Visualization of the Evolutionary Path: an Influenza Case Study

Visualization of viral evolution is one of the essential tasks in bioinformatics, through which virologists characterize a virus. The fundamental visualization tool for such a task is constructing a dendrogram, also called the phylogenetic tree. In this paper, we propose the visualization and characterization of the evolutionary path, starting from the root to isolated virus in the leaf of the phylogenetic tree. The suggested approach constructs the sequences of inner nodes (ancestors) within the phylogenetic tree and uses one-hot-encoding to represent the genetic sequence in a binary format. By employing embedding methods, such as multi-dimensional scaling, we project the path into 2D and 3D spaces. The final visualization demonstrates the dynamic of viral evolution locally (for an individual strain) and globally (for all isolated viruses). The results suggest applications of our approach in: detecting earlier changes in the characteristics of strains; exploring emerging novel strains; modeling antigenic evolution; and study of evolution dynamics. All of these potential applications are critical in the fight against viruses.

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Different Within-Host Viral Evolution Dynamics in Severely Immunosuppressed Cases with Persistent SARS-CoV-2

Biomedicines ◽

10.3390/biomedicines9070808 ◽

2021 ◽

Vol 9 (7) ◽

pp. 808

Author(s):

Laura Pérez-Lago ◽

Teresa Aldámiz-Echevarría ◽

Rita García-Martínez ◽

Leire Pérez-Latorre ◽

Marta Herranz ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Evolutionary Dynamics ◽

Viral Evolution ◽

Special Focus ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

New Variant ◽

History Of ◽

Evolution Dynamics ◽

The Uk

A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.7, has recently been reported in the UK, causing global alarm. Most likely, the new variant emerged in a persistently infected patient, justifying a special focus on these cases. Our aim in this study was to explore certain clinical profiles involving severe immunosuppression that may help explain the prolonged persistence of viable viruses. We present three severely immunosuppressed cases (A, B, and C) with a history of lymphoma and prolonged SARS-CoV-2 shedding (2, 4, and 6 months), two of whom finally died. Whole-genome sequencing of 9 and 10 specimens from Cases A and B revealed extensive within-patient acquisition of diversity, 12 and 28 new single nucleotide polymorphisms, respectively, which suggests ongoing SARS-CoV-2 replication. This diversity was not observed for Case C after analysing 5 sequential nasopharyngeal specimens and one plasma specimen, and was only observed in one bronchoaspirate specimen, although viral viability was still considered based on constant low Ct values throughout the disease and recovery of the virus in cell cultures. The acquired viral diversity in Cases A and B followed different dynamics. For Case A, new single nucleotide polymorphisms were quickly fixed (13–15 days) after emerging as minority variants, while for Case B, higher diversity was observed at a slower emergence: fixation pace (1–2 months). Slower SARS-CoV-2 evolutionary pace was observed for Case A following the administration of hyperimmune plasma. This work adds knowledge on SARS-CoV-2 prolonged shedding in severely immunocompromised patients and demonstrates viral viability, noteworthy acquired intra-patient diversity, and different SARS-CoV-2 evolutionary dynamics in persistent cases.

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Monitoring Alveolar Ridge Remodelling Post-Extraction Using Sequential Intraoral Scanning over a Period of Four Months

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph17186638 ◽

2020 ◽

Vol 17 (18) ◽

pp. 6638

Author(s):

Khaled E. Ahmed

Keyword(s):

Computer Aided Design ◽

Three Dimensional ◽

Dimensional Changes ◽

Intraoral Scanning ◽

Computer Aided ◽

Potential Applications ◽

Cad Cam ◽

Aided Design ◽

2D And 3D

The potential applications of computer-aided design/computer-aided manufacturing (CAD/CAM) and intraoral scanning exceed the delivery of standard prosthodontic interventions. The aim of this study was to clinically present a developed assessment technique, that relies on the use of sequential intraoral scanning, three-dimensional superimposition, and 2D and 3D deviation analyses based on a standardised protocol, as an auxiliary tool in monitoring dimensional changes of residual ridge post-extraction with a follow-up period of four months.

