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2. Breaking Free with AI: The Deconfinement Transition

Author

Ermann, Christian, Baker, Stephen, and Anber, Mohamed M.

Subjects
High Energy Physics - Theory, Condensed Matter - Disordered Systems and Neural Networks, High Energy Physics - Lattice
Abstract

Employing supervised machine learning techniques, we investigate the deconfinement phase transition within $4$-dimensional $SU(2)$ Yang-Mills (YM) theory, compactified on a small circle and endowed with center-stabilizing potential. This exploration encompasses scenarios both without and with matter in either the fundamental or adjoint representations. Central to our study is a profound duality relationship, intricately mapping the YM theory onto an XY-spin model with $\mathbb Z_p$-preserving perturbations. The parameter $p$ embodies the essence of the matter representation, with values of $p=1$ and $p=4$ for fundamental and adjoint representations, respectively, while $p=2$ corresponds to pure YM theory. The logistic regression method struggles to produce satisfactory results, particularly in predicting the transition temperature. Contrarily, convolutional neural networks (CNNs) exhibit remarkable prowess, effectively foreseeing critical temperatures in cases where $p=2$ and $p=4$. Furthermore, by harnessing CNNs, we compute critical exponents at the transition, aligning favorably with computations grounded in conventional order parameters. Taking our investigation a step further, we use CNNs to lend meaning to phases within YM theory with fundamental matter. Notably, this theory lacks conventional order parameters. Interestingly, CNNs manage to predict a transition temperature in this context. However, the fragility of this prediction under variations in the boundaries of the training window undermines its utility as a robust order parameter. This outcome underscores the constraints inherent in employing supervised machine learning techniques as innovative substitutes for traditional order parameters., Comment: 12 pages, 8 figures

Published
2023

7. CONTRIBUTORS

Author

Abahuje, Egide, primary, Abrahim, Orit, additional, Adetifa, Ifedayo M.O., additional, Ajjampur, Sitara S.R., additional, Alexander, Suceena, additional, PhD, Chiara Altare,, additional, Alves, Fabiana, additional, Andrianaivoarimanana, Voahangy, additional, Angelakis, Emmanouil, additional, Aronson, Jeffrey K., additional, Atukorala, Inoshi G., additional, Baily, Guy, additional, Baker, Stephen, additional, Barrett, Alan D.T., additional, Basnyat, Buddha, additional, Bastawrous, Andrew, additional, Bates, Imelda, additional, Bausch, Daniel G., additional, Baxter, Cheryl, additional, Beare, Nicholas A.V., additional, Beeching, Nick J., additional, Bekker, Linda-Gail, additional, Berlin, Anita, additional, FRS, Zulfiqar A. Bhutta, additional, Bloom, David E., additional, Blumberg, Lucille, additional, Boelaert, Marleen, additional, Brett-Major, David, additional, Brooker, Simon J., additional, Brouwer, Matthijs C., additional, Brunetti, Enrico, additional, Bull, Susan, additional, Bundy, Donald A.P., additional, Burri, Christian, additional, Bustinduy, Amaya L., additional, Caillet, Céline, additional, Chai, Jong Yil, additional, Chang, Thashi, additional, Chappuis, François, additional, Chibi, Buyisile, additional, Chiodini, Peter L., additional, Chowdhury, Rajiv, additional, Chowdhury, Sudipta Dhar, additional, Clemens, John D., additional, Cooke, Graham S., additional, Cotton, Mark F., additional, Currie, Bart J., additional, Cusack, Tomas-Paul, additional, Dance, David A.B., additional, Davis, Emily H., additional, Day, Nicholas P.J., additional, Deen, Jacqueline, additional, Dondorp, Arjen M., additional, Dünser, Martin W., additional, Eitzen, Edward, additional, Chebib, Hassan El, additional, Enria, Delia, additional, Faust, Christina, additional, Fekadu, Abebaw, additional, Fink, Günther, additional, Fischer, Peter U., additional, Fletcher, Tom, additional, Franco-Paredes, Carlos, additional, French, Neil, additional, Frumkin, Howard, additional, Garcia, Hector H., additional, Gerada, Alessandro, additional, Glass, Roger I., additional, Gordon, Stephen B., additional, Gottstein, Bruno, additional, Goyal, Alpesh, additional, Grey, Jonathan, additional, Gupta, Yashdeep, additional, Haines, Andy, additional, Hampson, Katie, additional, Hanlon, Charlotte, additional, Harrison, Mark, additional, Haswell, Melissa R., additional, Hawkesworth, Sophie, additional, Hay, Roderick J., additional, Heckmann, Jeannine M., additional, Heimesaat, Markus M., additional, Henao-Martínez, Andrés F., additional, Hien, Tran Tinh, additional, Hoerauf, Achim, additional, Irfan, Omar, additional, PhD, Euzebiusz Jamrozik, additional, Jobe, Modou, additional, John, George T., additional, Jones, Nick K., additional, Jones, Malcolm K., additional, Junghanss, Thomas, additional, Kaewkes, Sasithorn, additional, Karim, Quarraisha Abdool, additional, Keiser, Jennifer, additional, Kelly, Paul, additional, Khan, Amira M., additional, King, Charles H., additional, Kishore, Sandeep P., additional, Lang, Trudie, additional, Le, Thuy, additional, Liesenfeld, Oliver, additional, Lockwood, Diana N.J., additional, Mabey, David C.W., additional, Madkour, M. Monir, additional, Manesh, Abi, additional, Masekela, Refiloe, additional, Mäser, Pascal, additional, Mayaud, Philippe, additional, Mbanya, Dora, additional, McCarthy, James S., additional, McCartney, Daniel J., additional, McGready, Rose, additional, McKee, Martin, additional, Mc, Namara, Paul S., additional, Meara, John G., additional, Meintjes, Graeme, additional, Merson, Laura, additional, Mola, Glen, additional, Morassutti, Alessandra L., additional, Morris-Jones, Rachael, additional, Mortimer, Kevin J., additional, Muliyil, Divya Elizabeth, additional, Mumcuoglu, Kosta Y., additional, Munoz, Flor M., additional, Murphy, Adrianna, additional, Mutabingwa, Theonest, additional, Nawa, Yukifumi, additional, Newton, Paul N., additional, Nightingale, Sam, additional, Nokes, D. James, additional, Nosten, François H., additional, O’Hea, Jennifer, additional, Olliaro, Piero, additional, Ong, Jason J., additional, Oommen, Anu Mary, additional, Parashar, Umesh D., additional, Paris, Daniel H., additional, Parker, Michael, additional, Pluschke, Gerd, additional, Preidis, Geoffrey A., additional, Prentice, Andrew M., additional, Quail, Geoffrey, additional, Quinn, Thomas C., additional, Rabie, Helena, additional, Rajashekharaiah, Harsha, additional, Rajerison, Minoarisoa, additional, Ranganathan, Kannan, additional, Raoult, Didier, additional, Rassi,, Anis, additional, Ravi, Vasanthapuram, additional, Reddy, K. Srinath, additional, Rees, Claire, additional, Reynolds, Steven J., additional, Richter, Joachim, additional, Rijken, Marcus J., additional, Riviello, Robert, additional, Robinson, Janet, additional, Salazar, Juan C., additional, Schultz, Marcus J., additional, Schwarz, Dan, additional, Sendagire, Ibrahim, additional, Sharma, Savitri, additional, Shawon, Shajedur Rahman, additional, Singh, Bhagteshwar, additional, Sithithaworn, Paiboon, additional, Siwila, Joyce, additional, Solomon, Tom, additional, Spiegel, Paul, additional, Sridhar, Devi, additional, Sripa, Banchob, additional, Srour, M. Leila, additional, Stojković, Marija, additional, Strader, Christopher, additional, Suárez, Jose A., additional, Sundar, Shyam, additional, Tamarozzi, Francesca, additional, Tandon, Nikhil, additional, Tate, Jacqueline E., additional, Thachil, Jecko, additional, Thomson, Madeleine C., additional, Thwaites, Guy, additional, Thwaites, C. Louise, additional, van Daalen, Kim R., additional, Beek, Diederik van de, additional, van Doorn, H. Rogier, additional, Vega-Lopez, Francisco, additional, von Seidlein, MD, PhD, Lorenz, additional, Wakeham, Katie, additional, Walker, Stephen L., additional, Wallace, Ryan M., additional, Ward, Honorine, additional, Warrell, David A., additional, Weber, Tim Frederik, additional, Weil, Gary J., additional, White, Nicholas J., additional, White, MB Ch, B, Graham B., additional, Wong, Vanessa, additional, Wood, Robin, additional, Wood, Georgina, additional, Wyllie, Sarah, additional, Yacoub, Sophie, additional, Yen, Lam Minh, additional, Young, Paul R., additional, and Zafren, Ken, additional

