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1. Community standards and future opportunities for synthetic communities in plant–microbiota research

Author

Northen, Trent R, Kleiner, Manuel, Torres, Marta, Kovács, Ákos T, Nicolaisen, Mette Haubjerg, Krzyżanowska, Dorota M, Sharma, Shilpi, Lund, George, Jelsbak, Lars, Baars, Oliver, Kindtler, Nikolaj Lunding, Wippel, Kathrin, Dinesen, Caja, Ferrarezi, Jessica A, Marian, Malek, Pioppi, Adele, Xu, Xinming, Andersen, Tonni, Geldner, Niko, Schulze-Lefert, Paul, Vorholt, Julia A, and Garrido-Oter, Ruben

Subjects
Microbiology, Biological Sciences, Responsible Consumption and Production, Plants, Microbiota, Agriculture, Bacteria, Synthetic Biology, Medical Microbiology
Abstract

Harnessing beneficial microorganisms is seen as a promising approach to enhance sustainable agriculture production. Synthetic communities (SynComs) are increasingly being used to study relevant microbial activities and interactions with the plant host. Yet, the lack of community standards limits the efficiency and progress in this important area of research. To address this gap, we recommend three actions: (1) defining reference SynComs; (2) establishing community standards, protocols and benchmark data for constructing and using SynComs; and (3) creating an infrastructure for sharing strains and data. We also outline opportunities to develop SynCom research through technical advances, linking to field studies, and filling taxonomic blind spots to move towards fully representative SynComs.

Published
2024

12. Vulnerability Detection and Assessment for SQL Injection, Cross-site Scripting, and Other Common Vulnerabilities

Author

Kandhari, Harsimar, Jain, Sanskar, Sharma, Shilpi, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Choudrie, Jyoti, editor, Mahalle, Parikshit N., editor, Perumal, Thinagaran, editor, and Joshi, Amit, editor

Published
2024
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13. Enhancing Security in Wireless Sensor Networks: A Broadcast/Multicast Authentication Framework with Identity-Based Signature Schemes

Author

Sharma, Shilpi, Kumar, Bijendra, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Fortino, Giancarlo, editor, Kumar, Akshi, editor, Swaroop, Abhishek, editor, and Shukla, Pancham, editor

Published
2024
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14. A Novel Classification Scheme for Credit Card Fraud Detection Using Data Mining

Author

Kohli, Himani, Sharma, Shilpi, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Tan, Kay Chen, Series Editor, Shukla, Balvinder, editor, Murthy, B. K., editor, Hasteer, Nitasha, editor, Kaur, Harpreet, editor, and Van Belle, Jean-Paul, editor

Published
2024
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30. Terpenes and Terpenoids

Author

Sinha, Dwaipayan, primary, Chatterjee, Moumita, additional, Choudhury, Srijonee, additional, Seal, Sanchita, additional, Das, Tapas, additional, Sharma, Shilpi, additional, Banerjee, Swastika, additional, and Chowdhury, Shahana, additional

Published
2023
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31. Comparison of Cloudlet-Based Mobile Cloud Computing Models and the Rise of Cloud Manufacturing

Author

Chauhan, Devansh, Rao, Nipun, Masih, Alvin, Sharma, Dolly, Sharma, Shilpi, Chaari, Fakher, Series Editor, Gherardini, Francesco, Series Editor, Ivanov, Vitalii, Series Editor, Cavas-Martínez, Francisco, Editorial Board Member, di Mare, Francesca, Editorial Board Member, Haddar, Mohamed, Editorial Board Member, Kwon, Young W., Editorial Board Member, Trojanowska, Justyna, Editorial Board Member, Xu, Jinyang, Editorial Board Member, Phanden, Rakesh Kumar, editor, Kumar, Ravinder, editor, Pandey, Pulak Mohan, editor, and Chakraborty, Ayon, editor

Published
2023
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32. Performance Evaluation of HSRP and GLBP Over OSPF and RIP Routing Protocols

Author

Agarwal, Aayush, Sharma, Shilpi, Xavier, Evin Tom, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Dubey, Ashwani Kumar, editor, Sugumaran, Vijayan, editor, and Chong, Peter Han Joo, editor

Published
2023
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33. Flexible Reverse Engineering of Desktop and Web Applications

Author

Sharma, Shilpi, Vashisth, Shubham, Dhall, Ishika, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Möller, Sebastian, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Chatterjee, Prasenjit, editor, Pamucar, Dragan, editor, Yazdani, Morteza, editor, and Panchal, Dilbagh, editor

Published
2023
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34. Analysis of Public Perception of Autonomous Vehicles Based on Unlabelled Data from Twitter

Author

Gupta, Achal Shankar, Sharma, Shilpi, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Tuba, Milan, editor, Akashe, Shyam, editor, and Joshi, Amit, editor

Published
2023
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35. Reliable Biometric Authentication with Privacy Protection

Author

Sharma, Shilpi Barman, Dhall, Ishika, Nayak, Soumya Ranjan, Chatterjee, Pushpita, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Möller, Sebastian, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Dhar, Sourav, editor, Do, Dinh-Thuan, editor, Sur, Samarendra Nath, editor, and Liu, Howard Chuan-Ming, editor

Published
2023
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41. Wind Speed Prediction in the Region of India Using Artificial Intelligence

Author

Deepta, Eeshita, Juyal, Neha, Sharma, Shilpi, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Möller, Sebastian, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Unhelker, Bhuvan, editor, Pandey, Hari Mohan, editor, and Raj, Gaurav, editor

Published
2022
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46. Plasma Membrane-Associated Restriction Factors and Their Counteraction by HIV-1 Accessory Proteins.

