Author: "Zia F" - Searchworks@Jio Institute Digital Library Search Results

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1. Relative Measurement and Extrapolation of the Scintillation Quenching Factor of $\alpha$-Particles in Liquid Argon using DEAP-3600 Data

Author: The DEAP Collaboration, Adhikari, P., Alpízar-Venegas, M., Amaudruz, P. -A., Anstey, J., Auty, D. J., Batygov, M., Beltran, B., Bina, C. E., Bonivento, W., Boulay, M. G., Bueno, J. F., Cai, B., Cárdenas-Montes, M., Choudhary, S., Cleveland, B. T., Crampton, R., Daugherty, S., DelGobbo, P., Di Stefano, P., Dolganov, G., Doria, L., Duncan, F. A., Dunford, M., Ellingwood, E., Erlandson, A., Farahani, S. S., Fatemighomi, N., Fiorillo, G., Ford, R. J., Gahan, D., Gallacher, D., Abia, P. García, Garg, S., Giampa, P., Giménez-Alcázar, A., Goeldi, D., Gorel, P., Graham, K., Hallin, A. L., Hamstra, M., Haskins, S., Hu, J., Hucker, J., Hugues, T., Ilyasov, A., Jigmeddorj, B., Jillings, C. J., Kaur, G., Yazdi, M. Khoshraftar, Kemp, A., Kuźniak, M., La Zia, F., Lai, M., Langrock, S., Lehnert, B., Levashko, N., Lissia, M., Luzzi, L., Machulin, I., Maru, A., Mason, J., McDonald, A. B., McElroy, T., McLaughlin, J. B., Mielnichuk, C., Mirasola, L., Moharana, A., Monroe, J., Murray, A., Ng, C., Oliviéro, G., Olszewski, M., Pal, S., Papi, D., Park, B., Perry, M., Pesudo, V., Pollmann, T. R., Rad, F., Rethmeier, C., Retière, F., Roszkowski, L., Santorelli, R., Schuckman II, F. G., Seth, S., Shalamova, V., Skensved, P., Smirnova, T., Sobotkiewich, K., Sonley, T., Sosiak, J., Soukup, J., Stainforth, R., Stringer, M., Tang, J., Vázquez-Jáuregui, E., Viel, S., Vyas, B., Walczak, M., Walding, J., Ward, M., Westerdale, S., and Wormington, R.
Subjects: Physics - Instrumentation and Detectors, High Energy Physics - Experiment
Abstract: The knowledge of scintillation quenching of $\alpha$-particles plays a paramount role in understanding $\alpha$-induced backgrounds and improving the sensitivity of liquid argon-based direct detection of dark matter experiments. We performed a relative measurement of scintillation quenching in the MeV energy region using radioactive isotopes ($^{222}$Rn, $^{218}$Po and $^{214}$Po isotopes) present in trace amounts in the DEAP-3600 detector and quantified the uncertainty of extrapolating the quenching factor to the low-energy region., Comment: 9 pages, 6 figures (added 1 figure, revised 3 figures), 2 tables, revised sections 3, 4, 5. Accepted in Eur. Phys. J. C
Published: 2024

2. Precision Measurement of the Specific Activity of $^{39}$Ar in Atmospheric Argon with the DEAP-3600 Detector

Author: Adhikari, P., Ajaj, R., Alpízar-Venegas, M., Amaudruz, P. -A., Anstey, J., Araujo, G. R., Auty, D. J., Baldwin, M., Batygov, M., Beltran, B., Benmansour, H., Bina, C. E., Bonatt, J., Bonivento, W., Boulay, M. G., Broerman, B., Bueno, J. F., Burghardt, P. M., Butcher, A., Cadeddu, M., Cai, B., Cárdenas-Montes, M., Cavuoti, S., Chen, M., Chen, Y., Choudhary, S., Cleveland, B. T., Corning, J. M., Crampton, R., Cranshaw, D., Daughtery, S., DelGobbo, P., Dering, K., Di Stefano, P., DiGioseffo, J., Dolganov, G., Doria, L., Duncan, F. A., Dunford, M., Ellingwood, E., Erlandson, A., Farahani, S. S., Fatemighomi, N., Fiorillo, G., Florian, S., Flower, A., Ford, R. J., Gagnon, R., Gallacher, D., Abia, P. García, Garg, S., Giampa, P., Giménez-Alcázar, A., Goeldi, D., Golovko, V. V., Gorel, P., Graham, K., Grant, D. R., Grobov, A., Hallin, A. L., Hamstra, M., Harvey, P. J., Haskins, S., Hearns, C., Hu, J., Hucker, J., Hugues, T., Ilyasov, A., Jigmeddorj, B., Jillings, C. J., Joy, A., Kamaev, O., Kaur, G., Kemp, A., Kuźniak, M., La Zia, F., Lai, M., Langrock, S., Lehnert, B., Leonhardt, A., LePage-Bourbonnais, J., Levashko, N., Lidgard, J., Lindner, T., Lissia, M., Lock, J., Machulin, I., Majewski, P., Maru, A., Mason, J., McDonald, A. B., McElroy, T., McGinn, T., McLaughlin, J. B., Mehdiyev, R., Mielnichuk, C., Mirasola, L., Monroe, J., Nadeau, P., Nantais, C., Ng, C., Noble, A. J., O'Dwyer, E., Oliviéro, G., Ouellet, C., Pal, S., Papi, D., Pasuthip, P., Peeters, S. J. M., Perry, M., Pesudo, V., Picciau, E., Piro, M. -C., Pollmann, T. R., Rad, F., Rand, E. T., Rethmeier, C., Retière, F., García, I. Rodríguez, Roszkowski, L., Ruhland, J. B., Santorelli, R., Schuckman II, F. G., Seeburn, N., Seth, S., Shalamova, V., Singhrao, K., Skensved, P., Smith, N. J. T., Smith, B., Sobotkiewich, K., Sonley, T., Sosiak, J., Soukup, J., Stainforth, R., Stone, C., Strickland, V., Stringer, M., Sur, B., Tang, J., Vázquez-Jáuregui, E., Veloce, L., Viel, S., Vyas, B., Walczak, M., Walding, J., Ward, M., Westerdale, S., Willis, J., and Zuñiga-Reyes, A.
Subjects: Physics - Instrumentation and Detectors, High Energy Physics - Experiment
Abstract: The specific activity of the beta decay of $^{39}$Ar in atmospheric argon is measured using the DEAP-3600 detector. DEAP-3600, located 2 km underground at SNOLAB, uses a total of (3269 $\pm$ 24) kg of liquid argon distilled from the atmosphere to search for dark matter. This detector with very low background uses pulseshape discrimination to differentiate between nuclear recoils and electron recoils and is well-suited to measure the decay of $^{39}$Ar. With 167 live-days of data, the measured specific activity at the time of atmospheric extraction is [0.964 $\pm$ 0.001 (stat) $\pm$ 0.024 (sys)] Bq/kg$_{\rm atmAr}$ which is consistent with results from other experiments. A cross-check analysis using different event selection criteria provides a consistent result.
Published: 2023
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3. The liquid-argon scintillation pulseshape in DEAP-3600

Author: The DEAP collaboration, Adhikari, P., Ajaj, R., Batygov, G. R. Araujoand M., Beltran, B., Bina, C. E., Boulay, M. G., Broerman, B., Bueno, J. F., Butcher, A., Cai, B., Cárdenas-Montes, M., Cavuoti, S., Chen, Y., Cleveland, B. T., Corning, J. M., Dering, S. J. Daughertyand K., Doria, L., Dunford, F. A. Duncan andM., Erlandson, A., Fatemighomi, N., Fiorillo, G., Flower, A., Ford, R. J., Gagnon, R., Gallacher, D., Garcés, E. A., Abia, P. García, Garg, S., Giampa, P., Goeldi, D., Golovko, V. V., Gorel, P., Graham, K., Grant, D. R., Grobov, A., Hallin, A. L., Hamstra, M., Harvey, P. J., Hearns, C., Ilyasov, A., Joy, A., Jillings, C. J., Kamaev, O., Kaur, G., Kemp, A., Kochanek, I., Kuźniak, M., Langrock, S., La Zia, F., Lehnert, B., Levashko, N., Li, X., Litvinov, O., Lock, J., Longo, G., Machulin, I., Majewski, P., McDonald, A. B., McElroy, T., McGinn, T., McLaughlin, J. B., Mehdiyev, R., Mielnichuk, C., Monroe, J., Nadeau, P., Nantais, C., Ng, C., Noble, A. J., Oliviéro, G., Ouellet, C., Pal, S., Pasuthip, P., Peeters, S. J. M., Pesudo, V., Piro, M. -C., Pollmann, T. R., Rand, E. T., Rethmeier, C., Retière, F., García, E. Sanchez, Sánchez-Pastor, T., Santorelli, R., Seeburn, N., Skensved, P., Smith, B., Smith, N. J. T., Sonley, T., Stainforth, R., Stone, C., Strickland, V., Sur, B., Vázquez-Jáuregui, E., Veloce, L., Viel, S., Walding, J., Waqar, M., Ward, M., Westerdale, S., Willis, J., and Zuñiga-Reyes, A.
Subjects: Physics - Instrumentation and Detectors
Abstract: DEAP-3600 is a liquid-argon scintillation detector looking for dark matter. Scintillation events in the liquid argon (LAr) are registered by 255 photomultiplier tubes (PMTs), and pulseshape discrimination (PSD) is used to suppress electromagnetic background events. The excellent PSD performance of LAr makes it a viable target for dark matter searches, and the LAr scintillation pulseshape discussed here is the basis of PSD. The observed pulseshape is a combination of LAr scintillation physics with detector effects. We present a model for the pulseshape of electromagnetic background events in the energy region of interest for dark matter searches. The model is composed of a) LAr scintillation physics, including the so-called intermediate component, b) the time response of the TPB wavelength shifter, including delayed TPB emission at $\mathcal O$(ms) time-scales, and c) PMT response. TPB is the wavelength shifter of choice in most LAr detectors. We find that approximately 10\% of the intensity of the wavelength-shifted light is in a long-lived state of TPB. This causes light from an event to spill into subsequent events to an extent not usually accounted for in the design and data analysis of LAr-based detectors.
Published: 2020
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4. Electromagnetic Backgrounds and Potassium-42 Activity in the DEAP-3600 Dark Matter Detector

Author: Ajaj, R., Araujo, G. R., Batygov, M., Beltran, B., Bina, C. E., Boulay, M. G., Broerman, B., Bueno, J. F., Burghardt, P. M., Butcher, A., Cárdenas-Montes, M., Cavuoti, S., Chen, M., Chen, Y., Cleveland, B. T., Dering, K., Duncan, F. A., Dunford, M., Erlandson, A., Fatemighomi, N., Fiorillo, G., Flower, A., Ford, R. J., Gallacher, D., Abia, P. García, Garg, S., Giampa, P., Goeldi, D., Golovko, V. V., Gorel, P., Graham, K., Grant, D. R., Hallin, A. L., Hamstra, M., Harvey, P. J., Hearns, C., Joy, A., Jillings, C. J., Kamaev, O., Kaur, G., Kemp, A., Kochanek, I., Kuźniak, M., Langrock, S., La Zia, F., Lehnert, B., Li, X., Litvinov, O., Lock, J., Longo, G., Majewski, P., McDonald, A. B., McElroy, T., McGinn, T., McLaughlin, J. B., Mehdiyev, R., Mielnichuk, C., Monroe, J., Nadeau, P., Nantais, C., Ng, C., Noble, A. J., Ouellet, C., Pasuthip, P., Peeters, S. J. M., Pesudo, V., Piro, M. -C., Pollmann, T. R., Rand, E. T., Rethmeier, C., Retière, F., García, E. Sanchez, Santorelli, R., Seeburn, N., Skensved, P., Smith, B., Smith, N. J. T., Sonley, T., Stainforth, R., Stone, C., Strickland, V., Sur, B., Vázquez-Jáuregui, E., Veloce, L., Viel, S., Walding, J., Waqar, M., Ward, M., Westerdale, S., Willis, J., and Zuñiga-Reyes, A.
Subjects: Nuclear Experiment, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract: The DEAP-3600 experiment is searching for WIMP dark matter with a 3.3 tonne single phase liquid argon (LAr) target, located 2.1 km underground at SNOLAB. The experimental signature of dark matter interactions is keV-scale $^{40}$Ar nuclear recoils (NR) producing 128 nm LAr scintillation photons observed by PMTs. The largest backgrounds in DEAP-3600 are electronic recoils (ER) induced by $\beta$ and $\gamma$-rays originating from internal and external radioactivity in the detector material. A background model of the ER interactions in DEAP-3600 was developed and is described in this work. The model is based on several components which are expected from radioisotopes in the LAr, from ex-situ material assay measurements, and from dedicated independent in-situ analyses. This prior information is used in a Bayesian fit of the ER components to a 247.2 d dataset to model the radioactivity in the surrounding detector materials. While excellent discrimination between ERs and NRs is reached with pulse shape discrimination, utilizing the large difference between fast and slow components of LAr scintillation light, detailed knowledge of the ER background and activity of detector components, sets valuable constraints on other key types of backgrounds in the detector: neutrons and alphas. In addition, the activity of $^{42}$Ar in LAr in DEAP-3600 is determined by measuring the daughter decay of $^{42}$K. This cosmogenically activated trace isotope is a relevant background at higher energies for other rare event searches using atmospheric argon e.g. DarkSide-20k, GERDA or LEGEND. The specific activity of $^{42}$Ar in the atmosphere is found to be $40.4 \pm 5.9$ $\mu$Bq/kg of argon.
Published: 2019
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5. Search for dark matter with a 231-day exposure of liquid argon using DEAP-3600 at SNOLAB

Author: Ajaj, R., Amaudruz, P. -A., Araujo, G. R., Baldwin, M., Batygov, M., Beltran, B., Bina, C. E., Bonatt, J., Boulay, M. G., Broerman, B., Bueno, J. F., Burghardt, P. M., Butcher, A., Cai, B., Cavuoti, S., Chen, M., Chen, Y., Cleveland, B. T., Cranshaw, D., Dering, K., DiGioseffo, J., Doria, L., Duncan, F. A., Dunford, M., Erlandson, A., Fatemighomi, N., Fiorillo, G., Florian, S., Flower, A., Ford, R. J., Gagnon, R., Gallacher, D., Garcés, E. A., Garg, S., Giampa, P., Goeldi, D., Golovko, V. V., Gorel, P., Graham, K., Grant, D. R., Hallin, A. L., Hamstra, M., Harvey, P. J., Hearns, C., Joy, A., Jillings, C. J., Kamaev, O., Kaur, G., Kemp, A., Kochanek, I., Kuźniak, M., Langrock, S., La Zia, F., Lehnert, B., Li, X., Lidgard, J., Lindner, T., Litvinov, O., Lock, J., Longo, G., Majewski, P., McDonald, A. B., McElroy, T., McGinn, T., McLaughlin, J. B., Mehdiyev, R., Mielnichuk, C., Monroe, J., Nadeau, P., Nantais, C., Ng, C., Noble, A. J., O'Dwyer, E., Ouellet, C., Pasuthip, P., Peeters, S. J. M., Piro, M. -C., Pollmann, T. R., Rand, E. T., Rethmeier, C., Retière, F., Seeburn, N., Singhrao, K., Skensved, P., Smith, B., Smith, N. J. T., Sonley, T., Soukup, J., Stainforth, R., Stone, C., Strickland, V., Sur, B., Tang, J., Vázquez-Jáuregui, E., Veloce, L., Viel, S., Walding, J., Waqar, M., Ward, M., Westerdale, S., Willis, J., and Zuñiga-Reyes, A.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, High Energy Physics - Experiment, Nuclear Experiment
Abstract: DEAP-3600 is a single-phase liquid argon (LAr) direct-detection dark matter experiment, operating 2 km underground at SNOLAB (Sudbury, Canada). The detector consists of 3279 kg of LAr contained in a spherical acrylic vessel. This paper reports on the analysis of a 758 tonne\cdot day exposure taken over a period of 231 live-days during the first year of operation. No candidate signal events are observed in the WIMP-search region of interest, which results in the leading limit on the WIMP-nucleon spin-independent cross section on a LAr target of $3.9\times10^{-45}$ cm$^{2}$ ($1.5\times10^{-44}$ cm$^{2}$) for a 100 GeV/c$^{2}$ (1 TeV/c$^{2}$) WIMP mass at 90\% C. L. In addition to a detailed background model, this analysis demonstrates the best pulse-shape discrimination in LAr at threshold, employs a Bayesian photoelectron-counting technique to improve the energy resolution and discrimination efficiency, and utilizes two position reconstruction algorithms based on PMT charge and photon arrival times.
Published: 2019
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6. Design and Construction of the DEAP-3600 Dark Matter Detector