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Solid State Synthesis and Characterization of Tin-Based Low-Dimensional Materials

MRS Proceedings ◽

10.1557/proc-755-dd6.19 ◽

2002 ◽

Vol 755 ◽

Cited By ~ 1

Author(s):

Tolulope O. Salami ◽

Scott R. J. Oliver

Keyword(s):

Variable Temperature ◽

Layered Compounds ◽

Layered Compound ◽

X Ray Diffraction ◽

Group 14 ◽

Potential Applications ◽

Low Dimensional ◽

2D And 3D ◽

Extended Materials

ABSTRACTWe report the synthetic conditions, physical properties and potential applications of late group 14 metal (Sn) 0D, 1D, 2D and 3D extended materials. The structures are primarily neutral chain and anionic layered compounds. The latter are charge-balanced by ammonium cations, as in and BING-7 [Sn(C2O4)F-] [NH4+] and BING-8 [Sn(PO4H)F-] [NH4+]. The neutral layered compound and chain compounds BING-1 [Na4Sn4(C2O4)F6], BING-2 [KSn(C2O4)F] and BING-4 [Sn(C2O4)(C5H5N)] have also been synthesized solvothermally. Thermogravimetric analysis (TGA) under nitrogen and in-situ variable temperature X-ray diffraction show that the materials decompose in the 200°C to 300°C range to more stable phases. Nuclear magnetic resonance (NMR) was used to monitor the ion-exchange properties of some of the materials. The intercalation properties of these materials are still being investigated.

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Ln-Ag heterometallic coordination polymers

Reviews in Inorganic Chemistry ◽

10.1515/revic-2014-0009 ◽

2015 ◽

Vol 35 (2) ◽

pp. 81-113 ◽

Cited By ~ 5

Author(s):

Ming Fang ◽

Bin Zhao

Keyword(s):

Coordination Polymer ◽

Coordination Polymers ◽

Luminescent Properties ◽

Research Development ◽

Carboxylate Ligands ◽

One Dimensional ◽

Potential Applications ◽

Heterometallic Coordination Polymers ◽

Intense Activity ◽

2D And 3D

AbstractThe last few years have seen an increasing interest in the study of lanthanide-silver (Ln-Ag) heterometallic coordination polymers due to their potential applications. It has led to intense activity of chemists to produce Ln-Ag heterometallic coordination polymers and investigate their properties. In this review, we summarize recent research development in the fascinating and challenging field of Ln-Ag heterometallic coordination polymers. This review covers 182 Ln-Ag heterometallic coordination polymers, which are categorized by the kind of ligand as N-heterocyclic carboxylate ligands and others. There are three categories of Ln-Ag coordination polymer based on N-heterocyclic carboxylate ligands: one dimensional (1D), 2D, and 3D. The 3D part was divided into Ln-Ag coordination polymers based on pyridine carboxylate ligands and other N-heterocyclic carboxylate ligands. This perspective illustrates the coordination features of compounds constructed by N-heterocyclic carboxylate ligands. Luminescent properties are also discussed.

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Advanced Technology for 3D Nanoprinting

Proceedings International ◽

10.33263/proceedings22.035035 ◽

2020 ◽

Vol 2 (2) ◽

pp. 35

Keyword(s):

Research And Development ◽

Scanning Probe Microscopy ◽

Advanced Technology ◽

Scanning Probe ◽

Materials Chemistry ◽

New Materials ◽

Feature Size ◽

Potential Applications ◽

3D Printers ◽

2D And 3D

Today, additive manufacturing research and development rely heavily on 3D printing. While there is a wide choice of commercial 3D printers, few reach nanometer resolution and feature size. The difficulties arise from special high precision required for materials delivery and registry among layers in the printing process. Scanning probe microscopy (SPM) has been widely used by the research and development community to visualize specimens with unprecedented resolution: reaching nanometer levels routinely and atomic and molecular levels on occasion. , The localization of SPM at atomic and molecular scale, has been harnessed to control interactions of molecules toward 2D and 3D nanolithography. Combining SPM’s spatial precision with advanced local delivery methodologies, including microfluidics, this presentation demonstrates feasibility and examples to reach 3D nanoprinting as well as new materials chemistry. Potential applications will also be discussed.