Published
2024
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15. The rapid detection of respiratory pathogens in critically ill children

Author

Clark, John A., Conway Morris, Andrew, Curran, Martin D., White, Deborah, Daubney, Esther, Kean, Iain R. L., Navapurkar, Vilas, Bartholdson Scott, Josefin, Maes, Mailis, Bousfield, Rachel, Török, M. Estée, Inwald, David, Zhang, Zhenguang, Agrawal, Shruti, Kanaris, Constantinos, Khokhar, Fahad, Gouliouris, Theodore, Baker, Stephen, and Pathan, Nazima

Published
2023
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18. Incidence of typhoid fever in Burkina Faso, Democratic Republic of the Congo, Ethiopia, Ghana, Madagascar, and Nigeria (the Severe Typhoid in Africa programme): a population-based study

Author

Marks, Florian, Im, Justin, Park, Se Eun, Pak, Gi Deok, Jeon, Hyon Jin, Wandji Nana, Lady Rosny, Phoba, Marie-France, Mbuyi-Kalonji, Lisette, Mogeni, Ondari D, Yeshitela, Biruk, Panzner, Ursula, Cruz Espinoza, Ligia María, Beyene, Tigist, Owusu-Ansah, Michael, Twumasi-Ankrah, Sampson, Yeshambaw, Melese, Alemu, Ashenafi, Adewusi, Oluwafemi J, Adekanmbi, Olukemi, Higginson, Ellen, Adepoju, Akinlolu, Agbi, Sarah, Cakpo, Enoch G, Ogunleye, Veronica O, Tunda, Gaëlle Nkoji, Ikhimiukor, Odion O, Mbuyamba, Jules, Toy, Trevor, Agyapong, Francis Opoku, Osei, Isaac, Amuasi, John, Razafindrabe, Tsiriniaina Jean Luco, Raminosoa, Tiana Mirana, Nyirenda, Gabriel, Randriamampionona, Njariharinjakampionona, Seo, Hyeong Won, Seo, Hyejin, Siribie, Mohamadou, Carey, Megan E, Owusu, Michael, Meyer, Christian G, Rakotozandrindrainy, Ndrainaharimira, Sarpong, Nimarko, Razafindrakalia, Mathilde, Razafimanantsoa, Ravomialisoa, Ouedraogo, Moussa, Kim, Yeonseon J, Lee, Jooah, Zellweger, Raphaël M, Kang, Sophie S Y, Park, Ju Yeon, Crump, John A, Hardy, Liselotte, Jacobs, Jan, Garrett, Denise O, Andrews, Jason R, Poudyal, Nimesh, Kim, Deok Ryun, Clemens, John D, Baker, Stephen G, Kim, Jerome H, Dougan, Gordon, Sugimoto, Jonathan D, Van Puyvelde, Sandra, Kehinde, Aderemi, Popoola, Oluwafemi A, Mogasale, Vittal, Breiman, Robert F, MacWright, William R, Aseffa, Abraham, Tadesse, Birkneh Tilahun, Haselbeck, Andrea, Adu-Sarkodie, Yaw, Teferi, Mekonnen, Bassiahi, Abdramane Soura, Okeke, Iruka N, Lunguya-Metila, Octavie, Owusu-Dabo, Ellis, and Rakotozandrindrainy, Raphaël