Author: Amaudruz, P. -A., Baldwin, M., Batygov, M., Beltran, B., Bina, C. E., Bishop, D., Bonatt, J., Boorman, G., Boulay, M. G., Broerman, B., Bromwich, T., Bueno, J. F., Burghardt, P. M., Butcher, A., Cai, B., Chan, S., Chen, M., Chouinard, R., Churchwell, S., Cleveland, B. T., Cranshaw, D., Dering, K., DiGioseffo, J., Dittmeier, S., Duncan, F. A., Dunford, M., Erlandson, A., Fatemighomi, N., Florian, S., Flower, A., Ford, R. J., Gagnon, R., Giampa, P., Golovko, V. V., Gorel, P., Gornea, R., Grace, E., Graham, K., Grant, D. R., Gulyev, E., Hall, A., Hallin, A. L., Hamstra, M., Harvey, P. J., Hearns, C., Jillings, C. J., Kamaev, O., Kemp, A., Kuźniak, M., Langrock, S., La Zia, F., Lehnert, B., Li, O., Lidgard, J. J., Liimatainen, P., Lim, C., Lindner, T., Linn, Y., Liu, S., Majewski, P., Mathew, R., McDonald, A. B., McElroy, T., McFarlane, K., McGinn, T., McLaughlin, J. B., Mead, S., Mehdiyev, R., Mielnichuk, C., Monroe, J., Muir, A., Nadeau, P., Nantais, C., Ng, C., Noble, A. J., O'Dwyer, E., Ohlmann, C., Olchanski, K., Olsen, K. S., Ouellet, C., Pasuthip, P., Peeters, S. J. M., Pollmann, T. R., Rand, E. T., Rau, W., Rethmeier, C., Retière, F., Seeburn, N., Shaw, B., Singhrao, K., Skensved, P., Smith, B., Smith, N. J. T., Sonley, T., Soukup, J., Stainforth, R., Stone, C., Strickland, V., Sur, B., Tang, J., Taylor, J., Veloce, L., Vázquez-Jáuregui, E., Walding, J., Ward, M., Westerdale, S., White, R., Woolsey, E., and Zielinski, J.
Subjects: Astrophysics - Instrumentation and Methods for Astrophysics, High Energy Physics - Experiment
Abstract: The Dark matter Experiment using Argon Pulse-shape discrimination (DEAP) has been designed for a direct detection search for particle dark matter using a single-phase liquid argon target. The projected cross section sensitivity for DEAP-3600 to the spin-independent scattering of Weakly Interacting Massive Particles (WIMPs) on nucleons is $10^{-46}~\rm{cm}^{2}$ for a 100 GeV/$c^2$ WIMP mass with a fiducial exposure of 3 tonne-years. This paper describes the physical properties and construction of the DEAP-3600 detector., Comment: minor corrections in version 2. 70 pages, 24 figures, to be submitted to Astroparticle Physics Journal
Published: 2017
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7. Electromagnetic backgrounds and potassium-42 activity in the DEAP-3600 dark matter detector

Author: Ajaj, R, Araujo, GR, Batygov, M, Beltran, B, Bina, CE, Boulay, MG, Broerman, B, Bueno, JF, Burghardt, PM, Butcher, A, Cai, B, Cárdenas-Montes, M, Cavuoti, S, Chen, M, Chen, Y, Cleveland, BT, Dering, K, Duncan, FA, Dunford, M, Erlandson, A, Fatemighomi, N, Fiorillo, G, Flower, A, Ford, RJ, Gagnon, R, Gallacher, D, García Abia, P, Garg, S, Giampa, P, Goeldi, D, Golovko, VV, Gorel, P, Graham, K, Grant, DR, Hallin, AL, Hamstra, M, Harvey, PJ, Hearns, C, Joy, A, Jillings, CJ, Kamaev, O, Kaur, G, Kemp, A, Kochanek, I, Kuźniak, M, Langrock, S, La Zia, F, Lehnert, B, Li, X, Litvinov, O, Lock, J, Longo, G, Majewski, P, McDonald, AB, McElroy, T, McGinn, T, McLaughlin, JB, Mehdiyev, R, Mielnichuk, C, Monroe, J, Nadeau, P, Nantais, C, Ng, C, Noble, AJ, Ouellet, C, Pasuthip, P, Peeters, SJM, Pesudo, V, Piro, MC, Pollmann, TR, Rand, ET, Rethmeier, C, Retière, F, Sanchez García, E, Santorelli, R, Seeburn, N, Skensved, P, Smith, B, Smith, NJT, Sonley, T, Stainforth, R, Stone, C, Strickland, V, Sur, B, Vázquez-Jáuregui, E, Veloce, L, Viel, S, Walding, J, Waqar, M, Ward, M, Westerdale, S, Willis, J, and Zuñiga-Reyes, A
Subjects: nucl-ex, astro-ph.IM
Abstract: The DEAP-3600 experiment is searching for weakly interacting massive particles dark matter with a 3.3 ×103 kg single phase liquid argon (LAr) target, located 2.1 km underground at SNOLAB. The experimental signature of dark matter interactions is kilo electron volt-scale Ar40 nuclear recoils producing 128 nm LAr scintillation photons observed by photomultiplier tubes. The largest backgrounds in DEAP-3600 are electronic recoils (ERs) induced by β and γ rays originating from internal and external radioactivity in the detector material. A background model of the ER interactions in DEAP-3600 was developed and is described in this work. The model is based on several components which are expected from radioisotopes in the LAr, from ex situ material assay measurements, and from dedicated independent in situ analyses. This prior information is used in a Bayesian fit of the ER components to a 247.2 d dataset to model the radioactivity in the surrounding detector materials. Pulse-shape discrimination separates ER and NR events. However, detailed knowledge of the ER background and activity of detector components sets valuable constraints on NR backgrounds including neutrons and alphas. In addition, the activity of Ar42 in LAr in DEAP-3600 is determined by measuring the daughter decay of K42. This cosmogenically activated trace isotope is a relevant background at higher energies for other rare event searches using atmospheric argon, e.g., DarkSide-20k, GERDA, or LEGEND. The specific activity of Ar42 in the atmosphere is found to be 40.4±5.9 μBq/kg of argon.
Published: 2019

8. In-situ characterization of the Hamamatsu R5912-HQE photomultiplier tubes used in the DEAP-3600 experiment

Author: Amaudruz, P-A, Batygov, M, Beltran, B, Bina, CE, Bishop, D, Bonatt, J, Boorman, G, Boulay, MG, Broerman, B, Bromwich, T, Bueno, JF, Butcher, A, Cai, B, Chan, S, Chen, M, Chouinard, R, Churchwell, S, Cleveland, BT, Cranshaw, D, Dering, K, Dittmeier, S, Duncan, FA, Dunford, M, Erlandson, A, Fatemighomi, N, Ford, RJ, Gagnon, R, Giampa, P, Golovko, VV, Gorel, P, Gornea, R, Grace, E, Graham, K, Grant, DR, Gulyev, E, Hall, A, Hallin, AL, Hamstra, M, Harvey, PJ, Hearns, C, Jillings, CJ, Kamaev, O, Kemp, A, Kuźniak, M, Langrock, S, La Zia, F, Lehnert, B, Li, O, Lidgard, JJ, Liimatainen, P, Lim, C, Lindner, T, Linn, Y, Liu, S, Mathew, R, McDonald, AB, McElroy, T, McFarlane, K, McLaughlin, J, Mead, S, Mehdiyev, R, Mielnichuk, C, Monroe, J, Muir, A, Nadeau, P, Nantais, C, Ng, C, Noble, AJ, O’Dwyer, E, Ohlmann, C, Olchanski, K, Olsen, KS, Ouellet, C, Pasuthip, P, Peeters, SJM, Pollmann, TR, Rand, ET, Rau, W, Rethmeier, C, Retière, F, Seeburn, N, Shaw, B, Singhrao, K, Skensved, P, Smith, B, Smith, NJT, Sonley, T, Stainforth, R, Stone, C, Strickland, V, Sur, B, Tang, J, Taylor, J, Veloce, L, Vázquez-Jáuregui, E, Walding, J, Ward, M, Westerdale, S, White, R, and Woolsey, E
Subjects: Nuclear and Plasma Physics, Particle and High Energy Physics, Physical Sciences, PMT, Hamamatsu R5912-HQE, Single photoelectron charge distribution, Afterpulsing, Late and double pulsing, Dark noise, Dark matter detection, physics.ins-det, Astronomical and Space Sciences, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Other Physical Sciences, Nuclear & Particles Physics, Nuclear and plasma physics
Abstract: The Hamamatsu R5912-HQE photomultiplier-tube (PMT) is a novel high-quantum efficiency PMT. It is currently used in the DEAP-3600 dark matter detector and is of significant interest for future dark matter and neutrino experiments where high signal yields are needed. We report on the methods developed for in-situ characterization and monitoring of DEAP's 255 R5912-HQE PMTs. This includes a detailed discussion of typical measured single-photoelectron charge distributions, correlated noise (afterpulsing), dark noise, double, and late pulsing characteristics. The characterization is performed during the detector commissioning phase using laser light injected through a light diffusing sphere and during normal detector operation using LED light injected through optical fibres.
Published: 2019

9. In-situ characterization of the Hamamatsu R5912-HQE photomultiplier tubes used in the DEAP-3600 experiment

Author: Amaudruz, PA, Batygov, M, Beltran, B, Bina, CE, Bishop, D, Bonatt, J, Boorman, G, Boulay, MG, Broerman, B, Bromwich, T, Bueno, JF, Butcher, A, Cai, B, Chan, S, Chen, M, Chouinard, R, Churchwell, S, Cleveland, BT, Cranshaw, D, Dering, K, Dittmeier, S, Duncan, FA, Dunford, M, Erlandson, A, Fatemighomi, N, Ford, RJ, Gagnon, R, Giampa, P, Golovko, VV, Gorel, P, Gornea, R, Grace, E, Graham, K, Grant, DR, Gulyev, E, Hall, A, Hallin, AL, Hamstra, M, Harvey, PJ, Hearns, C, Jillings, CJ, Kamaev, O, Kemp, A, Kuźniak, M, Langrock, S, La Zia, F, Lehnert, B, Li, O, Lidgard, JJ, Liimatainen, P, Lim, C, Lindner, T, Linn, Y, Liu, S, Mathew, R, McDonald, AB, McElroy, T, McFarlane, K, McLaughlin, J, Mead, S, Mehdiyev, R, Mielnichuk, C, Monroe, J, Muir, A, Nadeau, P, Nantais, C, Ng, C, Noble, AJ, O'Dwyer, E, Ohlmann, C, Olchanski, K, Olsen, KS, Ouellet, C, Pasuthip, P, Peeters, SJM, Pollmann, TR, Rand, ET, Rau, W, Rethmeier, C, Retière, F, Seeburn, N, Shaw, B, Singhrao, K, Skensved, P, Smith, B, Smith, NJT, Sonley, T, Stainforth, R, Stone, C, Strickland, V, Sur, B, Tang, J, Taylor, J, Veloce, L, Vázquez-Jáuregui, E, Walding, J, Ward, M, Westerdale, S, White, R, and Woolsey, E
Subjects: PMT, Hamamatsu R5912-HQE, Single photoelectron charge distribution, Afterpulsing, Late and double pulsing, Dark noise, Dark matter detection, physics.ins-det, Nuclear & Particles Physics, Astronomical and Space Sciences, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Other Physical Sciences
Abstract: The Hamamatsu R5912-HQE photomultiplier-tube (PMT) is a novel high-quantum efficiency PMT. It is currently used in the DEAP-3600 dark matter detector and is of significant interest for future dark matter and neutrino experiments where high signal yields are needed. We report on the methods developed for in-situ characterization and monitoring of DEAP's 255 R5912-HQE PMTs. This includes a detailed discussion of typical measured single-photoelectron charge distributions, correlated noise (afterpulsing), dark noise, double, and late pulsing characteristics. The characterization is performed during the detector commissioning phase using laser light injected through a light diffusing sphere and during normal detector operation using LED light injected through optical fibres.
Published: 2019

10. Design and construction of the DEAP-3600 dark matter detector

Author: Amaudruz, P-A, Baldwin, M, Batygov, M, Beltran, B, Bina, CE, Bishop, D, Bonatt, J, Boorman, G, Boulay, MG, Broerman, B, Bromwich, T, Bueno, JF, Burghardt, PM, Butcher, A, Cai, B, Chan, S, Chen, M, Chouinard, R, Churchwell, S, Cleveland, BT, Cranshaw, D, Dering, K, DiGioseffo, J, Dittmeier, S, Duncan, FA, Dunford, M, Erlandson, A, Fatemighomi, N, Florian, S, Flower, A, Ford, RJ, Gagnon, R, Giampa, P, Golovko, VV, Gorel, P, Gornea, R, Grace, E, Graham, K, Grant, DR, Gulyev, E, Hall, A, Hallin, AL, Hamstra, M, Harvey, PJ, Hearns, C, Jillings, CJ, Kamaev, O, Kemp, A, Kuźniak, M, Langrock, S, La Zia, F, Lehnert, B, Li, O, Lidgard, JJ, Liimatainen, P, Lim, C, Lindner, T, Linn, Y, Liu, S, Majewski, P, Mathew, R, McDonald, AB, McElroy, T, McFarlane, K, McGinn, T, McLaughlin, JB, Mead, S, Mehdiyev, R, Mielnichuk, C, Monroe, J, Muir, A, Nadeau, P, Nantais, C, Ng, C, Noble, AJ, O’Dwyer, E, Ohlmann, C, Olchanski, K, Olsen, KS, Ouellet, C, Pasuthip, P, Peeters, SJM, Pollmann, TR, Rand, ET, Rau, W, Rethmeier, C, Retière, F, Seeburn, N, Shaw, B, Singhrao, K, Skensved, P, Smith, B, Smith, NJT, Sonley, T, Soukup, J, Stainforth, R, Stone, C, Strickland, V, Sur, B, and Tang, J
Subjects: Nuclear and Plasma Physics, Particle and High Energy Physics, Physical Sciences, Dark matter, WIMP, Liquid Argon, DEAP, SNOLAB, Low background, astro-ph.IM, hep-ex, Astronomical and Space Sciences, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Nuclear & Particles Physics, Astronomical sciences, Particle and high energy physics
Abstract: The Dark matter Experiment using Argon Pulse-shape discrimination (DEAP) has been designed for a direct detection search for particle dark matter using a single-phase liquid argon target. The projected cross section sensitivity for DEAP-3600 to the spin-independent scattering of Weakly Interacting Massive Particles (WIMPs) on nucleons is 10−46cm2 for a 100 GeV/c2 WIMP mass with a fiducial exposure of 3 tonne-years. This paper describes the physical properties and construction of the DEAP-3600 detector.
Published: 2019

