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835 results on '"Mathews, D."'

1. A Flexible Data Acquisition System Architecture for the Nab Experiment

Author

Mathews, D. G., Acharya, H., Crawford, C. B., Gervais, M. H., Jezghani, A. P., McCrea, M., Nelsen, A., Atencio, A., Birge, N., Broussard, L. J., Choi, J. H., Gonzalez, F. M., Li, H., Macsai, N., Mendelsohn, A., Mammei, R. R., Riley, G. V., and Whitehead, R. A.

Subjects
Physics - Instrumentation and Detectors, Nuclear Experiment
Abstract

The Nab experiment will measure the electron-neutrino correlation and Fierz interference term in free neutron beta decay to test the Standard Model and probe Beyond the Standard Model Physics. Using National Instrument's PXIe-5171 Reconfigurable Oscilloscope module, we have developed a data acquisition system that is not only capable of meeting Nab's specifications, but flexible enough to be adapted in situ as the experimental environment dictates. The L1 and L2 trigger logic can be reconfigured to optimize the system for coincidence event detection at runtime through configuration files and LabVIEW controls. This system is capable of identifying L1 triggers at at least $1$ MHz, while reading out a peak signal rate of approximately $2$ GB/s. During commissioning, the system ran at a sustained readout rate of $400$ MB/s of signal data originating from roughly $6$ kHz L2 triggers, well within the peak performance of the system., Comment: 11 pages, 6 figures

Published
2024

2. Fundamental Neutron Physics: a White Paper on Progress and Prospects in the US

Author

Alarcon, R., Aleksandrova, A., Baeßler, S., Beck, D. H., Bhattacharya, T., Blatnik, M., Bowles, T. J., Bowman, J. D., Brewington, J., Broussard, L. J., Bryant, A., Burdine, J. F., Caylor, J., Chen, Y., Choi, J. H., Christie, L., Chupp, T. E., Cianciolo, V., Cirigliano, V., Clayton, S. M., Collett, B., Crawford, C., Dekens, W., Demarteau, M., DeMille, D., Dodson, G., Filippone, B. W., Floyd, N., Fomin, N., Fry, J, Fuyuto, K., Gardner, S., Godri, R., Golub, R., Gonzalez, F., Greene, G. L., Gudkov, V., Gupta, R., Hamblen, J., Hayen, L., Hendrus, J C., Hickerson, K., Hills, F. B., Holley, A. T., Hoogerheide, S., Hubert, M., Huffman, P. R., Imam, S. K., Ito, T. M., Jin, L., Jones, G., Komives, A., Korobkina, E., Korsch, W., Leung, K. K. H., Liu, C. -Y., Liu, K. -F., Long, J. C., Mathews, D., Mendelsohn, A., Mereghetti, E., Mohanmurthy, P., Morris, C. L., Mueller, P., Mumm, H. P., Nelsen, A., Nicholson, A., Nico, J., O'Shaughnessy, C. M., Palamure, P. A., Pastore, S., Pattie Jr., R. W., Phan, N. S., Pioquinto, J. A., Plaster, B., Počanić, D., Rahangdale, H., Redwine, R., Reid, A., Salvat, D. J., Saunders, A., Schaper, D., Seng, C. -Y., Singh, M., Shindler, A., Snow, W. M., Tang, Z., Walker-Loud, A., Wong, D. K. -T., Wietfeldt, F., and Young, A. R.

Subjects
Nuclear Experiment, High Energy Physics - Experiment
Abstract

Fundamental neutron physics, combining precision measurements and theory, probes particle physics at short range with reach well beyond the highest energies probed by the LHC. Significant US efforts are underway that will probe BSM CP violation with orders of magnitude more sensitivity, provide new data on the Cabibbo anomaly, more precisely measure the neutron lifetime and decay, and explore hadronic parity violation. World-leading results from the US Fundamental Neutron Physics community since the last Long Range Plan, include the world's most precise measurement of the neutron lifetime from UCN$\tau$, the final results on the beta-asymmetry from UCNA and new results on hadronic parity violation from the NPDGamma and n-${^3}$He runs at the FNPB (Fundamental Neutron Physics Beamline), precision measurement of the radiative neutron decay mode and n-${}^4$He at NIST. US leadership and discovery potential are ensured by the development of new high-impact experiments including BL3, Nab, LANL nEDM and nEDM@SNS. On the theory side, the last few years have seen results for the neutron EDM from the QCD $\theta$ term, a factor of two reduction in the uncertainty for inner radiative corrections in beta-decay which impacts CKM unitarity, and progress on {\it ab initio} calculations of nuclear structure for medium-mass and heavy nuclei which can eventually improve the connection between nuclear and nucleon EDMs. In order to maintain this exciting program and capitalize on past investments while also pursuing new ideas and building US leadership in new areas, the Fundamental Neutron Physics community has identified a number of priorities and opportunities for our sub-field covering the time-frame of the last Long Range Plan (LRP) under development. This white paper elaborates on these priorities., Comment: arXiv admin note: text overlap with arXiv:2304.03451

Published
2023

3. Fundamental Symmetries, Neutrons, and Neutrinos (FSNN): Whitepaper for the 2023 NSAC Long Range Plan

Author

Acharya, B., Adams, C., Aleksandrova, A. A., Alfonso, K., An, P., Baeßler, S., Balantekin, A. B., Barbeau, P. S., Bellini, F., Bellini, V., Beminiwattha, R. S., Bernauer, J. C., Bhattacharya, T., Bishof, M., Bolotnikov, A. E., Breur, P. A., Brodeur, M., Brodsky, J. P., Broussard, L. J., Brunner, T., Burdette, D. P., Caylor, J., Chiu, M., Cirigliano, V., Clark, J. A., Clayton, S. M., Daniels, T. V., Darroch, L., Davoudi, Z., de Gouvêa, A., Dekens, W., Demarteau, M., DeMille, D., Deshpande, A., Detwiler, J. A., Dodson, G. W., Dolinski, M. J., Elliott, S. R., Engel, J., Erler, J., Filippone, B. W., Fomin, N., Formaggio, J. A., Friesen, F. Q. L., Fry, J., Fujikawa, B. K., Fuller, G., Fuyuto, K., Gallant, A. T., Gallina, G., Ruiz, A. Garcia, Ruiz, R. F. Garcia, Gardner, S., Gonzalez, F. M., Gratta, G., Gruszko, J., Gudkov, V., Guiseppe, V. E., Gutierrez, T. D., Hansen, E. V., Hardy, C. A., Haxton, W. C., Hayen, L., Hedges, S., Heeger, K. M., Heffner, M., Heise, J., Henning, R., Hergert, H., Hertzog, D. W., Aguilar, D. Hervas, Holt, J. D., Hoogerheide, S. F., Hoppe, E. W., Horoi, M., Howell, C. R., Huang, M., Hutzler, N. R., Imam, K., Ito, T. M., Jamil, A., Janssens, R. V., Jayich, A. M., Jones, B. J. P., Kammel, P., Liu, K. F., Khachatryan, V., King, P. M., Klein, J. R., Kneller, J. P., Kolomensky, Yu. G., Korsch, W., Krücken, R., Kumar, K. S., Launey, K. D., Lawrence, D., Leach, K. G., Lehnert, B., Lenardo, B. G., Li, Z., Lin, H. -W., Longfellow, B., Lopez-Caceres, S., Lunardini, C., MacLellan, R., Markoff, D. M., Maruyama, R. H., Mathews, D. G., Melconian, D., Mereghetti, E., Mohanmurthy, P., Moore, D. C., Mueller, P. E., Mumm, H. P., Nazarewicz, W., Newby, J., Nicholson, A. N., Novitski, E., Ondze, J. C. Nzobadila, O'Donnell, T., Gann, G. D. Orebi, Orrell, J. L., Ouellet, J. L., Parno, D. S., Paschke, K. D., Pastore, S., Pattie Jr, R. W., Petrov, A. A., Pitt, M. L., Plaster, B., Pocanic, D., Pocar, A., Poon, A. W. P., Radford, D. C., Rahangdale, H., Rasco, B. C., Rasiwala, H., Redwine, R. P., Ritz, A., Rogers, L., Ron, G., Saldanha, R., Sangiorgio, S., Sargsyan, G. H., Saunders, A., Savard, G., Schaper, D. C., Scholberg, K., Scielzo, N. D., Seng, C. -Y., Shindler, A., Singh, J. T., Singh, M., Singh, V., Snow, W. M., Soma, A. K., Souder, P. A., Speller, D. H., Stachurska, J., Surukuchi, P. T., Oregui, B. Tapia, Tomalak, O., Torres, J. A., Tyuka, O. A., VanDevender, B. A., Varriano, L., Vogt, R., Walker-Loud, A., Wamba, K., Watkins, S. L., Wietfeldt, F. E., Williams, W. D., Wilson, J. T., Winslow, L., Yan, X. L., Yang, L., Young, A. R., Zheng, X., and Zhou, Y.

Subjects
Nuclear Experiment, Nuclear Theory
Abstract

This whitepaper presents the research priorities decided on by attendees of the 2022 Town Meeting for Fundamental Symmetries, Neutrons and Neutrinos, which took place December 13-15, 2022 in Chapel Hill, NC, as part of the Nuclear Science Advisory Committee (NSAC) 2023 Long Range Planning process. A total of 275 scientists registered for the meeting. The whitepaper makes a number of explicit recommendations and justifies them in detail.

