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Journal articles on the topic 'Swarm virus'

Author: Grafiati

Published: 5 June 2025

Last updated: 1 August 2025

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1

Zelinka, Ivan, Swagatam Das, Lubomir Sikora, and Roman Šenkeřík. "Swarm virus - Next-generation virus and antivirus paradigm?" Swarm and Evolutionary Computation 43 (December 2018): 207–24. http://dx.doi.org/10.1016/j.swevo.2018.05.003.

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2

Kalke, Kiira, Jenni Lehtinen, Jelena Gnjatovic, et al. "Herpes Simplex Virus Type 1 Clinical Isolates Respond to UL29-Targeted siRNA Swarm Treatment Independent of Their Acyclovir Sensitivity." Viruses 12, no. 12 (2020): 1434. http://dx.doi.org/10.3390/v12121434.

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Acyclovir is the drug of choice for the treatment of herpes simplex virus (HSV) infections. Acyclovir-resistant HSV strains may emerge, especially during long-term drug use, and subsequently cause difficult-to-treat exacerbations. Previously, we set up a novel treatment approach, based on enzymatically synthesized pools of siRNAs, or siRNA swarms. These swarms can cover kilobases-long target sequences, reducing the likelihood of resistance to treatment. Swarms targeting the UL29 essential gene of HSV-1 have demonstrated high efficacy against HSV-1 in vitro and in vivo. Here, we assessed the an

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3

Caldwell, Haley S., Erica Lasek-Nesselquist, Paisley Follano, Laura D. Kramer, and Alexander T. Ciota. "Divergent Mutational Landscapes of Consensus and Minority Genotypes of West Nile Virus Demonstrate Host and Gene-Specific Evolutionary Pressures." Genes 11, no. 11 (2020): 1299. http://dx.doi.org/10.3390/genes11111299.

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Our current understanding of the natural evolution of RNA viruses comes largely from consensus level genetic analyses which ignore the diverse mutant swarms that comprise within-host viral populations. The breadth and composition of viral mutant swarms impact viral fitness and adaptation, and the capacity for swarm plasticity is likely to be particularly important for arthropod-borne viruses (arboviruses) that cycle between taxonomically divergent hosts. Despite this, characterization of the relationship between the selective pressures and genetic signatures of the mutant swarm and consensus s

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4

Thanh, Cong Truong, Plucar Jan, Bao Diep Quoc, and Zelinka Ivan. "X-ware: a proof of concept malware utilizing artificial intelligence." International Journal of Electrical and Computer Engineering (IJECE) 12, no. 2 (2022): 1937–44. https://doi.org/10.11591/ijece.v12i2.pp1937-1944.

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Recent years have witnessed a dramatic growth in utilizing computational intelligence techniques for various domains. Coherently, malicious actors are expected to utilize these techniques against current security solutions. Despite the importance of these new potential threats, there remains a paucity of evidence on leveraging these research literature techniques. This article investigates the possibility of combining artificial neural networks and swarm intelligence to generate a new type of malware. We successfully created a proof of concept malware named X-ware, which we tested against the

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5

Rahmalia, Dinita, Arif Rohmatullah, and Mohammad Syaiful Pradana. "Estimasi Parameter Super Pairwise Alignment pada Kombinasi Virus Dengue Menggunakan Particle Swarm Optimization." Techno.Com 18, no. 3 (2019): 264–74. http://dx.doi.org/10.33633/tc.v18i3.2528.

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Di Indonesia terdapat empat jenis virus dengue atau demam berdarah. Untuk melihat tingkat kesamaan (similarity) antara dua sekuens virus, dibutuhkan proses pensejajaran pada sekuens virus. Metode yang digunakan untuk pensejajaran pada dua sekuens virus adalah Super Pairwise Alignment (SPA). Nilai fungsi objective pada SPA adalah nilai penalty antara dua sekuens virus. Karena nilai fungsi objective tergantung pada parameter SPA, maka pada penelitian ini nilai parameter SPA akan diestimasi menggunakan metode heuristik seperti Particle Swarm Optimization (PSO). Simulasi diterapkan pada enam kombi

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6

Ciota, Alexander T., Dylan J. Ehrbar, Greta A. Van Slyke, Graham G. Willsey, and Laura D. Kramer. "Cooperative interactions in the West Nile virus mutant swarm." BMC Evolutionary Biology 12, no. 1 (2012): 58. http://dx.doi.org/10.1186/1471-2148-12-58.

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7

Husniah, Hilda Farida, and Toni Arifin. "Implementasi Algoritma Naïve Bayes Berbasis Particle Swarm Optimization Untuk Memprediksi Penyakit Hepatitis." Jurnal Ilmu Komputer 14, no. 1 (2021): 36. http://dx.doi.org/10.24843/jik.2021.v14.i01.p05.