Published
2024
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19. A Deep Learning Approach to Segment High-Content Images of the E. coli Bacteria

Author

Duong, Dat Q., Tran, Tuan-Anh, Kieu, Phuong Nhi Nguyen, Nguyen, Tien K., Le, Bao, Baker, Stephen, Nguyen, Binh T., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Blanc-Talon, Jaques, editor, Delmas, Patrice, editor, Philips, Wilfried, editor, and Scheunders, Paul, editor

Published
2023
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20. Iraq: Washington prepares for another war

Author

Baker, Stephen H., RADM, Ret and Donovan, Michael

Subjects
IRAQ - Foreign Relations - United States, UNITED STATES - Foreign Relations - Iraq, CHEMICAL BIOLOGICAL WEAPONS - Iraq
Published
2002

21. FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2

Author

Brevini, Teresa, Maes, Mailis, Webb, Gwilym J., John, Binu V., Fuchs, Claudia D., Buescher, Gustav, Wang, Lu, Griffiths, Chelsea, Brown, Marnie L., Scott, III, William E., Pereyra-Gerber, Pehuén, Gelson, William T. H., Brown, Stephanie, Dillon, Scott, Muraro, Daniele, Sharp, Jo, Neary, Megan, Box, Helen, Tatham, Lee, Stewart, James, Curley, Paul, Pertinez, Henry, Forrest, Sally, Mlcochova, Petra, Varankar, Sagar S., Darvish-Damavandi, Mahnaz, Mulcahy, Victoria L., Kuc, Rhoda E., Williams, Thomas L., Heslop, James A., Rossetti, Davide, Tysoe, Olivia C., Galanakis, Vasileios, Vila-Gonzalez, Marta, Crozier, Thomas W. M., Bargehr, Johannes, Sinha, Sanjay, Upponi, Sara S., Fear, Corrina, Swift, Lisa, Saeb-Parsy, Kourosh, Davies, Susan E., Wester, Axel, Hagström, Hannes, Melum, Espen, Clements, Darran, Humphreys, Peter, Herriott, Jo, Kijak, Edyta, Cox, Helen, Bramwell, Chloe, Valentijn, Anthony, Illingworth, Christopher J. R., Dahman, Bassam, Bastaich, Dustin R., Ferreira, Raphaella D., Marjot, Thomas, Barnes, Eleanor, Moon, Andrew M., Barritt, IV, Alfred S., Gupta, Ravindra K., Baker, Stephen, Davenport, Anthony P., Corbett, Gareth, Gorgoulis, Vassilis G., Buczacki, Simon J. A., Lee, Joo-Hyeon, Matheson, Nicholas J., Trauner, Michael, Fisher, Andrew J., Gibbs, Paul, Butler, Andrew J., Watson, Christopher J. E., Mells, George F., Dougan, Gordon, Owen, Andrew, Lohse, Ansgar W., Vallier, Ludovic, and Sampaziotis, Fotios

Published
2023
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24. Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study

Author

Banda, Happy C, Biswas, Prasanta K, Bhuiyan, Md A I, Blohmke, Christoph, Darton, Thomas C, Dolecek, Christiane, Dongol, Sabina, Mujadidi, Yama F, Hill, Jennifer, Hoang, Nhu T, Jere, Tikhala M, Mbewe, Maurice, Msuku, Harrison, Nga, Tran V T, Nkhata, Rose, Rahman, Sadia IA, Rahman, Nazia, Saad, Neil J, Tan, Trinh V, Thindwa, Deus, Voysey, Merryn, Wachepa, Richard, Dyson, Zoe A, Ashton, Philip M, Khanam, Farhana, Chunga Chirambo, Angeziwa, Shakya, Mila, Meiring, James E, Tonks, Susan, Karkey, Abhilasha, Msefula, Chisomo, Clemens, John D, Dunstan, Sarah J, Baker, Stephen, Dougan, Gordon, Pitzer, Virginia E, Basnyat, Buddha, Qadri, Firdausi, Heyderman, Robert S, Gordon, Melita A, Pollard, Andrew J, and Holt, Kathryn E

Published
2024
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26. Natural inflation, strong dynamics, and the role of generalized anomalies

Author

Anber, Mohamed M. and Baker, Stephen

Subjects
High Energy Physics - Theory, Astrophysics - Cosmology and Nongalactic Astrophysics, High Energy Physics - Phenomenology
Abstract

We revisit models of natural inflation and show that the single-field effective theory described by the potential $V(a)\sim \cos\frac{a}{f}$ breaks down as the inflaton $a$ makes large-field excursions, even for values of $f$ smaller than the Planck scale. In order to remedy the problem, we modify the potential in order to account for the heavy degrees of freedom (hadrons) that become intertwined with the light inflaton as the latter rolls down its potential. By embedding the low energy degrees of freedom into an ultraviolet complete gauge theory, we argue that the intertwining between the two scales can be explained as the result of a generalized mixed 't Hooft anomaly between the discrete chiral symmetry and background fractional fluxes in the baryon number, color, and flavor directions. Further, we study the multi-field inflation and show that it entertains rich dynamics. Inflating near the hilltop excites the hadrons and spoils the slow-roll parameters, in contradistinction with the expectations in the single-field inflation. Nevertheless, we identify a safe zone where inflation can proceed successfully. We determine the conditions under which the Universe inflates by at least $60$ e-foldings and inflation leads to a power spectrum and tensor to scalar ratio that are consistent with the Cosmic Microwave Background data., Comment: 15 pages, comments added, references added, matches the published version

Published
2020
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27. Aetiology and Potential Animal Exposure in Central Nervous System Infections in Vietnam

