A pairwise distance distribution correction (DDC) algorithm to eliminate blinking-caused artifacts in SMLM

AbstractIn single-molecule localization based super-resolution microscopy (SMLM), a fluorophore stochastically switches between fluorescent- and dark-states, leading to intermittent emission of fluorescence, a phenomenon known as blinking. Intermittent emissions create multiple localizations belonging to the same molecule, resulting in blinking-artifacts within SMLM images. These artifacts are often interpreted as true biological assemblies, confounding quantitative analyses and interpretations. Multiple methods have been developed to eliminate these artifacts, but they either require additional experiments, arbitrary thresholds, or specific photo-kinetic models. Here we present a method, termed Distance Distribution Correction (DDC), to eliminate blinking-caused repeat localizations without any additional calibrations. The approach relies on the finding that the true pairwise distance distribution of different fluorophores in an SMLM image can be naturally obtained from the imaging sequence by using distances between localizations separated by a time much longer than the average fluorescence survival time. We show that using the true pairwise distribution we can define and then maximize the likelihood of obtaining a particular set of localizations void of blinking-artifacts, generating an accurate reconstruction of the underlying cellular structure. Using both simulated and experimental data, we show that DDC surpasses all previous existing blinking-artifact correction methodologies, resulting in drastic improvements in obtaining the closest estimate of the true spatial organization and number of fluorescent emitters in a wide range of applications. The simplicity and robustness of DDC will allow it to become the field standard in SMLM imaging, enabling the most accurate reconstruction and quantification of SMLM images to date.

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Distance Distribution between Complex Network Nodes in Hyperbolic Space

Complex Systems ◽

10.25088/complexsystems.25.3.223 ◽

2016 ◽

Vol 25 (3) ◽

pp. 223-236 ◽

Cited By ~ 5

Author(s):

Gregorio Alanis-Lobato ◽

Miguel A. Andrade-Navarro ◽

Keyword(s):

Complex Network ◽

Hyperbolic Space ◽

Distance Distribution ◽

Network Nodes

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

International Journal of Educational Technology in Higher Education ◽

10.1186/s41239-021-00269-8 ◽

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.

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

Scientific Reports ◽

10.1038/s41598-021-83060-z ◽

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.

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Distributed Formation Estimation Via Pairwise Distance Measurements

IEEE Robotics and Automation Letters ◽

10.1109/lra.2021.3062347 ◽

2021 ◽

Vol 6 (2) ◽

pp. 3017-3024

Author(s):

Thomas Ziegler ◽

Marco Karrer ◽

Patrik Schmuck ◽

Margarita Chli

Keyword(s):

Pairwise Distance ◽

Distance Measurements

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Analytical solution of the PELDOR inverse problem using the integral Mellin transform

Physical Chemistry Chemical Physics ◽

10.1039/c7cp04059h ◽

2017 ◽

Vol 19 (48) ◽

pp. 32381-32388 ◽

Cited By ~ 5

Author(s):

Anna G. Matveeva ◽

Vyacheslav M. Nekrasov ◽

Alexander G. Maryasov

Keyword(s):

Inverse Problem ◽

Distribution Function ◽

Analytical Solution ◽

Short Distance ◽

Mellin Transform ◽

Distance Distribution ◽

Distance Distribution Function ◽

Distance Range ◽

Model Free ◽

Model Free Approach

The model-free approach used does not introduce systematic distortions in the computed distance distribution function between two spins and appears to result in noise grouping in the short distance range.

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

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2014.0013 ◽

2015 ◽

Vol 370 (1662) ◽

pp. 20140013 ◽

Cited By ~ 12

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.

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