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1. Topological and Dynamic Properties of the Sublinearly Morse Boundary and the Quasi-Redirecting Boundary

Author

Garcia, Jacob, Qing, Yulan, and Vest, Elliott

Subjects
Mathematics - Metric Geometry, Mathematics - Group Theory, Mathematics - Geometric Topology
Abstract

Sublinearly Morse boundaries of proper geodesic spaces are introduced by Qing, Rafi and Tiozzo. Expanding on this work, Qing and Rafi recently developed the quasi-redirecting boundary, denoted $\partial G$, to include all directions of metric spaces at infinity. Both boundaries are topological spaces that consist of equivalence classes of quasi-geodesic rays and are quasi-isometrically invariant. In this paper, we study these boundaries when the space is equipped with a geometric group action. In particular, we show that $G$ acts minimally on $\partial_\kappa G$ and that contracting elements of G induces a weak north-south dynamic on $\partial_\kappa G$. We also prove, when $\partial G$ exists and $|\partial_\kappa G|\geq3$, $G$ acts minimally on $\partial G$ and $\partial G$ is a second countable topological space. The last section concerns the restriction to proper CAT(0) spaces and finite dimensional \CAT cube complexes. We show that when $G$ acts geometrically on a finite dimensional CAT(0) cube complex (whose QR boundary is assumed to exist), then a nontrivial QR boundary implies the existence of a Morse element in $G$. Lastly, we show that if $X$ is a proper cocompact CAT(0) space, then $\partial G$ is a visibility space., Comment: 27 pages, 11 figures

Published
2024

2. Characterizations of Stability via Morse Limit Sets

Author

Garcia, Jacob

Subjects
Mathematics - Metric Geometry, Mathematics - Group Theory, Mathematics - Geometric Topology
Abstract

Subgroup stability is a strong notion of quasiconvexity that generalizes convex cocompactness in a variety of settings. In this paper, we characterize stability of a subgroup by properties of its limit set on the Morse boundary. Given $H

Published
2023

3. Analysis of Anonymous Student Narratives About Experiences with Emergency Medicine Residency Programs

Author

Estes, Molly, Garcia, Jacob, Ren, Ronnie, Olaf, Mark, Moffett, Shannon, Galuska, Michael, and Zhang, Xiao Chi

Subjects
anonymous online community, trainee feedback, Residency Program, social media, clerkship rotation, Emergency Medicine, Residency Recruitment, program development
Abstract

Background: Academic emergency medicine (EM) communities have viewed anonymous online communities (AOC) such as Reddit or specialty-specific “applicant spreadsheets” as poor advising resources. Despite this, robust EM AOCs exist, with large user bases and heavy readership. Insights about applicants’ authentic experiences can be critical for applicants and program leadership decision-making. To date, there are no EM studies to qualitatively assess EM AOC narratives during the application cycle. Our goal was to perform a qualitative analysis of students’ EM program experiences through a publicly available AOC.Methods: This was a qualitative analysis of a publicly available, time-stamped, user-locked AOC dataset: “Official 2020–2021 Emergency Medicine Applicant Spreadsheet.” We extracted and then de-identified all data from selected sub-sheets entitled “Virtual Interview Impressions” and “Rotation Impressions.” Four investigators used constant comparative method to analyze the data inductively, and they subsequently met to generate common themes discussed by students. Preliminary thematic analysis was conducted on a random sample of 37/183 (20%) independent narratives to create the initial codebook. This was used and updated iteratively to analyze the entire narrative set consisting of 841 discrete statements. Finally, two unique codes were created to distinguish whether the identified sub-themes, or program attributes, were likely “modifiable” or “non-modifiable.”Results: We identified six major themes: living and working conditions; interpersonal relationships; learning experiences, postgraduate readiness, and online/virtual supplements. Common sub-themes included patient population (13%); resident personality (7%); program leadership personality (7%); relationship with faculty/leadership (6%); geography (4%); practice setting (4%); program reputation (4%), and postgraduate year-3 experiences (4%). Modifiable sub-themes outnumbered non-modifiable sub-themes, 60.7% to 39.3%.Conclusion: In this analysis of selected medical students’ narratives in an AOC, the majority of identified themes represented topics that may serve as external feedback for EM residency programs and their clerkships. Selective use of AOCs may set a precedent for future program assessments by applicants and inform program leadership of important programmatic elements in the eyes of applicants. It elucidates important themes in their interactions or learning experiences with programs and creates opportunities for learner-centric program improvement.

Published
2024

5. Identification of complex Plasmodium falciparum genetic backgrounds circulating in Africa: a multicountry genomic epidemiology analysis

Author

Miotto, Olivo, Amambua-Ngwa, Alfred, Amenga-Etego, Lucas N, Abdel Hamid, Muzamil M, Adam, Ishag, Aninagyei, Enoch, Apinjoh, Tobias, Awandare, Gordon A, Bejon, Philip, Bertin, Gwladys I, Bouyou-Akotet, Marielle, Claessens, Antoine, Conway, David J, D'Alessandro, Umberto, Diakite, Mahamadou, Djimdé, Abdoulaye, Dondorp, Arjen M, Duffy, Patrick, Fairhurst, Rick M, Fanello, Caterina I, Ghansah, Anita, Ishengoma, Deus S, Lawniczak, Mara, Maïga-Ascofaré, Oumou, Auburn, Sarah, Rosanas-Urgell, Anna, Wasakul, Varanya, White, Nina F D, Harrott, Alexandria, Almagro-Garcia, Jacob, Pearson, Richard D, Goncalves, Sonia, Ariani, Cristina, Bozdech, Zbynek, Hamilton, William L, Simpson, Victoria, and Kwiatkowski, Dominic P

Published
2024
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7. Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana

Author

Girgis, Sophia T., Adika, Edem, Nenyewodey, Felix E., Senoo Jnr, Dodzi K., Ngoi, Joyce M., Bandoh, Kukua, Lorenz, Oliver, van de Steeg, Guus, Harrott, Alexandria J. R., Nsoh, Sebastian, Judge, Kim, Pearson, Richard D., Almagro-Garcia, Jacob, Saiid, Samirah, Atampah, Solomon, Amoako, Enock K., Morang’a, Collins M., Asoala, Victor, Adjei, Elrmion S., Burden, William, Roberts-Sengier, William, Drury, Eleanor, Pierce, Megan L., Gonçalves, Sónia, Awandare, Gordon A., Kwiatkowski, Dominic P., Amenga-Etego, Lucas N., and Hamilton, William L.

