scholarly journals Recognition of arthropod species names using bigram-based classification

2020 ◽  
Author(s):  
Jennien Raffington ◽  
Dirk Steinke ◽  
Dan Tulpan
Keyword(s):  
Specific Information ◽  
Scientific Publications ◽  
Species Discovery ◽  
The Public ◽  
Arthropod Species ◽  
Relationship Extraction ◽  
As Species ◽  
External Software ◽  
Species Specific ◽  
Bayesian Logistic Regression

Abstract BackgroundThe task of recognizing species names in scientific articles is a quintessential step for a large number of applications in high-throughput text mining and data analytics, such as species-specific information collection, construction of species food networks and trophic relationship extraction. These tasks become even more important in fast-paced species-discovery areas such as entomology, where an impressive number of new arthropod species are discovered each year. This article explores the use of twocharacter n-grams (bigrams) in machine learning models for arthropod species name recognition. This particular method has been previously applied successfully to the task of language identification [1] but the application to species name identification had yet to be explored.ResultsArthropod species names, regular English words used in scientific publications and person names were collected from the public domain and bigrams were extracted and used as classifier features. A number of learning classifiers spanning 7 algorithmic categories (tree-based, rule-based, artificial neural network, Bayesian, boosting, lazy and kernel-based) were tested and the highest accuracies were consistently obtained with LIBLINEAR [2], Bayesian Logistic Regression [3], the Multilayer Perceptron [4], Random Forest [5], and the LIBSVM [6] classifiers. When compared with dictionary-based external software tools such as GNRD [7] and TaxonFinder [8], our top-3 classifiers were insensitive to words capitalization and were able to correctly classify novel species names that are absent in dictionary-based approaches with accuracies between 88.6% and 91.6%.ConclusionsOur results suggest that character bigram-based classification is a suitable method for distinguishing arthropod species names from regular English words and person names commonly found in scientific literature. Moreover, our method can also be used to reduce the number of false positives produced by dictionary-based methods.

scholarly journals Interactive web-based visualization and sharing of phylogenetic trees using phylogeny.IO

2019 ◽  
Vol 47 (W1) ◽  
pp. W266-W269 ◽  
Author(s):  
Nikola Jovanovic ◽  
Alexander S Mikheyev
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Study ◽  
Specific Information ◽  
Data Sets ◽  
Complex Data ◽  
Web Based ◽  
As Species ◽  
Complex Data Sets ◽  
Data Layers ◽  
Species Specific

Abstract Traditional static publication formats make visualization, exploration, and sharing of massive phylogenetic trees difficult. A phylogenetic study often involves hundreds of taxa, and the resulting tree has to be split across multiple journal pages, or be shrunk onto one, which jeopardizes legibility. Furthermore, additional data layers, such as species-specific information or time calibrations are often displayed in separate figures, making the entire picture difficult for readers to grasp. Web-based technologies, such as the Data Driven Document (D3) JavaScript library, were created to overcome such challenges by allowing interactive displays of complex data sets. The new phylogeny.IO web server (https://phylogeny.io) overcomes this issue by allowing users to easily import, annotate, and share interactive phylogenetic trees. It allows a range of static (e.g. such as shapes and colors) and dynamic (e.g. pop-up text and images) annotations. Annotated trees can be saved on the server for subsequent modification or they may be shared as IFrame HTML objects, easily embeddable in any web page. The principal goal of phylogeny.IO is not to produce publication-ready figures, but rather to provide a simple and intuitive annotation interface that allows easy and rapid sharing of figures in blogs, lecture notes, press releases, etc.

Mitigating Impacts of Natural Hazards on Fishery Ecosystems

2008 ◽  
Keyword(s):  
Natural Hazards ◽  
Natural Hazard ◽  
Individual Species ◽  
Variable Response ◽  
The Public ◽  
Levels Of Organization ◽  
As Species ◽  
Historical Databases ◽  
Biological Attributes ◽  
Species Specific

