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1. 'Birds in the Clouds': Adventures in Data Engineering

Author

Cherel, N., Reesman, J., Sahuguet, A., Auer, T., and Fink, D.

Subjects
Computer Science - Computers and Society
Abstract

Leveraging their eBird crowdsourcing project, the Cornell Lab of Ornithology generates sophisticated Spatio-Temporal Exploratory Model (STEM) maps of bird migrations. Such maps are highly relevant for both scientific and educational purposes, but creating them requires advanced modeling techniques that rely on long and potentially expensive computations. In this paper, we share our experience porting the eBird STEM data pipeline from a physical cluster to the cloud, providing a seamless deployment at a lower cost. Using open source tools and cloud "marketplaces", we managed to divide the operating costs by a factor of 6, making it possible to scale our pipeline on a research budget., Comment: Presented at the Data For Good Exchange 2017

Published
2017

3. The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)

Author

Poldrack, R, Markiewicz, C, Appelhoff, S, Ashar, Y, Auer, T, Baillet, S, Bansal, S, Beltrachini, L, Benar, C, Bertazzoli, G, Bhogawar, S, Blair, R, Bortoletto, M, Boudreau, M, Brooks, T, Calhoun, V, Castelli, F, Clement, P, Cohen, A, Cohen-Adad, J, D'Ambrosio, S, de Hollander, G, de la Iglesia-Vayá, M, de la Vega, A, Delorme, A, Devinsky, O, Draschkow, D, Duff, E, Dupre, E, Earl, E, Esteban, O, Feingold, F, Flandin, G, Galassi, A, Gallitto, G, Ganz, M, Gau, R, Gholam, J, Ghosh, S, Giacomel, A, Gillman, A, Gleeson, P, Gramfort, A, Guay, S, Guidali, G, Halchenko, Y, Handwerker, D, Hardcastle, N, Herholz, P, Hermes, D, Honey, C, Innis, R, Ioanas, H, Jahn, A, Karakuzu, A, Keator, D, Kiar, G, Kincses, B, Laird, A, Lau, J, Lazari, A, Legarreta, J, Li, A, Li, X, Love, B, Lu, H, Marcantoni, E, Maumet, C, Mazzamuto, G, Meisler, S, Mikkelsen, M, Mutsaerts, H, Nichols, T, Nikolaidis, A, Nilsonne, G, Niso, G, Norgaard, M, Okell, T, Oostenveld, R, Ort, E, Park, P, Pawlik, M, Pernet, C, Pestilli, F, Petr, J, Phillips, C, Poline, J, Pollonini, L, Raamana, P, Ritter, P, Rizzo, G, Robbins, K, Rockhill, A, Rogers, C, Rokem, A, Rorden, C, Routier, A, Saborit-Torres, J, Salo, T, Schirner, M, Smith, R, Spisak, T, Sprenger, J, Swann, N, Szinte, M, Takerkart, S, Thirion, B, Thomas, A, Torabian, S, Varoquaux, G, Voytek, B, Welzel, J, Wilson, M, Yarkoni, T, Gorgolewski, K, Poldrack, Russell A., Markiewicz, Christopher J., Appelhoff, Stefan, Ashar, Yoni K., Auer, Tibor, Baillet, Sylvain, Bansal, Shashank, Beltrachini, Leandro, Benar, Christian G., Bertazzoli, Giacomo, Bhogawar, Suyash, Blair, Ross W., Bortoletto, Marta, Boudreau, Mathieu, Brooks, Teon L., Calhoun, Vince D., Castelli, Filippo Maria, Clement, Patricia, Cohen, Alexander L., Cohen-Adad, Julien, D'Ambrosio, Sasha, de Hollander, Gilles, de la Iglesia-Vayá, María, de la Vega, Alejandro, Delorme, Arnaud, Devinsky, Orrin, Draschkow, Dejan, Duff, Eugene Paul, DuPre, Elizabeth, Earl, Eric, Esteban, Oscar, Feingold, Franklin W., Flandin, Guillaume, Galassi, Anthony, Gallitto, Giuseppe, Ganz, Melanie, Gau, Rémi, Gholam, James, Ghosh, Satrajit S., Giacomel, Alessio, Gillman, Ashley G., Gleeson, Padraig, Gramfort, Alexandre, Guay, Samuel, Guidali, Giacomo, Halchenko, Yaroslav O., Handwerker, Daniel A., Hardcastle, Nell, Herholz, Peer, Hermes, Dora, Honey, Christopher J., Innis, Robert B., Ioanas, Horea-Ioan, Jahn, Andrew, Karakuzu, Agah, Keator, David B., Kiar, Gregory, Kincses, Balint, Laird, Angela R., Lau, Jonathan C., Lazari, Alberto, Legarreta, Jon Haitz, Li, Adam, Li, Xiangrui, Love, Bradley C., Lu, Hanzhang, Marcantoni, Eleonora, Maumet, Camille, Mazzamuto, Giacomo, Meisler, Steven L., Mikkelsen, Mark, Mutsaerts, Henk, Nichols, Thomas E., Nikolaidis, Aki, Nilsonne, Gustav, Niso, Guiomar, Norgaard, Martin, Okell, Thomas W., Oostenveld, Robert, Ort, Eduard, Park, Patrick J., Pawlik, Mateusz, Pernet, Cyril