Published
2023
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9. Student-Forum Heuristics for Emergency Medicine Residency Program Application-Preliminary Thematic Analysis

Author

Garcia, Jacob, Estes, Molly, Ren, Ronnie, and Zhang, Xiao Chi

Abstract

Learning Objectives: To perform a qualitative analysis of students’ EM program experiences through a publicly available AOC.Background: Academic Emergency Medicine (EM) communities have viewed anonymous online communities (AOCs) such as Reddit or specialty-specific “applicant spreadsheets” as poor advising sources. Despite this, robust EM AOCs exist, with large user bases and heavy readership. Insights about applicants’ authentic experiences can be critical for applicants and program leadership decision-making. To date, there are no EM studies to qualitatively assess EM AOC narratives during the application cycle.Objectives: To perform a qualitative analysis of students’ EM program experiences through a publicly available AOC.Methods: This is a qualitative, single-blinded, retrospective review of a publicly-available, time-stamped, user-locked AOC dataset: “EM Applicant Spreadsheet, 2020-21.” All data were extracted from the Excel sub-sheets entitled ‘Virtual Interview Impressions’ and ‘Rotation Impressions’ and then de-identified. Four investigators independently analyzed the data using an inductive approach and findings were combined to generate common themes discussed by students.Results: Preliminary thematic analysis was conducted on a random 20% sample (N=37) of 183 independent narratives. Major themes were: Living- and Working-Conditions, Interpersonal Relationships, Learning Experiences, Post Graduate Readiness, and Online/Virtual Supplements (Table 1). Sub-themes included: patient population (13%), resident personality (7%), program leadership personality (7%), relationship with faculty/leadership (6%), geography (4%), practice setting (4%), program reputation (4%), and PGY-3 experiences (4%).Conclusions: This study could help set a precedent for future program assessments by applicants. It elucidates important themes in their interactions or learning experiences with programs and creates opportunities for learner-centric program improvement.

Published
2022

10. Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination.

Author

Jacob, Christopher G, Thuy-Nhien, Nguyen, Mayxay, Mayfong, Maude, Richard J, Quang, Huynh Hong, Hongvanthong, Bouasy, Vanisaveth, Viengxay, Ngo Duc, Thang, Rekol, Huy, van der Pluijm, Rob, von Seidlein, Lorenz, Fairhurst, Rick, Nosten, François, Hossain, Md Amir, Park, Naomi, Goodwin, Scott, Ringwald, Pascal, Chindavongsa, Keobouphaphone, Newton, Paul, Ashley, Elizabeth, Phalivong, Sonexay, Maude, Rapeephan, Leang, Rithea, Huch, Cheah, Dong, Le Thanh, Nguyen, Kim-Tuyen, Nhat, Tran Minh, Hien, Tran Tinh, Nguyen, Hoa, Zdrojewski, Nicole, Canavati, Sara, Sayeed, Abdullah Abu, Uddin, Didar, Buckee, Caroline, Fanello, Caterina I, Onyamboko, Marie, Peto, Thomas, Tripura, Rupam, Amaratunga, Chanaki, Myint Thu, Aung, Delmas, Gilles, Landier, Jordi, Parker, Daniel M, Chau, Nguyen Hoang, Lek, Dysoley, Suon, Seila, Callery, James, Jittamala, Podjanee, Hanboonkunupakarn, Borimas, Pukrittayakamee, Sasithon, Phyo, Aung Pyae, Smithuis, Frank, Lin, Khin, Thant, Myo, Hlaing, Tin Maung, Satpathi, Parthasarathi, Satpathi, Sanghamitra, Behera, Prativa K, Tripura, Amar, Baidya, Subrata, Valecha, Neena, Anvikar, Anupkumar R, Ul Islam, Akhter, Faiz, Abul, Kunasol, Chanon, Drury, Eleanor, Kekre, Mihir, Ali, Mozam, Love, Katie, Rajatileka, Shavanthi, Jeffreys, Anna E, Rowlands, Kate, Hubbart, Christina S, Dhorda, Mehul, Vongpromek, Ranitha, Kotanan, Namfon, Wongnak, Phrutsamon, Almagro Garcia, Jacob, Pearson, Richard D, Ariani, Cristina V, Chookajorn, Thanat, Malangone, Cinzia, Nguyen, T, Stalker, Jim, Jeffery, Ben, Keatley, Jonathan, Johnson, Kimberly J, Muddyman, Dawn, Chan, Xin Hui S, Sillitoe, John, Amato, Roberto, Simpson, Victoria, Gonçalves, Sonia, Rockett, Kirk, Day, Nicholas P, Dondorp, Arjen M, Kwiatkowski, Dominic P, and Miotto, Olivo

Subjects
asia, drug resistance, epidemiology, genetic surveillance, global health, infectious disease, malaria, microbiology, Biochemistry and Cell Biology
Abstract

BackgroundNational Malaria Control Programmes (NMCPs) currently make limited use of parasite genetic data. We have developed GenRe-Mekong, a platform for genetic surveillance of malaria in the Greater Mekong Subregion (GMS) that enables NMCPs to implement large-scale surveillance projects by integrating simple sample collection procedures in routine public health procedures.MethodsSamples from symptomatic patients are processed by SpotMalaria, a high-throughput system that produces a comprehensive set of genotypes comprising several drug resistance markers, species markers and a genomic barcode. GenRe-Mekong delivers Genetic Report Cards, a compendium of genotypes and phenotype predictions used to map prevalence of resistance to multiple drugs.ResultsGenRe-Mekong has worked with NMCPs and research projects in eight countries, processing 9623 samples from clinical cases. Monitoring resistance markers has been valuable for tracking the rapid spread of parasites resistant to the dihydroartemisinin-piperaquine combination therapy. In Vietnam and Laos, GenRe-Mekong data have provided novel knowledge about the spread of these resistant strains into previously unaffected provinces, informing decision-making by NMCPs.ConclusionsGenRe-Mekong provides detailed knowledge about drug resistance at a local level, and facilitates data sharing at a regional level, enabling cross-border resistance monitoring and providing the public health community with valuable insights. The project provides a rich open data resource to benefit the entire malaria community.FundingThe GenRe-Mekong project is funded by the Bill and Melinda Gates Foundation (OPP11188166, OPP1204268). Genotyping and sequencing were funded by the Wellcome Trust (098051, 206194, 203141, 090770, 204911, 106698/B/14/Z) and Medical Research Council (G0600718). A proportion of samples were collected with the support of the UK Department for International Development (201900, M006212), and Intramural Research Program of the National Institute of Allergy and Infectious Diseases.

