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1. Optical Direct Write of Dolan--Niemeyer-Bridge Junctions for Transmon Qubits

Author

Monroe, J. T., Kowsari, D., Zheng, K., Gaikwad, C., Brewster, J., Wisbey, D. S., and Murch, K. W.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Quantum Physics
Abstract

We characterize highly coherent transmon qubits fabricated with a direct-write photolithography system. Multi-layer evaporation and oxidation allows us to change the critical current density by reducing the effective tunneling area and increasing the barrier thickness. Surface treatments before resist application and again before evaporation result in high coherence devices. With optimized surface treatments we achieve energy relaxation $T_1$ times in excess of $80\ \mu$s for three dimensional transmon qubits with Josephson junction lithographic areas of 2 $\mu\mathrm{m}^2$., Comment: 7 pages, 3 figures

Published
2021
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2. Discovery and spectroscopy of the young Jovian planet 51 Eri b with the Gemini Planet Imager

Author

Macintosh, B., Graham, J. R., Barman, T., De Rosa, R. J., Konopacky, Q., Marley, M. S., Marois, C., Nielsen, E. L., Pueyo, L., Rajan, A., Rameau, J., Saumon, D., Wang, J. J., Patience, J., Ammons, M., Arriaga, P., Artigau, E., Beckwith, S., Brewster, J., Bruzzone, S., Bulger, J., Burningham, B., Burrows, A. S., Chen, C., Chiang, E., Chilcote, J. K., Dawson, R. I., Dong, R., Doyon, R., Draper, Z. H., Duchêne, G., Esposito, T. M., Fabrycky, D., Fitzgerald, M. P., Follette, K. B., Fortney, J. J., Gerard, B., Goodsell, S., Greenbaum, A. Z., Hibon, P., Hinkley, S., Cotten, T. H., Hung, L. -W., Ingraham, P., Johnson-Groh, M., Kalas, P., Lafreniere, D., Larkin, J. E., Lee, J., Line, M., Long, D., Maire, J., Marchis, F., Matthews, B. C., Max, C. E., Metchev, S., Millar-Blanchaer, M. A., Mittal, T., Morley, C. V., Morzinski, K. M., Murray-Clay, R., Oppenheimer, R., Palmer, D. W., Patel, R., Perrin, M. D., Poyneer, L. A., Rafikov, R. R., Rantakyrö, F. T., Rice, E. L., Rojo, P., Rudy, A. R., Ruffio, J. -B., Ruiz, M. T., Sadakuni, N., Saddlemyer, L., Salama, M., Savransky, D., Schneider, A. C., Sivaramakrishnan, A., Song, I., Soummer, R., Thomas, S., Vasisht, G., Wallace, J. K., Ward-Duong, K., Wiktorowicz, S. J., Wolff, S. G., and Zuckerman, B.

Subjects
Astrophysics - Earth and Planetary Astrophysics
Abstract

Directly detecting thermal emission from young extrasolar planets allows measurement of their atmospheric composition and luminosity, which is influenced by their formation mechanism. Using the Gemini Planet Imager, we discovered a planet orbiting the \$sim$20 Myr-old star 51 Eridani at a projected separation of 13 astronomical units. Near-infrared observations show a spectrum with strong methane and water vapor absorption. Modeling of the spectra and photometry yields a luminosity of L/LS=1.6-4.0 x 10-6 and an effective temperature of 600-750 K. For this age and luminosity, "hot-start" formation models indicate a mass twice that of Jupiter. This planet also has a sufficiently low luminosity to be consistent with the "cold- start" core accretion process that may have formed Jupiter., Comment: 29 pages, 3 figures, 2 tables, and Supplementary Materials. published in Science Express on Aug 13 2015. List of authors and the magnitudes of the star were correted

Published
2015
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4. Discovery and spectroscopy of the young jovian planet 51 Eri b with the Gemini Planet Imager.

Author

Macintosh, B, Graham, JR, Barman, T, De Rosa, RJ, Konopacky, Q, Marley, MS, Marois, C, Nielsen, EL, Pueyo, L, Rajan, A, Rameau, J, Saumon, D, Wang, JJ, Patience, J, Ammons, M, Arriaga, P, Artigau, E, Beckwith, S, Brewster, J, Bruzzone, S, Bulger, J, Burningham, B, Burrows, AS, Chen, C, Chiang, E, Chilcote, JK, Dawson, RI, Dong, R, Doyon, R, Draper, ZH, Duchêne, G, Esposito, TM, Fabrycky, D, Fitzgerald, MP, Follette, KB, Fortney, JJ, Gerard, B, Goodsell, S, Greenbaum, AZ, Hibon, P, Hinkley, S, Cotten, TH, Hung, L-W, Ingraham, P, Johnson-Groh, M, Kalas, P, Lafreniere, D, Larkin, JE, Lee, J, Line, M, Long, D, Maire, J, Marchis, F, Matthews, BC, Max, CE, Metchev, S, Millar-Blanchaer, MA, Mittal, T, Morley, CV, Morzinski, KM, Murray-Clay, R, Oppenheimer, R, Palmer, DW, Patel, R, Perrin, MD, Poyneer, LA, Rafikov, RR, Rantakyrö, FT, Rice, EL, Rojo, P, Rudy, AR, Ruffio, J-B, Ruiz, MT, Sadakuni, N, Saddlemyer, L, Salama, M, Savransky, D, Schneider, AC, Sivaramakrishnan, A, Song, I, Soummer, R, Thomas, S, Vasisht, G, Wallace, JK, Ward-Duong, K, Wiktorowicz, SJ, Wolff, SG, and Zuckerman, B

