1
|
Moussa AM, Abdou S, Elsayed KM, Rashwan M, Asif A, Khatoon S, Alshamari MA. Enhanced Arabic disaster data classification using domain adaptation. PLoS One 2024; 19:e0301255. [PMID: 38574077 PMCID: PMC10994337 DOI: 10.1371/journal.pone.0301255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
Natural disasters, like pandemics and earthquakes, are some of the main causes of distress and casualties. Governmental crisis management processes are crucial when dealing with these types of problems. Social media platforms are among the main sources of information regarding current events and public opinion. So, they have been used extensively to aid disaster detection and prevention efforts. Therefore, there is always a need for better automatic systems that can detect and classify disaster data of social media. In this work, we propose enhanced Arabic disaster data classification models. The suggested models utilize domain adaptation to provide state-of-the-art accuracy. We used a standard dataset of Arabic disaster data collected from Twitter for testing the proposed models. Experimental results show that the provided models significantly outperform the previous state-of-the-art results.
Collapse
Affiliation(s)
- Abdullah M. Moussa
- The Engineering Company for the Development of Digital Systems, Giza, Egypt
| | - Sherif Abdou
- Faculty of Computers and Artificial Intelligence, Cairo University, Giza, Egypt
| | - Khaled M. Elsayed
- Faculty of Computers and Artificial Intelligence, Cairo University, Giza, Egypt
| | | | - Amna Asif
- School of Computing and Communications, Lancaster University Leipzig, Leipzig, Germany
| | - Shaheen Khatoon
- School of Architecture, Computing & Engineering, University of East London, London, United Kingdom
| | - Majed A. Alshamari
- College of Computer Sciences and Information Technology, King Faisal University, AlAhsa, Saudi Arabia
| |
Collapse
|
2
|
Elmanakhly AR, Safwat N, Tohamy STK, Elsayed KM, ElSherif HM, Elsayed M, El-Tarabili RM, Alhomrani M, Alamri AS, Ghoneim MM, Alshahrani MA, Saif A, Mansour AT, Bendary MM. Comparative phenotypic and genotypic analysis of community-acquired and hospital-acquired intra-abdominal infections among liver transplanted patients. J Appl Microbiol 2024; 135:lxae076. [PMID: 38515285 DOI: 10.1093/jambio/lxae076] [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: 02/09/2024] [Revised: 03/09/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024]
Abstract
AIM During liver transplantation, both hospital-acquired (HA) and community-acquired (CA) intra-abdominal infections (IAIs) are involved causing life-threatening diseases. Therefore, comparative studies of aerobic and facultative anaerobic HA-IAIs and CA-IAIs after liver transplantation surgery are necessary. METHODS AND RESULTS The species of detected isolates (310) from intra-abdominal fluid were identified and classified into hospital-acquired intra-abdominal infections (HA-IAIs) and community-acquired intra-abdominal infections (CA-IAIs). Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii were the most commonly detected species. The resistant phenotypes were commonly detected among the HA-IAIs; however, the virulent phenotypes were the predominant strains of CA-IAIs. Regrettably, the resistance profiles were shocking, indicating the inefficacy of monotherapy in treating these isolates. Therefore, we confirmed the use of empirical combination therapies of amikacin and meropenem for treating all IAIs (FICI ≤ 0.5). Unfortunately, the high diversity and low clonality of all identified HA and CA-IAIs were announced with D-value in the range of 0.992-1. CONCLUSION This diversity proves that there are infinite numbers of infection sources inside and outside healthcare centers.