Published
2021

11. Temporal trends in microplastic accumulation in placentas from pregnancies in Hawaiʻi

Author

Weingrill, Rodrigo Barbano, Lee, Men-Jean, Benny, Paula, Riel, Jonathan, Saiki, Kevin, Garcia, Jacob, Oliveira, Lais Farias Azevedo de Magalhaes, Fonseca, Eduardo Jorge da Silva, Souza, Samuel Teixeira de, D'Amato, Flavio de Oliveira Silva, Silva, Ueslen Rocha, Dutra, Mariana Lima, Marques, Aldilane Lays Xavier, Borbely, Alexandre Urban, and Urschitz, Johann

Published
2023
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12. Conicality of Morse Limit Sets and Stability

Author

Garcia, Jacob Daniel

Subjects
Mathematics, Geometric Group Theory, Geometric Topology, Group Theory, Metric Geometry
Abstract

One of the most successful techniques for studying groups acting on metric spaceshas been to study actions on spaces which admit hyperbolic properties. We study a groupG acting by isometries on a proper, geodesic metric space X by studying interactionsbetween the group action on the space and hyperbolic-like boundaries for X. We presentresults regarding two different hyperbolic-like boundaries on X: the Morse boundary andthe sublinearly Morse boundary. Both of these boundaries are quasi-isometry invariants forproper geodesic metric spaces.Subgroup stability is a strong notion of quasiconvexity that generalizes convexcocompactness in a variety of settings. A characterization of convex cocompact Kleinian groups is that the limit set of the group is composed entirely of conical limit pointsin the boundary of the three dimensional hyperbolic space. We show that stable subgroups admit an identical conical limit pointcharacterization in the Morse boundary. We also, additionally, show that stable subgroupsare characterized by having an entirely horospherical limit set.A group G is non-elementary if G is not virtually cyclic and if its boundary is notempty. We show that every non-elementary group acts minimally on its sublinearly Morseboundary, i.e., for any element in the sublinearly Morse boundary, the G orbit of that element is dense in theboundary. This result, which is joint with Yulan Qing and Elliott Vest, is an importantstep towards understanding the dynamics of groups acting on their own sublinearly Morseboundary.

Published
2024

13. Fibrations, unique path lifting, and continuous monodromy

Author

Fischer, Hanspeter and Garcia, Jacob D.

Subjects
Mathematics - Algebraic Topology, 57M10, 55Q05, 55R65
Abstract

Given a path-connected space $X$ and $H\leq\pi_1(X,x_0)$, there is essentially only one construction of a map $p_H:(\widetilde{X}_H,\widetilde{x}_0)\rightarrow(X,x_0)$ with connected and locally path-connected domain that can possibly have the following two properties: $(p_{H})_{\#}\pi_1(\widetilde{X}_H,\widetilde{x}_0)=H$ and $p_H$ has the unique lifting property. $\widetilde{X}_H$ consists of equivalence classes of paths starting at $x_0$, appropriately topologized, and $p_H$ is the endpoint projection. For $p_H$ to have these two properties, $T_1$ fibers are necessary and unique path lifting is sufficient. However, $p_H$ always admits the standard lifts of paths. We show that $p_H$ has unique path lifting if it has continuous (standard) monodromies toward a $T_1$ fiber over $x_0$. Assuming, in addition, that $H$ is locally quasinormal (e.g., if $H$ is normal) we show that $X$ is homotopically path Hausdorff relative to $H$. We show that $p_H$ is a fibration if $X$ is locally path connected, $H$ is locally quasinormal, and all (standard) monodromies are continuous., Comment: 9 pages; revised abstract and introduction for version 2

Published
2019
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16. Global alteration of T-lymphocyte metabolism by PD-L1 checkpoint involves a block of de novo nucleoside phosphate synthesis

Author

Palaskas, Nicolaos Jay, Garcia, Jacob David, Shirazi, Roksana, Shin, Daniel Sanghoon, Puig-Saus, Cristina, Braas, Daniel, Ribas, Antoni, and Graeber, Thomas Glen

Subjects
Biochemistry and Cell Biology, Biological Sciences, Immunotherapy, Cancer, 2.1 Biological and endogenous factors, 5.1 Pharmaceuticals, Cancer microenvironment, DNA metabolism, Metabolomics, RNA metabolism, Tumour immunology, Biochemistry and cell biology
Abstract

Metabolic obstacles of the tumor microenvironment remain a challenge to T-cell-mediated cancer immunotherapies. To better understand the interplay of immune checkpoint signaling and immune metabolism, this study developed and used an optimized metabolite extraction protocol for non-adherent primary human T-cells, to broadly profile in vitro metabolic changes effected by PD-1 signaling by mass spectrometry-based metabolomics and isotopomer analysis. Inhibitory signaling reduced aerobic glycolysis and glutaminolysis. A general scarcity across the panel of metabolites measured supported widespread metabolic regulation by PD-1. Glucose carbon fate analysis supported tricarboxylic acid cycle reliance on pyruvate carboxylation, catabolic-state fluxes into acetyl-CoA and succinyl-CoA, and a block in de novo nucleoside phosphate synthesis that was accompanied by reduced mTORC1 signaling. Nonetheless, exogenous administration of nucleosides was not sufficient to ameliorate proliferation of T-cells in the context of multiple metabolic insufficiencies due to PD-L1 treatment. Carbon fate analysis did not support the use of primarily glucose-derived carbons to fuel fatty acid beta oxidation, in contrast to reports on T-memory cells. These findings add to our understanding of metabolic dysregulation by PD-1 signaling and inform the effort to rationally develop metabolic interventions coupled with immune-checkpoint blockade for increased treatment efficacy.

Published
2019

19. Turnover Prediction Of Shares using Data Mining techniques : A Case Study

Author

Shashaank, D. S., Sruthi, V., Vijayalakshimi, M. L. S, and Garcia, Jacob Shomona

Subjects
Computer Science - Learning
Abstract

Predicting the turnover of a company in the ever fluctuating Stock market has always proved to be a precarious situation and most certainly a difficult task in hand. Data mining is a well-known sphere of Computer Science that aims on extracting meaningful information from large databases. However, despite the existence of many algorithms for the purpose of predicting the future trends, their efficiency is questionable as their predictions suffer from a high error rate. The objective of this paper is to investigate various classification algorithms to predict the turnover of different companies based on the Stock price. The authorized dataset for predicting the turnover was taken from www.bsc.com and included the stock market values of various companies over the past 10 years. The algorithms were investigated using the "R" tool. The feature selection algorithm, Boruta, was run on this dataset to extract the important and influential features for classification. With these extracted features, the Total Turnover of the company was predicted using various classification algorithms like Random Forest, Decision Tree, SVM and Multinomial Regression. This prediction mechanism was implemented to predict the turnover of a company on an everyday basis and hence could help navigate through dubious stock market trades. An accuracy rate of 95% was achieved by the above prediction process. Moreover, the importance of stock market attributes was established as well.