Subjects
astro-ph.EP, General Science & Technology
Abstract

Directly detecting thermal emission from young extrasolar planets allows measurement of their atmospheric compositions and luminosities, which are influenced by their formation mechanisms. Using the Gemini Planet Imager, we discovered a planet orbiting the ~20-million-year-old star 51 Eridani at a projected separation of 13 astronomical units. Near-infrared observations show a spectrum with strong methane and water-vapor absorption. Modeling of the spectra and photometry yields a luminosity (normalized by the luminosity of the Sun) of 1.6 to 4.0 × 10(-6) and an effective temperature of 600 to 750 kelvin. For this age and luminosity, "hot-start" formation models indicate a mass twice that of Jupiter. This planet also has a sufficiently low luminosity to be consistent with the "cold-start" core-accretion process that may have formed Jupiter.

Published
2015

10. PacBio long-read amplicon sequencing enables scalable high-resolution population allele typing of the complex CYP2D6 locus

Author

Charnaud, S, Munro, JE, Semenec, L, Mazhari, R, Brewster, J, Bourke, C, Ruybal-Pesantez, S, James, R, Lautu-Gumal, D, Karunajeewa, H, Mueller, I, Bahlo, M, Charnaud, S, Munro, JE, Semenec, L, Mazhari, R, Brewster, J, Bourke, C, Ruybal-Pesantez, S, James, R, Lautu-Gumal, D, Karunajeewa, H, Mueller, I, and Bahlo, M

Abstract

The CYP2D6 enzyme is estimated to metabolize 25% of commonly used pharmaceuticals and is of intense pharmacogenetic interest due to the polymorphic nature of the CYP2D6 gene. Accurate allele typing of CYP2D6 has proved challenging due to frequent copy number variants (CNVs) and paralogous pseudogenes. SNP-arrays, qPCR and short-read sequencing have been employed to interrogate CYP2D6, however these technologies are unable to capture longer range information. Long-read sequencing using the PacBio Single Molecule Real Time (SMRT) sequencing platform has yielded promising results for CYP2D6 allele typing. However, previous studies have been limited in scale and have employed nascent data processing pipelines. We present a robust data processing pipeline "PLASTER" for accurate allele typing of SMRT sequenced amplicons. We demonstrate the pipeline by typing CYP2D6 alleles in a large cohort of 377 Solomon Islanders. This pharmacogenetic method will improve drug safety and efficacy through screening prior to drug administration.

Published
2022

11. Acquisition of antibodies to Plasmodium falciparum and Plasmodium vivax antigens in pregnant women living in a low malaria transmission area of Brazil

Author

Kassa, MW, Hasang, W, Barateiro, A, Damelang, T, Brewster, J, Dombrowski, JGG, Longley, RJJ, Chung, AW, Wunderlich, G, Mueller, I, Aitken, EH, Marinho, CRF, Rogerson, SJJ, Kassa, MW, Hasang, W, Barateiro, A, Damelang, T, Brewster, J, Dombrowski, JGG, Longley, RJJ, Chung, AW, Wunderlich, G, Mueller, I, Aitken, EH, Marinho, CRF, and Rogerson, SJJ

