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Balkrishna A, Kumar A, Rohela A, Arya V, Gautam AK, Sharma H, Rai P, Kumari A, Amarowicz R. Traditional uses, hepatoprotective potential, and phytopharmacology of Tinospora cordifolia: a narrative review. J Pharm Pharmacol 2024; 76:183-200. [PMID: 38280221 DOI: 10.1093/jpp/rgae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/09/2024] [Indexed: 01/29/2024]
Abstract
OBJECTIVES Despite significant advancements in modern medicine, effective hepatoprotective medication with minimal side effects is still lacking. In this context. Tinospora cordifolia, an Indian Ayurvedic liana, has attracted much attention. KEY FINDINGS Traditionally, T. cordifolia has been found to be effective in the treatment of jaundice; according to the literature, T. cordifolia is a hepatoprotective agent, and the CCl4 model is the most frequently used to evaluate its potential. Its hepatoprotective effects might be attributed to alkaloids (berberine, palmatine, and jatrorrhizine) and sinapic acid. Berberine decreases inflammation by inhibiting the proinflammatory cascade triggered by TNF-α and reduces nitrosative stress by inhibiting iNOS. T. cordifolia also exhibits anticancer, anti-inflammatory, antimicrobial, antioxidant, and other activities; it is safe at concentrations up to 2000 mg/kg. Its biological action can be attributed to polyphenols, alkaloids, steroids, terpenoids, and glycosides. T. cordifolia has also been found to be an active ingredient in several polyherbal formulations used to treat chemical-mediated hepatotoxicity. CONCLUSION T. cordifolia's hepatoprotective effects are mediated by the inhibition of lipid peroxidation, the management of oxidative stress, and other factors. T. cordifolia can be used to manage liver disorders and as a hepatoprotective supplement in the food industry. The bioprospecting of its alkaloids can lead to the development of novel formulations against hepatic ailments.
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Affiliation(s)
- Acharya Balkrishna
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, India
- Centre of Excellence, Patanjali Ayurved Hospital, Haridwar, India
| | - Ashwani Kumar
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, India
| | - Akansha Rohela
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, India
| | - Vedpriya Arya
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, India
- Centre of Excellence, Patanjali Ayurved Hospital, Haridwar, India
| | - Ajay Kumar Gautam
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, India
| | - Hemant Sharma
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, India
| | - Priyanka Rai
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, India
| | - Amita Kumari
- Patanjali Herbal Research Department, Patanjali Research Foundation, Haridwar, India
| | - Ryszard Amarowicz
- Department of Chemical and Physical Properties of Food, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
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Mewara A, Gile GH, Mathison B, Zhao H, Pritt B, Bradbury RS. Lophomonas as a respiratory pathogen-jumping the gun. J Clin Microbiol 2024; 62:e0084523. [PMID: 37902329 PMCID: PMC10793291 DOI: 10.1128/jcm.00845-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023] Open
Abstract
Human infections with the protozoan Lophomonas have been increasingly reported in the medical literature over the past three decades. Initial reports were based on microscopic identification of the purported pathogen in respiratory specimens. Later, a polymerase chain reaction (PCR) was developed to detect Lophomonas blattarum, following which there has been a significant increase in reports. In this minireview, we thoroughly examine the published reports of Lophomonas infection to evaluate its potential role as a human pathogen. We examined the published images and videos of purported Lophomonas, compared its morphology and motility characteristics with host bronchial ciliated epithelial cells and true L. blattarum derived from cockroaches, analyzed the published PCR that is being used for its diagnosis, and reviewed the clinical data of patients reported in the English and Chinese literature. From our analysis, we conclude that the images and videos from human specimens do not represent true Lophomonas and are predominantly misidentified ciliated epithelial cells. Additionally, we note that there is insufficient clinical evidence to attribute the cases to Lophomonas infection, as the clinical manifestations are non-specific, possibly caused by other infections and comorbidities, and there is no associated tissue pathology attributable to Lophomonas. Finally, our analysis reveals that the published PCR is not specific to Lophomonas and can amplify DNA from commensal trichomonads. Based on this thorough review, we emphasize the need for rigorous scientific scrutiny before a microorganism is acknowledged as a novel human pathogen and discuss the potential harms of misdiagnoses for patient care and scientific literature.
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Affiliation(s)
- Abhishek Mewara
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Gillian H. Gile
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Blaine Mathison
- Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Huan Zhao
- Federation University, Melbourne, Australia
| | - Bobbi Pritt
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
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Weiskirchen R. Research reporting guidelines for cell lines: more than just a recommendation. Ann Transl Med 2023; 11:421. [PMID: 38213802 PMCID: PMC10777224 DOI: 10.21037/atm-23-1208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/25/2023] [Indexed: 01/13/2024]
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Cajka T, Hricko J, Rudl Kulhava L, Paucova M, Novakova M, Fiehn O, Kuda O. Exploring the Impact of Organic Solvent Quality and Unusual Adduct Formation during LC-MS-Based Lipidomic Profiling. Metabolites 2023; 13:966. [PMID: 37755246 PMCID: PMC10536874 DOI: 10.3390/metabo13090966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/28/2023] Open
Abstract
Liquid chromatography-mass spectrometry (LC-MS) is the key technique for analyzing complex lipids in biological samples. Various LC-MS modes are used for lipid separation, including different stationary phases, mobile-phase solvents, and modifiers. Quality control in lipidomics analysis is crucial to ensuring the generated data's reliability, reproducibility, and accuracy. While several quality control measures are commonly discussed, the impact of organic solvent quality during LC-MS analysis is often overlooked. Additionally, the annotation of complex lipids remains prone to biases, leading to potential misidentifications and incomplete characterization of lipid species. In this study, we investigate how LC-MS-grade isopropanol from different vendors may influence the quality of the mobile phase used in LC-MS-based untargeted lipidomic profiling of biological samples. Furthermore, we report the occurrence of an unusual, yet highly abundant, ethylamine adduct [M+46.0651]+ that may form for specific lipid subclasses during LC-MS analysis in positive electrospray ionization mode when acetonitrile is part of the mobile phase, potentially leading to lipid misidentification. These findings emphasize the importance of considering solvent quality in LC-MS analysis and highlight challenges in lipid annotation.
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Affiliation(s)
- Tomas Cajka
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic; (J.H.); (L.R.K.); (M.P.); (M.N.); (O.K.)
| | - Jiri Hricko
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic; (J.H.); (L.R.K.); (M.P.); (M.N.); (O.K.)
| | - Lucie Rudl Kulhava
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic; (J.H.); (L.R.K.); (M.P.); (M.N.); (O.K.)
| | - Michaela Paucova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic; (J.H.); (L.R.K.); (M.P.); (M.N.); (O.K.)
| | - Michaela Novakova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic; (J.H.); (L.R.K.); (M.P.); (M.N.); (O.K.)
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA;
| | - Ondrej Kuda
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic; (J.H.); (L.R.K.); (M.P.); (M.N.); (O.K.)
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Iftikhar M, Shah M, Ullah Z, Shakoor HA, Ullah S. Achieving Critical View of Safety via a New Technique: The Triple One (111) Technique. Cureus 2023; 15:e44098. [PMID: 37750143 PMCID: PMC10518118 DOI: 10.7759/cureus.44098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Misidentification of anatomical structures is one of the most common causes of bile duct injury following laparoscopic cholecystectomy. Achieving Critical View of Safety (CVS) is a standard step in conducting safe cholecystectomy all over the world. In our institute, we achieve CVS via a unique technique called Triple One or 111 and find it very helpful and easy to achieve CVS. Moreover, the rate of conversion has also decreased while achieving CVS via this technique. The unique aspect of the Triple One technique is that by following this method, even new laparoscopic surgeons can achieve CVS very easily in difficult cases and, hence, it decreases the chances of vasculobiliary injury (VBI). OBJECTIVE This study aimed to determine how effective the Triple One technique is in achieving CVS as well as in lessening the chances of VBI. MATERIAL AND METHODS A total of 545 patients were admitted through the outpatient department, ranging in age from 30 to 70 years, with a mean of 50 years. The study comprised patients with American Society of Anaesthesiologists (ASA) I & II, acute and chronic cholecystitis, and symptomatic cholelithiasis. The study excluded patients with co-morbidities, prior abdominal procedures, and suspected complications. On the second postoperative day, all patients received their discharge papers and on the seventh postoperative day, follow-up was completed. RESULTS Successful gallbladder extraction using the Triple One technique was achieved in 540 (99%) cases. The other five (1%) cases converted to open cholecystectomy because of the difficult gallbladder anatomy and extensive scarring. No VBI or bile duct injury was noted. No mortality was recorded during the study period. CONCLUSION By incorporating CVS using the Triple One technique into our policies and curriculum, we may encourage safe cholecystectomy practices and prevent bile duct injuries.
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Affiliation(s)
- Muhammad Iftikhar
- General Surgery Department, Hayatabad Medical Complex Peshawar, Peshawar, PAK
| | - Muhammad Shah
- General Surgery Department, Hayatabad Medical Complex Peshawar, Peshawar, PAK
| | - Zia Ullah
- Anatomy Department, Peshawar Institute of Medical Sciences, Peshawar, PAK
| | | | - Shahid Ullah
- General Surgery Department, Hayatabad Medical Complex Peshawar, Peshawar, PAK
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Iliadis M, Harris B, Vakhitova Z, Flynn A, Tyson D. Police Body-Worn Cameras as a Response to Domestic and Family Violence: Practitioner Insights Into the Consequences for Victim/Survivors. Violence Against Women 2023:10778012231185541. [PMID: 37487222 DOI: 10.1177/10778012231185541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Body-worn cameras (BWCs) have been promoted internationally to enhance responses to domestic and family violence (DFV). However, little is known about their utility, benefits, and limitations. Drawing upon the insights of DFV practitioners who support victim/survivors in the Australian states of Queensland and Western Australia, this article finds that while BWCs can capture some DFV incidents, they are unable to show their full context and impacts. BWC footage may also have consequences for "nonideal" victim/survivors, including wrongful criminalization and the removal of children. Ultimately, we argue that trauma-informed responses are vital for BWC use in DFV cases to improve frontline responses.
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Affiliation(s)
- Mary Iliadis
- School of Humanities and Social Sciences, Deakin University, Melbourne, Victoria, Australia
| | | | | | - Asher Flynn
- Monash University, Melbourne, Victoria, Australia
| | - Danielle Tyson
- School of Humanities and Social Sciences, Deakin University, Melbourne, Victoria, Australia
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Kumaran D, Laflamme C, Ramirez-Arcos S. A multiphasic approach to solve misidentification of Cutibacterium acnes as Atopobium vaginae during routine bacterial screening of platelet concentrates using the VITEK 2 system. Access Microbiol 2023; 5:acmi000539.v3. [PMID: 37424557 PMCID: PMC10323807 DOI: 10.1099/acmi.0.000539.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/16/2023] [Indexed: 07/11/2023] Open
Abstract
Skin flora bacteria, such as Cutibacterium acnes , are the predominant contaminants of blood products used for transfusion. Platelet concentrates (PCs), a therapeutic product used to treat patients with platelet deficiencies, are stored at ambient temperature under agitation, providing ideal conditions for bacterial proliferation. At Canadian Blood Services, PCs are screened for microbial contamination using the automated BACT/ALERT culture system. Positive cultures are processed and contaminating organisms are identified using the VITEK 2 system. Over a period of approximately 2 years, several PC isolates were identified as Atopobium vaginae to a high level of confidence. However, since A. vaginae is associated with bacterial vaginosis and is not a common PC contaminant, a retrospective investigation revealed that in all cases C. acnes was misidentified as A. vaginae . Our investigation demonstrated that the media type used to grow PC bacterial isolates can have a significant impact on the results obtained on the VITEK 2 system. Furthermore, other identification methods such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALD-TOF MS) and PCR amplification of the 16S RNA gene were only partially successful in the identification of C. acnes . Therefore, our findings support a multiphasic approach when PC isolates are identified as A. vaginae by the VITEK 2 system for proper identification of C. acnes using macroscopic, microscopic and other biochemical analyses.
