Assessment of incorporation of the International Committee for Classification of Corneal Dystrophies (IC3D) in literature

2020 ◽  
Vol 41 (5) ◽  
pp. 507-509
Author(s):  
Saif Aldeen AlRyalat ◽  
Bahaa Al-Din Jaber
Keyword(s):  
International Committee ◽  
Corneal Dystrophies

Corneal Dystrophy in Dutch Belted Rabbits as a Possible Model of Thiel-Behnke Subtype of Epithelial-Stromal TGFβ-Induced Corneal Dystrophy

2020 ◽  
pp. 019262332096809
Author(s):  
JoAnn C. L. Schuh ◽  
Dana L. Holve ◽  
Karen E. Mundwiler
Keyword(s):  
Transforming Growth Factor ◽  
Transforming Growth Factor Β ◽  
Corneal Opacity ◽  
Corneal Dystrophy ◽  
International Committee ◽  
Corneal Dystrophies ◽  
Transmission Electron ◽  
Oct Imaging ◽  
Small Clusters

The International Committee for Classification of Corneal Dystrophies (IC3D) categorized corneal dystrophies in humans using anatomic, genotypic, and clinicopathologic phenotypic features. Relative to the IC3D classification, a review of the veterinary literature confirmed that corneal dystrophy is imprecisely applied to any corneal opacity and to multiple poorly characterized histologic abnormalities of the cornea in animals. True corneal dystrophy occurs in mice with targeted mutations and spontaneously in pet dogs and cats and in Dutch belted (DB) rabbits, but these instances lack complete phenotyping or genotyping. Corneal dystrophy in DB rabbits can be an important confounding finding in ocular toxicology studies but has only been described once. Therefore, the ophthalmology and pathology of corneal dystrophy in 13 DB rabbits were characterized to determine whether the findings were consistent with or a possible model of any corneal dystrophy subtypes in humans. Slit lamp and optical coherence tomography (OCT) imaging were used to characterize corneal dystrophy over 4 months in young DB rabbits. The hyperechoic OCT changes correlated with light microscopic findings in the anterior stroma, consisting of highly disordered collagen fibers and enlarged keratocytes. Histochemical stains did not reveal abnormal deposits. Small clusters of 8 to 16 nm diameter curly fibers identified by transmission electron microscopy were consistent with Thiel-Behnke (TBCD) subtype of epithelial-stromal transforming growth factor β-induced dystrophies. Sporadic corneal dystrophy in DB rabbits appears to be a potential animal model of TBCD, but genotypic characterization will be required to confirm this categorization.

Corneal Dystrophies

2022 ◽  
pp. 322-340
Keyword(s):  
Late Onset ◽  
Corneal Thickness ◽  
Corneal Dystrophy ◽  
International Committee ◽  
Level Of Evidence ◽  
Corneal Dystrophies ◽  
Tgfbi Gene ◽  
Epithelial Basement Membrane ◽  
Posterior Polymorphous Corneal Dystrophy

Corneal dystrophies have classically referred to inherited, bilateral disease without systemic findings, although there are several exceptions to this definition. Hereditary pattern is not present in most patients with epithelial basement membrane dystrophy (EBMD). Unilateral corneal changes may be found in some patients with posterior polymorphous corneal dystrophy (PPCD). TGFBI gene mutation (p.His572del) is associated with a unilateral, late-onset variant of lattice corneal dystrophy. Among all dystrophies, macular corneal dystrophy and posterior amorphous corneal dystrophy are associated with decreased corneal thickness. The International Committee for Classification of Corneal Dystrophies (IC3D) was created in 2005 to revise the corneal dystrophy nomenclature and create a current and accurate corneal dystrophy classification system. Evidential categories were created in the IC3D classification for reflecting the natural evolution of a corneal dystrophy and indicate the level of evidence supporting the existence of a given dystrophy.

