scholarly journals The System of Register Labels in plWordNet

2015 ◽  
pp. 161-175
Author(s):  
Marek Maziarz ◽  
Maciej Piasecki ◽  
Stan Szpakowicz
Keyword(s):  
Comparative Analysis ◽  
Large Scale ◽  
Homogeneous System ◽  
Lexical Resources ◽  
System A ◽  
Intensive Exercise ◽  
Wide Range ◽  
Practical Effect ◽  
High Consistency ◽  
Register Assignment

The System of Register Labels in plWordNetStylistic registers influence word usage. Both traditional dictionaries and wordnets assign lexical units to registers, and there is a wide range of solutions. A system of register labels can be flat or hierarchical, with few labels or many, homogeneous or decomposed into sets of elementary features. We review the register label systems in lexicography, and then discuss our model, designed for plWordNet, a large wordnet for Polish. There follows a detailed comparative analysis of several register systems in Polish lexical resources. We also present the practical effect of the adoption of our flat, small and homogeneous system: a relatively high consistency of register assignment in plWordNet, as measured by inter-annotator agreement on a manageable sample. Large-scale conclusions for the whole plWordNet remain to be made once the annotation has been completed, but the experience half-way through this labour-intensive exercise is very encouraging.

Glutton: large-scale integration of non-model organism transcriptome data for comparative analysis

2016 ◽  
Author(s):  
Alan Medlar ◽  
Laura Laakso ◽  
Andreia Miraldo ◽  
Ari Löytynoja
Keyword(s):  
Comparative Analysis ◽  
Large Scale ◽  
De Novo ◽  
Sequence Data ◽  
Model Organism ◽  
Model Organisms ◽  
Rna Seq ◽  
Reference Species ◽  
Wide Range ◽  
The Impact

AbstractHigh-throughput RNA-seq data has become ubiquitous in the study of non-model organisms, but its use in comparative analysis remains a challenge. Without a reference genome for mapping, sequence data has to be de novo assembled, producing large numbers of short, highly redundant contigs. Preparing these assemblies for comparative analyses requires the removal of redundant isoforms, assignment of orthologs and converting fragmented transcripts into gene alignments. In this article we present Glutton, a novel tool to process transcriptome assemblies for downstream evolutionary analyses. Glutton takes as input a set of fragmented, possibly erroneous transcriptome assemblies. Utilising phylogeny-aware alignment and reference data from a closely related species, it reconstructs one transcript per gene, finds orthologous sequences and produces accurate multiple alignments of coding sequences. We present a comprehensive analysis of Glutton’s performance across a wide range of divergence times between study and reference species. We demonstrate the impact choice of assembler has on both the number of alignments and the correctness of ortholog assignment and show substantial improvements over heuristic methods, without sacrificing correctness. Finally, using inference of Darwinian selection as an example of downstream analysis, we show that Glutton-processed RNA-seq data give results comparable to those obtained from full length gene sequences even with distantly related reference species. Glutton is available from http://wasabiapp.org/software/glutton/ and is licensed under the GPLv3.

scholarly journals AnnotationBustR: an R package to extract subsequences from GenBank annotations

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5179 ◽  
Author(s):  
Samuel R. Borstein ◽  
Brian C. O’Meara
Keyword(s):  
Comparative Analysis ◽  
Dna Sequences ◽  
Large Scale ◽  
Retrieval System ◽  
Single Gene ◽  
R Package ◽  
Fasta File ◽  
Search Terms ◽  
Large Numbers ◽  
Wide Range

BackgroundDNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequence records on GenBank contain more than one gene or are portions of genomes. Inconsistencies in the way genes are annotated and the numerous synonyms a single gene may be listed under provide major challenges for extracting large numbers of subsequences for comparative analysis across taxa. At present, there is no easy way to extract portions from many GenBank accessions based on annotations where gene names may vary extensively.ResultsThe R packageAnnotationBustRallows users to extract sequences based on GenBank annotations through the ACNUC retrieval system given search terms of gene synonyms and accession numbers.AnnotationBustRextracts subsequences of interest and then writes them to a FASTA file for users to employ in their research endeavors.ConclusionFASTA files of extracted subsequences and accession tables generated byAnnotationBustRallow users to quickly find and extract subsequences from GenBank accessions. These sequences can then be incorporated in various analyses, like the construction of phylogenies to test a wide range of ecological and evolutionary hypotheses.

scholarly journals AnnotationBustR: An R package to extract subsequences from GenBank annotations

2017 ◽  
Author(s):  
Samuel R. Borstein ◽  
Brian C. O'Meara
Keyword(s):  
Comparative Analysis ◽  
Dna Sequences ◽  
Large Scale ◽  
Retrieval System ◽  
Single Gene ◽  
R Package ◽  
Fasta File ◽  
Search Terms ◽  
Large Numbers ◽  
Wide Range