11. Design and construction of the DEAP-3600 dark matter detector

Author: Amaudruz, PA, Baldwin, M, Batygov, M, Beltran, B, Bina, CE, Bishop, D, Bonatt, J, Boorman, G, Boulay, MG, Broerman, B, Bromwich, T, Bueno, JF, Burghardt, PM, Butcher, A, Cai, B, Chan, S, Chen, M, Chouinard, R, Churchwell, S, Cleveland, BT, Cranshaw, D, Dering, K, DiGioseffo, J, Dittmeier, S, Duncan, FA, Dunford, M, Erlandson, A, Fatemighomi, N, Florian, S, Flower, A, Ford, RJ, Gagnon, R, Giampa, P, Golovko, VV, Gorel, P, Gornea, R, Grace, E, Graham, K, Grant, DR, Gulyev, E, Hall, A, Hallin, AL, Hamstra, M, Harvey, PJ, Hearns, C, Jillings, CJ, Kamaev, O, Kemp, A, Kuźniak, M, Langrock, S, La Zia, F, Lehnert, B, Li, O, Lidgard, JJ, Liimatainen, P, Lim, C, Lindner, T, Linn, Y, Liu, S, Majewski, P, Mathew, R, McDonald, AB, McElroy, T, McFarlane, K, McGinn, T, McLaughlin, JB, Mead, S, Mehdiyev, R, Mielnichuk, C, Monroe, J, Muir, A, Nadeau, P, Nantais, C, Ng, C, Noble, AJ, O'Dwyer, E, Ohlmann, C, Olchanski, K, Olsen, KS, Ouellet, C, Pasuthip, P, Peeters, SJM, Pollmann, TR, Rand, ET, Rau, W, Rethmeier, C, Retière, F, Seeburn, N, Shaw, B, Singhrao, K, Skensved, P, Smith, B, Smith, NJT, Sonley, T, Soukup, J, Stainforth, R, Stone, C, Strickland, V, Sur, B, and Tang, J
Subjects: Dark matter, WIMP, Liquid Argon, DEAP, SNOLAB, Low background, astro-ph.IM, hep-ex, Astronomical and Space Sciences, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Nuclear & Particles Physics
Abstract: The Dark matter Experiment using Argon Pulse-shape discrimination (DEAP) has been designed for a direct detection search for particle dark matter using a single-phase liquid argon target. The projected cross section sensitivity for DEAP-3600 to the spin-independent scattering of Weakly Interacting Massive Particles (WIMPs) on nucleons is 10−46cm2 for a 100 GeV/c2 WIMP mass with a fiducial exposure of 3 tonne-years. This paper describes the physical properties and construction of the DEAP-3600 detector.
Published: 2019

12. First results from the DEAP-3600 dark matter search with argon at SNOLAB

Author: Collaboration, DEAP-3600, Amaudruz, P. -A., Baldwin, M., Batygov, M., Beltran, B., Bina, C. E., Bishop, D., Bonatt, J., Boorman, G., Boulay, M. G., Broerman, B., Bromwich, T., Bueno, J. F., Burghardt, P. M., Butcher, A., Cai, B., Chan, S., Chen, M., Chouinard, R., Cleveland, B. T., Cranshaw, D., Dering, K., DiGioseffo, J., Dittmeier, S., Duncan, F. A., Dunford, M., Erlandson, A., Fatemighomi, N., Florian, S., Flower, A., Ford, R. J., Gagnon, R., Giampa, P., Golovko, V. V., Gorel, P., Gornea, R., Grace, E., Graham, K., Gulyev, E., Hakobyan, R., Hall, A., Hallin, A. L., Hamstra, M., Harvey, P. J., Hearns, C., Jillings, C. J., Kamaev, O., Kemp, A., Kuźniak, M., Langrock, S., La Zia, F., Lehnert, B., Lidgard, J. J., Lim, C., Lindner, T., Linn, Y., Liu, S., Majewski, P., Mathew, R., McDonald, A. B., McElroy, T., McGinn, T., McLaughlin, J. B., Mead, S., Mehdiyev, R., Mielnichuk, C., Monroe, J., Muir, A., Nadeau, P., Nantais, C., Ng, C., Noble, A. J., O'Dwyer, E., Ohlmann, C., Olchanski, K., Olsen, K. S., Ouellet, C., Pasuthip, P., Peeters, S. J. M., Pollmann, T. R., Rand, E. T., Rau, W., Rethmeier, C., Retière, F., Seeburn, N., Shaw, B., Singhrao, K., Skensved, P., Smith, B., Smith, N. J. T., Sonley, T., Soukup, J., Stainforth, R., Stone, C., Strickland, V., Sur, B., Tang, J., Taylor, J., Veloce, L., Vázquez-Jáuregui, E., Walding, J., Ward, M., Westerdale, S., Woolsey, E., and Zielinski, J.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, High Energy Physics - Experiment, High Energy Physics - Phenomenology
Abstract: This paper reports the first results of a direct dark matter search with the DEAP-3600 single-phase liquid argon (LAr) detector. The experiment was performed 2 km underground at SNOLAB (Sudbury, Canada) utilizing a large target mass, with the LAr target contained in a spherical acrylic vessel of 3600 kg capacity. The LAr is viewed by an array of PMTs, which would register scintillation light produced by rare nuclear recoil signals induced by dark matter particle scattering. An analysis of 4.44 live days (fiducial exposure of 9.87 tonne-days) of data taken with the nearly full detector during the initial filling phase demonstrates the detector performance and the best electronic recoil rejection using pulse-shape discrimination in argon, with leakage $<1.2\times 10^{-7}$ (90% C.L.) between 16 and 33 keV$_{ee}$. No candidate signal events are observed, which results in the leading limit on WIMP-nucleon spin-independent cross section on argon, $<1.2\times 10^{-44}$ cm$^2$ for a 100 GeV/c$^2$ WIMP mass (90% C.L.)., Comment: Accepted for publication in Physical Review Letters
Published: 2017
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13. In-situ characterization of the Hamamatsu R5912-HQE photomultiplier tubes used in the DEAP-3600 experiment

Author: DEAP Collaboration, Amaudruz, P. -A., Batygov, M., Beltran, B., Bina, C. E., Bishop, D., Bonatt, J., Boorman, G., Boulay, M. G., Broerman, B., Bromwich, T., Bueno, J. F., Butcher, A., Cai, B., Chan, S., Chen, M., Chouinard, R., Churchwell, S., Cleveland, B. T., Cranshaw, D., Dering, K., Dittmeier, S., Duncan, F. A., Dunford, M., Erlandson, A., Fatemighomi, N., Ford, R. J., Gagnon, R., Giampa, P., Golovko, V. V., Gorel, P., Gornea, R., Grace, E., Graham, K., Grant, D. R., Gulyev, E., Hall, A., Hallin, A. L., Hamstra, M., Harvey, P. J., Hearns, C., Jillings, C. J., Kamaev, O., Kemp, A., Kuźniak, M., Langrock, S., La Zia, F., Lehnert, B., Li, O., Lidgard, J. J., Liimatainen, P., Lim, C., Lindner, T., Linn, Y., Liu, S., Mathew, R., McDonald, A. B., McElroy, T., McFarlane, K., McLaughlin, J., Mead, S., Mehdiyev, R., Mielnichuk, C., Monroe, J., Muir, A., Nadeau, P., Nantais, C., Ng, C., Noble, A. J., O'Dwyer, E., Ohlmann, C., Olchanski, K., Olsen, K. S., Ouellet, C., Pasuthip, P., Peeters, S. J. M., Pollmann, T. R., Rand, E. T., Rau, W., Rethmeier, C., Retiére, F., Seeburn, N., Shaw, B., Singhrao, K., Skensved, P., Smith, B., Smith, N. J. T., Sonley, T., Stainforth, R., Stone, C., Strickland, V., Sur, B., Tang, J., Taylor, J., Veloce, L., Vázquez-Jáuregui, E., Walding, J., Ward, M., Westerdale, S., White, R., Woolsey, E., and Zielinski, J.
Subjects: Physics - Instrumentation and Detectors
Abstract: The Hamamatsu R5912-HQE photomultiplier-tube (PMT) is a novel high-quantum efficiency PMT. It is currently used in the DEAP-3600 dark matter detector and is of significant interest for future dark matter and neutrino experiments where high signal yields are needed. We report on the methods developed for in-situ characterization and monitoring of DEAP's 255 R5912-HQE PMTs. This includes a detailed discussion of typical measured single-photoelectron charge distributions, correlated noise (afterpulsing), dark noise, double, and late pulsing characteristics. The characterization is performed during the detector commissioning phase using laser light injected through a light diffusing sphere and during normal detector operation using LED light injected through optical fibres.
Published: 2017
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14. Design and construction of the DEAP-3600 dark matter detector

Author: Amaudruz, P.-A., Baldwin, M., Batygov, M., Beltran, B., Bina, C.E., Bishop, D., Bonatt, J., Boorman, G., Boulay, M.G., Broerman, B., Bromwich, T., Bueno, J.F., Burghardt, P.M., Butcher, A., Cai, B., Chan, S., Chen, M., Chouinard, R., Churchwell, S., Cleveland, B.T., Cranshaw, D., Dering, K., DiGioseffo, J., Dittmeier, S., Duncan, F.A., Dunford, M., Erlandson, A., Fatemighomi, N., Florian, S., Flower, A., Ford, R.J., Gagnon, R., Giampa, P., Golovko, V.V., Gorel, P., Gornea, R., Grace, E., Graham, K., Grant, D.R., Gulyev, E., Hall, A., Hallin, A.L., Hamstra, M., Harvey, P.J., Hearns, C., Jillings, C.J., Kamaev, O., Kemp, A., Kuźniak, M., Langrock, S., La Zia, F., Lehnert, B., Li, O., Lidgard, J.J., Liimatainen, P., Lim, C., Lindner, T., Linn, Y., Liu, S., Majewski, P., Mathew, R., McDonald, A.B., McElroy, T., McFarlane, K., McGinn, T., McLaughlin, J.B., Mead, S., Mehdiyev, R., Mielnichuk, C., Monroe, J., Muir, A., Nadeau, P., Nantais, C., Ng, C., Noble, A.J., O’Dwyer, E., Ohlmann, C., Olchanski, K., Olsen, K.S., Ouellet, C., Pasuthip, P., Peeters, S.J.M., Pollmann, T.R., Rand, E.T., Rau, W., Rethmeier, C., Retière, F., Seeburn, N., Shaw, B., Singhrao, K., Skensved, P., Smith, B., Smith, N.J.T., Sonley, T., Soukup, J., Stainforth, R., Stone, C., Strickland, V., Sur, B., Tang, J., Taylor, J., Veloce, L., Vázquez-Jáuregui, E., Walding, J., Ward, M., Westerdale, S., White, R., Woolsey, E., and Zielinski, J.
Published: 2019
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15. Measurement of the scintillation time spectra and pulse-shape discrimination of low-energy beta and nuclear recoils in liquid argon with DEAP-1

Author: Amaudruz, P. -A., Batygov, M., Beltran, B., Bonatt, J., Boudjemline, K., Boulay, M. G., Broerman, B., Bueno, J. F., Butcher, A., Cai, B., Caldwell, T., Chen, M., Chouinard, R., Cleveland, B. T., Cranshaw, D., Dering, K., Duncan, F., Fatemighomi, N., Ford, R., Gagnon, R., Giampa, P., Giuliani, F., Gold, M., Golovko, V. V., Gorel, P., Grace, E., Graham, K., Grant, D. R., Hakobyan, R., Hallin, A. L., Hamstra, M., Harvey, P., Hearns, C., Hofgartner, J., Jillings, C. J., Kuźniak, M., Lawson, I., La Zia, F., Li, O., Lidgard, J. J., Liimatainen, P., Lippincott, W. H., Mathew, R., McDonald, A. B., McElroy, T., McFarlane, K., Mehdiyev, R., McKinsey, D. N., Monroe, J., Muir, A., Nantais, C., Nicolics, K., Nikkel, J., Noble, A. J., O'Dwyer, E., Olsen, K., Ouellet, C., Pasuthip, P., Peeters, S. J. M., Pollmann, T., Rau, W., Retière, F., Ronquest, M., Seeburn, N., Skensved, P., Smith, B., Sonley, T., Tang, J., Vázquez-Jáuregui, E., Veloce, L., Walding, J., and Ward, M.
Subjects: Astrophysics - Instrumentation and Methods for Astrophysics
Abstract: The DEAP-1 low-background liquid argon detector was used to measure scintillation pulse shapes of electron and nuclear recoil events and to demonstrate the feasibility of pulse-shape discrimination (PSD) down to an electron-equivalent energy of 20 keV. In the surface dataset using a triple-coincidence tag we found the fraction of beta events that are misidentified as nuclear recoils to be $<1.4\times 10^{-7}$ (90% C.L.) for energies between 43-86 keVee and for a nuclear recoil acceptance of at least 90%, with 4% systematic uncertainty on the absolute energy scale. The discrimination measurement on surface was limited by nuclear recoils induced by cosmic-ray generated neutrons. This was improved by moving the detector to the SNOLAB underground laboratory, where the reduced background rate allowed the same measurement with only a double-coincidence tag. The combined data set contains $1.23\times10^8$ events. One of those, in the underground data set, is in the nuclear-recoil region of interest. Taking into account the expected background of 0.48 events coming from random pileup, the resulting upper limit on the electronic recoil contamination is $<2.7\times10^{-8}$ (90% C.L.) between 44-89 keVee and for a nuclear recoil acceptance of at least 90%, with 6% systematic uncertainty on the absolute energy scale. We developed a general mathematical framework to describe PSD parameter distributions and used it to build an analytical model of the distributions observed in DEAP-1. Using this model, we project a misidentification fraction of approx. $10^{-10}$ for an electron-equivalent energy threshold of 15 keV for a detector with 8 PE/keVee light yield. This reduction enables a search for spin-independent scattering of WIMPs from 1000 kg of liquid argon with a WIMP-nucleon cross-section sensitivity of $10^{-46}$ cm$^2$, assuming negligible contribution from nuclear recoil backgrounds., Comment: Accepted for publication in Astroparticle Physics
Published: 2009
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16. The liquid-argon scintillation pulseshape in DEAP-3600

Author: Adhikari, P., Ajaj, R., Araujo, G. R., Batygov, M., Beltran, B., Bina, C. E., Boulay, M. G., Broerman, B., Bueno, J. F., Butcher, A., Cai, B., Cárdenas-Montes, M., Cavuoti, S., Chen, Y., Cleveland, B. T., Corning, J. M., Daugherty, S. J., Di Stefano, P., Dering, K., Doria, L., Duncan, F. A., Dunford, M., Erlandson, A., Fatemighomi, N., Fiorillo, G., Flower, A., Ford, R. J., Gagnon, R., Gallacher, D., Garcés , E. A., Abia, P. García, Garg, S., Giampa, P., Goeldi, D., Golovko, V. V., Gorel, P., Graham, K., Grant, D. R., Grobov, A., Hallin, A. L., Hamstra, M., Harvey, P. J., Hearns, C., Ilyasov, A., Joy, A., Jillings, C. J., Kamaev, O., Kaur, G., Kemp, A., Kochanek, I., Kuźniak, M., Langrock, S., La Zia, F., Lehnert, B., Levashko, N., Li, X., Litvinov, O., Lock, J., Longo, G., Machulin, I., Majewski, P., McDonald, A. B., McElroy, T., McGinn, T., McLaughlin, J. B., Mehdiyev, R., Mielnichuk, C., Monroe, J., Nadeau, P., Nantais, C., Ng, C., Noble, A. J., Oliviéro, G., Ouellet, C., Pal, S., Pasuthip, P., Peeters, S. J. M., Pesudo, V., Piro, M.-C., Pollmann, T. R., Rand, E. T., Rethmeier, C., Retière, F., García, E. Sanchez, Sánchez-Pastor, T., Santorelli, R., Seeburn, N., Skensved, P., Smith, B., Smith, N. J. T., Sonley, T., Stainforth, R., Stone, C., Strickland, V., Stringer, M., Sur, B., Vázquez-Jáuregui, E., Veloce, L., Viel, S., Walding, J., Waqar, M., Ward, M., Westerdale, S., Willis, J., and Zuñiga-Reyes, A.
Published: 2020
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17. The effect of a perioperative ketamine infusion on the incidence of chronic postsurgical pain - a pilot study

Author: Peyton, PJ, Wu, C, Jacobson, T, Hogg, M, Zia, F, and Leslie, K
Published: 2017

