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Rani P, Kotwal S, Manhas J, Sharma V, Sharma S. Machine Learning and Deep Learning Based Computational Approaches in Automatic Microorganisms Image Recognition: Methodologies, Challenges, and Developments. ARCHIVES OF COMPUTATIONAL METHODS IN ENGINEERING : STATE OF THE ART REVIEWS 2022; 29:1801-1837. [PMID: 34483651 PMCID: PMC8405717 DOI: 10.1007/s11831-021-09639-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/24/2021] [Indexed: 05/12/2023]
Abstract
Microorganisms or microbes comprise majority of the diversity on earth and are extremely important to human life. They are also integral to processes in the ecosystem. The process of their recognition is highly tedious, but very much essential in microbiology to carry out different experimentation. To overcome certain challenges, machine learning techniques assist microbiologists in automating the entire process. This paper presents a systematic review of research done using machine learning (ML) and deep leaning techniques in image recognition of different microorganisms. This review investigates certain research questions to analyze the studies concerning image pre-processing, feature extraction, classification techniques, evaluation measures, methodological limitations and technical development over a period of time. In addition to this, this paper also addresses the certain challenges faced by researchers in this field. Total of 100 research publications in the chronological order of their appearance have been considered for the time period 1995-2021. This review will be extremely beneficial to the researchers due to the detailed analysis of different methodologies and comprehensive overview of effectiveness of different ML techniques being applied in microorganism image recognition field.
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Affiliation(s)
- Priya Rani
- Computer Science and IT, University of Jammu, Jammu, India
| | - Shallu Kotwal
- Information Technology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Jatinder Manhas
- Computer Science and IT, Bhaderwah Campus, University of Jammu, Jammu, India
| | - Vinod Sharma
- Computer Science and IT, University of Jammu, Jammu, India
| | - Sparsh Sharma
- Department of Computer Science and Engineering, NIT Srinagar, Srinagar, J&K India
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Zhai X, Kong WG, Cheng GF, Cao JF, Dong F, Han GK, Song YL, Qin CJ, Xu Z. Molecular Characterization and Expression Analysis of Intercellular Adhesion Molecule-1 (ICAM-1) Genes in Rainbow Trout ( Oncorhynchus mykiss) in Response to Viral, Bacterial and Parasitic Challenge. Front Immunol 2021; 12:704224. [PMID: 34489953 PMCID: PMC8417878 DOI: 10.3389/fimmu.2021.704224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 08/02/2021] [Indexed: 01/10/2023] Open
Abstract
The intercellular adhesion molecule-1 (ICAM-1), known as CD54, is a transmembrane cell surface glycoprotein that interacts with two integrins (i.e., LFA-1 and Mac-l) important for trans-endothelial migration of leukocytes. The level of ICAM-1 expression is upregulated in response to some inflammatory stimulations, including pathogen infection and proinflammatory cytokines. Yet, to date, our knowledge regarding the functional role of ICAM-1 in teleost fish remains largely unknown. In this study, we cloned and characterized the sequence of ICAM-1 in rainbow trout (Oncorhynchus mykiss) for the first time, which exhibited that the molecular features of ICAM-1 in fishes were relatively conserved compared with human ICAM-1. The transcriptional level of ICAM-1 was detected in 12 different tissues, and we found high expression of this gene in the head kidney, spleen, gills, skin, nose, and pharynx. Moreover, upon stimulation with infectious hematopoietic necrosis virus (IHNV), Flavobacterium columnare G4 (F. columnare), and Ichthyophthirius multifiliis (Ich) in rainbow trout, the morphological changes were observed in the skin and gills, and enhanced expression of ICAM-1 mRNA was detected both in the systemic and mucosal tissues. These results indicate that ICAM-1 may be implicated in the mucosal immune responses to viral, bacterial, and parasitic infections in teleost fish, meaning that ICAM-1 emerges as a master regulator of mucosal immune responses against pathogen infections in teleost fish.