Author

Brindle, Hannah E., Nadjm, Behzad, Choisy, Marc, Christley, Rob, Griffiths, Michael, Baker, Stephen, Bryant, Juliet E., Campbell, James I., Nguyen, Van Vinh Chau, Nguyen, Thi Ngoc Diep, Vu, Ty Thi Hang, Nguyen, Van Hung, Hoang, Bao Long, Le, Xuan Luat, Pham, Ha My, Ta, Thi Dieu Ngan, Ho, Dang Trung Nghia, Tran, Thua Nguyen, Nguyen, Thi Han Ny, Tran, My Phuc, Pham, Thi Hong Phuong, Le, Van Tan, Nguyen, Dac Thuan, Hau, Thi Thu Trang, Nguyen, Ngoc Vinh, Wertheim, Heiman F. L., Thwaites, Guy E., and van Doorn, H. Rogier

Published
2022
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28. SARS-CoV-2 evolution during treatment of chronic infection

Author

Baker, Stephen, Dougan, Gordon, Hess, Christoph, Kingston, Nathalie, Lehner, Paul J, Lyons, Paul A, Matheson, Nicholas J, Owehand, Willem H, Saunders, Caroline, Summers, Charlotte, Thaventhiran, James ED, Toshner, Mark, Weekes, Michael P, Bucke, Ashlea, Calder, Jo, Canna, Laura, Domingo, Jason, Elmer, Anne, Fuller, Stewart, Harris, Julie, Hewitt, Sarah, Kennet, Jane, Jose, Sherly, Kourampa, Jenny, Meadows, Anne, O’Brien, Criona, Price, Jane, Publico, Cherry, Rastall, Rebecca, Ribeiro, Carla, Rowlands, Jane, Ruffolo, Valentina, Tordesillas, Hugo, Bullman, Ben, Dunmore, Benjamin J, Fawke, Stuart, Gräf, Stefan, Hodgson, Josh, Huang, Christopher, Hunter, Kelvin, Jones, Emma, Legchenko, Ekaterina, Matara, Cecilia, Martin, Jennifer, Mescia, Federica, O’Donnell, Ciara, Pointon, Linda, Pond, Nicole, Shih, Joy, Sutcliffe, Rachel, Tilly, Tobias, Treacy, Carmen, Tong, Zhen, Wood, Jennifer, Wylot, Marta, Bergamaschi, Laura, Betancourt, Ariana, Bower, Georgie, Cossetti, Chiara, De Sa, Aloka, Epping, Madeline, Gleadall, Nick, Grenfell, Richard, Hinch, Andrew, Huhn, Oisin, Jackson, Sarah, Jarvis, Isobel, Lewis, Daniel, Marsden, Joe, Nice, Francesca, Okecha, Georgina, Omarjee, Ommar, Perera, Marianne, Richoz, Nathan, Romashova, Veronika, Yarkoni, Natalia Savinykh, Sharma, Rahul, Stefanucci, Luca, Stephens, Jonathan, Strezlecki, Mateusz, Turner, Lori, De Bie, Eckart MDD, Bunclark, Katherine, Josipovic, Masa, Mackay, Michael, Rossi, Sabrina, Selvan, Mayurun, Spencer, Sarah, Yong, Cissy, Ansaripour, Ali, Michael, Alice, Mwaura, Lucy, Patterson, Caroline, Polwarth, Gary, Polgarova, Petra, di Stefano, Giovanni, Fahey, Codie, Michel, Rachel, and Bong, Sze-How

Subjects
Immunization, Pneumonia & Influenza, Lung, Prevention, Genetics, Vaccine Related, Biotechnology, Pneumonia, Emerging Infectious Diseases, Biodefense, Infectious Diseases, 2.1 Biological and endogenous factors, Aetiology, Infection, Good Health and Well Being, Adenosine Monophosphate, Aged, Alanine, Antibodies, Neutralizing, Antibodies, Viral, COVID-19, Chronic Disease, Evolution, Molecular, Genome, Viral, High-Throughput Nucleotide Sequencing, Humans, Immune Evasion, Immune Tolerance, Immunization, Passive, Immunosuppression Therapy, Male, Mutagenesis, Mutant Proteins, Mutation, Phylogeny, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Time Factors, Viral Load, Virus Shedding, COVID-19 Drug Treatment, COVID-19 Serotherapy, CITIID-NIHR BioResource COVID-19 Collaboration, COVID-19 Genomics UK (COG-UK) Consortium, General Science & Technology
Abstract

The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for virus infection through the engagement of the human ACE2 protein1 and is a major antibody target. Here we show that chronic infection with SARS-CoV-2 leads to viral evolution and reduced sensitivity to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma, by generating whole-genome ultra-deep sequences for 23 time points that span 101 days and using in vitro techniques to characterize the mutations revealed by sequencing. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (ΔH69/ΔV70) in the S1 N-terminal domain of the spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype were reduced in frequency, before returning during a final, unsuccessful course of convalescent plasma treatment. In vitro, the spike double mutant bearing both ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. The spike deletion mutant ΔH69/ΔV70 had a twofold higher level of infectivity than wild-type SARS-CoV-2, possibly compensating for the reduced infectivity of the D796H mutation. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals.

Published
2021

29. Victory at an unknown cost

Author

Baker, Stephen H., RADM

Subjects
WEAPONS OF MASS DESTRUCTION, CHEMICAL BIOLOGICAL WEAPONS - Iraq, URBAN WARFARE, IRAQ - Politics and Government, WAR - Political Aspects
Published
2002

31. The frequency and associated factors of typhoid carriage in patients undergoing cholecystectomy for gallbladder disease in Pakistan: A cross-sectional study

Author

Qureshi, Sonia, primary, Maria, Noshi, additional, Chawla, Tabish, additional, Iqbal, Junaid, additional, Kazi, Abdul Momin, additional, Adnan, Mehreen, additional, Hotwani, Aneeta, additional, Rahman, Najeeb, additional, Sadiq, Muhammed Wahhaab, additional, Charles, Richelle, additional, Baker, Stephen, additional, and Qamar, Farah Naz, additional

Published
2024
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34. D28. Are Drains Protective in Greater Resection Weights? A Retrospective Cohort Study of 1,098 Reduction Mammoplasties Using the Superomedial Pedicle Wise-pattern Technique

Author

Lava, Christian X., primary, Huffman, Samuel S., additional, Li, Karen R., additional, Snee, Isabel A, additional, Bell, Alice C., additional, Bekeny, Jenna C., additional, Parikh, Rajiv P., additional, Jabbour, Samer F., additional, Tom, Laura K., additional, Baker, Stephen B., additional, and Fan, Kenneth L., additional

Published
2024
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35. The identification of novel immunogenic antigens as potential Shigella vaccine components.