R., Pestilli, Franco, Petr, Jan, Phillips, Christophe, Poline, Jean-Baptiste, Pollonini, Luca, Raamana, Pradeep Reddy, Ritter, Petra, Rizzo, Gaia, Robbins, Kay A., Rockhill, Alexander P., Rogers, Christine, Rokem, Ariel, Rorden, Chris, Routier, Alexandre, Saborit-Torres, Jose Manuel, Salo, Taylor, Schirner, Michael, Smith, Robert E., Spisak, Tamas, Sprenger, Julia, Swann, Nicole C., Szinte, Martin, Takerkart, Sylvain, Thirion, Bertrand, Thomas, Adam G., Torabian, Sajjad, Varoquaux, Gael, Voytek, Bradley, Welzel, Julius, Wilson, Martin, Yarkoni, Tal, Gorgolewski, Krzysztof J., Poldrack, R, Markiewicz, C, Appelhoff, S, Ashar, Y, Auer, T, Baillet, S, Bansal, S, Beltrachini, L, Benar, C, Bertazzoli, G, Bhogawar, S, Blair, R, Bortoletto, M, Boudreau, M, Brooks, T, Calhoun, V, Castelli, F, Clement, P, Cohen, A, Cohen-Adad, J, D'Ambrosio, S, de Hollander, G, de la Iglesia-Vayá, M, de la Vega, A, Delorme, A, Devinsky, O, Draschkow, D, Duff, E, Dupre, E, Earl, E, Esteban, O, Feingold, F, Flandin, G, Galassi, A, Gallitto, G, Ganz, M, Gau, R, Gholam, J, Ghosh, S, Giacomel, A, Gillman, A, Gleeson, P, Gramfort, A, Guay, S, Guidali, G, Halchenko, Y, Handwerker, D, Hardcastle, N, Herholz, P, Hermes, D, Honey, C, Innis, R, Ioanas, H, Jahn, A, Karakuzu, A, Keator, D, Kiar, G, Kincses, B, Laird, A, Lau, J, Lazari, A, Legarreta, J, Li, A, Li, X, Love, B, Lu, H, Marcantoni, E, Maumet, C, Mazzamuto, G, Meisler, S, Mikkelsen, M, Mutsaerts, H, Nichols, T, Nikolaidis, A, Nilsonne, G, Niso, G, Norgaard, M, Okell, T, Oostenveld, R, Ort, E, Park, P, Pawlik, M, Pernet, C, Pestilli, F, Petr, J, Phillips, C, Poline, J, Pollonini, L, Raamana, P, Ritter, P, Rizzo, G, Robbins, K, Rockhill, A, Rogers, C, Rokem, A, Rorden, C, Routier, A, Saborit-Torres, J, Salo, T, Schirner, M, Smith, R, Spisak, T, Sprenger, J, Swann, N, Szinte, M, Takerkart, S, Thirion, B, Thomas, A, Torabian, S, Varoquaux, G, Voytek, B, Welzel, J, Wilson, M, Yarkoni, T, Gorgolewski, K, Poldrack, Russell A., Markiewicz, Christopher J., Appelhoff, Stefan, Ashar, Yoni K., Auer, Tibor, Baillet, Sylvain, Bansal, Shashank, Beltrachini, Leandro, Benar, Christian G., Bertazzoli, Giacomo, Bhogawar, Suyash, Blair, Ross W., Bortoletto, Marta, Boudreau, Mathieu, Brooks, Teon L., Calhoun, Vince D., Castelli, Filippo Maria, Clement, Patricia, Cohen, Alexander L., Cohen-Adad, Julien, D'Ambrosio, Sasha, de Hollander, Gilles, de la Iglesia-Vayá, María, de la Vega, Alejandro, Delorme, Arnaud, Devinsky, Orrin, Draschkow, Dejan, Duff, Eugene Paul, DuPre, Elizabeth, Earl, Eric, Esteban, Oscar, Feingold, Franklin W., Flandin, Guillaume, Galassi, Anthony, Gallitto, Giuseppe, Ganz, Melanie, Gau, Rémi, Gholam, James, Ghosh, Satrajit S., Giacomel, Alessio, Gillman, Ashley G., Gleeson, Padraig, Gramfort, Alexandre, Guay, Samuel, Guidali, Giacomo, Halchenko, Yaroslav O., Handwerker, Daniel A., Hardcastle, Nell, Herholz, Peer, Hermes, Dora, Honey, Christopher J., Innis, Robert B., Ioanas, Horea-Ioan, Jahn, Andrew, Karakuzu, Agah, Keator, David B., Kiar, Gregory, Kincses, Balint, Laird, Angela R., Lau, Jonathan C., Lazari, Alberto, Legarreta, Jon Haitz, Li, Adam, Li, Xiangrui, Love, Bradley C., Lu, Hanzhang, Marcantoni, Eleonora, Maumet, Camille, Mazzamuto, Giacomo, Meisler, Steven L., Mikkelsen, Mark, Mutsaerts, Henk, Nichols, Thomas E., Nikolaidis, Aki, Nilsonne, Gustav, Niso, Guiomar, Norgaard, Martin, Okell, Thomas W., Oostenveld, Robert, Ort, Eduard, Park, Patrick J., Pawlik, Mateusz, Pernet, Cyril R., Pestilli, Franco, Petr, Jan, Phillips, Christophe, Poline, Jean-Baptiste, Pollonini, Luca, Raamana, Pradeep Reddy, Ritter, Petra, Rizzo, Gaia, Robbins, Kay A., Rockhill, Alexander P., Rogers, Christine, Rokem, Ariel, Rorden, Chris, Routier, Alexandre, Saborit-Torres, Jose Manuel, Salo, Taylor, Schirner, Michael, Smith, Robert E., Spisak, Tamas, Sprenger, Julia, Swann, Nicole C., Szinte, Martin, Takerkart, Sylvain, Thirion, Bertrand, Thomas, Adam G., Torabian, Sajjad, Varoquaux, Gael, Voytek, Bradley, Welzel, Julius, Wilson, Martin, Yarkoni, Tal, and Gorgolewski, Krzysztof J.