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Penyakit Hepatitis merupakan penyakit peradangan pada sel-sel hati, yang disebabkan oleh infeksi (virus, bakteri, parasite), obat-obatan (termasuk obat tradisional), mengkonsumsi alkohol, lemak yang berlebihan dan penyakit autoimmune. Penyebab terjadinya Hepatitis adalah sering disebabkan oleh Virus Hepatitis B dan C. Prevalensi Hepatitis di Indonesia pada tahun 2013 sebesar 1,2% meningkat dua kali dibandingkan Riskesdas tahun 2007 yang sebesar 0,6%. Nusa Tenggara Timur merupakan provinsi dengan prevalensi Hepatitis tertinggi pada tahun 2013 yaitu sebesar 4,3%. Para peneliti berusaha membuat t

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8

Sahara, Sucitra, Rizqi Agung Permana, and Hariyanto Hariyanto. "Particle Swarm Optimization pada Analisa Review Software Antivirus Menggunakan Metode K-Nearest Neighbors." INFORMATICS FOR EDUCATORS AND PROFESSIONAL : Journal of Informatics 4, no. 2 (2020): 123. http://dx.doi.org/10.51211/itbi.v4i2.1313.

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Abstrak: Virus pada komputer menjadi hal yang membahayakan bagi para pengguna komputer perorangan maupun perusahaan yang telah menerapkan sistem terkomputerisasi. Virus program yang didesain untuk tujuan jahat dapat merusak bagian tertentu dari komputer, bahkan yang paling merugikan adalah dapat merusak data penting pada perusahaan. Dalam hal ini maka diciptakanlah sebuah software anti virus, perkembangan anti virus selalu lebih lambat dari virus itu sendiri, sehingga peneliti akan mengadakan penyeleksian software anti virus pada suatu opini atau berdasarkan komentar masyarakat yang telah meng

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9

Halim, Abdul, and Andri Safuwan. "ANALISIS SENTIMEN OPINI WARGANET TWITTER TERHADAP TES SCREENING GENOSE PENDETEKSI VIRUS COVID-19 MENGGUNAKAN METODE NAÏVE BAYES BERBASIS PARTICLE SWARM OPTIMIZATION." Jurnal Informatika Teknologi dan Sains 5, no. 1 (2023): 170–78. http://dx.doi.org/10.51401/jinteks.v5i1.2229.

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Munculnya pandemi COVID-19 mengakibatkan masyarakat harus selalu memeriksakan kesehatannya, terutama dalam menentukan gejala awal seseorang terpapar virus COVID-19 itu sendiri. Pada penelitian ini dilakukan analisis sentimen tweet masyarakat terkait screening genose test sebagai alat deteksi dini virus covid-19 dengan mengklasifikasikan respon yang mengandung sentimen positif dan negatif melalui jejaring sosial Twitter. Metode yang digunakan dalam penelitian ini adalah Nave Bayes Based Particle Swarm Optimization. Dengan proses crawling data dari twitter menggunakan RapidMiner. Preprocessing d

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10

Ghorbani, Amir, John M. Ngunjiri, and Chang-Won Lee. "Influenza A Virus Subpopulations and Their Implication in Pathogenesis and Vaccine Development." Annual Review of Animal Biosciences 8, no. 1 (2020): 247–67. http://dx.doi.org/10.1146/annurev-animal-021419-083756.

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The concept of influenza A virus (IAV) subpopulations emerged approximately 75 years ago, when Preben von Magnus described “incomplete” virus particles that interfere with the replication of infectious virus. It is now widely accepted that infectious particles constitute only a minor portion of biologically active IAV subpopulations. The IAV quasispecies is an extremely diverse swarm of biologically and genetically heterogeneous particle subpopulations that collectively influence the evolutionary fitness of the virus. This review summarizes the current knowledge of IAV subpopulations, focusing

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11

O'Connor, David H., and Dennis R. Burton. "Immune responses and HIV: a little order from the chaos." Journal of Experimental Medicine 203, no. 3 (2006): 501–3. http://dx.doi.org/10.1084/jem.20060216.

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HIV is evolution gone mad and bad. The virus infects a person and rapidly diversifies to become a huge swarm of viruses, each equipped differently to resist the onslaught of diverse T cells and antibodies. We can't expect to predict details of the struggle between virus and immunity, right? Wrong—maybe we can make some predictions, say two new landmark studies with potentially huge consequences for AIDS vaccine design.

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12

Febryani, Rahayu, and Toni Arifin. "OPTIMASI NAÏVE BAYES MENGGUNAKAN PARTICLE SWARM OPTIMIZATION UNTUK TINGKAT KEBERHASILAN CRYOTHERAPY PADA PENYAKIT KUTIL." Jurnal Responsif : Riset Sains dan Informatika 3, no. 2 (2021): 174–83. http://dx.doi.org/10.51977/jti.v3i2.431.

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Penyakit kutil merupakan salah satu penyebab masalah kesehatan kulit yang ditandai dengan timbulnya benjolan kecil pada kulit, penyakit ini disebabkan oleh virus Human Papiloma Virus. Ada berbagai cara dalam penyembuhan penyakit kutil, salah satunya dengan melakukan cryotherapy. Metode cryotherapy adalah teknik pengobatan terapi dengan berendam didalam es atau air yang dingin selama kurang lebih 30 menit, dalam suhu -18 derajat celcius sampai 24 derajat celcius, sehingga sel-sel kanker dalam tubuh pasien membeku dan terbukti dapat memperpanjang umur pasien bahkan ada kemungkinan sembuh. Untuk

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13

Schmidt, Fabian, Brandon F. Keele, Gregory Q. Del Prete, et al. "Derivation of simian tropic HIV-1 infectious clone reveals virus adaptation to a new host." Proceedings of the National Academy of Sciences 116, no. 21 (2019): 10504–9. http://dx.doi.org/10.1073/pnas.1818059116.

