alfred Smee

2019 ◽  
Vol 16 (10) ◽  
pp. 4170-4178
Author(s):  
Sheifali Gupta ◽  
Gurleen Kaur ◽  
Deepali Gupta ◽  
Udit Jindal

This paper tends to the issue of coin recognition when dealing with shading and reflection variations under the same lighting conditions. In order to approach the problem, a database containing Brazilian coin images (both front and reverse side of the coin) consisting of five different denominations have been used which is provided by the kaggle-diverse and largest data community in the world. This work focuses on an automatic image classification process for Brazilian coins. The imagebased classification of coins primarily incorporates three stages where the initial step is Region of Interest (ROI) extraction; the subsequent advance is extraction of features and classification. The first step of ROI extraction is accomplished by segmenting the coin region using the proposed segmentation method. In the second step i.e., feature extraction; Histogram of Oriented Gradients (HOG) features are extracted from the image. The image is converted to a vector containing feature values. The third step is where the extracted features are mapped to the class and are known as classification. Three classification algorithms i.e., Support Vector Machine (SVM), Artificial Neural Network (ANN) and K-Nearest Neighbour are compared for classification of five coin denominations. With the proposed segmentation methodology, the best classification accuracy of 92% is achieved in the case of ANN classifier.


1990 ◽  
Vol 27 (01) ◽  
pp. 115-123
Author(s):  
J. George Shanthikumar ◽  
Hui-Wen Koo

Sufficient conditions under which two random vectors are ordered in the sense of uniform conditional stochastic order (Whitt (1980), (1982)) with respect to planar regions are given. A natural classification of distributions based on this notion of stochastic order is defined and studied. A negative dependence property of Block et al. (1985) is shown to hold for this class of distributions. An application of these results in statistics is also presented.


2012 ◽  
Vol 31 (1) ◽  
pp. 1-41 ◽  
Author(s):  
Davis Young

The preference of the authors of the quantitative igneous rock classification for an artificial rather than a natural system, coupled with their invention of a new nomenclature to accompany the classification, indicates that some essential elements of scientific work are not empirically ascertained but are proposed and accepted (or rejected) by the relevant scientific community as a matter of free choice. The use of igneous rocks as exemplars in the education of novice geology students is discussed. It is claimed that the CIPW classification could not have been produced by a single individual geologist. The factors that allowed for the collective success in the creation of the quantitative classification are examined.Upon publication of their monumental quantitative chemico-mineralogical classification (CIPW 1902, 1903), C. W. Cross, J. P. Iddings, L. V. Pirsson, and H. S. Washington immediately received numerous letters of congratulation. Initial published reviews ranged from highly supportive to suspicious. To help buttress their classification, Washington (1903) published a compilation of igneous rock chemical analyses and Iddings (1903) published several diagrams to drive home the point that a natural classification of igneous rocks was not feasible. Led by Washington, Pirsson, and Cross, several geologists began using the CIPW classification in their petrological studies and some contributed new sub-rang names. In the meantime, Iddings worked on the first volume of a projected two-volume work on igneous rocks based on the quantitative CIPW scheme. Unsympathetic to artificial, overly precise classifications, Harker in particular rejected the CIPW system and its norm calculations and European geologists generally were unenthusiastic. Cross (1910b) offered a major rebuttal to the criticisms, particularly those of Harker, in which he challenged the likelihood of producing a valid natural classification of igneous rocks. Iddings (1913) published the second volume on igneous rocks in which he developed an elaborate correlation between the old qualitative system and the new quantitative CIPW scheme. Washington and Pirsson produced many more petrological studies of Mediterranean volcanic rocks, New Hampshire, and Hawaii that incorporated the quantitative system. Washington (1917) produced a vastly expanded compilation of chemical analyses arranged in accord with the CIPW system. Criticisms, however, continued to mount from Fermor, Daly, Shand, and others, while Tyrrell and Johannsen were lukewarm toward the new classification. The criticism that the CIPW system was of little value in fieldwork repeatedly surfaced. Dissatisfaction with the quantitative scheme led to the publication of many new classifications by geologists, such as Hatch, Winchell, Lincoln, Shand, Holmes, Johannsen, and Niggli. With the creation of satisfactory quantitative mineralogical classifications, the increasing ability to determine the proportions of minerals quantitatively, and the death of Iddings and Pirsson, enthusiasm for the CIPW system gradually began to wane. By the 1960s the classification had become a thing of the past. The value of the norm calculation, however, gained recognition and has survived to the present, assisted no doubt by the capability for doing the necessary calculations by computer.


2004 ◽  
Vol 01 (01n02) ◽  
pp. 23-31 ◽  
Author(s):  
GIAMPAOLO CICOGNA

It is shown that the introduction of suitable "symmetry-adapted" variables for the study of differential equations can be efficient and useful even if the problem does not admit symmetries. This method not only provides new solutions but also leads to the introduction of weaker notions of symmetry, and allows a natural classification of the possible types of symmetry, each of which is characterized by a specific form of the equation when written in the appropriate variables. Some simple examples are briefly proposed.


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