Search results for "Ph D"
showing 10 items of 71 documents
Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi
2021
Made available in DSpace on 2021-06-25T11:52:41Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-03-04 European Regional Development Fund (Centre of Excellence EcolChange) University of Tartu (Estonian Research Council ) Moscow State University Natural Sciences and Engineering Research Council of Canada Discovery Grant Russian Science Foundation Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Swedish Research Council (Vetenskapsradet) The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 s…
Heuristics for the min–max arc crossing problem in graphs
2018
Abstract In this paper, we study the visualization of complex structures in the context of automatic graph drawing. Constructing geometric representations of combinatorial structures, such as networks or graphs, is a difficult task that requires an expert system. The automatic generation of drawings of graphs finds many applications from software engineering to social media. The objective of graph drawing expert systems is to generate layouts that are easy to read and understand. This main objective is achieved by solving several optimization problems. In this paper we focus on the most important one: reducing the number of arc crossings in the graph. This hard optimization problem has been…
Variable neighborhood descent for the incremental graph drawing
2017
Abstract Graphs are used to represent reality in several areas of knowledge. Drawings of graphs have many applications, from project scheduling to software diagrams. The main quality desired for drawings of graphs is readability, and crossing reduction is a fundamental aesthetic criterion for a good representation of a graph. In this paper we target the edge crossing reduction in the context of incremental graph drawing, in which we want to preserve the layout of a graph over successive drawings. We propose a hybrid method based on the GRASP (Greedy Randomized Adaptive Search Procedure) and VND (Variable Neighborhood Descent) methodologies and compare it with previous methods via simulation.
Application of Graph Clustering and Visualisation Methods to Analysis of Biomolecular Data
2018
In this paper we present an approach based on integrated use of graph clustering and visualisation methods for semi-supervised discovery of biologically significant features in biomolecular data sets. We describe several clustering algorithms that have been custom designed for analysis of biomolecular data and feature an iterated two step approach involving initial computation of thresholds and other parameters used in clustering algorithms, which is followed by identification of connected graph components, and, if needed, by adjustment of clustering parameters for processing of individual subgraphs.
EFMviz
2020
Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge. In this study, we developed an extension for the widely adopted COBRA Toolbox, EFMviz, for analysis and graphical visualization of EFMs as networks of reactions, metabolites and genes. The analysis workflow offers a platform for EFM visualization to improve EFM interpretability by connecting COBRA toolbox with the network analysis and visualization software Cytoscape. The biological applicability of EFMviz is demonstrated in two use cases on medium (Escherichia coli, iAF1…
Reactome graph database: Efficient access to complex pathway data
2018
Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its qu…
Performance optimisation of biological pathway data storage, retrieval, analysis and its interactive visualisation
2018
The aim of this research was to optimise the performance of the storage, retrieval, analysis and interactive visualisation of biomolecular pathways data. This was achieved by the adoption of new technologies and a variety of highly optimised data structures, algorithms and strategies across the different layers of the software. The first challenge to overcome was the creation of a long-lasting, large-scale web application to enable pathways navigation; the Pathway Browser. This tool had to aggregate different modules to allow users to browse pathway content and use their own data to perform pathway analysis. Another challenge was the development of a high-performance pathway analysis tool t…
Cognitive and social cognitive functioning in spinocerebellar ataxia : a preliminary characterization
2006
INTRODUCTION : The spinocerebellar ataxias (SCAs), are rare neurodegenerative disorders caused by distinct genetic mutations. Clinically, the SCAs are characterised by progressive ataxia and a variety of other features, including cognitive dysfunction. The latter is consistent with a growing body of evidence supporting a cognitive as well as motor role for the cerebellum. Recent suggestions of cerebellar involvement in social cognition have not been extensively explored in these conditions. The availability of definitive molecular diagnosis allows genetically defined subgroups of SCA patients, with distinct patterns of cerebellar and extracerebellar involvement, to be tested comparatively u…
Three-dimensional sonographic diagnosis of a large cystic neck lymphangioma.
2004
Lymphangiomas are fairly well-circumscribed benign masses of lymphatic vessels or channels that vary in size, are usually greatly dilated, and are lined with normal endothelial cells. They may be classified into 3 groups: lymphangioma simplex, consisting of capillary-sized channels; cavernous lymphangiomas, consisting of dilated channels with a fibrous adventitial covering; and cystic lymphangiomas, or hygromas, composed of multiple cysts of varying sizes that are lined with endothelial cells. Mixed types may coexist within a given lesion. Although lymphangiomas can occur in any part of the body where lymphatic ducts are located, 95% of them are found in the neck, the head, or the axilla. 1…
Search for neutral MSSM Higgs bosons at LEP
2006
The four LEP collaborations, ALEPH, DELPHI, L3 and OPAL, have searched for the neutral Higgs bosons which are predicted by the Minimal Supersymmetric Standard Model (MSSM). The data of the four collaborations are statistically combined and examined for their consistency with the background hypothesis and with a possible Higgs boson signal. The combined LEP data show no significant excess of events which would indicate the production of Higgs bosons. The search results are used to set upper bounds on the cross-sections of various Higgs-like event topologies. The results are interpreted within the MSSM in a number of "benchmark" models, including CP-conserving and CP-violating scenarios. Thes…