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Affiliation(s)
- Dilini Kumaran
- Canadian Blood Services, Ottawa, Ontario, Canada
- University of Ottawa, Ottawa, Ontario, Canada
| | | | - Sandra Ramirez-Arcos
- Canadian Blood Services, Ottawa, Ontario, Canada
- University of Ottawa, Ottawa, Ontario, Canada
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8
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Li F, Lin Y, Li S. Notes on two Stiphropus species from China (Araneae, Thomisidae). Biodivers Data J 2023; 11:e105695. [PMID: 37305448 PMCID: PMC10257076 DOI: 10.3897/bdj.11.e105695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/30/2023] [Indexed: 06/13/2023] Open
Abstract
Background The spider genus Stiphropus Gerstaecker, 1873 currently includes 21 extant species that are distributed in Africa (12) and Asia (9). Four species, S.falciformus Yang, Zhu & Song, 2006, S.myrmecophilus Huang & Lin, 2020, S.ocellatus Thorell, 1887 and S.soureni Sen, 1964, are currently known from China. New information The mismatched female of S.falciformus is reported as a new species: S.qianlei sp. n. (♂♀). The unknown male of S.soureni Sen, 1964 is described for the first time. Photos and morphological descriptions are provided.
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Affiliation(s)
- Fengyuan Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, ChinaState Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking UniversityBeijing 100871China
| | - Yejie Lin
- Hebei Key Laboratory of Animal Diversity, College of Life Science, Langfang Normal University, Langfang 065000, ChinaHebei Key Laboratory of Animal Diversity, College of Life Science, Langfang Normal UniversityLangfang 065000China
| | - Shuqiang Li
- Institute of Zoology, Chinese Academy of sciences, Beijing 100101, ChinaInstitute of Zoology, Chinese Academy of sciencesBeijing 100101China
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Sosa-Duque FJ, Tauber CA. Discovery and redescription of the true Nuvolumbrosus Navás and naming of a new Nuvol species (Neuroptera, Chrysopidae, Leucochrysini). Zookeys 2023; 1158:179-193. [PMID: 37215690 PMCID: PMC10193997 DOI: 10.3897/zookeys.1158.98572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/07/2023] [Indexed: 05/24/2023] Open
Abstract
Examination of a newly discovered specimen of Nuvol showed that our earlier species determination of Nuvolumbrosus Navás had been incorrect and that our "redescription" of the species actually applied to an undescribed species. Here, we redescribe the true N.umbrosus, based on a newly discovered male specimen. This specimen closely resembles Navás' description, and it was collected from the Atlantic Forest as was the original type specimen. In addition, we assign the previously misidentified Nuvol specimens from the Amazonian region to a separate species, Nuvolsatur Sosa & Tauber, sp. nov. As a result of these actions, the genus Nuvol now contains two morphologically and geographically distinct species. In addition, the abdomens and genitalia of both sexes of Nuvol are now described (although each from a separate species).
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Affiliation(s)
- Francisco José Sosa-Duque
- Universidade Federal Rural da Amazônia (UFRA) Campus de Capitão Poço, Pará, BrazilUniversidade Federal Rural da Amazônia UFRACampus de Capitão PoçoBrazil
| | - Catherine A. Tauber
- Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY 14853, USACornell UniversityIthacaUnited States of America
- Department of Entomology and Nematology, University of California, Davis, CA 95616, USAUniversity of CaliforniaDavisUnited States of America
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Weiskirchen S, Schröder SK, Buhl EM, Weiskirchen R. A Beginner's Guide to Cell Culture: Practical Advice for Preventing Needless Problems. Cells 2023; 12. [PMID: 36899818 DOI: 10.3390/cells12050682] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/18/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023] Open
Abstract
The cultivation of cells in a favorable artificial environment has become a versatile tool in cellular and molecular biology. Cultured primary cells and continuous cell lines are indispensable in investigations of basic, biomedical, and translation research. However, despite their important role, cell lines are frequently misidentified or contaminated by other cells, bacteria, fungi, yeast, viruses, or chemicals. In addition, handling and manipulating of cells is associated with specific biological and chemical hazards requiring special safeguards such as biosafety cabinets, enclosed containers, and other specialized protective equipment to minimize the risk of exposure to hazardous materials and to guarantee aseptic work conditions. This review provides a brief introduction about the most common problems encountered in cell culture laboratories and some guidelines on preventing or tackling respective problems.
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de Jong AW, Al-Obaid K, Mohd Tap R, Gerrits van den Ende B, Groenewald M, Joseph L, Ahmad S, Hagen F. Candida khanbhai sp. nov., a new clinically relevant yeast within the Candida haemulonii species complex. Med Mycol 2023; 61:7000835. [PMID: 36694950 PMCID: PMC9936790 DOI: 10.1093/mmy/myad009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/10/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Invasive fungal infections caused by non-albicans Candida species are increasingly reported. Recent advances in diagnostic and molecular tools enabled better identification and detection of emerging pathogenic yeasts. The Candida haemulonii species complex accommodates several rare and recently described pathogenic species, C. duobushaemulonii, C. pseudohaemulonii, C. vulturna, and the most notorious example is the outbreak-causing multi-drug resistant member C. auris. Here, we describe a new clinically relevant yeast isolated from geographically distinct regions, representing the proposed novel species C. khanbhai, a member of the C. haemulonii species complex. Moreover, several members of the C. haemulonii species complex were observed to be invalidly described, including the clinically relevant species C. auris and C. vulturna. Hence, the opportunity was taken to correct this here, formally validating the names of C. auris, C. chanthaburiensis, C. konsanensis, C. metrosideri, C. ohialehuae, and C. vulturna.
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Affiliation(s)
- Auke W de Jong
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Khaled Al-Obaid
- Department of Microbiology, Mubarak Al-Kabir Hospital, Jabriya, Kuwait
| | - Ratna Mohd Tap
- Mycology Section, Bacteriology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Selangor, Malaysia
| | | | - Marizeth Groenewald
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Leena Joseph
- Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Ferry Hagen
- To whom correspondence should be addressed. Ferry Hagen, PhD, FESCMID, FECMM. Westerdijk Fungal Biodiversity Institute (WI-KNAW), Department of Medical Mycology, Uppsalalaan 8, 3584CT Utrecht, The Netherlands. Tel: +31-030-2122-600; E-mail: ,
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Altayb HN, Hosawi S, Baothman O, Kazmi I, Chaieb K, Abu Zeid IM, Elbadawi HS, Lopes BS, Moglad E. Molecular insights into novel environmental strains of Klebsiella quasipneumoniae harboring different antimicrobial-resistance genes. Front Public Health 2023; 10:1068888. [PMID: 36711372 PMCID: PMC9878601 DOI: 10.3389/fpubh.2022.1068888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023] Open
Abstract
Introduction The emergence of bacterial pathogens in environmental hosts represents a major risk to public health. This study aimed at characterizing seven novel environmental strains of K. quasipneumoniae using a genomic approach which was misidentified by phenotypic methods in a previous batch of 27 species thought to be K. pneumoniae. Methods Whole-genome sequencing was performed using the Illumina platform, and the generated raw reads were de novo assembled. Comparative genomic, resistome, virulome, mobilome, and phylogeny were then investigated using dierent bioinformatics tools. Results Six strains were identified as K. quasipneumoniae subsp similipneumoniae and one as K. quasipneumoniae subsp. quasipneumoniae. All isolates were resistant to ampicillin, cephalexin, and amoxicillin-clavulanic acid and harbored the fosA, bla OKP types, oqxB, and oqxA genes. One isolate additionally harbored a gene cassettes consisting of bla SHV-1, bla OXA-1, aac(6')-Ib-cr, catB genes. The aminoglycoside-modifying enzyme gene aph(3")-Ia was bracketed by two insertion elements. Plasmid analyses showed that IncFIBK was the most prevalent plasmid, circulating in six isolates, while one isolate exhibited seven different plasmids. The isolates have virulence genes responsible for capsule formation, lipopolysaccharide, iron uptake aerobactin (iutA), salmochelins (iroE, iroN), enterobactin siderophore, adherence, and biofilm formation (mrkA, mrkB, mrkC, mrkD, mrkF, and mrkH). Conclusion Our study highlights the ecology and transmission of K. quasipneumoniae (which have the ability to disseminate to other environmental sources including animals) outside the clinical setting and the contribution of water, vegetables, and table surfaces as potential reservoirs of farm-to-fork transmission of disease via local markets in Khartoum, Sudan.
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Affiliation(s)
- Hisham N. Altayb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia,Center of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia,*Correspondence: Hisham N. Altayb ✉
| | - Salman Hosawi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Othman Baothman
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kamel Chaieb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Isam M. Abu Zeid
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hana S. Elbadawi
- Microbiology and Parasitology Department, Soba University Hospital, University of Khartoum, Khartoum, Sudan
| | - Bruno Silvester Lopes
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom,National Horizons Centre, Teesside University, Darlington, United Kingdom,Bruno Silvester Lopes ✉
| | - Ehssan Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
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Abbate C, Trimarchi PD, Fumagalli GG, Gallucci A, Tomasini E, Fracchia S, Rebecchi I, Morello E, Fontanella A, Parisi PM, Tartarone F, Giunco F, Ciccone S, Nicolini P, Lucchi T, Arosio B, Inglese S, Rossi PD. Diencephalic versus Hippocampal Amnesia in Alzheimer's Disease: The Possible Confabulation- Misidentification Phenotype. J Alzheimers Dis 2023; 91:363-388. [PMID: 36442200 PMCID: PMC9881034 DOI: 10.3233/jad-220919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is clinically heterogeneous, including the classical-amnesic (CA-) phenotype and some variants. OBJECTIVE We aim to describe a further presentation we (re)named confabulation-misidentification (CM-) phenotype. METHODS We performed a retrospective longitudinal case-series study of 17 AD outpatients with the possible CM-phenotype (CM-ADs). Then, in a cross-sectional study, we compared the CM-ADs to a sample of 30 AD patients with the CA-phenotype (CA-ADs). The primary outcome was the frequency of cognitive and behavioral features. Data were analyzed as differences in percentage by non-parametric Chi Square and mean differences by parametric T-test. RESULTS Anterograde amnesia (100%) with early confabulation (88.2%), disorientation (88.2%) and non-infrequently retrograde amnesia (64.7%) associated with reduced insight (88.2%), moderate prefrontal executive impairment (94.1%) and attention deficits (82.3%) dominated the CM-phenotype. Neuropsychiatric features with striking misidentification (52.9%), other less-structured delusions (70.6%), and brief hallucinations (64.7%) were present. Marked behavioral disturbances were present early in some patients and very common at later stages. At the baseline, the CM-ADs showed more confabulation (p < 0.001), temporal disorientation (p < 0.02), misidentification (p = 0.013), other delusions (p = 0.002), and logorrhea (p = 0.004) than the CA-ADs. In addition, more social disinhibition (p = 0.018), reduction of insight (p = 0.029), and hallucination (p = 0.03) persisted at 12 months from baseline. Both the CA- and CM-ADs showed anterior and medial temporal atrophy. Compared to HCs, the CM-ADs showed more right fronto-insular atrophy, while the CA-ADs showed more dorsal parietal, precuneus, and right parietal atrophy. CONCLUSION We described an AD phenotype resembling diencephalic rather than hippocampal amnesia and overlapping the past-century description of presbyophrenia.
