Design networks with bounded pairwise distance

1999 ◽  
Author(s):  
Yevgeniy Dodis ◽  
Sanjeev Khanna
Keyword(s):  
Pairwise Distance

scholarly journals Chatbot to improve learning punctuation in Spanish and to enhance open and flexible learning environments

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Esteban Vázquez-Cano ◽  
Santiago Mengual-Andrés ◽  
Eloy López-Meneses
Keyword(s):  
Learning Process ◽  
Latent Dirichlet Allocation ◽  
Distance Matrix ◽  
Ease Of Use ◽  
Three Dimensions ◽  
Pairwise Distance ◽  
Control Group ◽  
Quantitative Methodology ◽  
Quasi Experimental ◽  
Experimental Group

AbstractThe objective of this article is to analyze the didactic functionality of a chatbot to improve the results of the students of the National University of Distance Education (UNED / Spain) in accessing the university in the subject of Spanish Language. For this, a quasi-experimental experiment was designed, and a quantitative methodology was used through pretest and posttest in a control and experimental group in which the effectiveness of two teaching models was compared, one more traditional based on exercises written on paper and another based on interaction with a chatbot. Subsequently, the perception of the experimental group in an academic forum about the educational use of the chatbot was analyzed through text mining with tests of Latent Dirichlet Allocation (LDA), pairwise distance matrix and bigrams. The quantitative results showed that the students in the experimental group substantially improved the results compared to the students with a more traditional methodology (experimental group / mean: 32.1346 / control group / mean: 28.4706). Punctuation correctness has been improved mainly in the usage of comma, colon and periods in different syntactic patterns. Furthermore, the perception of the students in the experimental group showed that they positively value chatbots in their teaching–learning process in three dimensions: greater “support” and companionship in the learning process, as they perceive greater interactivity due to their conversational nature; greater “feedback” and interaction compared to the more traditional methodology and, lastly, they especially value the ease of use and the possibility of interacting and learning anywhere and anytime.

scholarly journals Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sajjad Asaf ◽  
Abdul Latif Khan ◽  
Muhammad Numan ◽  
Ahmed Al-Harrasi
Keyword(s):  
Chloroplast Genome ◽  
Related Species ◽  
Evolutionary Genetics ◽  
Single Copy ◽  
Avicennia Marina ◽  
Pairwise Distance ◽  
Trna Genes ◽  
Evolutionary Divergence ◽  
Mangrove Tree ◽  
High Degree

AbstractAvicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members’ specifically A. marina and related species.

scholarly journals Distributed Formation Estimation Via Pairwise Distance Measurements

2021 ◽  
Vol 6 (2) ◽  
pp. 3017-3024
Author(s):  
Thomas Ziegler ◽  
Marco Karrer ◽  
Patrik Schmuck ◽  
Margarita Chli
Keyword(s):  
Pairwise Distance ◽  
Distance Measurements

scholarly journals Global evolutionary isolation measures can capture key local conservation species in Nearctic and Neotropical bird communities

2015 ◽  
Vol 370 (1662) ◽  
pp. 20140013 ◽  
Author(s):  
David W. Redding ◽  
Arne O. Mooers ◽  
Çağan H. Şekercioğlu ◽  
Ben Collen
Keyword(s):  
Evolutionary History ◽  
Local Level ◽  
Local Scale ◽  
Bird Communities ◽  
Community Level ◽  
Pairwise Distance ◽  
Conservation Priorities ◽  
Local Conservation ◽  
Trait Diversity ◽  
Evolutionary Distinctiveness

Understanding how to prioritize among the most deserving imperilled species has been a focus of biodiversity science for the past three decades. Though global metrics that integrate evolutionary history and likelihood of loss have been successfully implemented, conservation is typically carried out at sub-global scales on communities of species rather than among members of complete taxonomic assemblages. Whether and how global measures map to a local scale has received little scrutiny. At a local scale, conservation-relevant assemblages of species are likely to be made up of relatively few species spread across a large phylogenetic tree, and as a consequence there are potentially relatively large amounts of evolutionary history at stake. We ask to what extent global metrics of evolutionary history are useful for conservation priority setting at the community level by evaluating the extent to which three global measures of evolutionary isolation (evolutionary distinctiveness (ED), average pairwise distance (APD) and the pendant edge or unique phylogenetic diversity (PD) contribution) capture community-level phylogenetic and trait diversity for a large sample of Neotropical and Nearctic bird communities. We find that prioritizing the most ED species globally safeguards more than twice the total PD of local communities on average, but that this does not translate into increased local trait diversity. By contrast, global APD is strongly related to the APD of those same species at the community level, and prioritizing these species also safeguards local PD and trait diversity. The next step for biologists is to understand the variation in the concordance of global and local level scores and what this means for conservation priorities: we need more directed research on the use of different measures of evolutionary isolation to determine which might best capture desirable aspects of biodiversity.

