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6. Human movement and environmental barriers shape the emergence of dengue

Author

Harish, Vinyas, Colón-González, Felipe J., Moreira, Filipe R. R., Gibb, Rory, Kraemer, Moritz U. G., Davis, Megan, Reiner, Jr., Robert C., Pigott, David M., Perkins, T. Alex, Weiss, Daniel J., Bogoch, Isaac I., Vazquez-Prokopec, Gonzalo, Saide, Pablo Manrique, Barbosa, Gerson L., Sabino, Ester C., Khan, Kamran, Faria, Nuno R., Hay, Simon I., Correa-Morales, Fabián, Chiaravalloti-Neto, Francisco, and Brady, Oliver J.

Published
2024
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7. Efficacy and safety of fixed dose combination of Sitagliptin, metformin, and pioglitazone in type 2 Diabetes (IMPACT study): a randomized controlled trial

Author

Aashish, Mondal, Arindam, Naskar, Siddiqi, Sheelu Shafiq, Bhosle, Deepak, Mallikarjuna, V. J., Amol, Dange, Sanket, Sorate, Omkar, Gavali, Parth, Patel, Dhruvi, Hasnani, Durga, Prasad, Pradeep, Dalwadi, Suresh, Kumar, Vaishali, Pathak, Mayura, Chaudhari, Indraneel, Basu, Jayashri, Shembalkar, Arif, Fariooqui, Raghavendra, S. K., Deepak, Varade, Ravindra, Thakkar, Shaishav, Bhanushali, Vijay, Gaikwad, Khan, Kamran, Mahajani, V. V., Sharma, A. D., Mayabhate, Mayur, Pawar, R. R., Aiwale, A. S., and Vinayaka, Shahavi

Published
2024
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10. Gyroid-like metamaterials: Topology optimization and Deep Learning

Author

Viswanath, Asha, Abueidda, Diab W, Modrek, Mohamad, Khan, Kamran A, Koric, Seid, and Al-Rub, Rashid K. Abu

Subjects
Computer Science - Computational Engineering, Finance, and Science
Abstract

Triply periodic minimal surface (TPMS) metamaterials characterized by mathematically-controlled topologies exhibit better mechanical properties compared to uniform structures. The unit cell topology of such metamaterials can be further optimized to improve a desired mechanical property for a specific application. However, such inverse design involves multiple costly 3D finite element analyses in topology optimization and hence has not been attempted. Data-driven models have recently gained popularity as surrogate models in the geometrical design of metamaterials. Gyroid-like unit cells are designed using a novel voxel algorithm, a homogenization-based topology optimization, and a Heaviside filter to attain optimized densities of 0-1 configuration. Few optimization data are used as input-output for supervised learning of the topology optimization process from a 3D CNN model. These models could then be used to instantaneously predict the optimized unit cell geometry for any topology parameters, thus alleviating the need to run any topology optimization for future design. The high accuracy of the model was demonstrated by a low mean square error metric and a high dice coefficient metric. This accelerated design of 3D metamaterials opens the possibility of designing any computationally costly problems involving complex geometry of metamaterials with multi-objective properties or multi-scale applications.

Published
2023

11. Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1.

Author

Tsui, Joseph, McCrone, John, Lambert, Ben, Bajaj, Sumali, Inward, Rhys, Bosetti, Paolo, Pena, Rosario, Tegally, Houriiyah, Hill, Verity, Zarebski, Alexander, Peacock, Thomas, Liu, Luyang, Wu, Neo, Davis, Megan, Bogoch, Isaac, Khan, Kamran, Kall, Meaghan, Abdul Aziz, Nurin, Colquhoun, Rachel, OToole, Áine, Jackson, Ben, Dasgupta, Abhishek, Wilkinson, Eduan, de Oliveira, Tulio, Connor, Thomas, Loman, Nicholas, Colizza, Vittoria, Fraser, Christophe, Volz, Erik, Ji, Xiang, Gutierrez, Bernardo, Chand, Meera, Dellicour, Simon, Cauchemez, Simon, Raghwani, Jayna, Suchard, Marc, Lemey, Philippe, Rambaut, Andrew, Pybus, Oliver, and Kraemer, Moritz

Subjects
Humans, Africa, Southern, COVID-19, Genomics, SARS-CoV-2, Phylogeny
Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) now arise in the context of heterogeneous human connectivity and population immunity. Through a large-scale phylodynamic analysis of 115,622 Omicron BA.1 genomes, we identified >6,000 introductions of the antigenically distinct VOC into England and analyzed their local transmission and dispersal history. We find that six of the eight largest English Omicron lineages were already transmitting when Omicron was first reported in southern Africa (22 November 2021). Multiple datasets show that importation of Omicron continued despite subsequent restrictions on travel from southern Africa as a result of export from well-connected secondary locations. Initiation and dispersal of Omicron transmission lineages in England was a two-stage process that can be explained by models of the countrys human geography and hierarchical travel network. Our results enable a comparison of the processes that drive the invasion of Omicron and other VOCs across multiple spatial scales.