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Affiliation(s)
- Carlo Abbate
- Istituto Palazzolo, IRCCS Fondazione Don Carlo Gnocchi Onlus, Milan, Italy,Correspondence to: Carlo Abbate, PhD, Istituto Palazzolo, IRCCS
Fondazione Don Carlo Gnocchi ONLUS, via Don Luigi Palazzolo, 21,
20149 Milan, Italy. Tel.: +39 02 39703657; E-mail:
| | | | - Giorgio G. Fumagalli
- Neurology Unit, IRCCS Fondazione Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessia Gallucci
- Istituto Palazzolo, IRCCS Fondazione Don Carlo Gnocchi Onlus, Milan, Italy,Ph.D. Program in Neuroscience, School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Emanuele Tomasini
- Istituto Palazzolo, IRCCS Fondazione Don Carlo Gnocchi Onlus, Milan, Italy
| | - Stefania Fracchia
- Istituto Palazzolo, IRCCS Fondazione Don Carlo Gnocchi Onlus, Milan, Italy
| | - Isabella Rebecchi
- Istituto Palazzolo, IRCCS Fondazione Don Carlo Gnocchi Onlus, Milan, Italy
| | - Elisabetta Morello
- Istituto Palazzolo, IRCCS Fondazione Don Carlo Gnocchi Onlus, Milan, Italy
| | - Anna Fontanella
- Istituto Palazzolo, IRCCS Fondazione Don Carlo Gnocchi Onlus, Milan, Italy
| | - Paola M.R. Parisi
- Istituto Palazzolo, IRCCS Fondazione Don Carlo Gnocchi Onlus, Milan, Italy
| | - Federica Tartarone
- Istituto Palazzolo, IRCCS Fondazione Don Carlo Gnocchi Onlus, Milan, Italy
| | - Fabrizio Giunco
- Istituto Palazzolo, IRCCS Fondazione Don Carlo Gnocchi Onlus, Milan, Italy
| | - Simona Ciccone
- Geriatric Unit, IRCCS Fondazione Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Paola Nicolini
- Geriatric Unit, IRCCS Fondazione Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Tiziano Lucchi
- Geriatric Unit, IRCCS Fondazione Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Beatrice Arosio
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Silvia Inglese
- Geriatric Unit, IRCCS Fondazione Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Paolo D. Rossi
- Geriatric Unit, IRCCS Fondazione Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
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14
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Pap A, Kiraly IE, Medzihradszky KF, Darula Z. Multiple Layers of Complexity in O-Glycosylation Illustrated With the Urinary Glycoproteome. Mol Cell Proteomics 2022; 21:100439. [PMID: 36334872 PMCID: PMC9758497 DOI: 10.1016/j.mcpro.2022.100439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/17/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
While N-glycopeptides are relatively easy to characterize, O-glycosylation analysis is more complex. In this article, we illustrate the multiple layers of O-glycopeptide characterization that make this task so challenging. We believe our carefully curated dataset represents perhaps the largest intact human glycopeptide mixture derived from individuals, not from cell lines. The samples were collected from healthy individuals, patients with superficial or advanced bladder cancer (three of each group), and a single bladder inflammation patient. The data were scrutinized manually and interpreted using three different search engines: Byonic, Protein Prospector, and O-Pair, and the tool MS-Filter. Despite all the recent advances, reliable automatic O-glycopeptide assignment has not been solved yet. Our data reveal such diversity of site-specific O-glycosylation that has not been presented before. In addition to the potential biological implications, this dataset should be a valuable resource for software developers in the same way as some of our previously released data has been used in the development of O-Pair and O-Glycoproteome Analyzer. Based on the manual evaluation of the performance of the existing tools with our data, we lined up a series of recommendations that if implemented could significantly improve the reliability of glycopeptide assignments.
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Affiliation(s)
- Adam Pap
- Laboratory of Proteomics Research, Biological Research Centre, Eotvos Lorand Research Network (ELKH) Szeged, Hungary
| | | | - Katalin F. Medzihradszky
- Laboratory of Proteomics Research, Biological Research Centre, Eotvos Lorand Research Network (ELKH) Szeged, Hungary,For correspondence: Zsuzsanna Darula; Katalin F. Medzihradszky
| | - Zsuzsanna Darula
- Laboratory of Proteomics Research, Biological Research Centre, Eotvos Lorand Research Network (ELKH) Szeged, Hungary,Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine Szeged, Hungary,For correspondence: Zsuzsanna Darula; Katalin F. Medzihradszky
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15
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Morioka D, Kobayashi R, Hayashi H, Kawakatsu S, Suzuki A. Clonazepam-induced misidentification in prodromal dementia with Lewy bodies. Psychogeriatrics 2022; 22:767-769. [PMID: 35808967 DOI: 10.1111/psyg.12873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/08/2022] [Accepted: 06/19/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Daichi Morioka
- Department of Psychiatry, Yamagata University School of Medicine, Yamagata, Japan
| | - Ryota Kobayashi
- Department of Psychiatry, Yamagata University School of Medicine, Yamagata, Japan
| | - Hiroshi Hayashi
- Department of Occupational Therapy, Fukushima Medical University School of Health Sciences, Fukushima, Japan
| | - Shinobu Kawakatsu
- Department of Neuropsychiatry, Aizu Medical Center, Fukushima Medical University, Aizuwakamatsu, Japan
| | - Akihito Suzuki
- Department of Psychiatry, Yamagata University School of Medicine, Yamagata, Japan
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16
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Chianca GC, Antunes LAA, Ornellas PO, Neves FPG, Póvoa HCC, Iorio NLPP. Virulence of Lactobacillus spp. misidentified as Enterococcus faecalis from children's carious dentine. Acta Odontol Scand 2022; 80:21-28. [PMID: 34107230 DOI: 10.1080/00016357.2021.1934534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Objective: This study aimed to search for Enterococcus faecalis in children's deep carious dentine and characterize their virulence traits.Material and Methods: Eight isolates from 15 carious molars identified by 16S rDNA species-specific PCR as E. faecalis were included. These eight isolates were subject to identification by MALDI-TOF and characterized regarding: (i) bacterial aggregation and biofilm formation on polystyrene and glass, with/without saliva, as single or dual-species (associated to Streptococcus mutans); (ii) environmental pH measurement before and after 24 h incubation; (iii) acidogenicity; (iv) gelatinase production; (v) macrophage adherence; and (vi) toxicity towards Caenorhabditis elegans. Statistical analyses were performed using two-way ANOVA/Tukey or Fisher's exact tests.Results: All isolates initially identified as E. faecalis by PCR were correctly identified as Lactobacillus by MALDI-TOF, being designated as Lactobacillus misidentified as Enterococcus (LME). These isolates produced biofilm in the presence of saliva and in the dual-species assays. Bacterial aggregation was only observed in the dual-species model. After 24 h, environmental pH dropped from 7.5 to 4.5 for seven of eight isolates, and to 4.0 in all dual-species models. LME isolates were acidogenic, none of them produced gelatinase or adhered to macrophages, but all presented toxicity towards C. elegans.Conclusions: No E. faecalis were identified in the children's caries lesions. All LME isolates presented important virulence traits, including biofilm formation and high acidogenicity, which cause enamel demineralization, that might increase the risk of dental caries in children carrying LME. Thus, the correct identification and in-depth virulence characterization of microorganisms isolated from dental caries are important to understand the dynamics of this disease.
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Affiliation(s)
- Gabriela Ceccon Chianca
- Department of Basic Science, Universidade Federal Fluminense (UFF), Nova Friburgo, Rio de Janeiro, Brazil
- Faculdade de Farmácia, Universidade Estácio de Sá (UNESA), Nova Friburgo, Rio de Janeiro, Brazil
| | - Lívia Azeredo Alves Antunes
- Department of Specific Formation, Universidade Federal Fluminense (UFF), Nova Friburgo, Rio de Janeiro, Brazil
| | - Pâmela Oliveira Ornellas
- Department of Specific Formation, Universidade Federal Fluminense (UFF), Nova Friburgo, Rio de Janeiro, Brazil
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17
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Eldred LE, Thorn RG, Smith DR. Simple Matching Using QIIME 2 and RDP Reveals Misidentified Sequences and an Underrepresentation of Fungi in Reference Datasets. Front Genet 2021; 12:768473. [PMID: 34899856 PMCID: PMC8662557 DOI: 10.3389/fgene.2021.768473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/08/2021] [Indexed: 11/21/2022] Open
Abstract
Simple nucleotide matching identification methods are not as accurate as once thought at identifying environmental fungal sequences. This is largely because of incorrect naming and the underrepresentation of various fungal groups in reference datasets. Here, we explore these issues by examining an environmental metabarcoding dataset of partial large subunit rRNA sequences of Basidiomycota and basal fungi. We employed the simple matching method using the QIIME 2 classifier and the RDP Classifier in conjunction with the latest releases of the SILVA (138.1, 2020) and RDP (11, 2014) reference datasets and then compared the results with a manual phylogenetic binning approach. Of the 71 query sequences tested, 21 and 42% were misidentified using QIIME 2 and the RDP Classifier, respectively. Of these simple matching misidentifications, more than half resulted from the underrepresentation of various groups of fungi in the SILVA and RDP reference datasets. More comprehensive reference datasets with fewer misidentified sequences will increase the accuracy of simple matching identifications. However, we argue that the phylogenetic binning approach is a better alternative to simple matching since, in addition to better accuracy, it provides evolutionary information about query sequences.