Published
2023

4. Using Nab to determine correlations in unpolarized neutron decay

Author

Broussard, L. J., Baeßler, S., Bailey, T. L., Birge, N., Bowman, J. D., Crawford, C. B., Cude-Woods, C., Fellers, D. E., Fomin, N., Frlež, E., Gericke, M. T. W., Hayen, L., Jezghani, A. P., Li, H., Macsai, N., Makela, M. F., Mammei, R. R., Mathews, D., McGaughey, P. L., Mueller, P. E., Počanić, D., Royse, C. A., Salas-Bacci, A., Sjue, S. K. L., Ramsey, J. C., Severijns, N., Smith, E. C., Wexler, J., Whitehead, R. A., Young, A. R., and Zeck, B. A.

Subjects
Nuclear Experiment, Physics - Instrumentation and Detectors
Abstract

The Nab experiment will measure the ratio of the weak axial-vector and vector coupling constants $\lambda=g_A/g_V$ with precision $\delta\lambda/\lambda\sim3\times10^{-4}$ and search for a Fierz term $b_F$ at a level $\Delta b_F<10^{-3}$. The Nab detection system uses thick, large area, segmented silicon detectors to very precisely determine the decay proton's time of flight and the decay electron's energy in coincidence and reconstruct the correlation between the antineutrino and electron momenta. Excellent understanding of systematic effects affecting timing and energy reconstruction using this detection system are required. To explore these effects, a series of ex situ studies have been undertaken, including a search for a Fierz term at a less sensitive level of $\Delta b_F<10^{-2}$ in the beta decay of $^{45}$Ca using the UCNA spectrometer., Comment: Proceedings of the 7th International Syposium on Symmetries in Subatomic Physics SSP2018, Aachen (Germany), 10 - 15 Jun 2018. This is a pre-print of an article published in Hyperfine Interactions. The final authenticated version is available online at: https://doi.org/10.1007/s10751-018-1538-7

Published
2018
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5. The Nab Experiment: A Precision Measurement of Unpolarized Neutron Beta Decay

Author

Fry, J., Alarcon, R., Baessler, S., Balascuta, S., Barron-Palos, L., Bailey, T., Bass, K., Birge, N., Blose, A., Borissenko, D., Bowman, J. D., Broussard, L. J., Bryant, A. T., Byrne, J., Calarco, J. R., Caylor, J., Chang, K., Chupp, T., Cianciolo, T. V., Crawford, C., Ding, X., Doyle, M., Fan, W., Farrar, W., Fomin, N., Frlez, E., Gericke, M. T., Gervais, M., Gluck, F., Greene, G. L., Grzywacz, R. K., Gudkov, V., Hamblen, J., Hayes, C., Hendrus, C., Ito, T., Jezghani, A., Li, H., Makela, M., Macsai, N., Mammei, J., Mammei, R., Martinez, M., Mathews, D. G., McCrea, M., McGaughey, P., McLaughlin, C. D., Mueller, P., van Petten, D., Penttila, S. I., Perryman, D. E., Picker, R., Pierce, J., Pocanic, D., Qian, Y., Ramsey, J., Randall, G., Riley, G., Rykaczewski, K. P., Salas-Bacci, A., Samiei, S., Scott, E. M., Shelton, T., Sjue, S. K., Smith, A., Smith, E., Stevens, E., Wexler, J., Whitehead, R., Wilburn, W. S., Young, A., and Zeck, B.

Subjects
Nuclear Experiment
Abstract

Neutron beta decay is one of the most fundamental processes in nuclear physics and provides sensitive means to uncover the details of the weak interaction. Neutron beta decay can evaluate the ratio of axial-vector to vector coupling constants in the standard model, $\lambda = g_A / g_V$, through multiple decay correlations. The Nab experiment will carry out measurements of the electron-neutrino correlation parameter $a$ with a precision of $\delta a / a = 10^{-3}$ and the Fierz interference term $b$ to $\delta b = 3\times10^{-3}$ in unpolarized free neutron beta decay. These results, along with a more precise measurement of the neutron lifetime, aim to deliver an independent determination of the ratio $\lambda$ with a precision of $\delta \lambda / \lambda = 0.03\%$ that will allow an evaluation of $V_{ud}$ and sensitively test CKM unitarity, independent of nuclear models. Nab utilizes a novel, long asymmetric spectrometer that guides the decay electron and proton to two large area silicon detectors in order to precisely determine the electron energy and an estimation of the proton momentum from the proton time of flight. The Nab spectrometer is being commissioned at the Fundamental Neutron Physics Beamline at the Spallation Neutron Source at Oak Ridge National Lab. We present an overview of the Nab experiment and recent updates on the spectrometer, analysis, and systematic effects., Comment: Presented at PPNS2018

Published
2018
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6. Thirty critical research needs for managing an ecologically and culturally unique remote marine environment: The Kimberley region of Western Australia

Author

Cvitanovic, C., Mackay, M., Kelly, R., Wilson, S.K., Waples, K., Nash, K.L., van Putten, E.I., Field, S., Botterill-James, T., Austin, B.J., Beckley, L.E., Boschetti, F., Depczynski, M., Dobbs, R.J., Evans, R.D., Feng, M., Goater, R.K., Halford, A.R., Kendrick, A., Kendrick, G.A., Lincoln, G.D.B., Ludgerus, L.J., Lowe, R.J., McMahon, K., Munro, J.K., Newman, S.J., Nutt, C., Pearson, L., O'Leary, M.J., Richards, Z.T., Robbins, W.D., Rogers, D.I., Salgado Kent, C.P., Schoepf, V., Travers, M.J., Thums, M., Tucker, A.D., Underwood, J.N., Whiting, S., and Mathews, D.

Published
2021
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7. Fundamental Symmetries, Neutrons, and Neutrinos (FSNN): Whitepaper for the 2023 NSAC Long Range Plan

Author

Acharya, B, primary, Adams, C, additional, Aleksandrova, A, additional, Alfonso, K, additional, An, P, additional, Baessler, S, additional, Balantekin, A, additional, Barbeau, P, additional, Bellini, F, additional, Bellini, V, additional, Beminiwatha, R, additional, Bernauer, J, additional, Bhattacharya, T, additional, Bishof, M, additional, Bolotnikov, A, additional, Breur, P, additional, Brodeur, M, additional, Brodsky, J, additional, Broussard, L, additional, Brunner, T, additional, Burdette, D, additional, Caylor, J, additional, Chiu, M, additional, Cirigliano, V, additional, Clark, J, additional, Clayton, S, additional, Daniels, T, additional, Darroch, L, additional, Davoudi, Z, additional, de Gouvea, A, additional, Dekens, W, additional, Demarteau, M, additional, DeMille, D, additional, Deshpande, A, additional, Detwiler, J, additional, Dodson, G, additional, Kolinski, M, additional, Elliott, S, additional, Engel, J, additional, Erler, J, additional, Filippone, B, additional, Fomin, N, additional, Formaggio, J, additional, Fry, J, additional, Fujikawa, B, additional, Fuller, G, additional, Fuyuto, K, additional, Gallant, A, additional, Gallina, G, additional, Garcia Ruiz, A, additional, Garcia Ruiz, R, additional, Gardner, S, additional, Gonzalez, F, additional, Gratta, G, additional, Gruszko, J, additional, Gudkov, V, additional, Giuseppe, V, additional, Gutierrez, T, additional, Hansen, E, additional, Hardy, C, additional, Haxton, W, additional, Hayer, L, additional, Hedges, S, additional, Heeger, K, additional, Heffner, M, additional, Heise, J, additional, Henning, R, additional, Hergert, H, additional, Hertzog, D, additional, Hervas Aguilar, D, additional, Holt, J, additional, Hoogerheide, S, additional, Hoppe, E, additional, Horoi, M, additional, Howell, C, additional, Huang, M, additional, Hutzler, N, additional, Imam, K, additional, Ito, T, additional, Jamil, A, additional, Janssens, R, additional, Jayich, A, additional, Kammel, P, additional, Liu, K, additional, Khachatryan, V, additional, King, P, additional, Klein, J, additional, Kneller, J, additional, Kolomensky, Y, additional, Korsch, W, additional, Krucken, R, additional, Kumar, K, additional, Launey, K, additional, Lawrence, D, additional, Leach, K, additional, Lehnert, B, additional, Lenardo, B, additional, Li, Z, additional, Lin, H, additional, Longfellow, B, additional, Lopez-Caceres, S, additional, Lunardini, C, additional, MacLellan, R, additional, Markoff, D, additional, Maruyama, R, additional, Mathews, D, additional, Melconian, D, additional, Mereghetti, E, additional, Mohanmurthy, P, additional, Moore, D, additional, Mueller, P, additional, Mumm, H, additional, Nazarewicz, W, additional, Newby, J, additional, Nicholson, A, additional, Novitski, E, additional, Nzobadila Ondze, J, additional, O'Donnell, T, additional, Orebi Gann, G, additional, Orrell, J, additional, Ouellet, J, additional, Parno, D, additional, Paschke, K, additional, Pastore, S, additional, Pattie Jr, R, additional, Petrov, A, additional, Pitt, M, additional, Plaster, B, additional, Pocanic, D, additional, Pocar, A, additional, Radford, D, additional, Rahangdale, H, additional, Rasco, B, additional, Rasiwala, H, additional, Redwine, R, additional, Ritz, A, additional, Rogers, L, additional, Ron, G, additional, Saldanha, R, additional, Sangiorgio, S, additional, Sargsyan, G, additional, Saunders, A, additional, Savard, G, additional, Schaper, D, additional, Scholberg, K, additional, Scielzo, N, additional, Seng, C, additional, Shindler, A, additional, Singh, J, additional, Singh, M, additional, Singh, V, additional, Snow, W, additional, Soma, A, additional, Souder, P, additional, Speller, D, additional, Stachurska, J, additional, Surukuchi, P, additional, Tapia Oregui, B, additional, Tomalak, O, additional, Torres, J, additional, Tyuka, O, additional, VanDevender, B, additional, Varriano, L, additional, Vogt, R, additional, Walker-Loud, A, additional, Wamba, K, additional, Watkins, S, additional, Wietfeldt, F, additional, Williams, W, additional, Wilson, J, additional, Winslow, L, additional, Yan, X, additional, Yang, L, additional, Young, A, additional, Zheng, X, additional, and Zhou, Y, additional