Author

de Alwis, Ruklanthi, Liang, Li, Taghavian, Omid, Werner, Emma, The, Hao, Thu, Trang, Duong, Vu, Davies, D, Felgner, Philip, and Baker, Stephen

Subjects
Antibody Formation, Antigens, Bacterial, Bacterial Proteins, Computational Biology, Dysentery, Bacillary, Fetal Blood, Genome, Human, Humans, Immunization, Immunoglobulin G, Seroconversion, Shigella Vaccines
Abstract

BACKGROUND: Shigella is a major diarrheal pathogen for which there is presently no vaccine. Whole genome sequencing provides the ability to predict and derive novel antigens for use as vaccines. Here, we aimed to identify novel immunogenic Shigella antigens that could serve as Shigella vaccine candidates, either alone, or when conjugated to Shigella O-antigen. METHODS: Using a reverse vaccinology approach, where genomic analysis informed the Shigella immunome via an antigen microarray, we aimed to identify novel immunogenic Shigella antigens. A core genome analysis of Shigella species, pathogenic and non-pathogenic Escherichia coli, led to the selection of 234 predicted immunogenic Shigella antigens. These antigens were expressed and probed with acute and convalescent serum from microbiologically confirmed Shigella infections. RESULTS: Several Shigella antigens displayed IgG and IgA seroconversion, with no difference in sero-reactivity across by sex or age. IgG sero-reactivity to key Shigella antigens was observed at birth, indicating transplacental antibody transfer. Six antigens (FepA, EmrK, FhuA, MdtA, NlpB, and CjrA) were identified in in vivo testing as capable of producing binding IgG and complement-mediated bactericidal antibody. CONCLUSIONS: These findings provide six novel immunogenic Shigella proteins that could serve as candidate vaccine antigens, species-specific carrier proteins, or targeted adjuvants.

Published
2021

38. Correction: Aetiology and Potential Animal Exposure in Central Nervous System Infections in Vietnam

Author

Brindle, Hannah E., Nadjm, Behzad, Choisy, Marc, Christley, Rob, Griffiths, Michael, Baker, Stephen, Bryant, Juliet E., Campbell, James I., Nguyen, Van Vinh Chau, Nguyen, Thi Ngoc Diep, Vu, Ty Thi Hang, Nguyen, Van Hung, Hoang, Bao Long, Le, Xuan Luat, Pham, Ha My, Ta, Thi Dieu Ngan, Ho, Dang Trung Nghia, Tran, Thua Nguyen, Nguyen, Thi Han Ny, Tran, My Phuc, Pham, Thi Hong Phuong, Le, Van Tan, Nguyen, Dac Thuan, Hau, Thi Thu Trang, Nguyen, Ngoc Vinh, Wertheim, Heiman F. L., Thwaites, Guy E., and van Doorn, H. Rogier

Published
2022
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39. The Surveillance for Enteric Fever in Asia Project (SEAP), Severe Typhoid Fever Surveillance in Africa (SETA), Surveillance of Enteric Fever in India (SEFI), and Strategic Typhoid Alliance Across Africa and Asia (STRATAA) Population-based Enteric Fever Studies: A Review of Methodological Similarities and Differences

Author

Carey, Megan E, MacWright, William R, Im, Justin, Meiring, James E, Gibani, Malick M, Park, Se Eun, Longley, Ashley, Jeon, Hyon Jin, Hemlock, Caitlin, Yu, Alexander T, Soura, Abdramane, Aiemjoy, Kristen, Owusu-Dabo, Ellis, Terferi, Mekonnen, Islam, Sahidul, Lunguya, Octavie, Jacobs, Jan, Gordon, Melita, Dolecek, Christiane, Baker, Stephen, Pitzer, Virginia E, Yousafzai, Mohammad Tahir, Tonks, Susan, Clemens, John D, Date, Kashmira, Qadri, Firdausi, Heyderman, Robert S, Saha, Samir K, Basnyat, Buddha, Okeke, Iruka N, Qamar, Farah N, Voysey, Merryn, Luby, Stephen, Kang, Gagandeep, Andrews, Jason, Pollard, Andrew J, John, Jacob, Garrett, Denise, and Marks, Florian

Subjects
Infectious Diseases, Vaccine Related, Digestive Diseases, Immunization, Clinical Research, Rare Diseases, Emerging Infectious Diseases, Biodefense, Prevention, Foodborne Illness, Prevention of disease and conditions, and promotion of well-being, 3.4 Vaccines, Aetiology, 2.4 Surveillance and distribution, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being, Clean Water and Sanitation, Africa South of the Sahara, Asia, Humans, India, Salmonella typhi, Typhoid Fever, Typhoid-Paratyphoid Vaccines, blood culture, enteric fever surveillance, Salmonella Typhi, typhoid fever, Salmonella Typhi, Biological Sciences, Medical and Health Sciences, Microbiology
Abstract

Building on previous multicountry surveillance studies of typhoid and others salmonelloses such as the Diseases of the Most Impoverished program and the Typhoid Surveillance in Africa Project, several ongoing blood culture surveillance studies are generating important data about incidence, severity, transmission, and clinical features of invasive Salmonella infections in sub-Saharan Africa and South Asia. These studies are also characterizing drug resistance patterns in their respective study sites. Each study answers a different set of research questions and employs slightly different methodologies, and the geographies under surveillance differ in size, population density, physician practices, access to healthcare facilities, and access to microbiologically safe water and improved sanitation. These differences in part reflect the heterogeneity of the epidemiology of invasive salmonellosis globally, and thus enable generation of data that are useful to policymakers in decision-making for the introduction of typhoid conjugate vaccines (TCVs). Moreover, each study is evaluating the large-scale deployment of TCVs, and may ultimately be used to assess post-introduction vaccine impact. The data generated by these studies will also be used to refine global disease burden estimates. It is important to ensure that lessons learned from these studies not only inform vaccination policy, but also are incorporated into sustainable, low-cost, integrated vaccine-preventable disease surveillance systems.