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Affiliation(s)
- Lauren E Eldred
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - R Greg Thorn
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, Canada
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18
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Aguirre‐Sarabia I, Díaz‐Arce N, Pereda‐Agirre I, Mendibil I, Urtizberea A, Gerritsen HD, Burns F, Holmes I, Landa J, Coscia I, Quincoces I, Santurtún M, Zanzi A, Martinsohn JT, Rodríguez‐Ezpeleta N. Evidence of stock connectivity, hybridization, and misidentification in white anglerfish supports the need of a genetics-informed fisheries management framework. Evol Appl 2021; 14:2221-2230. [PMID: 34603494 PMCID: PMC8477593 DOI: 10.1111/eva.13278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 11/27/2022] Open
Abstract
Understanding population connectivity within a species as well as potential interactions with its close relatives is crucial to define management units and to derive efficient management actions. However, although genetics can reveal mismatches between biological and management units and other relevant but hidden information such as species misidentification or hybridization, the uptake of genetic methods by the fisheries management process is far from having been consolidated. Here, we have assessed the power of genetics to better understand the population connectivity of white (Lophius piscatorius) and its interaction with its sister species, the black anglerfish (Lophius budegassa). Our analyses, based on thousands of genome-wide single nucleotide polymorphisms, show three findings that are crucial for white anglerfish management. We found (i) that white anglerfish is likely composed of a single panmictic population throughout the Northeast Atlantic, challenging the three-stock based management, (ii) that a fraction of specimens classified as white anglerfish using morphological characteristics are genetically identified as black anglerfish (L. budegassa), and iii) that the two Lophius species naturally hybridize leading to a population of hybrids of up to 20% in certain areas. Our results set the basics for a genetics-informed white anglerfish assessment framework that accounts for stock connectivity, revises and establishes new diagnostic characters for Lophius species identification, and evaluates the effect of hybrids in the current and future assessments of the white anglerfish. Furthermore, our study contributes to provide additional evidence of the potentially negative consequences of ignoring genetic data for assessing fisheries resources.
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Affiliation(s)
- Imanol Aguirre‐Sarabia
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
| | - Natalia Díaz‐Arce
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
| | - Iker Pereda‐Agirre
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
| | - Iñaki Mendibil
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
| | - Agurtzane Urtizberea
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
| | | | - Finlay Burns
- Marine LaboratoryMarine Scotland ScienceAberdeenshireUK
| | - Ian Holmes
- Lowestoft LaboratoryCentre for Environment, Fisheries and Aquaculture ScienceLowestoftSuffolkUK
| | - Jorge Landa
- Centro Oceanográfico de SantanderInstituto Español de Oceanografía (IEO)SantanderSpain
| | - Ilaria Coscia
- School of Science, Engineering and EnvironmentUniversity of SalfordSalfordUK
| | - Iñaki Quincoces
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
| | - Marina Santurtún
- Marine ResearchAZTI Basque Research and Technology Alliance (BRTA)SukarrietaBizkaiaSpain
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Abstract
Authentic DNA sequences are crucial for reliable evolutionary inference. Concerns about the identification of DNA sequences have been voiced several times in the past but few quantitative studies exist. Mitogenomes play important roles in phylogenetics, phylogeography, population genetics, and DNA identification. However, the large number of mitogenomes being published routinely, often in brief data papers, has raised questions about their authenticity. In this study, we quantify problematic mitogenomes of birds and their reusage in other papers. Of 1,876 complete or partial mitogenomes of birds published until January 1, 2020, the authenticity of 1,559 could be assessed with sequences of conspecifics. Of these, 78 (5.0%) were found to be problematic, including 45 curated reference sequences. Problems were due to misidentification (33), chimeras of two or three species (23), sequencing errors/numts (18), incorrect sequence assembly (1), mislabeling at GenBank but not in the final paper (2), or vice versa (1). The number of problematic mitogenomes has increased sharply since 2012. Worryingly, these problematic sequences have been reused 436 times in other papers, including 385 times in phylogenies. No less than 53% of all mitogenomic phylogenies/networks published until January 1, 2020 included at least one problematic mitogenome. Problematic mitogenomes have resulted in incorrect phylogenetic hypotheses and proposals for unwarranted taxonomic revision, and may have compromised comparative analyses and measurements of divergence times. Our results indicate that a major upgrade of quality control measures is warranted. We propose a comprehensive set of measures that may serve as a new standard for publishing mitogenome sequences.
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Affiliation(s)
- George Sangster
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Jolanda A Luksenburg
- Institute of Environmental Sciences, Leiden University, The Netherlands
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
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20
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Brown C, Daniel R, Addo N, Knight S. The experiences of medical students, residents, fellows, and attendings in the emergency department: Implicit bias to microaggressions. AEM Educ Train 2021; 5:S49-S56. [PMID: 34616973 PMCID: PMC8480501 DOI: 10.1002/aet2.10670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/13/2021] [Accepted: 05/19/2021] [Indexed: 05/23/2023]
Abstract
OBJECTIVES Microaggressions and implicit bias occur frequently in medicine. No previous study, however, has examined the implicit bias and microaggressions that emergency medicine (EM) providers experience. Our primary objective was to understand how often EM providers experience implicit bias and microaggressions. Our secondary objective was to evaluate the types of microaggressions they experience and whether their own identifying characteristics are risk factors. METHODS A questionnaire was administered to EM providers across the United States. Outcome measures of experiencing or witnessing a microaggression, overt discrimination, or implicit bias were described using frequencies, proportions, and logistic regressions. Where a univariate association between outcome measures and demographic characteristics was found, multivariate regression to estimate odds ratios (ORs) and 95% confidence intervals (95% CIs) was performed. Proportional odds logistic regression models were used to evaluate the specific type of microaggressions experienced and if there was an association with demographic variables. RESULTS A total of 277 medical providers (48% trainees-medical students, residents, and fellows-and 52% attending physicians) completed the survey. A total of 181 (65%) respondents reported experiencing a microaggression. Female (OR = 5.9 [95% CI = 3.1 to 11.2]) and non-White respondents (OR = 2.4 [95% CI = 1.2 to 4.5]) were more likely to report experiencing any microaggression. Misidentification, the most common form of microaggression, was more common with trainees compared to attending physicians (proportional OR [POR] = 2.6 [95% CI = 1.7 to 4.0]) and non-White, compared to White, respondents (POR = 2.2 [95% CI = 1.3 to 3.6]). Misidentification as nonclinician staff was associated with gender (POR = 53 [95% CI = 24 to 116]) and 52% of female respondents reported being mistaken for nonclinician staff almost daily. Seventy-six percent of respondents reported being called a vulgar term by a patient and 21% by a staff member. CONCLUSIONS EM providers, particularly women and non-Whites, who responded to our survey experienced and witnessed bias and microaggressions, most commonly misidentification, in the ED.
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Affiliation(s)
- Cortlyn Brown
- Department of Emergency MedicineAtrium Health CarolinasCharlotteNorth CarolinaUSA
| | - Rosny Daniel
- Department of Emergency MedicineUniversity of California at San FranciscoSan FranciscoCaliforniaUSA
| | - Newton Addo
- Department of Emergency MedicineUniversity of California at San FranciscoSan FranciscoCaliforniaUSA
| | - Starr Knight
- Division of General Internal MedicineDepartment of MedicineZuckerberg San Francisco General HospitalUniversity of California at San FranciscoSan FranciscoCaliforniaUSA
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21
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Dennert K, Kumar R. Traceability Methods for Cell Line Authentication and Mycoplasma Detection. SLAS Technol 2021; 26:630-636. [PMID: 34282690 DOI: 10.1177/24726303211030290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Many laboratories struggle with mycoplasma contamination and cell line misidentification when growing cells in culture. These well-documented issues affect the scientific research community and have detrimental downstream effects. Research published with suspect cultures can produce misleading results. There is increasing pressure to verify the integrity of experimental and established cell lines before publishing. Therefore, laboratories need to define how and when to perform these critical tests, analyze the results, and determine action plans if disparities exist. Our laboratory is committed to producing cell lines of the highest quality for use in experiments; thus, we created a surveillance strategy for these potential problems. We developed processes for both testing and tracing cell line authentication and mycoplasma detection data. Using these methods, we can protect the integrity of our patient and commercial cell lines, maintaining reliable cultures for our research.
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Affiliation(s)
- Kate Dennert
- Advocate Aurora Research Institute Discovery Lab, Aurora Sinai Medical Center, Advocate Aurora Health, Milwaukee, WI, USA
| | - Rajeev Kumar
- Advocate Aurora Research Institute Discovery Lab, Aurora Sinai Medical Center, Advocate Aurora Health, Milwaukee, WI, USA
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22
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Abstract
We report a case of melioidosis in China and offer a comparison of 5 commercial detection systems for Burkholderia pseudomallei. The organism was misidentified by the VITEK 2 Compact, Phoenix, VITEK mass spectrometry, and API 20NE systems but was eventually identified by the Bruker Biotyper system and 16S rRNA sequencing.
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23
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McKibben FE, Frey JK. Linking camera-trap data to taxonomy: Identifying photographs of morphologically similar chipmunks. Ecol Evol 2021; 11:9741-9764. [PMID: 34306659 PMCID: PMC8293720 DOI: 10.1002/ece3.7801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/29/2021] [Accepted: 05/27/2021] [Indexed: 11/12/2022] Open
Abstract
Remote cameras are a common method for surveying wildlife and recently have been promoted for implementing large-scale regional biodiversity monitoring programs. The use of camera-trap data depends on the correct identification of animals captured in the photographs, yet misidentification rates can be high, especially when morphologically similar species co-occur, and this can lead to faulty inferences and hinder conservation efforts. Correct identification is dependent on diagnosable taxonomic characters, photograph quality, and the experience and training of the observer. However, keys rooted in taxonomy are rarely used for the identification of camera-trap images and error rates are rarely assessed, even when morphologically similar species are present in the study area. We tested a method for ensuring high identification accuracy using two sympatric and morphologically similar chipmunk (Neotamias) species as a case study. We hypothesized that the identification accuracy would improve with use of the identification key and with observer training, resulting in higher levels of observer confidence and higher levels of agreement among observers. We developed an identification key and tested identification accuracy based on photographs of verified museum specimens. Our results supported predictions for each of these hypotheses. In addition, we validated the method in the field by comparing remote-camera data with live-trapping data. We recommend use of these methods to evaluate error rates and to exclude ambiguous records in camera-trap datasets. We urge that ensuring correct and scientifically defensible species identifications is incumbent on researchers and should be incorporated into the camera-trap workflow.
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Affiliation(s)
- Fiona E. McKibben
- Department of Fish, Wildlife and Conservation EcologyNew Mexico State UniversityLas CrucesNMUSA
| | - Jennifer K. Frey
- Department of Fish, Wildlife and Conservation EcologyNew Mexico State UniversityLas CrucesNMUSA
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McDonald JL, Hodgson D. Counting Cats: The integration of expert and citizen science data for unbiased inference of population abundance. Ecol Evol 2021; 11:4325-4338. [PMID: 33976813 PMCID: PMC8093703 DOI: 10.1002/ece3.7330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/25/2021] [Accepted: 01/31/2021] [Indexed: 11/07/2022] Open
Abstract
Free-roaming animal populations are hard to count, and professional experts are a limited resource. There is vast untapped potential in the data collected by nonprofessional scientists who volunteer their time to population monitoring, but citizen science (CS) raises concerns around data quality and biases. A particular concern in abundance modeling is the presence of false positives that can occur due to misidentification of nontarget species. Here, we introduce Integrated Abundance Models (IAMs) that integrate citizen and expert data to allow robust inference of population abundance meanwhile accounting for biases caused by misidentification. We used simulation experiments to confirm that IAMs successfully remove the inflation of abundance estimates caused by false-positive detections and can provide accurate estimates of both bias and abundance. We illustrate the approach with a case study on unowned domestic cats, which are commonly confused with owned, and infer their abundance by analyzing a combination of CS data and expert data. Our case study finds that relying on CS data alone, either through simple summation or via traditional modeling approaches, can vastly inflate abundance estimates. IAMs provide an adaptable framework, increasing the opportunity for further development of the approach, tailoring to specific systems and robust use of CS data.