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To replicate in a new host, lentiviruses must adapt to exploit required host factors and evade species-specific antiviral proteins. Understanding how host protein variation drives lentivirus adaptation allowed us to expand the host range of HIV-1 to pigtail macaques. We have previously derived a viral swarm (in the blood of infected animals) that can cause AIDS in this new host. To further exploit this reagent, we generated infectious molecular clones (IMCs) from the viral swarm. We identified clones with high replicative capacity in pigtail peripheral blood mononuclear cells (PBMC) in vitro a

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14

Baban, Payam Qaderi, Farzad Mir, and Farshad Ebrahimi. "Power System Stability Improvement Based on Virus Particle Swarm Optimization Algorithm." European Journal of Electrical Engineering and Computer Science 7, no. 3 (2023): 35–40. http://dx.doi.org/10.24018/ejece.2023.7.3.526.

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This article discusses the development of a Power System Stabilizer (PSS) utilizing the Virus Particle Swarm Optimization Algorithm (VEPSO) to enhance power system stability. PSS is commonly used in the industry to suppress power system oscillations. The proposed algorithm was implemented on a Single Machine Infinite Bus (SMIB) system, and the PSS controller coefficients were optimized using VEPSO. The system was simulated under a specific disturbance in the generator input power, and the generator's dynamic responses were presented. The VEPSO algorithm's results, such as faster convergence, w

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15

Del Prete, Gregory Q., Haesun Park, Christine M. Fennessey, et al. "Molecularly Tagged Simian Immunodeficiency Virus SIVmac239 Synthetic Swarm for Tracking Independent Infection Events." Journal of Virology 88, no. 14 (2014): 8077–90. http://dx.doi.org/10.1128/jvi.01026-14.

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ABSTRACTFollowing mucosal human immunodeficiency virus type 1 transmission, systemic infection is established by one or only a few viral variants. Modeling single-variant, mucosal transmission in nonhuman primates using limiting-dose inoculations with a diverse simian immunodeficiency virus isolate stock may increase variability between animals since individual variants within the stock may have substantial functional differences. To decrease variability between animals while retaining the ability to enumerate transmitted/founder variants by sequence analysis, we modified the SIVmac239 clone t

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16

Lin, Kuan-Cheng, Sih-Yang Chen, and Jason C. Hung. "Botnet Detection Using Support Vector Machines with Artificial Fish Swarm Algorithm." Journal of Applied Mathematics 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/986428.

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Because of the advances in Internet technology, the applications of the Internet of Things have become a crucial topic. The number of mobile devices used globally substantially increases daily; therefore, information security concerns are increasingly vital. The botnet virus is a major threat to both personal computers and mobile devices; therefore, a method of botnet feature characterization is proposed in this study. The proposed method is a classified model in which an artificial fish swarm algorithm and a support vector machine are combined. A LAN environment with several computers which h

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17

W Callaghan, Chris. "Knowledge Management and Problem Solving in Real Time: The Role of Swarm Intelligence." Interdisciplinary Journal of Information, Knowledge, and Management 11 (2016): 177–99. http://dx.doi.org/10.28945/3528.

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Knowledge management research applied to the development of real-time research capability, or capability to solve societal problems in hours and days instead of years and decades, is perhaps increasingly important, given persistent global problems such as the Zika virus and rapidly developing antibiotic resistance. Drawing on swarm intelligence theory, this paper presents an approach to real-time research problem-solving in the form of a framework for understanding the complexity of real-time research and the challenges associated with maximizing collaboration. The objective of this research i

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18

O'Rourke, Sara M., Becky Schweighardt, William G. Scott, et al. "Novel Ring Structure in the gp41 Trimer of Human Immunodeficiency Virus Type 1 That Modulates Sensitivity and Resistance to Broadly Neutralizing Antibodies." Journal of Virology 83, no. 15 (2009): 7728–38. http://dx.doi.org/10.1128/jvi.00688-09.

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ABSTRACT The identification of the determinants of sensitivity and resistance to broadly neutralizing antibodies is a high priority for human immunodeficiency virus (HIV) research. An analysis of the swarm of closely related envelope protein variants in an HIV-infected individual revealed a mutation that markedly affected sensitivity to neutralization by antibodies and antiviral entry inhibitors targeting both gp41 and gp120. This mutation mapped to the C34 helix of gp41 and disrupted an unexplored structural feature consisting of a ring of hydrogen bonds in the gp41 trimer. This mutation appe

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19

Paavilainen, Henrik, Jenni Lehtinen, Alesia Romanovskaya, et al. "Topical treatment of herpes simplex virus infection with enzymatically created siRNA swarm." Antiviral Therapy 22, no. 7 (2017): 631–37. http://dx.doi.org/10.3851/imp3153.