Abstract

BACKGROUND: Pregnant women have increased susceptibility to Plasmodium falciparum malaria and acquire protective antibodies over successive pregnancies. Most studies that investigated malaria antibody responses in pregnant women are from high transmission areas in sub-Saharan Africa, while reports from Latin America are scarce and inconsistent. The present study sought to explore the development of antibodies against P. falciparum and Plasmodium vivax antigens in pregnant women living in a low transmission area in the Brazilian Amazon. METHODS: In a prospective cohort study, plasma samples from 408 pregnant women (of whom 111 were infected with P. falciparum, 96 had infections with P. falciparum and P. vivax, and 201 had no Plasmodium infection) were used to measure antibody levels. Levels of IgG and opsonizing antibody to pregnancy-specific variant surface antigens (VSAs) on infected erythrocytes (IEs), 10 recombinant VAR2CSA Duffy binding like (DBL domains), 10 non-pregnancy-specific P. falciparum merozoite antigens, and 10 P. vivax antigens were measured by flow cytometry, ELISA, and multiplex assays. Antibody levels and seropositivity among the groups were compared. RESULTS: Antibodies to VSAs on P. falciparum IEs were generally low but were higher in currently infected women and women with multiple P. falciparum episodes over pregnancy. Many women (21%-69%) had antibodies against each individual VAR2CSA DBL domain, and antibodies to DBLs correlated with each other (r ≥ 0.55, p < 0.0001), but not with antibody to VSA or history of infection. Infection with either malaria species was associated with higher seropositivity rate for antibodies against P. vivax proteins, adjusted odds ratios (95% CI) ranged from 5.6 (3.2, 9.7), p < 0.0001 for PVDBPII-Sal1 to 15.7 (8.3, 29.7), p < 0.0001 for PvTRAg_2. CONCLUSIONS: Pregnant Brazilian women had low levels of antibodies to pregnancy-specific VSAs that increased with exposure. They frequently recognized both VAR2CSA DBL d

Published
2022

13. EUSO-SPB2 Telescope Optics and Testing

Author

Kungel, V., Bachman, R., Brewster, J., Dawes, M., Desiato, J., Eser, J., Finch, W., Huelett, L., Olinto, A. V., Pace, J., Pech, M., Reardon, P., Schovanek, P., Wang, C., Wiencke, L., Abdellaoui, G., Abe, S., Adams, J.H., Allard, D., Alonso, G., Anchordoqui, L., Anzalone, A., Arnone, E., Asano, K., Attallah, R., Attoui, H., Ave Pernas, M., Bagheri, M., Baláz, J., Bakiri, M., Barghini, D., Bartocci, S., Battisti, M., Bayer, J., Beldjilali, B., Belenguer, T., Belkhalfa, N., Bellotti, R., Belov, A. A., Benmessai, K., Bertaina, M., Bertone, P. F., Biermann, P. L., Bisconti, F., Blaksley, C., Blanc, N., Blin-Bondil, S., Bobik, P., Bogomilov, M., Bolmgren, K., Bozzo, E., Briz, S., Bruno, A., Caballero, K. S., Cafagna, F., Cambié, G., Campana, D., Capdevielle, J.-N., Capel, F., Caramete, A., Caramete, L., Carlson, P., Caruso, R., Casolino, M., Cassardo, C., Castellina, A., Catalano, O., Cellino, A., Černý, K., Chikawa, M., Chiritoi, G., Christl, M. J., Colalillo, R., Conti, L., Cotto, G., Crawford, H. J., Cremonini, R., Creusot, A., Castro Gónzalez, A. De, Taille, C. De La, Peral, L. Del, Diaz Damian, A., Diesing, R., Dinaucourt, P., Djakonow, A., Djemil, T., Ebersoldt, A., Ebisuzaki, T., Fenu, F., Fernández-González, S., Ferrarese, S., Filippatos, G., Fornaro, C., Fouka, M., Franceschi, A., Franchini, S., Fuglesang, C., Fujii, T., Fukushima, M., Galeotti, P., García-Ortega, E., Gardiol, D., Garipov, G. K., Gascón, E., Gazda, E., Genci, J., Golzio, A., González Alvarado, C., Gorodetzky, P., Green, A., Guarino, F., Guépin, C., Guzmán, A., Hachisu, Y., Haungs, A., Hernández Carretero, J., Hulett, L., Ikeda, D., Inoue, N., Inoue, S., Isgrò, F., Itow, Y., Jammer, T., Jeong, S., Joven, E., Judd, E. G., Jochum, J., Kajino, F., Kajino, T., Kalli, S., Kaneko, I., Karadzhov, Y., Kasztelan, M., Katahira, K., Kawai, K., Kawasaki, Y., Kedadra, A., Khales, H., Khrenov, B. A., Kim, J.-S., Kim, S.-W., Kleifges, M., Klimov, P. A., Kolev, D., Kreykenbohm, I., Krizmanic, J. F., Królik, K., Kurihara, Y., Kusenko, A., Kuznetsov, E., Lahmar, H., Lakhdari, F., Licandro, J., López Campano, L., López Martínez, F., Mackovjak, S., Mahdi, M., Mandát, D., Manfrin, M., Marcelli, L., Marcos, J. L., Marszał, W., Martín, Y., Martinez, O., Mase, K., Matev, R., Matthews, J. N., Mebarki, N., Medina-Tanco, G., Menshikov, A., Merino, A., Mese, M., Meseguer, J., Meyer, S. S., Mimouni, J., Miyamoto, H., Mizumoto, Y., Monaco, A., Morales De Los Ríos, J. A., Mastafa, M., Nagataki, S., Naitamor, S., Napolitano, T., Nachtman, J. M., Neronov, A., Nomoto, K., Nonaka, T., Ogawa, T., Ogio, S., Ohmori, H., Onel, Y., Osteria, G., Otte, A. N., Pagliaro, A., Painter, W., Panasyuk, M. I., Panico, B., Parizot, E., Park, I. H., Pastircak, B., Paul, T., Pérez-Grande, I., Perfetto, F., Peter, T., Picozza, P., Pindado, S., Piotrowski, L. W., Piraino, S., Plebaniak, Z., Pollini, A., Popescu, E. M., Prevete, R., Prévôt, G., Prieto, H., Przybylak, M., Puehlhofer, G., Putis, M., Reno, M. H., Reyes, M., Ricci, M., Rodríguez Frías, M. D., Romero Matamala, O. F., Ronga, F., Sabau, M. D., Saccá, G., Sáez Cano, G., Sagawa, H., Sahnoune, Z., Saito, A., Sakaki, N., Salazar, H., Sanchez Balanzar, J. C., Sánchez, J. L., Santangelo, A., Sanz-Andrés, A., Sanz Palomino, M., Saprykin, O. A., Sarazin, F., Sato, M., Scagliola, A., Schanz, T., Schieler, H., Schovánek, P., Scotti, V., Serra, M., Sharakin, S. A., Shimizu, H. M., Shinozaki, K., Soriano, J. F., Sotgiu, A., Stan, I., Strharský, I., Sugiyama, N., Supanitsky, D., Suzuki, M., Szabelski, J., Tajima, N., Tajima, T., Takahashi, Y., Takeda, M., Takizawa, Y., Talai, M. C., Tameda, Y., Tenzer, C., Thomas, S. B., Tibolla, O., Tkachev, L. G., Tomida, T., Tone, N., Toscano, S., Traïche, M., Tsunesada, Y., Tsuno, K., Turriziani, S., Uchihori, Y., Vaduvescu, O., Valdés-Galicia, J. F., Vallania, P., Valore, L., Vankova-Kirilova, G., Venters, T. M., Vigorito, C., Villaseñor, L., Vlcek, B., Ballmoos, P. Von, Vrabel, M., Wada, S., Watanabe, J., Watts, J., Weigand Muñoz, R., Weindl, A., Wille, M., Wilms, J., Winn, D., Yamamoto, T., Yang, J., Yano, H., Yashin, I. V., Yonetoku, D., Yoshida, S., Young, R., Zgura, I. S., Zotov, M. Yu, Zuccaro Marchi, A., and JEM-EUSO Collaboration

