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3. Understanding Organisms Using Ecological Observatory Networks.

Author

Dantzer, B, Mabry, K, Bernhardt, J, Cox, R, Francis, C, Ghalambor, C, Hoke, K, Jha, S, Ketterson, E, Levis, N, McCain, K, Safran, R, Schwartz, T, Throop, H, Zaman, L, Martin, L, Paull, S, Patricelli, Gail, and Pinter-Wollman, Noa

Abstract

Human activities are rapidly changing ecosystems around the world. These changes have widespread implications for the preservation of biodiversity, agricultural productivity, prevalence of zoonotic diseases, and sociopolitical conflict. To understand and improve the predictive capacity for these and other biological phenomena, some scientists are now relying on observatory networks, which are often composed of systems of sensors, teams of field researchers, and databases of abiotic and biotic measurements across multiple temporal and spatial scales. One well-known example is NEON, the US-based National Ecological Observatory Network. Although NEON and similar networks have informed studies of population, community, and ecosystem ecology for years, they have been minimally used by organismal biologists. NEON provides organismal biologists, in particular those interested in NEONs focal taxa, with an unprecedented opportunity to study phenomena such as range expansions, disease epidemics, invasive species colonization, macrophysiology, and other biological processes that fundamentally involve organismal variation. Here, we use NEON as an exemplar of the promise of observatory networks for understanding the causes and consequences of morphological, behavioral, molecular, and physiological variation among individual organisms.