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20

Curran, Rebecca, Claire L. Jameson, Joanna K. Craggs, et al. "Evolutionary trends of the first hypervariable region of the hepatitis C virus E2 protein in individuals with differing liver disease severity." Journal of General Virology 83, no. 1 (2002): 11–23. http://dx.doi.org/10.1099/0022-1317-83-1-11.

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Hepatitis C virus (HCV) exists as a complex swarm of genetically related viruses known as a quasispecies. Recent work has shown that quasispecies complexity and evolutionary rates are associated with the outcome of acute infection. Knowledge of how the virus population evolves at different stages of chronic infection is less clear. We have studied rates of evolution of the first hypervariable region (HVR1) of the E2 envelope protein in six individuals with disparate liver disease severity. These data show that virus populations present in individuals with mild non-progressive liver disease evo

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21

Davis, Nancy L., Ian J. Caley, Kevin W. Brown, et al. "Vaccination of Macaques against Pathogenic Simian Immunodeficiency Virus with Venezuelan Equine Encephalitis Virus Replicon Particles." Journal of Virology 74, no. 1 (2000): 371–78. http://dx.doi.org/10.1128/jvi.74.1.371-378.2000.

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ABSTRACT Vaccine vectors derived from Venezuelan equine encephalitis virus (VEE) that expressed simian immunodeficiency virus (SIV) immunogens were tested in rhesus macaques as part of the effort to design a safe and effective vaccine for human immunodeficiency virus. Immunization with VEE replicon particles induced both humoral and cellular immune responses. Four of four vaccinated animals were protected against disease for at least 16 months following intravenous challenge with a pathogenic SIV swarm, while two of four controls required euthanasia at 10 and 11 weeks. Vaccination reduced the

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Strickland, Samantha L., Rebecca R. Gray, Susanna L. Lamers, et al. "Efficient transmission and persistence of low‐frequency SIVmac251 variants in CD8-depleted rhesus macaques with different neuropathology." Journal of General Virology 93, no. 5 (2012): 925–38. http://dx.doi.org/10.1099/vir.0.039586-0.

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Infection of CD8-depleted rhesus macaques with the genetically heterogeneous simian immunodeficiency virus (SIV)mac251 viral swarm provides a rapid-disease model for simian acquired immune deficiency syndrome and SIV-encephalitis (SIVE). The objective was to evaluate how the diversity of the swarm influences the initial seeding of the infection that may potentially affect disease progression. Plasma, lymphoid and non-lymphoid (brain and lung) tissues were collected from two infected macaques euthanized at 21 days post-infection (p.i.), as well as longitudinal specimens and post-mortem tissues

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Handayani, Rissa Nurfitriana, and Djajasukma Tjahjadi. "OPTIMASI SUPPORT VECTOR MACHINE MENGGUNAKAN PARTICLE SWARM OPTIMIZATION UNTUK KLASIFIKASI MULTICLASS DATASET." Jurnal Responsif : Riset Sains dan Informatika 5, no. 1 (2023): 120–26. http://dx.doi.org/10.51977/jti.v5i1.1069.

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Data mining merupakan proses pengembangan model yang bertujuan untuk memahami pola dari hasil analisis data dan prediksi. Kumpulan data atau yang biasa disebut dataset terdiri dari atribut, data dan kelas. Salah satu permasalahan yang terdapat pada dataset yaitu multiclass dataset. Multiclass merupakan dataset yang memiliki kelas klasifikasi polynominal. Algoritma Support Vector Machine (SVM) banyak digunakan oleh peneliti untuk metode klasifikasi. SVM dipilih karena mampu menentukan hyperplane terpisah untuk memaksimalkan margin antara 2 kelas yang berbeda. Namum, SVM terdapat kekurangan pada

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Dr.K.Lenin. "ACTIVE POWER LOSS REDUCTION BY INNOVATIVE ALGORITHMS." GLOBAL JOURNAL OF ENGINEERING SCIENCE AND RESEARCHES 5, no. 8 (2018): 131–38. https://doi.org/10.5281/zenodo.1343476.

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This paper presents Attraction & Repulsion Particle Swarm Optimization (APSO), Random Virus Algorithm (RVA) for solving optimal Reactive Power Optimization problem. The modified model uses a diversity measure to have the algorithm alternate between exploring and exploiting behavior. In this work two phases are introduced i.e., attraction and <em>repulsion</em>. By measuring the diversity we let the swarm alternate between these phases. As long as the diversity is above a certain threshold <em>d<sub>low </sub></em>the particles attract each other. When the diversity declines below <em>d<sub

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Truong, Thanh Cong, Jan Plucar, Bao Quoc Diep, and Ivan Zelinka. "X-ware: a proof of concept malware utilizing artificial intelligence." International Journal of Electrical and Computer Engineering (IJECE) 12, no. 2 (2022): 1937. http://dx.doi.org/10.11591/ijece.v12i2.pp1937-1944.