Published
2015

22. Pf-HaploAtlas: an interactive web app for spatiotemporal analysis of Plasmodium falciparum genes.

Author

Lee, Chiyun, Ünlü, Eyyüb S, White, Nina F D, Almagro-Garcia, Jacob, Ariani, Cristina, and Pearson, Richard D

Subjects
WHOLE genome sequencing, GENETIC variation, VACCINE effectiveness, PLASMODIUM falciparum, GENOMICS, PHARMACOGENOMICS
Abstract

Motivation Monitoring the genomic evolution of Plasmodium falciparum— the most widespread and deadliest of the human-infecting malaria species—is critical for making decisions in response to changes in drug resistance, diagnostic test failures, and vaccine effectiveness. The MalariaGEN data resources are the world's largest whole genome sequencing databases for Plasmodium parasites. The size and complexity of such data is a barrier to many potential end users in both public health and academic research. A user-friendly method for accessing and exploring data on the genetic variation of P. falciparum would greatly enable efforts in studying and controlling malaria. Results We developed Pf-HaploAtlas, a web application enabling exploratory data analysis of genomic variation without requiring advanced technical expertise. The app provides analysis-ready data catalogues and visualizations of amino acid haplotypes for all 5102 core P. falciparum genes. Pf-HaploAtlas facilitates comprehensive spatial and temporal exploration of genes and variants of interest by using data from 16 203 samples, from 33 countries, and spread between the years 1984 and 2018. The scope of Pf-HaploAtlas will expand with each new MalariaGEN Plasmodium data release. Availability and implementation Pf-HaploAtlas is available online for public use at https://apps.malariagen.net/pf-haploatlas , which allows users to download the underlying amino acid haplotype data for further analyses, and its source code is freely available on GitHub under the MIT licence at https://github.com/malariagen/pf-haploatlas. [ABSTRACT FROM AUTHOR]

Published
2024
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23. Lisocabtagene maraleucel for patients with relapsed or refractory large B-cell lymphomas (TRANSCEND NHL 001): a multicentre seamless design study

Author

Abramson, Jeremy S, Palomba, M Lia, Gordon, Leo I, Lunning, Matthew A, Wang, Michael, Arnason, Jon, Mehta, Amitkumar, Purev, Enkhtsetseg, Maloney, David G, Andreadis, Charalambos, Sehgal, Alison, Solomon, Scott R, Ghosh, Nilanjan, Albertson, Tina M, Garcia, Jacob, Kostic, Ana, Mallaney, Mary, Ogasawara, Ken, Newhall, Kathryn, Kim, Yeonhee, Li, Daniel, and Siddiqi, Tanya

Published
2020
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24. Global and local patterns of population structure and their role in the evolution and demography of Plasmodium falciparum

Author

Almagro-Garcia, Jacob, McVean, Gilean, and Kwiatkowski, Dominic

Subjects
616.9, Malaria
Abstract

In this thesis, I study the role of genetic population structure in the evolution and demography of Plasmodium falciparum by focusing on the recent onset of artemisinin resistance in Southeast Asia, an alarming event for global public health. I describe the population structure of Plasmodium falciparum in the Thai-Cambodian border region, characterizing sympatric but differentiated subpopulations associated with artemisinin resistance. I show evidence that they are the product of recent founder events and seem the primary force spreading resistance. Next, I study a superset of the kelch13 mutations associated with artemisinin resistance, assessing their relationship with population structure and recent founder effects. Each resistant subpopulation possesses a distinct kelch13 allele that, in conjunction with a particular genetic background, seem to have driven recent founder effects. I examine the demography of these resistance alleles using patterns of haplotype sharing and show that the primary mode of spread consists of independent mutational events, with limited gene flow within countries in East Southeast Asia. Subsequently, I assess the origin of kelch13 mutations observed in African isolates, concluding that they are indigenous and have originated independently. These observations undermine localized resistance containment as a strategy for malaria control and suggest that population structure and founder effects may predate and facilitate the emergence of resistance. Therefore, monitoring these phenomena could warn about the development of resistance before phenotypic evidence materializes. Next, given the importance of demographic inference to inform malaria control programs and the advent of large genomic datasets, I develop a fast and scalable method to build the ancestral haplotype graph. I show that this data structure, composed of a collection of local haplotype trees, is informative about the recent genealogical history of the sequences and can be used to summarize and study shared haplotype patterns along the genome. I describe a set of algorithms with quasilinear time complexity as a first step in the development of scalable demographic inferential methods that can be applied to several thousands of sequences. I also evaluate how mixed infections affect the analysis of deep sequencing data and review the FWS statistic, a relative measure of inbreeding and complexity of infection. In doing so, I show that the original FWS estimator discards the diversity encoded by rare variants and provide an alternative estimator without such bias that is simpler, more intuitive and has a better resolution.

Published
2016

25. A complexPlasmodium falciparumcryptotype circulating at low frequency across the African continent

Author

Miotto, Olivo, primary, Amambua-Ngwa, Alfred, additional, Amenga-Etego, Lucas, additional, Abdel Hamid, Muzamil M, additional, Adam, Ishag, additional, Aninagyei, Enoch, additional, Apinjoh, Tobias, additional, Awandare, Gordon A, additional, Bejon, Philip, additional, Bertin, Gwladys I, additional, Bouyou-Akotet, Marielle, additional, Claessens, Antoine, additional, Conway, David J, additional, D’Alessandro, Umberto, additional, Diakite, Mahamadou, additional, Djimdé, Abdoulaye, additional, Dondorp, Arjen M, additional, Duffy, Patrick, additional, Fairhurst, Rick M, additional, Fanello, Caterina I, additional, Ghansah, Anita, additional, Ishengoma, Deus, additional, Lawniczak, Mara, additional, Maïga-Ascofaré, Oumou, additional, Auburn, Sarah, additional, Rosanas-Urgell, Anna, additional, Wasakul, Varanya, additional, White, Nina FD, additional, Almagro-Garcia, Jacob, additional, Pearson, Richard D, additional, Goncalves, Sonia, additional, Ariani, Cristina, additional, Bozdech, Zbynek, additional, Hamilton, William, additional, Simpson, Victoria, additional, and Kwiatkowski, Dominic P, additional

Published
2024
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31. Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study