Published
2020

40. Environmental Surveillance as a Tool for Identifying High-risk Settings for Typhoid Transmission

Author

Andrews, Jason R, Yu, Alexander T, Saha, Senjuti, Shakya, Jivan, Aiemjoy, Kristen, Horng, Lily, Qamar, Farah, Garrett, Denise, Baker, Stephen, Saha, Samir, and Luby, Stephen P

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, Prevention, Vaccine Related, Emerging Infectious Diseases, Foodborne Illness, Biodefense, Infectious Diseases, Rare Diseases, Digestive Diseases, 2.2 Factors relating to the physical environment, Aetiology, Infection, Good Health and Well Being, Clean Water and Sanitation, Environmental Monitoring, Humans, Salmonella paratyphi A, Salmonella typhi, Typhoid Fever, Typhoid-Paratyphoid Vaccines, typhoid, enteric fever, Salmonella, water, environment, Salmonella, Biological Sciences, Medical and Health Sciences, Microbiology, Clinical sciences
Abstract

Enteric fever remains a major cause of morbidity in developing countries with poor sanitation conditions that enable fecal contamination of water distribution systems. Historical evidence has shown that contamination of water systems used for household consumption or agriculture are key transmission routes for Salmonella Typhi and Salmonella Paratyphi A. The World Health Organization now recommends that typhoid conjugate vaccines (TCV) be used in settings with high typhoid incidence; consequently, governments face a challenge regarding how to prioritize typhoid against other emerging diseases. A key issue is the lack of typhoid burden data in many low- and middle-income countries where TCV could be deployed. Here we present an argument for utilizing environmental sampling for the surveillance of enteric fever organisms to provide data on community-level typhoid risk. Such an approach could complement traditional blood culture-based surveillance or even replace it in settings where population-based clinical surveillance is not feasible. We review historical studies characterizing the transmission of enteric fever organisms through sewage and water, discuss recent advances in the molecular detection of typhoidal Salmonella in the environment, and outline challenges and knowledge gaps that need to be addressed to establish environmental sampling as a tool for generating actionable data that can inform public health responses to enteric fever.

Published
2020

44. Global, regional, and national incidence and mortality burden of non-COVID-19 lower respiratory infections and aetiologies, 1990–2021: a systematic analysis from the Global Burden of Disease Study 2021