scholarly journals Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling

2020 ◽  
Vol 21 (3) ◽  
pp. 944 ◽  
Author(s):  
Valery V. Panyukov ◽  
Sergey S. Kiselev ◽  
Olga N. Ozoline
Keyword(s):  
Distance Matrix ◽  
Pairwise Distance ◽  
Clinical Samples ◽  
E Coli ◽  
Taxonomic Profiling ◽  
New Methods ◽  
Natural Microflora ◽  
Microbiome Profiling ◽  
Pairwise Distance Matrix

The need for a comparative analysis of natural metagenomes stimulated the development of new methods for their taxonomic profiling. Alignment-free approaches based on the search for marker k-mers turned out to be capable of identifying not only species, but also strains of microorganisms with known genomes. Here, we evaluated the ability of genus-specific k-mers to distinguish eight phylogroups of Escherichia coli (A, B1, C, E, D, F, G, B2) and assessed the presence of their unique 22-mers in clinical samples from microbiomes of four healthy people and four patients with Crohn’s disease. We found that a phylogenetic tree inferred from the pairwise distance matrix for unique 18-mers and 22-mers of 124 genomes was fully consistent with the topology of the tree, obtained with concatenated aligned sequences of orthologous genes. Therefore, we propose strain-specific “barcodes” for rapid phylotyping. Using unique 22-mers for taxonomic analysis, we detected microbes of all groups in human microbiomes; however, their presence in the five samples was significantly different. Pointing to the intraspecies heterogeneity of E. coli in the natural microflora, this also indicates the feasibility of further studies of the role of this heterogeneity in maintaining population homeostasis.

Quantifying paleogeography using biogeography: a test case for the Ordovician and Silurian of Avalonia based on brachiopods and trilobites

Paleobiology ◽  
2002 ◽  
Vol 28 (3) ◽  
pp. 343-363 ◽  
Author(s):  
David C. Lees ◽  
Richard A. Fortey ◽  
L. Robin M. Cocks
Keyword(s):  
Goodness Of Fit ◽  
Total Evidence ◽  
Pairwise Distance ◽  
Test Case ◽  
Data Sets ◽  
Plate Tectonic ◽  
Plate Model ◽  
Optimal Arrangement ◽  
Evidence Analysis ◽  
Better Than

Despite substantial advances in plate tectonic modeling in the last three decades, the postulated position of terranes in the Paleozoic has seldom been validated by faunal data. Fewer studies still have attempted a quantitative approach to distance based on explicit data sets. As a test case, we examine the position of Avalonia in the Ordovician (Arenig, Llanvirn, early Caradoc, and Ashgill) to mid-Silurian (Wenlock) with respect to Laurentia, Baltica, and West Gondwana. Using synoptic lists of 623 trilobite genera and 622 brachiopod genera for these four plates, summarized as Venn diagrams, we have devised proportional indices of mean endemism (ME, normalized by individual plate faunas to eliminate area biogeographic effects) and complementarity (C) for objective paleobiogeographic comparisons. These can discriminate the relative position of Avalonia by assessing the optimal arrangement of inter-centroid distances (measured as great circles) between relevant pairs of continental masses. The proportional indices are used to estimate the “goodness-of-fit” of the faunal data to two widely used dynamic plate tectonic models for these time slices, those of Smith and Rush (1998) and Ross and Scotese (1997). Our faunal data are more consistent with the latter model, which we use to suggest relationships between faunal indices for the five time slices and new rescaled inter-centroid distances between all six plate pairs. We have examined linear and exponential models in relation to continental separation for these indices. For our generic data, the linear model fits distinctly better overall. The fits of indices generated by using independent trilobite and brachiopod lists are mostly similar to each other at each time slice and for a given plate, reflecting a common biogeographic signal; however, the indices vary across the time slices. Combining groups into the same matrix in a “total evidence” analysis performs better still as a measure of distance for mean endemism in the “Scotese” plate model. Four-plate mean endemism performs much better than complementarity as an indicator of pairwise distance for either plate model in the test case.

A new species of Zhangixalus (Anura: Rhacophoridae), previously confused with Zhangixalus smaragdinus (Blyth, 1852)

Zootaxa ◽  
2019 ◽  
Vol 4711 (2) ◽  
pp. 275-292
Author(s):  
GUOHUA YU ◽  
HONG HUI ◽  
MIAN HOU ◽  
ZHENGJUN WU ◽  
DINGQI RAO ◽  
...  
Keyword(s):  
New Species ◽  
Pairwise Distance ◽  
Outer Side ◽  
Molecular Evidence ◽  
Adult Males ◽  
Upper Eyelid ◽  
White Stripe ◽  
Lower Jaw ◽  
Southern Yunnan Of China ◽  
A New Species