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Homing Peptide-Based Targeting of Tenascin-C and Fibronectin in Endometriosis

Nanomaterials ◽

10.3390/nano11123257 ◽

2021 ◽

Vol 11 (12) ◽

pp. 3257

Author(s):

Lorena Simón-Gracia ◽

Kristina Kiisholts ◽

Vilma Petrikaitė ◽

Allan Tobi ◽

Merli Saare ◽

...

Keyword(s):

Cell Lines ◽

Therapeutic Strategies ◽

Normal Endometrium ◽

Benign Condition ◽

Tenascin C ◽

Potential Applications ◽

Homing Peptide ◽

Antimitotic Drug ◽

Therapeutic Compounds ◽

2D And 3D

The current diagnostic and therapeutic strategies for endometriosis are limited. Although endometriosis is a benign condition, some of its traits, such as increased cell invasion, migration, tissue inflammation, and angiogenesis are similar to cancer. Here we explored the application of homing peptides for precision delivery of diagnostic and therapeutic compounds to endometriotic lesions. First, we audited a panel of peptide phages for the binding to the cultured immortalized endometriotic epithelial 12Z and eutopic stromal HESC cell lines. The bacteriophages displaying PL1 peptide that engages with angiogenic extracellular matrix overexpressed in solid tumors showed the strongest binding to both cell lines. The receptors of PL1 peptide, tenascin C domain C (TNC-C) and fibronectin Extra Domain-B (Fn-EDB), were expressed in both cells. Silver nanoparticles functionalized with synthetic PL1 peptide showed specific internalization in 12Z and HESC cells. Treatment with PL1-nanoparticles loaded with the potent antimitotic drug monomethyl auristatin E decreased the viability of endometriotic cells in 2D and 3D cultures. Finally, PL1-nanoparticless bound to the cryosections of clinical peritoneal endometriotic lesions in the areas positive for TNC-C and Fn-EDB immunoreactivities and not to sections of normal endometrium. Our findings suggest potential applications for PL1-guided nanoparticles in precision diagnosis and therapy of endometriosis.

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Repetitive elements and their genetic applications in zebrafish

Biochemistry and Cell Biology ◽

10.1139/o97-045 ◽

1997 ◽

Vol 75 (5) ◽

pp. 507-523 ◽

Cited By ~ 12

Author(s):

Zsuzsanna Izsvák ◽

Zoltan Ivics ◽

Perry B Hackett

Keyword(s):

Insertional Mutagenesis ◽

Repetitive Sequences ◽

Genetic Research ◽

Strain Differences ◽

Gene Families ◽

Repetitive Elements ◽

Model Systems ◽

Evolutionary Forces ◽

Individual Strain ◽

Potential Applications

Repetitive elements provide important clues about chromosome dynamics, evolutionary forces, and mechanisms for exchange of genetic information between organisms. Repetitive sequences, especially the mobile elements, have many potential applications in genetic research. DNA transposons and retroposons are routinely used for insertional mutagenesis, gene mapping, gene tagging, and gene transfer in several model systems. Once they are developed for the zebrafish, they will greatly facilitate the identification, mapping, and isolation of genes involved in development as well as the investigation of the evolutionary processes that have been shaping eukaryotic genomes. In this review repetitive elements are characterized in terms of their lengths and other physical properties, copy numbers, modes of amplification, and mobilities within a single genome and between genomes. Examples of how they can be used to screen genomes for species and individual strain differences are presented. This review does not cover repetitive gene families that encode well-studied products such as rRNAs, tRNAs, and the like.