Author

Bender, Rose Grace, primary, Sirota, Sarah Brooke, additional, Swetschinski, Lucien R, additional, Dominguez, Regina-Mae Villanueva, additional, Novotney, Amanda, additional, Wool, Eve E, additional, Ikuta, Kevin S, additional, Vongpradith, Avina, additional, Rogowski, Emma Lynn Best, additional, Doxey, Matthew, additional, Troeger, Christopher E, additional, Albertson, Samuel B, additional, Ma, Jianing, additional, He, Jiawei, additional, Maass, Kelsey Lynn, additional, A.F.Simões, Eric, additional, Abdoun, Meriem, additional, Abdul Aziz, Jeza Muhamad, additional, Abdulah, Deldar Morad, additional, Abu Rumeileh, Samir, additional, Abualruz, Hasan, additional, Aburuz, Salahdein, additional, Adepoju, Abiola Victor, additional, Adha, Rishan, additional, Adikusuma, Wirawan, additional, Adra, Saryia, additional, Afraz, Ali, additional, Aghamiri, Shahin, additional, Agodi, Antonella, additional, Ahmadzade, Amir Mahmoud, additional, Ahmed, Haroon, additional, Ahmed, Ayman, additional, Akinosoglou, Karolina, additional, AL-Ahdal, Tareq Mohammed Ali, additional, Al-amer, Rasmieh Mustafa, additional, Albashtawy, Mohammed, additional, AlBataineh, Mohammad T., additional, Alemi, Hediyeh, additional, Al-Gheethi, Adel Ali Saeed, additional, Ali, Abid, additional, Ali, Syed Shujait Shujait, additional, Alqahtani, Jaber S, additional, AlQudah, Mohammad, additional, Al-Tawfiq, Jaffar A., additional, Al-Worafi, Yaser Mohammed, additional, Alzoubi, Karem H, additional, Amani, Reza, additional, Amegbor, Prince M, additional, Ameyaw, Edward Kwabena, additional, Amuasi, John H, additional, Anil, Abhishek, additional, Anyanwu, Philip Emeka, additional, Arafat, Mosab, additional, Areda, Damelash, additional, Arefnezhad, Reza, additional, Atalell, Kendalem Asmare, additional, Ayele, Firayad, additional, Azzam, Ahmed Y, additional, Babamohamadi, Hassan, additional, Babin, François-Xavier, additional, Bahurupi, Yogesh, additional, Baker, Stephen, additional, Banik, Biswajit, additional, Barchitta, Martina, additional, Barqawi, Hiba Jawdat, additional, Basharat, Zarrin, additional, Baskaran, Pritish, additional, Batra, Kavita, additional, Batra, Ravi, additional, Bayileyegn, Nebiyou Simegnew, additional, Beloukas, Apostolos, additional, Berkley, James A, additional, Beyene, Kebede A, additional, Bhargava, Ashish, additional, Bhattacharjee, Priyadarshini, additional, Bielicki, Julia A, additional, Bilalaga, Mariah Malak, additional, Bitra, Veera R, additional, Brown, Colin Stewart, additional, Burkart, Katrin, additional, Bustanji, Yasser, additional, Carr, Sinclair, additional, Chahine, Yaacoub, additional, Chattu, Vijay Kumar, additional, Chichagi, Fatemeh, additional, Chopra, Hitesh, additional, Chukwu, Isaac Sunday, additional, Chung, Eunice, additional, Dadana, Sriharsha, additional, Dai, Xiaochen, additional, Dandona, Lalit, additional, Dandona, Rakhi, additional, Darban, Isaac, additional, Dash, Nihar Ranjan, additional, Dashti, Mohsen, additional, Dashtkoohi, Mohadese, additional, Dekker, Denise Myriam, additional, Delgado-Enciso, Ivan, additional, Devanbu, Vinoth Gnana Chellaiyan, additional, Dhama, Kuldeep, additional, Diao, Nancy, additional, Do, Thao Huynh Phuong, additional, Dokova, Klara Georgieva, additional, Dolecek, Christiane, additional, Dziedzic, Arkadiusz Marian, additional, Eckmanns, Tim, additional, Ed-Dra, Abdelaziz, additional, Efendi, Ferry, additional, Eftekharimehrabad, Aziz, additional, Eyre, David William, additional, Fahim, Ayesha, additional, Feizkhah, Alireza, additional, Felton, Timothy William, additional, Ferreira, Nuno, additional, Flor, Luisa S, additional, Gaihre, Santosh, additional, Gebregergis, Miglas W, additional, Gebrehiwot, Mesfin, additional, Geffers, Christine, additional, Gerema, Urge, additional, Ghaffari, Kazem, additional, Goldust, Mohamad, additional, Goleij, Pouya, additional, Guan, Shi-Yang, additional, Gudeta, Mesay Dechasa, additional, Guo, Cui, additional, Gupta, Veer Bala, additional, Gupta, Ishita, additional, Habibzadeh, Farrokh, additional, Hadi, Najah R, additional, Haeuser, Emily, additional, Hailu, Wase Benti, additional, Hajibeygi, Ramtin, additional, Haj-Mirzaian, Arvin, additional, Haller, Sebastian, additional, Hamiduzzaman, Mohammad, additional, Hanifi, Nasrin, additional, Hansel, Jan, additional, Hasnain, Md Saquib, additional, Haubold, Johannes, additional, Hoan, Nguyen Quoc, additional, Huynh, Hong-Han, additional, Iregbu, Kenneth Chukwuemeka, additional, Islam, Md. Rabiul, additional, Jafarzadeh, Abdollah, additional, Jairoun, Ammar Abdulrahman, additional, Jalili, Mahsa, additional, Jomehzadeh, Nabi, additional, Joshua, Charity Ehimwenma, additional, Kabir, Md. Awal, additional, Kamal, Zul, additional, Kanmodi, Kehinde Kazeem, additional, Kantar, Rami S., additional, Karimi Behnagh, Arman, additional, Kaur, Navjot, additional, Kaur, Harkiran, additional, Khamesipour, Faham, additional, Khan, M Nuruzzaman, additional, Khan suheb, Mahammed Ziauddin, additional, Khanal, Vishnu, additional, Khatab, Khaled, additional, Khatib, Mahalaqua Nazli, additional, Kim, Grace, additional, Kim, Kwanghyun, additional, Kitila, Aiggan Tamene Tamene, additional, Komaki, Somayeh, additional, Krishan, Kewal, additional, Krumkamp, Ralf, additional, Kuddus, Md Abdul, additional, Kurniasari, Maria Dyah, additional, Lahariya, Chandrakant, additional, Latifinaibin, Kaveh, additional, Le, Nhi Huu Hanh, additional, Le, Thao Thi Thu, additional, Le, Trang Diep Thanh, additional, Lee, Seung Won, additional, LEPAPE, Alain, additional, Lerango, Temesgen L., additional, Li, Ming-Chieh, additional, Mahboobipour, Amir Ali, additional, Malhotra, Kashish, additional, Mallhi, Tauqeer Hussain, additional, Manoharan, Anand, additional, Martinez-Guerra, Bernardo Alfonso, additional, Mathioudakis, Alexander G., additional, Mattiello, Rita, additional, May, Jürgen, additional, McManigal, Barney, additional, McPhail, Steven M, additional, Mekene Meto, Tesfahun, additional, Mendez-Lopez, Max Alberto Mendez, additional, Meo, Sultan Ayoub, additional, Merati, Mohsen, additional, Mestrovic, Tomislav, additional, Mhlanga, Laurette, additional, Minh, Le Huu Nhat, additional, Misganaw, Awoke, additional, Mishra, Vinaytosh, additional, Misra, Arup Kumar, additional, Mohamed, Nouh Saad, additional, Mohammadi, Esmaeil, additional, Mohammed, Mesud, additional, Mohammed, Mustapha, additional, Mokdad, Ali H, additional, Monasta, Lorenzo, additional, Moore, Catrin E, additional, Motappa, Rohith, additional, Mougin, Vincent, additional, Mousavi, Parsa, additional, Mulita, Francesk, additional, Mulu, Atsedemariam Andualem, additional, Naghavi, Pirouz, additional, Naik, Ganesh R, additional, Nainu, Firzan, additional, Nair, Tapas Sadasivan, additional, Nargus, Shumaila, additional, Negaresh, Mohammad, additional, Nguyen, Hau Thi Hien, additional, Nguyen, Dang H, additional, Nguyen, Van Thanh, additional, Nikolouzakis, Taxiarchis Konstantinos, additional, Noman, Efaq Ali, additional, Nri-Ezedi, Chisom Adaobi, additional, Odetokun, Ismail A., additional, Okwute, Patrick Godwin, additional, Olana, Matifan Dereje, additional, Olanipekun, Titilope O, additional, Olasupo, Omotola O., additional, Olivas-Martinez, Antonio, additional, Ordak, Michal, additional, Ortiz-Brizuela, Edgar, additional, Ouyahia, Amel, additional, Padubidri, Jagadish Rao, additional, Pak, Anton, additional, Pandey, Anamika, additional, Pantazopoulos, Ioannis, additional, Parija, Pragyan Paramita, additional, Parikh, Romil R, additional, Park, Seoyeon, additional, Parthasarathi, Ashwaghosha, additional, Pashaei, Ava, additional, Peprah, Prince, additional, Pham, Hoang Tran, additional, Poddighe, Dimitri, additional, Pollard, Andrew, additional, Ponce-De-Leon, Alfredo, additional, Prakash, Peralam Yegneswaran, additional, Prates, Elton Junio Sady, additional, Quan, Nguyen Khoi, additional, Raee, Pourya, additional, Rahim, Fakher, additional, Rahman, Mosiur, additional, Rahmati, Masoud, additional, Ramasamy, Shakthi Kumaran, additional, Ranjan, Shubham, additional, Rao, Indu Ramachandra, additional, Rashid, Ahmed Mustafa, additional, Rattanavong, Sayaphet, additional, Ravikumar, Nakul, additional, Reddy, Murali Mohan Rama Krishna, additional, Redwan, Elrashdy Moustafa Mohamed, additional, Reiner, Robert C, additional, Reyes, Luis Felipe, additional, Roberts, Tamalee, additional, Rodrigues, Mónica, additional, Rosenthal, Victor Daniel, additional, Roy, Priyanka, additional, Runghien, Tilleye, additional, Saeed, Umar, additional, Saghazadeh, Amene, additional, Saheb Sharif-Askari, Narjes, additional, Saheb Sharif-Askari, Fatemeh, additional, Sahoo, Soumya Swaroop, additional, Sahu, Monalisha, additional, Sakshaug, Joseph W, additional, Salami, Afeez Abolarinwa, additional, Saleh, Mohamed A., additional, Salehi omran, Hossein, additional, Sallam, Malik, additional, Samadzadeh, Sara, additional, Samodra, Yoseph Leonardo, additional, Sanjeev, Rama Krishna, additional, Sarasmita, Made Ary, additional, Saravanan, Aswini, additional, Sartorius, Benn, additional, Saulam, Jennifer, additional, Schumacher, Austin E, additional, Seyedi, Seyed Arsalan, additional, Shafie, Mahan, additional, Shahid, Samiah, additional, Sham, Sunder, additional, Shamim, Muhammad Aaqib, additional, Shamshirgaran, Mohammad Ali, additional, Shastry, Rajesh P., additional, Sherchan, Samendra P, additional, Shiferaw, Desalegn, additional, Shittu, Aminu, additional, Siddig, Emmanuel Edwar, additional, Sinto, Robert, additional, Sood, Aayushi, additional, Sorensen, Reed J D, additional, Stergachis, Andy, additional, Stoeva, Temenuga Zhekova, additional, Swain, Chandan Kumar, additional, Szarpak, Lukasz, additional, Tamuzi, Jacques Lukenze, additional, Temsah, Mohamad-Hani, additional, Tessema, Melkamu B Tessema, additional, Thangaraju, Pugazhenthan, additional, Tran, Nghia Minh, additional, Tran, Ngoc-Ha, additional, Tumurkhuu, Munkhtuya, additional, Ty, Sree Sudha, additional, Udoakang, Aniefiok John, additional, Ulhaq, Inam, additional, Umar, Tungki Pratama, additional, Umer, Abdurezak Adem, additional, Vahabi, Seyed Mohammad, additional, Vaithinathan, Asokan Govindaraj, additional, Van den Eynde, Jef, additional, Walson, Judd L, additional, Waqas, Muhammad, additional, Xing, Yuhan, additional, Yadav, Mukesh Kumar, additional, Yahya, Galal, additional, Yon, Dong Keon, additional, Zahedi Bialvaei, Abed, additional, Zakham, Fathiah, additional, Zeleke, Abyalew Mamuye, additional, Zhai, Chunxia, additional, Zhang, Zhaofeng, additional, Zhang, Haijun, additional, Zielińska, Magdalena, additional, Zheng, Peng, additional, Aravkin, Aleksandr Y, additional, Vos, Theo, additional, Hay, Simon I, additional, Mosser, Jonathan F., additional, Lim, Stephen S, additional, Naghavi, Mohsen, additional, Murray, Christopher J L, additional, and Kyu, Hmwe Hmwe, additional