Author

Ramirez, Peter W, Sharma, Shilpi, Singh, Rajendra, Stoneham, Charlotte A, Vollbrecht, Thomas, and Guatelli, John

Subjects
Animals, Humans, HIV-1, HIV Infections, Membrane Glycoproteins, Membrane Proteins, Antigens, CD, Viral Regulatory and Accessory Proteins, Host-Pathogen Interactions, GPI-Linked Proteins, BST-2, CD4, Nef, SERINC5, Vpu, HIV/AIDS, Infectious Diseases, Vaccine Related, Clinical Research, 2.1 Biological and endogenous factors, 2.2 Factors relating to the physical environment, 1.1 Normal biological development and functioning, Infection
Abstract

The plasma membrane is a site of conflict between host defenses and many viruses. One aspect of this conflict is the host's attempt to eliminate infected cells using innate and adaptive cell-mediated immune mechanisms that recognize features of the plasma membrane characteristic of viral infection. Another is the expression of plasma membrane-associated proteins, so-called restriction factors, which inhibit enveloped virions directly. HIV-1 encodes two countermeasures to these host defenses: The membrane-associated accessory proteins Vpu and Nef. In addition to inhibiting cell-mediated immune-surveillance, Vpu and Nef counteract membrane-associated restriction factors. These include BST-2, which traps newly formed virions at the plasma membrane unless counteracted by Vpu, and SERINC5, which decreases the infectivity of virions unless counteracted by Nef. Here we review key features of these two antiviral proteins, and we review Vpu and Nef, which deplete them from the plasma membrane by co-opting specific cellular proteins and pathways of membrane trafficking and protein-degradation. We also discuss other plasma membrane proteins modulated by HIV-1, particularly CD4, which, if not opposed in infected cells by Vpu and Nef, inhibits viral infectivity and increases the sensitivity of the viral envelope glycoprotein to host immunity.

Published
2019

47. The C-Terminal End of HIV-1 Vpu Has a Clade-Specific Determinant That Antagonizes BST-2 and Facilitates Virion Release

Author

Sharma, Shilpi, Jafari, Moein, Bangar, Amandip, William, Karen, Guatelli, John, and Lewinski, Mary K

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Infectious Diseases, HIV/AIDS, Sexually Transmitted Infections, 2.2 Factors relating to the physical environment, 2.1 Biological and endogenous factors, Infection, Antigens, CD, Cell Line, Cell Membrane, GPI-Linked Proteins, HIV Infections, HIV Seropositivity, HIV-1, HeLa Cells, Human Immunodeficiency Virus Proteins, Humans, Viral Regulatory and Accessory Proteins, Virion, Virus Assembly, Virus Release, beta-Transducin Repeat-Containing Proteins, BST-2, Vpu, host-pathogen interactions, human immunodeficiency virus, molecular biology, restriction factors, virology, virus-host interactions, Hela Cells, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Virology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

The cellular protein bone marrow stromal antigen-2 (BST-2)/tetherin acts against a variety of enveloped viruses by restricting their release from the plasma membrane. The HIV-1 accessory protein Vpu counteracts BST-2 by downregulating it from the cell surface and displacing it from virion assembly sites. Previous comparisons of Vpus from transmitted/founder viruses and between viruses isolated during acute and chronic infection led to the identification of a tryptophan at position 76 in Vpu (W76) as a key determinant for the displacement of BST-2 from virion assembly sites. Although present in Vpus from clades B, D, and G, W76 is absent from Vpus from clades A, C, and H. Mutagenesis of the C-terminal region of Vpu from two clade C viruses led to the identification of a conserved LL sequence that is functionally analogous to W76 of clade B. Alanine substitution of these leucines partially impaired virion release. This impairment was even greater when the mutations were combined with mutations of the Vpu β-TrCP binding site, resulting in Vpu proteins that induced high surface levels of BST-2 and reduced the efficiency of virion release to less than that of virus lacking vpu Microscopy confirmed that these C-terminal leucines in clade C Vpu, like W76 in clade B, contribute to virion release by supporting the displacement of BST-2 from virion assembly sites. These results suggest that although encoded differently, the ability of Vpu to displace BST-2 from sites of virion assembly on the plasma membrane is evolutionarily conserved among clade B and C HIV-1 isolates.IMPORTANCE Although targeted by a variety of restriction mechanisms, HIV-1 establishes chronic infection in most cases, in part due to the counteraction of these host defenses by viral accessory proteins. Using conserved motifs, the accessory proteins exploit the cellular machinery to degrade or mistraffic host restriction factors, thereby counteracting them. The Vpu protein counteracts the virion-tethering factor BST-2 in part by displacing it from virion assembly sites along the plasma membrane, but a previously identified determinant of that activity is clade specific at the level of protein sequence and not found in the clade C viruses that dominate the pandemic. Here, we show that clade C Vpu provides this activity via a leucine-containing sequence rather than the tryptophan-containing sequence found in clade B Vpu. This difference seems likely to reflect the different evolutionary paths taken by clade B and clade C HIV-1 in human populations.

Published
2019

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