Subjects
Physics, ddc:530
Abstract

The Extreme Universe Space Observatory - Super Pressure Balloon (EUSO-SPB2) mission will fly two custom telescopes that feature Schmidt optics to measure Cherenkov- and fluorescence emission of extensive air showers from cosmic rays at the PeV and EeV-scale, and search for τ-neutrinos. Both telescopes have 1-meter diameter apertures and UV/UV-visible sensitivity. The Cherenkov telescope uses a bifocal mirror segment alignment, to distinguish between a direct cosmic ray that hits the camera versus the Cherenkov light from outside the telescope. Telescope integration and laboratory calibration will be performed in Colorado. To estimate the point spread function and efficiency of the integrated telescopes, a test beam system that delivers a 1-meter diameter parallel beam of light is being fabricated. End-to-end tests of the fully integrated instruments will be carried out in a field campaign at dark sites in the Utah desert using cosmic rays, stars, and artificial light sources. Laser tracks have long been used to characterize the performance of fluorescence detectors in the field. For EUSO-SPB2 an improvement in the method that includes a correction for aerosol attenuation is anticipated by using a bi-dynamic Lidar configuration in which both the laser and the telescope are steerable. We plan to conduct these field tests in Fall 2021 and Spring 2022 to accommodate the scheduled launch of EUSO-SPB2 in 2023 from Wanaka, New Zealand.