<em>Abstract.</em>—Natural hazards are inevitable but unpredictable—both spatially and temporally. Because of their ubiquitous distribution in aquatic ecosystems, fish and their associated fisheries could potentially serve as important in situ bioindicators of natural hazard effects. Many fish attributes suit this purpose, including response variables at individual, species, and community levels of organization. Given that resources for investigations are often limited, some attributes are more efficient, effective, and biologically meaningful than others. To help establish research plans to investigate natural hazard effects, a matrix was created with regard to space, time, and variable response (i.e., biological attributes) potential. A series of additional criteria appropriate for investigation and based on biological attributes according to levels of organization such as species, stocks, populations, and communities is provided. More subjective criteria, such as the presence of historical databases that are species-specific, were included, as well as the economic and social value of the fishery as viewed by the public. Last, a national or international network of research facilities should be established that is both multijurisdictional and multidisciplinary to fully evaluate the spatial and temporal effects of natural hazards on fishery ecosystems. Integration of long-term fisheries- and species-response data will allow a full evaluation of fish responses to natural hazards as well as help set goals for mitigation and restoration efforts.

Electron Microscopy in the Study of Natural Phytoplankton Assemblages

1985 ◽  
Vol 43 ◽  
pp. 620-623
Author(s):  
Linda Sicko-Goad
Keyword(s):  
Electron Microscopy ◽  
Aquatic Environment ◽  
Size Range ◽  
Physical Parameters ◽  
Specific Information ◽  
Phytoplankton Assemblages ◽  
Phytoplankton Productivity ◽  
Ecosystem Effects ◽  
Time Of Year ◽  
Species Specific

Although the use of electron microscopy and its varied methodologies is not usually associated with ecological studies, the types of species specific information that can be generated by these techniques are often quite useful in predicting long-term ecosystem effects. The utility of these techniques is especially apparent when one considers both the size range of particles found in the aquatic environment and the complexity of the phytoplankton assemblages.The size range and character of organisms found in the aquatic environment are dependent upon a variety of physical parameters that include sampling depth, location, and time of year. In the winter months, all the Laurentian Great Lakes are uniformly mixed and homothermous in the range of 1.1 to 1.7°C. During this time phytoplankton productivity is quite low.

Professional and Communicative Proficiency of a Mentor as a Tool of Image Building in Public Service

Communicology ◽  
2020 ◽  
Vol 8 (1) ◽  
pp. 74-88
Author(s):  
D.A. Kemenev
Keyword(s):  
Public Service ◽  
Role Models ◽  
Communicative Competence ◽  
Public Servants ◽  
Scientific Publications ◽  
Communicative Skills ◽  
The Public ◽  
Public Servant ◽  
Professional Business ◽  
Image Building

The article investigates the imageological aspect of mentor’s communicative competence in public service and reveals the communicative functions of mentor’s image in relation to the mentees. The author determines the communicative skills necessary for the mentor in all processes and stages of this personnel technology. Based on the analysis of scientific publications, the author discloses and justifies the role models of mentor’s behavior in relation to the mentees from the perspective of the mentor’s image, authority, and communicative competence. The author has conducted an expert survey among public servants, which allowed identify the main professional, business, moral, psychological, and integral qualities that are the most effectively developed by the public servant in the process of performing mentor’s functions. As a result, the author suggests a structural-logical model of the communicative competence of a mentor in the public service in the process of perceiving its communicative knowledge, skills, and competencies for achieving the effectiveness of mentoring.

scholarly journals Incumbent and Entrant Bidding in Scoring Rule Auctions: A Study on Italian Canteen Services

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Riccardo Camboni ◽  
Paola Valbonesi
Keyword(s):  
Theoretical Model ◽  
Production Cost ◽  
Specific Information ◽  
Scoring Rule ◽  
The Public ◽  
Simple Theoretical Model ◽  
Original Dataset

AbstractWe empirically investigate incumbents’ and entrants’ bids on an original dataset of 192 scoring rule auctions for canteen services in Italy. Our findings show that winning rebates are lower (i.e., prices paid by the public buyer are higher) when the contract is awarded to the incumbent supplier. This result is not explained by the observable characteristics of the auction or the service awarded. We develop a simple theoretical model showing that the result is consistent with a setting in which the buyer exploits specific information on the incumbent supplier’s production cost.

scholarly journals Flight-call as species-specific signal in South American parrots and the effect of species relatedness in call similarity

