Volatilization of Organotin Species from Municipal Waste Deposits: Novel Species Identification and Modeling of Atmospheric Stability

2011 ◽  
Vol 45 (3) ◽  
pp. 943-950 ◽  
Author(s):  
Eva M. Krupp ◽  
John K. Merle ◽  
Karsten Haas ◽  
Gary Foote ◽  
Nicolas Maubec ◽  
...  
Keyword(s):  
Species Identification ◽  
Novel Species ◽  
Atmospheric Stability ◽  
Municipal Waste ◽  
Organotin Species ◽  
Waste Deposits

scholarly journals Mosquito species identification using convolutional neural networks with a multitiered ensemble model for novel species detection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Adam Goodwin ◽  
Sanket Padmanabhan ◽  
Sanchit Hira ◽  
Margaret Glancey ◽  
Monet Slinowsky ◽  
...  
Keyword(s):  
Neural Networks ◽  
Species Identification ◽  
Convolutional Neural Networks ◽  
Novel Species ◽  
Novelty Detection ◽  
Mosquito Species ◽  
Image Database ◽  
Closed Set ◽  
Open Set

AbstractWith over 3500 mosquito species described, accurate species identification of the few implicated in disease transmission is critical to mosquito borne disease mitigation. Yet this task is hindered by limited global taxonomic expertise and specimen damage consistent across common capture methods. Convolutional neural networks (CNNs) are promising with limited sets of species, but image database requirements restrict practical implementation. Using an image database of 2696 specimens from 67 mosquito species, we address the practical open-set problem with a detection algorithm for novel species. Closed-set classification of 16 known species achieved 97.04 ± 0.87% accuracy independently, and 89.07 ± 5.58% when cascaded with novelty detection. Closed-set classification of 39 species produces a macro F1-score of 86.07 ± 1.81%. This demonstrates an accurate, scalable, and practical computer vision solution to identify wild-caught mosquitoes for implementation in biosurveillance and targeted vector control programs, without the need for extensive image database development for each new target region.

Klebsiella oxytoca Complex: Update on Taxonomy, Antimicrobial Resistance, and Virulence

2021 ◽  
Author(s):  
Jing Yang ◽  
Haiyan Long ◽  
Ya Hu ◽  
Yu Feng ◽  
Alan McNally ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Species Identification ◽  
Novel Species ◽  
Klebsiella Oxytoca ◽  
Content Type ◽  
Phenotypic Tests

Klebsiella oxytoca is actually a complex of nine species— Klebsiella grimontii , Klebsiella huaxiensis , Klebsiella michiganensis , K. oxytoca , Klebsiella pasteurii , Klebsiella spallanzanii , and three unnamed novel species. Phenotypic tests can assign isolates to the complex, but precise species identification requires genome-based analysis.

A taxonomic revision of the catshark genus Haploblepharus Garman 1913  (Chondrichthyes: Carcharhiniformes: Scyliorhinidae)

Zootaxa ◽  
2007 ◽  
Vol 1451 (1) ◽  
pp. 1-40 ◽  
Author(s):  
BRETT A. HUMAN
Keyword(s):  
South Africa ◽  
Species Identification ◽  
Novel Species ◽  
Taxonomic Revision ◽  
Identification Key ◽  
Range Extension ◽  
Type Material ◽  
Comprehensive Review ◽  
Colour Variation ◽  
Alpha Level

This paper examines the alpha level taxonomy of the genus Haploblepharus Garman, 1913 (Chondrichthyes; Scyliorhinidae). Three species are endemic to South Africa, with one species occurring in Namibia and South Africa. Haploblepharus pictus exhibits considerable colour variation which has led to some confusion between that species and H. edwardsii, resulting in a significant range extension for H. pictus. A neotype is designated for H. edwardsii, and problematic Haploblepharus juveniles are tentatively assigned to H. kistnasamyi. A novel species identification key is presented for Haploblepharus, and a comprehensive review of the taxonomy (including type material and synonyms) and distribution of all taxa is presented. The genus Haploblepharus contains four contemporary taxa: H. edwardsii (Schinz, 1822), H. pictus (Müller & Henle, 1838), H. fuscus Smith, 1950, and H. kistnasamyi Human & Compagno, 2006.

scholarly journals Precise Species Identification for Enterobacter: a Genome Sequence-Based Study with Reporting of Two Novel Species, Enterobacter quasiroggenkampii sp. nov. and Enterobacter quasimori sp. nov.