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<p>Recent years have witnessed a dramatic growth in utilizing computational intelligence techniques for various domains. Coherently, malicious actors are expected to utilize these techniques against current security solutions. Despite the importance of these new potential threats, there remains a paucity of evidence on leveraging these research literature techniques. This article investigates the possibility of combining artificial neural networks and swarm intelligence to generate a new type of malware. We successfully created a proof of concept malware named X-ware, which we tested aga

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26

Hermanto, Hermanto, and Astrid Noviriandini. "ANALISA SENTIMEN TERHADAP BELAJAR ONLINE PADA MASA COVID-19 MENGGUNAKAN ALGORITMA SUPPORT VECTOR MACHINE BERBASIS PARTICLE SARM OPTIMIZATION." Jurnal Informatika Kaputama (JIK) 5, no. 1 (2021): 129–36. http://dx.doi.org/10.59697/jik.v5i1.311.

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Coronavirus 19 (COVID-19) merupakan infeksi virus menular yang saat ini sudah merambah ke berbagai negara salah satunya di Indoenesia. Pemantauan penyebaran COVID-19 di Indonesia ditangani langsung oleh Pemerintah Indonesia terutama. Pemerintah Indonesia langsung menindak lanjuti kasus tersebut. Salah satu tindakan pemerintah adalah melakukan Social Distancing selama 14 hari untuk meminimalisir penyebaran virus tersebut. Kegiatan pembelajaran online ini dilakukan untuk mengganti kegiatan pembelajaran secara langsung. Pembelajaran online memiliki beberapa kelemahan yakni penggunaan jaringan int

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Tang, Mingsheng, Xinjun Mao, and Zahia Guessoum. "Research on an Infectious Disease Transmission by Flocking Birds." Scientific World Journal 2013 (2013): 1–7. http://dx.doi.org/10.1155/2013/196823.

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The swarm intelligence is becoming a hot topic. The flocking of birds is a natural phenomenon, which is formed and organized without central or external controls for some benefits (e.g., reduction of energy consummation). However, the flocking also has some negative effects on the human, as the infectious disease H7N9 will easily be transmited from the denser flocking birds to the human. Zombie-city model has been proposed to help analyzing and modeling the flocking birds and the artificial society. This paper focuses on the H7N9 virus transmission in the flocking birds and from the flocking b

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Arzt, Jonathan, Ian Fish, Steven J. Pauszek, et al. "The evolution of a super-swarm of foot-and-mouth disease virus in cattle." PLOS ONE 14, no. 4 (2019): e0210847. http://dx.doi.org/10.1371/journal.pone.0210847.

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Jain, Mansi, Mitika Arora, Mukul Upadhyaya, and Rohit Aggarwal. "Social Distance detection using Deep Learning." International Journal for Research in Applied Science and Engineering Technology 10, no. 5 (2022): 1448–51. http://dx.doi.org/10.22214/ijraset.2022.42421.

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Abstract: Our research paper presented below is about social distance among people in public places by utilizing Deep learning technique on captured video by at public place Camera for detecting and controlling distance between them so that virus spread can be contained. This application is created to give alarms to individuals for keeping social separation in jam-packed areas. The real time video used to analysis objects by using object detection method and YOLOv3 calculation. We can figure out whether individuals are following social separating or not and in view of that we are alarming by m

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Bilal, Anas, Guangmin Sun, Sarah Mazhar, and Zhang Junjie. "Neuro-optimized numerical treatment of HIV infection model." International Journal of Biomathematics 14, no. 05 (2021): 2150033. http://dx.doi.org/10.1142/s1793524521500339.

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In this paper, a neuro-optimized numerical method is presented for approximation of HIV virus progression model in the human body. The model is composed of coupled nonlinear system of differential equations (DEs) containing healthy and infected T-Cells and HIV free virus particles. The coupled system is transformed into feedforward artificial neural network (ANN) with Mexican hat wavelet function in the hidden layers. Two meta-heuristic algorithms based on chaotic particle swarm optimization (CPSO) and its hybrid version with local search technique are exploited to tune the parameters of ANN i

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Reynolds, Matthew R., Andrea M. Weiler, Shari M. Piaskowski та ін. "Macaques Vaccinated with Simian Immunodeficiency Virus SIVmac239Δnef Delay Acquisition and Control Replication after Repeated Low-Dose Heterologous SIV Challenge". Journal of Virology 84, № 18 (2010): 9190–99. http://dx.doi.org/10.1128/jvi.00041-10.

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ABSTRACT An effective human immunodeficiency virus (HIV) vaccine will likely need to reduce mucosal transmission and, if infection occurs, control virus replication. To determine whether our best simian immunodeficiency virus (SIV) vaccine can achieve these lofty goals, we vaccinated eight Indian rhesus macaques with SIVmac239Δnef and challenged them intrarectally (i.r.) with repeated low doses of the pathogenic heterologous swarm isolate SIVsmE660. We detected a significant reduction in acquisition of SIVsmE660 in comparison to that for naïve controls (log rank test; P = 0.023). After 10 muc

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Alves, Beatriz S. G., Alice Bacon, Keri Langridge, et al. "Epidemiology of a Hybrid Swarm: Evidence of 11 Feline Infectious Agents Circulating in a Population of Sympatric European Wildcat Hybrids and Free-Living Domestic Cats, in Scotland." Transboundary and Emerging Diseases 2023 (October 5, 2023): 1–16. http://dx.doi.org/10.1155/2023/6692514.

