Search results for "Tree"
showing 10 items of 1841 documents
Learning the structure of HMM's through grammatical inference techniques
2002
A technique is described in which all the components of a hidden Markov model are learnt from training speech data. The structure or topology of the model (i.e. the number of states and the actual transitions) is obtained by means of an error-correcting grammatical inference algorithm (ECGI). This structure is then reduced by using an appropriate state pruning criterion. The statistical parameters that are associated with the obtained topology are estimated from the same training data by means of the standard Baum-Welch algorithm. Experimental results showing the applicability of this technique to speech recognition are presented. >
TRAFFIC FLOW HYPOTHETICAL MODELLING FOR AIR QUALITY IMPROVEMENT AND PLANNING PURPOSES
2019
The main emphasis of this research was to describe air pollution level and dispersion in a typical street canyon (Valdemara Street in Riga (Latvia) city centre), afterward to postulate potential development scenarios and perform modelling in order to understand the influence on air pollution level. For this purpose special mathematical model was used - Operational Street Pollution Model (OSPM), which was developed by the National Environmental Research Institute in Denmark. Following development scenarios were tested: (1) realistic environmentally friendly - decrease of traffic flow by 50 %, as according to street interviews about 36 - 50 % of drivers are ready to change driving habits from…
What do we know about growth of vessel elements of secondary xylem in woody plants?
2021
Despite extensive knowledge about vessel element growth and the determination of the axial course of vessels, these processes are still not fully understood. They are usually explained as resulting primarily from hormonal regulation in stems. This review focuses on an increasingly discussed aspect - mechanical conditions in the vascular cambium. Mechanical conditions in cambial tissue are important for the growth of vessel elements, as well as other cambial derivatives. In relation to the type of stress acting on cambial cells (compressive versus tensile stress) we: (i) discuss the shape of the enlarging vessel elements observed in anatomical sections; (ii) present hypotheses regarding the …
Structural and evolutionary analysis of the copia-like elements in the Arabidopsis thaliana genome.
2001
The analysis of 460 kb of genomic sequence of Arabidopsis thaliana chromosome III allowed us to identify two new transposable elements named AtC1 and AtC2. AtC1 shows identical long terminal repeats (LTRs) and all the structural features characteristic of the copia-like active elements. AtC2 is also a full copia-like element, but a putative stop codon in the open reading frame (ORF) would produce a truncated protein. In order to identify the copia-like fraction of the A. thaliana genome, a careful computer-based analysis of the available sequences (which correspond to 92% of the genome) was performed. Approximately 300 nonredundant copia-like sequences homologous to AtC1 and AtC2 were detec…
piRNAclusterDB 2.0: update and expansion of the piRNA cluster database.
2021
Abstract PIWI-interacting RNAs (piRNAs) and their partnering PIWI proteins defend the animal germline against transposable elements and play a crucial role in fertility. Numerous studies in the past have uncovered many additional functions of the piRNA pathway, including gene regulation, anti-viral defense, and somatic transposon repression. Further, comparative analyses across phylogenetic groups showed that the PIWI/piRNA system evolves rapidly and exhibits great evolutionary plasticity. However, the presence of so-called piRNA clusters as the major source of piRNAs is common to nearly all metazoan species. These genomic piRNA-producing loci are highly divergent across taxa and critically…
bilbo, a non-LTR retrotransposon of Drosophila subobscura: a clue to the evolution of LINE-like elements in Drosophila
1997
We used the repetitive character of transposable elements to isolate a non-LTR retrotransposon in Drosophila subobscura. bilbo, as we have called it, has homology to TRIM and LOA elements. Sequence analysis showed a 5' untranslated region (UTR), an open reading frame (ORF) with no RNA-binding domains, a downstream ORF that had structural homology to that of the I factor, and, finally, a 3' UTR which ended in several 5-nt repeats. The results of our phylogenetic and structural analyses shed light on the evolution of Drosophila non-LTR retrotransposons and support the hypothesis that an ancestor of these elements was structurally complex.
Suitability of chloroplast LSU rDNA and its diverse group I introns for species recognition and phylogenetic analyses of lichen-forming Trebouxia alg…
2009
To date, species identification of lichen photobionts has been performed principally on the basis of microscopic examinations and molecular data from nuclear-encoded genes. In plants, the chloroplast genome has been more readily exploited than the nuclear genome for systematic investigations. At the present time, very little information is available about the chloroplast genome of lichen-forming algae. For this reason, we have sequenced a portion of the gene encoding for the chloroplast large sub-unit rRNA (LSU rDNA) as a new molecular marker. Sequencing of the chloroplast LSU rDNAs revealed the existence of an unusual diversity of group I introns (a total of 31) within 15 analyzed Trebouxi…
Disentangling Sources of Gene Tree Discordance in Phylogenomic Datasets: Testing Ancient Hybridizations in Amaranthaceae s.l.
2019
Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data…
New insights into the OCST problem
2009
This paper considers the Euclidean variant of the optimal communciation spanning tree (OCST) problem. Researches have analyzed the structure of the problem and found that high quality solutions prefer edges of low cost. Further, edges pointing to the center of the network are more likely to be included in good solutions. We add to the literature and provide additional insights into the structure of the OCST problem. Therefore, we investigate properies of the whole tree, such as node degrees and the Wiener index. The results reveal that optimal solutions are structured in a star-like manner. There are few nodes with high node degrees, these nodes are located next to the graph's center. The m…
A relational model for unstructured documents
1987
The logical structure of a document is usually a tree in which the order of the nodes is important at least at some level of the tree. We call a document unstructured if its structure is a single-level ordered tree. The purpose of this paper is to present a many-sorted algebra for handling unstructured documents. The documents in the model are represented by relations. An algebra for handling documents of one type can be extended to an algebra for handling documents of several types. Further, an algebra for handling documents can be extended by the relational algebra for handling documents and relations in a common algebra. The model of this paper can be regarded as a part of a general docu…