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Affiliation(s)
- Jenni L. McDonald
- Veterinary Department, Cats ProtectionNational Cat CentreHaywards HeathUK
- Bristol Veterinary SchoolUniversity of BristolBristolUK
| | - Dave Hodgson
- Centre for Ecology and ConservationCollege of Life and Environmental SciencesUniversity of ExeterPenrynUK
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25
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Guilbault E, Renner I, Mahony M, Beh E. How to make use of unlabeled observations in species distribution modeling using point process models. Ecol Evol 2021; 11:5220-5243. [PMID: 34026002 PMCID: PMC8131797 DOI: 10.1002/ece3.7411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/07/2021] [Accepted: 02/11/2021] [Indexed: 11/23/2022] Open
Abstract
Species distribution modeling, which allows users to predict the spatial distribution of species with the use of environmental covariates, has become increasingly popular, with many software platforms providing tools to fit such models. However, the species observations used can have varying levels of quality and can have incomplete information, such as uncertain or unknown species identity.In this paper, we develop two algorithms to classify observations with unknown species identities which simultaneously predict several species distributions using spatial point processes. Through simulations, we compare the performance of these algorithms using 7 different initializations to the performance of models fitted using only the observations with known species identity.We show that performance varies with differences in correlation among species distributions, species abundance, and the proportion of observations with unknown species identities. Additionally, some of the methods developed here outperformed the models that did not use the misspecified data. We applied the best-performing methods to a dataset of three frog species (Mixophyes).These models represent a helpful and promising tool for opportunistic surveys where misidentification is possible or for the distribution of species newly separated in their taxonomy.
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Affiliation(s)
- Emy Guilbault
- Faculty of ScienceSchool of Mathematical and Physical SciencesThe University of NewcastleCallaghanNSWAustralia
| | - Ian Renner
- Faculty of ScienceSchool of Mathematical and Physical SciencesThe University of NewcastleCallaghanNSWAustralia
| | - Michael Mahony
- Faculty of ScienceSchool of Environmental and Life SciencesThe University of NewcastleCallaghanNSWAustralia
| | - Eric Beh
- Faculty of ScienceSchool of Mathematical and Physical SciencesThe University of NewcastleCallaghanNSWAustralia
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26
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Nagahama Y, Okina T, Suzuki N, Matsuda M. Prevalence of the core clinical features and the other neuropsychiatric symptoms in dementia with Lewy bodies. Psychogeriatrics 2021; 21:443-445. [PMID: 33759303 DOI: 10.1111/psyg.12687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 11/26/2022]
Affiliation(s)
- Yasuhiro Nagahama
- Department of Psychiatry and Neurology, Kawasaki Memorial Hospital, Kawasaki, Japan.,Department of Geriatric Neurology, Shiga General Hospital, Moriyama, Japan
| | - Tomoko Okina
- Department of Geriatric Neurology, Shiga General Hospital, Moriyama, Japan
| | - Norio Suzuki
- Department of Geriatric Neurology, Shiga General Hospital, Moriyama, Japan
| | - Minoru Matsuda
- Department of Geriatric Neurology, Shiga General Hospital, Moriyama, Japan.,Department of Neurology, Izuminomori Clinic, Sendai, Japan
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27
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Abstract
'We advise the authors to find a native English speaker to proofread the manuscript'. This is a standard feedback journals give to non-native English speakers. Journals are justifiably concerned with grammar but do not show the same rigour about another step crucial to biological research: specimen identification. Surveying the author guidelines of 100 journals, we found that only 6% of them request explicitly citation of the literature used in specimen identification. Authors hamper readers from contesting specimen identification whenever vouchers, identification methods, and taxon concepts are not provided. However, unclear taxonomic procedures violate the basic scientific principle of reproducibility. The scientific community must continuously look for practical alternatives to improve taxonomic identification and taxonomic verification. We argue that voucher pictures are an accessible, cheap and time-effective alternative to mitigate (not abolish) bad taxonomy by exposing preventable misidentifications. Voucher pictures allow scientists to judge specimen identification actively, based on available data. The popularization of high-quality image devices, photo-identification technologies and computer vision algorithms yield accurate scientific photo-documentation, improving taxonomic procedures. Taxonomy is timeless, transversal and essential to most scientific disciplines in biological sciences. It is time to demand rigour in taxonomic identifications.
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Affiliation(s)
- Filipe Michels Bianchi
- Laboratório de Entomologia Sistemática, Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Leonardo Tresoldi Gonçalves
- Laboratório de Drosophila, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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28
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Strausfeld NJ. Mushroom bodies and reniform bodies coexisting in crabs cannot both be homologs of the insect mushroom body. J Comp Neurol 2021; 529:3265-3271. [PMID: 33829500 DOI: 10.1002/cne.25152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 11/06/2022]
Abstract
In one species of shore crab (Brachyura, Varunidae), a center that supports long-term visual habituation and that matches the reniform body's morphology has been claimed as a homolog of the insect mushroom body despite lacking traits that define it as such. The discovery in a related species of shore crab of a mushroom body possessing those defining traits renders that interpretation unsound. Two phenotypically distinct, coexisting centers cannot both be homologs of the insect mushroom body. The present commentary outlines the history of research leading to misidentification of the reniform body as a mushroom body. One conclusion is that if both centers support learning and memory, this would be viewed as a novel and fascinating attribute of the pancrustacean brain.
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29
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Sangster G, Luksenburg JA. The published complete mitochondrial genome of the milk shark ( Rhizoprionodon acutus) is a misidentified Pacific spadenose shark ( Scoliodon macrorhynchos) (Chondrichthyes: Carcharhiniformes). Mitochondrial DNA B Resour 2021; 6:828-830. [PMID: 33763593 PMCID: PMC7954409 DOI: 10.1080/23802359.2021.1884019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The recently published mitogenome of milk shark Rhizoprionodon acutus (MN602076/NC_046016) was fully resolved in an unexpected phylogenetic position in the original mitogenome announcement, which rendered the genus Scoliodon paraphyletic. Here, we show that this mitogenome is actually that of a misidentified Pacific spadenose shark (Scoliodon macrorhynchos). The error is documented to avoid the perpetuation of erroneous sequence information in the literature.
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Affiliation(s)
| | - Jolanda A Luksenburg
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands.,Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
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30
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Durso AM, Bolon I, Kleinhesselink AR, Mondardini MR, Fernandez-Marquez JL, Gutsche-Jones F, Gwilliams C, Tanner M, Smith CE, Wüster W, Grey F, Ruiz de Castañeda R. Crowdsourcing snake identification with online communities of professional herpetologists and avocational snake enthusiasts. R Soc Open Sci 2021; 8:201273. [PMID: 33614073 PMCID: PMC7890515 DOI: 10.1098/rsos.201273] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
Species identification can be challenging for biologists, healthcare practitioners and members of the general public. Snakes are no exception, and the potential medical consequences of venomous snake misidentification can be significant. Here, we collected data on identification of 100 snake species by building a week-long online citizen science challenge which attracted more than 1000 participants from around the world. We show that a large community including both professional herpetologists and skilled avocational snake enthusiasts with the potential to quickly (less than 2 min) and accurately (69-90%; see text) identify snakes is active online around the clock, but that only a small fraction of community members are proficient at identifying snakes to the species level, even when provided with the snake's geographical origin. Nevertheless, participants showed great enthusiasm and engagement, and our study provides evidence that innovative citizen science/crowdsourcing approaches can play significant roles in training and building capacity. Although identification by an expert familiar with the local snake fauna will always be the gold standard, we suggest that healthcare workers, clinicians, epidemiologists and other parties interested in snakebite could become more connected to these communities, and that professional herpetologists and skilled avocational snake enthusiasts could organize ways to help connect medical professionals to crowdsourcing platforms. Involving skilled avocational snake enthusiasts in decision making could build the capacity of healthcare workers to identify snakes more quickly, specifically and accurately, and ultimately improve snakebite treatment data and outcomes.
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Affiliation(s)
- A. M. Durso
- Institute of Global Health, Department of Community Health and Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Biological Sciences, Florida Gulf Coast University, Ft. Myers, FL, USA
| | - I. Bolon
- Institute of Global Health, Department of Community Health and Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - A. R. Kleinhesselink
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - M. R. Mondardini
- Citizen Science Center Zürich, ETHZ and University of Zürich, Zurich, Switzerland
| | | | - F. Gutsche-Jones
- Citizen Science Center Zürich, ETHZ and University of Zürich, Zurich, Switzerland
| | - C. Gwilliams
- Citizen Science Center Zürich, ETHZ and University of Zürich, Zurich, Switzerland
| | - M. Tanner
- Citizen Science Center Zürich, ETHZ and University of Zürich, Zurich, Switzerland
| | | | - W. Wüster
- Bangor University College of Natural Sciences, Bangor, UK
| | - F. Grey
- Citizen Cyberlab, University of Geneva, Geneva, Switzerland
| | - R. Ruiz de Castañeda
- Institute of Global Health, Department of Community Health and Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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31
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Jurado-Martín I, Marcos-Arias C, Tamayo E, Guridi A, de Groot PWJ, Quindós G, Eraso E. Candida duobushaemulonii: An Old But Unreported Pathogen. J Fungi (Basel) 2020; 6:E374. [PMID: 33348882 DOI: 10.3390/jof6040374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 01/02/2023] Open
Abstract
Candidiasis caused by species of the Candida haemulonii complex (Candida haemulonii and Candida duobushaemulonii) and closely related species, Candida auris and Candida pseudohaemulonii are increasing. These species often show reduced susceptibility to antifungal drugs, such as azoles and amphotericin B or, less frequently, echinocandins. However, conventional phenotypic identification methods are unable to accurately differentiate these species and, therefore, their prevalence may have been underestimated. In this study, 150 isolates that were probably misidentified were reanalyzed using two novel PCR approaches. We found that one isolate previously identified in 1996 as Candida intermedia was C. duobushaemulonii, being one of the oldest isolates of this species described to date. We also found that this isolate had reduced susceptibility to fluconazole, itraconazole, and amphotericin B.
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32
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Sangster G, Luksenburg JA. The published complete mitochondrial genome of Eptesicus serotinus is a chimera of Vespertilio sinensis and Hypsugo alaschanicus (Mammalia: Chiroptera). Mitochondrial DNA B Resour 2020; 5:2661-2664. [PMID: 33457897 PMCID: PMC7781936 DOI: 10.1080/23802359.2020.1785349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The mitogenome of Eptesicus serotinus (Serotine bat) was published in 2013 with GenBank accession number KF111725 and NCBI Reference Sequence number NC_022474. This sequence was placed with Vespertilio sinensis (Asian parti-colored bat) in a COI gene tree but with Hypsugo alashanicus (Alashanian pipistrelle) in a cytochrome b gene tree. Direct comparison of mitogenomes showed that 92.4% of this mitogenome is similar to Vespertilio sinensis, 5.9% to Hypsugo alaschanicus, and that 1.6% of the mitogenome could not be attributed to either species, or any other species. This mitogenome has been re-used in at least 17 phylogenies. Our findings suggest that mitogenomes are best verified with multiple gene trees, followed by direct comparison of sequences. We conclude that greater vigilance is warranted to ensure that problematic sequences do not enter the scientific record, and are not re-used in subsequent studies.