Published
2023
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9. Prognostic relevance of gait-related cognitive functions for dementia conversion in amnestic mild cognitive impairment

Author

Tuena, C, Maestri, S, Serino, S, Pedroli, E, Stramba-Badiale, M, Riva, G, Silbert, L, Lind, B, Crissey, R, Kaye, J, Carter, R, Dolen, S, Quinn, J, Schneider, L, Pawluczyk, S, Becerra, M, Teodoro, L, Dagerman, K, Spann, B, Brewer, J, Fleisher, A, Vanderswag, H, Ziolkowski, J, Heidebrink, J, Zbizek-Nulph, L, Lord, J, Albers, C, Petersen, R, Mason, S, Knopman, D, Johnson, K, Villanueva-Meyer, J, Pavlik, V, Pacini, N, Lamb, A, Kass, J, Doody, R, Shibley, V, Chowdhury, M, Rountree, S, Dang, M, Stern, Y, Honig, L, Mintz, A, Ances, B, Morris, J, Winkfield, D, Carroll, M, Stobbs-Cucchi, G, Oliver, A, Creech, M, Mintun, M, Schneider, S, Geldmacher, D, Love, M, Griffith, R, Clark, D, Brockington, J, Marson, D, Grossman, H, Goldstein, M, Greenberg, J, Mitsis, E, Shah, R, Lamar, M, Samuels, P, Duara, R, Greig-Custo, M, Rodriguez, R, Albert, M, Onyike, C, Farrington, L, Rudow, S, Brichko, R, Kielb, S, Smith, A, Raj, B, Fargher, K, Sadowski, M, Wisniewski, T, Shulman, M, Faustin, A, Rao, J, Castro, K, Ulysse, A, Chen, S, Doraiswamy, P, Petrella, J, James, O, Wong, T, Borges-Neto, S, Karlawish, J, Wolk, D, Vaishnavi, S, Clark, C, Arnold, S, Smith, C, Jicha, G, Khouli, R, Raslau, F, Lopez, O, Oakley, M, Simpson, D, Porsteinsson, A, Martin, K, Kowalski, N, Keltz, M, Goldstein, B, Makino, K, Ismail, M, Brand, C, Thai, G, Pierce, A, Yanez, B, Sosa, E, Witbracht, M, Kelley, B, Nguyen, T, Womack, K, Mathews, D, Quiceno, M, Levey, A, Lah, J, Hajjar, I, Burns, J, Swerdlow, R, Brooks, W, Silverman, D, Kremen, S, Apostolova, L, Tingus, K, Lu, P, Bartzokis, G, Woo, E, Teng, E, Graff-Radford, N, Parfitt, F, Poki-Walker, K, Farlow, M, Hake, A, Matthews, B, Brosch, J, Herring, S, van Dyck, C, Mecca, A, Good, S, Macavoy, M, Carson, R, Varma, P, Chertkow, H, Vaitekunas, S, Hosein, C, Black, S, Stefanovic, B, Heyn, C, Hsiung, G, Kim, E, Mudge, B, Sossi, V, Feldman, H, Assaly, M, Finger, E, Pasternak, S, Rachinsky, I, Kertesz, A, Drost, D, Rogers, J, Grant, I, Muse, B, Rogalski, E, Robson, J, Mesulam, M, Kerwin, D, Wu, C, Johnson, N, Lipowski, K, Weintraub, S, Bonakdarpour, B, Pomara, N, Hernando, R, Sarrael, A, Rosen, H, Miller, B, Weiner, M, Perry, D, Turner, R, Reynolds, B, Mccann, K, Poe, J, Marshall, G, Sperling, R, Yesavage, J, Taylor, J, Chao, S, Coleman, J, White, J, Lane, B, Rosen, A, Tinklenberg, J, Belden, C, Atri, A, Clark, K, Zamrini, E, Sabbagh, M, Killiany, R, Stern, R, Mez, J, Kowall, N, Budson, A, Obisesan, T, Ntekim, O, Wolday, S, Khan, J, Nwulia, E, Nadarajah, S, Lerner, A, Ogrocki, P, Tatsuoka, C, Fatica, P, Fletcher, E, Maillard, P, Olichney, J, Decarli, C, Carmichael, O, Bates, V, Capote, H, Rainka, M, Borrie, M, Lee, T, Bartha, R, Johnson, S, Asthana, S, Carlsson, C, Perrin, A, Burke, A, Scharre, D, Kataki, M, Tarawneh, R, Hart, D, Zimmerman, E, Celmins, D, Miller, D, Ponto, L, Smith, K, Koleva, H, Shim, H, Nam, K, Schultz, S, Williamson, J, Craft, S, Cleveland, J, Yang, M, Sink, K, Ott, B, Drake, J, Tremont, G, Daiello, L, Ritter, A, Bernick, C, Munic, D, O'Connelll, A, Mintzer, J, Wiliams, A, Masdeu, J, Shi, J, Garcia, A, Newhouse, P, Potkin, S, Salloway, S, Malloy, P, Correia, S, Kittur, S, Pearlson, G, Blank, K, Anderson, K, Flashman, L, Seltzer, M, Hynes, M, Santulli, R, Relkin, N, Chiang, G, Lee, A, Lin, M, Ravdin, L, Tuena C., Maestri S., Serino S., Pedroli E., Stramba-Badiale M., Riva G., Silbert L. C., Lind B., Crissey R., Kaye J. A., Carter R., Dolen S., Quinn J., Schneider L. S., Pawluczyk S., Becerra M., Teodoro L., Dagerman K., Spann B. M., Brewer J., Fleisher A., Vanderswag H., Ziolkowski J., Heidebrink J. L., Zbizek-Nulph L., Lord J. L., Albers C. S., Petersen R., Mason S. S., Knopman D., Johnson K., Villanueva-Meyer J., Pavlik V., Pacini N., Lamb A., Kass J. S., Doody R. S., Shibley V., Chowdhury M., Rountree S., Dang M., Stern Y., Honig L. S., Mintz A., Ances B., Morris J. C., Winkfield D., Carroll M., Stobbs-Cucchi G., Oliver A., Creech M. L., Mintun M. A., Schneider S., Geldmacher D., Love M. N., Griffith R., Clark D., Brockington J., Marson D., Grossman H., Goldstein M. A., Greenberg J., Mitsis E., Shah R. C., Lamar M., Samuels P., Duara R., Greig-Custo M. T., Rodriguez R., Albert M., Onyike C., Farrington L., Rudow S., Brichko R., Kielb S., Smith A., Raj B. A., Fargher K., Sadowski M., Wisniewski T., Shulman M., Faustin A., Rao J., Castro K. M., Ulysse A., Chen S., Doraiswamy P. M., Petrella J. R., James O., Wong T. Z., Borges-Neto S., Karlawish J. H., Wolk D. A., Vaishnavi S., Clark C. M., Arnold S. E., Smith C. D., Jicha G. A., Khouli R. E., Raslau F. D., Lopez O. L., Oakley M. A., Simpson D. M., Porsteinsson A. P., Martin K., Kowalski N., Keltz M., Goldstein B. S., Makino K. M., Ismail M. S., Brand C., Thai G., Pierce A., Yanez B., Sosa E., Witbracht M., Kelley B., Nguyen T., Womack K., Mathews D., Quiceno M., Levey A. I., Lah J. J., Hajjar I., Burns J. M., Swerdlow R. H., Brooks W. M., Silverman D. H. S., Kremen S., Apostolova L., Tingus K., Lu P. H., Bartzokis G., Woo E., Teng E., Graff-Radford N. R., Parfitt F., Poki-Walker K., Farlow M. R., Hake A. M., Matthews B. R., Brosch J. R., Herring S., van Dyck C. H., Mecca A. P., Good S. P., MacAvoy M. G., Carson R. E., Varma P., Chertkow H., Vaitekunas S., Hosein C., Black S., Stefanovic B., Heyn C., Hsiung G. -Y. R., Kim E., Mudge B., Sossi V., Feldman H., Assaly M., Finger E., Pasternak S., Rachinsky I., Kertesz A., Drost D., Rogers J., Grant I., Muse B., Rogalski E., Robson J., Mesulam M. -M., Kerwin D., Wu C. -K., Johnson N., Lipowski K., Weintraub S., Bonakdarpour B., Pomara N., Hernando R., Sarrael A., Rosen H. J., Miller B. L., Weiner M. W., Perry D., Turner R. S., Reynolds B., MCCann K., Poe J., Marshall G. A., Sperling R. A., Johnson K. A., Yesavage J., Taylor J. L., Chao S., Coleman J., White J. D., Lane B., Rosen A., Tinklenberg J., Belden C. M., Atri A., Clark K. A., Zamrini E., Sabbagh M., Killiany R., Stern R., Mez J., Kowall N., Budson A. E., Obisesan T. O., Ntekim O. E., Wolday S., Khan J. I., Nwulia E., Nadarajah S., Lerner A., Ogrocki P., Tatsuoka C., Fatica P., Fletcher E., Maillard P., Olichney J., DeCarli C., Carmichael O., Bates V., Capote H., Rainka M., Borrie M., Lee T. -Y., Bartha R., Johnson S., Asthana S., Carlsson C. M., Perrin A., Burke A., Scharre D. W., Kataki M., Tarawneh R., Hart D., Zimmerman E. A., Celmins D., Miller D. D., Ponto L. L. B., Smith K. E., Koleva H., Shim H., Nam K. W., Schultz S. K., Williamson J. D., Craft S., Cleveland J., Yang M., Sink K. M., Ott B. R., Drake J., Tremont G., Daiello L. A., Drake J. D., Ritter A., Bernick C., Munic D., O'Connelll A., Mintzer J., Wiliams A., Masdeu J., Shi J., Garcia A., Newhouse P., Potkin S., Salloway S., Malloy P., Correia S., Kittur S., Pearlson G. D., Blank K., Anderson K., Flashman