Author

Abathina, Amadou, Abubakar, Ismaela, Achidi, Eric, Agbenyega, Tsiri, Aiyegbo, Mohammed, Akoto, Alex, Allen, Angela, Allen, Stephen, Amenga-Etego, Lucas, Amodu, Folakemi, Amodu, Olukemi, Anchang-Kimbi, Judith, Ansah, Nana, Ansah, Patrick, Ansong, Daniel, Antwi, Sampson, Anyorigiya, Thomas, Apinjoh, Tobias, Asafo-Agyei, Emmanuel, Asoala, Victor, Atuguba, Frank, Auburn, Sarah, Bah, Abdou, Bamba, Kariatou, Bancone, Germana, Band, Gavin, Barnwell, David, Barry, Abdoulaye, Bauni, Evasius, Besingi, Richard, Bojang, Kalifa, Bougouma, Edith, Bull, Susan, Busby, George, Camara, Abdoulie, Camara, Landing, Campino, Susana, Carter, Richard, Carucci, Dan, Casals-Pascual, Climent, Ceesay, Ndey, Ceesay, Pa, Chau, Tran, Chuong, Ly, Clark, Taane, Clarke, Geraldine, Cole-Ceesay, Ramou, Conway, David, Cook, Katharine, Cook, Olivia, Cornelius, Victoria, Corran, Patrick, Correa, Simon, Cox, Sharon, Craik, Rachel, Danso, Bakary, Davis, Timothy, Day, Nicholas, Deloukas, Panos, Dembele, Awa, deVries, Jantina, Dewasurendra, Rajika, Diakite, Mahamadou, Diarra, Elizabeth, Dibba, Yaya, Diss, Andrea, Djimdé, Abdoulaye, Dolo, Amagana, Doumbo, Ogobara, Doyle, Alan, Drakeley, Chris, Drury, Eleanor, Duffy, Patrick, Dunstan, Sarah, Ebonyi, Augustine, Elhassan, Ahmed, Elhassan, Ibrahim, Elzein, Abier, Enimil, Anthony, Esangbedo, Pamela, Evans, Jennifer, Evans, Julie, Farrar, Jeremy, Fernando, Deepika, Fitzpatrick, Kathryn, Fullah, Janet, Garcia, Jacob, Ghansah, Anita, Gottleib, Michael, Green, Angie, Hart, Lee, Hennsman, Meike, Hien, Tran, Hieu, Nguyen, Hilton, Eliza, Hodgson, Abraham, Horstmann, Rolf, Hubbart, Christina, Hughes, Catherine, Hussein, Ayman, Hutton, Robert, Ibrahim, Muntaser, Ishengoma, Deus, Jaiteh, Jula, Jallow, Mariatou, Jallow, Muminatou, Jammeh, Kebba, Jasseh, Momodou, Jeffreys, Anna, Jobarteh, Amie, Johnson, Kimberly, Joseph, Sarah, Jyothi, Dushyanth, Kachala, David, Kamuya, Dorcas, Kanyi, Haddy, Karunajeewa, Harin, Karunaweera, Nadira, Keita, Momodou, Kerasidou, Angeliki, Khan, Aja, Kivinen, Katja, Kokwaro, Gilbert, Konate, Amadou, Konate, Salimata, Koram, Kwadwo, Kwiatkowski, Dominic, Laman, Moses, Le, Si, Leffler, Ellen, Lemnge, Martha, Lin, Enmoore, Ly, Alioune, Macharia, Alexander, MacInnis, Bronwyn, Mai, Nguyen, Makani, Julie, Malangone, Cinzia, Mangano, Valentina, Manjurano, Alphaxard, Manneh, Lamin, Manning, Laurens, Manske, Magnus, Marsh, Kevin, Marsh, Vicki, Maslen, Gareth, Maxwell, Caroline, Mbunwe, Eric, McCreight, Marilyn, Mead, Daniel, Mendy, Alieu, Mendy, Anthony, Mensah, Nathan, Michon, Pascal, Miles, Alistair, Miotto, Olivo, Modiano, David, Mohamed, Hiba, Molloy, Sile, Molyneux, Malcolm, Molyneux, Sassy, Moore, Mike, Moyes, Catherine, Mtei, Frank, Mtove, George, Mueller, Ivo, Mugri, Regina, Munthali, Annie, Mutabingwa, Theonest, Nadjm, Behzad, Ndi, Andre, Ndila, Carolyne, Newton, Charles, Niangaly, Amadou, Njie, Haddy, Njie, Jalimory, Njie, Madi, Njie, Malick, Njie, Sophie, Njiragoma, Labes, Nkrumah, Francis, Ntunthama, Neema, Nyika, Aceme, Nyirongo, Vysaul, O'Brien, John, Obu, Herbert, Oduro, Abraham, Ofori, Alex, Olaniyan, Subulade, Olaosebikan, Rasaq, Oluoch, Tom, Omotade, Olayemi, Oni, Olajumoke, Onykwelu, Emmanuel, Opi, Daniel, Orimadegun, Adebola, O'Riordan, Sean, Ouedraogo, Issa, Oyola, Samuel, Parker, Michael, Pearson, Richard, Pensulo, Paul, Peshu, Norbert, Phiri, Ajib, Phu, Nguyen, Pinder, Margaret, Pirinen, Matti, Plowe, Chris, Potter, Claire, Poudiougou, Belco, Puijalon, Odile, Quyen, Nguyen, Ragoussis, Ioannis, Ragoussis, Jiannis, Rasheed, Oba, Reeder, John, Reyburn, Hugh, Riley, Eleanor, Risley, Paul, Rockett, Kirk, Rodford, Joanne, Rogers, Jane, Rogers, William, Rowlands, Kate, Ruano-Rubio, Valentín, Sabally-Ceesay, Kumba, Sadiq, Abubacar, Saidy-Khan, Momodou, Saine, Horeja, Sakuntabhai, Anavaj, Sall, Abdourahmane, Sambian, David, Sambou, Idrissa, SanJoaquin, Miguel, Sepúlveda, Nuno, Shah, Shivang, Shelton, Jennifer, Siba, Peter, Silva, Nilupa, Simmons, Cameron, Simpore, Jaques, Singhasivanon, Pratap, Sinh, Dinh, Sirima, Sodiomon, Sirugo, Giorgio, Sisay-Joof, Fatoumatta, Sissoko, Sibiry, Small, Kerrin, Somaskantharajah, Elilan, Spencer, Chris, Stalker, Jim, Stevens, Marryat, Suriyaphol, Prapat, Sylverken, Justice, Taal, Bintou, Tall, Adama, Taylor, Terrie, Teo, Yik, Thai, Cao, Thera, Mahamadou, Titanji, Vincent, Toure, Ousmane, Troye-Blomberg, Marita, Usen, Stanley, Uyoga, Sophie, Vanderwal, Aaron, Wangai, Hannah, Watson, Renee, Williams, Thomas, Wilson, Michael, Wrigley, Rebecca, Yafi, Clarisse, Yamoah, Lawrence, Ndila, Carolyne M, Macharia, Alexander W, Nyutu, Gideon, Ojal, John, Shebe, Mohammed, Awuondo, Kennedy O, Mturi, Neema, Tsofa, Benjamin, Clark, Taane G, Kariuki, Silvia, Mackinnon, Margaret, Maitland, Kathryn, Kwiatkowski, Dominic P, Rockett, Kirk A, and Williams, Thomas N

Published
2018
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35. Temporal trends in microplastic accumulation in placentas from pregnancies in Hawaiʻi

Author

Barbano Weingrill, Rodrigo, primary, Lee, Men-Jean, additional, Benny, Paula, additional, Riel, Jonathan, additional, Saiki, Kevin, additional, Garcia, Jacob, additional, Farias Azevedo de Magalhaes Oliveira, Lais, additional, Jorge da Silva Fonseca, Eduardo, additional, Teixeira de Souza, Samuel, additional, de Oliveira Silva D'Amato, Flavio, additional, Rocha Silva, Ueslen, additional, Lima Dutra, Mariana, additional, Lays Xavier Marques, Aldilane, additional, Urban Borbely, Alexandre, additional, and Urschitz, Johann, additional

Published
2023
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38. Effect of oxidation on excited state dynamics of neutral TinO2n−x (n < 10, x < 4) clusters.

Author

Garcia, Jacob M., Heald, Lauren F., Shaffer, Ryan E., and Sayres, Scott G.