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Affiliation(s)
- George Sangster
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Jolanda A Luksenburg
- Institute of Environmental Sciences, Leiden University, Leiden, The Netherlands.,Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
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33
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Taylor GS, Martoni F. Case of mistaken identity: resolving the taxonomy between Trioza eugeniae Froggatt and T. adventicia Tuthill (Psylloidea: Triozidae). Bull Entomol Res 2020; 110:340-351. [PMID: 31865924 DOI: 10.1017/s0007485319000695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The 'Eugenia psyllid' or 'Lilly pilly psyllid', widely recognized in Australia and in the USA as Trioza eugeniae Froggatt (Hemiptera: Triozidae), is not T. eugeniae, but rather T. adventicia Tuthill. In this study we assessed morphological comparisons of materials from throughout the native and introduced ranges and re-examined original descriptions of both taxa, together with Froggatt's type specimens of T. eugeniae. Furthermore, through DNA barcoding analyses, we confirmed the validity of both T. adventicia and T. eugeniae as separate species. We re-described both species to include additional characters not previously included and designated a lectotype for T. eugeniae. T. eugeniae has smaller fore wings that are slightly more elongate. These lack infuscation around veins R and R1, vein Rs is relatively longer, meeting the costa closer to the wing apex; with certain veins bearing long, fine divergent setae, a character not previously described. It has consistently three inner and one outer metatibial spurs. The male parameres appear narrowly pyriform with a weak dorsolateral lobe and weakly sclerotized apices. T. adventicia has larger fore wings that are slightly more ovate with dark infuscation around veins R and R1; vein Rs is relatively shorter, meeting the costa further from the wing apex, with veins lacking long, fine divergent setae. The usual configuration of two inner and one outer metatibial spurs, previously used to separate the two species, appears inconsistent. The male parameres appear a little more broadly pyriform with slightly more sclerotized apices. T. eugeniae refers to a distinct species which has a restricted distribution only in its native range in southern subcoastal New South Wales, Australia. T. adventicia refers to a separate species, with a natural distribution in eastern subcoastal Australia, but has been introduced widely in southern Australia, to New Zealand and the USA. This study elucidates a long history of misidentification of T. eugeniae in the nursery industry and in almost 30 years of literature on its biological control in the USA. Regardless, the biological control program, unknowingly, targeted the correct species of psyllid, T. adventicia, in its foreign exploration and importation of the appropriate parasitoid as a biocontrol agent in the USA. Despite being firmly entrenched in both the nursery trade and scientific literature, the name T. eugeniae is misapplied. While the acceptance of the valid name, T. adventicia, might be regarded as both problematic and protracted, this is the correct taxonomical attribution.
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Affiliation(s)
- Gary S Taylor
- Department of Genetics & Evolution, Australian Centre for Evolutionary Biology & Biodiversity, School of Biological Sciences, The University of Adelaide, North Terrace, SA5005, Australia
| | - Francesco Martoni
- Agriculture Victoria Research, AgriBio Centre, Bundoora, VIC3083, Australia
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34
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Strickfaden KM, Fagre DA, Golding JD, Harrington AH, Reintsma KM, Tack JD, Dreitz VJ. Dependent double-observer method reduces false-positive errors in auditory avian survey data. Ecol Appl 2020; 30:e02026. [PMID: 31630467 PMCID: PMC7078931 DOI: 10.1002/eap.2026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/27/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
Bias introduced by detection errors is a well-documented issue for abundance and occupancy estimates of wildlife. Detection errors bias estimates of detection and abundance or occupancy in positive and negative directions, which can produce misleading results. There have been considerable design- and model-based methods to address false-negative errors, or missed detections. However, false-positive errors, or detections of individuals that are absent but counted as present because of misidentifications or double counts, are often assumed to not occur in ecological studies. The dependent double-observer survey method is a design-based approach speculated to reduce false positives because observations have the ability to be confirmed by two observers. However, whether this method reduces false positives compared to single-observer methods has not been empirically tested. We used prairie songbirds as a model system to test if a dependent double-observer method reduced false positives compared to a single-observer method. We used vocalizations of ten species to create auditory simulations and used naive and expert observers to survey these simulations using single-observer and dependent double-observer methods. False-positive rates were significantly lower using the dependent double-observer survey method in both observer groups. Expert observers reported a 3.2% false-positive rate in dependent double-observer surveys and a 9.5% false-positive rate in single-observer surveys, while naive observers reported a 39.1% false-positive rate in dependent double-observer surveys and a 49.1% false-positive rate in single-observer surveys. Misidentification errors arose in all survey scenarios and almost all species combinations. However, expert observers using the dependent double-observer method performed significantly better than other survey scenarios. Given the use of double-observer methods and the accumulating evidence that false positives occur in many survey methods across different taxa, this study is an important step forward in acknowledging and addressing false positives.
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Affiliation(s)
- Kaitlyn M. Strickfaden
- Avian Science Center and Wildlife Biology ProgramDepartment of Ecosystem and Conservation SciencesW.A. Franke College of Forestry and ConservationUniversity of Montana32 Campus DriveMissoulaMontana59812USA
| | - Danielle A. Fagre
- Avian Science Center and Wildlife Biology ProgramDepartment of Ecosystem and Conservation SciencesW.A. Franke College of Forestry and ConservationUniversity of Montana32 Campus DriveMissoulaMontana59812USA
| | - Jessie D. Golding
- Avian Science Center and Wildlife Biology ProgramDepartment of Ecosystem and Conservation SciencesW.A. Franke College of Forestry and ConservationUniversity of Montana32 Campus DriveMissoulaMontana59812USA
- National Genomics Center for Wildlife and Fish ConservationRocky Mountain Research Station, U.S. Forest Service800 E Beckwith AvenueMissoulaMontana59801USA
| | - Alan H. Harrington
- Avian Science Center and Wildlife Biology ProgramDepartment of Ecosystem and Conservation SciencesW.A. Franke College of Forestry and ConservationUniversity of Montana32 Campus DriveMissoulaMontana59812USA
- Animal and Rangeland SciencesOregon State UniversityCorvallisOregon97331USA
| | - Kaitlyn M. Reintsma
- Avian Science Center and Wildlife Biology ProgramDepartment of Ecosystem and Conservation SciencesW.A. Franke College of Forestry and ConservationUniversity of Montana32 Campus DriveMissoulaMontana59812USA
| | - Jason D. Tack
- Avian Science Center and Wildlife Biology ProgramDepartment of Ecosystem and Conservation SciencesW.A. Franke College of Forestry and ConservationUniversity of Montana32 Campus DriveMissoulaMontana59812USA
- United States Fish and Wildlife ServiceHabitat and Population Evaluation Team32 Campus DriveMissoulaMontana59812USA
| | - Victoria J. Dreitz
- Avian Science Center and Wildlife Biology ProgramDepartment of Ecosystem and Conservation SciencesW.A. Franke College of Forestry and ConservationUniversity of Montana32 Campus DriveMissoulaMontana59812USA
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35
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Liu F, Chen J, Du Y, Jiang W, Gong L, Mu J. Misidentification of Acute Psychiatric Symptoms in the Emergency Room: Clinical Experience in China. Front Psychiatry 2020; 11:579484. [PMID: 33584361 PMCID: PMC7874002 DOI: 10.3389/fpsyt.2020.579484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/04/2020] [Indexed: 11/17/2022] Open
Abstract
Introduction: Patients who come to the emergency department because of acute psychiatric symptoms are often not admitted to the correct department timely. The purpose of this study is to identify the clinical characteristics of patients with acute psychiatric symptoms in order to achieve early and correct triage in the emergency room. Methodology: We conducted a cross-analysis of inpatients who first came to the emergency department with acute psychiatric symptoms and then admitted to the department of neurology or psychiatry between years 2012 and 2018. Among them, 70 patients were rediagnosed and retransferred, with 38 patients to the department of neurology and 32 patients to the department of psychiatry. The clinical characteristics, laboratory examination, and Neuropsychiatric Inventory (NPI) were analyzed. Results: Patients who were rediagnosed with neurological diseases were more prone to have somatic symptoms (headache, dizziness) (P < 0.05). Because of the atypical early clinical manifestations in the emergency room, fever and positive neurological signs do not necessarily represent the diagnosis of neurological diseases. On the other hand, the absence of these manifestations does not guarantee the diagnosis of psychiatric illness. According to NPI, abnormal behaviors, changes in appetite, and sleep disturbances were more obvious in patients with neurological diseases (P < 0.05), whereas patients with psychiatric disorders often showed prominent irritability (P < 0.05). Conclusions: Acute psychiatric symptoms are usually complex and diverse. The triage and diagnosisshould be based on multiple factors. After triage, clinical symptoms should be dynamically observed.
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Affiliation(s)
- Fang Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jianjun Chen
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Yang Du
- Department of Neurology, Suining Central Hospital, Sichuan, China
| | - Wenxia Jiang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lei Gong
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun Mu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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36
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Stemler J, Salmanton-García J, Seidel D, Alexander BD, Bertz H, Hoenigl M, Herbrecht R, Meintker L, Meißner A, Mellinghoff SC, Sal E, Zarrouk M, Koehler P, Cornely OA. Risk factors and mortality in invasive Rasamsonia spp. infection: Analysis of cases in the FungiScope ® registry and from the literature. Mycoses 2019; 63:265-274. [PMID: 31769549 DOI: 10.1111/myc.13039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND The new Rasamsonia spp. complex can develop invasive infection in immunosuppression or chronic pulmonary disease. It has potential to be misidentified as other genera due to morphological similarities. Nowadays, there is a gap of knowledge on this fungi. OBJECTIVES To provide knowledge base of risk factors and therapeutic decisions in invasive Rasamsonia spp. complex infection. PATIENTS/METHODS Cases of invasive infection due to Rasamsonia spp. (formerly Geosmithia/Penicillium spp.) from FungiScope® registry and all reported cases from a literature were included. RESULTS We identified 23 invasive infections due to Rasamsonia spp., six (26.1%) in the FungiScope® registry. Main risk factors were chronic granulomatous disease (n = 12, 52.2%), immunosuppressive treatment (n = 10, 43.5%), haematopoietic stem cell transplantation (n = 7, 30.4%), graft-versus-host disease and major surgery (n = 4, 17.4%, each). Predominantly affected organs were the lungs (n = 21, 91.3%), disease disseminated in seven cases (30.4%). Fungal misidentification occurred in 47.8% (n = 11), and sequencing was used in 69.6% of the patients (n = 16) to diagnose. Breakthrough infection occurred in 13 patients (56.5%). All patients received antifungal treatment, mostly posaconazole (n = 11), caspofungin (n = 10) or voriconazole (n = 9). Combination therapy was administered in 13 patients (56.5%). Susceptibility testing showed high minimum inhibitory concentrations for azoles and amphotericin B, but not for echinocandins. No preferable treatment influencing favourable outcome was identified. Overall mortality was 39% (n = 9). CONCLUSION Rasamsonia spp. are emerging fungi causing life-threatening infections, especially in immunocompromised and critically ill patients. Mortality is high. Treatment is challenging and clinicians dealing with this patient population should become aware of this infection constituting a medical emergency.