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Hybridisation between wild and domestic species poses a serious challenge to conservation management and can, potentially, lead to extinction. Alongside it, disease transmission will inevitably occur. However, the link between these two phenomena has historically been neglected. In Scotland, the European wildcat is particularly threatened by hybridisation with the domestic cat, a process promoted by long-term habitat loss, human encroachment, and persecution. Between 2015 and 2019, free-living cats (n = 120) were captured in six conservation priority areas of northern Scotland. Samples were co

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Faulinda, Ely Nastiti, Musa Shahrulniza, and Yafi Eiad. "A hybrid deep learning optimization for predicting the spread of a new emerging infectious disease." IAES International Journal of Artificial Intelligence (IJ-AI) 13, no. 2 (2024): 2036–48. https://doi.org/10.11591/ijai.v13.i2.pp2036-2048.

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In this study, a novel approach geared toward predicting the estimated number of coronavirus disease (COVID-19) cases was developed. Combining long short-term memory (LSTM) neural networks with particle swarm optimization (PSO) along with grey wolf optimization (GWO) employ hybrid optimization algorithm techniques. This investigation utilizes COVID-19 original data from the Ministry of Health of Indonesia, period 2020-2021. The developed LSTM-PSO-GWO hybrid optimization algorithm can improve the performance and accuracy of predicting the spread of the COVID-19 virus in Indonesia. In initiating

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Lamers, Susanna L., David J. Nolan, Samantha L. Strickland, et al. "Longitudinal analysis of intra-host simian immunodeficiency virus recombination in varied tissues of the rhesus macaque model for neuroAIDS." Journal of General Virology 94, no. 11 (2013): 2469–79. http://dx.doi.org/10.1099/vir.0.055335-0.

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Human immunodeficiency virus intra-host recombination has never been studied in vivo both during early infection and throughout disease progression. The CD8-depleted rhesus macaque model of neuroAIDS was used to investigate the impact of recombination from early infection up to the onset of neuropathology in animals inoculated with a simian immunodeficiency virus (SIV) swarm. Several lymphoid and non-lymphoid tissues were collected longitudinally at 21 days post-infection (p.i.), 61 days p.i. and necropsy (75–118 days p.i.) from four macaques that developed SIV-encephalitis or meningitis, as w

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Setianingsih, Susi, Maria Ulfa Chasanah, Yogiek Indra Kurniawan, and Lasmedi Afuan. "IMPLEMENTATION OF PARTICLE SWARM OPTIMIZATION IN K-NEAREST NEIGHBOR ALGORITHM AS OPTIMIZATION HEPATITIS C CLASSIFICATION." Jurnal Teknik Informatika (Jutif) 4, no. 2 (2023): 457–65. http://dx.doi.org/10.52436/1.jutif.2023.4.2.980.

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Hepatitis has become a public health problem that is generally caused by infection with the hepatitis virus. One type of hepatitis caused by a virus is Hepatitis C. This disease can cause patients to experience inflammation of the liver. In the worst conditions, it can even lead to death. Initial predictions need to be made to increase the awareness of each individual against the threat of Hepatitis C by using the K-Nearest Neighbor method. K-Nearest Neighbor is a classification method that can give a pretty good percentage result in classifying, especially when using large training data. Howe

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Dittes, Julia, Marc O. Schäfer, Heike Aupperle-Lellbach, Christoph K. W. Mülling, and Ilka U. Emmerich. "Overt Infection with Chronic Bee Paralysis Virus (CBPV) in Two Honey Bee Colonies." Veterinary Sciences 7, no. 3 (2020): 142. http://dx.doi.org/10.3390/vetsci7030142.

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Chronic Bee Paralysis Virus (CBPV), a widespread honey bee RNA virus, causes massive worker bee losses, mostly in strong colonies. Two different syndromes, with paralysis, ataxia and flight incapacity on one hand and black hairless individuals with shortened abdomens on the other, can affect a colony simultaneously. This case report presents two Apis mellifera carnica colonies with symptoms of paralysis and hairless black syndrome in 2019. Via RT-PCR, a highly positive result for CBPV was detected in both samples. Further problems, such as a Nosema infection and Varroa infestation, were presen

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Shimelis, Ephrem, Shimels Tesfaye, and Fanos Tadesse. "Diagnostic Overview of Foot-And-Mouth Disease Viruse (FMDV)." South Asian Research Journal of Agriculture and Fisheries 5, no. 04 (2023): 36–44. http://dx.doi.org/10.36346/sarjaf.2023.v05i04.002.