Subjects
*EXCITED states, *OXIDATION states, *CHARGE carriers, *TITANIUM oxides, *FEMTOSECOND pulses, *PHOTOEXCITATION
Abstract

Excited state lifetimes of neutral titanium oxide clusters (TinO2n−x, n < 10, x < 4) were measured using a sequence of 400 nm pump and 800 nm probe femtosecond laser pulses. Despite large differences in electronic properties between the closed shell stoichiometric TinO2n clusters and the suboxide TinO2n−x (x = 1–3) clusters, the transient responses for all clusters contain a fast response of 35 fs followed by a sub-picosecond (ps) excited state lifetime. In this non-scalable size regime, subtle changes in the sub-ps lifetimes are attributed to variations in the coordination of Ti atoms and localization of charge carriers following UV photoexcitation. In general, clusters exhibit longer lifetimes with increased size and also with the addition of O atoms. This suggests that the removal of O atoms develops stronger Ti–Ti interactions as the system transitions from a semiconducting character to a fast metallic electronic relaxation mechanism. [ABSTRACT FROM AUTHOR]

Published
2021
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40. ADVANCED CHARACTERIZATION OF MATERIALS USING ATOM PROBE TOMOGRAPHY.

Author

Garcia, Jacob M. and Chiaramonti, Ann N.

Subjects
*ATOM-probe tomography, *PHYSICAL & theoretical chemistry, *MATERIALS science, *SECONDARY ion mass spectrometry, *FIELD ion microscopy, *TUNNEL junctions (Materials science)
Abstract

The article discusses the advanced characterization of materials in electronic devices using atom probe tomography (APT). APT, providing sub-nanometer 3D maps with high analytical sensitivity, is highlighted for its role in understanding failure modes influenced by material choice, processing methods, and service conditions. Topics include the evolution of APT, experimental overview, scope of material characterization, and examples of its applications in electronic devices.

Published
2024
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41. Abstract CT137: ENLIGHTen-01: a phase 1 study of fluorescein-specific (FITC-E2)-car T cells in combination with folate-fluorescein (UB-TT170) for osteosarcoma

Author

Albert, Catherine M., primary, Pinto, Navin R., additional, Taylor, Mallory, additional, Wilson, Ashley, additional, Rawlings-Rhea, Stephanie, additional, Narayanaswamy, Prabha, additional, Huang, Wenjun, additional, Seidel, Kristy, additional, Mgebroff, Stephanie, additional, Brown, Christopher, additional, Garcia, Jacob, additional, Teoh, Jeffrey, additional, Orentas, Rimas J., additional, Gardner, Rebecca A., additional, Jensen, Michael C., additional, and Park, Julie R., additional

Published
2023
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42. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

Author

Abdel Hamid, Muzamil Mahdi, Abdelraheem, Mohamed Hassan, Acheampong, Desmond Omane, Ahouidi, Ambroise, Ali, Mozam, Almagro-Garcia, Jacob, Amambua-Ngwa, Alfred, Amaratunga, Chanaki, Amenga-Etego, Lucas, Andagalu, Ben, Anderson, Tim, Andrianaranjaka, Voahangy, Aniebo, Ifeyinwa, Aninagyei, Enoch, Ansah, Felix, Ansah, Patrick, Apinjoh, Tobias, Arnaldo, Paulo, Ashley, Elizabeth, Auburn, Sarah, Awandare, Gordon, Ba, Hampate, Baraka, Vito, Barry, Alyssa, Bejon, Philip, Bertin, Gwladys, Boni, Maciej, Borrmann, Steffen, Bousema, Teun, Bouyou-Akotet, Marielle, Branch, Oralee, Bull, Peter, Cheah, Huch, Chindavongsa, Keobouphaphone, Chookajorn, Thanat, Chotivanich, Kesinee, Claessens, Antoine, Conway, David, Corredor, Vladimir, Courtier, Erin, Craig, Alister, d'Alessandro, Umberto, Dama, Souleymane, Day, Nicholas, Denis, Brigitte, Dhorda, Mehul, Diakite, Mahamadou, Djimde, Abdoulaye, Dolecek, Christiane, Dondorp, Arjen, Doumbia, Seydou, Drakeley, Chris, Drury, Eleanor, Duffy, Patrick, Echeverry, Diego, Egwang, Thomas, Enosse, Sonia Maria Mauricio, Erko, Berhanu, Fairhurst, Rick, Faiz, Abdul, Fanello, Caterina, Fleharty, Mark, Forbes, Matthew, Fukuda, Mark, Gamboa, Dionicia, Ghansah, Anita, Golassa, Lemu, Goncalves, Sonia, Harrison, G, Healy, Sara Anne, Hendry, Jason, Hernandez-Koutoucheva, Anastasia, Hien, Tran Tinh, Hill, Catherine, Hombhanje, Francis, Hott, Amanda, Htut, Ye, Hussein, Mazza, Imwong, Mallika, Ishengoma, Deus, Jackson, Scott, Jacob, Chris, Jeans, Julia, Johnson, Kimberly, Kamaliddin, Claire, Kamau, Edwin, Keatley, Jon, Kochakarn, Theerarat, Konate, Drissa, Konaté, Abibatou, Kone, Aminatou, Kwiatkowski, Dominic, Kyaw, Myat, Kyle, Dennis, Lawniczak, Mara, Lee, Samuel, Lemnge, Martha, Lim, Pharath, Lon, Chanthap, Loua, Kovana, Mandara, Celine, Marfurt, Jutta, Marsh, Kevin, Maude, Richard James, Mayxay, Mayfong, Maïga-Ascofaré, Oumou, Miotto, Olivo, Mita, Toshihiro, Mobegi, Victor, Mohamed, Abdelrahim Osman, Mokuolu, Olugbenga, Montgomery, Jaqui, Morang'A, Collins Misita, Mueller, Ivo, Murie, Kathryn, Newton, Paul, Ngo Duc, Thang, Nguyen, Thuy, Nguyen, Thuy-Nhien, Nguyen Thi Kim, Tuyen, Nguyen Van, Hong, Noedl, Harald, Nosten, François, Noviyanti, Rintis, Ntui, Vincent Ntui-Njock, Nzila, Alexis, Ochola-Oyier, Lynette Isabella, Ocholla, Harold, Oduro, Abraham, Omedo, Irene, Onyamboko, Marie, Ouedraogo, Jean-Bosco, Oyebola, Kolapo, Oyibo, Wellington Aghoghovwia, Pearson, Richard, Peshu, Norbert, Phyo, Aung, Plowe, Christopher, Price, Ric, Pukrittayakamee, Sasithon, Quang, Huynh Hong, Randrianarivelojosia, Milijaona, Rayner, Julian, Ringwald, Pascal, Rosanas-Urgell, Anna, Rovira-Vallbona, Eduard, Ruano-Rubio, Valentin, Ruiz, Lastenia, Saunders, David, Shayo, Alex, Siba, Peter, Simpson, Victoria, Sissoko, Mahamadou, Smith, Christen, Su, Xin-Zhuan, Sutherland, Colin, Takala-Harrison, Shannon, Talman, Arthur, Tavul, Livingstone, Thanh, Ngo Viet, Thathy, Vandana, Thu, Aung Myint, Toure, Mahamoudou, Tshefu, Antoinette, Verra, Federica, Vinetz, Joseph, Wellems, Thomas, Wendler, Jason, White, Nicholas, Whitton, Georgia, Yavo, William, van der Pluijm, Rob, MalariaGEN, University of Khartoum, University of Cape Coast [Ghana], Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), The Wellcome Trust Sanger Institute [Cambridge], London School of Hygiene and Tropical Medicine [Fajara, Gambia], London School of Hygiene and Tropical Medicine (LSHTM), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), West African Centre for Cell Biology of Infectious Pathogens [Legon, Ghana] (WACCBIP), University of Ghana, Navrongo Health Research Centre [Navrongo, Ghana] (NHRC), Kenya Medical Research Institute (KEMRI), Texas Biomedical Research Institute [San Antonio, TX], Université d'Antananarivo, University of Buéa, Instituto Nacional de Saude [Maputo, Mozambique] (INS), Centre for Tropical Medicine and Global Health [Oxford, UK], Nuffield Department of Medicine [Oxford, UK] (Big Data Institute), University of Oxford-University of Oxford, Mahidol Oxford Tropical Medicine Research Unit (MORU), University of Oxford-Mahidol University [Bangkok]-Wellcome Trust, Menzies School of Health Research [Australia], Charles Darwin University [Australia], Nuffield Department of Clinical Medicine [Oxford], University of Oxford, Institut de Recherche pour le Développement (IRD), Laboratory of Pathogen and Host Immunity [Montpellier] (LPHI), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), and Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)