Background. DNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequences on GenBank contain more than one gene or are portions of genomes, and inconsistencies in the way genes are annotated and the numerous synonyms a single gene may be listed under provide major challenges for extracting large numbers of subsequences for comparative analysis across taxa. At present, there is no easy way to extract portions from multiple GenBank accessions based on annotations where gene names may vary extensively. Results. The R package AnnotationBustR allows users to extract sequences based on GenBank annotations through the ACNUC retrieval system given search terms of gene synonyms and accession numbers. AnnotationBustR extracts portions of interest and then writes them to a FASTA file for users to employ in their research endeavors. Conclusion. FASTA files of extracted subsequences and accession tables generated by AnnotationBustR allow users to quickly find and extract subsequences from GenBank accessions. These sequences can then be incorporated in various analyses, like the construction of phylogenies to test a wide range of ecological and evolutionary hypotheses.

scholarly journals AnnotationBustR: An R package to extract subsequences from GenBank annotations

2017 ◽  
Author(s):  
Samuel R. Borstein ◽  
Brian C. O'Meara
Keyword(s):  
Comparative Analysis ◽  
Dna Sequences ◽  
Large Scale ◽  
Retrieval System ◽  
Single Gene ◽  
R Package ◽  
Fasta File ◽  
Search Terms ◽  
Large Numbers ◽  
Wide Range

Background. DNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequences on GenBank contain more than one gene or are portions of genomes, and inconsistencies in the way genes are annotated and the numerous synonyms a single gene may be listed under provide major challenges for extracting large numbers of subsequences for comparative analysis across taxa. At present, there is no easy way to extract portions from multiple GenBank accessions based on annotations where gene names may vary extensively. Results. The R package AnnotationBustR allows users to extract sequences based on GenBank annotations through the ACNUC retrieval system given search terms of gene synonyms and accession numbers. AnnotationBustR extracts portions of interest and then writes them to a FASTA file for users to employ in their research endeavors. Conclusion. FASTA files of extracted subsequences and accession tables generated by AnnotationBustR allow users to quickly find and extract subsequences from GenBank accessions. These sequences can then be incorporated in various analyses, like the construction of phylogenies to test a wide range of ecological and evolutionary hypotheses.

scholarly journals An S-band Receiver and Backend System for MeerKAT

2017 ◽  
Vol 13 (S337) ◽  
pp. 175-178 ◽  
Author(s):  
Ewan D. Barr
Keyword(s):  
Large Scale ◽  
Scientific Applications ◽  
System A ◽  
Receiver System ◽  
Wide Range ◽  
Working Together ◽  
Fast Transient

AbstractThe MPIfR is working together with SKA-SA and the Universities of Manchester and Oxford to deploy three instruments on MeerKAT: An S-band receiver system, a dedicated beamforming cluster and a flexible pulsar search cluster. Together these instruments will provide MeerKAT with powerful tools for supporting a wide range of scientific applications and in particular will enable large-scale pulsar and fast transient surveys to be performed. In these proceedings we describe the design, implementation and deployment timeline for these instruments.

scholarly journals AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments

2019 ◽  
Author(s):  
Andrew J. Page ◽  
Sarah Bastkowski ◽  
Muhammad Yasir ◽  
A. Keith Turner ◽  
Thanh Le Viet ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Stress Responses ◽  
Cell Biology ◽  
Large Scale ◽  
Transposon Mutagenesis ◽  
Data Sets ◽  
Wide Range ◽  
Multiple Data Sets ◽  
Triclosan Resistance ◽  
The Impact

AbstractBackgroundBacteria have evolved over billions of years to survive in a wide range of environments. Currently, there is an incomplete understanding of the genetic basis for mechanisms underpinning survival in stressful conditions, such as the presence of anti-microbials. Transposon mutagenesis has been proven to be a powerful tool to identify genes and networks which are involved in survival and fitness under a given condition by simultaneously assaying the fitness of millions of mutants, thereby relating genotype to phenotype and contributing to an understanding of bacterial cell biology. A recent refinement of this approach allows the roles of essential genes in conditional stress survival to be inferred by altering their expression. These advancements combined with the rapidly falling costs of sequencing now allows comparisons between multiple experiments to identify commonalities in stress responses to different conditions. This capacity however poses a new challenge for analysis of multiple data sets in conjunction.ResultsTo address this analysis need, we have developed ‘AlbaTraDIS’; a software application for rapid large-scale comparative analysis of TraDIS experiments that predicts the impact of transposon insertions on nearby genes. AlbaTraDIS can identify genes which are up or down regulated, or inactivated, between multiple conditions, producing a filtered list of genes for further experimental validation as well as several accompanying data visualisations. We demonstrate the utility of our new approach by applying it to identify genes used byEscherichia colito survive in a wide range of different concentrations of the biocide Triclosan. AlbaTraDIS automatically identified all well characterised Triclosan resistance genes, including the primary target,fabI. A number of new loci were also implicated in Triclosan resistance and the predicted phenotypes for a selection of these were validated experimentally and results showed high consistency with predictions.ConclusionsAlbaTraDIS provides a simple and rapid method to analyse multiple transposon mutagenesis data sets allowing this technology to be used at large scale. To our knowledge this is the only tool currently available that can perform these tasks. AlbaTraDIS is written in Python 3 and is available under the open source licence GNU GPL 3 fromhttps://github.com/quadram-institute-bioscience/albatradis.