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Foot-and-mouth disease (FMD) is one of the highly contagious diseases of domestic animals. Sensitive, speciﬁc, and quick detection of FMD virus antigens and antibodies is an essential corner stone diagnostic tool at each tier of control strategy. Continued development of molecular and genetic technologies combined with novel analytical techniques will benefit many areas of FMD research and understanding. Genome sequencing provides excellent insight into the evolutionary and epidemiological dynamics of such viruses. The advent of next generation sequencing (NGS) technologies enables evolutionar

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Sironen, Tarja, Eva R. Kallio, Antti Vaheri, Åke Lundkvist, and Alexander Plyusnin. "Quasispecies dynamics and fixation of a synonymous mutation in hantavirus transmission." Journal of General Virology 89, no. 5 (2008): 1309–13. http://dx.doi.org/10.1099/vir.0.83662-0.

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RNA-dependent RNA polymerases, the key enzymes in replication of RNA viruses, have a low fidelity; thus, these viruses replicate as a swarm of mutants termed viral quasispecies. Constant generation of new mutations allows RNA viruses to adapt swiftly to a novel environment through selection of both pre-existing and de novo-generated genetic variants. Here, quasispecies dynamics were studied in vivo in controlled hantavirus transmission from experimentally infected to naïve rodents through infested cage bedding. An elementary step of virus microevolution was apparent, as one synonymous mutation

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Moelling, Karin. "Within-Host and Between-Host Evolution in SARS-CoV-2—New Variant’s Source." Viruses 13, no. 5 (2021): 751. http://dx.doi.org/10.3390/v13050751.

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Some of the newly emerging corona viral variants show high numbers of mutations. This is unexpected for a virus with a low mutation rate due to an inherent proof-reading system. Could such a variant arise under very special conditions occurring in a host where the virus replicates and mutates in a rather unlimited fashion, such as in immune compromised patients? The virus was shown to replicate in an immunosuppressed cancer patient for more than 105 days and might be a source of new variants. These patients are asymptomatic and the virus may therefore escape detection and attention and be high

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Jridi, Chiraz, Jean-François Martin, Véronique Marie-Jeanne, Gérard Labonne, and Stéphane Blanc. "Distinct Viral Populations Differentiate and Evolve Independently in a Single Perennial Host Plant." Journal of Virology 80, no. 5 (2006): 2349–57. http://dx.doi.org/10.1128/jvi.80.5.2349-2357.2006.

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ABSTRACT The complex structure of virus populations has been the object of intensive study in bacteria, animals, and plants for over a decade. While it is clear that tremendous genetic diversity is rapidly generated during viral replication, the distribution of this diversity within a single host remains an obscure area in this field of science. Among animal viruses, only Human immunodeficiency virus and Hepatitis C virus populations have recently been thoroughly investigated at an intrahost level, where they are structured as metapopulations, demonstrating that the host cannot be considered s

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Musafir, Raqqasyi Rahmatullah, and Syaiful Anam. "PARAMETER ESTIMATION OF COVID-19 COMPARTMENT MODEL IN INDONESIA USING PARTICLE SWARM OPTIMIZATION." Jurnal Berkala Epidemiologi 10, no. 3 (2022): 283–92. http://dx.doi.org/10.20473/jbe.v10i32022.283-292.

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Background: The government established a vaccination program to deal with highly reactive COVID-19 cases in Indonesia. In obtaining accurate predictions of the dynamics of the compartment model of COVID-19 spread, a good parameter estimation technique was required.. Purpose: This research aims to apply Particle Swarm Optimization as a parameter estimation method to obtain parameters value from the Susceptible-Vaccinated-Infected-Recovered compartment model of COVID-19 cases. Methods: This research was conducted in April-May 2020 in Indonesia with exploratory design research. The researchers us

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Ciota, Alexander T., Evan M. Koch, Graham G. Willsey, et al. "Temporal and spatial alterations in mutant swarm size of St. Louis encephalitis virus in mosquito hosts." Infection, Genetics and Evolution 11, no. 2 (2011): 460–68. http://dx.doi.org/10.1016/j.meegid.2010.12.007.

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Yin, Lili, Xiaokang Du, Chao Ma, and Hengwen Gu. "Virtual Screening of Drug Proteins Based on the Prediction Classification Model of Imbalanced Data Mining." Processes 10, no. 7 (2022): 1420. http://dx.doi.org/10.3390/pr10071420.

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We propose a virtual screening method based on imbalanced data mining in this paper, which combines virtual screening techniques with imbalanced data classification methods to improve the traditional virtual screening process. First, in the actual virtual screening process, we apply k-means and smote heuristic oversampling method to deal with imbalanced data. Meanwhile, to enhance the accuracy of the virtual screening process, a particle swarm optimization algorithm is introduced to optimize the parameters of the support vector machine classifier, and the concept of ensemble learning is brough

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Purwaningsih, Esty. "Penerapan Particle Swarm Optimization pada Metode Neural Network untuk Perawatan Penyakit Kutil melalui Immunotherapy." Jurnal Sistem dan Teknologi Informasi (Justin) 8, no. 2 (2020): 207. http://dx.doi.org/10.26418/justin.v8i2.39869.