Published
2022

15. PLANETARY SCIENCE: Discovery and spectroscopy of the young jovian planet 51 Eri b with the Gemini Planet Imager

Author

Macintosh, B., Graham, J. R., Barman, T., De Rosa, R. J., Konopacky, Q., Marley, M. S., Marois, C., Nielsen, E. L., Pueyo, L., Rajan, A., Rameau, J., Saumon, D., Wang, J. J., Patience, J., Ammons, M., Arriaga, P., Artigau, E., Beckwith, S., Brewster, J., Bruzzone, S., Bulger, J., Burningham, B., Burrows, A. S., Chen, C., Chiang, E., Chilcote, J. K., Dawson, R. I., Dong, R., Doyon, R., Draper, Z. H., Duchêne, G., Esposito, T. M., Fabrycky, D., Fitzgerald, M. P., Follette, K. B., Fortney, J. J., Gerard, B., Goodsell, S., Greenbaum, A. Z., Hibon, P., Hinkley, S., Cotten, T. H., Hung, L.-W., Ingraham, P., Johnson-Groh, M., Kalas, P., Lafreniere, D., Larkin, J. E., Lee, J., Line, M., Long, D., Maire, J., Marchis, F., Matthews, B. C., Max, C. E., Metchev, S., Millar-Blanchaer, M. A., Mittal, T., Morley, C. V., Morzinski, K. M., Murray-Clay, R., Oppenheimer, R., Palmer, D. W., Patel, R., Perrin, M. D., Poyneer, L. A., Rafikov, R. R., Rantakyrö, F. T., Rice, E. L., Rojo, P., Rudy, A. R., Ruffio, J.-B., Ruiz, M. T., Sadakuni, N., Saddlemyer, L., Salama, M., Savransky, D., Schneider, A. C., Sivaramakrishnan, A., Song, I., Soummer, R., Thomas, S., Vasisht, G., Wallace, J. K., Ward-Duong, K., Wiktorowicz, S. J., Wolff, S. G., and Zuckerman, B.

Published
2015

23. IgG Antibody Responses Are Preferential Compared With IgM for Use as Serological Markers for Detecting Recent Exposure to Plasmodium vivax Infection

Author

Longley, RJ, White, MT, Brewster, J, Liu, Zoe, Bourke, C, Takashima, E, Harbers, M, Tham, W-H, Healer, J, Chitnis, CE, Monteiro, W, Lacerda, M, Sattabongkot, J, Tsuboi, T, Mueller, I, Longley, RJ, White, MT, Brewster, J, Liu, Zoe, Bourke, C, Takashima, E, Harbers, M, Tham, W-H, Healer, J, Chitnis, CE, Monteiro, W, Lacerda, M, Sattabongkot, J, Tsuboi, T, and Mueller, I

Abstract

Abstract To achieve malaria elimination, new tools are required to explicitly target Plasmodium vivax. Recently, a novel panel of P. vivax proteins were identified and validated as serological markers for detecting recent exposure to P. vivax within the last 9 months. In order to improve the sensitivity and specificity of these markers, immunoglobulin M (IgM) in addition to immunoglobulin G (IgG) antibody responses were compared with a down-selected panel of 20 P. vivax proteins. IgM was tested using archival plasma samples from observational cohort studies conducted in malaria-endemic regions of Thailand and Brazil. IgM responses to these proteins generally had poorer classification performance than IgG.

Published
2021

24. Application of 23 Novel Serological Markers for Identifying Recent Exposure to Plasmodium vivax Parasites in an Endemic Population of Western Thailand

Author

Chotirat, S, Nekkab, N, Kumpitak, C, Hietanen, J, White, MT, Kiattibutr, K, Sa-angchai, P, Brewster, J, Schoffer, K, Takashima, E, Tsuboi, T, Harbers, M, Chitnis, CE, Healer, J, Tham, W-H, Nguitragool, W, Mueller, I, Sattabongkot, J, Longley, RJ, Chotirat, S, Nekkab, N, Kumpitak, C, Hietanen, J, White, MT, Kiattibutr, K, Sa-angchai, P, Brewster, J, Schoffer, K, Takashima, E, Tsuboi, T, Harbers, M, Chitnis, CE, Healer, J, Tham, W-H, Nguitragool, W, Mueller, I, Sattabongkot, J, and Longley, RJ

Abstract

Thailand is aiming for malaria elimination by the year 2030. However, the high proportion of asymptomatic infections and the presence of the hidden hypnozoite stage of Plasmodium vivax are impeding these efforts. We hypothesized that a validated surveillance tool utilizing serological markers of recent exposure to P. vivax infection could help to identify areas of ongoing transmission. The objective of this exploratory study was to assess the ability of P. vivax serological exposure markers to detect residual transmission "hot-spots" in Western Thailand. Total IgG levels were measured against a panel of 23 candidate P. vivax serological exposure markers using a multiplexed bead-based assay. A total of 4,255 plasma samples from a cross-sectional survey conducted in 2012 of endemic areas in the Kanchanaburi and Ratchaburi provinces were assayed. We compared IgG levels with multiple epidemiological factors that are associated with an increased risk of P. vivax infection in Thailand, including age, gender, and spatial location, as well as Plasmodium infection status itself. IgG levels to all proteins were significantly higher in the presence of a P. vivax infection (n = 144) (T-test, p < 0.0001). Overall seropositivity rates varied from 2.5% (PVX_097625, merozoite surface protein 8) to 16.8% (PVX_082670, merozoite surface protein 7), with 43% of individuals seropositive to at least 1 protein. Higher IgG levels were associated with older age (>18 years, p < 0.05) and males (17/23 proteins, p < 0.05), supporting the paradigm that men have a higher risk of infection than females in this setting. We used a Random Forests algorithm to predict which individuals had exposure to P. vivax parasites in the last 9-months, based on their IgG antibody levels to a panel of eight previously validated P. vivax proteins. Spatial clustering was observed at the village and regional level, with a moderate correlation between PCR prevalence and sero-prevalence as predicted by the algorithm.