We describe a new species of Zhangixalus from southern Yunnan of China, Vietnam, and Thailand based on morphological and molecular evidence. The new species had been confused with Zhangixalus smaragdinus (Blyth, 1852) in the past. Zhangixalus pachyproctus sp. nov. can be distinguished from Z. smaragdinus morphologically by the protruding vent in adult males, large thick grey reticular mottles below the white stripe on flank, more oblique snout in profile and wider head, longer snout, greater internarial distance, larger tympanum and longer hindlimb. The new species can be distinguished from other species of Zhangixalus with green dorsum by the following combination of characters: body size larger (SVL of adult males: 74.2–83.3 mm; SVL of adult female: 102.4 mm); dorsum smooth; narrow white stripes along edge of the lower jaw, body sides, outer side of limbs and above the vent; absence of brown bands on canthus rostralis, upper eyelid and supratympanic fold; webbing between fingers and toes complete except between the first two fingers; and internal single subgular vocal sac. Phylogeny based on comparison of 16S rRNA sequences suggests that the new species is the sister taxon to Z. smaragdinus and the two species differ by 7.63% in the uncorrected pairwise distance of 16S sequences. 

scholarly journals Extraction of accurate cytoskeletal actin velocity distributions from noisy measurements

2020 ◽  
Author(s):  
Cayla M. Miller ◽  
Elgin Korkmazhan ◽  
Alexander R. Dunn
Keyword(s):  
Single Molecule ◽  
Actin Filaments ◽  
Dynamical Behavior ◽  
Jump Process ◽  
Pairwise Distance ◽  
Actin Dynamics ◽  
Cell Cortex ◽  
Superresolution Microscopy ◽  
Distance Distributions ◽  
Primary Fibroblasts

Dynamic remodeling of the actin cytoskeleton allows cells to migrate, change shape, and exert mechanical forces on their surroundings. How the complex dynamical behavior of the cytoskeleton arises from the interactions of its molecular components remains incompletely understood. Tracking the movement of individual actin filaments in living cells can in principle provide a powerful means of addressing this question. However, single-molecule fluorescence imaging measurements that could provide this information are limited by low signal-to-noise ratios, with the result that the localization errors for individual fluorophore fiducials attached to filamentous (F)-actin are comparable to the distances traveled by actin filaments between measurements. In this study we tracked the movement F-actin labeled with single-molecule densities of the fluorogenic label SiR-actin in primary fibroblasts and endothelial cells. We then used a Bayesian statistical approach to estimate true, underlying actin filament velocity distributions from the tracks of individual actin-associated fluorophores along with quantified localization uncertainties. This analysis approach is broadly applicable to inferring statistical pairwise distance distributions arising from noisy point localization measurements such as occur in superresolution microscopy. We found that F-actin velocity distributions were better described by a statistical jump process, in which filaments exist in mechanical equilibria punctuated by abrupt, jump-like movements, than by models incorporating combinations of diffusive motion and drift. A model with exponentially distributed time- and length-scales for filament jumps recapitulated F-actin velocity distributions measured for the cell cortex, integrin-based adhesions, and actin stress fibers, indicating that a common physical model can potentially describe F-actin dynamics in a variety of cellular contexts.

scholarly journals Control of artefactual variation in reported inter-sample relatedness during clinical use of a Mycobacterium tuberculosis sequencing pipeline

2018 ◽  
Author(s):  
David H Wyllie ◽  
Nicholas Sanderson ◽  
Richard Myers ◽  
Tim Peto ◽  
Esther Robinson ◽  
...  
Keyword(s):  
Consensus Sequence ◽  
Read Depth ◽  
Pairwise Distance ◽  
Contact Tracing ◽  
Clinical Samples ◽  
Bacterial Dna ◽  
Consensus Sequences ◽  
Minor Variant ◽  
Validation Set ◽  
Genomic Regions

ABSTRACTContact tracing requires reliable identification of closely related bacterial isolates. When we noticed the reporting of artefactual variation between M. tuberculosis isolates during routine next generation sequencing of Mycobacterium spp, we investigated its basis in 2,018 consecutive M. tuberculosis isolates. In the routine process used, clinical samples were decontaminated and inoculated into broth cultures; from positive broth cultures DNA was extracted, sequenced, reads mapped, and consensus sequences determined. We investigated the process of consensus sequence determination, which selects the most common nucleotide at each position. Having determined the high-quality read depth and depth of minor variants across 8,006 M. tuberculosis genomic regions, we quantified the relationship between the minor variant depth and the amount of non-Mycobacterial bacterial DNA, which originates from commensal microbes killed during sample decontamination. In the presence of non-Mycobacterial bacterial DNA, we found significant increases in minor variant frequencies of more than 1.5 fold in 242 regions covering 5.1% of the M. tuberculosis genome. Included within these were four high variation regions strongly influenced by the amount of non-Mycobacterial bacterial DNA. Excluding these four regions from pairwise distance comparisons reduced biologically implausible variation from 5.2% to 0% in an independent validation set derived from 226 individuals. Thus, we have demonstrated an approach identifying critical genomic regions contributing to clinically relevant artefactual variation in bacterial similarity searches. The approach described monitors the outputs of the complex multi-step laboratory and bioinformatics process, allows periodic process adjustments, and will have application to quality control of routine bacterial genomics.

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