Published
2023

17. Context-specific emergence and growth of the SARS-CoV-2 Delta variant

Author

McCrone, John T, Hill, Verity, Bajaj, Sumali, Pena, Rosario Evans, Lambert, Ben C, Inward, Rhys, Bhatt, Samir, Volz, Erik, Ruis, Christopher, Dellicour, Simon, Baele, Guy, Zarebski, Alexander E, Sadilek, Adam, Wu, Neo, Schneider, Aaron, Ji, Xiang, Raghwani, Jayna, Jackson, Ben, Colquhoun, Rachel, O’Toole, Áine, Peacock, Thomas P, Twohig, Kate, Thelwall, Simon, Dabrera, Gavin, Myers, Richard, Faria, Nuno R, Huber, Carmen, Bogoch, Isaac I, Khan, Kamran, du Plessis, Louis, Barrett, Jeffrey C, Aanensen, David M, Barclay, Wendy S, Chand, Meera, Connor, Thomas, Loman, Nicholas J, Suchard, Marc A, Pybus, Oliver G, Rambaut, Andrew, and Kraemer, Moritz UG

Subjects
Emerging Infectious Diseases, Infectious Diseases, Good Health and Well Being, COVID-19, Cities, Contact Tracing, England, Genome, Viral, Humans, Quarantine, SARS-CoV-2, Travel, COVID-19 Genomics UK (COG-UK) Consortium, General Science & Technology
Abstract

The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide1,2. The emergence of the Delta variant in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 SARS-CoV-2 genomes from England together with 93,649 genomes from the rest of the world to reconstruct the emergence of Delta and quantify its introduction to and regional dissemination across England in the context of changing travel and social restrictions. Using analysis of human movement, contact tracing and virus genomic data, we find that the geographic focus of the expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced more than 1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers reduced onward transmission from importations; however, the transmission chains that later dominated the Delta wave in England were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove the nationwide dissemination of Delta, with some cities receiving more than 2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing-and not the number of importations-were associated with the faster relative spread of Delta. The invasion dynamics of Delta depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce the transmission of current and future variants of concern, such as Omicron (Pango lineage B.1.1.529).

Published
2022

27. The Securitisation of Language Borders and the (Re)production of Inequalities

Author

Khan, Kamran

Abstract

This article will focus on inequalities for migrants which are (re)produced by the promise of equality through citizenship and settlement test regimes. I theorize the links between language and borders by drawing on scholarship on security before offering an analysis of language border proliferation. Drawing on other studies and my own work, I will also outline various inequalities. First, how language can act as a proxy for the race through testing which is disproportionately more problematic for non-Europeans. Second, how a lack of access to test centers can discriminate in testing that takes place in the country of origin prior to arrival while also reducing access to test centers in the country of arrival once settled. Third, how tests can affect women, particularly mothers who may lack access to language support and may also have care duties. I will also outline the effects of delays and in relation to language borders. In all of the above, citizenship testing is better situated as a form of border making consistent with the increasing securitization of broader society whether through offshore detention, walls, or increased surveillance.

Published
2022
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40. Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria

Author

Olawoye, Idowu B., Oluniyi, Paul E., Oguzie, Judith U., Uwanibe, Jessica N., Kayode, Tolulope A., Olumade, Testimony J., Ajogbasile, Fehintola V., Parker, Edyth, Eromon, Philomena E., Abechi, Priscilla, Sobajo, Tope A., Ugwu, Chinedu A., George, Uwem E., Ayoade, Femi, Akano, Kazeem, Oyejide, Nicholas E., Nosamiefan, Iguosadolo, Fred-Akintunwa, Iyanuoluwa, Adedotun-Sulaiman, Kemi, Brimmo, Farida B., Adegboyega, Babatunde B., Philip, Courage, Adeleke, Richard A., Chukwu, Grace C., Ahmed, Muhammad I., Ope-Ewe, Oludayo O., Otitoola, Shobi G., Ogunsanya, Olusola A., Saibu, Mudasiru F., Sijuwola, Ayotunde E., Ezekiel, Grace O., John, Oluwagboadurami G., Akin-John, Julie O., Akinlo, Oluwasemilogo O., Fayemi, Olanrewaju O., Ipaye, Testimony O., Nwodo, Deborah C., Omoniyi, Abolade E., Omwanghe, Iyobosa B., Terkuma, Christabel A., Okolie, Johnson, Ayo-Ale, Olubukola, Ikponmwosa, Odia, Benevolence, Ebo, Naregose, Grace O., Patience, Akhilomen E., Blessing, Osiemi, Micheal, Airende, Jacqueline, Agbukor, Aiyepada, John O., Ebhodaghe, Paulson, Racheal, Omiunu, Rita, Esumeh, Rosemary, Giwa E., Solomon, Ehikhametalor, Anieno, Ekanem, Edna, Yerumoh, Chris, Aire O., Donatus, Adomeh I., Ogbaini-Emovon, Ephraim, Tatfeng, Mirabeau Y., Omunakwe, Hannah E., Bob-Manuel, Mienye, Ahmed, Rahaman A., Onwuamah, Chika K., Shaibu, Joseph O., Okwuraiwe, Azuka, Ataga, Anthony E., Bock-Oruma, Andrew, Daramola, Funmi, Yusuf, Ibrahim F., Fajola, Akinwumi, Ntia, Nsikak-Abasi, Ekpo, Julie J., Moses, Anietie E., Moore-Igwe, Beatrice W., Fakayode, Oluwatosin E., Akinola, Monilade, Kida, Ibrahim M., Oderinde, Bamidele S., Wudiri, Zara W., Adeyemi, Oluwapelumi O., Akanbi, Olusola A., Ahumibe, Anthony, Akinpelu, Afolabi, Ayansola, Oyeronke, Babatunde, Olajumoke, Omoare, Adesuyi A., Chukwu, Chimaobi, Mba, Nwando G., Omoruyi, Ewean C., Olisa, Olasunkanmi, Akande, Olatunji K., Nwafor, Ifeanyi E., Ekeh, Matthew A., Ndoma, Erim, Ewah, Richard L., Duruihuoma, Rosemary O., Abu, Augustine, Odeh, Elizabeth, Onyia, Venatius, Ojide, Chiedozie K., Okoro, Sylvanus, Igwe, Daniel, Ogah, Emeka O., Khan, Kamran, Ajayi, Nnennaya A., Ugwu, Collins N., Ukwaja, Kingsley N., Ugwu, Ngozi I., Abejegah, Chukwuyem, Adedosu, Nelson, Ayodeji, Olufemi, Liasu, Ahmed A., Isamotu, Rafiu O., Gadzama, Galadima, Petros, Brittany A., Siddle, Katherine J., Schaffner, Stephen F., Akpede, George, Erameh, Cyril Oshomah, Baba, Marycelin M., Oladiji, Femi, Audu, Rosemary, Ndodo, Nnaemeka, Fowotade, Adeola, Okogbenin, Sylvanus, Okokhere, Peter O., Park, Danny J., Mcannis, Bronwyn L., Adetifa, Ifedayo M., Ihekweazu, Chikwe, Salako, Babatunde L., Tomori, Oyewale, Happi, Anise N., Folarin, Onikepe A., Andersen, Kristian G., Sabeti, Pardis C., and Happi, Christian T.

Published
2023
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42. Banach and Suzuki-type fixed point theorems in Generalized $n$-metric spaces with an application

Author

Khan, Kamran Alam

Subjects
Mathematics - General Topology, 47H10, 54H25, 54E50, 90C39
Abstract

Mustafa and Sims [12] introduced the notion of $G$-metric as a possible generalization of usual notion of a metric space. The author generalized the notion of G-metric to more than three variables and introduced the concept of Generalized $n$-metric spaces [10]. In this paper, We prove Banach fixed point theorem and a Suzuki-type fixed point theorem in Generalized $n$-metric spaces. We also discuss applications to certain functional equations arising in dynamic programming., Comment: arXiv admin note: substantial text overlap with arXiv:1809.08997

Published
2021

44. Feasibility of double-blinded, placebo-controlled interventional study for assessing catheter ablation efficacy in persistent atrial fibrillation: Insights from the ORBITA AF feasibility study

Author

Kanthasamy, Vijayabharathy, Schilling, Richard, Zongo, Olivier, Khan, Kamran, Earley, Mark, Monk, Vivienne, Hunter, Ross, Mangiafico, Valentina, Ang, Richard, Creta, Antonio, Aluwhalia, Nikhil, Honarbakhsh, Shohreh, Dhinoja, Mehul, Gupta, Dhiraj, and Finlay, Malcolm

Published
2024
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45. Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions

Author

Parker, Edyth, Anderson, Catelyn, Zeller, Mark, Tibi, Ahmad, Havens, Jennifer L, Laroche, Geneviève, Benlarbi, Mehdi, Ariana, Ardeshir, Robles-Sikisaka, Refugio, Latif, Alaa Abdel, Watts, Alexander, Awidi, Abdalla, Jaradat, Saied A, Gangavarapu, Karthik, Ramesh, Karthik, Kurzban, Ezra, Matteson, Nathaniel L, Han, Alvin X, Hughes, Laura D, McGraw, Michelle, Spencer, Emily, Nicholson, Laura, Khan, Kamran, Suchard, Marc A, Wertheim, Joel O, Wohl, Shirlee, Côté, Marceline, Abdelnour, Amid, Andersen, Kristian G, and Abu-Dayyeh, Issa