Published
2021

25. Heterogeneity in response to serological exposure markers of recent Plasmodium vivax infections in contrasting epidemiological contexts

Author

Phillips, MA, Rosado, J, White, MT, Longley, RJ, Lacerda, M, Monteiro, W, Brewster, J, Sattabongkot, J, Guzman-Guzman, M, Llanos-Cuentas, A, Vinetz, JM, Gamboa, D, Mueller, I, Phillips, MA, Rosado, J, White, MT, Longley, RJ, Lacerda, M, Monteiro, W, Brewster, J, Sattabongkot, J, Guzman-Guzman, M, Llanos-Cuentas, A, Vinetz, JM, Gamboa, D, and Mueller, I

Abstract

BACKGROUND: Antibody responses as serological markers of Plasmodium vivax infection have been shown to correlate with exposure, but little is known about the other factors that affect antibody responses in naturally infected people from endemic settings. To address this question, we studied IgG responses to novel serological exposure markers (SEMs) of P. vivax in three settings with different transmission intensity. METHODOLOGY: We validated a panel of 34 SEMs in a Peruvian cohort with up to three years' longitudinal follow-up using a multiplex platform and compared results to data from cohorts in Thailand and Brazil. Linear regression models were used to characterize the association between antibody responses and age, the number of detected blood-stage infections during follow-up, and time since previous infection. Receiver Operating Characteristic (ROC) analysis was used to test the performance of SEMs to identify P. vivax infections in the previous 9 months. PRINCIPAL FINDINGS: Antibody titers were associated with age, the number of blood-stage infections, and time since previous P. vivax infection in all three study sites. The association between antibody titers and time since previous P. vivax infection was stronger in the low transmission settings of Thailand and Brazil compared to the higher transmission setting in Peru. Of the SEMs tested, antibody responses to RBP2b had the highest performance for classifying recent exposure in all sites, with area under the ROC curve (AUC) = 0.83 in Thailand, AUC = 0.79 in Brazil, and AUC = 0.68 in Peru. CONCLUSIONS: In low transmission settings, P. vivax SEMs can accurately identify individuals with recent blood-stage infections. In higher transmission settings, the accuracy of this approach diminishes substantially. We recommend using P. vivax SEMs in low transmission settings pursuing malaria elimination, but they are likely to be less effective in high transmission settings focused on malaria control.

Published
2021

28. A comparison of non-magnetic and magnetic beads for measuring IgG antibodies against Plasmodium vivax antigens in a multiplexed bead-based assay using Luminex technology (Bio-Plex 200 or MAGPIX)

Author

Carvalho, LH, Mazhari, R, Brewster, J, Fong, R, Bourke, C, Liu, ZSJ, Takashima, E, Tsuboi, T, Tham, W-H, Harbers, M, Chitnis, C, Healer, J, Ome-Kaius, M, Sattabongkot, J, Kazura, J, Robinson, LJ, King, C, Mueller, I, Longley, RJ, Carvalho, LH, Mazhari, R, Brewster, J, Fong, R, Bourke, C, Liu, ZSJ, Takashima, E, Tsuboi, T, Tham, W-H, Harbers, M, Chitnis, C, Healer, J, Ome-Kaius, M, Sattabongkot, J, Kazura, J, Robinson, LJ, King, C, Mueller, I, and Longley, RJ

Abstract

Multiplexed bead-based assays that use Luminex® xMAP® technology have become popular for measuring antibodies against proteins of interest in many fields, including malaria and more recently SARS-CoV-2/COVID-19. There are currently two formats that are widely used: non-magnetic beads or magnetic beads. Data are lacking regarding the comparability of results obtained using these two types of beads, and for assays run on different instruments. Whilst non-magnetic beads can only be run on flow-based instruments (such as the Luminex® 100/200™ or Bio-Plex® 200), magnetic beads can be run on both these and the newer MAGPIX® instruments. In this study we utilized a panel of purified recombinant Plasmodium vivax proteins and samples from malaria-endemic areas to measure P. vivax-specific IgG responses using different combinations of beads and instruments. We directly compared: i) non-magnetic versus magnetic beads run on a Bio-Plex® 200, ii) magnetic beads run on the Bio-Plex® 200 versus MAGPIX® and iii) non-magnetic beads run on a Bio-Plex® 200 versus magnetic beads run on the MAGPIX®. We also performed an external comparison of our optimized assay. We observed that IgG antibody responses, measured against our panel of P. vivax proteins, were moderately-strongly correlated in all three of our comparisons (pearson r>0.5 for 18/19 proteins), however higher amounts of protein were required for coupling to magnetic beads. Our external comparison indicated that results generated in different laboratories using the same coupled beads are also highly comparable (pearson r>0.7), particularly if a reference standard curve is used.