Abstract

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.

Published
2024

4. The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)

Author

Poldrack, R. A., Markiewicz, C. J., Appelhoff, S., Ashar, Y. K., Auer, T., Baillet, S., Bansal, S., Beltrachini, L., Bertazzoli, G., Bhogawar, S., Blair, R. W., Bortoletto, M., Boudreau, M., Brooks, T. L., Bénar, C. G., Calhoun, V. D., Castelli, F. M., Clement, P., Cohen, A. L., Cohen-Adad, J., Dambrosio, S., Delorme, A., Devinsky, O., Draschkow, D., Duff, E. P., Dupre, E., Earl, E., Esteban, O., Feingold, F. W., Flandin, G., Galassi, A., Gallitto, G., Ganz, M., Gholam, J., Ghosh, S. S., Giacomel, A., Gillman, A. G., Gleeson, P., Gramfort, A., Guay, S., Guidali, G., Halchenko, Y. O., Handwerker, D. A., Hardcastle, N., Herholz, P., Hermes, D., Honey, C. J., Innis, R. B., Ioanas, H.-I., Jahn, A., Karakuzu, A., Keator, D. B., Kiar, G., Kincses, B., Laird, A. R., Lau, J. C., Lazari, A., Legarreta, J. H., Li, A., Li, X., Love, B. C., Lu, H., Maumet, C., Mazzamuto, G., Meisler, S. L., Mikkelsen, M., Mutsaerts, H., Nichols, T. E., Nikolaidis, A., Nilsonne, G., Niso, G., Norgaard, M., Okell, T. W., Oostenveld, R., Ort, E., Park, P. J., Pawlik, M., Pernet, C. R., Pestilli, F., (0000-0002-3201-6002) Petr, J., Phillips, C., Poline, J.-B., Pollonini, L., Raamana, P. R., Ritter, P., Rizzo, G., Robbins, K. A., Rockhill, A. P., Rogers, C., Rokem, A., Rorden, C., Routier, A., Saborit-Torres, J. M., Salo, T., Schirner, M., Smith, R. E., Spisak, T., Sprenger, J., Swann, N. C., Szinte, M., Takerkart, S., Thirion, B., Thomas, A. G., Torabian, S., Varoquaux, G., Vaya, M. D. L. I., Voytek, B., Welzel, J., Wilson, M., Hollander, G., Vega, A., Gorgolewski, K. J., Poldrack, R. A., Markiewicz, C. J., Appelhoff, S., Ashar, Y. K., Auer, T., Baillet, S., Bansal, S., Beltrachini, L., Bertazzoli, G., Bhogawar, S., Blair, R. W., Bortoletto, M., Boudreau, M., Brooks, T. L., Bénar, C. G., Calhoun, V. D., Castelli, F. M., Clement, P., Cohen, A. L., Cohen-Adad, J., Dambrosio, S., Delorme, A., Devinsky, O., Draschkow, D., Duff, E. P., Dupre, E., Earl, E., Esteban, O., Feingold, F. W., Flandin, G., Galassi, A., Gallitto, G., Ganz, M., Gholam, J., Ghosh, S. S., Giacomel, A., Gillman, A. G., Gleeson, P., Gramfort, A., Guay, S., Guidali, G., Halchenko, Y. O., Handwerker, D. A., Hardcastle, N., Herholz, P., Hermes, D., Honey, C. J., Innis, R. B., Ioanas, H.-I., Jahn, A., Karakuzu, A., Keator, D. B., Kiar, G., Kincses, B., Laird, A. R., Lau, J. C., Lazari, A., Legarreta, J. H., Li, A., Li, X., Love, B. C., Lu, H., Maumet, C., Mazzamuto, G., Meisler, S. L., Mikkelsen, M., Mutsaerts, H., Nichols, T. E., Nikolaidis, A., Nilsonne, G., Niso, G., Norgaard, M., Okell, T. W., Oostenveld, R., Ort, E., Park, P. J., Pawlik, M., Pernet, C. R., Pestilli, F., (0000-0002-3201-6002) Petr, J., Phillips, C., Poline, J.-B., Pollonini, L., Raamana, P. R., Ritter, P., Rizzo, G., Robbins, K. A., Rockhill, A. P., Rogers, C., Rokem, A., Rorden, C., Routier, A., Saborit-Torres, J. M., Salo, T., Schirner, M., Smith, R. E., Spisak, T., Sprenger, J., Swann, N. C., Szinte, M., Takerkart, S., Thirion, B., Thomas, A. G., Torabian, S., Varoquaux, G., Vaya, M. D. L. I., Voytek, B., Welzel, J., Wilson, M., Hollander, G., Vega, A., and Gorgolewski, K. J.