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Human papillomaviruses (HPVs) merupakan virus yang menimbulkan infeksi pada permukaan kulit dan dapt menyebabkan tumor sampai dengan kanker, salh satu penyakit yang disebabkan oleh HPVs adalah kutil. Immunotheraphy dapat dimanfaatkan untuk mengobati penyakit kutil. Sehingga penelitian ini melakukan penerapan metode neural network dengan algoritma PSO yang bertujuan untuk mengetahui nilai akurasi dari metode neural network dengan algoritma PSO yang berperan membantu menganalisis apakah peran immunotherapy lebih efektif dalam penyembuhan penyakit kutil dan kanker kulit. Setelah dilakukan penguji

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Larsen, L. E., K. Tjørnehøj, and B. Viuff. "Extensive Sequence Divergence among Bovine Respiratory Syncytial Viruses Isolated during Recurrent Outbreaks in Closed Herds." Journal of Clinical Microbiology 38, no. 11 (2000): 4222–27. http://dx.doi.org/10.1128/jcm.38.11.4222-4227.2000.

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The nucleotides coding for the extracellular part of the G glycoprotein and the full SH protein of bovine respiratory syncytial virus (BRSV) were sequenced from viruses isolated from numerous outbreaks of BRSV infection. The isolates included viruses isolated from the same herd (closed dairy farms and veal calf production units) in different years and from all confirmed outbreaks in Denmark within a short period. The results showed that identical viruses were isolated within a herd during outbreaks and that viruses from recurrent infections varied by up to 11% in sequence even in closed herds.

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Domingo, Esteban, and Celia Perales. "Viral Quasispecies and Lethal Mutagenesis." European Review 24, no. 1 (2016): 39–48. http://dx.doi.org/10.1017/s1062798715000411.

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Virology has undergone a profound transformation with the incorporation of quasispecies theory to the understanding of the composition and dynamics of viral populations as they cause disease. RNA viral populations do not consist of a genome class with a defined nucleotide sequence but of a cloud or swarm or related mutants due to high mutation rates (number of incorrect nucleotides introduced per nucleotide copied) during replication. DNA and RNA viruses whose multiplication is catalysed by a low fidelity polymerase replicate close to an error threshold for maintenance of their genetic informa

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O'Rourke, Sara M., Becky Schweighardt, Pham Phung, et al. "Mutation at a Single Position in the V2 Domain of the HIV-1 Envelope Protein Confers Neutralization Sensitivity to a Highly Neutralization-Resistant Virus." Journal of Virology 84, no. 21 (2010): 11200–11209. http://dx.doi.org/10.1128/jvi.00790-10.

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ABSTRACT Understanding the determinants of neutralization sensitivity and resistance is important for the development of an effective human immunodeficiency virus type 1 (HIV-1) vaccine. In these studies, we have made use of the swarm of closely related envelope protein variants (quasispecies) from an extremely neutralization-resistant clinical isolate in order to identify mutations that conferred neutralization sensitivity to antibodies in sera from HIV-1-infected individuals. Here, we describe a virus with a rare mutation at position 179 in the V2 domain of gp120, where replacement of aspart

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Yi, Yanjie, Anjali Singh, Farida Shaheen, Andrew Louden, ChuHee Lee, and Ronald G. Collman. "Contrasting Use of CCR5 Structural Determinants by R5 and R5X4 Variants within a Human Immunodeficiency Virus Type 1 Primary Isolate Quasispecies." Journal of Virology 77, no. 22 (2003): 12057–66. http://dx.doi.org/10.1128/jvi.77.22.12057-12066.2003.

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ABSTRACT Macrophagetropic R5 human immunodeficiency virus type 1 (HIV-1) isolates often evolve into dualtropic R5X4 variants during disease progression. The structural basis for CCR5 coreceptor function has been studied in a limited number of prototype strains and suggests that R5 and R5X4 Envs interact differently with CCR5. However, differences between unrelated viruses may reflect strain-specific factors and do not necessarily represent changes resulting from R5 to R5X4 evolution of a virus in vivo. Here we addressed CCR5 domains involved in fusion for a large set of closely related yet fun

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Ciota, Alexander T., Dylan J. Ehrbar, Greta A. Van Slyke, et al. "Quantification of intrahost bottlenecks of West Nile virus in Culex pipiens mosquitoes using an artificial mutant swarm." Infection, Genetics and Evolution 12, no. 3 (2012): 557–64. http://dx.doi.org/10.1016/j.meegid.2012.01.022.

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Immonen, Taina T., Celine Camus, Carolyn Reid, et al. "Genetically barcoded SIV reveals the emergence of escape mutations in multiple viral lineages during immune escape." Proceedings of the National Academy of Sciences 117, no. 1 (2019): 494–502. http://dx.doi.org/10.1073/pnas.1914967117.

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The rapidity of replication coupled with a high mutation rate enables HIV to evade selective pressures imposed by host immune responses. Investigating the ability of HIV to escape different selection forces has generally relied on population-level measures, such as the time to detectable escape mutations in plasma and the rate these mutations subsequently take over the virus population. Here we employed a barcoded synthetic swarm of simian immunodeficiency virus (SIV) in rhesus macaques to investigate the generation and selection of escape mutations within individual viral lineages at the Mamu

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