Collapse
Affiliation(s)
- Arwa R Elmanakhly
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information, Cairo 19648, Egypt
| | - Nesreen Safwat
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information, Cairo 19648, Egypt
| | - Sally T K Tohamy
- Department of Microbiology and Immunology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 19648, Egypt
| | - Khaled M Elsayed
- Department of Microbiology, Faculty of Pharmacy, Misr international university (MIU), Cairo 19648, Egypt
| | - Heba M ElSherif
- Department of Microbiology, Faculty of Pharmacy, Misr international university (MIU), Cairo 19648, Egypt
| | - Mahitab Elsayed
- Department of clinical pharmacy, faculty of Pharmacy, Modern University for Technology and Information, Cairo 19648, Egypt
| | - Reham M El-Tarabili
- Department of Bacteriology, Immunology and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Majid Alhomrani
- Department of Clinical Laboratories Sciences, The Faculty of Applied Medical Science, Taif University, Taif 26432, Saudi Arabia
- Reseacher center for health science, Deanship of Scientific Research, Taif University, Taif 26432, Saudi Arabia
| | - Abdulhakeem S Alamri
- Department of Clinical Laboratories Sciences, The Faculty of Applied Medical Science, Taif University, Taif 26432, Saudi Arabia
- Reseacher center for health science, Deanship of Scientific Research, Taif University, Taif 26432, Saudi Arabia
| | - Mohammed M Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, Al Maarefa University, Ad Diriyah 13713, Saudi Arabia
| | - Mohammed A Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, P.O. Box 1988, Najran 61441, Saudi Arabia
| | - Ahmed Saif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62217, Saudia Arabia
| | - Abdallah T Mansour
- Fish and Animal Production and Aquaculture Department, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
- Fish and Animal Production Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria 21531, Egypt
| | - Mahmoud M Bendary
- Department of Microbiology and Immunology, Faculty of Pharmacy, Port Said University, Port Said 42511, Egypt
| |
Collapse
|
3
|
Fujinami D, Motomura H, Oshima H, Mahin AA, Elsayed KM, Zendo T, Sugita Y, Sonomoto K, Kohda D. Correction to "Mosaic Cooperativity in Slow Polypeptide Topological Isomerization Revealed by Residue-Specific NMR Thermodynamic Analysis". J Phys Chem Lett 2021; 12:10766-10767. [PMID: 34714649 DOI: 10.1021/acs.jpclett.1c03473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
|
4
|
Fujinami D, Motomura H, Oshima H, Mahin AA, Elsayed KM, Zendo T, Sugita Y, Sonomoto K, Kohda D. Mosaic Cooperativity in Slow Polypeptide Topological Isomerization Revealed by Residue-Specific NMR Thermodynamic Analysis. J Phys Chem Lett 2020; 11:1934-1939. [PMID: 32067463 DOI: 10.1021/acs.jpclett.9b03591] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Slow polypeptide conformational changes on time scales of >1 s are generally assumed to be highly cooperative two-state transitions, reflecting the high energy barrier. However, few experimental characterizations have tested the validity of this assumption. We performed residue-specific NMR thermodynamic analysis of the 27-residue lantibiotic peptide, nukacin ISK-1, to characterize the isomerization between two topological states on the second time scale. Unexpectedly, the thermal transition behaviors were distinct among peptide regions, indicating that the topological isomerization process is a mosaic of different degrees of cooperativity. The conformational change path between the two NMR structures was deduced by a targeted molecular dynamics simulation. The unique side-chain threading motions through the monosulfide rings are the structural basis of the high energy barrier, and the nonlocal interactions in the hydrophobic core are the structural basis of the cooperativity. Taken together, we provide an energetic description of the topological isomerization of nukacin ISK-1.
Collapse
Affiliation(s)
- Daisuke Fujinami
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Hajime Motomura
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Hiraku Oshima
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Abdullah-Al Mahin
- Laboratory of Microbial Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 819-0395, Japan
| | - Khaled M Elsayed
- Laboratory of Microbial Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 819-0395, Japan
| | - Takeshi Zendo
- Laboratory of Microbial Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Kenji Sonomoto
- Laboratory of Microbial Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 819-0395, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| |
Collapse
|
5
|
Fujinami D, -Mahin AA, Elsayed KM, Islam MR, Nagao JI, Roy U, Momin S, Zendo T, Kohda D, Sonomoto K. The lantibiotic nukacin ISK-1 exists in an equilibrium between active and inactive lipid-II binding states. Commun Biol 2018; 1:150. [PMID: 30272026 PMCID: PMC6156582 DOI: 10.1038/s42003-018-0150-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/17/2018] [Indexed: 11/28/2022] Open
Abstract
The lantibiotic nukacin ISK-1 exerts antimicrobial activity through binding to lipid II. Here, we perform NMR analyses of the structure of nukacin ISK-1 and the interaction with lipid II. Unexpectedly, nukacin ISK-1 exists in two structural states in aqueous solution, with an interconversion rate on a time scale of seconds. The two structures differ in the relative orientations of the two lanthionine rings, ring A and ring C. Chemical shift perturbation induced by the titration of lipid II reveals that only one state was capable of binding to lipid II. On the molecular surface of the active state, a multiple hydrogen-bonding site formed by amino acid residues in the ring A region is adjacent to a hydrophobic surface formed by residues in the ring C region, and we propose that these sites interact with the pyrophosphate moiety and the isoprene chain of the lipid II molecule, respectively. Fujinami et al. show that an antimicrobial peptide Nukacin ISK-1 exists in an equilibrium between two states, only one of which can bind to the ISK-1’s target lipid-II, an important bacterial cell wall precursor. This study provides unexpected insights into the action modes of antibiotics.