Electron microscopy study of reactively sputter-deposited Ti/N films on silicon

1992 ◽  
Vol 50 (2) ◽  
pp. 1362-1363
Author(s):  
V. C. Kannan ◽  
A. K. Singh ◽  
R. B. Irwin ◽  
S. Chittipeddi ◽  
F. D. Nkansah ◽  
...  
Keyword(s):  
Integrated Circuits ◽  
Large Scale ◽  
Hexagonal Phase ◽  
Microscopy Study ◽  
Electron Microscopy Study ◽  
Process Conditions ◽  
Tin Films ◽  
Wide Range ◽  
Fcc Phase ◽  
Circuits Vlsi

Titanium nitride (TiN) films have historically been used as diffusion barrier between silicon and aluminum, as an adhesion layer for tungsten deposition and as an interconnect material etc. Recently, the role of TiN films as contact barriers in very large scale silicon integrated circuits (VLSI) has been extensively studied. TiN films have resistivities on the order of 20μ Ω-cm which is much lower than that of titanium (nearly 66μ Ω-cm). Deposited TiN films show resistivities which vary from 20 to 100μ Ω-cm depending upon the type of deposition and process conditions. TiNx is known to have a NaCl type crystal structure for a wide range of compositions. Change in color from metallic luster to gold reflects the stabilization of the TiNx (FCC) phase over the close packed Ti(N) hexagonal phase. It was found that TiN (1:1) ideal composition with the FCC (NaCl-type) structure gives the best electrical property.

THE SOME QUESTIONS OF AUTONOMOUS MOTION AND MANAGEMENT OF LAND-MOBILE ROBOTIC COMPLEXES FOR UKRAINIAN GROUND FORCESE

2019 ◽  
pp. 53-58
Author(s):  
О. Кravchuk ◽  
V. Symonenkov ◽  
I. Symonenkova ◽  
O. Hryhorev
Keyword(s):  
Large Scale ◽  
Armed Forces ◽  
Distributed Information ◽  
Wide Range ◽  
Highly Effective ◽  
Information Management Systems ◽  
Robotic Devices ◽  
Principles And Standards ◽  
And Control ◽  
The Eu

Today, more than forty countries of the world are engaged in the development of military-purpose robots. A number of unique mobile robots with a wide range of capabilities are already being used by combat and intelligence units of the Armed forces of the developed world countries to conduct battlefield intelligence and support tactical groups. At present, the issue of using the latest information technology in the field of military robotics is thoroughly investigated, and the creation of highly effective information management systems in the land-mobile robotic complexes has acquired a new phase associated with the use of distributed information and sensory systems and consists in the transition from application of separate sensors and devices to the construction of modular information subsystems, which provide the availability of various data sources and complex methods of information processing. The purpose of the article is to investigate the ways to increase the autonomy of the land-mobile robotic complexes using in a non-deterministic conditions of modern combat. Relevance of researches is connected with the necessity of creation of highly effective information and control systems in the perspective robotic means for the needs of Land Forces of Ukraine. The development of the Armed Forces of Ukraine management system based on the criteria adopted by the EU and NATO member states is one of the main directions of increasing the effectiveness of the use of forces (forces), which involves achieving the principles and standards necessary for Ukraine to become a member of the EU and NATO. The inherent features of achieving these criteria will be the transition to a reduction of tasks of the combined-arms units and the large-scale use of high-precision weapons and land remote-controlled robotic devices. According to the views of the leading specialists in the field of robotics, the automation of information subsystems and components of the land-mobile robotic complexes can increase safety, reliability, error-tolerance and the effectiveness of the use of robotic means by standardizing the necessary actions with minimal human intervention, that is, a significant increase in the autonomy of the land-mobile robotic complexes for the needs of Land Forces of Ukraine.

Stirring and aeration system for the upgrading of small waste water treatment plants

1994 ◽  
Vol 29 (12) ◽  
pp. 149-156 ◽  
Author(s):  
Marcus Höfken ◽  
Katharina Zähringer ◽  
Franz Bischof
Keyword(s):  
Waste Water ◽  
Water Treatment ◽  
Large Scale ◽  
Waste Water Treatment ◽  
Water Treatment Plants ◽  
Waste Water Treatment Plants ◽  
Basic Fluid ◽  
Aeration System ◽  
Technical Realization ◽  
Wide Range

A novel agitating system has been developed which allows for individual or combined operation of stirring and aeration processes. Basic fluid mechanical considerations led to the innovative hyperboloid design of the stirrer body, which ensures high efficiencies in the stirring and the aeration mode, gentle circulation with low shear forces, excellent controllability, and a wide range of applications. This paper presents the basic considerations which led to the operating principle, the technical realization of the system and experimental results in a large-scale plant. The characteristics of the system and the differences to other stirring and aeration systems are illustrated. Details of the technical realization are shown, which conform to the specific demands of applications in the biological treatment of waste water. Special regard is given to applications in the upgrading of small compact waste water treatment plants.

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