18. Measurement of the scintillation time spectra and pulse-shape discrimination of low-energy β and nuclear recoils in liquid argon with DEAP-1

Author: Amaudruz, P.-A., Batygov, M., Beltran, B., Bonatt, J., Boudjemline, K., Boulay, M.G., Broerman, B., Bueno, J.F., Butcher, A., Cai, B., Caldwell, T., Chen, M., Chouinard, R., Cleveland, B.T., Cranshaw, D., Dering, K., Duncan, F., Fatemighomi, N., Ford, R., Gagnon, R., Giampa, P., Giuliani, F., Gold, M., Golovko, V.V., Gorel, P., Grace, E., Graham, K., Grant, D.R., Hakobyan, R., Hallin, A.L., Hamstra, M., Harvey, P., Hearns, C., Hofgartner, J., Jillings, C.J., Kuźniak, M., Lawson, I., La Zia, F., Li, O., Lidgard, J.J., Liimatainen, P., Lippincott, W.H., Mathew, R., McDonald, A.B., McElroy, T., McFarlane, K., McKinsey, D.N., Mehdiyev, R., Monroe, J., Muir, A., Nantais, C., Nicolics, K., Nikkel, J., Noble, A.J., O’Dwyer, E., Olsen, K., Ouellet, C., Pasuthip, P., Peeters, S.J.M., Pollmann, T., Rau, W., Retière, F., Ronquest, M., Seeburn, N., Skensved, P., Smith, B., Sonley, T., Tang, J., Vázquez-Jáuregui, E., Veloce, L., Walding, J., and Ward, M.
Published: 2016
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19. Assessment of agreement and interchangeability between the TEG5000 and TEG6S thromboelastography haemostasis analysers: a prospective validation study

Author: Lloyd-Donald, P., Churilov, L., Zia, F., Bellomo, R., Hart, G., McCall, P., Mårtensson, J., Glassford, N., and Weinberg, L.
Published: 2019
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20. Arqueologia da Personalidade

Author: ZIA, F. R., primary
Published: 2023
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21. Input precision, output excellence: the importance of data quality control and method selection in disease risk mapping —authors’ reply

Author: Zia Farooq, Joacim Rocklöv, Jonas Wallin, Najmeh Abiri, Maquines Odhiambo Sewe, Henrik Sjödin, and Jan C. Semenza
Subjects: Public aspects of medicine, RA1-1270
Published: 2024
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22. Knowledge and Practice of Health-care Workers regarding Hand Hygiene during Third Wave of COVID-19

Author: Fatima, M.l, primary, Waqar, M., additional, Qamar, H., additional, Akram, M., additional, Zia, F., additional, and Hussain, R., additional
Published: 2021
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23. Effects of a short message service (SMS) by cellular phone to improve compliance with fasting guidelines in patients undergoing elective surgery: a retrospective observational study

Author: Zia, F, Cosic, L, Wong, A, Levin, A, Lu, P, Mitchell, C, Shaw, M, Rosewarne, F, Weinberg, L, Zia, F, Cosic, L, Wong, A, Levin, A, Lu, P, Mitchell, C, Shaw, M, Rosewarne, F, and Weinberg, L
Abstract: BACKGROUND: Contemporary perioperative fasting guidelines aim to alleviate patient discomfort before surgery and enhance postoperative recovery whilst seeking to reduce the risk of pulmonary aspiration during anesthesia. The impact of a short message service (SMS) reminder on fasting guideline compliance is unknown. Therefore, we performed a retrospective observational study and quality improvement project aiming to quantify the extent of excessive and prolonged fasting, and then assessed the impact of a SMS reminder in reducing fasting times. METHODS: After ethics committee approval we performed a retrospective observational study investigating preoperative fasting times of adult patients undergoing elective surgery. First, we assessed whether the fasting guideline times were adhered to (Standard Care group). All patients received internationally recommended fasting guidelines in the form of a written hospital policy document. We then implemented an additional prompt via a mobile phone SMS 1 day prior to surgery containing a reminder of fasting guideline times (SMS group). The primary aims were to compare fasting times between the Standard Care group and the SMS group. RESULTS: The fasting times of 160 patients in the Standard Care group and 110 patients in the SMS group were evaluated. Adherence to the fasting guidelines for solids occurred in 14 patients (8.8%) in the Standard Care group vs. Twenty-two patients (13.6%) in the SMS group (p=0.01). Adherence to the fasting guidelines for fluids occurred in 4 patients (2.5%) in the Standard Care group vs. Ten patients (6.3%) in the SMS group (p=0.023). Patients in the Standard Care group had a longer median (inter-quartile range (IQR)) fasting time for fluids compared the SMS group [6.5 h (IQR 4.5:11) vs 3.5 h (IQR 3:8.5), p< 0.0001]. Median fasting times for solids were 11 h (IQR 7:14) in the Standard Care group and 11.5 h (IQR 7:13.5) in the SMS group (p=0.756). CONCLUSION: Adherence to internationally recommended
Published: 2021

24. Hematopoietic stem cell transplantation in Oman

Author: Dennison, D, Al Kindi, S, Pathare, A, Daar, S, Nusrat, N, Ur Rehman, J, Zia, F, Khan, H, Khan, M, Alghazaly, A, Al Zadjali, S, Tauro, M, Al Lawatia, A T, and Ganguly, S S
Published: 2008
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25. The liquid-argon scintillation pulseshape in DEAP-3600

Author: Adhikari, P. (P.), Ajaj, R. (R.), Araujo, G.R. (G. R.), Batygov, M. (M.), Beltran, B. (B.), Bina, C.E. (C. E.), Boulay, M.G. (Mark Guy), Broerman, B. (B.), Bueno, J.F. (J. F.), Butcher, A. (A.), Cai, B. (B.), Cárdenas-Montes, M. (M.), Cavuoti, S. (S.), Chen, Y. (Y.), Cleveland, B.T. (B. T.), Corning, J.M. (J. M.), Daugherty, S.J. (S. J.), Di Stefano, P. (P.), Dering, K. (K.), Doria, L. (L.), Duncan, F.A. (F. A.), Dunford, M. (M.), Erlandson, A. (A.), Fatemighomi, N. (N.), Fiorillo, G. (G.), Flower, A. (A.), Ford, R.J. (R. J.), Gagnon, R. (R.), Gallacher, D. (D.), Garcés, E.A. (E. A.), Abia, P.G. (P. García), Garg, S. (S.), Giampa, P. (P.), Goeldi, D. (D.), Golovko, V.V. (V. V.), Gorel, P. (P.), Graham, K. (K.), Grant, D.R. (D. R.), Grobov, A. (A.), Hallin, A.L. (A. L.), Hamstra, M. (M.), Harvey, P.J. (P. J.), Hearns, C. (C.), Ilyasov, A. (A.), Joy, A. (A.), Jillings, C.J. (C. J.), Kamaev, O. (O.), Kaur, G. (G.), Kemp, A. (A.), Kochanek, I. (I.), Kuźniak, M. (M.), Langrock, S. (S.), La Zia, F. (F.), Lehnert, B. (B.), Levashko, N. (N.), Li, X. (X.), Litvinov, O. (O.), Lock, J. (J.), Longo, G. (G.), Machulin, I. (I.), Majewski, P. (P.), McDonald, A.B. (A. B.), McElroy, T. (T.), McGinn, T. (T.), McLaughlin, J.B. (J. B.), Mehdiyev, R. (R.), Mielnichuk, C. (C.), Monroe, J. (J.), Nadeau, P. (P.), Nantais, C. (C.), Ng, C. (C.), Noble, A.J. (A. J.), Oliviéro, G. (G.), Ouellet, C. (C.), Pal, S. (S.), Pasuthip, P. (P.), Peeters, S.J.M. (S. J.M.), Pesudo, V. (V.), Piro, M.-C. (M. C.), Pollmann, T.R. (T. R.), Rand, E.T. (E. T.), Rethmeier, C. (C.), Retière, F. (F.), García, E.S. (E. Sanchez), Sánchez-Pastor, T. (T.), Santorelli, R. (R.), Seeburn, N. (N.), Skensved, P. (P.), Smith, B. (B.), Smith, N.J.T. (N. J.T.), Sonley, T. (T.), Stainforth, R. (R.), Stone, C. (C.), Strickland, V. (V.), Stringer, M. (M.), Sur, B. (B.), Vázquez-Jáuregui, E. (E.), Veloce, L. (L.), Viel, S. (S.), Walding, J. (J.), Waqar, M. (M.), Ward, M. (M.), Westerdale, S. (S.), Willis, J. (J.), Zuñiga-Reyes, A. (A.), Adhikari, P. (P.), Ajaj, R. (R.), Araujo, G.R. (G. R.), Batygov, M. (M.), Beltran, B. (B.), Bina, C.E. (C. E.), Boulay, M.G. (Mark Guy), Broerman, B. (B.), Bueno, J.F. (J. F.), Butcher, A. (A.), Cai, B. (B.), Cárdenas-Montes, M. (M.), Cavuoti, S. (S.), Chen, Y. (Y.), Cleveland, B.T. (B. T.), Corning, J.M. (J. M.), Daugherty, S.J. (S. J.), Di Stefano, P. (P.), Dering, K. (K.), Doria, L. (L.), Duncan, F.A. (F. A.), Dunford, M. (M.), Erlandson, A. (A.), Fatemighomi, N. (N.), Fiorillo, G. (G.), Flower, A. (A.), Ford, R.J. (R. J.), Gagnon, R. (R.), Gallacher, D. (D.), Garcés, E.A. (E. A.), Abia, P.G. (P. García), Garg, S. (S.), Giampa, P. (P.), Goeldi, D. (D.), Golovko, V.V. (V. V.), Gorel, P. (P.), Graham, K. (K.), Grant, D.R. (D. R.), Grobov, A. (A.), Hallin, A.L. (A. L.), Hamstra, M. (M.), Harvey, P.J. (P. J.), Hearns, C. (C.), Ilyasov, A. (A.), Joy, A. (A.), Jillings, C.J. (C. J.), Kamaev, O. (O.), Kaur, G. (G.), Kemp, A. (A.), Kochanek, I. (I.), Kuźniak, M. (M.), Langrock, S. (S.), La Zia, F. (F.), Lehnert, B. (B.), Levashko, N. (N.), Li, X. (X.), Litvinov, O. (O.), Lock, J. (J.), Longo, G. (G.), Machulin, I. (I.), Majewski, P. (P.), McDonald, A.B. (A. B.), McElroy, T. (T.), McGinn, T. (T.), McLaughlin, J.B. (J. B.), Mehdiyev, R. (R.), Mielnichuk, C. (C.), Monroe, J. (J.), Nadeau, P. (P.), Nantais, C. (C.), Ng, C. (C.), Noble, A.J. (A. J.), Oliviéro, G. (G.), Ouellet, C. (C.), Pal, S. (S.), Pasuthip, P. (P.), Peeters, S.J.M. (S. J.M.), Pesudo, V. (V.), Piro, M.-C. (M. C.), Pollmann, T.R. (T. R.), Rand, E.T. (E. T.), Rethmeier, C. (C.), Retière, F. (F.), García, E.S. (E. Sanchez), Sánchez-Pastor, T. (T.), Santorelli, R. (R.), Seeburn, N. (N.), Skensved, P. (P.), Smith, B. (B.), Smith, N.J.T. (N. J.T.), Sonley, T. (T.), Stainforth, R. (R.), Stone, C. (C.), Strickland, V. (V.), Stringer, M. (M.), Sur, B. (B.), Vázquez-Jáuregui, E. (E.), Veloce, L. (L.), Viel, S. (S.), Walding, J. (J.), Waqar, M. (M.), Ward, M. (M.), Westerdale, S. (S.), Willis, J. (J.), and Zuñiga-Reyes, A. (A.)
Abstract: DEAP-3600 is a liquid-argon scintillation detector looking for dark matter. Scintillation events in the liquid argon (LAr) are registered by 255 photomultiplier tubes (PMTs), and pulseshape discrimination (PSD) is used to suppress electromagnetic background events. The excellent PSD performance of LAr makes it a viable target for dark matter searches, and the LAr scintillation pulseshape discussed h
Published: 2020
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26. Contextual role of architectural background images in digital comics

Author: Anissa Febrina, Muhammad Heru Arie Edytia, and Zia Faizurrahmany El Faridy
Subjects: architectural background, digital comic, narrative, comparative analysis, Architecture, NA1-9428
Abstract: This research aims to determine the role of architectural background images in digital comics and their proportional contribution to the overall reading interest. Digital comics are a form of media with sequential panels of images that project two-dimensional scenes positioned in a certain context. The context is presented in the background and is used as a story-building element in the comics. The study is interested in identifying important criteria of the architectural background as part of the digital comics narrative and measuring its relevance. This research uses the quantitative comparative method, with non-probability purposive sampling of 15 respondents. This research measured readers' interest in digital comics with and without an architectural background using a Likert scale and percentage interval scale to determine. Comparative analysis is done using two samples with the t-test. This research found that the percentage of readers' interest interval scale for digital comics with an architectural background is significantly higher in comparison with digital comics without an architectural background. The study demonstrates the various roles of architectural image as part of the story narrative, from clarification of the storyline and demonstrating representation of reality, to creating points of interest and focus.
Published: 2023
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27. An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis

Author: Vinh G. Tran, Somesh Mishra, Sarang S. Bhagwat, Saman Shafaei, Yihui Shen, Jayne L. Allen, Benjamin A. Crosly, Shih-I Tan, Zia Fatma, Joshua D. Rabinowitz, Jeremy S. Guest, Vijay Singh, and Huimin Zhao
Subjects: Science
Abstract: Abstract Microbial production of succinic acid (SA) at an industrially relevant scale has been hindered by high downstream processing costs arising from neutral pH fermentation for over three decades. Here, we metabolically engineer the acid-tolerant yeast Issatchenkia orientalis for SA production, attaining the highest titers in sugar-based media at low pH (pH 3) in fed-batch fermentations, i.e. 109.5 g/L in minimal medium and 104.6 g/L in sugarcane juice medium. We further perform batch fermentation using sugarcane juice medium in a pilot-scale fermenter (300×) and achieve 63.1 g/L of SA, which can be directly crystallized with a yield of 64.0%. Finally, we simulate an end-to-end low-pH SA production pipeline, and techno-economic analysis and life cycle assessment indicate our process is financially viable and can reduce greenhouse gas emissions by 34–90% relative to fossil-based production processes. We expect I. orientalis can serve as a general industrial platform for production of organic acids.
Published: 2023
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28. Assessment of agreement and interchangeability between the TEG5000 and TEG6S thromboelastography haemostasis analysers: a prospective validation study

Author: Lloyd-Donald, P, Churilov, L, Zia, F, Bellomo, R, Hart, G, McCall, P, Martensson, J, Glassford, N, Weinberg, L, Lloyd-Donald, P, Churilov, L, Zia, F, Bellomo, R, Hart, G, McCall, P, Martensson, J, Glassford, N, and Weinberg, L
Abstract: BACKGROUND: TEG6S® and TEG5000® (Haemonetics Corp, USA) are haemostasis analysers that measure viscoelasticity properties of whole blood. Both use different mechanisms to assess similar components of the coagulation process. The aim of this study was to assess agreement and interchangeability between the TEG6S and TEG5000 analysers. METHODS: 3.5 mL whole blood was collected from 25 adult patients in a tertiary intensive care unit (ICU). Analysis was performed using TEG6S and TEG5000 haemostatic platforms. Agreement between platforms was measured using Lin's concordance coefficient (Lin's CC), further validated using intraclass correlation coefficients and reduced major axis regression (RMAR). RESULTS: Sixteen (64%) patients were male; mean (range) age: 59yo (23-86). TEG6S and TEG5000 systems were broadly interchangeable. The majority of TEG variables demonstrated almost perfect or substantial agreement and minimal proportional bias (maximum amplitude demonstrated a fixed bias). LY30%, however, demonstrated poor agreement and a proportional bias. Lin's CC coefficients (95% CI, RMAR slope, intercept) between TEG6S and TEG5000 variables were: R time: 0.78 (0.64-0.92, 0.76, 0.92); K time: 0.82 (0.69-0.94, 1.30, - 0.93); alpha angle: 0.79 (0.64-0.95, 1.04, - 1.43); maximum amplitude (MA): 0.90 (0.83-0.96, 0.99, - 5.0); LY30%: 0.34 (0.1-0.58, 0.43, 0.04). CONCLUSIONS: Adult patients with critical illness demonstrate almost perfect agreement in the R time and MA, substantial agreement in K time and alpha angle, but poor agreement in LY30%, as measured by the TEG6S and TEG5000 analysers. With the exception of LY30%, the TEG6S and TEG5000 platforms appear interchangeable. This has important implications for use in clinical practice and multi-site research programs. TRIAL REGISTRATION: ANZCRT number: 12617000062325 , registered 12/Jan17. Retrospectively registered.
Published: 2019