Abstract

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, and the mechanisms by which it has been extended. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.

Published
2024

5. eBird Status and Trends

Author

Fink, D, primary, Auer, T, additional, Johnston, A, additional, Strimas-Mackey, M, additional, Ligocki, S, additional, Robinson, O, additional, Hochachka, W, additional, Jaromczyk, L, additional, Crowley, C, additional, Dunham, K, additional, Stillman, A, additional, Davies, I, additional, Rodewald, A, additional, Ruiz-Gutierrez, V, additional, and Wood, C, additional

Published
2023
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6. The Knight field and the local nuclear dipole-dipole field in an (In,Ga)As quantum dot ensemble

Author

Auer, T., Oulton, R., Bauschulte, A., Yakovlev, D. R., Bayer, M., Verbin, S. Yu., Cherbunin, R. V., Reuter, D., and Wieck, A. D.

Subjects
Condensed Matter - Other Condensed Matter
Abstract

We present a comprehensive investigation of the electron-nuclear system of negatively charged InGaAs/GaAs self-assembled quantum dots under the influence of weak external magnetic fields (up to 2 mT). We demonstrate that, in contrast to conventional semiconductor systems, these small fields have a profound influence on the electron spin dynamics, via the hyperfine interaction. Quantum dots, with their comparatively limited number of nuclei, present electron-nuclear behavior that is unique to low-dimensional systems. We show that the conventional Hanle effect used to measure electron spin relaxation times, for example, cannot be used in these systems when the spin lifetimes are long. An individual nucleus in the QD is subject to milli-Tesla effective fields, arising from the interaction with its nearest-neighbors and with the electronic Knight field. The alignment of each nucleus is influenced by application of external fields of the same magnitude. A polarized nuclear system, which may have an effective field strength of several Tesla, may easily be influenced by these milli-Tesla fields. This in turn has a dramatic effect on the electron spin dynamics, and we use this technique to gain a measure of both the dipole-dipole field and the maximum Knight field in our system, thus allowing us to estimate the maximum Overhauser field that may be generated at zero external magnetic field. We also show that one may fine-tune the angle which the Overhauser field makes with the optical axis., Comment: 13 pages, 7 figures

Published
2008
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7. Systematic study of carrier correlations in the electron-hole recombination dynamics of quantum dots

Author

Berstermann, T., Auer, T., Kurtze, H., Schwab, M., Yakovlev, D. R., Bayer, M., Wiersig, J., Gies, C., Jahnke, F., Reuter, D., and Wieck, A. D.

Subjects
Condensed Matter - Other Condensed Matter
Abstract

The ground state carrier dynamics in self-assembled (In,Ga)As/GaAs quantum dots has been studied using time-resolved photoluminescence and transmission. By varying the dot design with respect to confinement and doping, the dynamics is shown to follow in general a non-exponential decay. Only for specific conditions in regard to optical excitation and carrier population, for example, the decay can be well described by a mono-exponential form. For resonant excitation of the ground state transition a strong shortening of the luminescence decay time is observed as compared to the non-resonant case. The results are consistent with a microscopic theory that accounts for deviations from a simple two-level picture., Comment: 8 pages, 7 figures

Published
2007
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8. Radiative emission dynamics of quantum dots in a single cavity micropillar

Author

Schwab, M., Kurtze, H., Auer, T., Berstermann, T., Bayer, M., Wiersig, J., Baer, N., Gies, C., Jahnke, F., Reithmaier, J. P., Forchel, A., Benyoucef, M., and Michler, P.

Subjects
Condensed Matter - Other Condensed Matter
Abstract

The light emission of self-assembled (In,Ga)As/GaAs quantum dots embedded in single GaAs-based micropillars has been studied by time-resolved photoluminescence spectroscopy. The altered spontaneous emission is found to be accompanied by a non-exponential decay of the photoluminescence where the decay rate strongly depends on the excitation intensity. A microscopic theory of the quantum dot photon emission is used to explain both, the non-exponential decay and its intensity dependence. Also the transition from spontaneous to stimulated emission is studied., Comment: 9 pages, 6 figures, figure captions corrected

Published
2006
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9. Tailored quantum dots for entangled photon pair creation

Author

Greilich, A., Schwab, M., Berstermann, T., Auer, T., Oulton, R., Yakovlev, D. R., Bayer, M., Stavarache, V., Reuter, D., and Wieck, A.

Subjects
Physics - Optics
Abstract

We compare the asymmetry-induced exchange splitting delta_1 of the bright-exciton ground-state doublet in self-assembled (In,Ga)As/GaAs quantum dots, determined by Faraday rotation, with its homogeneous linewidth gamma, obtained from the radiative decay in time-resolved photoluminescence. Post-growth thermal annealing of the dot structures leads to a considerable increase of the homogeneous linewidth, while a strong reduction of the exchange splitting is simultaneously observed. The annealing can be tailored such that delta_1 and gamma become comparable, whereupon the carriers are still well confined. This opens the possibility to observe polarization entangled photon pairs through the biexciton decay cascade., Comment: 4 pages, 4 figures

Published
2006
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10. Millisecond spin lifetimes in quantum dots at zero applied magnetic field due to strong electron-nuclear interaction

Author

Greilich, A., Oulton, R., Verbin, S. Yu., Cherbunin, R. V., Auer, T., Yakovlev, D. R., Bayer, M., Stavarache, V., Reuter, D., and Wieck, A.