Published
2020

39. Large Spun Formed Friction-Stir Welded Tank Domes for Liquid Propellant Tanks Made from AA2195: A Technology Demonstration for the Next Generation of Heavy Lift Launchers

Author

Stachulla, M, Pernpeinter, R, Brewster J, Curreri, P, and Hoffman, E

Subjects
Spacecraft Design, Testing And Performance
Abstract

Improving structural efficiency while reducing manufacturing costs are key objectives when making future heavy-lift launchers more performing and cost efficient. The main enabling technologies are the application of advanced high performance materials as well as cost effective manufacture processes. This paper presents the status and main results of a joint industrial research & development effort to demonstrate TRL 6 of a novel manufacturing process for large liquid propellant tanks for launcher applications. Using high strength aluminium-lithium alloy combined with the spin forming manufacturing technique, this development aims at thinner wall thickness and weight savings up to 25% as well as a significant reduction in manufacturing effort. In this program, the concave spin forming process is used to manufacture tank domes from a single flat plate. Applied to aluminium alloy, this process allows reaching the highest possible material strength status T8, eliminating numerous welding steps which are typically necessary to assemble tank domes from 3D-curved panels. To minimize raw material costs for large diameter tank domes for launchers, the dome blank has been composed from standard plates welded together prior to spin forming by friction stir welding. After welding, the dome blank is contoured in order to meet the required wall thickness distribution. For achieving a material state of T8, also in the welding seams, the applied spin forming process allows the required cold stretching of the 3D-curved dome, with a subsequent ageing in a furnace. This combined manufacturing process has been demonstrated up to TRL 6 for tank domes with a 5.4 m diameter. In this paper, the manufacturing process as well as test results are presented. Plans are shown how this process could be applied to future heavy-lift launch vehicles developments, also for larger dome diameters.

Published
2010

45. Some factors affecting the uptake of plant nutrients from the soil

Author

Brewster, J and Brewster, J. L.