Subjects
data resource, lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4], plasmodium falciparum, genomics, malaria, Medicine (miscellaneous), genomic epidemiology, General Biochemistry, Genetics and Molecular Biology, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

Contains fulltext : 291985.pdf (Publisher’s version ) (Open Access) We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.

Published
2023
Full Text
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45. Qualidade de vida relacionada com a saúde, quedas e sarcopenia em idosos cabo-verdianos

Author

Garcia, Jacob Mendes Furtado, Loureiro, Vânia, and Bento, Pedro

Subjects
Qualidade de vida, Idosos, Acidente por queda, Envelhecimento ativo
Abstract

Introdução: O presente estudo pretende medir os níveis de Qualidade de Vida Relacionado com a Saúde, Quedas e Sarcopenia dos idosos com mais de 55 anos que residem no concelho de Santa Cruz em cabo verde. O objetivo geral do trabalho de investigação foi caraterizar a qualidade de vida relacionada com a saúde (QdVRS) e a prevalência de quedas e de sarcopenia na população idosa de Cabo-Verde. Metodologia - O estudo, baseado na aplicação de questionários, foi levado a cabo através da aplicação presencial dos questionários pelo investigador, com recurso à utilização da plataforma Google Forms. De seguida serão explicados os diferentes instrumentos de investigação aplicados no estudo. No estudo foram aplicados diferentes instrumentos: questionário de caraterização sociodemográfica, questionário histórico de quedas, questionário de estado de saúde e questionário SARC-F. Trata-se de um estudo exploratório e descritivo, transversal corelaciona, orientado por uma metodologia quantitativa, com uma amostra de 42 indivíduos idosos. Analise de dados- Verificou-se que uma elevada prevalência de quedas (73,2%) entre os idosos participantes no estudo e 80% idosos, que reportaram queda, referem que caíram entre 1 a 3 vezes. Não se verificaram diferenças estatisticamente significativas entre géneros. Relativamente ao medo de cair, a maior parte dos idosos (75,6%) refere que tem medo. A prevalência de sarcopenia surge associada a idosos que reportaram queda nos últimos 12 meses (39%) e a idosos que têm medo de cair (43,9%). Conclusão - Este estudo permitiu concluir que os idosos da amostra sobre atividade física e a qualidade de vida dos idosos, deverão ser um processo compartilhado, em que a principal preocupação é a integração das questões económicas, sociais e ambientais com as condições de vida e a utilização dos recursos existentes. A prevalência de sarcopenia aumentou conforme o avançar da idade em ambos os sexos, o que confirma a perda de massa e função muscular que ocorre com o avançar da idade e medo de cair, em idoso cabo-verdianos.