29. VPAC1 Receptors and Lung Cancer

Author: MOODY, T. W., WALTERS, J., CASIBANG, M., ZIA, F., and GOZES, Y.
Published: 2000

30. In-situ characterization of the Hamamatsu R5912-HQE photomultiplier tubes used in the DEAP-3600 experiment

Author: Amaudruz, P.-A., primary, Batygov, M., additional, Beltran, B., additional, Bina, C.E., additional, Bishop, D., additional, Bonatt, J., additional, Boorman, G., additional, Boulay, M.G., additional, Broerman, B., additional, Bromwich, T., additional, Bueno, J.F., additional, Butcher, A., additional, Cai, B., additional, Chan, S., additional, Chen, M., additional, Chouinard, R., additional, Churchwell, S., additional, Cleveland, B.T., additional, Cranshaw, D., additional, Dering, K., additional, Dittmeier, S., additional, Duncan, F.A., additional, Dunford, M., additional, Erlandson, A., additional, Fatemighomi, N., additional, Ford, R.J., additional, Gagnon, R., additional, Giampa, P., additional, Golovko, V.V., additional, Gorel, P., additional, Gornea, R., additional, Grace, E., additional, Graham, K., additional, Grant, D.R., additional, Gulyev, E., additional, Hall, A., additional, Hallin, A.L., additional, Hamstra, M., additional, Harvey, P.J., additional, Hearns, C., additional, Jillings, C.J., additional, Kamaev, O., additional, Kemp, A., additional, Kuźniak, M., additional, Langrock, S., additional, La Zia, F., additional, Lehnert, B., additional, Li, O., additional, Lidgard, J.J., additional, Liimatainen, P., additional, Lim, C., additional, Lindner, T., additional, Linn, Y., additional, Liu, S., additional, Mathew, R., additional, McDonald, A.B., additional, McElroy, T., additional, McFarlane, K., additional, McLaughlin, J., additional, Mead, S., additional, Mehdiyev, R., additional, Mielnichuk, C., additional, Monroe, J., additional, Muir, A., additional, Nadeau, P., additional, Nantais, C., additional, Ng, C., additional, Noble, A.J., additional, O’Dwyer, E., additional, Ohlmann, C., additional, Olchanski, K., additional, Olsen, K.S., additional, Ouellet, C., additional, Pasuthip, P., additional, Peeters, S.J.M., additional, Pollmann, T.R., additional, Rand, E.T., additional, Rau, W., additional, Rethmeier, C., additional, Retière, F., additional, Seeburn, N., additional, Shaw, B., additional, Singhrao, K., additional, Skensved, P., additional, Smith, B., additional, Smith, N.J.T., additional, Sonley, T., additional, Stainforth, R., additional, Stone, C., additional, Strickland, V., additional, Sur, B., additional, Tang, J., additional, Taylor, J., additional, Veloce, L., additional, Vázquez-Jáuregui, E., additional, Walding, J., additional, Ward, M., additional, Westerdale, S., additional, White, R., additional, Woolsey, E., additional, and Zielinski, J., additional
Published: 2019
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31. Decision-support tools to build climate resilience against emerging infectious diseases in Europe and beyond

Author: Joacim Rocklöv, Jan C. Semenza, Shouro Dasgupta, Elizabeth J.Z. Robinson, Ahmed Abd El Wahed, Tilly Alcayna, Cristina Arnés-Sanz, Meghan Bailey, Till Bärnighausen, Frederic Bartumeus, Carme Borrell, Laurens M. Bouwer, Pierre-Antoine Bretonnière, Aditi Bunker, Chloe Chavardes, Kim R. van Daalen, João Encarnação, Nube González-Reviriego, Junwen Guo, Katie Johnson, Marion P.G. Koopmans, María Máñez Costa, Antonios Michaelakis, Tomás Montalvo, Anna Omazic, John R.B. Palmer, Raman Preet, Marina Romanello, Mohammad Shafiul Alam, Reina S. Sikkema, Marta Terrado, Marina Treskova, Diana Urquiza, Rachel Lowe, Henrik Sjodin, Zia Farooq, Maquines Sewe, Frances MacGuire, Evangelia Zavitsanou, Panos Milonas, Dimitrios Papachristos, Marina Bisia, Georgios Balatsos, Spyros Antonatos, Jaime Martinez-Urtaza, Joaquin Triñanes, Mark Williams, Berj Dekramanjian, Karl Broome, Otis Johnson, Laurens Bouwer, Maria Máñez Costa, Adriana Martin, Lola Kotova, Thea Wübbelmann, Fiona Walsh, Pascale Stiles, Jerome Baron, Charles Hatfield, Julian Heidecke, Pratik Singh, Francesco Bosello, Sara Mehryar, Pauline de Best, Tijmen Hartung, Ayat Abourashed, Jesus Bellver, Catuxa Cerecedo, Martín Lotto Bautista, Bruno Moreira de Carvalho, Chloe Fletcher, Julieta Rosenbluth, Marina Corradini, Jaume Ramon, Liam Patrick Brodie, Alba Llabres, Arianna Ceruti, Uwe Truyen, Sasha Rodrigues, Erik Ågren, Giulio Grandi, Stefan Widgren, Masud Parvage, Martin Bergström, Rashidul Haque, Wasif Ali Khan, Andrea Valsecchi, Laura Barahona, Elisenda Realp, and Stephan de Roode
Subjects: Climate change, Infectious disease, One Health, Planetary health, Human health, Climate policy, Public aspects of medicine, RA1-1270
Abstract: Summary: Climate change is one of several drivers of recurrent outbreaks and geographical range expansion of infectious diseases in Europe. We propose a framework for the co-production of policy-relevant indicators and decision-support tools that track past, present, and future climate-induced disease risks across hazard, exposure, and vulnerability domains at the animal, human, and environmental interface. This entails the co-development of early warning and response systems and tools to assess the costs and benefits of climate change adaptation and mitigation measures across sectors, to increase health system resilience at regional and local levels and reveal novel policy entry points and opportunities. Our approach involves multi-level engagement, innovative methodologies, and novel data streams. We take advantage of intelligence generated locally and empirically to quantify effects in areas experiencing rapid urban transformation and heterogeneous climate-induced disease threats. Our goal is to reduce the knowledge-to-action gap by developing an integrated One Health—Climate Risk framework.
Published: 2023
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32. A phase II study of durvalumab, a PD-L1 inhibitor and olaparib in recurrent ovarian cancer (OvCa)

Author: Lee, J.-M., primary, Annunziata, C.M., additional, Houston, N., additional, Kohn, E.C., additional, Lipkowitz, S., additional, Minasian, L., additional, Nichols, E., additional, Trepel, J., additional, Trewhitt, K., additional, Zia, F., additional, and Zimmer, A.D.S., additional
Published: 2018
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33. European projections of West Nile virus transmission under climate change scenarios

Author: Zia Farooq, Henrik Sjödin, Jan C. Semenza, Yesim Tozan, Maquines Odhiambo Sewe, Jonas Wallin, and Joacim Rocklöv
Subjects: West Nile virus, Zoonoses, Europe, XGBoost, WNV risk projections, Climate change, Medicine (General), R5-920
Abstract: West Nile virus (WNV), a mosquito-borne zoonosis, has emerged as a disease of public health concern in Europe. Recent outbreaks have been attributed to suitable climatic conditions for its vectors favoring transmission. However, to date, projections of the risk for WNV expansion under climate change scenarios is lacking. Here, we estimate the WNV-outbreaks risk for a set of climate change and socioeconomic scenarios. We delineate the potential risk-areas and estimate the growth in the population at risk (PAR).We used supervised machine learning classifier, XGBoost, to estimate the WNV-outbreak risk using an ensemble climate model and multi-scenario approach. The model was trained by collating climatic, socioeconomic, and reported WNV-infections data (2010−22) and the out-of-sample results (1950–2009, 2023–99) were validated using a novel Confidence-Based Performance Estimation (CBPE) method. Projections of area specific outbreak risk trends, and corresponding population at risk were estimated and compared across scenarios.Our results show up to 5-fold increase in West Nile virus (WNV) risk for 2040-60 in Europe, depending on geographical region and climate scenario, compared to 2000-20. The proportion of disease-reported European land areas could increase from 15% to 23-30%, putting 161 to 244 million people at risk. Across scenarios, Western Europe appears to be facing the largest increase in the outbreak risk of WNV. The increase in the risk is not linear but undergoes periods of sharp changes governed by climatic thresholds associated with ideal conditions for WNV vectors. The increased risk will require a targeted public health response to manage the expansion of WNV with climate change in Europe.
Published: 2023
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34. Author Correction: An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis

Author: Vinh G. Tran, Somesh Mishra, Sarang S. Bhagwat, Saman Shafaei, Yihui Shen, Jayne L. Allen, Benjamin A. Crosly, Shih-I Tan, Zia Fatma, Joshua D. Rabinowitz, Jeremy S. Guest, Vijay Singh, and Huimin Zhao
Subjects: Science
Published: 2024
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35. 936PD - A phase II study of durvalumab, a PD-L1 inhibitor and olaparib in recurrent ovarian cancer (OvCa)

Author: Lee, J.-M., Annunziata, C.M., Houston, N., Kohn, E.C., Lipkowitz, S., Minasian, L., Nichols, E., Trepel, J., Trewhitt, K., Zia, F., and Zimmer, A.D.S.
Published: 2018
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36. Modified Hodge test: A simple and effective test for detection of carbapenemase production

Author: Amjad, A, Mirza, IA, Abbasi, SA, Farwa, U, Malik, N, and Zia, F
Subjects: carbapenemases, Short Communication, disc diffusion, lcsh:QR1-502, Modified Hodge test, lcsh:Microbiology
Abstract: Background and Objectives: Resistance among bacterial isolates is the leading cause of increased mortality and morbidity worldwide. Carbapenems once thought to be effective are becoming ineffective mostly due to the emergence of carbapenemase. This study was designed to determine in vitro efficacy of Modified Hodge test for detection of carbapenemase production in Gram negative rods. Material and Methods: The study was done in the Department of Microbiology, Armed Forces Institute of Pathology Rawalpindi Pakistan from January 2010 to December 2010. A total of 200 Gram negative rods from different clinical samples were taken. Those isolates which showed intermediate or susceptible zones i.e 16mm-21mm on disc diffusion were included in the study. These isolates were then subjected to Modified Hodge test. Result: Out of 200 isolates, 138 (69%) were positive for carbapenemase production by Modified Hodge test. Out of 138 MHT positive organisms, the frequency of E. coli was 38%, followed by Pseudomonas aeruginosa (30%), Klebsiella pneumoniae (17%), Acinetobacter baumannii (12%), Citrobacter diversus (2%) and Enterobacter agglomerans (1.4%). Conclusion: Modified Hodge test is a simple test which can be performed in the routine lab for detection of carbapenemases in isolates showing intermediate or sensitive zone diameter on disc diffusion.
Published: 2011

37. Artificial intelligence to predict West Nile virus outbreaks with eco-climatic drivers

Author: Zia Farooq, Joacim Rocklöv, Jonas Wallin, Najmeh Abiri, Maquines Odhiambo Sewe, Henrik Sjödin, and Jan C. Semenza
Subjects: West Nile virus, Culex vectors, Europe, XGBoost, SHAP, Outbreaks management, Public aspects of medicine, RA1-1270
Abstract: Summary: Background: In Europe, the frequency, intensity, and geographic range of West Nile virus (WNV)-outbreaks have increased over the past decade, with a 7.2-fold increase in 2018 compared to 2017, and a markedly expanded geographic area compared to 2010. The reasons for this increase and range expansion remain largely unknown due to the complexity of the transmission pathways and underlying disease drivers. In a first, we use advanced artificial intelligence to disentangle the contribution of eco-climatic drivers to WNV-outbreaks across Europe using decade-long (2010-2019) data at high spatial resolution. Methods: We use a high-performance machine learning classifier, XGBoost (eXtreme gradient boosting) combined with state-of-the-art XAI (eXplainable artificial intelligence) methodology to describe the predictive ability and contribution of different drivers of the emergence and transmission of WNV-outbreaks in Europe, respectively. Findings: Our model, trained on 2010-2017 data achieved an AUC (area under the receiver operating characteristic curve) score of 0.97 and 0.93 when tested with 2018 and 2019 data, respectively, showing a high discriminatory power to classify a WNV-endemic area. Overall, positive summer/spring temperatures anomalies, lower water availability index (NDWI), and drier winter conditions were found to be the main determinants of WNV-outbreaks across Europe. The climate trends of the preceding year in combination with eco-climatic predictors of the first half of the year provided a robust predictive ability of the entire transmission season ahead of time. For the extraordinary 2018 outbreak year, relatively higher spring temperatures and the abundance of Culex mosquitoes were the strongest predictors, in addition to past climatic trends. Interpretation: Our AI-based framework can be deployed to trigger rapid and timely alerts for active surveillance and vector control measures in order to intercept an imminent WNV-outbreak in Europe. Funding: The work was partially funded by the Swedish Research Council FORMAS for the project ARBOPREVENT (grant agreement 2018-05973).
Published: 2022
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38. Haemodialysis catheter-related giant right atrial and superior cava thrombi

Author: Weinberg, L., primary, Zia, F., additional, Tay, S., additional, and Roubos, N., additional
Published: 2015
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39. The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

