Review
Oncology
Henning Leske, Raymond Dalgleish, Alexander J. Lazar, Guido Reifenberger, Ian A. Cree
Summary: The description of genetic alterations in tumors is crucial, with guidelines often not adhered to for histone gene sequence variations, leading to confusion for pathologists, oncologists, and researchers. A proposed standard for reporting histone sequence variants according to HGVS principles aims to clarify these issues.
JOURNAL OF PATHOLOGY
(2021)
Article
Environmental Sciences
G. Masachessi, V. E. Prez, J. F. Michelena, A. Lizasoain, L. J. Ferreyra, L. C. Martinez, M. O. Giordano, P. A. Barril, J. Pavan, M. B. Pisano, A. A. Farias, M. B. Isa, V. E. Re, R. Colina, S. Nates
Summary: An environmental survey conducted in San Roque Dam, Cordoba, Argentina revealed high detection frequencies of PBV, HAdV, and iEV, which were consistent over the years and not affected by seasonal patterns. The study suggests using these viruses to enhance the evaluation of microbiological quality in freshwater in Argentina.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Review
Biochemistry & Molecular Biology
Mark J. Pallen, Andrea Telatin, Aharon Oren
Summary: Latin binomials, popularized by Linnaeus in the 18th century, have provided a stable and clear system of nomenclature in biology. However, with the increasing exploration of the microbial world, there is a need for a large number of new names for Archaea and Bacteria. To address this issue, an automated approach using Latin and Greek roots for creating linguistically correct names has been proposed, demonstrating the potential for creating millions of new names for Bacteria and Archaea.
TRENDS IN MICROBIOLOGY
(2021)
Editorial Material
Geochemistry & Geophysics
Frederic Hatert, Stuart J. Mills, Frank C. Hawthorne, Mike S. Rumsey
Summary: The classification and nomenclature of mineral species is regulated by IMA-CNMNC, which is essential for Earth Sciences due to minerals constituting the majority of planetary and interstellar materials. Hazen's proposed classification scheme, although complementary to IMA-CNMNC, has faced unjustified criticisms and factual errors.
AMERICAN MINERALOGIST
(2021)
Article
Ophthalmology
Douglas A. Jabs, Alastair K. Denniston, Anat Galor, Susan Lightman, Peter McCluskey, Neal Oden, Alan G. Palestine, James T. Rosenbaum, Sophia M. Saleem, Jennifer E. Thorne, Brett E. Trusko
Summary: Machine learning was utilized to determine classification criteria for TINU, with a low misclassification rate observed for TINU in both training and validation sets, indicating the criteria's utility for clinical and translational research.
AMERICAN JOURNAL OF OPHTHALMOLOGY
(2021)
Article
Food Science & Technology
Schrei Erik Andre, Bolanos Rodolfo
Summary: This paper presents a nomenclature system for agricultural food ingredients classification that takes into account multiple factors, with the purpose to contribute to the specificity and future differentiation between commodities and agricultural products with unique qualities.
INTERNATIONAL JOURNAL OF GASTRONOMY AND FOOD SCIENCE
(2021)
Article
Microbiology
Aharon Oren, Jan Mares, Rosmarie Rippka
Summary: The decision by ICSP to place the rank of phylum under ICNP rules allows the valid publication of the phylum name Cyanobacteriota with Cyanobacterium as the type genus. The names Cyanobacterium and Cyanobacterium stanieri are proposed for valid publication under ICN provisions, and the phylum name Cyanobacteriota is proposed under ICNP rules.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Constantina Theofanopoulou, Gregory Gedman, James A. Cahill, Cedric Boeckx, Erich D. Jarvis
Summary: The study indicates that oxytocin and vasopressin are adjacent paralogous genes that likely resulted from a local duplication through DNA transposable elements near the origin of vertebrates, with vasotocin retaining more of the parental sequence. Six major oxytocin-vasotocin receptors were identified among vertebrates, potentially originating from a single receptor shared with the common ancestor of invertebrates through whole-genome and large segmental duplications.
Article
Ophthalmology
Lucy I. Mudie, Amit K. Reddy, Jennifer L. Patnaik, Paula Pecen, Emmeline Kim, Kaylee Cole, Alan G. Palestine
Summary: The study evaluated the application of the new Standardization of Uveitis Nomenclature (SUN) classification criteria in an academic uveitis practice. The results showed that half of the patients had uveitis that was not covered by the SUN classification system. However, in cases where classification was possible, there was a good agreement between SUN classification and clinical diagnosis by a uveitis specialist.
AMERICAN JOURNAL OF OPHTHALMOLOGY
(2022)
Article
Ophthalmology
Douglas A. Jabs, Andrew D. Dick, Michal Kramer, Cristina Muccioli, Neal Oden, Annabelle A. Okada, Alan G. Palestine, Narsing A. Rao, Russell W. Read, Jennifer E. Thorne, Brett E. Trusko
Summary: This study aimed to determine classification criteria for sympathetic ophthalmia using machine learning techniques. Key criteria for sympathetic ophthalmia include bilateral uveitis with a history of unilateral ocular trauma or surgery, and anterior chamber and vitreous inflammation. The criteria had a low misclassification rate and appeared to perform sufficiently well for clinical and translational research.