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Wenjing Wu ◽  
Yu Feng ◽  
Zhiyong Zong
Keyword(s):  
Species Identification ◽  
Novel Species ◽  
Enterobacter Cloacae ◽  
Clinical Samples ◽  
Correct Identification ◽  
Content Type ◽  
A Genome ◽  
Enterobacter Hormaechei ◽  
Taxonomic Assignments ◽  
Genome Analyses

ABSTRACT The genus Enterobacter comprises common pathogens and has a complicated taxonomy. Precise taxonomic assignation lays a foundation for microbiology. In this study, we updated the Enterobacter taxonomy based on robust genome analyses. We found that all Enterobacter subspecies assignments were incorrect. Enterobacter cloacae subsp. dissolvens and Enterobacter hormaechei subsp. hoffmannii are species (Enterobacter dissolvens and Enterobacter hoffmannii, respectively) rather than subspecies. Enterobacter xiangfangensis, Enterobacter hormaechei subsp. oharae, and Enterobacter hormaechei subsp. steigerwaltii are not Enterobacter hormaechei subspecies but belong to the same species (Enterobacter xiangfangensis). Enterobacter timonensis should be removed to Pseudenterobacter, a novel genus. We then reported two novel species, Enterobacter quasiroggenkampii and Enterobacter quasimori, by genome- and phenotype-based characterization. We also applied the updated taxonomy to curate 1,997 Enterobacter genomes in GenBank. Species identification was changed following our updated taxonomy for the majority of publicly available strains (1,542, 77.2%). The most common Enterobacter species was E. xiangfangensis. We identified 14 novel tentative Enterobacter genomospecies. This study highlights that updated and curated taxonomic assignments are the premise of correct identification. IMPORTANCE Enterobacter species are major human pathogens. Precise species identification lays a foundation for microbiology, but the taxonomy of Enterobacter is complicated and confusing. In this study, first, we significantly updated the taxonomy of Enterobacter by rigorous genome analyses and found that all subspecies assignments of Enterobacter were incorrect. Second, we characterized and reported two novel Enterobacter species with clinical significance. Third, we curated 1,997 Enterobacter genome sequences deposited in GenBank and found that the species identification of most Enterobacter strains needed to be corrected. Fourth, we found that the most common Enterobacter species seen in clinical samples is Enterobacter xiangfangensis rather than Enterobacter cloacae. Fifth, we identified 14 tentative novel Enterobacter and 18 tentative novel non-Enterobacter species. This study highlights that updated and curated taxonomic assignments are the premise of correct species identification. We recommend that future Enterobacter studies need to use the updated taxonomy to avoid misleading information.

A taxonomic revision of the catshark genus Holohalaelurus Fowler 1934 (Chondrichthyes: Carcharhiniformes: Scyliorhinidae), with descriptions of two new species

Zootaxa ◽  
2006 ◽  
Vol 1315 (1) ◽  
pp. 1 ◽  
Author(s):  
BRETT A. HUMAN
Keyword(s):  
New Species ◽  
East Africa ◽  
Species Identification ◽  
Southern Africa ◽  
Novel Species ◽  
Taxonomic Revision ◽  
Comprehensive Review ◽  
Type Series ◽  
Two New Species ◽  
Alpha Level