L. A., Seltzer M., Hynes M. L., Santulli R. B., Relkin N., Chiang G., Lee A., Lin M., Ravdin L., Tuena, C, Maestri, S, Serino, S, Pedroli, E, Stramba-Badiale, M, Riva, G, Silbert, L, Lind, B, Crissey, R, Kaye, J, Carter, R, Dolen, S, Quinn, J, Schneider, L, Pawluczyk, S, Becerra, M, Teodoro, L, Dagerman, K, Spann, B, Brewer, J, Fleisher, A, Vanderswag, H, Ziolkowski, J, Heidebrink, J, Zbizek-Nulph, L, Lord, J, Albers, C, Petersen, R, Mason, S, Knopman, D, Johnson, K, Villanueva-Meyer, J, Pavlik, V, Pacini, N, Lamb, A, Kass, J, Doody, R, Shibley, V, Chowdhury, M, Rountree, S, Dang, M, Stern, Y, Honig, L, Mintz, A, Ances, B, Morris, J, Winkfield, D, Carroll, M, Stobbs-Cucchi, G, Oliver, A, Creech, M, Mintun, M, Schneider, S, Geldmacher, D, Love, M, Griffith, R, Clark, D, Brockington, J, Marson, D, Grossman, H, Goldstein, M, Greenberg, J, Mitsis, E, Shah, R, Lamar, M, Samuels, P, Duara, R, Greig-Custo, M, Rodriguez, R, Albert, M, Onyike, C, Farrington, L, Rudow, S, Brichko, R, Kielb, S, Smith, A, Raj, B, Fargher, K, Sadowski, M, Wisniewski, T, Shulman, M, Faustin, A, Rao, J, Castro, K, Ulysse, A, Chen, S, Doraiswamy, P, Petrella, J, James, O, Wong, T, Borges-Neto, S, Karlawish, J, Wolk, D, Vaishnavi, S, Clark, C, Arnold, S, Smith, C, Jicha, G, Khouli, R, Raslau, F, Lopez, O, Oakley, M, Simpson, D, Porsteinsson, A, Martin, K, Kowalski, N, Keltz, M, Goldstein, B, Makino, K, Ismail, M, Brand, C, Thai, G, Pierce, A, Yanez, B, Sosa, E, Witbracht, M, Kelley, B, Nguyen, T, Womack, K, Mathews, D, Quiceno, M, Levey, A, Lah, J, Hajjar, I, Burns, J, Swerdlow, R, Brooks, W, Silverman, D, Kremen, S, Apostolova, L, Tingus, K, Lu, P, Bartzokis, G, Woo, E, Teng, E, Graff-Radford, N, Parfitt, F, Poki-Walker, K, Farlow, M, Hake, A, Matthews, B, Brosch, J, Herring, S, van Dyck, C, Mecca, A, Good, S, Macavoy, M, Carson, R, Varma, P, Chertkow, H, Vaitekunas, S, Hosein, C, Black, S, Stefanovic, B, Heyn, C, Hsiung, G, Kim, E, Mudge, B, Sossi, V, Feldman, H, Assaly, M, Finger, E, Pasternak, S, Rachinsky, I, Kertesz, A, Drost, D, Rogers, J, Grant, I, Muse, B, Rogalski, E, Robson, J, Mesulam, M, Kerwin, D, Wu, C, Johnson, N, Lipowski, K, Weintraub, S, Bonakdarpour, B, Pomara, N, Hernando, R, Sarrael, A, Rosen, H, Miller, B, Weiner, M, Perry, D, Turner, R, Reynolds, B, Mccann, K, Poe, J, Marshall, G, Sperling, R, Yesavage, J, Taylor, J, Chao, S, Coleman, J, White, J, Lane, B, Rosen, A, Tinklenberg, J, Belden, C, Atri, A, Clark, K, Zamrini, E, Sabbagh, M, Killiany, R, Stern, R, Mez, J, Kowall, N, Budson, A, Obisesan, T, Ntekim, O, Wolday, S, Khan, J, Nwulia, E, Nadarajah, S, Lerner, A, Ogrocki, P, Tatsuoka, C, Fatica, P, Fletcher, E, Maillard, P, Olichney, J, Decarli, C, Carmichael, O, Bates, V, Capote, H, Rainka, M, Borrie, M, Lee, T, Bartha, R, Johnson, S, Asthana, S, Carlsson, C, Perrin, A, Burke, A, Scharre, D, Kataki, M, Tarawneh, R, Hart, D, Zimmerman, E, Celmins, D, Miller, D, Ponto, L, Smith, K, Koleva, H, Shim, H, Nam, K, Schultz, S, Williamson, J, Craft, S, Cleveland, J, Yang, M, Sink, K, Ott, B, Drake, J, Tremont, G, Daiello, L, Ritter, A, Bernick, C, Munic, D, O'Connelll, A, Mintzer, J, Wiliams, A, Masdeu, J, Shi, J, Garcia, A, Newhouse, P, Potkin, S, Salloway, S, Malloy, P, Correia, S, Kittur, S, Pearlson, G, Blank, K, Anderson, K, Flashman, L, Seltzer, M, Hynes, M, Santulli, R, Relkin, N, Chiang, G, Lee, A, Lin, M, Ravdin, L, Tuena C., Maestri S., Serino S., Pedroli E., Stramba-Badiale M., Riva G., Silbert L. C., Lind B., Crissey R., Kaye J. A., Carter R., Dolen S., Quinn J., Schneider L. S., Pawluczyk S., Becerra M., Teodoro L., Dagerman K., Spann B. M., Brewer J., Fleisher A., Vanderswag H., Ziolkowski J., Heidebrink J. L., Zbizek-Nulph L., Lord J. L., Albers C. S., Petersen R., Mason S. S., Knopman D., Johnson K., Villanueva-Meyer J., Pavlik V., Pacini N., Lamb A., Kass J. S., Doody R. S., Shibley V., Chowdhury M., Rountree S., Dang M., Stern Y., Honig L. S., Mintz A., Ances B., Morris J. C., Winkfield D., Carroll M., Stobbs-Cucchi G., Oliver A., Creech M. L., Mintun M. A., Schneider S., Geldmacher D., Love M. N., Griffith R., Clark D., Brockington J., Marson D., Grossman H., Goldstein M. A., Greenberg J., Mitsis E., Shah R. C., Lamar M., Samuels P., Duara R., Greig-Custo M. T., Rodriguez R., Albert M., Onyike C., Farrington L., Rudow S., Brichko R., Kielb S., Smith A., Raj B. A., Fargher K., Sadowski M., Wisniewski T., Shulman M., Faustin A., Rao J., Castro K. M., Ulysse A., Chen S., Doraiswamy P. M., Petrella J. R., James O., Wong T. Z., Borges-Neto S., Karlawish J. H., Wolk D. A., Vaishnavi S., Clark C. M., Arnold S. E., Smith C. D., Jicha G. A., Khouli R. E., Raslau F. D., Lopez O. L., Oakley M. A., Simpson D. M., Porsteinsson A. P., Martin K., Kowalski N., Keltz M., Goldstein B. S., Makino K. M., Ismail M. S., Brand C., Thai G., Pierce A., Yanez B., Sosa E., Witbracht M., Kelley B., Nguyen T., Womack K., Mathews D., Quiceno M., Levey A. I., Lah J. J., Hajjar I., Burns J. M., Swerdlow R. H., Brooks W. M., Silverman D. H. S., Kremen S., Apostolova L., Tingus K., Lu P. H., Bartzokis G., Woo E., Teng E., Graff-Radford N. R., Parfitt F., Poki-Walker K., Farlow M. R., Hake A. M., Matthews B. R., Brosch J. R., Herring S., van Dyck C. H., Mecca A. P., Good S. P., MacAvoy M. G., Carson R. E., Varma P., Chertkow H., Vaitekunas S., Hosein C., Black S., Stefanovic B., Heyn C., Hsiung G. -Y. R., Kim E., Mudge B., Sossi V., Feldman H., Assaly M., Finger E., Pasternak S., Rachinsky I., Kertesz A., Drost D., Rogers J., Grant I., Muse B., Rogalski E., Robson J., Mesulam M. -M., Kerwin D., Wu C. -K., Johnson N., Lipowski K., Weintraub S., Bonakdarpour B., Pomara N., Hernando R., Sarrael A., Rosen H. J., Miller B. L., Weiner M. W., Perry D., Turner R. S., Reynolds B., MCCann K., Poe J., Marshall G. A., Sperling R. A., Johnson K. A., Yesavage J., Taylor J. L., Chao S., Coleman J., White J. D., Lane B., Rosen A., Tinklenberg J., Belden C. M., Atri A., Clark K. A., Zamrini E., Sabbagh M., Killiany R., Stern R., Mez J., Kowall N., Budson A. E., Obisesan T. O., Ntekim O. E., Wolday S., Khan J. I., Nwulia E., Nadarajah S., Lerner A., Ogrocki P., Tatsuoka C., Fatica P., Fletcher E., Maillard P., Olichney J., DeCarli C., Carmichael O., Bates V., Capote H., Rainka M., Borrie M., Lee T. -Y., Bartha R., Johnson S., Asthana S., Carlsson C. M., Perrin A., Burke A., Scharre D. W., Kataki M., Tarawneh R., Hart D., Zimmerman E. A., Celmins D., Miller D. D., Ponto L. L. B., Smith K. E., Koleva H., Shim H., Nam K. W., Schultz S. K., Williamson J. D., Craft S., Cleveland J., Yang M., Sink K. M., Ott B. R., Drake J., Tremont G., Daiello L. A., Drake J. D., Ritter A., Bernick C., Munic D., O'Connelll A., Mintzer J., Wiliams A., Masdeu J., Shi J., Garcia A., Newhouse P., Potkin S., Salloway S., Malloy P., Correia S., Kittur S., Pearlson G. D., Blank K., Anderson K., Flashman L. A., Seltzer M., Hynes M. L., Santulli R. B., Relkin N., Chiang G., Lee A., Lin M., and Ravdin L.