Author: Collaboration, LBNE, Adams, C., Adams, D. A., Akiri, T., Alion, T., Anderson, K., Andreopoulos, C., Andrews, M., Anghel, I., Anjos, JCCD, Antonello, M., Arrieta-Diaz, E., Artuso, M., Asaadi, J., Bai, X., Baibussinov, B., Baird, M., Balantekin, A. B., Baller, B., Baptista, B., Barker, D., Barker, G., Barletta, W. A., Barr, G., Bartoszek, L., Bashyal, A., Bass, M., Bellini, V., Benetti, P. A., Berger, B. E., Bergevin, M., Berman, E., Berns, H. G., Bernstein, A., Bernstein, R., Bhandari, B., Bhatnagar, V., Bhuyan, B., Bian, J., Bishai, M., Blake, A., Blaszczyk, F., Blaufuss, E., Bleakley, B., Blucher, E., Blusk, S., Bocean, V., Boffelli, F., Boissevain, J. G., Bolton, T., Bonesini, M., Boyd, S., Brandt, A., Breedon, R., Bromberg, C., Brown, R., Brunetti, G., Buchanan, N., Bugg, B., Busenitz, J., Calligarich, E., Camilleri, Leslie, Carminati, G., Carr, Rachel E., Castromonte, C., Cavanna, F., Centro, S., Chen, A., Chen, H., Chen, K., Cherdack, D., Chi, C. Y., Childress, S., Choudhary, B. C., Christodoulou, G., Christofferson, C. A., Church, E., Cline, D., Coan, T., Cocco, A., Coelho, J., Coleman, S., Conrad, Janet M., Convery, M., Corey, R., Corwin, L., Cranshaw, J., Cronin-Hennessy, D., Curioni, A., Motta, H. D., Davenne, T., Davies, G. S., Dazeley, S., De, K., Gouvea, A. D., Jong, J K. D., Demuth, D., Densham, C., Diwan, M., Djurcic, Zelimir, Dolfini, R., Dolph, J., Drake, G., Dye, S., Dyuang, H., Edmunds, D., Elliott, S., Elnimr, M., Eno, S., Enomoto, S., Escobar, C. O., Evans, J., Falcone, A., Falk, L., Farbin, A., Farnese, C., Fava, A., Felde, J., Fernandes, S., Ferroni, F., Feyzi, F., Fields, L., Finch, A., Fitton, M., Fleming, B., Fowler, J., Fox, W., Friedland, A., Fuess, S., Fujikawa, B. K., Gallagher, H., Gandhi, R., Garvey, G. T., Gehman, V. M., Geronimo, G. D., Gibin, D., Gill, R., Gomes, R. A., Goodman, M. C., Goon, J., Graf, N., Graham, M., Gran, R., Grant, C., Grant, N., Greenlee, H., Greenler, L., Grullon, S., Guardincerri, E., Guarino, V., Guarnaccia, E., Guedes, G. P., Guenette, R., Guglielmi, A., Guzzo, M. M., Habig, A. T., Hackenburg, R. W., Hadavand, H., Hahn, A., Haigh, M., Haines, T., Handler, T., Hans, S., Hartnell, J., Harton, J., Hatcher, R., Hatzikoutelis, A., Hays, S., Hazen, E., Headley, M., Heavey, A., Heeger, K., Heise, J., Hellauer, R., Hewes, J., Himmel, A., Hogan, M., Holanda, P., Holin, A., Horton-Smith, Glenn A., Howell, J., Hurh, P., Huston, J., Hylen, J., Imlay, R., Insler, J., Introzzi, G., Isvan, Z., Jackson, C., Jacobsen, J., Jaffe, D. E., James, C., Jen, C. M., Johnson, M., Johnson, R., Johnson, S., Johnston, W., Johnstone, J., Jones, B. J. P., Jostlein, H., Junk, T., Kadel, R., Kaess, K., Karagiorgi, Georgia S., Kaspar, J., Katori, T., Kayser, B., Kearns, E., Keener, P., Kemp, E., Kettell, S. H., Kirby, M., Klein, J., Koizumi, G., Kopp, S., Kormos, L., Kropp, W., Kudryavtsev, V. A., Kumar, A., Kumar, J., Kutter, T., Zia, F. L., Lande, K., Lane, C., Lang, K., Lanni, F., Lanza, R., Latorre, T., Learned, J., Lee, D., Lee, K., Li, Q., Li, S., Li, Y., Li, Z., Libo, J., Linden, S., Ling, J., Link, Jonathan M., Littenberg, L., Liu, H., Liu, Q., Liu, T., Losecco, J., Louis, W., Lundberg, B., Lundin, T., Lundy, J., Machado, A. A., Maesano, C., Magill, S., Mahler, G., Malon, D., Malys, S., Mammoliti, F., Mandal, S. K., Mann, A., Mantsch, P., Marchionni, A., Marciano, W. J., Mariani, Camillo, Maricic, Jelena, Marino, A., Marshak, M., Marshall, J., Matsuno, S., Mauger, C., Mavrokoridis, K., Mayer, N., McCauley, N., McCluskey, E., McDonald, K., McFarland, K. S., McKee, D., McKeown, R., McTaggart, R., Mehdiyev, R., Mei, D., Menegolli, A., Meng, G., Meng, Y., Mertins, D., Messier, M., Metcalf, W., Milincic, R., Miller, W., Mills, G., Mishra, S. R., Mokhov, N., Montanari, C., Montanari, D., Moore, C., Morfin, J., Morgan, B., Morse, W., Moss, Z., Moura, C. A., Mufson, S., Muller, D., Musser, J., Naples, D., Napolitano, J., Newcomer, M., Nichol, R., Nicholls, T., Niner, E., Norris, B., Nowak, J., O'Keeffe, H., Oliveira, R., Olson, T., Page, B., Pakvasa, S., Palamara, O., Paley, J., Paolone, V., Papadimitriou, V., Park, S., Parsa, Z., Partyka, K., Paulos, B., Pavlovic, Z., Peeters, S., Perch, A., Perkin, J. D., Petti, R., Petukhov, A., Pietropaolo, F., Plunkett, R., Polly, C. C., Pordes, S., Potekhin, M., Potenza, R., Prakash, A., Prokofiev, O., Qian, X., Raaf, J. L., Radeka, V., Rakhno, I., Ramachers, Y. A., Rameika, R., Ramsey, J., Rappoldi, A., Raselli, G. L., Ratoff, P., Ravindra, S., Rebel, B., Reichenbacher, J., Reitzner, D., Rescia, S., Richardson, M., Rielage, K., Riesselmann, K., Robinson, M., Rochester, L., Ronquest, M., Rosen, M., Rossella, M., Rubbia, C., Rucinski, R., Sahijpal, S., Sahoo, H., Sala, P., Salmiera, D., Samios, N., Sanchez, Maria Cristina, Scaramelli, A., Schellman, H., Schmitt, R., Schmitz, D., Schneps, J., Scholberg, K., Segreto, E., Seibert, S., Sexton-Kennedy, L., Shaevitz, Marjorie Hansen, Shanahan, P., Sharma, R., Shaw, T., Simos, N., Singh, V., Sinnis, G., Sippach, W., Skwarnicki, T., Smy, M., Sobel, H., Soderberg, M., Sondericker, J., Sondheim, W., Sousa, A., Spooner, N. J. C., Stancari, M., Stancu, Ion, Stefan, D., Stefanik, A., Stewart, J., Stone, S., Strait, J., Strait, M., Striganov, S., Sullivan, G., Sun, Y., Suter, L., Svenson, A., Svoboda, R., Szczerbinska, B., Szelc, A., Szydagis, M., Söldner-Rembold, S., Talaga, R., Tamsett, M., Tariq, S., Tayloe, R., Taylor, C., Taylor, D., Teymourian, A., Themann, H., Thiesse, M., Thomas, J., Thompson, L. F., Thomson, M., Thorn, C., Thorpe, M., Tian, X., Tiedt, D., Toki, W., Tolich, N., Torti, M., Toups, M., Touramanis, C., Tripathi, M., Tropin, I., Tsai, Y. T., Tull, C., Tzanov, M., Urheim, J., Usman, S., Vagins, M. R., Valdiviesso, G. A., Berg, R. V., Water, R. V. D., Gemmeren, P. V., Varanini, F., Varner, G., Vaziri, K., Velev, G., Ventura, S., Vignoli, C., Viren, B., Wahl, D., Waldron, A., Walter, C. W., Wang, H., Wang, W., Warburton, K., Warner, D., Wasserman, R., Watson, B., Weber, A., Wei, W., Wells, D., Wetstein, M., White, A., White, H., Whitehead, L., Whittington, D., Willhite, J., Wilson, R. J., Winslow, L., Wood, K., Worcester, E., Worcester, M., Xin, T., Yarritu, K., Ye, J., Yeh, M., Yu, B., Yu, J., Yuan, T., Zani, A., Zeller, Geralyn P., Zhang, C., Zimmerman, E. D., Zwaska, R., Collaboration, LBNE, Adams, C., Adams, D. A., Akiri, T., Alion, T., Anderson, K., Andreopoulos, C., Andrews, M., Anghel, I., Anjos, JCCD, Antonello, M., Arrieta-Diaz, E., Artuso, M., Asaadi, J., Bai, X., Baibussinov, B., Baird, M., Balantekin, A. B., Baller, B., Baptista, B., Barker, D., Barker, G., Barletta, W. A., Barr, G., Bartoszek, L., Bashyal, A., Bass, M., Bellini, V., Benetti, P. A., Berger, B. E., Bergevin, M., Berman, E., Berns, H. G., Bernstein, A., Bernstein, R., Bhandari, B., Bhatnagar, V., Bhuyan, B., Bian, J., Bishai, M., Blake, A., Blaszczyk, F., Blaufuss, E., Bleakley, B., Blucher, E., Blusk, S., Bocean, V., Boffelli, F., Boissevain, J. G., Bolton, T., Bonesini, M., Boyd, S., Brandt, A., Breedon, R., Bromberg, C., Brown, R., Brunetti, G., Buchanan, N., Bugg, B., Busenitz, J., Calligarich, E., Camilleri, Leslie, Carminati, G., Carr, Rachel E., Castromonte, C., Cavanna, F., Centro, S., Chen, A., Chen, H., Chen, K., Cherdack, D., Chi, C. Y., Childress, S., Choudhary, B. C., Christodoulou, G., Christofferson, C. A., Church, E., Cline, D., Coan, T., Cocco, A., Coelho, J., Coleman, S., Conrad, Janet M., Convery, M., Corey, R., Corwin, L., Cranshaw, J., Cronin-Hennessy, D., Curioni, A., Motta, H. D., Davenne, T., Davies, G. S., Dazeley, S., De, K., Gouvea, A. D., Jong, J K. D., Demuth, D., Densham, C., Diwan, M., Djurcic, Zelimir, Dolfini, R., Dolph, J., Drake, G., Dye, S., Dyuang, H., Edmunds, D., Elliott, S., Elnimr, M., Eno, S., Enomoto, S., Escobar, C. O., Evans, J., Falcone, A., Falk, L., Farbin, A., Farnese, C., Fava, A., Felde, J., Fernandes, S., Ferroni, F., Feyzi, F., Fields, L., Finch, A., Fitton, M., Fleming, B., Fowler, J., Fox, W., Friedland, A., Fuess, S., Fujikawa, B. K., Gallagher, H., Gandhi, R., Garvey, G. T., Gehman, V. M., Geronimo, G. D., Gibin, D., Gill, R., Gomes, R. A., Goodman, M. C., Goon, J., Graf, N., Graham, M., Gran, R., Grant, C., Grant, N., Greenlee, H., Greenler, L., Grullon, S., Guardincerri, E., Guarino, V., Guarnaccia, E., Guedes, G. P., Guenette, R., Guglielmi, A., Guzzo, M. M., Habig, A. T., Hackenburg, R. W., Hadavand, H., Hahn, A., Haigh, M., Haines, T., Handler, T., Hans, S., Hartnell, J., Harton, J., Hatcher, R., Hatzikoutelis, A., Hays, S., Hazen, E., Headley, M., Heavey, A., Heeger, K., Heise, J., Hellauer, R., Hewes, J., Himmel, A., Hogan, M., Holanda, P., Holin, A., Horton-Smith, Glenn A., Howell, J., Hurh, P., Huston, J., Hylen, J., Imlay, R., Insler, J., Introzzi, G., Isvan, Z., Jackson, C., Jacobsen, J., Jaffe, D. E., James, C., Jen, C. M., Johnson, M., Johnson, R., Johnson, S., Johnston, W., Johnstone, J., Jones, B. J. P., Jostlein, H., Junk, T., Kadel, R., Kaess, K., Karagiorgi, Georgia S., Kaspar, J., Katori, T., Kayser, B., Kearns, E., Keener, P., Kemp, E., Kettell, S. H., Kirby, M., Klein, J., Koizumi, G., Kopp, S., Kormos, L., Kropp, W., Kudryavtsev, V. A., Kumar, A., Kumar, J., Kutter, T., Zia, F. L., Lande, K., Lane, C., Lang, K., Lanni, F., Lanza, R., Latorre, T., Learned, J., Lee, D., Lee, K., Li, Q., Li, S., Li, Y., Li, Z., Libo, J., Linden, S., Ling, J., Link, Jonathan M., Littenberg, L., Liu, H., Liu, Q., Liu, T., Losecco, J., Louis, W., Lundberg, B., Lundin, T., Lundy, J., Machado, A. A., Maesano, C., Magill, S., Mahler, G., Malon, D., Malys, S., Mammoliti, F., Mandal, S. K., Mann, A., Mantsch, P., Marchionni, A., Marciano, W. J., Mariani, Camillo, Maricic, Jelena, Marino, A., Marshak, M., Marshall, J., Matsuno, S., Mauger, C., Mavrokoridis, K., Mayer, N., McCauley, N., McCluskey, E., McDonald, K., McFarland, K. S., McKee, D., McKeown, R., McTaggart, R., Mehdiyev, R., Mei, D., Menegolli, A., Meng, G., Meng, Y., Mertins, D., Messier, M., Metcalf, W., Milincic, R., Miller, W., Mills, G., Mishra, S. R., Mokhov, N., Montanari, C., Montanari, D., Moore, C., Morfin, J., Morgan, B., Morse, W., Moss, Z., Moura, C. A., Mufson, S., Muller, D., Musser, J., Naples, D., Napolitano, J., Newcomer, M., Nichol, R., Nicholls, T., Niner, E., Norris, B., Nowak, J., O'Keeffe, H., Oliveira, R., Olson, T., Page, B., Pakvasa, S., Palamara, O., Paley, J., Paolone, V., Papadimitriou, V., Park, S., Parsa, Z., Partyka, K., Paulos, B., Pavlovic, Z., Peeters, S., Perch, A., Perkin, J. D., Petti, R., Petukhov, A., Pietropaolo, F., Plunkett, R., Polly, C. C., Pordes, S., Potekhin, M., Potenza, R., Prakash, A., Prokofiev, O., Qian, X., Raaf, J. L., Radeka, V., Rakhno, I., Ramachers, Y. A., Rameika, R., Ramsey, J., Rappoldi, A., Raselli, G. L., Ratoff, P., Ravindra, S., Rebel, B., Reichenbacher, J., Reitzner, D., Rescia, S., Richardson, M., Rielage, K., Riesselmann, K., Robinson, M., Rochester, L., Ronquest, M., Rosen, M., Rossella, M., Rubbia, C., Rucinski, R., Sahijpal, S., Sahoo, H., Sala, P., Salmiera, D., Samios, N., Sanchez, Maria Cristina, Scaramelli, A., Schellman, H., Schmitt, R., Schmitz, D., Schneps, J., Scholberg, K., Segreto, E., Seibert, S., Sexton-Kennedy, L., Shaevitz, Marjorie Hansen, Shanahan, P., Sharma, R., Shaw, T., Simos, N., Singh, V., Sinnis, G., Sippach, W., Skwarnicki, T., Smy, M., Sobel, H., Soderberg, M., Sondericker, J., Sondheim, W., Sousa, A., Spooner, N. J. C., Stancari, M., Stancu, Ion, Stefan, D., Stefanik, A., Stewart, J., Stone, S., Strait, J., Strait, M., Striganov, S., Sullivan, G., Sun, Y., Suter, L., Svenson, A., Svoboda, R., Szczerbinska, B., Szelc, A., Szydagis, M., Söldner-Rembold, S., Talaga, R., Tamsett, M., Tariq, S., Tayloe, R., Taylor, C., Taylor, D., Teymourian, A., Themann, H., Thiesse, M., Thomas, J., Thompson, L. F., Thomson, M., Thorn, C., Thorpe, M., Tian, X., Tiedt, D., Toki, W., Tolich, N., Torti, M., Toups, M., Touramanis, C., Tripathi, M., Tropin, I., Tsai, Y. T., Tull, C., Tzanov, M., Urheim, J., Usman, S., Vagins, M. R., Valdiviesso, G. A., Berg, R. V., Water, R. V. D., Gemmeren, P. V., Varanini, F., Varner, G., Vaziri, K., Velev, G., Ventura, S., Vignoli, C., Viren, B., Wahl, D., Waldron, A., Walter, C. W., Wang, H., Wang, W., Warburton, K., Warner, D., Wasserman, R., Watson, B., Weber, A., Wei, W., Wells, D., Wetstein, M., White, A., White, H., Whitehead, L., Whittington, D., Willhite, J., Wilson, R. J., Winslow, L., Wood, K., Worcester, E., Worcester, M., Xin, T., Yarritu, K., Ye, J., Yeh, M., Yu, B., Yu, J., Yuan, T., Zani, A., Zeller, Geralyn P., Zhang, C., Zimmerman, E. D., and Zwaska, R.
Abstract: The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.
Published: 2014