Subjects
Condensed Matter - Other Condensed Matter
Abstract

A key to achieving ultra-long electron spin memory in quantum dots (QDs) at 0~$T$ is the polarization of the nuclei, such that the electron spin is stabilized along the nuclear magnetic field. We demonstrate that spin-polarized electrons in n-doped QDs align the nuclear field via the hyperfine interaction. A feedback onto the electrons occurs, leading to stabilization of electron polarization. We suggest that the coupled electron-nuclear system forms a rigid nuclear spin polaron state as predicted by I.A.~Merkulov, for which spin memory is retained over millisecond lifetimes., Comment: 3 figures

Published
2005

14. eBird Status and Trends

Author

Fink, D, primary, Auer, T, additional, Johnston, A, additional, Strimas-Mackey, M, additional, Robinson, O, additional, Ligocki, S, additional, Hochachka, W, additional, Jaromczyk, L, additional, Rodewald, A, additional, Wood, C, additional, Davies, I, additional, and Spencer, A, additional

Published
2022
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15. Artificial intelligence-based body composition predicts postoperative complications and mortality in advanced heart failure patients receiving long-term mechanical circulatory support

Author

Just-Lauer, I A, primary, Schoenrath, F, additional, Roehrich, L, additional, Auer, T A, additional, Fehrenbach, U, additional, Potapov, E J, additional, Solowjowa, N, additional, Balzer, F, additional, Geisel, D, additional, Braun, J, additional, and Boening, G, additional

Published
2022
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17. Computer-assisted interstitial brachytherapy

Author

Freysinger, W., Hensler, E., Gunkel, A. R., Bale, R. J., Vogele, M., Martin, A., Auer, T., Eichberger, P., Szankay, A., Auberger, T., Künzel, K. H., Gaber, O., Thumfart, W. F., Lukas, P. H., Wells, William M., editor, Colchester, Alan, editor, and Delp, Scott, editor

Published
1998
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22. eBird Status and Trends

Author

Fink, D, primary, Auer, T, additional, Johnston, A, additional, Strimas-Mackey, M, additional, Robinson, O, additional, Ligocki, S, additional, Hochachka, W, additional, Jaromczyk, L, additional, Wood, C, additional, Davies, I, additional, Iliff, M, additional, and Seitz, L, additional

Published
2021
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25. Minimalinvasive Versorgung einer Herniation des linken Harnleiters ins Foramen ischiadicum majus

Author

Hager, B, Auer, T, Gutschi, S, and Pummer, K

Subjects
ddc: 610, 610 Medical sciences, Medicine
Abstract

Eine ureterale Hernie ist eine seltene Ursache für eine Obstruktion. Meist tritt sie inguinal, femoral oder obturatorisch auf. Herniationen des Harnleiters in das Foramen ischiadicum majus sind sehr selten mit etwa 50 beschriebenen Fällen seit 1947. Durch das Foramen ischiadicum majus zieht[zum vollständigen Text gelangen Sie über die oben angegebene URL], 46. Gemeinsame Tagung der Bayerischen Urologenvereinigung und der Österreichischen Gesellschaft für Urologie und Andrologie

Published
2020
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26. Centering inclusivity in the design of online conferences-An OHBM-Open Science perspective