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Affiliation(s)
- Xue Zhai
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Wei-Guang Kong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Center for Fish Biology and Fishery Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Gao-Feng Cheng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Jia-Feng Cao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Fen Dong
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Guang-Kun Han
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Yan-Ling Song
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Chuan-Jie Qin
- Department of Life Science, Key Laboratory of Sichuan Province for Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River, Neijiang Normal University, Neijiang, China
| | - Zhen Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Center for Fish Biology and Fishery Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Increased Prevalence of Severe Fever with Thrombocytopenia Syndrome in Eastern China Clustered with Multiple Genotypes and Reasserted Virus during 2010-2015. Sci Rep 2017; 7:6503. [PMID: 28747674 PMCID: PMC5529542 DOI: 10.1038/s41598-017-06853-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/19/2017] [Indexed: 11/13/2022] Open
Abstract
Severe fever with thrombocytopenia syndrome (SFTS) is a novel tick-borne viral disease with high mortality. Since January 2010, we have conducted an epidemiological surveillance and etiological study of SFTS in Jiangsu and Anhui provinces. From January 2010 through December 2015, a total of 286 SFTS cases were confirmed in Jiangsu and Anhui provinces with a case fatality rate of 16.1%. The majority of confirmed SFTS cases were distributed in the border area of Jiangsu and Anhui provinces. Our findings suggest that the SFTS prevalence rate rose since 2010 and reached its highest in 2015. Phylogenetic analysis demonstrated that the majority of the SFTSV strains (83.6%) from Jiangsu and Anhui provinces belonged to genotypes A and D. Notably, we identified three strains of SFTSV clustered into the genotype E. This is the first report of the genotype E SFTSV strains in mainland of China. A reassortment between genotype A and D was found in the central region of the endemic areas, where three SFTSV genotypes (A, C and D) were co-circulating.
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de Araújo EF, Feriotti C, Galdino NADL, Preite NW, Calich VLG, Loures FV. The IDO-AhR Axis Controls Th17/Treg Immunity in a Pulmonary Model of Fungal Infection. Front Immunol 2017; 8:880. [PMID: 28791025 PMCID: PMC5523665 DOI: 10.3389/fimmu.2017.00880] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/10/2017] [Indexed: 12/20/2022] Open
Abstract
In infectious diseases, the enzyme indoleamine 2,3 dioxygenase-1 (IDO1) that catalyzes the tryptophan (Trp) degradation along the kynurenines (Kyn) pathway has two main functions, the control of pathogen growth by reducing available Trp and immune regulation mediated by the Kyn-mediated expansion of regulatory T (Treg) cells via aryl hydrocarbon receptor (AhR). In pulmonary paracoccidioidomycosis (PCM) caused by the dimorphic fungus Paracoccidioides brasiliensis, IDO1 was shown to control the disease severity of both resistant and susceptible mice to the infection; however, only in resistant mice, IDO1 is induced by TGF-β signaling that confers a stable tolerogenic phenotype to dendritic cells (DCs). In addition, in pulmonary PCM, the tolerogenic function of plasmacytoid dendritic cells was linked to the IDO1 activity. To further evaluate the function of IDO1 in pulmonary PCM, IDO1-deficient (IDO1-/-) C57BL/6 mice were intratracheally infected with P. brasiliensis yeasts and the infection analyzed at three postinfection periods regarding several parameters of disease severity and immune response. The fungal loads and tissue pathology of IDO1-/- mice were higher than their wild-type controls resulting in increased mortality rates. The evaluation of innate lymphoid cells showed an upregulated differentiation of the innate lymphoid cell 3 phenotype accompanied by a decreased expansion of ILC1 and NK cells in the lungs of infected IDO1-/- mice. DCs from these mice expressed elevated levels of costimulatory molecules and cytokine IL-6 associated with reduced production of IL-12, TNF-α, IL-1β, TGF-β, and IL-10. This response was concomitant with a marked reduction in AhR production. The absence of IDO1 expression caused an increased influx of activated Th17 cells to the lungs with a simultaneous reduction in Th1 and Treg cells. Accordingly, the suppressive cytokines IL-10, TGF-β, IL-27, and IL-35 appeared in reduced levels in the lungs of IDO1-/- mice. In conclusion, the immunological balance mediated by the axis IDO/AhR is fundamental to determine the balance between Th17/Treg cells and control the severity of pulmonary PCM.
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Affiliation(s)
- Eliseu Frank de Araújo
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Claudia Feriotti
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | | | - Nycolas Willian Preite
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Vera Lúcia Garcia Calich
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Flávio Vieira Loures
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
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Jandaghi NZS, Azad TM, Naseri M, Yavarian J, Nategh R. Molecular and genetic characteristics of hemagglutinin and neuraminidase in Iranian 2009 pandemic influenza A(H1N1) viruses. Arch Virol 2010; 155:717-21. [DOI: 10.1007/s00705-010-0629-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 02/08/2010] [Indexed: 10/19/2022]
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