40. The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

Author: Center for Neutrino Physics, Physics, Collaboration, LBNE, Adams, C., Adams, D. A., Akiri, T., Alion, T., Anderson, K., Andreopoulos, C., Andrews, M., Anghel, I., Anjos, JCCD, Antonello, M., Arrieta-Diaz, E., Artuso, M., Asaadi, J., Bai, X., Baibussinov, B., Baird, M., Balantekin, A. B., Baller, B., Baptista, B., Barker, D., Barker, G., Barletta, W. A., Barr, G., Bartoszek, L., Bashyal, A., Bass, M., Bellini, V., Benetti, P. A., Berger, B. E., Bergevin, M., Berman, E., Berns, H. G., Bernstein, A., Bernstein, R., Bhandari, B., Bhatnagar, V., Bhuyan, B., Bian, J., Bishai, M., Blake, A., Blaszczyk, F., Blaufuss, E., Bleakley, B., Blucher, E., Blusk, S., Bocean, V., Boffelli, F., Boissevain, J. G., Bolton, T., Bonesini, M., Boyd, S., Brandt, A., Breedon, R., Bromberg, C., Brown, R., Brunetti, G., Buchanan, N., Bugg, B., Busenitz, J., Calligarich, E., Camilleri, Leslie, Carminati, G., Carr, Rachel E., Castromonte, C., Cavanna, F., Centro, S., Chen, A., Chen, H., Chen, K., Cherdack, D., Chi, C. Y., Childress, S., Choudhary, B. C., Christodoulou, G., Christofferson, C. A., Church, E., Cline, D., Coan, T., Cocco, A., Coelho, J., Coleman, S., Conrad, Janet M., Convery, M., Corey, R., Corwin, L., Cranshaw, J., Cronin-Hennessy, D., Curioni, A., Motta, H. D., Davenne, T., Davies, G. S., Dazeley, S., De, K., Gouvea, A. D., Jong, J K. D., Demuth, D., Densham, C., Diwan, M., Djurcic, Zelimir, Dolfini, R., Dolph, J., Drake, G., Dye, S., Dyuang, H., Edmunds, D., Elliott, S., Elnimr, M., Eno, S., Enomoto, S., Escobar, C. O., Evans, J., Falcone, A., Falk, L., Farbin, A., Farnese, C., Fava, A., Felde, J., Fernandes, S., Ferroni, F., Feyzi, F., Fields, L., Finch, A., Fitton, M., Fleming, B., Fowler, J., Fox, W., Friedland, A., Fuess, S., Fujikawa, B. K., Gallagher, H., Gandhi, R., Garvey, G. T., Gehman, V. M., Geronimo, G. D., Gibin, D., Gill, R., Gomes, R. A., Goodman, M. C., Goon, J., Graf, N., Graham, M., Gran, R., Grant, C., Grant, N., Greenlee, H., Greenler, L., Grullon, S., Guardincerri, E., Guarino, V., Guarnaccia, E., Guedes, G. P., Guenette, R., Guglielmi, A., Guzzo, M. M., Habig, A. T., Hackenburg, R. W., Hadavand, H., Hahn, A., Haigh, M., Haines, T., Handler, T., Hans, S., Hartnell, J., Harton, J., Hatcher, R., Hatzikoutelis, A., Hays, S., Hazen, E., Headley, M., Heavey, A., Heeger, K., Heise, J., Hellauer, R., Hewes, J., Himmel, A., Hogan, M., Holanda, P., Holin, A., Horton-Smith, Glenn A., Howell, J., Hurh, P., Huston, J., Hylen, J., Imlay, R., Insler, J., Introzzi, G., Isvan, Z., Jackson, C., Jacobsen, J., Jaffe, D. E., James, C., Jen, C. M., Johnson, M., Johnson, R., Johnson, S., Johnston, W., Johnstone, J., Jones, B. J. P., Jostlein, H., Junk, T., Kadel, R., Kaess, K., Karagiorgi, Georgia S., Kaspar, J., Katori, T., Kayser, B., Kearns, E., Keener, P., Kemp, E., Kettell, S. H., Kirby, M., Klein, J., Koizumi, G., Kopp, S., Kormos, L., Kropp, W., Kudryavtsev, V. A., Kumar, A., Kumar, J., Kutter, T., Zia, F. L., Lande, K., Lane, C., Lang, K., Lanni, F., Lanza, R., Latorre, T., Learned, J., Lee, D., Lee, K., Li, Q., Li, S., Li, Y., Li, Z., Libo, J., Linden, S., Ling, J., Link, Jonathan M., Littenberg, L., Liu, H., Liu, Q., Liu, T., Losecco, J., Louis, W., Lundberg, B., Lundin, T., Lundy, J., Machado, A. A., Maesano, C., Magill, S., Mahler, G., Malon, D., Malys, S., Mammoliti, F., Mandal, S. K., Mann, A., Mantsch, P., Marchionni, A., Marciano, W. J., Mariani, Camillo, Maricic, Jelena, Marino, A., Marshak, M., Marshall, J., Matsuno, S., Mauger, C., Mavrokoridis, K., Mayer, N., McCauley, N., McCluskey, E., McDonald, K., McFarland, K. S., McKee, D., McKeown, R., McTaggart, R., Mehdiyev, R., Mei, D., Menegolli, A., Meng, G., Meng, Y., Mertins, D., Messier, M., Metcalf, W., Milincic, R., Miller, W., Mills, G., Mishra, S. R., Mokhov, N., Montanari, C., Montanari, D., Moore, C., Morfin, J., Morgan, B., Morse, W., Moss, Z., Moura, C. A., Mufson, S., Muller, D., Musser, J., Naples, D., Napolitano, J., Newcomer, M., Nichol, R., Nicholls, T., Niner, E., Norris, B., Nowak, J., O'Keeffe, H., Oliveira, R., Olson, T., Page, B., Pakvasa, S., Palamara, O., Paley, J., Paolone, V., Papadimitriou, V., Park, S., Parsa, Z., Partyka, K., Paulos, B., Pavlovic, Z., Peeters, S., Perch, A., Perkin, J. D., Petti, R., Petukhov, A., Pietropaolo, F., Plunkett, R., Polly, C. C., Pordes, S., Potekhin, M., Potenza, R., Prakash, A., Prokofiev, O., Qian, X., Raaf, J. L., Radeka, V., Rakhno, I., Ramachers, Y. A., Rameika, R., Ramsey, J., Rappoldi, A., Raselli, G. L., Ratoff, P., Ravindra, S., Rebel, B., Reichenbacher, J., Reitzner, D., Rescia, S., Richardson, M., Rielage, K., Riesselmann, K., Robinson, M., Rochester, L., Ronquest, M., Rosen, M., Rossella, M., Rubbia, C., Rucinski, R., Sahijpal, S., Sahoo, H., Sala, P., Salmiera, D., Samios, N., Sanchez, Maria Cristina, Scaramelli, A., Schellman, H., Schmitt, R., Schmitz, D., Schneps, J., Scholberg, K., Segreto, E., Seibert, S., Sexton-Kennedy, L., Shaevitz, Marjorie Hansen, Shanahan, P., Sharma, R., Shaw, T., Simos, N., Singh, V., Sinnis, G., Sippach, W., Skwarnicki, T., Smy, M., Sobel, H., Soderberg, M., Sondericker, J., Sondheim, W., Sousa, A., Spooner, N. J. C., Stancari, M., Stancu, Ion, Stefan, D., Stefanik, A., Stewart, J., Stone, S., Strait, J., Strait, M., Striganov, S., Sullivan, G., Sun, Y., Suter, L., Svenson, A., Svoboda, R., Szczerbinska, B., Szelc, A., Szydagis, M., Söldner-Rembold, S., Talaga, R., Tamsett, M., Tariq, S., Tayloe, R., Taylor, C., Taylor, D., Teymourian, A., Themann, H., Thiesse, M., Thomas, J., Thompson, L. F., Thomson, M., Thorn, C., Thorpe, M., Tian, X., Tiedt, D., Toki, W., Tolich, N., Torti, M., Toups, M., Touramanis, C., Tripathi, M., Tropin, I., Tsai, Y. T., Tull, C., Tzanov, M., Urheim, J., Usman, S., Vagins, M. R., Valdiviesso, G. A., Berg, R. V., Water, R. V. D., Gemmeren, P. V., Varanini, F., Varner, G., Vaziri, K., Velev, G., Ventura, S., Vignoli, C., Viren, B., Wahl, D., Waldron, A., Walter, C. W., Wang, H., Wang, W., Warburton, K., Warner, D., Wasserman, R., Watson, B., Weber, A., Wei, W., Wells, D., Wetstein, M., White, A., White, H., Whitehead, L., Whittington, D., Willhite, J., Wilson, R. J., Winslow, L., Wood, K., Worcester, E., Worcester, M., Xin, T., Yarritu, K., Ye, J., Yeh, M., Yu, B., Yu, J., Yuan, T., Zani, A., Zeller, Geralyn P., Zhang, C., Zimmerman, E. D., Zwaska, R., Center for Neutrino Physics, Physics, Collaboration, LBNE, Adams, C., Adams, D. A., Akiri, T., Alion, T., Anderson, K., Andreopoulos, C., Andrews, M., Anghel, I., Anjos, JCCD, Antonello, M., Arrieta-Diaz, E., Artuso, M., Asaadi, J., Bai, X., Baibussinov, B., Baird, M., Balantekin, A. B., Baller, B., Baptista, B., Barker, D., Barker, G., Barletta, W. A., Barr, G., Bartoszek, L., Bashyal, A., Bass, M., Bellini, V., Benetti, P. A., Berger, B. E., Bergevin, M., Berman, E., Berns, H. G., Bernstein, A., Bernstein, R., Bhandari, B., Bhatnagar, V., Bhuyan, B., Bian, J., Bishai, M., Blake, A., Blaszczyk, F., Blaufuss, E., Bleakley, B., Blucher, E., Blusk, S., Bocean, V., Boffelli, F., Boissevain, J. G., Bolton, T., Bonesini, M., Boyd, S., Brandt, A., Breedon, R., Bromberg, C., Brown, R., Brunetti, G., Buchanan, N., Bugg, B., Busenitz, J., Calligarich, E., Camilleri, Leslie, Carminati, G., Carr, Rachel E., Castromonte, C., Cavanna, F., Centro, S., Chen, A., Chen, H., Chen, K., Cherdack, D., Chi, C. Y., Childress, S., Choudhary, B. C., Christodoulou, G., Christofferson, C. A., Church, E., Cline, D., Coan, T., Cocco, A., Coelho, J., Coleman, S., Conrad, Janet M., Convery, M., Corey, R., Corwin, L., Cranshaw, J., Cronin-Hennessy, D., Curioni, A., Motta, H. D., Davenne, T., Davies, G. S., Dazeley, S., De, K., Gouvea, A. D., Jong, J K. D., Demuth, D., Densham, C., Diwan, M., Djurcic, Zelimir, Dolfini, R., Dolph, J., Drake, G., Dye, S., Dyuang, H., Edmunds, D., Elliott, S., Elnimr, M., Eno, S., Enomoto, S., Escobar, C. O., Evans, J., Falcone, A., Falk, L., Farbin, A., Farnese, C., Fava, A., Felde, J., Fernandes, S., Ferroni, F., Feyzi, F., Fields, L., Finch, A., Fitton, M., Fleming, B., Fowler, J., Fox, W., Friedland, A., Fuess, S., Fujikawa, B. K., Gallagher, H., Gandhi, R., Garvey, G. T., Gehman, V. M., Geronimo, G. D., Gibin, D., Gill, R., Gomes, R. A., Goodman, M. C., Goon, J., Graf, N., Graham, M., Gran, R., Grant, C., Grant, N., Greenlee, H., Greenler, L., Grullon, S., Guardincerri, E., Guarino, V., Guarnaccia, E., Guedes, G. P., Guenette, R., Guglielmi, A., Guzzo, M. M., Habig, A. T., Hackenburg, R. W., Hadavand, H., Hahn, A., Haigh, M., Haines, T., Handler, T., Hans, S., Hartnell, J., Harton, J., Hatcher, R., Hatzikoutelis, A., Hays, S., Hazen, E., Headley, M., Heavey, A., Heeger, K., Heise, J., Hellauer, R., Hewes, J., Himmel, A., Hogan, M., Holanda, P., Holin, A., Horton-Smith, Glenn A., Howell, J., Hurh, P., Huston, J., Hylen, J., Imlay, R., Insler, J., Introzzi, G., Isvan, Z., Jackson, C., Jacobsen, J., Jaffe, D. E., James, C., Jen, C. M., Johnson, M., Johnson, R., Johnson, S., Johnston, W., Johnstone, J., Jones, B. J. P., Jostlein, H., Junk, T., Kadel, R., Kaess, K., Karagiorgi, Georgia S., Kaspar, J., Katori, T., Kayser, B., Kearns, E., Keener, P., Kemp, E., Kettell, S. H., Kirby, M., Klein, J., Koizumi, G., Kopp, S., Kormos, L., Kropp, W., Kudryavtsev, V. A., Kumar, A., Kumar, J., Kutter, T., Zia, F. L., Lande, K., Lane, C., Lang, K., Lanni, F., Lanza, R., Latorre, T., Learned, J., Lee, D., Lee, K., Li, Q., Li, S., Li, Y., Li, Z., Libo, J., Linden, S., Ling, J., Link, Jonathan M., Littenberg, L., Liu, H., Liu, Q., Liu, T., Losecco, J., Louis, W., Lundberg, B., Lundin, T., Lundy, J., Machado, A. A., Maesano, C., Magill, S., Mahler, G., Malon, D., Malys, S., Mammoliti, F., Mandal, S. K., Mann, A., Mantsch, P., Marchionni, A., Marciano, W. J., Mariani, Camillo, Maricic, Jelena, Marino, A., Marshak, M., Marshall, J., Matsuno, S., Mauger, C., Mavrokoridis, K., Mayer, N., McCauley, N., McCluskey, E., McDonald, K., McFarland, K. S., McKee, D., McKeown, R., McTaggart, R., Mehdiyev, R., Mei, D., Menegolli, A., Meng, G., Meng, Y., Mertins, D., Messier, M., Metcalf, W., Milincic, R., Miller, W., Mills, G., Mishra, S. R., Mokhov, N., Montanari, C., Montanari, D., Moore, C., Morfin, J., Morgan, B., Morse, W., Moss, Z., Moura, C. A., Mufson, S., Muller, D., Musser, J., Naples, D., Napolitano, J., Newcomer, M., Nichol, R., Nicholls, T., Niner, E., Norris, B., Nowak, J., O'Keeffe, H., Oliveira, R., Olson, T., Page, B., Pakvasa, S., Palamara, O., Paley, J., Paolone, V., Papadimitriou, V., Park, S., Parsa, Z., Partyka, K., Paulos, B., Pavlovic, Z., Peeters, S., Perch, A., Perkin, J. D., Petti, R., Petukhov, A., Pietropaolo, F., Plunkett, R., Polly, C. C., Pordes, S., Potekhin, M., Potenza, R., Prakash, A., Prokofiev, O., Qian, X., Raaf, J. L., Radeka, V., Rakhno, I., Ramachers, Y. A., Rameika, R., Ramsey, J., Rappoldi, A., Raselli, G. L., Ratoff, P., Ravindra, S., Rebel, B., Reichenbacher, J., Reitzner, D., Rescia, S., Richardson, M., Rielage, K., Riesselmann, K., Robinson, M., Rochester, L., Ronquest, M., Rosen, M., Rossella, M., Rubbia, C., Rucinski, R., Sahijpal, S., Sahoo, H., Sala, P., Salmiera, D., Samios, N., Sanchez, Maria Cristina, Scaramelli, A., Schellman, H., Schmitt, R., Schmitz, D., Schneps, J., Scholberg, K., Segreto, E., Seibert, S., Sexton-Kennedy, L., Shaevitz, Marjorie Hansen, Shanahan, P., Sharma, R., Shaw, T., Simos, N., Singh, V., Sinnis, G., Sippach, W., Skwarnicki, T., Smy, M., Sobel, H., Soderberg, M., Sondericker, J., Sondheim, W., Sousa, A., Spooner, N. J. C., Stancari, M., Stancu, Ion, Stefan, D., Stefanik, A., Stewart, J., Stone, S., Strait, J., Strait, M., Striganov, S., Sullivan, G., Sun, Y., Suter, L., Svenson, A., Svoboda, R., Szczerbinska, B., Szelc, A., Szydagis, M., Söldner-Rembold, S., Talaga, R., Tamsett, M., Tariq, S., Tayloe, R., Taylor, C., Taylor, D., Teymourian, A., Themann, H., Thiesse, M., Thomas, J., Thompson, L. F., Thomson, M., Thorn, C., Thorpe, M., Tian, X., Tiedt, D., Toki, W., Tolich, N., Torti, M., Toups, M., Touramanis, C., Tripathi, M., Tropin, I., Tsai, Y. T., Tull, C., Tzanov, M., Urheim, J., Usman, S., Vagins, M. R., Valdiviesso, G. A., Berg, R. V., Water, R. V. D., Gemmeren, P. V., Varanini, F., Varner, G., Vaziri, K., Velev, G., Ventura, S., Vignoli, C., Viren, B., Wahl, D., Waldron, A., Walter, C. W., Wang, H., Wang, W., Warburton, K., Warner, D., Wasserman, R., Watson, B., Weber, A., Wei, W., Wells, D., Wetstein, M., White, A., White, H., Whitehead, L., Whittington, D., Willhite, J., Wilson, R. J., Winslow, L., Wood, K., Worcester, E., Worcester, M., Xin, T., Yarritu, K., Ye, J., Yeh, M., Yu, B., Yu, J., Yuan, T., Zani, A., Zeller, Geralyn P., Zhang, C., Zimmerman, E. D., and Zwaska, R.
Abstract: The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.
Published: 2014