Published
2024
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45. Limited evidence of spill over of antimicrobial resistantKlebsiella pneumoniaefrom animal/environmental reservoirs to humans in India

Author

Jacob, Jobin John, primary, V, Aravind, additional, Beresford-Jones, Benjamin S., additional, Y, Binesh Lal, additional, Shankar, Chaitra, additional, M, Yesudoss, additional, Abdullah, Fiza, additional, Priya T, Monisha, additional, Kulkarni, Sanika, additional, Baker, Stephen, additional, Veeraraghavan, Balaji, additional, and Walia, Kamini, additional

Published
2024
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46. A metagenomic prospective cohort study on gut microbiome composition and clinical infection in small bowel transplantation

Author

Madhav, Archana, primary, Bousfield, Rachel, additional, Pereira-Dias, Joana, additional, Cormie, Claire, additional, Forrest, Sally, additional, Keane, Jacqueline, additional, Kermack, Leanne, additional, Higginson, Ellen, additional, Dougan, Gordon, additional, Spiers, Harry, additional, Massey, Dunecan, additional, Sharkey, Lisa, additional, Rutter, Charlotte, additional, Woodward, Jeremy, additional, Russell, Neil, additional, Amin, Irum, additional, Butler, Andrew, additional, Atkinson, Kayleigh, additional, Dymond, Tom, additional, Bartholdson Scott, Josefin, additional, Baker, Stephen, additional, and Gkrania-Klotsas, Effrossyni, additional

Published
2024
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50. Tumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients

Author

Tran, Hoang N. H., Thu, Trang Nguyen Hoang, Nguyen, Phu Huu, Vo, Chi Nguyen, Doan, Khanh Van, Nguyen Ngoc Minh, Chau, Nguyen, Ngoc Tuan, Ta, Van Ngoc Duc, Vu, Khuong An, Hua, Thanh Danh, Nguyen, To Nguyen Thi, Van, Tan Trinh, Pham Duc, Trung, Duong, Ba Lap, Nguyen, Phuc Minh, Hoang, Vinh Chuc, Pham, Duy Thanh, Thwaites, Guy E., Hall, Lindsay J., Slade, Daniel J., Baker, Stephen, Tran, Vinh Hung, and Chung The, Hao

Published
2022
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