AMERICAN JOURNAL OF OPHTHALMOLOGY
(2021)
Article
Virology
Lester J. Perez, Gavin A. Cloherty, Michael G. Berg
Summary: This study revealed the unreliability of using a 200 nt sequence of RdRp for the phylogenetic analysis of Picobirnaviruses, and proposed the use of full-length RdRp sequences instead. MAFFT alignment and maximum likelihood trees were identified as the optimal methods for determining phylogenetic relationships. The research showed that PBVs can be divided into three species, each with different genotypes.
Article
Ophthalmology
Douglas A. Jabs, Rubens Belfort, Bahram Bodaghi, Elizabeth Graham, Vishali Gupta, Gary N. Holland, Susan L. Lightman, Neal Oden, Alan G. Palestine, Justine R. Smith, Jennifer E. Thorne, Brett E. Trusko
Summary: This study aimed to determine classification criteria for tubercular uveitis by using machine learning techniques. Key criteria for tubercular uveitis included specific uveitic syndromes and evidence of tuberculosis infection. The accuracy of the diagnosis of tubercular uveitis was high, with low misclassification rates.
AMERICAN JOURNAL OF OPHTHALMOLOGY
(2021)
Editorial Material
Microbiology
Sybren de Hoog, Thomas J. Walsh, Sarah A. Ahmed, Ana Alastruey-Izquierdo, Barbara D. Alexander, Maiken Cavling Arendrup, Esther Babady, Feng-Yan Bai, Joan-Miquel Balada-Llasat, Andrew Borman, Anuradha Chowdhary, Andrew Clark, Robert C. Colgrove, Oliver A. Cornely, Tanis C. Dingle, Philippe J. Dufresne, Jeff Fuller, Jean-Pierre Gangneux, Connie Gibas, Heather Glasgow, Yvonne Graeser, Jacques Guillot, Andreas H. Groll, Gerhard Haase, Kimberly Hanson, Amanda Harrington, David L. Hawksworth, Randall T. Hayden, Martin Hoenigl, Vit Hubka, Kristie Johnson, Julianne V. Kus, Ruoyu Li, Jacques F. Meis, Michaela Lackner, Fanny Lanternier, Sixto M. Leal Jr, Francesca Lee, Shawn R. Lockhart, Paul Luethy, Isabella Martin, Kyung J. Kwon-Chung, Wieland Meyer, M. Hong Nguyen, Luis Ostrosky-Zeichner, Elizabeth Palavecino, Preeti Pancholi, Peter G. Pappas, Gary W. Procop, Scott A. Redhead, Daniel D. Rhoads, Stefan Riedel, Bryan Stevens, Kaede Ota Sullivan, Paschalis Vergidis, Emmanuel Roilides, Amir Seyedmousavi, Lili Tao, Vania A. Vicente, Roxana G. Vitale, Qi-Ming Wang, Nancy L. Wengenack, Lars Westblade, Nathan Wiederhold, Lewis White, Christina M. Wojewoda, Sean X. Zhang
Summary: The rapid pace of name changes of medically important fungi creates challenges for clinical laboratories and clinicians. Suggestions are made to reduce the number of name changes and provide diagnostic markers. It is recommended to maintain stability at the genus level and report both overarching species and molecular siblings. An open access online database of all medically important fungi names is essential, and new name changes should be reviewed routinely by a standing committee.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Microbiology
Lester J. Perez, Gavin A. Cloherty, Michael G. Berg
Summary: Picobirnaviruses (PBVs) are small double-segmented, double-stranded RNA viruses that are frequently associated with gastrointestinal and respiratory infections. The evolutionary analysis revealed that PBVs emerged simultaneously from avian Reovirus and fungal Partitivirus ancestors, indicating parallel evolution from different hosts has driven the genetic similarities among PBV species. These findings provide insights into the origins and genetic diversification of the Picobirnaviridae family.
MICROBIOLOGY SPECTRUM
(2023)
Article
Agriculture, Dairy & Animal Science
Xumin Ou, Sai Mao, Jingwen Dong, Jiayi Chen, Di Sun, Mingshu Wang, Dekang Zhu, Renyong Jia, Shun Chen, Mafeng Liu, Qiao Yang, Ying Wu, Xinxin Zhao, Shaqiu Zhang, Juan Huang, Qun Gao, Yunya Liu, Ling Zhang, Zhijiang Miao, Yunlong Li, Yang Li, Qiuwei Pan, Anchun Cheng
Summary: The nomenclature of duck viral hepatitis has caused confusion and misunderstanding due to the association of the same disease name with different genera of viruses. In order to address this issue, an updated disease classification based on the principles of human viral hepatitis and Koch's postulates has been proposed.