This paper examines the alpha level taxonomy of the genus Holohalaelurus Fowler 1934 (Chondrichthyes: Carcharhiniformes: Scyliorhinidae), which is endemic to southern and east Africa. A novel species identification key is presented for Holohalaelurus, and a comprehensive review of the taxonomy (including type material and synonyms) and distribution of all taxa is presented. Holohalaelurus regani (Gilchrist 1922) is restricted to southern Africa and the taxa that occur in tropical east Africa are discrete taxonomic units, resulting in the resurrection of H. melanostigma Norman 1939, and two new species, which are described here. Holohalaelurus polystigma (Regan 1921) is shown to be a junior synonym of H. punctatus (Gilchrist 1914), the validity of the type series for H. regani is discussed, and neotypes are designated for H. regani and H. punctatus. The genus Holohalaelurus contains the contemporary taxa H. punctatus (Gilchrist 1914), H. regani (Gilchrist 1922), H. melanostigma Norman 1939, H. favus sp. nov., and H. grennian sp. nov.

scholarly journals Precise Species Identification and Taxonomy Update for the Genus Kluyvera With Reporting Kluyvera sichuanensis sp. nov.

2020 ◽  
Vol 11 ◽  
Author(s):  
Lina Liu ◽  
Yu Feng ◽  
Li Wei ◽  
Fu Qiao ◽  
Zhiyong Zong
Keyword(s):  
Species Identification ◽  
Genome Sequencing ◽  
Dna Hybridization ◽  
Novel Species ◽  
Bacterial Species ◽  
Genome Sequences ◽  
Bacterial Genomes ◽  
Carbapenem Resistant ◽  
The Family ◽  
Human Infections

Kluyvera is a genus within the family Enterobacteriaceae and can cause various human infections but remains poorly studied. A carbapenem-resistant blaNDM–1-carrying Kluyvera strain 090646T was isolated from a hospital sink in Chengdu, Sichuan province, China. Whole genome sequencing of the strain revealed that it had 28.2 to 42.3% in silico DNA-DNA hybridization (isDDH) scores and 84.15 to 90.10% average nucleotide identity (ANI) values with other Kluyvera species. Both values are well below the ≥ 70.0% isDDH and ≥ 95–96% ANI cutoffs to define bacterial species, suggesting that the strain represents a novel species of the genus Kluyvera, for which the name Kluyvera sichuanensis. nov. is proposed. Type strain of K. sichuanensis is 090646T (=GDMCC 1.1872T =KCTC 82166T). Strain 090646T can be differentiated from other Kluyvera species by its ability to utilize D-sorbitol but not β-galactosidase (ONPG), D-mannose, glycerin, raffinose, nor sucrose. There were 47 genome sequences labeled as Kluyvera in GenBank, which were curated for precise species identification. Only 33 of the 47 genomes were indeed of Kluyvera and four novel Kluyvera genomospecies were identified, highlighting that the species assignation of bacterial genomes in GenBank need to be curated. Genome sequencing for more strains is required to understand the genus Kluyvera.

A taxonomic revision of the catshark genus Poroderma Smith, 1837 (Chondrichthyes: Carcharhiniformes: Scyliorhinidae)

Zootaxa ◽  
2006 ◽  
Vol 1229 (1) ◽  
pp. 1 ◽  
Author(s):  
BRETT A. HUMAN
Keyword(s):  
South Africa ◽  
Species Identification ◽  
Novel Species ◽  
Taxonomic Revision ◽  
Junior Synonym ◽  
Comprehensive Description ◽  
Comprehensive Review ◽  
Colour Variation ◽  
Alpha Level ◽  
Colour Form

This paper examines the alpha level taxonomy of the genus Poroderma Smith, 1837 (Chondrichthyes: Scyliorhinidae), which is endemic to South Africa. A novel species identification key is presented for Poroderma, and a comprehensive review of the taxonomy (including type material and synonyms) and distribution of all taxa is presented. Conoporoderma Fowler, 1934 is shown to be a junior synonym of Poroderma Smith, 1837, P. marleyi Fowler, 1934 is shown to be a junior synonym of P. pantherinum, and a new colour form of P. pantherinum is described. This review is the first to offer a comprehensive description of the colour variation exhibited by P. pantherinum. The genus Poroderma contains the contemporary taxa P. africanum (Gmelin, 1789) and P. pantherinum (Smith in Müller and Henle, 1838).

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