Subjects
Roots (Botany), Plants, Nutrition
Abstract

The thesis is primarily concerned with the rate of uptake of nutrients by plant roots in relation to the ability of soil to supply nutrients to roots by diffusion and by mass flow. In Chapter One, some current concepts of the chemistry and availability of plant nutrients in soil are briefly discussed. Particular attention is paid to work that stresses the role of the dynamic processes of diffusion, and the mass flow of dissolved nutrients in the transpiration stream, in supplying nutrients to roots. In Chapter Two, diffusion coefficients of nutrients in soil are discussed. In Chapter Three, the mathematical description of nutrient flow to a root system in soil is discussed. An equation is developed which relates the mean nutrient inflow into a root system to the concentration of nutrients initially present in the soil solution, to the mean concentration of nutrients in the soil solution at the surface of the root system,to the mean rate of flow of water to the roots, to the diffusion coefficient of the nutrient in the soil, and to the age of the roots. The mean nutrient inflow into a root system is defined as the mean rate of flow of nutrients into unit length of root. In Chapter Four, an experiment is described in which all the terms in the above mentioned equation were measured apart from the mean root surface concentration of nutrients. In the experiment, the growth and nutrient uptake of leek plants growing outdoors in a moist, fertilised, silty loam soil was followed. The plants were grown in large pots containing an ample reservoir of soil water, so that watering was unnecessary during growth. The growing period was from early May to mid-July. The nutrient uptake rate was followed by harvesting, and analysing for nutrients, samples of ten plants taken at approximately ten day intervals. Root length was measured at each harvest after washing the roots free from the soil. The pots were weighed every few days to determine the water lost by transpiration. At intervals during the growing period soil samples were taken from the pots, and the soil solution was extracted and analysed. From separate experiments, diffusion coefficients for nutrients in the soil were calculated. The data from the experiments yielded all the terms in the above mentioned equation except mean root surface concentration which could be calculated. The nutrients considered were N, P, K, Ca, Na, Mg, S and Cl. It was found that mass flow supplied on average more of all nutrients to the roots than they absorbed apart from K and P, which were supplied mainly by diffusion. For those nutrients that were found to be supplied by mass flow in excess of uptake, calculations indicated that the resultant mean accumulations at the root surface did not give rise to a solution concentration at the root surface greater than 120% of the initial concentration in the soil. In contrast it was calculated that the root surface concentration of K was less than half its initial level in the soil. P had a concentration dependent diffusion coefficient which meant that the quantity of P diffusing to a root had to be calculated numerically using a computer. The results of such a calculation are given in Chapter Five. It was found that even if the roots acted a zero sink for phosphate, the theoretical mean inflow of phosphate was somewhat less than the observed mean inflow. In Chapter Seven an experimental investigation is described into the accumulation of sulphate at the surface of a root in conditions of high mass flow. Autoradiography using S35 was the technique used. In accordance with theory, accumulations became large only when the soil was fairly dry. One of the difficulties in the mathematical analysis of nutrient flow to roots is the uncertainty about the inherent absorbing power of roots of different ages. In Section Three, experiments are described in which the uptake of short segments of leek root of different ages was measured. The leeks for these experiments were grown in solution culture and the mean inflow into the roots was measured by sampling and analysis as described for the pot experiment in soil. Some plants from solution were then selected and short segments of the roots of different ages were sealed into tubes containing two radioactively labelled nutrients, the rest of the root system being grown in unlabelled nutrient solution. P32, and either K42 or Sr85, Sr85 being taken as a label for Ca, were the labelled nutrients used. The plants were harvested after twenty four hours of exposure to labelled nutrients and the quantity of label absorbed was measured. There were no significant differences in the mean absorption of different aged roots, but different root segments varied very widely in their uptake in a way that could not be connected with their age. The possibility of such variation in absorbing power in roots in soil and its consequences in soil are discussed at the end of Chapter Eleven. In Chapter Twelve values for the mean inflow of nutrients into roots from a wide range of published experiments are tabulated. The rates are also given as specific absorption rates, this term meaning the rate of flow of nutrient into unit fresh weight of root. Similar values of mean inflow and specific absorption rate have been measured in widely different conditions, ranging from a few minutes uptake from solution to several weeks uptake from soil. Plant factors which affect mean nutrient inflows are discussed and possible future developments along the lines suggested by the experiment in Chapter Four are considered. In the final Chapter the evidence is stated on which is based current theory of nutrient flow to roots by mass flow and diffusion. In conclusion the insight the theory provides into the concept of nutrient availability in soil, into root competition for nutrients and into ideas about root system efficiency is considered.

Published
2016

47. A comparison of the trophic ecology of Beaufort Sea Gadidae using fatty acids and stable isotopes

Author

Brewster, J. D., Giraldo, Carolina, Choy, E. S., Macphee, S. A., Hoover, C., Lynn, B., Mcnicholl, D. G., Majewski, A., Rosenberg, B., Power, M., Reist, J. D., Loseto, L. L., Brewster, J. D., Giraldo, Carolina, Choy, E. S., Macphee, S. A., Hoover, C., Lynn, B., Mcnicholl, D. G., Majewski, A., Rosenberg, B., Power, M., Reist, J. D., and Loseto, L. L.

Abstract

Polar cod (Boreogadus saida) is one of the most studied Arctic marine fishes given its circumpolar distribution and centralised role in the Arctic marine food web. In contrast, relatively little is known about two other Arctic Gadidae: saffron cod (Eleginus gracilis) and Greenland cod (Gadus ogac). Climate change is expected to have an effect on sea ice-associated species, such as polar cod, but due to our lack of knowledge of other arctic gadid species it remains unclear how climate change will impact them and their interactions within the arctic marine ecosystem. Here, we explored the ecology of three Arctic Gadidae that co-occur in the Canadian Beaufort Sea. Stable isotope (SI) (niche overlap) and fatty acid (FA) (correspondence analysis and linear discriminant analysis) biomarkers were used to assess among- and within-species differences and trophic niche. Despite the close habitat proximity of saffron cod and polar cod while on the shelf, trophic niche characterisation revealed only a marginal overlap. Marginal niche overlaps also occurred for the two coastal species with similar diets, saffron cod and Greenland cod, likely reflecting regional-scale differences between two habitats. Within-species, polar cod collected from three habitats (shelf, upper- and lower-slope habitats) were not differentiated likely due to the movement of individuals between habitats. In contrast, Greenland cod had a narrow trophic niche and differentiation occurred between the two collection sites. The comparison of trophic niches defined by stable isotope and fatty acid proved a promising tool for new insights into the ecology of Arctic fishes.

Published
2018
Full Text
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48. Towards Science Profiles.

Author

Hodson, D. and Brewster, J.

Abstract

Discusses the use of student profiles in recording student progress related to science processes and skills, indicating that profile reporting is a fundamentally different way of describing and monitoring academic progress. Implications for the science curriculum are considered. (JN)

Published
1985

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