Collapse
Affiliation(s)
- Daisuke Fujinami
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Abdullah-Al -Mahin
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Laboratory of Microbial Technology, Kyushu University, Fukuoka, 812-8581, Japan.,Microbiology and Industrial Irradiation Division, Institute of Food and Radiation Biology, Atomic Energy Research Establishment, Ganakbari, Savar 1207, Dhaka, 1349, Bangladesh
| | - Khaled M Elsayed
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Laboratory of Microbial Technology, Kyushu University, Fukuoka, 812-8581, Japan.,Department of Microbiology, Faculty of Pharmacy, Misr International University, Cairo, 19648, Egypt
| | - Mohammad R Islam
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Laboratory of Microbial Technology, Kyushu University, Fukuoka, 812-8581, Japan.,Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Jun-Ichi Nagao
- Department of Functional Bioscience, Section of Infection Biology, Fukuoka Dental College, Fukuoka, 814-0175, Japan
| | - Urmi Roy
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Laboratory of Microbial Technology, Kyushu University, Fukuoka, 812-8581, Japan
| | - Sabrina Momin
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Laboratory of Microbial Technology, Kyushu University, Fukuoka, 812-8581, Japan
| | - Takeshi Zendo
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Laboratory of Microbial Technology, Kyushu University, Fukuoka, 812-8581, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
| | - Kenji Sonomoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Laboratory of Microbial Technology, Kyushu University, Fukuoka, 812-8581, Japan.
| |
Collapse
|
6
|
Elsayed KM, Islam MR, Abdullah-Al-Mahin, Nagao JI, Zendo T, Sonomoto K. LiaRS reporter assay: A simple tool to identify lipid II binding moieties in lantibiotic nukacin ISK-1. J Biosci Bioeng 2016; 123:398-401. [PMID: 27856233 DOI: 10.1016/j.jbiosc.2016.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/08/2016] [Accepted: 10/01/2016] [Indexed: 12/27/2022]
Abstract
Binding to lipid II is an important step in the mode of action of most lantibiotics targeting the bacterial cell wall. We applied the Bacillus subtilis two-component system, LiaRS, that is known to respond to antibiotics interfering with lipid II cycle, in order to evaluate lipid II binding activity of known bacteriocins and also to identify lipid II binding moieties in lantibiotic nukacin ISK-1. Using this method, we confirmed that the methyllanthionine ring in nukacin ISK-1 is crucial for lipid II binding as previously indicated. In this study, we further identified that the three N-terminal lysine residues (K1, K2, and K3) and the glycine (G5) residue in nukacin ISK-1 are also important in lipid II binding.
Collapse
Affiliation(s)
- Khaled M Elsayed
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Mohammad R Islam
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan; Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka 1000, Bangladesh
| | - Abdullah-Al-Mahin
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan; Microbiology and Industrial Irradiation Division, Institute of Food and Radiation Biology, Atomic Energy Research Establishment, Savar, Dhaka 1349, Bangladesh
| | - Jun-Ichi Nagao
- Section of Infection Biology, Department of Functional Bioscience, Fukuoka Dental College, 2-15-1 Tamura, Sawara-ku, Fukuoka 814-0913, Japan
| | - Takeshi Zendo
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Kenji Sonomoto
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
| |
Collapse
|
7
|
Elsayed KM, Perros HG. Analysis of an ATM statistical multiplexer with heterogeneous Markovian on/off sources and applications to call admission control. Journal of High Speed Networks 1997. [DOI: 10.3233/jhs-1997-6204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
| | - Harry G. Perros
- Department of Computer Science, North Carolina State University, Raleigh, NC 27695-8206, USA, Tel.: +919 515 2858, E-mail:
| |
Collapse
|