Abstract

Background: Increasing research suggests that gait abnormalities can be a risk factor for Alzheimer’s Disease (AD). Notably, there is growing evidence highlighting this risk factor in individuals with amnestic Mild Cognitive Impairment (aMCI), however further studies are needed. The aim of this study is to analyze cognitive tests results and brain-related measures over time in aMCI and examine how the presence of gait abnormalities (neurological or orthopedic) or normal gait affects these trends. Additionally, we sought to assess the significance of gait and gait-related measures as prognostic indicators for the progression from aMCI to AD dementia, comparing those who converted to AD with those who remained with a stable aMCI diagnosis during the follow-up. Methods: Four hundred two individuals with aMCI from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database were included. Robust linear mixed-effects models were used to study the impact of gait abnormalities on a comprehensive neuropsychological battery over 36 months while controlling for relevant medical variables at baseline. The impact of gait on brain measures was also investigated. Lastly, the Cox proportional-hazards model was used to explore the prognostic relevance of abnormal gait and neuropsychological associated tests. Results: While controlling for relevant covariates, we found that gait abnormalities led to a greater decline over time in attention (DSST) and global cognition (MMSE). Intriguingly, psychomotor speed (TMT-A) and divided attention (TMT-B) declined uniquely in the abnormal gait group. Conversely, specific AD global cognition tests (ADAS-13) and auditory-verbal memory (RAVLT immediate recall) declined over time independently of gait profile. All the other cognitive tests were not significantly affected by time or by gait profile. In addition, we found that ventricles size increased faster in the abnormal gait group compared to the normal gait group. In terms of prognosis, abno

Published
2023

12. The RNA Ontology Consortium: An open invitation to the RNA community

Author

Leontis, N B, Altman, R B, Berman, H M, Brenner, Steven E, Brown, J W, Engelke, D R, Harvey, S C, Holbrook, S R, Jossinet, F, Lewis, S E, Major, F, Mathews, D H, Richardson, J S, Williamson, J R, and Westhof, E

Subjects
biological ontology, RNA, sequence alignments, 3D structure, RNA motifs
Abstract

The aim of the RNA Ontology Consortium (ROC) is to create an integrated conceptual framework - an RNA Ontology (RO) - with a common, dynamic, controlled, and structured vocabulary to describe and characterize RNA sequences, secondary structures, three-dimensional structures, and dynamics pertaining to RNA function. The RO should produce tools for clear communication about RNA structure and function for multiple uses, including the integration of RNA electronic resources into the Semantic Web. These tools should allow the accurate description in computer-interpretable form of the coupling between RNA architecture, function, and evolution. The purposes for creating the RO are, therefore, (1) to integrate sequence and structural databases; (2) to allow different computational tools to interoperate; (3) to create powerful software tools that bring advanced computational methods to the bench scientist; and (4) to facilitate precise searches for all relevant information pertaining to RNA. For example, one initial objective of the ROC is to define, identify, and classify RNA structural motifs described in the literature or appearing in databases and to agree on a computer-interpretable definition for each of these motifs. To achieve these aims, the ROC will foster communication and promote collaboration among RNA scientists by coordinating frequent face-to-face workshops to discuss, debate, and resolve difficult conceptual issues. These meeting opportunities will create new directions at various levels of RNA research. The ROC will work closely with the PDB/NDB structural databases and the Gene, Sequence, and Open Biomedical Ontology Consortia to integrate the RO with existing biological ontologies to extend existing content while maintaining interoperability.

Published
2006

21. Can unsupervised learning methods applied to milk recording big data provide new insights into dairy cow health?

Author

Franceschini, S., Grelet, C., Leblois, J., Gengler, N., Soyeurt, H., Crowe, M., MeLoughlin, N., Fahey, A., Carter, F., Matthews, E., Santoro, A., Byrne, C., Rudd, P., O'Flaherty, R., Hallinan, S., Wathes, C., Salavati, M., Cheng, Z., Fouladi, A., Pollott, G., Werling, D., Bernardo, B. Sanz, Ferris, C., Wylie, A., Bell, M., Vaneetvelde, M., Hermans, K., Hostens, M., Opsomer, Geert, Moerman, S., De Koster, J., Bogaert, H., Vandepitte, J., Vanervelde, L., Vanranst, B., Ingvartsen, K., Sorensen, M. Tang, Hoglund, J., Dahl, S., Ostergaard, S., Rothmaan, J., Krogh, M., Meyer, E., Foldager, L., Gaillard, C., Ettema, J., Rousing, T., Larsen, T., De Oilveira, V. H. Silva, Marchitelli, C., McClure, F., Mathews, D., Kearney, F., Cromie, A., McClure, M., Zheng, S., Chen, X., Chen, H., Zhao, J., Yang, L., Hua, G., Tan, C., Wang, G., Bonneau, M., Sciarretta, M., Pearn, A., Evertson, A., Kosten, L., Fogh, A., Andersen, T., Lucy, M., Elsik, C., Conant, G., Taylor, J., Triant, D., Georges, M., Colinet, F., Pampona, M. Ramos, Hammami, H., Bastin, C., Takeda, H., Laine, A., Van Laere, A., Mota, R., Darbagshahi, S. Nadri, Dehareng, F., Vanlierde, A., Froidmont, E., Becker, F., Schulze, M., Vera, S. Palma, and GplusE Consortium, H.

Subjects
INDICATORS, Big Data, BOVINE-MILK, PREDICTION, LACTOFERRIN CONTENT, Cattle Diseases, Glucose-6-Phosphate, Mastitis, unsupervised learning, Pregnancy, MASTITIS, Genetics, Animals, Lactation, Veterinary Sciences, milk, animal health, Mastitis/veterinary, BLOOD BETA-HYDROXYBUTYRATE, MIDINFRARED SPECTROSCOPY, LARGE-SCALE, mid-infrared, NEGATIVE-ENERGY BALANCE, Animal Science and Zoology, Cattle, Female, ANIMAL-WELFARE, Biomarkers, Food Science, Unsupervised Machine Learning
Abstract

Among the dairy sector's current concerns, the as-sessment of global animal health status is a complex challenge. Its multidimensionality means that global monitoring tools are rarely considered. Instead, specific disease detection is often studied separately and, due to financial and ethical issues, uses small-scale data sets focusing on few biomarkers. Several studies have already been conducted using milk Fourier transform mid-infrared (FT-MIR) spectroscopy to detect mastitis and lameness or to quantify health-related biomarkers in milk or blood. Those studies are relevant but they focus mainly on one biomarker or disease. To solve this issue and the small-scale data set, in this study, we proposed a holistic approach using big data obtained from milk recording, including milk yield, somatic cell count, and 27 FT-MIR-based predictors related to milk composition and animal health status. Using 740,454 records collected from 114,536 first-parity Holstein cows in southern Belgium, we performed repeated unsupervised learning algorithms based on Ward's agglomerative hierarchical clustering method to find potential interesting patterns. A divide-and-conquer approach was used to overcome the limitation of computational resources in clustering a relatively large data set. Five groups of records were identified. Differences observed in the fourth group suggested a relationship to metabolic disorders. The fifth group seemed to be related to mastitis. In a second step, we performed a partial least squares discriminant analysis (PLS-DA) to predict the probability of belonging to those specific groups for the entire data set. The obtained global ac-curacy was 0.77 and the balanced accuracy (i.e., the mean between sensitivity and specificity) of discrimi-nating the fourth and fifth groups was 0.88 and 0.96, respectively. Then, a validation of the interpretation of those groups was performed using 204 milk and blood reference records. The predicted probability associated with the metabolic disorders issue had significant cor-relations of 0.54 with blood beta-hydroxybutyrate, 0.44 with blood nonesterified fatty acids, -0.32 with blood glucose, -0.23 with milk glucose-6-phosphate, and 0.38 with milk isocitrate. In contrast, the predicted prob-ability of belonging to the mastitis group had correla-tions of 0.69 with milk lactate dehydrogenase, 0.46 with milk N-acetyl-beta-D-glucosaminidase, -0.18 with milk free glucose, and 0.16 with milk glucose-6-phosphate. Consequently, these results suggest that the obtained quantitative traits indirectly reflect some of the main health disorders in dairy farming and could be used to monitor dairy cows on a large scale. By using unsuper-vised learning on large-scale milk recording data and then validating the pattern using reference laboratory measures, we propose a new approach to quickly assess dairy cow health status.