Author

Levitis, E, van Praag, CDG, Gau, R, Heunis, S, DuPre, E, Kiar, G, Bottenhorn, KL, Glatard, T, Nikolaidis, A, Whitaker, KJ, Mancini, M, Niso, G, Afyouni, S, Alonso-Ortiz, E, Appelhoff, S, Arnatkeviciute, A, Atay, SM, Auer, T, Baracchini, G, Bayer, JMM, Beauvais, MJS, Bijsterbosch, JD, Bilgin, IP, Bollmann, S, Botvinik-Nezer, R, Bright, MG, Calhoun, VD, Chen, X, Chopra, S, Hu, C-P, Close, TG, Cookson, SL, Craddock, RC, De la Vega, A, De Leener, B, Demeter, D, Di Maio, P, Dickie, EW, Eickhoff, SB, Esteban, O, Finc, K, Frigo, M, Ganesan, S, Ganz, M, Garner, KG, Garza-Villarreal, EA, Gonzalez-Escamilla, G, Goswami, R, Griffiths, JD, Grootswagers, T, Guay, S, Guest, O, Handwerker, DA, Herholz, P, Heuer, K, Huijser, DC, Iacovella, V, Joseph, MJE, Karakuzu, A, Keator, DB, Kobeleva, X, Kumar, M, Laird, AR, Larson-Prior, LJ, Lautarescu, A, Lazari, A, Legarreta, JH, Li, X-Y, Lv, J, Mansour, SL, Meunier, D, Moraczewski, D, Nandi, T, Nastase, SA, Nau, M, Noble, S, Norgaard, M, Obungoloch, J, Oostenveld, R, Orchard, ER, Poldrack, RA, Qiu, A, Raamana, PR, Rokem, A, Rutherford, S, Sharan, M, Shaw, TB, Syeda, WT, Testerman, MM, Toro, R, Valk, SL, Van den Bossche, S, Varoquaux, G, Vasa, F, Veldsman, M, Vohryzek, J, Wagner, AS, Walsh, RJ, White, T, Wong, F-T, Xie, X, Yan, C-G, Yang, Y-F, Yee, Y, Zanitti, GE, Van Gulick, AE, Duff, E, Maumet, C, Levitis, E, van Praag, CDG, Gau, R, Heunis, S, DuPre, E, Kiar, G, Bottenhorn, KL, Glatard, T, Nikolaidis, A, Whitaker, KJ, Mancini, M, Niso, G, Afyouni, S, Alonso-Ortiz, E, Appelhoff, S, Arnatkeviciute, A, Atay, SM, Auer, T, Baracchini, G, Bayer, JMM, Beauvais, MJS, Bijsterbosch, JD, Bilgin, IP, Bollmann, S, Botvinik-Nezer, R, Bright, MG, Calhoun, VD, Chen, X, Chopra, S, Hu, C-P, Close, TG, Cookson, SL, Craddock, RC, De la Vega, A, De Leener, B, Demeter, D, Di Maio, P, Dickie, EW, Eickhoff, SB, Esteban, O, Finc, K, Frigo, M, Ganesan, S, Ganz, M, Garner, KG, Garza-Villarreal, EA, Gonzalez-Escamilla, G, Goswami, R, Griffiths, JD, Grootswagers, T, Guay, S, Guest, O, Handwerker, DA, Herholz, P, Heuer, K, Huijser, DC, Iacovella, V, Joseph, MJE, Karakuzu, A, Keator, DB, Kobeleva, X, Kumar, M, Laird, AR, Larson-Prior, LJ, Lautarescu, A, Lazari, A, Legarreta, JH, Li, X-Y, Lv, J, Mansour, SL, Meunier, D, Moraczewski, D, Nandi, T, Nastase, SA, Nau, M, Noble, S, Norgaard, M, Obungoloch, J, Oostenveld, R, Orchard, ER, Poldrack, RA, Qiu, A, Raamana, PR, Rokem, A, Rutherford, S, Sharan, M, Shaw, TB, Syeda, WT, Testerman, MM, Toro, R, Valk, SL, Van den Bossche, S, Varoquaux, G, Vasa, F, Veldsman, M, Vohryzek, J, Wagner, AS, Walsh, RJ, White, T, Wong, F-T, Xie, X, Yan, C-G, Yang, Y-F, Yee, Y, Zanitti, GE, Van Gulick, AE, Duff, E, and Maumet, C

Abstract

As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g., caregiving responsibilities. Yet, the mere existence of online conferences is no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the set-up of the conference can provide more visibility to well-established researchers and reduce opportunities for early-career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design. Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume.

Published
2021

28. eBird Status and Trends

Author

Fink, D, primary, Auer, T, additional, Johnston, A, additional, Strimas-Mackey, M, additional, Robinson, O, additional, Ligocki, S, additional, Hochachka, W, additional, Wood, C, additional, Davies, I, additional, Iliff, M, additional, and Seitz, L, additional

Published
2020
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34. Best practices for making reliable inferences from citizen science data: case study using eBird to estimate species distributions

Author

Johnston, A, Hochachka, WM, Strimas-Mackey, ME, Gutierrez, V Ruiz, Robinson, OJ, Miller, ET, Auer, T, Kelling, ST, and Fink, D

Abstract

Citizen science data are valuable for addressing a wide range of ecological research questions, and there has been a rapid increase in the scope and volume of data available. However, data from large-scale citizen science projects typically present a number of challenges that can inhibit robust ecological inferences. These challenges include: species bias, spatial bias, variation in effort, and variation in observer skill. To demonstrate key challenges in analysing citizen science data, we use the example of estimating species distributions with data from eBird, a large semi-structured citizen science project. We estimate three widely applied metrics for describing species distributions: encounter rate, occupancy probability, and relative abundance. For each method, we outline approaches for data processing and modelling that are suitable for using citizen science data for estimating species distributions. Model performance improved when data processing and analytical methods addressed the challenges arising from citizen science data. The largest gains in model performance were achieved with two key processes 1) the use of complete checklists rather than presence-only data, and 2) the use of covariates describing variation in effort and detectability for each checklist. Including these covariates accounted for heterogeneity in detectability and reporting, and resulted in substantial differences in predicted distributions. The data processing and analytical steps we outlined led to improved model performance across a range of sample sizes. When using citizen science data it is imperative to carefully consider the appropriate data processing and analytical procedures required to address the bias and variation. Here, we describe the consequences and utility of applying our suggested approach to semi-structured citizen science data to estimate species distributions. The methods we have outlined are also likely to improve other forms of inference and will enable researchers to conduct robust analyses and harness the vast ecological knowledge that exists within citizen science data.

Published
2019
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39. Optimizing the conservation of migratory species over their full annual cycle

Author

Schuster, R. (Richard), Wilson, S. (Scott), Rodewald, A.D. (Amanda D.), Arcese, P. (Peter), Fink, D. (Daniel), Auer, T. (Tom), Bennett, J.R. (Joseph R.), Schuster, R. (Richard), Wilson, S. (Scott), Rodewald, A.D. (Amanda D.), Arcese, P. (Peter), Fink, D. (Daniel), Auer, T. (Tom), and Bennett, J.R. (Joseph R.)