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Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree

10.1101/040980 ◽

2016 ◽

Cited By ~ 1

Author(s):

M Azim Ansari ◽

Xavier Didelot

Keyword(s):

Bayesian Inference ◽

Phylogenetic Tree ◽

Human Leukocyte ◽

Ancestral State ◽

Tree Leaves ◽

Inference Method ◽

Leukocyte Antigen ◽

Potential Applications ◽

Bayesian Inference Method ◽

Phenotype Distribution

The distribution of a phenotype on a phylogenetic tree is often a quantity of interest. Many phenotypes have imperfect heritability, so that a measurement of the phenotype for an individual can be thought of as a single realisation from the phenotype distribution of that individual. If all individuals in a phylogeny had the same phenotype distribution, measured phenotypes would be randomly distributed on the tree leaves. This is however often not the case, implying that the phenotype distribution evolves over time. Here we propose a new model based on this principle of evolving phenotype distribution on the branches of a phylogeny, which is different from ancestral state reconstruction where the phenotype itself is assumed to evolve. We develop an efficient Bayesian inference method to estimate the parameters of our model and to test the evidence for changes in the phenotype distribution. We use multiple simulated datasets to show that our algorithm has good sensitivity and specificity properties. Since our method identifies branches on the tree on which the phenotype distribution has changed, it is able to break down a tree into components for which this distribution is unique and constant. We present two applications of our method, one investigating the association between HIV genetic variation and human leukocyte antigen, and the other studying host range distribution in a lineage of Salmonella enterica, and we discuss many other potential applications. All the methods described in this paper are implemented in a software package called TreeBreaker which is freely available for download at https://github.com/ansariazim/TreeBreaker

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UNIFIED TOPOLOGICAL FRAMEWORK FOR RETRIEVING 2D AND 3D MULTI-SCALE SPATIAL INFORMATION

ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences ◽

10.5194/isprs-archives-xlii-4-w9-265-2018 ◽

2018 ◽

Vol XLII-4/W9 ◽

pp. 265-272

Author(s):

H. Karim ◽

A. Abdul Rah ◽

A. Jamali

Keyword(s):

Conceptual Framework ◽

Information Science ◽

Spatial Information ◽

Geographical Information ◽

Topological Graph ◽

Single View ◽

Level Of Details ◽

Potential Applications ◽

And Performance ◽

2D And 3D

<p><strong>Abstract.</strong> Different applications or users need different model (differ requirement on level of details; geometry and information), less focuses in topological element. Improper manage geometry, attribute and topology elements in multi-scape environment will cause data repetition/redundancy, storage capacity and performance issues. This research focuses on utilizing topological graph which is important for various Geographical Information Science applications such as 3D indoor, network analysis, and sharing information/attribute from multiple level of details (LoD). A conceptual framework towards a unified data structure/model for representing several levels of details (LoDs) which integrates 2D and 3D topological and geometrical spaces in a single view is presented. The proposed framework has a potential of adopting into the CityGML/IndoorGML standards with representing different CityGML LoDs in a single view representation. Potential applications of the proposed conceptual framework including solar energy and utility mapping are discussed.</p>

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Metal Salen- and Salphen-Containing Organic Polymers: Synthesis and Applications

Organic Materials ◽

10.1055/s-0040-1708501 ◽

2020 ◽

Vol 02 (02) ◽

pp. 182-203

Author(s):

Sven M. Elbert ◽

Michael Mastalerz

Keyword(s):

Heterogeneous Catalysis ◽

Functional Groups ◽

Polymeric Materials ◽

Building Blocks ◽

Luminescent Materials ◽

Organic Polymers ◽

Gas Sorption ◽

Metal Centers ◽

Potential Applications ◽

2D And 3D

The properties of organic polymeric materials can be chemically fine-tuned by the implementation of functional groups or units within the backbone. Especially the inclusion of coordinated metal centers offers a nearly infinite toolbox to adjust properties and thus potential applications. In particular, salen and salphen complexes are widely known to be highly efficient homogenous catalysts. They are also used as luminescent materials and devices or as supramolecular building blocks. This review focusses on the class of salen- and salphen-containing organic polymers, from 1D to 3D. Besides the comparison of synthetic polymerization methods, properties and applications are discussed, with an emphasis on porous 2D and 3D polymeric metal salphens and salens for heterogeneous catalysis and gas sorption.

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