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Affiliation(s)
- Jannik Stemler
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), European Diamond Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), partner site Bonn - Cologne, Cologne, Germany
| | - Jon Salmanton-García
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), European Diamond Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Danila Seidel
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), European Diamond Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Barbara D Alexander
- Infectious Diseases Division, Duke University Medical Center, Durham, NC, USA
| | - Hartmut Bertz
- Department of Internal Medicine I, Medical Center of Freiburg University, Faculty of Medicine, Freiburg University, Freiburg, Germany
| | - Martin Hoenigl
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA, USA.,Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Raoul Herbrecht
- Department of Oncology and Hematology, Hôpitaux Universitaires de Strasbourg and Université de Strasbourg, Inserm, UMR-S1113/IRFAC, Strasbourg, France
| | - Lisa Meintker
- Department of Medicine 5 for Hematology and Oncology, Erlangen University Hospital, Friedrich-Alexander-University of Erlangen-Nuremberg, Erlangen, Germany
| | - Arne Meißner
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), European Diamond Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, Germany.,Department of Hospital Hygiene and Infection Control, University Hospital of Cologne, Cologne, Germany
| | - Sibylle C Mellinghoff
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), European Diamond Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), partner site Bonn - Cologne, Cologne, Germany
| | - Ertan Sal
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), European Diamond Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Marouan Zarrouk
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), European Diamond Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), partner site Bonn - Cologne, Cologne, Germany
| | - Philipp Koehler
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), European Diamond Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Oliver A Cornely
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), European Diamond Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), partner site Bonn - Cologne, Cologne, Germany.,Clinical Trials Centre Cologne (ZKS Köln), University of Cologne, Cologne, Germany
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Muthumbi EM, Gordon NC, Mochamah G, Nyongesa S, Odipo E, Mwarumba S, Mturi N, Etyang AO, Dance DAB, Scott JAG, Morpeth SC. Population-Based Estimate of Melioidosis, Kenya. Emerg Infect Dis 2019; 25:984-987. [PMID: 31002067 PMCID: PMC6478202 DOI: 10.3201/eid2505.180545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Melioidosis is thought to be endemic, although underdiagnosed, in Africa. We identified 5 autochthonous cases of Burkholderia pseudomallei infection in a case series in Kenya. Incidence of B. pseudomallei bacteremia in Kenya’s Kilifi County is low, at 1.5 cases per million person-years, but this result might be an underestimate.
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Buil JB, van der Lee HAL, Curfs-Breuker I, Verweij PE, Meis JF. External Quality Assessment Evaluating the Ability of Dutch Clinical Microbiological Laboratories to Identify Candida auris. J Fungi (Basel) 2019; 5:jof5040094. [PMID: 31591307 PMCID: PMC6958413 DOI: 10.3390/jof5040094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/30/2019] [Accepted: 09/30/2019] [Indexed: 12/22/2022] Open
Abstract
Background: Candida auris is a yeast that is causing nosocomial outbreaks in healthcare facilities around the world. There is a risk of the misidentification of C. auris with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)—when libraries are used that lack C. auris spectra, or when conventional biochemical methods are used. Methods: We conducted an external quality assessment to evaluate the ability of Dutch clinical microbiological laboratories to identify C. auris, and to raise awareness about the risk of misidentification. Results: 35/47 participating laboratories were able to identify C. auris correctly. Only 2/14 labs that potentially misidentified C. auris with their primary identification methods specified that they would perform additional tests to exclude C. auris when appropriate. 45/47 labs used MALDI-TOF MS systems to identify Candida species. Conclusions: There was a lack of awareness about the potential misidentification of C. auris in many labs that used MALDI-TOF MS with libraries that lacked C. auris spectra, and labs that used Vitek 2. However, as the currently available MALDI-TOF MS libraries in The Netherlands contain several C. auris spectra, we expect that currently almost all participating laboratories are able to identify C. auris correctly, as 45/47 participating laboratories use MALDI-TOF MS as their primary yeast identification method.
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Affiliation(s)
- Jochem B Buil
- Department of Medical Microbiology, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
- Center of Expertise in Mycology Radboudumc/CWZ, 6525GA Nijmegen, The Netherlands.
| | - Henrich A L van der Lee
- Department of Medical Microbiology, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
- Center of Expertise in Mycology Radboudumc/CWZ, 6525GA Nijmegen, The Netherlands.
| | - Ilse Curfs-Breuker
- Department of Medical Microbiology, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
- Center of Expertise in Mycology Radboudumc/CWZ, 6525GA Nijmegen, The Netherlands.
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), 6532SZ Nijmegen, The Netherlands.
| | - Paul E Verweij
- Department of Medical Microbiology, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
- Center of Expertise in Mycology Radboudumc/CWZ, 6525GA Nijmegen, The Netherlands.
| | - Jacques F Meis
- Department of Medical Microbiology, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
- Center of Expertise in Mycology Radboudumc/CWZ, 6525GA Nijmegen, The Netherlands.
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital (CWZ), 6532SZ Nijmegen, The Netherlands.
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Robin T, Capes-Davis A, Bairoch A. CLASTR: The Cellosaurus STR similarity search tool - A precious help for cell line authentication. Int J Cancer 2019; 146:1299-1306. [PMID: 31444973 DOI: 10.1002/ijc.32639] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/02/2019] [Accepted: 08/14/2019] [Indexed: 11/06/2022]
Abstract
Despite an increased awareness of the problematic of cell line cross-contamination and misidentification, it remains nowadays a major source of erroneous experimental results in biomedical research. To prevent it, researchers are expected to frequently test the authenticity of the cell lines they are working on. STR profiling was selected as the international reference method to perform cell line authentication. While the experimental protocols and manipulations for generating a STR profile are well described, the available tools and workflows to analyze such data are lacking. The Cellosaurus knowledge resource aimed to improve the situation by compiling all the publicly available STR profiles from the literature and other databases. As a result, it grew to become the largest database in terms of human STR profiles, with 6,474 distinct cell lines having an associated STR profile (release July 31, 2019). Here we present CLASTR, the Cellosaurus STR similarity search tool enabling users to compare one or more STR profiles with those available in the Cellosaurus cell line knowledge resource. It aims to help researchers in the process of cell line authentication by providing numerous functionalities. The tool is publicly accessible on the SIB ExPASy server (https://web.expasy.org/cellosaurus-str-search) and its source code is available on GitHub under the GPL-3.0 license.
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Affiliation(s)
- Thibault Robin
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland.,Microbiology and Molecular Medicine Department, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland.,Computer Science Department, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Amanda Capes-Davis
- CellBank Australia, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Amos Bairoch
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland.,Microbiology and Molecular Medicine Department, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Pandey U, Naccache SN, Dien Bard J. Back to the Basics: Biochemical Testing for Pathogen Identification in the Era of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). J Clin Microbiol 2019; 57:e00498-19. [PMID: 31315960 DOI: 10.1128/JCM.00498-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Lavesque N, Daffe G, Grall J, Zanol J, Benoit Gouillieux, Hutchings P. Guess who? On the importance of using appropriate name: case study of Marphysasanguinea (Montagu, 1813). Zookeys 2019; 859:1-15. [PMID: 31327919 PMCID: PMC6616095 DOI: 10.3897/zookeys.859.34117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/14/2019] [Indexed: 11/12/2022] Open
Abstract
The common bait worm Marphysasanguinea (Montagu, 1813), originally described from the south coast of England, is the type species of the genus. This species has been widely reported from all around the world and has been considered as cosmopolitan until recently. This is partly because the original description was very brief and poorly illustrated, and also because all species superficially look similar. In order to clarify the situation, M.sanguinea was redescribed and a neotype was designated by Hutchings and Karageorgpoulos in 2003. Recently, specimens from Cornwall, close to the type locality, were sampled, examined morphologically, and used to obtain COI gene sequences for this species. Molecular results permitted us to confirm the identity and presence of M.sanguinea along the French coasts and to highlight the presence of inaccurate sequences of this species on GenBank. Use of this "false" cosmopolitan species at a worldwide scale by many biologists is also discussed in this paper.
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Affiliation(s)
- Nicolas Lavesque
- Univ. Bordeaux, EPOC, UMR 5805, Station Marine d’Arcachon, 33120 Arcachon, FranceUniversité de BordeauxArcachonFrance
- CNRS, EPOC, UMR 5805, Station Marine d’Arcachon, 33120 Arcachon, FranceStation Marine d’ArcachonArcachonFrance
| | - Guillemine Daffe
- CNRS, Université de Bordeaux, Observatoire Aquitain des Sciences de l’Univers, UMS 2567 POREA, 33615 Pessac, FranceUniversité de BordeauxPessacFrance
| | - Jacques Grall
- Université de Brest, CNRS, UMS 3113, Observatoire, Séries Faune-Flore, OSU-IUEM, 29280 Plouzané, FranceUniversité de BrestPlouzanéFrance
| | - Joana Zanol
- Laboratório de Biodiversidade de Annelida, Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, BrazilUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Benoit Gouillieux
- Univ. Bordeaux, EPOC, UMR 5805, Station Marine d’Arcachon, 33120 Arcachon, FranceUniversité de BordeauxArcachonFrance
- CNRS, EPOC, UMR 5805, Station Marine d’Arcachon, 33120 Arcachon, FranceStation Marine d’ArcachonArcachonFrance
| | - Pat Hutchings
- Australian Museum Research Institute, Australian Museum, Sydney, AustraliaAustralian MuseumSydneyAustralia
- Department of Biological Sciences, Macquarie University, North Ryde 2109, AustraliaMacquarie UniversityNorth RydeAustralia
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Nic Lughadha EM, Graziele Staggemeier V, Vasconcelos TNC, Walker BE, Canteiro C, Lucas EJ. Harnessing the potential of integrated systematics for conservation of taxonomically complex, megadiverse plant groups. Conserv Biol 2019; 33:511-522. [PMID: 30779869 PMCID: PMC6850456 DOI: 10.1111/cobi.13289] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 05/30/2023]
Abstract
The value of natural history collections for conservation science research is increasingly recognized, despite their well-documented limitations in terms of taxonomic, geographic, and temporal coverage. Specimen-based analyses are particularly important for tropical plant groups for which field observations are scarce and potentially unreliable due to high levels of diversity-amplifying identification challenges. Specimen databases curated by specialists are rich sources of authoritatively identified, georeferenced occurrence data, and such data are urgently needed for large genera. We compared entries in a monographic database for the large Neotropical genus Myrcia in 2007 and 2017. We classified and quantified differences in specimen records over this decade and determined the potential impact of these changes on conservation assessments. We distinguished misidentifications from changes due to taxonomic remodeling and considered the effects of adding specimens and georeferences. We calculated the potential impact of each change on estimates of extent of occurrence (EOO), the most frequently used metric in extinction-risk assessments of tropical plants. We examined whether particular specimen changes were associated with species for which changes in EOO over the decade were large enough to change their conservation category. Corrections to specimens previously misidentified or lacking georeferences were overrepresented in such species, whereas changes associated with taxonomic remodeling (lumping and splitting) were underrepresented. Among species present in both years, transitions to less threatened status outnumbered those to more threatened (8% vs 3%, respectively). Species previously deemed data deficient transitioned to threatened status more often than to not threatened (10% vs 7%, respectively). Conservation scientists risk reaching unreliable conclusions if they use specimen databases that are not actively curated to reflect changing knowledge.