Discriminating arboviral species

2021 ◽  
Vol 102 (4) ◽  
Author(s):  
Yiyuan Li ◽  
Angela C. O’Donnell ◽  
Howard Ochman
Keyword(s):  
Evolutionary History ◽  
Viral Vectors ◽  
Species Concept ◽  
International Committee ◽  
Biological Species ◽  
Biological Species Concept ◽  
Substantial Variation ◽  
Artificial Boundaries ◽  
Human Infections

Mosquito-borne arboviruses, including a diverse array of alphaviruses and flaviviruses, lead to hundreds of millions of human infections each year. Current methods for species-level classification of arboviruses adhere to guidelines prescribed by the International Committee on Taxonomy of Viruses (ICTV), and generally apply a polyphasic approach that might include information about viral vectors, hosts, geographical distribution, antigenicity, levels of DNA similarity, disease association and/or ecological characteristics. However, there is substantial variation in the criteria used to define viral species, which can lead to the establishment of artificial boundaries between species and inconsistencies when inferring their relatedness, variation and evolutionary history. In this study, we apply a single, uniform principle – that underlying the Biological Species Concept (BSC) – to define biological species of arboviruses based on recombination between genomes. Given that few recombination events have been documented in arboviruses, we investigate the incidence of recombination within and among major arboviral groups using an approach based on the ratio of homoplastic sites (recombinant alleles) to non-homoplastic sites (vertically transmitted alleles). This approach supports many ICTV-designations but also recognizes several cases in which a named species comprises multiple biological species. These findings demonstrate that this metric may be applied to all lifeforms, including viruses, and lead to more consistent and accurate delineation of viral species.

scholarly journals Taxonomic patterns in the zoonotic potential of mammalian viruses

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5979 ◽  
Author(s):  
Alex D. Washburne ◽  
Daniel E. Crowley ◽  
Daniel J. Becker ◽  
Kevin J. Olival ◽  
Matthew Taylor ◽  
...  
Keyword(s):  
Infectious Disease ◽  
At Risk ◽  
Life Histories ◽  
Coarse Graining ◽  
International Committee ◽  
Zoonotic Potential ◽  
Human Host ◽  
Disease Biology ◽  
Taxonomic Patterns

Predicting and simplifying which pathogens may spill over from animals to humans is a major priority in infectious disease biology. Many efforts to determine which viruses are at risk of spillover use a subset of viral traits to find trait-based associations with spillover. We adapt a new method—phylofactorization—to identify not traits but lineages of viruses at risk of spilling over. Phylofactorization is used to partition the International Committee on Taxonomy of Viruses viral taxonomy based on non-human host range of viruses and whether there exists evidence the viruses have infected humans. We identify clades on a range of taxonomic levels with high or low propensities to spillover, thereby simplifying the classification of zoonotic potential of mammalian viruses. Phylofactorization by whether a virus is zoonotic yields many disjoint clades of viruses containing few to no representatives that have spilled over to humans. Phylofactorization by non-human host breadth yields several clades with significantly higher host breadth. We connect the phylogenetic factors above with life-histories of clades, revisit trait-based analyses, and illustrate how cladistic coarse-graining of zoonotic potential can refine trait-based analyses by illuminating clade-specific determinants of spillover risk.

Summary of recommendations of nomenclature committees relevant to clay mineralogy: report of the Association Internationale pour l'Etude des Argiles (AIPEA) Nomenclature Committee for 2006

Clay Minerals ◽  
2006 ◽  
Vol 41 (4) ◽  
pp. 863-877 ◽  
Author(s):  
S. Guggenheim ◽  
J. M. Adams ◽  
D. C. Bain ◽  
F. Bergaya ◽  
M. F. Brigatti ◽  
...  
Keyword(s):  
Clay Minerals ◽  
International Collaboration ◽  
International Association ◽  
Clay Mineralogy ◽  
International Committee ◽  
Nomenclature Committee ◽  
Group Meetings