2017 ◽  
Vol 25 (3) ◽  
pp. 143-151 ◽  
Author(s):  
Carlos B. de Araújo ◽  
Paulo A. M. Marques ◽  
Jacques M. E. Vielliard
Keyword(s):  
South American ◽  
Specific Signal ◽  
As Species ◽  
Species Specific

scholarly journals Preparedness of Young People for a Sustainable Lifestyle: Awareness and Willingness

2021 ◽  
Vol 13 (13) ◽  
pp. 7204
Author(s):  
Anastazija Dimitrova ◽  
Antonín Vaishar ◽  
Milada Šťastná
Keyword(s):  
Young People ◽  
Environmental Issues ◽  
Financial Resources ◽  
Specific Information ◽  
Public And Private ◽  
The Public ◽  
Global Problem ◽  
Sustainable Lifestyle ◽  
Local Companies ◽  
The Relationship

This article discusses the relationship between a consumer lifestyle and the environment. The willingness to adapt to a sustainable lifestyle was tested through a questionnaire among students of Mendel University in Brno, who are theoretically well-informed people. Overall, 417 students answered, i.e., 19% of the respondents. The students generally recognised the need to address environmental issues, and 90.6% intended to change their lifestyle in this direction. Among the barriers, they mentioned in particular lack of time, lack of financial resources, lack of specific information and insufficient conditions. Addressing this issue requires close co-operation in education between governmental and non-governmental organisations in both the public and private sectors. The COVID-19 pandemic has affected the situation in that it has drawn attention to the response of local companies to the global problem.

scholarly journals Trichothecene Genotypes of Fusarium graminearum Populations Isolated from Winter Wheat Crops in Serbia

Toxins ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 460 ◽  
Author(s):  
Vesna Krnjaja ◽  
Slavica Stanković ◽  
Ana Obradović ◽  
Tanja Petrović ◽  
Violeta Mandić ◽  
...  
Keyword(s):  
Fusarium Graminearum ◽  
Gene Clusters ◽  
Sensu Stricto ◽  
Molecular Techniques ◽  
Weather Data ◽  
Morphological Observation ◽  
Specific Primer ◽  
Head Blight ◽  
As Species ◽  
Species Specific

Fusarium graminearum as the main causal agent of Fusarium head blight (FHB) and its ability to produce trichothecenes was investigated by molecular techniques. A total of 37 strains isolated from the wheat, harvested in Serbia in 2005, 2008 and 2015, and previously designated by morphological observation as F. graminearum, were used for trichothecene genotypes characterization. The strains were identified using the species-specific primer set FG16R/FG16F while genotypic characterization was done using specific TRI13 and TRI3 sequences of the trichothecene gene clusters. The PCR assays identified all strains as species of F. graminearum sensu stricto with the DON/15-ADON genotype. The quantification of the mycotoxin (DON) was performed using the biochemical assay. The high levels of DON (>20,000 µg kg−1) were recorded in all of the strains from 2005, four strains from 2008 and two strains from 2015. Weather data of the investigated seasons, showed that the optimal temperature, frequent rains and high relative humidity (RH) was very favourable for the development of F. graminearum, affecting the DON biosynthesis.

scholarly journals Accelerating Scientific Publication in Biology

2015 ◽  
Author(s):  
Ronald D Vale
Keyword(s):  
Scientific Community ◽  
Scientific Publication ◽  
Scientific Publications ◽  
Postdoctoral Training ◽  
The Public ◽  
New Information ◽  
Funding Agencies ◽  
New Findings ◽  
Time Required ◽  
Catalytic Effects

Scientific publications enable results and ideas to be transmitted throughout the scientific community. The number and type of journal publications also have become the primary criteria used in evaluating career advancement. Our analysis suggests that publication practices have changed considerably in the life sciences over the past thirty years. More experimental data is now required for publication, and the average time required for graduate students to publish their first paper has increased and is approaching the desirable duration of Ph.D. training. Since publication is generally a requirement for career progression, schemes to reduce the time of graduate student and postdoctoral training may be difficult to implement without also considering new mechanisms for accelerating communication of their work. The increasing time to publication also delays potential catalytic effects that ensue when many scientists have access to new information. The time has come for life scientists, funding agencies, and publishers to discuss how to communicate new findings in a way that best serves the interests of the public and the scientific community.

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