Published
2022
Full Text
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22. Low-dose cyclosporine treatment for sight-threatening uveitis: Efficacy, toxicity, and tolerance

Author

Mathews D, Mathews John, and Jones N

Subjects
Cyclosporine, immunosuppression, steroid, uveitis, Ophthalmology, RE1-994
Abstract

Aim : To ascertain the effectiveness, tolerability, and safety of low-dose cyclosporine in the management of sight-threatening uveitis. Materials and Methods: This was a retrospective clinical case series of patients using oral low-dose cyclosporine for the management of sight-threatening uveitis in the uvea clinic (UC). Patients receiving cyclosporine were identified from the clinic database. Main outcome measures were degree of intraocular inflammation, visual acuity and dose reduction of oral steroid for effectiveness and adverse symptoms, systemic hypertension, and raised serum creatinine for tolerability and safety. Results: Intraocular inflammation was improved or stable in 97% of patients, visual acuity was improved or stable in 91%, and oral steroid dosage was reduced in 73% (by half or more in 51%). Adverse symptoms were almost universal, the commonest being peripheral paresthesia/burning in 70% and fatigue in 67%. Significant systemic hypertension developed in 27% and raised creatinine in 30%, necessitating dose reduction. Cyclosporine was discontinued in 35%, being intolerable in 20% and ineffective in 15%. Conclusions: Cyclosporine was found to be effective in reducing inflammation and protecting vision in sight-threatening uveitis. It was safe with proper monitoring, including in children. It had a significant toxicity profile and a high incidence of adverse symptoms which required close supervision, and a prompt dose reduction or drug exchange.

Published
2010

30. ISSCR Guidelines for Stem Cell Research and Clinical Translation: The 2021 update

Author

Lovell-Badge, R, Anthony, E, Barker, RA, Bubela, T, Brivanlou, AH, Carpenter, M, Charo, RA, Clark, A, Clayton, E, Cong, Y, Daley, GQ, Fu, J, Fujita, M, Greenfield, A, Goldman, SA, Hill, L, Hyun, I, Isasi, R, Kahn, J, Kato, K, Kim, J-S, Kimmelman, J, Knoblich, JA, Mathews, D, Montserrat, N, Mosher, J, Munsie, M, Nakauchi, H, Naldini, L, Naughton, G, Niakan, K, Ogbogu, U, Pedersen, R, Rivron, N, Rooke, H, Rossant, J, Round, J, Saitou, M, Sipp, D, Steffann, J, Sugarman, J, Surani, A, Takahashi, J, Tang, F, Turner, L, Zettler, PJ, Zhai, X, Lovell-Badge, R, Anthony, E, Barker, RA, Bubela, T, Brivanlou, AH, Carpenter, M, Charo, RA, Clark, A, Clayton, E, Cong, Y, Daley, GQ, Fu, J, Fujita, M, Greenfield, A, Goldman, SA, Hill, L, Hyun, I, Isasi, R, Kahn, J, Kato, K, Kim, J-S, Kimmelman, J, Knoblich, JA, Mathews, D, Montserrat, N, Mosher, J, Munsie, M, Nakauchi, H, Naldini, L, Naughton, G, Niakan, K, Ogbogu, U, Pedersen, R, Rivron, N, Rooke, H, Rossant, J, Round, J, Saitou, M, Sipp, D, Steffann, J, Sugarman, J, Surani, A, Takahashi, J, Tang, F, Turner, L, Zettler, PJ, and Zhai, X

Abstract

The International Society for Stem Cell Research has updated its Guidelines for Stem Cell Research and Clinical Translation in order to address advances in stem cell science and other relevant fields, together with the associated ethical, social, and policy issues that have arisen since the last update in 2016. While growing to encompass the evolving science, clinical applications of stem cells, and the increasingly complex implications of stem cell research for society, the basic principles underlying the Guidelines remain unchanged, and they will continue to serve as the standard for the field and as a resource for scientists, regulators, funders, physicians, and members of the public, including patients. A summary of the key updates and issues is presented here.

Published
2021

31. Thirty critical research needs for managing an ecologically and culturally unique remote marine environment: The Kimberley region of Western Australia

Author

Cvitanovic, C, Mackay, M, Kelly, R, Wilson, SK, Waples, K, Nash, KL, van Putten, EI, Field, S, Botterill-James, T, Austin, BJ, Beckley, LE, Boschetti, F, Depczynski, M, Dobbs, RJ, Evans, RD, Feng, M, Goater, RK, Halford, AR, Kendrick, A, Kendrick, G, Lincoln, GDB, Ludgerus, LJ, Lowe, RJ, McMahon, K, Munro, JK, Newman, SJ, Nutt, C, Pearson, L, O'Leary, MJ, Richards, ZT, Robbins, WD, Rogers, DI, Salgado Kent, CP, Schoepf, V, Travers, MJ, Thums, M, Tucker, AD, Underwood, JN, Whiting, S, Mathews, D, Cvitanovic, C, Mackay, M, Kelly, R, Wilson, SK, Waples, K, Nash, KL, van Putten, EI, Field, S, Botterill-James, T, Austin, BJ, Beckley, LE, Boschetti, F, Depczynski, M, Dobbs, RJ, Evans, RD, Feng, M, Goater, RK, Halford, AR, Kendrick, A, Kendrick, G, Lincoln, GDB, Ludgerus, LJ, Lowe, RJ, McMahon, K, Munro, JK, Newman, SJ, Nutt, C, Pearson, L, O'Leary, MJ, Richards, ZT, Robbins, WD, Rogers, DI, Salgado Kent, CP, Schoepf, V, Travers, MJ, Thums, M, Tucker, AD, Underwood, JN, Whiting, S, and Mathews, D

Abstract

The Kimberley marine environment in Western Australia is widely recognised for its outstanding natural features, vast and remote sea and landscapes, and Indigenous cultural significance. To ensure that adequate baseline information is available to understand, monitor and manage this remote and relatively understudied region, scientific exploration was undertaken between 2012 and 2018 as part of the Kimberley Marine Research Program (KMRP). Whilst this program generated significant amounts of new knowledge about the region, important research gaps remain, that if answered, should improve the capacity of managers to conserve the region's values more effectively. Here, we apply established participatory horizon scanning methods to draw on the expertise and understanding of 24 scientists and 18 managers (12 natural resource managers and 6 healthy country managers) involved in the KMRP, and assess their most essential remaining research needs for informing management of the region. Through this process, we identify a total of 184 research questions spanning seven themes: (i) habitats, (ii) fauna, (iii) ecological processes, (iv) pressures, (v) management, (vi) oceanography, and (vii) geomorphology. Of the 184 questions that formed the basis of this study, 29% related to the theme of ‘management’, followed by questions relating to ‘fauna’ (21%) and ‘pressures’ (20%). Questions assigned to the theme of ‘habitats’ (13%), ‘ecological processes’ (10%), and ‘oceanography’ (6%) were less common, whilst questions that related to ‘geomorphology’ only constituted 1% of all questions provided by study participants. Subtle differences in the types of questions posed by the scientist and manager groups were also evident, with questions relating to ‘ecological process’ and ‘oceanography’ overwhelmingly provided by scientists; questions in the themes ‘fauna’ and ‘management’ were mainly provided by Healthy Country Managers; and questions posed by natural resource managers were distribu

Published
2021

38. Chloride versus sulfate salinity effects on alfalfa shoot growth and ionic balance

Author

Soltanpour, P.N., Al-Wardy, M.M., Ippolito, J.A., Rodriquez, J.B., Self, J., Gillaume, M., and Mathews, D.