Abstract

Limited knowledge of the distribution, abundance, and habitat associations of migratory species hinders effective conservation actions. We use Neotropical migratory birds as a model group to compare approaches to prioritize land conservation needed to support ≥30% of the global abundances of 117 species. Specifically, we compare scenarios from spatial optimization models to achieve conservation targets by: 1) area requirements for conserving >30% abundance of each species for each week of the year independently vs. combined; 2) including vs. ignoring spatial clustering of species abundance; and 3) incorporating vs. avoiding human-dominated landscapes. Solutions integrating information across the year require 56% less area than those integrating weekly abundances, with additional reductions when shared-use landscapes are included. Although incorporating spatial population structure requires more area, geographical representation among priority sites improves substantially. These findings illustrate that globally-sourced citizen science data can elucidate key trade-offs among opportunity costs and spatiotemporal representation of conservation efforts.

Published
2019
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44. Transarterial Chemoebolization in Hepatocellular Carcinoma: A Binational Japanese-German Study

Author

Auer TA, Sofue K, Ueshima E, Rauer N, Yamaguchi T, Gebauer B, Hamm B, Murakami T, and Althoff CE

Subjects
hcc, tace, liver, hepatocellular carcinoma, interventional oncology, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Timo A Auer,1,2 Keitaro Sofue,3 Eisuke Ueshima,3 Nina Rauer,1 Takeru Yamaguchi,3 Bernhard Gebauer,1 Bernd Hamm,1 Takamichi Murakami,3 Christian E Althoff1 1Department of Radiology, Charité - University Medicine Berlin, Berlin, Germany; 2Berlin Institute of Health (BIH), Berlin, Germany; 3Department of Radiology, Kobe University Graduate School of Medicine, Kobe, JapanCorrespondence: Timo A Auer, Department of Radiology, Campus Virchow-Klinikum, Charité – Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany, Tel +49-30-450-557001, Fax +49-30-450-557901, Email timo-alexander.auer@charite.deObjective: The purpose of this study was to investigate outcomes of transarterial chemoembolization (TACE) in treating hepatocellular carcinoma (HCC) comparing the different approaches used in Germany and Japan.Methods: This binational IRB-approved retrospective dual-center study included a total of 94 HCC patients subdivided in a German and a Japanese cohort. For each patient, liver and tumor volumetry was performed using computed tomography (CT) and magnetic resonance imaging (MRI). Furthermore, a comprehensive risk profile, including body constitution and liver and kidney function was established. Primary endpoints were progression-free and overall survival (PFS/OS).Results: PFS in the German cohort was 168 vs 224d in the Japanese cohort (p=0.640). When subdivided by BCLC stage, no significant differences were reported (p=0.160– 0.429). OS was significantly longer in the Japanese cohort with 856 vs. 303d (p< 0.001). OS for BCLC A was significantly longer in the Japanese cohort (1960 vs. 428d; p< 0.001), while survival rates did not differ significantly in BCLC B (785 vs 330d; p=0.067) and C-stages (208 vs 302d; p=0.186). Older age (p=0.034), poorer liver/kidney function (p=0.025-0-035), and a higher liver/tumor ratio (p< 0.001) were found to correlate with shorter survival. ECOG scores were significantly higher in the German cohort (p=0.002).Conclusion: While OS is longer in TACE-treated patients in the Japanese cohort compared to the German cohort, the two approaches seem to be equally effective as PFS does not differ significantly. The different survival rates may be caused by the different clinical performance status of the selected collectives. In very early and early stage HCC, TACE in Japan seems to be an effective treatment option while in Germany for patients in those stages TACE remains a second-line option for patients not available for surgery or ablation.Keywords: HCC, TACE, liver, hepatocellular carcinoma, interventional oncology

Published
2022

47. 25 Years of cooling research in office buildings: Review for the integration of cooling strategies into the building façade (1990–2014)

Author

Prieto Hoces, A.I. (author), Knaack, U. (author), Klein, T. (author), Auer, T (author), Prieto Hoces, A.I. (author), Knaack, U. (author), Klein, T. (author), and Auer, T (author)

Abstract

This paper seeks to present a panorama of cooling related research in office buildings, categorising reported research experiences from the past 25 years in order to identify knowledge gaps and define current paths and trends for further exploration. The general goal behind this research is to support the design of sustainable office buildings in warm climates through examination of past experiences, thus the paper focuses on strategies at building level and specially related with façade design. Peer reviewed journal articles were selected as the source for the study, given the reliability of the information published under peer-review processes. Several queries were carried out throughout three online journal article databases (Web of Science, SCOPUS and ScienceDirect), considering published papers from 1990 onwards. The resulting article database was then explored trough descriptive analysis and in-depth review of some articles to expand on specific topics in order to thoroughly visualise scientific interest and tendencies within the field of study for the last 25 years. As results of the review it is possible to state the high current relevance of cooling research, having experienced an increase of publications under different climate contexts and varied topics ranging from passive to solar cooling, which is seen as a research field on its own. Also, in terms of research methods, software simulations seem to be the primary tool for cooling research, which makes sense for performance driven developments. On the other hand, the main knowledge gaps identified are the need for specific research regarding possibilities for application and architectural integration of cooling systems; the lack of articles addressing some specific cooling strategies, such as the use of evaporative and ground cooling; and the need for more information about the operation of cooling systems, especially taking users’ perception and their behaviour into account., Design of Constrution

Published
2017
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48. BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods

Author

Schneidman, D, Gorgolewski, KJ, Alfaro-Almagro, F, Auer, T, Bellec, P, Capota, M, Chakravarty, MM, Churchill, NW, Cohen, AL, Craddock, RC, Devenyi, GA, Eklund, A, Esteban, O, Flandin, G, Ghosh, SS, Guntupalli, JS, Jenkinson, M, Keshavan, A, Kiar, G, Liem, F, Raamana, PR, Raffelt, D, Steele, CJ, Quirion, P-O, Smith, RE, Strother, SC, Varoquaux, G, Wang, Y, Yarkoni, T, Poldrack, RA, Schneidman, D, Gorgolewski, KJ, Alfaro-Almagro, F, Auer, T, Bellec, P, Capota, M, Chakravarty, MM, Churchill, NW, Cohen, AL, Craddock, RC, Devenyi, GA, Eklund, A, Esteban, O, Flandin, G, Ghosh, SS, Guntupalli, JS, Jenkinson, M, Keshavan, A, Kiar, G, Liem, F, Raamana, PR, Raffelt, D, Steele, CJ, Quirion, P-O, Smith, RE, Strother, SC, Varoquaux, G, Wang, Y, Yarkoni, T, and Poldrack, RA

Abstract

The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). The portability of these applications (BIDS Apps) is achieved by using container technologies that encapsulate all binary and other dependencies in one convenient package. BIDS Apps run on all three major operating systems with no need for complex setup and configuration and thanks to the comprehensiveness of the BIDS standard they require little manual user input. Previous containerized data processing solutions were limited to single user environments and not compatible with most multi-tenant High Performance Computing systems. BIDS Apps overcome this limitation by taking advantage of the Singularity container technology. As a proof of concept, this work is accompanied by 22 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms.

Published
2017

49. Impairment of functional integration of the default mode network correlates with cognitive outcome at three months after stroke

Author

Dacosta-Aguayo R, Graña M, Iturria-Medina Y, Fernández-Andújar M, López-Cancio E, Cáceres C, Bargalló N, Barrios M, Clemente I, Toran P, Forés R, Dávalos A, Auer T, and Mataro M

Subjects
default mode network, graph-computation analysis, probabilistic independent component analysis, seed-based connectivity analysis
Abstract

Resting-state studies conducted with stroke patients are scarce. The study of brain activity and connectivity at rest provides a unique opportunity for the investigation of brain rewiring after stroke and plasticity changes. This study sought to identify dynamic changes in the functional organization of the default mode network (DMN) of stroke patients at three months after stroke. Eleven patients (eight male and three female; age range: 48-72) with right cortical and subcortical ischemic infarctions and 17 controls (eleven males and six females; age range: 57-69) were assessed by neurological and neuropsychological examinations and scanned with resting-state functional magnetic ressonance imaging. First, we explored group differences in functional activity within the DMN by means of probabilistic independent component analysis followed by a dual regression approach. Second, we estimated functional connectivity between 11 DMN nodes both locally by means of seed-based connectivity analysis, as well as globally by means of graph-computation analysis. We found that patients had greater DMN activity in the left precuneus and the left anterior cingulate gyrus when compared with healthy controls (P < 0.05 family-wise error corrected). Seed-based connectivity analysis showed that stroke patients had significant impairment (P = 0.014; threshold = 2.00) in the connectivity between the following five DMN nodes: left superior frontal gyrus (lSFG) and posterior cingulate cortex (t = 2.01); left parahippocampal gyrus and right superior frontal gyrus (t = 2.11); left parahippocampal gyrus and lSFG (t = 2.39); right parietal and lSFG (t = 2.29). Finally, mean path length obtained from graph-computation analysis showed positive correlations with semantic fluency test (r(s) = 0.454; P = 0.023), phonetic fluency test (r(s) = 0.523; P = 0.007) and the mini mental state examination (r(s) = 0.528; P = 0.007). In conclusion, the ability to regulate activity of the DMN appears to be a central part of normal brain function in stroke patients. Our study expands the understanding of the changes occurring in the brain after stroke providing a new avenue for investigating lesion-induced network plasticity.

Published
2015

50. Sharing brain mapping statistical results with the neuroimaging data model.

Author

Maumet, C, Auer, T, Bowring, A, Chen, G, Das, S, Flandin, G, Ghosh, S, Glatard, T, Gorgolewski, KJ, Helmer, KG, Jenkinson, M, Keator, DB, Nichols, BN, Poline, J-B, Reynolds, R, Sochat, V, Turner, J, Nichols, TE, Maumet, C, Auer, T, Bowring, A, Chen, G, Das, S, Flandin, G, Ghosh, S, Glatard, T, Gorgolewski, KJ, Helmer, KG, Jenkinson, M, Keator, DB, Nichols, BN, Poline, J-B, Reynolds, R, Sochat, V, Turner, J, and Nichols, TE

Abstract

Only a tiny fraction of the data and metadata produced by an fMRI study is finally conveyed to the community. This lack of transparency not only hinders the reproducibility of neuroimaging results but also impairs future meta-analyses. In this work we introduce NIDM-Results, a format specification providing a machine-readable description of neuroimaging statistical results along with key image data summarising the experiment. NIDM-Results provides a unified representation of mass univariate analyses including a level of detail consistent with available best practices. This standardized representation allows authors to relay methods and results in a platform-independent regularized format that is not tied to a particular neuroimaging software package. Tools are available to export NIDM-Result graphs and associated files from the widely used SPM and FSL software packages, and the NeuroVault repository can import NIDM-Results archives. The specification is publically available at: http://nidm.nidash.org/specs/nidm-results.html.

Published
2016

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