Subjects
Life on Land, COVID-19, Humans, Middle East, Pandemics, SARS-CoV-2, Travel
Abstract

Regional connectivity and land travel have been identified as important drivers of SARS-CoV-2 transmission. However, the generalizability of this finding is understudied outside of well-sampled, highly connected regions. In this study, we investigated the relative contributions of regional and intercontinental connectivity to the source-sink dynamics of SARS-CoV-2 for Jordan and the Middle East. By integrating genomic, epidemiological and travel data we show that the source of introductions into Jordan was dynamic across 2020, shifting from intercontinental seeding in the early pandemic to more regional seeding for the travel restrictions period. We show that land travel, particularly freight transport, drove introduction risk during the travel restrictions period. High regional connectivity and land travel also drove Jordan's export risk. Our findings emphasize regional connectedness and land travel as drivers of transmission in the Middle East.

Published
2022

46. An Electronic Textile Embedded Smart Cementitious Composite

Author

Irfan, Muhammad S, Ali, Muhammad A, Khan, Kamran A, Umer, Rehan, Kanellopoulos, Antonios, and Samad, Yarjan A

Subjects
Physics - Applied Physics
Abstract

Structural health monitoring (SHM) using self-sensing cement-based materials has been reported before, where nano-fillers have been incorporated in cementitious matrices as functional sensing elements. A percolation threshold is always required in order for conductive nano-fillers modified concrete to be useful for SHM. Nonetheless, the best pressure/strain sensitivity results achieved for any self-sensing cementitious matrix are <0.01 MPa-1. In this work, we introduce novel reduced graphene oxide (RGO) based electronic textile (e-textile) embedded in plain and polymer-binder-modified cementitious matrix for SHM applications. As a proof of concept, it was demonstrated that these coated fabric-based sensors can be successfully embedded within the cement-based structures, which are independent of any percolation threshold due to the interconnected fabric inside the host matrix. The piezo-resistive response was measured by applying direct and cyclic compressive loads (0.1 to 3.9 MPa). A pressure sensitivity of 1.5 MPa-1 and an ultra-high gauge factor of 2000 was obtained for the system of the self-sensing cementitious structure with embedded e-textiles. The sensitivity of this new system with embedded e-textile is many orders of magnitude higher than nanoparticle based self-sensing of cementitious composites. The manufactured e-textile sensors showed mechanical stability and functional durability over long-term cyclic compression tests of 1000 cycles.

Published
2020

48. Emergence of an early SARS-CoV-2 epidemic in the United States.

Author

Zeller, Mark, Gangavarapu, Karthik, Anderson, Catelyn, Smither, Allison R, Vanchiere, John A, Rose, Rebecca, Snyder, Daniel J, Dudas, Gytis, Watts, Alexander, Matteson, Nathaniel L, Robles-Sikisaka, Refugio, Marshall, Maximilian, Feehan, Amy K, Sabino-Santos, Gilberto, Bell-Kareem, Antoinette R, Hughes, Laura D, Alkuzweny, Manar, Snarski, Patricia, Garcia-Diaz, Julia, Scott, Rona S, Melnik, Lilia I, Klitting, Raphaëlle, McGraw, Michelle, Belda-Ferre, Pedro, DeHoff, Peter, Sathe, Shashank, Marotz, Clarisse, Grubaugh, Nathan D, Nolan, David J, Drouin, Arnaud C, Genemaras, Kaylynn J, Chao, Karissa, Topol, Sarah, Spencer, Emily, Nicholson, Laura, Aigner, Stefan, Yeo, Gene W, Farnaes, Lauge, Hobbs, Charlotte A, Laurent, Louise C, Knight, Rob, Hodcroft, Emma B, Khan, Kamran, Fusco, Dahlene N, Cooper, Vaughn S, Lemey, Phillipe, Gardner, Lauren, Lamers, Susanna L, Kamil, Jeremy P, Garry, Robert F, Suchard, Marc A, and Andersen, Kristian G

Subjects
Humans, Risk Factors, Disease Outbreaks, Phylogeny, Travel, United States, Louisiana, Texas, Databases as Topic, Epidemics, COVID-19, SARS-CoV-2, genomic epidemiology, mobility, phylogenetics, viral emergence, viral sequencing, Emerging Infectious Diseases, Biodefense, Prevention, Vaccine Related, Lung, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract

The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.

Published
2021

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