41. TALEN outperforms Cas9 in editing heterochromatin target sites

Author: Surbhi Jain, Saurabh Shukla, Che Yang, Meng Zhang, Zia Fatma, Manasi Lingamaneni, Shireen Abesteh, Stephan Thomas Lane, Xiong Xiong, Yuchuan Wang, Charles M. Schroeder, Paul R. Selvin, and Huimin Zhao
Subjects: Science
Abstract: While Cas9 outperforms TALENs in euchromatin, it is less efficient in heterochromatic regions. Here the authors, using single-molecule imaging, show that Cas9 uses a less efficient search strategy compared to TALENs in these regions.
Published: 2021
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42. Intrahepatic microbes govern liver immunity by programming NKT cells

Author: Joshua C. Leinwand, Bidisha Paul, Ruonan Chen, Fangxi Xu, Maria A. Sierra, Madan M. Paluru, Sumant Nanduri, Carolina G. Alcantara, Sorin A.A. Shadaloey, Fan Yang, Salma A. Adam, Qianhao Li, Michelle Bandel, Inderdeep Gakhal, Lara Appiah, Yuqi Guo, Mridula Vardhan, Zia Flaminio, Emilie R. Grodman, Ari Mermelstein, Wei Wang, Brian Diskin, Berk Aykut, Mohammad Khan, Gregor Werba, Smruti Pushalkar, Mia McKinstry, Zachary Kluger, Jaimie J. Park, Brandon Hsieh, Kristen Dancel-Manning, Feng-Xia Liang, James S. Park, Anjana Saxena, Xin Li, Neil D. Theise, Deepak Saxena, and George Miller
Subjects: Hepatology, Microbiology, Medicine
Abstract: The gut microbiome shapes local and systemic immunity. The liver is presumed to be a protected sterile site. As such, a hepatic microbiome has not been examined. Here, we showed a liver microbiome in mice and humans that is distinct from that of the gut and is enriched in Proteobacteria. It undergoes dynamic alterations with age and is influenced by the environment and host physiology. Fecal microbial transfer experiments revealed that the liver microbiome is populated from the gut in a highly selective manner. Hepatic immunity is dependent on the microbiome, specifically the bacteroidetes species. Targeting bacteroidetes with oral antibiotics reduced hepatic immune cells by approximately 90%, prevented antigen-presenting cell (APC) maturation, and mitigated adaptive immunity. Mechanistically, our findings are consistent with presentation of bacteroidetes-derived glycosphingolipids to NKT cells promoting CCL5 signaling, which drives hepatic leukocyte expansion and activation, among other possible host-microbe interactions. Collectively, we reveal a microbial/glycosphingolipid/NKT/CCL5 axis that underlies hepatic immunity.
Published: 2022
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43. The Effect of one Course of Swimming Exercise before Induction of Multiple Sclerosis (MS) on Nerve Growth Factor Levels in Rat’s Brain

Author: hamid hosseini and zia fallahmohammadi
Subjects: multiple sclerosis, swimming exercise, nerve growth factor, Medicine, Medicine (General), R5-920
Abstract: Background and Aim: Multiple Sclerosis is a chronic inflammatory disease with unknown etiology in the nervous system. However, exercise routinely for these patients is beneficial, but the effect of pretreatment swimming exercise in this disease has not been fixed. Therefore, the aim of these study was to investigate pretreatment effect of swimming exercise on NGF levels in female Lewis rats with experimental autoimmune encephalomyelitis. Materials and Methods: This experimental in vitro study was conducted on female Lewis rats. In this study, animals were randomly divided into 4 groups (each group 5), including healthy control, EAE control, healthy swimming and EAE swimming. The training protocol included swimming exercise 1 hour/day, 5 days/week for six weeks. Results: This study shows that NGF levels in EAE swimming group were significantly increased compared to the same controls (P= 0.006). Also the weight of EAE swimming training group significantly increased compared with control (P=0.001). Conclusion: According to these findings, concluded that pretreatment with sub-chronic swimming exercise, through increased levels of NGF, is effective in inhibiting EAE. Hence, perhaps, the protocol used in this study to enhance the protection of nerve cells in the brain tissue of MS Risk Factors and ultimately recommended to promote brain health.
Published: 2020

44. Electronic Cigarette Use Promotes a Unique Periodontal Microbiome

Author: Scott C. Thomas, Fangxi Xu, Smruti Pushalkar, Ziyan Lin, Nirali Thakor, Mridula Vardhan, Zia Flaminio, Alireza Khodadadi-Jamayran, Rebeca Vasconcelos, Adenike Akapo, Erica Queiroz, Maria Bederoff, Malvin N. Janal, Yuqi Guo, Deanna Aguallo, Terry Gordon, Patricia M. Corby, Angela R. Kamer, Xin Li, and Deepak Saxena
Subjects: dysbiosis, electronic cigarette, microbiome, periodontitis, subgingival plaque, Microbiology, QR1-502
Abstract: ABSTRACT Electronic cigarettes (e-cigs) have become prevalent as an alternative to conventional cigarette smoking, particularly in youth. E-cig aerosols contain unique chemicals which alter the oral microbiome and promote dysbiosis in ways we are just beginning to investigate. We conducted a 6-month longitudinal study involving 84 subjects who were either e-cig users, conventional smokers, or nonsmokers. Periodontal condition, cytokine levels, and subgingival microbial community composition were assessed, with periodontal, clinical, and cytokine measures reflecting cohort habit and positively correlating with pathogenic taxa (e.g., Treponema, Saccharibacteria, and Porphyromonas). α-Diversity increased similarly across cohorts longitudinally, yet each cohort maintained a unique microbiome. The e-cig microbiome shared many characteristics with the microbiome of conventional smokers and some with nonsmokers, yet it maintained a unique subgingival microbial community enriched in Fusobacterium and Bacteroidales (G-2). Our data suggest that e-cig use promotes a unique periodontal microbiome, existing as a stable heterogeneous state between those of conventional smokers and nonsmokers and presenting unique oral health challenges. IMPORTANCE Electronic cigarette (e-cig) use is gaining in popularity and is often perceived as a healthier alternative to conventional smoking. Yet there is little evidence of the effects of long-term use of e-cigs on oral health. Conventional cigarette smoking is a prominent risk factor for the development of periodontitis, an oral disease affecting nearly half of adults over 30 years of age in the United States. Periodontitis is initiated through a disturbance in the microbial biofilm communities inhabiting the unique space between teeth and gingival tissues. This disturbance instigates host inflammatory and immune responses and, if left untreated, leads to tooth and bone loss and systemic diseases. We found that the e-cig user’s periodontal microbiome is unique, eliciting unique host responses. Yet some similarities to the microbiomes of both conventional smokers and nonsmokers exist, with strikingly more in common with that of cigarette smokers, suggesting that there is a unique periodontal risk associated with e-cig use.
Published: 2022
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45. Polarized Cell Migration during Cell-to-Cell Transmission of Herpes Simplex Virus in Human Skin Keratinocytes

Author: Abaitua, Fernando, primary, Zia, F. Rabiya, additional, Hollinshead, Michael, additional, and O'Hare, Peter, additional
Published: 2013
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46. Successful treatment of severe thrombocytopenia with romiplostim in a pregnant patient with systemic lupus erythematosus

Author: Alkaabi, JK, primary, Alkindi, S, additional, Riyami, N Al, additional, Zia, F, additional, Balla, LMA, additional, and Balla, SM, additional
Published: 2012
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47. Preventive effect of injections of vitamin D on the levels of Klotho in the brain tissue of female lewis rats with experimental autoimmune ensephalomyelitis

Author: seyedeh fatemeh fatemi, zia fallah mohammadi, vahid Talebi, and Sayed mojtaba Hosseini
Subjects: Experimental autoimmune encephalomyelitis, Vitamin D, Klotho., Medicine (General), R5-920
Abstract: Introdution: The aim of this study was to investigate the effect of vitamin D supplementation on Klotho levels of the brain tissue. Methods: In this laboratory experimental study, 25 female Lewis rats, after 2 weeks adaptation to lab environmental, were randomly divided into 5 groups: 1-control; 2- control+ EAE; 3-sham; 4vitamin D; 5-vitaminD + EAE. Results: The data were analyzed using one way ANOVA, and to examine the weight changes Mann-Whitney test was used to the research groups. In order to induce EAE, 0.4 ml of solution, a combination of guinea Hindi pig spinal cord and adjuvant ratio was injected to each animal. Klotho levels were measured by ELISA. Finding: There was significantly different in Klotho levels of brain tissue of control+ EAE compared to control group (P=0/001). There was significant difference in Klotho levels of the brain tissue in EAE +vitamin D group compared to control group (P=0/001). In addition, the weight of vitamin D+EAE group was more than control+EAE group (P=0/006). Conclusion: Pre-treatment with vitamin D supplementation increases the Klotho levels of brain tissue and may have protective role against EAE.
Published: 2019

48. The effect of regular interval training on histochemical symptoms and cytokine and neurotrophic levels of brain tissue of the Lewis rats in experimental model of multiple sclerosis

Author: Sayed Mojtaba Hosseini, Zia Fallahmohammadi, and Vahid Talebi
Subjects: Cytokine, Experimental autoimmune encephalomyelitis, Interleukin 10, BDNF, TNF-α, Medicine (General), R5-920
Abstract: Background: Multiple sclerosis is an inflammatory and chronic disease of the central nervous system. Regarding the possible effects of exercise in preventing this disease, the aim of this study was to investigate the effect of 6 weeks of high intensity interval training on TNF-α, IL-10 and BDNF levels in rat brain tissue of the experimental autoimmune encephalomyelitis (EAE) model. Materials and Methods: In this experimental study, 25 Lewis female rats, 6 weeks old, were randomly divided into 5 groups. Interval training was performed for 6 weeks and 5 days a week. An interval training program was conducted in the second week and during 6 weeks of training in each session including 10 repetitions of 1 minute. The EAE model was induced at the end of the sixth week of exercise. TNF-α, BDNF and IL-10 were measured in the brain tissue. Results: The results of coloring showed that the amount of inflammation of the nerve tissue decreased in the interval training groups. Interval training in Lewis female rats with experimental autoimmune encephalomyelitis showed a significant decrease in TNF-α (P=0.001), but did not significantly change the IL-10 (P=0.07) and BDNF (P=0.54) levels. In addition, trained rats showed delayed clinical symptoms. Conclusions: It seems that interval exercises with the duration and severity of the present study protocol may delay the incidence and severity of clinical symptoms and thus increase cellular protection in Lewis rats against the onset of experimental autoimmune encephalomyelitis.
Published: 2018

49. Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production

Author: Patrick F. Suthers, Hoang V. Dinh, Zia Fatma, Yihui Shen, Siu Hung Joshua Chan, Joshua D. Rabinowitz, Huimin Zhao, and Costas D. Maranas
Subjects: Genome-scale model, Non-model yeast, Constraint-based modeling, Metabolic engineering, Biotechnology, TP248.13-248.65, Biology (General), QH301-705.5
Abstract: Many platform chemicals can be produced from renewable biomass by microorganisms, with organic acids making up a large fraction. Intolerance to the resulting low pH growth conditions, however, remains a challenge for the industrial production of organic acids by microorganisms. Issatchenkia orientalis SD108 is a promising host for industrial production because it is tolerant to acidic conditions as low as pH 2.0. With the goal to systematically assess the metabolic capabilities of this non-model yeast, we developed a genome-scale metabolic model for I. orientalis SD108 spanning 850 genes, 1826 reactions, and 1702 metabolites. In order to improve the model’s quantitative predictions, organism-specific macromolecular composition and ATP maintenance requirements were determined experimentally and implemented. We examined its network topology, including essential genes and flux coupling analysis and drew comparisons with the Yeast 8.3 model for Saccharomyces cerevisiae. We explored the carbon substrate utilization and examined the organism’s production potential for the industrially-relevant succinic acid, making use of the OptKnock framework to identify gene knockouts which couple production of the targeted chemical to biomass production. The genome-scale metabolic model iIsor850 is a data-supported curated model which can inform genetic interventions for overproduction.
Published: 2020
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50. Reduced Kidney Function Is Associated with Increasing Red Blood Cell Folate Concentration and Changes in Folate Form Distributions (NHANES 2011–2018)

Author: Arick Wang, Lorraine F. Yeung, Nilka Ríos Burrows, Charles E. Rose, Zia Fazili, Christine M. Pfeiffer, and Krista S. Crider
Subjects: folate concentration, chronic kidney disease, folic acid, folate metabolism, Nutrition. Foods and food supply, TX341-641
Abstract: Background: Current studies examining the effects of high concentrations of red blood cell (RBC) or serum folates assume that high folate concentrations are an indicator of high folic acid intakes, often ignoring the contributions of other homeostatic and biological processes, such as kidney function. Objective: The current study examined the relative contributions of declining kidney function, as measured by the risk of chronic kidney disease (CKD), and usual total folic acid intake on the concentrations of RBC folate and serum folate (total as well as individual folate forms). Design: Cross-sectional data from the National Health and Nutrition Examination Survey (NHANES) collected in 2-year cycles were combined from 2011 to 2018. A total of 18,127 participants aged ≥16 years with available folate measures, kidney biomarker data (operationalized as a categorical CKD risk variable describing the risk of progression), and reliable dietary recall data were analyzed. Results: RBC folate concentrations increased as CKD risk increased: low risk, 1089 (95% CI: 1069, 1110) nmol/L; moderate risk, 1189 (95% CI: 1158, 1220) nmol/L; high risk, 1488 (95% CI: 1419, 1561) nmol/L; and highest risk, 1443 (95% CI: 1302, 1598) nmol/L (p < 0.0001). Similarly, serum total folate concentrations increased as CKD risk increased: low risk: 37.1 (95% CI: 26.3, 38.0) nmol/L; moderate risk: 40.2 (95% CI: 38.8, 41.7) nmol/L; high risk: 48.0 (95% CI: 44.3, 52.1) nmol/L; the highest Risk: 42.8 (95% CI: 37.8, 48.4) nmol/L (p < 0.0001). The modeled usual intake of folic acid showed no difference among CKD risk groups, with a population median of 225 (interquartile range: 108–390) µg/day. Conclusion: Both RBC and serum folate concentrations increased with declining kidney function without increased folic acid intake. When analyzing associations between folate concentrations and disease outcomes, researchers may want to consider the confounding role of kidney function.
Published: 2022
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