Subjects
Alfalfa -- Growth, Soils, Salts in -- Physiological aspects, Soil fertility -- Research, Chlorides -- Environmental aspects, Sulfides -- Environmental aspects, Earth sciences
Abstract

Information on Cl vs. S[O.sub.4] salinity effects on alfalfa (Medicago sativa L) dry matter yield (DM) and cation-anion balance is limited. Consequently, we compared Cl and S[O.sub.4] salinity effects on shoot DM and ionic balance for Archer and Ladak varieties of alfalfa. A modified, flowing Hoagland solution, buffered with CaC[O.sub.3], was the control: electrical conductivity (EC) = 0.7 dS [m.sup.-1]. Chloride or S[O.sub.4] salts of K, Ca and Mg were added to the control to get iso-EC solutions (2-11 dS [m.sup.-1]). Shoot cations (Ca, Mg, K, and Na) and their sum (C), anions (Cl, S[O.sub.4], N[O.sub.3] and [H.sub.2]P[O.sub.4]) and their sum (A), and DM were measured. Organic anions ((C-A) were calculated in [mmol.sub.c] [kg.sup.-1]. The calculated hydroponic osmotic potentials ([Pi]) were from 1.4 to 1.7 times lower in Cl than in iso-conductive S[O.sub.4] solutions. As EC increased, DM decreased equally for both varieties in iso-conductive Cl and S[O.sub.4] solutions. Solution [Pi] decreased, shoot [H.sub.2]P[O.sub.4] declined below its critical level of 65 [mmol.sub.c] [kg.sup.-1], shoot C stayed constant, shoot A increased; and therefore, shoot C-A decreased. The shoot C-A was lower in S[O.sub.4] solutions. In Cl solutions shoot Cl exceeded the toxic level of 282 [mmol.sub.c] [kg.sup.-1]. The DM was correlated positively with [Pi], shoot [H.sub.2]P[O.sub.4], and C-A, and negatively with shoot Cl and S[O.sub.4]. We conclude that (i) iso-conductive Cl or S[O.sub.4] salinity depress DM equally, but isoosmotic S[O.sub.4] is more depressive; (ii) the yield declines are probably due to any one or a combination of low water potential, toxic shoot Cl and possibly S[O.sub.4], and deficiencies of shoot P and organic anions; (iii) neutral organic solutes were probably responsible for osmotic adjustment, since total ionic charges (2C) stayed constant; and (iv) P deficiency occurred despite high solution P, due to Cl or S[O.sub.4] competition in saline environments.

Published
1999

43. A blood-based signature of cerebrospinal fluid A beta(1-42) status

Author

Goudey, B., Fung, B.J., Schieber, C., Faux, N.G., Weiner, M.W., Aisen, P., Petersen, R., Jack, C.R., Jagust, W., Trojanowki, J.Q., Toga, A.W., Beckett, L., Green, R.C., Saykin, A.J., Morris, J., Shaw, L.M., Kaye, J., Quinn, J., Silbert, L., Lind, B., Carter, R., Dolen, S., Schneider, L.S., Pawluczyk, S., Beccera, M., Teodoro, L., Spann, B.M., Brewer, J., Vanderswag, H., Fleisher, A., Heidebrink, J.L., Lord, J.L., Mason, S.S., Albers, C.S., Knopman, D., Johnson, K., Doody, R.S., Villanueva-Meyer, J., Chowdhury, M., Rountree, S., Dang, M., Stern, Y., Honig, L.S., Bell, K.L., Ances, B., Morris, J.C., Carroll, M., Creech, M.L., Franklin, E., Mintun, M.A., Schneider, S., Oliver, A., Marson, D., Griffth, R., Clark, D., Geldmacher, D., Brockington, J., Roberson, E., Natelson Love, M., Grossman, H., Mitsis, E., Shah, R.C., deToledo-Morrell, L., Duara, R., Varon, D., Greig, M.T., Roberts, P., Albert, M., Onyike, C., D'Agostino, D., Kielb, S., Galvin, J.E., Cerbone, B., Michel, C.A., Pogorelec, D.M., Rusinek, H., Leon, M.J. de, Glodzik, L., De Santi, S., Doraiswamy, P.M., Petrella, J.R., Borges-Neto, S., Wong, T.Z., Coleman, E., Smith, C.D., Jicha, G., Hardy, P., Sinha, P., Oates, E., Conrad, G., Porsteinsson, A.P., Goldstein, B.S., Martin, K., Makino, K.M., Ismail, M.S., Brand, C., Mulnard, R.A., Thai, G., McAdams-Ortiz, C., Womack, K., Mathews, D., Quiceno, M., Levey, A.I., Lah, J.J., Cellar, J.S., Burns, J.M., Swerdlow, R.H., Brooks, W.M., Apostolova, L., Tingus, K., Woo, E., Silverman, D.H.S., Lu, P.H., Bartzokis, G., Graff-Radford, N.R., Parftt, F., Kendall, T., Johnson, H., Farlow, M.R., Hake, A.M., Matthews, B.R., Brosch, J.R., Herring, S., Hunt, C., Dyck, .H. van, Carson, R.E., MacAvoy, M.G., Varma, P., Chertkow, H., Bergman, H., Hosein, C., Black, S., Stefanovic, B., Caldwell, C., Hsiung, Ging-Yuek Robin, Feldman, H., Mudge, B., Assaly, M., Finger, E., Pasternack, S., Rachisky, I., Trost, D., Kertesz, A., Bernick, C., Munic, D., Mesulam, M.-M., Lipowski, K., Weintraub, S., Bonakdarpour, B., Kerwin, D., Wu, C.-K., Johnson, N., Sadowsky, C., Villena, T., Turner, R.S., Reynolds, B., Sperling, R.A., Johnson, K.A., Marshall, G., Yesavage, J., Taylor, J.L., Lane, B., Rosen, A., Tinklenberg, J., Sabbagh, M.N., Belden, C.M., Jacobson, S.A., Sirrel, S.A., Kowall, N., Killiany, R., Budson, A.E., Norbash, A., Johnson, P.L., Obisesan, T.O., Wolday, S., Allard, J., Lerner, A., Ogrocki, P., Tatsuoka, C., Fatica, P., Fletcher, E., Maillard, P., Olichney, J., DeCarli, C., Carmichael, O., Kittur, S., Borrie, M., Lee, T.-Y., Bartha, R., Johnson, S., Asthana, S., Carlsson, C.M., Potkin, S.G., Preda, A., Nguyen, D., Tariot, P., Burke, A., Trncic, N., Reeder, S., Bates, V., Capote, H., Rainka, M., Scharre, D.W., Kataki, M., Adeli, A., Zimmerman, E.A., Celmins, D., Brown, A.D., Pearlson, G.D., Blank, K., Anderson, K., Flashman, L.A., Seltzer, M., Hynes, M.L., Santulli, R.B., Sink, K.M., Gordineer, L., Williamson, J.D., Garg, P., Watkins, F., Ott, B.R., Querfurth, H., Tremont, G., Salloway, S., Malloy, P., Correia, S., Rosen, H.J., Miller, B.L., Perry, D., Mintzer, J., Spicer, K., Bachman, D., Pomara, N., Hernando, R., Sarrael, A., Relkin, N., Chaing, G., Lin, M., Ravdin, L., Smith, A., Raj, B.A., Fargher, K., Saykin, A., Nho, K., Kling, M., Toledo, J., Shaw, L., Trojanowski, J., Farrer, L., Kastsenmueller, G., Arnold, M., Wishart, D., Wurtz, P., Bhattcharyya, S., Duijin, C. van, Mangravite, L., Han, X., Hankemeier, T., Fiehn, O., Barupal, D., Thiele, I., Heinken, A., Meikle, P., Price, N., Funk, C., Jia, W., Kueider-Paisley, A., Tenebaum, J., Black, C., Moseley, A., Thompson, W., Mahmoudiandehkorki, S., Baillie, R., Welsh-Bohmer, K., Plassman, B., and Epidemiology

Subjects
Male, 0301 basic medicine, Apolipoprotein E, Oncology, medicine.medical_specialty, Amyloid, Amyloid beta, lcsh:Medicine, Article, 03 medical and health sciences, Apolipoproteins E, 0302 clinical medicine, Cerebrospinal fluid, Alzheimer Disease, Predictive Value of Tests, Internal medicine, medicine, Humans, Dementia, Cognitive decline, lcsh:Science, Aged, Aged, 80 and over, Amyloid beta-Peptides, Multidisciplinary, biology, Chemokine CCL26, business.industry, lcsh:R, Alzheimer’s Disease Metabolomics Consortium, Alzheimer’s Disease Neuroimaging Initiative, medicine.disease, Peptide Fragments, 3. Good health, 030104 developmental biology, biology.protein, Chromogranin A, Female, lcsh:Q, Alzheimer's disease, business, Biomarkers, 030217 neurology & neurosurgery, Alzheimer's Disease Neuroimaging Initiative
Abstract

It is increasingly recognized that Alzheimer’s disease (AD) exists before dementia is present and that shifts in amyloid beta occur long before clinical symptoms can be detected. Early detection of these molecular changes is a key aspect for the success of interventions aimed at slowing down rates of cognitive decline. Recent evidence indicates that of the two established methods for measuring amyloid, a decrease in cerebrospinal fluid (CSF) amyloid β1−42 (Aβ1−42) may be an earlier indicator of Alzheimer’s disease risk than measures of amyloid obtained from Positron Emission Tomography (PET). However, CSF collection is highly invasive and expensive. In contrast, blood collection is routinely performed, minimally invasive and cheap. In this work, we develop a blood-based signature that can provide a cheap and minimally invasive estimation of an individual’s CSF amyloid status using a machine learning approach. We show that a Random Forest model derived from plasma analytes can accurately predict subjects as having abnormal (low) CSF Aβ1−42 levels indicative of AD risk (0.84 AUC, 0.78 sensitivity, and 0.73 specificity). Refinement of the modeling indicates that only APOEε4 carrier status and four plasma analytes (CGA, Aβ1−42, Eotaxin 3, APOE) are required to achieve a high level of accuracy. Furthermore, we show across an independent validation cohort that individuals with predicted abnormal CSF Aβ1−42 levels transitioned to an AD diagnosis over 120 months significantly faster than those with predicted normal CSF Aβ1−42 levels and that the resulting model also validates reasonably across PET Aβ1−42 status (0.78 AUC). This is the first study to show that a machine learning approach, using plasma protein levels, age and APOEε4 carrier status, is able to predict CSF Aβ1−42 status, the earliest risk indicator for AD, with high accuracy.