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Affiliation(s)
| | - Vanessa Graziele Staggemeier
- Royal Botanic Gardens, KewTW9 3AERichmondSurreyU.K.
- Universidade Estadual Paulista, Instituto de Biociências, Departamento de BotânicaLaboratório de FenologiaAvenida 24A 1515, CEP 13506–900Rio ClaroSão PauloBrazil
- Departamento de Ecologia, Centro de BiociênciasUniversidade Federal do Rio Grande do NorteCEP 59072–970NatalRio Grande do NorteBrazil
| | - Thais N. C. Vasconcelos
- Royal Botanic Gardens, KewTW9 3AERichmondSurreyU.K.
- Laboratório de Sistemática VegetalDepartamento de Botânica, Universidade de São Paulo, São PauloSP 05508–090Brazil
| | | | | | - Eve J. Lucas
- Royal Botanic Gardens, KewTW9 3AERichmondSurreyU.K.
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Abstract
Anchovies (Engraulidae) are one of the ecologically important groups and often difficult to identify due to their small size and overlapping morphological characters. In the present study, reference DNA barcodes were generated for 82 individuals representing 13 species of Engraulidae family using mitochondrial Cytochrome c oxidase subunit I (COI) and 16S rRNA genes. The average genetic distance value of COI gene for conspecific, congeneric and confamilial is 0.25, 20.45 and 22.28%, respectively. Mitochondrial 16S rRNA showed an average divergence value of 0.60, 10.28 and 14.37% for within species, between species and within families, respectively. Comparison of the present study reference barcodes with the reported sequences revealed high frequency of misidentification of species and possible occurrence of cryptic species in this family. Phylogenetic tree reconstructed using different methodologies revealed monophyletic nature of genus Stolephorus and the evolutionary relationship within genus Stolephorus is defined as ([S. insularis: S. tamilensis] S. dubiosus (S. waitei [S. commersonnii: S. indicus])).
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Affiliation(s)
- Shardul S Gangan
- a Fisheries Resources Harvest & Post-Harvest Division , ICAR - Central Institute of Fisheries Education , Mumbai , India
| | - A Pavan-Kumar
- b Fish Genetics and Biotechnology Division , ICAR - Central Institute of Fisheries Education , Mumbai , India
| | - Jaiswar A K
- a Fisheries Resources Harvest & Post-Harvest Division , ICAR - Central Institute of Fisheries Education , Mumbai , India
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Fontana L, Bonura E, Lyski Z, Messer W. Closing the Brief Case: Klebsiella variicola-Identifying the Misidentified. J Clin Microbiol 2019; 57:e00825-18. [PMID: 30602546 DOI: 10.1128/JCM.00825-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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46
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Bach E, Sant'Anna FH, Magrich Dos Passos JF, Balsanelli E, de Baura VA, Pedrosa FDO, de Souza EM, Passaglia LMP. Detection of misidentifications of species from the Burkholderia cepacia complex and description of a new member, the soil bacterium Burkholderia catarinensis sp. nov. Pathog Dis 2018; 75:3934654. [PMID: 28859310 DOI: 10.1093/femspd/ftx076] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/04/2017] [Indexed: 12/31/2022] Open
Abstract
The correct identification of bacteria from the Burkholderia cepacia complex (Bcc) is crucial for epidemiological studies and treatment of cystic fibrosis infections. However, genome-based identification tools are revealing many controversial Bcc species assignments. The aim of this work is to re-examine the taxonomic position of the soil bacterium B. cepacia 89 through polyphasic and genomic approaches. recA and 16S rRNA gene sequence analysis positioned strain 89 inside the Bcc group. However, based on the divergence score of seven concatenated allele sequences, and values of average nucleotide identity, and digital DNA:DNA hybridization, our results suggest that strain 89 is different from other Bcc species formerly described. Thus, we propose to classify Burkholderia sp. 89 as the novel species Burkholderia catarinensis sp. nov. with strain 89T (=DSM 103188T = BR 10601T) as the type strain. Moreover, our results call the attention to some probable misidentifications of Bcc genomes at the National Center for Biotechnology Information database.
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Affiliation(s)
- Evelise Bach
- Laboratório de Microbiologia Agrícola, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Bento Goncalves 9500, Porto Alegre, RS 91501-970, Brazil
| | - Fernando Hayashi Sant'Anna
- Laboratório de Microbiologia Agrícola, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Bento Goncalves 9500, Porto Alegre, RS 91501-970, Brazil
| | | | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Valter Antonio de Baura
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Luciane Maria Pereira Passaglia
- Laboratório de Microbiologia Agrícola, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Bento Goncalves 9500, Porto Alegre, RS 91501-970, Brazil
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Stavrou AA, Mixão V, Boekhout T, Gabaldón T. Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications. Yeast 2018; 35:425-429. [PMID: 29320804 PMCID: PMC6001429 DOI: 10.1002/yea.3303] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/30/2017] [Accepted: 12/21/2017] [Indexed: 11/05/2022] Open
Abstract
Online sequence databases such as NCBI GenBank serve as a tremendously useful platform for researchers to share and reuse published data. However, submission systems lack control for errors such as organism misidentification, which once entered in the database can be propagated and mislead downstream analyses. Here we present an illustrating case of misidentification of Candida albicans from a clinical sample as Naumovozyma dairenensis based on whole-genome shotgun data. Analyses of phylogenetic markers, read mapping and single nucleotide polymorphisms served to correct the identification. We propose that the routine use of such analyses could help to detect misidentifications arising from unsupervised analyses and correct them before they enter the databases. Finally, we discuss broader implications of such misidentifications and the difficulty of correcting them once they are in the records.
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Affiliation(s)
- Aimilia A Stavrou
- Westerdijk Fungal Biodiversity Institute, 3584, Utrecht, The Netherlands.,Institute for Biodiversity and ecosystem Dynamics, University of Amsterdam, 1012, WX, Amsterdam, The Netherlands
| | - Verónica Mixão
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584, Utrecht, The Netherlands.,Institute for Biodiversity and ecosystem Dynamics, University of Amsterdam, 1012, WX, Amsterdam, The Netherlands
| | - Toni Gabaldón
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Pg. Lluís Companys 23, 08010, Barcelona, Spain
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McLachlan E, Bousfield J, Howard R, Reeves S. Reduced parahippocampal volume and psychosis symptoms in Alzheimer's disease. Int J Geriatr Psychiatry 2018; 33:389-395. [PMID: 28741694 DOI: 10.1002/gps.4757] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/31/2017] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Establishing structural imaging correlates of psychosis symptoms in Alzheimer's disease (AD) could localise pathology and target symptomatic treatment. This study investigated whether psychosis symptoms are associated with visuoperceptual or frontal networks, and whether regional brain volume differences could be linked with the paranoid (persecutory delusions) or misidentification (misidentification phenomena and/or hallucinations) subtypes. METHODS A total of 104 patients with probable AD (AddNeuroMed; 47 psychotic, 57 non-psychotic), followed up for at least one year with structural MRI at baseline. Presence and subtype of psychosis symptoms were established using the Neuropsychiatric Inventory. Volume and cortical thickness measures in visuoperceptual and frontal networks were explored using multivariate analyses to compare with both a global (psychotic versus not) and subtype-specific approach, adjusting for potential confounding factors. RESULTS There was a significant main effect of psychosis subtypes on the ventral visual stream region of interest (F30,264 = 1.65, p = 0.021, np2 = 0.16). This was explained by reduced left parahippocampal gyrus volume (F1,97 = 11.1, p = 0.001, np2 = 0.10). When comparisons were made across psychosis subtypes, left parahippocampal volume reduction remained significant (F7,95 = 3.94, p = 0.011, np2 = 0.11) and was greatest for the misidentification and mixed subtypes compared to paranoid and non-psychotic groups. CONCLUSIONS These findings implicate the ventral visual stream in psychosis in AD, consistent with integrative theories regarding origins of psychosis, and provide further evidence for a role in the misidentification subtype. Specifically, reduced volume in the parahippocampal gyrus is implicated in misidentification delusion formation, which we hypothesise is due to its role in context attribution. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Emma McLachlan
- Department of Old Age Psychiatry, King's College London, UK.,Division of Psychiatry, University College London, UK
| | | | - Robert Howard
- Department of Old Age Psychiatry, King's College London, UK.,Division of Psychiatry, University College London, UK
| | - Suzanne Reeves
- Department of Old Age Psychiatry, King's College London, UK.,Division of Psychiatry, University College London, UK
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Pillonetto M, Arend LN, Faoro H, D'Espindula HRS, Blom J, Smits THM, Mira MT, Rezzonico F. Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus (Zhang 2008) and description of Phytobacter ursingii sp. nov. Int J Syst Evol Microbiol 2017; 68:176-184. [PMID: 29125457 DOI: 10.1099/ijsem.0.002477] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The species Phytobacter diazotrophicus and the associated genus Phytobacter were originally described by Zhanget al. [Arch Microbiol189 (2008), 431-439] on the basis of few endophytic nitrogen-fixing bacteria isolated from wild rice (Oryza rufipogon) in China. In this study, we demonstrate that a number of clinical isolates that were either described in the literature, preserved in culture collections, or obtained during a 2013 multi-state sepsis outbreak in Brazil also belong to the same genus. 16S rRNA gene sequencing, multilocus sequence analysis based on gyrB, rpoB, atpD and infB genes, as well as digital DNA-DNA hybridization support the existence of a second species within the genus Phytobacter. All isolates from the recent Brazilian outbreak, along with some older American clinical strains, were found to belong to the already described species Phytobacterdiazotrophicus, whereas three clinical strains retrieved in the USA over a time span of almost four decades, could be assigned to a new Phytobacter species. Implementation of an extended set of biochemical tests showed that the two Phytobacter species could phenotypically be discriminated from each other by the ability to utilize l-sorbose and d-serine. This feature was limited to the strains of the novel species described herein, for which the name Phytobacter ursingii sp. nov. is proposed, with ATCC 27989T (=CNCTC 5729T) as the designated type strain. An emended description of the species Phytobacter diazotrophicus and of the genus Phytobacter is also provided.
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Affiliation(s)
- Marcelo Pillonetto
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba-PR, Brazil.,Molecular Bacteriology Division, Central Public Health Laboratory, State of Paraná, São José dos Pinhais-PR, Brazil
| | - Lavinia N Arend
- Molecular Bacteriology Division, Central Public Health Laboratory, State of Paraná, São José dos Pinhais-PR, Brazil
| | | | - Helena R S D'Espindula
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba-PR, Brazil
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Marcelo T Mira
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba-PR, Brazil
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
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Kawahara-Matsumizu M, Yamagishi Y, Mikamo H. Misidentification of Neisseria cinerea as Neisseria meningitidis by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS). Jpn J Infect Dis 2017; 71:85-87. [PMID: 29093319 DOI: 10.7883/yoken.jjid.2017.183] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
| | - Yuka Yamagishi
- Department of Clinical Infectious Diseases, Aichi Medical University Graduate School of Medicine
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University Graduate School of Medicine
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