Published
2023

46. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

Author

MalariaGEN, Abdel Hamid, Muzamil Mahdi, Abdelraheem, Mohamed Hassan, Acheampong, Desmond Omane, Ahouidi, Ambroise, Ali, Mozam, Almagro-Garcia, Jacob, Amambua-Ngwa, Alfred, Amaratunga, Chanaki, Amenga-Etego, Lucas, Andagalu, Ben, Anderson, Tim, Andrianaranjaka, Voahangy, Aniebo, Ifeyinwa, Aninagyei, Enoch, Ansah, Felix, Ansah, Patrick O, Apinjoh, Tobias, Arnaldo, Paulo, Ashley, Elizabeth, Auburn, Sarah, Awandare, Gordon A, Ba, Hampate, Baraka, Vito, Barry, Alyssa, Bejon, Philip, Bertin, Gwladys I, Boni, Maciej F, Borrmann, Steffen, Bousema, Teun, Bouyou-Akotet, Marielle, Branch, Oralee, Bull, Peter C, Cheah, Huch, Chindavongsa, Keobouphaphone, Chookajorn, Thanat, Chotivanich, Kesinee, Claessens, Antoine, Conway, David J, Corredor, Vladimir, Courtier, Erin, Craig, Alister, D'Alessandro, Umberto, Dama, Souleymane, Day, Nicholas, Denis, Brigitte, Dhorda, Mehul, Diakite, Mahamadou, Djimde, Abdoulaye, Dolecek, Christiane, Dondorp, Arjen, Doumbia, Seydou, Drakeley, Chris, Drury, Eleanor, Duffy, Patrick, Echeverry, Diego F, Egwang, Thomas G, Enosse, Sonia Maria Mauricio, Erko, Berhanu, Fairhurst, Rick M, Faiz, Abdul, Fanello, Caterina A, Fleharty, Mark, Forbes, Matthew, Fukuda, Mark, Gamboa, Dionicia, Ghansah, Anita, Golassa, Lemu, Goncalves, Sonia, Harrison, GL Abby, Healy, Sara Anne, Hendry, Jason A, Hernandez-Koutoucheva, Anastasia, Hien, Tran Tinh, Hill, Catherine A, Hombhanje, Francis, Hott, Amanda, Htut, Ye, Hussein, Mazza, Imwong, Mallika, Ishengoma, Deus, Jackson, Scott A, Jacob, Chris G, Jeans, Julia, Johnson, Kimberly J, Kamaliddin, Claire, Kamau, Edwin, Keatley, Jon, Kochakarn, Theerarat, Konate, Drissa S, Konaté, Abibatou, Kone, Aminatou, Kwiatkowski, Dominic P, Kyaw, Myat P, Kyle, Dennis, Lawniczak, Mara, Lee, Samuel K, Lemnge, Martha, Lim, Pharath, Lon, Chanthap, Loua, Kovana M, Mandara, Celine I, Marfurt, Jutta, Marsh, Kevin, Maude, Richard James, Mayxay, Mayfong, Maïga-Ascofaré, Oumou, Miotto, Olivo, Mita, Toshihiro, Mobegi, Victor, Mohamed, Abdelrahim Osman, Mokuolu, Olugbenga A, Montgomery, Jaqui, Morang'a, Collins Misita, Mueller, Ivo, Murie, Kathryn, Newton, Paul N, Ngo Duc, Thang, Nguyen, Thuy, Nguyen, Thuy-Nhien, Nguyen Thi Kim, Tuyen, Nguyen Van, Hong, Noedl, Harald, Nosten, Francois, Noviyanti, Rintis, Ntui, Vincent Ntui-Njock, Nzila, Alexis, Ochola-Oyier, Lynette Isabella, Ocholla, Harold, Oduro, Abraham, Omedo, Irene, Onyamboko, Marie A, Ouedraogo, Jean-Bosco, Oyebola, Kolapo, Oyibo, Wellington Aghoghovwia, Pearson, Richard, Peshu, Norbert, Phyo, Aung P, Plowe, Christopher V, Price, Ric N, Pukrittayakamee, Sasithon, Quang, Huynh Hong, Randrianarivelojosia, Milijaona, Rayner, Julian C, Ringwald, Pascal, Rosanas-Urgell, Anna, Rovira-Vallbona, Eduard, Ruano-Rubio, Valentin, Ruiz, Lastenia, Saunders, David, Shayo, Alex, Siba, Peter, Simpson, Victoria J, Sissoko, Mahamadou S, Smith, Christen, Su, Xin-Zhuan, Sutherland, Colin, Takala-Harrison, Shannon, Talman, Arthur, Tavul, Livingstone, Thanh, Ngo Viet, Thathy, Vandana, Thu, Aung Myint, Toure, Mahamoudou, Tshefu, Antoinette, Verra, Federica, Vinetz, Joseph, Wellems, Thomas E, Wendler, Jason, White, Nicholas J, Whitton, Georgia, Yavo, William, Van Der Pluijm, Rob W, Amenga-Etego, Lucas [0000-0003-4468-0506], Anderson, Tim [0000-0002-0191-0204], Ansah, Patrick O [0000-0002-3214-5621], Ashley, Elizabeth [0000-0002-7620-4822], Ba, Hampate [0000-0002-9299-5775], Baraka, Vito [0000-0001-9694-9293], Bejon, Philip [0000-0002-2135-7549], Bertin, Gwladys I [0000-0002-2218-9591], Boni, Maciej F [0000-0002-0830-9630], Bousema, Teun [0000-0003-2666-094X], Chookajorn, Thanat [0000-0003-2876-6203], Claessens, Antoine [0000-0002-4277-0914], Conway, David J [0000-0002-8711-3037], Craig, Alister [0000-0003-0914-6164], D'Alessandro, Umberto [0000-0001-6341-5009], Day, Nicholas [0000-0003-2309-1171], Diakite, Mahamadou [0000-0002-4268-8857], Djimde, Abdoulaye [0000-0003-0062-2283], Dondorp, Arjen [0000-0001-5190-2395], Drakeley, Chris [0000-0003-4863-075X], Echeverry, Diego F [0000-0003-0301-4478], Erko, Berhanu [0000-0003-1685-752X], Faiz, Abdul [0000-0002-3460-7535], Fanello, Caterina A [0000-0003-1932-9562], Gamboa, Dionicia [0000-0002-1420-7729], Golassa, Lemu [0000-0002-1216-8711], Healy, Sara Anne [0000-0003-3078-6094], Ishengoma, Deus [0000-0003-2040-3416], Jackson, Scott A [0000-0002-3172-1607], Kamaliddin, Claire [0000-0001-8198-6235], Kamau, Edwin [0000-0002-5761-7883], Konate, Drissa S [0000-0002-4177-9642], Kwiatkowski, Dominic P [0000-0002-5023-0176], Kyle, Dennis [0000-0002-0238-965X], Lawniczak, Mara [0000-0002-3006-2080], Loua, Kovana M [0000-0003-0571-0944], Marsh, Kevin [0000-0001-8377-5466], Mayxay, Mayfong [0000-0002-6056-4516], Miotto, Olivo [0000-0001-8060-6771], Mita, Toshihiro [0000-0001-8180-2344], Mobegi, Victor [0000-0002-1962-5583], Morang'a, Collins Misita [0000-0002-6988-150X], Nguyen, Thuy-Nhien [0000-0002-4101-5706], Nosten, Francois [0000-0002-7951-0745], Ntui, Vincent Ntui-Njock [0000-0002-7532-9930], Oduro, Abraham [0000-0002-4191-7419], Onyamboko, Marie A [0000-0002-7501-5931], Ouedraogo, Jean-Bosco [0000-0003-0412-8733], Oyebola, Kolapo [0000-0002-1003-2570], Pearson, Richard [0000-0002-7386-3566], Phyo, Aung P [0000-0002-0383-9624], Price, Ric N [0000-0003-2000-2874], Rayner, Julian C [0000-0002-9835-1014], Rosanas-Urgell, Anna [0000-0002-0432-5203], Shayo, Alex [0000-0002-7099-8537], Su, Xin-Zhuan [0000-0003-3246-3248], Vinetz, Joseph [0000-0001-8344-2004], Wellems, Thomas E [0000-0003-3899-8454], and Apollo - University of Cambridge Repository

Subjects
data resource, plasmodium falciparum, genomics, malaria, genomic epidemiology
Abstract

We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.

Published
2023

47. Nanopore sequencing for real-time genomic surveillance ofPlasmodium falciparum

Author

Girgis, Sophia T., primary, Adika, Edem, additional, Nenyewodey, Felix E., additional, Senoo Jnr, Dodzi K., additional, Ngoi, Joyce M., additional, Bandoh, Kukua, additional, Lorenz, Oliver, additional, van de Steeg, Guus, additional, Nsoh, Sebastian, additional, Judge, Kim, additional, Pearson, Richard D., additional, Almagro-Garcia, Jacob, additional, Saiid, Samirah, additional, Atampah, Solomon, additional, Amoako, Enock K., additional, Morang’a, Collins M., additional, Asoala, Victor, additional, Adjei, Elrmion S., additional, Burden, William, additional, Roberts-Sengier, William, additional, Drury, Eleanor, additional, Gonçalves, Sónia, additional, Awandare, Gordon A., additional, Kwiatkowski, Dominic P., additional, Amenga-Etego, Lucas N., additional, and Hamilton, William L., additional

Published
2022
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