Published
2019
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46. Uncovering the heterogeneity and temporal complexity of neurodegenerative diseases with Subtype and Stage Inference

Author

Young, A. L., Marinescu, R. V., Oxtoby, N. P., Bocchetta, M., Yong, K., Firth, N. C., Cash, D. M., Thomas, D. L., Dick, K. M., Cardoso, J., van Swieten, J., Borroni, B., Galimberti, D., Masellis, M., Tartaglia, M. C., Rowe, J. B., Graff, C., Tagliavini, F., Frisoni, G. B., Laforce, R., Finger, E., de Mendonca, A., Sorbi, S., Warren, J. D., Crutch, S., Fox, N. C., Ourselin, S., Schott, J. M., Rohrer, J. D., Alexander, D. C., Andersson, C., Archetti, S., Arighi, A., Benussi, L., Binetti, G., Black, S., Cosseddu, M., Fallstrom, M., Ferreira, C., Fenoglio, C., Freedman, M., Fumagalli, G. G., Gazzina, S., Ghidoni, R., Grisoli, M., Jelic, V., Jiskoot, L., Keren, R., Lombardi, G., Maruta, C., Meeter, L., Mead, S., van Minkelen, R., Nacmias, B., Oijerstedt, L., Padovani, A., Panman, J., Pievani, M., Polito, C., Premi, E., Prioni, S., Rademakers, R., Redaelli, V., Rogaeva, E., Rossi, G., Rossor, M., Scarpini, E., Tang-Wai, D., Thonberg, H., Tiraboschi, P., Verdelho, A., Weiner, M. W., Aisen, P., Petersen, R., Jack, C. R., Jagust, W., Trojanowki, J. Q., Toga, A. W., Beckett, L., Green, R. C., Saykin, A. J., Morris, J., Shaw, L. M., Khachaturian, Z., Sorensen, G., Kuller, L., Raichle, M., Paul, S., Davies, P., Fillit, H., Hefti, F., Holtzman, D., Mesulam, M. M., Potter, W., Snyder, P., Schwartz, A., Montine, T., Thomas, R. G., Donohue, M., Walter, S., Gessert, D., Sather, T., Jiminez, G., Harvey, D., Bernstein, M., Thompson, P., Schuff, N., Borowski, B., Gunter, J., Senjem, M., Vemuri, P., Jones, D., Kantarci, K., Ward, C., Koeppe, R. A., Foster, N., Reiman, E. M., Chen, K., Mathis, C., Landau, S., Cairns, N. J., Householder, E., Taylor-Reinwald, L., Lee, V., Korecka, M., Figurski, M., Crawford, K., Neu, S., Foroud, T. M., Potkin, S., Shen, L., Faber, K., Kim, S., Nho, K., Thal, L., Buckholtz, N., Albert, M., Frank, R., Hsiao, J., Kaye, J., Quinn, J., Lind, B., Carter, R., Dolen, S., Schneider, L. S., Pawluczyk, S., Beccera, M., Teodoro, L., Spann, B. M., Brewer, J., Vanderswag, H., Fleisher, A., Heidebrink, J. L., Lord, J. L., Mason, S. S., Albers, C. S., Knopman, D., Johnson, K., Doody, R. S., Villanueva-Meyer, J., Chowdhury, M., Rountree, S., Dang, M., Stern, Y., Honig, L. S., Bell, K. L., Ances, B., Carroll, M., Leon, S., Mintun, M. A., Schneider, S., Oliver, A., Marson, D., Griffith, R., Clark, D., Geldmacher, D., Brockington, J., Roberson, E., Grossman, H., Mitsis, E., de Toledo-Morrell, L., Shah, R. C., Duara, R., Varon, D., Greig, M. T., Roberts, P., Onyike, C., D'Agostino, D., Kielb, S., Galvin, J. E., Cerbone, B., Michel, C. A., Rusinek, H., de Leon, M. J., Glodzik, L., De Santi, S., Doraiswamy, P. M., Petrella, J. R., Wong, T. Z., Arnold, S. E., Karlawish, J. H., Wolk, D., Smith, C. D., Jicha, G., Hardy, P., Sinha, P., Oates, E., Conrad, G., Lopez, O. L., Oakley, M. A., Simpson, D. M., Porsteinsson, A. P., Goldstein, B. S., Martin, K., Makino, K. M., Ismail, M. S., Brand, C., Mulnard, R. A., Thai, G., Mc-Adams-Ortiz, C., Womack, K., Mathews, D., Quiceno, M., Diaz-Arrastia, R., King, R., Weiner, M., Martin-Cook, K., Devous, M., Levey, A. I., Lah, J. J., Cellar, J. S., Burns, J. M., Anderson, H. S., Swerdlow, R. H., Apostolova, L., Tingus, K., Woo, E., Silverman, D. H., P. H., Lu, Bartzokis, G., Graff-Radford, N. R., Parfitt, F., Kendall, T., Johnson, H., Farlow, M. R., Hake, A. M., Matthews, B. R., Herring, S., Hunt, C., van Dyck, C. H., Carson, R. E., Macavoy, M. G., Chertkow, H., Bergman, H., Hosein, C., Stefanovic, B., Caldwell, C., Hsiung, G. -Y. R., Feldman, H., Mudge, B., Assaly, M., Kertesz, A., Rogers, J., Bernick, C., Munic, D., Kerwin, D., Mesulam, M. -M., Lipowski, K., C. -K., Wu, Johnson, N., Sadowsky, C., Martinez, W., Villena, T., Turner, R. S., Reynolds, B., Sperling, R. A., Johnson, K. A., Marshall, G., Frey, M., Lane, B., Rosen, A., Tinklenberg, J., Sabbagh, M. N., Belden, C. M., Jacobson, S. A., Sirrel, S. A., Kowall, N., Killiany, R., Budson, A. E., Norbash, A., Johnson, P. L., Allard, J., Lerner, A., Ogrocki, P., Hudson, L., Fletcher, E., Carmichael, O., Olichney, J., Decarli, C., Kittur, S., Borrie, M., Lee, T. -Y., Bartha, R., Johnson, S., Asthana, S., Carlsson, C. M., Potkin, S. G., Preda, A., Nguyen, D., Tariot, P., Reeder, S., Bates, V., Capote, H., Rainka, M., Scharre, D. W., Kataki, M., Adeli, A., Zimmerman, E. A., Celmins, D., Brown, A. D., Pearlson, G. D., Blank, K., Anderson, K., Santulli, R. B., Kitzmiller, T. J., Schwartz, E. S., Sink, K. M., Williamson, J. D., Garg, P., Watkins, F., Ott, B. R., Querfurth, H., Tremont, G., Salloway, S., Malloy, P., Correia, S., Rosen, H. J., Miller, B. L., Mintzer, J., Spicer, K., Bachman, D., Pasternak, S., Rachinsky, I., Drost, D., Pomara, N., Hernando, R., Sarrael, A., Schultz, S. K., Ponto, L. L. B., Shim, H., Smith, K. E., Relkin, N., Chaing, G., Raudin, L., Smith, A., Fargher, K., Raj, B. A., Neylan, T., Grafman, J., Davis, M., Morrison, R., Hayes, J., Finley, S., Friedl, K., Fleischman, D., Arfanakis, K., James, O., Massoglia, D., Fruehling, J. J., Harding, S., Peskind, E. R., Petrie, E. C., Li, G., Yesavage, J. A., Taylor, J. L., and Furst, A. J.

Published
2018

47. Application specific serial arithmetic arrays

Author

Winters, K, Mathews, D, and Thompson, T

Subjects
Solid-State Physics
Abstract

High performance systolic arrays of serial-parallel multiplier elements may be rapidly constructed for specific applications by applying hardware description language techniques to a library of full-custom CMOS building blocks. Single clock pre-charged circuits have been implemented for these arrays at clock rates in excess of 100 Mhz using economical 2-micron (minimum feature size) CMOS processes, which may be quickly configured for a variety of applications. A number of application-specific arrays are presented, including a 2-D convolver for image processing, an integer polynomial solver, and a finite-field polynomial solver.

Published
1990

48. Using Nab to determine correlations in unpolarized neutron decay

Author

Broussard, L. J., primary, Baeßler, S., additional, Bailey, T. L., additional, Birge, N., additional, Bowman, J. D., additional, Crawford, C. B., additional, Cude-Woods, C., additional, Fellers, D. E., additional, Fomin, N., additional, Frlež, E., additional, Gericke, M. T. W., additional, Hayen, L., additional, Jezghani, A. P., additional, Li, H., additional, Macsai, N., additional, Makela, M. F., additional, Mammei, R. R., additional, Mathews, D., additional, McGaughey, P. L., additional, Mueller, P. E., additional, Počanić, D., additional, Royse, C. A., additional, Salas-Bacci, A., additional, Sjue, S. K. L., additional, Ramsey, J. C., additional, Severijns, N., additional, Smith, E. C., additional, Wexler, J., additional, Whitehead, R. A., additional, Young, A. R., additional, and Zeck, B. A., additional

Published
2018
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