Brindley et al. (1951) reported the earliest efforts to obtain international collaboration on nomenclature and classification of clay minerals, initiated at the International Soil Congress in Amsterdam in 1950. Since then, national clay groups were formed, and they proposed various changes in nomenclature at group meetings of the International Clay Conferences. Most of the national clay groups have representation on the Nomenclature Committee of the Association Internationale pour l'Etude des Argiles (AIPEA, International Association for the Study of Clays), which was established in 1966. The precursor committee to the AIPEA Nomenclature Committee was the Nomenclature Subcommittee of the Comité International pour l'Etude des Argiles (OPEA, International Committee for the Study of Clays).

scholarly journals ClassiPhages 2.0: Sequence-based classification of phages using Artificial Neural Networks

2019 ◽  
Author(s):  
Cynthia Maria Chibani ◽  
Florentin Meinecke ◽  
Anton Farr ◽  
Sascha Dietrich ◽  
Heiko Liesegang
Keyword(s):  
Neural Networks ◽  
Artificial Neural Networks ◽  
Markov Models ◽  
International Committee ◽  
Biological Data ◽  
Sequencing Technologies ◽  
Artificial Neural ◽  
Taxonomic Markers ◽  
Artificial Neural Network Ann

AbstractBackground/ MotivationIn the era of affordable next generation sequencing technologies we are facing an exploding amount of new phage genome sequences. This requests high throughput phage classification tools that meet the standards of the International Committee on Taxonomy of Viruses (ICTV). However, an accurate prediction of phage taxonomic classification derived from phage sequences still poses a challenge due to the lack of performant taxonomic markers. Since machine learning methods have proved to be efficient for the classification of biological data we investigated how artificial neural networks perform on the task of phage taxonomy.ResultsIn this work, 5,920 constructed and refined profile Hidden Markov Models (HMMs), derived from 8,721 phage sequences classified into 12 well known phage families, were used to scan phage proteome datasets. The resulting Phage Family-proteome to Phage-derived-HMMs scoring matrix was used to develop and train an Artificial Neural Network (ANN) to find patterns for phage classification into one of the phage families. Results show that using the 100 fold cross-validation test, the proposed method achieved an overall accuracy of 84.18 %. The ANN was tested on a set of unclassified phages and resulted in a taxonomic prediction. The ANN prediction was benchmarked against the prediction resulting of multi-HMM hits, and showed that the ANN performance is dependent on the quality of the input matrix.ConclusionsWe believe that, as long as some phage families on public databases are underrepresented, multi-HMM hits can be used as a classification method to populate those phage families, which in turn will improve the performance and accuracy of the ANN. We believe that the proposed method is an effective and promising method for phage classification. The good performance of the ANN and HMM based predictor indicates the efficiency of the method for phage classification, where we foresee its improvement with an increasing number of sequenced viral genomes.

scholarly journals Severe acute respiratory syndrome-related coronavirus: The species and its viruses – a statement of the Coronavirus Study Group

2020 ◽  
Author(s):  
Alexander E. Gorbalenya ◽  
Susan C. Baker ◽  
Ralph S. Baric ◽  
Raoul J. de Groot ◽  
Christian Drosten ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Clinical Manifestations ◽  
International Committee ◽  
Study Group ◽  
Virus Species ◽  
Host Interactions ◽  
Naming Convention ◽  
Pathogenic Viruses ◽  
Tract Infections

AbstractThe present outbreak of lower respiratory tract infections, including respiratory distress syndrome, is the third spillover, in only two decades, of an animal coronavirus to humans resulting in a major epidemic. Here, the Coronavirus Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the official classification of viruses and taxa naming (taxonomy) of the Coronaviridae family, assessed the novelty of the human pathogen tentatively named 2019-nCoV. Based on phylogeny, taxonomy and established practice, the CSG formally recognizes this virus as a sister to severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus and designates it as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To facilitate communication, the CSG further proposes to use the following naming convention for individual isolates: SARS-CoV-2/Isolate/Host/Date/Location. The spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined. The independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying the entire (virus) species to complement research focused on individual pathogenic viruses of immediate significance. This research will improve our understanding of virus-host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.

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