Published
2023

6. Variability in the analysis of a single neuroimaging dataset by many teams

Author

Botvinik-Nezer, R., Holzmeister, F., Camerer, C. F., Dreber, A., Huber, J., Johannesson, M., Kirchler, M., Iwanir, R., Mumford, J. A., Adcock, R. A., Avesani, P., Baczkowski, B. M., Bajracharya, A., Bakst, L., Ball, S., Barilari, M., Bault, N., Beaton, D., Beitner, J., Benoit, R. G., Berkers, R. M. W. J., Bhanji, J. P., Biswal, B. B., Bobadilla-Suarez, S., Bortolini, T., Bottenhorn, K. L., Bowring, A., Braem, S., Brooks, H. R., Brudner, E. G., Calderon, C. B., Camilleri, J. A., Castrellon, J. J., Cecchetti, L., Cieslik, E. C., Cole, Z. J., Collignon, O., Cox, R. W., Cunningham, W. A., Czoschke, S., Dadi, K., Davis, C. P., Luca, A. D., Delgado, M. R., Demetriou, L., Dennison, J. B., Di, X., Dickie, E. W., Dobryakova, E., Donnat, C. L., Dukart, J., Duncan, N. W., Durnez, J., Eed, A., Eickhoff, S. B., Erhart, A., Fontanesi, L., Fricke, G. M., Fu, S., Galván, A., Gau, R., Genon, S., Glatard, T., Glerean, E., Goeman, J. J., Golowin, S. A. E., González-García, C., Gorgolewski, K. J., Grady, C. L., Green, M. A., Guassi Moreira, J. F., Guest, O., Hakimi, S., Hamilton, J. P., Hancock, R., Handjaras, G., Harry, B.B., Hawco, C., Herholz, P., Herman, G., Heunis, S., Hoffstaedter, F., Hogeveen, J., Holmes, S., Hu, C. P., Huettel, S. A., Hughes, M. E., Iacovella, V., Iordan, A. D., Isager, P. M., Isik, A. I., Jahn, Andrew, Johnson, Matthew R., Johnstone, Tom, Joseph, Michael J. E., Juliano, Anthony C., Kable, Joseph W., Kassinopoulos, Michalis, Koba, Cemal, Kong, Xiang-Zhen, Koscik, Timothy R., Kucukboyaci, Nuri Erkut, Kuhl, Brice A., Kupek, Sebastian, Laird, Angela R., Lamm, Claus, Langner, Robert, Lauharatanahirun, Nina, Lee, Hongmi, Lee, Sangil, Leemans, Alexander, Leo, Andrea, Lesage, Elise, Li, Flora, Li, Monica Y. C., Lim, Cheng Phui, Lintz, Evan N., Liphardt, Schuyler W., Losecaat Vermeer, Annabel B., Love, Bradley C., Mack, Michael L., Malpica, Norberto, Marins, Theo, Maumet, Camille, McDonald, Kelsey, McGuire, Joseph T., Méndez Leal, Adriana S., Meyer, Benjamin, Meyer, Kristin N., Mihai, Glad, Mitsis, Georgios D., Moll, Jorge, Nielson, Dylan M., Nilsonne, Gustav, Notter, Michael P., Olivetti, Emanuele, Onicas, Adrian I., Papale, Paolo, Patil, Kaustubh R., Peelle, Jonathan E., Pérez, Alexandre, Pischedda, Doris, Poline, Jean-Baptiste, Prystauka,Yanina, Ray, Shruti, Reuter-Lorenz, Patricia A., Reynolds, Richard C., Ricciardi, Emiliano, Rieck, Jenny R., Rodriguez-Thompson, Anais M., Romyn, Anthony, Salo, Taylor, Samanez-Larkin, Gregory R., Sanz-Morales, Emilio, Schlichting, Margaret L., Schultz, Douglas H., Shen, Qiang, Sheridan, Margaret A., Silvers, Jennifer A., Skagerlund, Kenny, Smith, Alec, Smith, David V., Sokol-Hessner, Peter, Steinkamp, Simon R., Tashjian, Sarah M., Thirion, Bertrand, Thorp, John N., Tinghög, Gustav, Tisdall, Loreen, Tompson, Steven H., Toro-Serey, Claudio, Torre Tresols, Juan Jesus, Tozzi, Leonardo, Truong, Vuong, Turella, Luca, van ‘t Veer, Anna E., Verguts, Tom, Vettel, Jean M., Vijayarajah, Sagana, Vo, Khoi, Wall, Matthew B., Weeda, Wouter D., Weis, Susanne, White, David J., Wisniewski, David, Xifra-Porxas, Alba, Yearling, Emily A., Yoon, Sangsuk, Yuan, Rui, Yuen, Kenneth S. L., Lei Zhang, Zhang, Xu, Zosky, Joshua E., Thomas E. Nichols, Poldrack, Rusell A., Schonberg, Tom, Melero Carrasco, Helena, Botvinik-Nezer, R., Holzmeister, F., Camerer, C. F., Dreber, A., Huber, J., Johannesson, M., Kirchler, M., Iwanir, R., Mumford, J. A., Adcock, R. A., Avesani, P., Baczkowski, B. M., Bajracharya, A., Bakst, L., Ball, S., Barilari, M., Bault, N., Beaton, D., Beitner, J., Benoit, R. G., Berkers, R. M. W. J., Bhanji, J. P., Biswal, B. B., Bobadilla-Suarez, S., Bortolini, T., Bottenhorn, K. L., Bowring, A., Braem, S., Brooks, H. R., Brudner, E. G., Calderon, C. B., Camilleri, J. A., Castrellon, J. J., Cecchetti, L., Cieslik, E. C., Cole, Z. J., Collignon, O., Cox, R. W., Cunningham, W. A., Czoschke, S., Dadi, K., Davis, C. P., Luca, A. D., Delgado, M. R., Demetriou, L., Dennison, J. B., Di, X., Dickie, E. W., Dobryakova, E., Donnat, C. L., Dukart, J., Duncan, N. W., Durnez, J., Eed, A., Eickhoff, S. B., Erhart, A., Fontanesi, L., Fricke, G. M., Fu, S., Galván, A., Gau, R., Genon, S., Glatard, T., Glerean, E., Goeman, J. J., Golowin, S. A. E., González-García, C., Gorgolewski, K. J., Grady, C. L., Green, M. A., Guassi Moreira, J. F., Guest, O., Hakimi, S., Hamilton, J. P., Hancock, R., Handjaras, G., Harry, B.B., Hawco, C., Herholz, P., Herman, G., Heunis, S., Hoffstaedter, F., Hogeveen, J., Holmes, S., Hu, C. P., Huettel, S. A., Hughes, M. E., Iacovella, V., Iordan, A. D., Isager, P. M., Isik, A. I., Jahn, Andrew, Johnson, Matthew R., Johnstone, Tom, Joseph, Michael J. E., Juliano, Anthony C., Kable, Joseph W., Kassinopoulos, Michalis, Koba, Cemal, Kong, Xiang-Zhen, Koscik, Timothy R., Kucukboyaci, Nuri Erkut, Kuhl, Brice A., Kupek, Sebastian, Laird, Angela R., Lamm, Claus, Langner, Robert, Lauharatanahirun, Nina, Lee, Hongmi, Lee, Sangil, Leemans, Alexander, Leo, Andrea, Lesage, Elise, Li, Flora, Li, Monica Y. C., Lim, Cheng Phui, Lintz, Evan N., Liphardt, Schuyler W., Losecaat Vermeer, Annabel B., Love, Bradley C., Mack, Michael L., Malpica, Norberto, Marins, Theo, Maumet, Camille, McDonald, Kelsey, McGuire, Joseph T., Méndez Leal, Adriana S., Meyer, Benjamin, Meyer, Kristin N., Mihai, Glad, Mitsis, Georgios D., Moll, Jorge, Nielson, Dylan M., Nilsonne, Gustav, Notter, Michael P., Olivetti, Emanuele, Onicas, Adrian I., Papale, Paolo, Patil, Kaustubh R., Peelle, Jonathan E., Pérez, Alexandre, Pischedda, Doris, Poline, Jean-Baptiste, Prystauka,Yanina, Ray, Shruti, Reuter-Lorenz, Patricia A., Reynolds, Richard C., Ricciardi, Emiliano, Rieck, Jenny R., Rodriguez-Thompson, Anais M., Romyn, Anthony, Salo, Taylor, Samanez-Larkin, Gregory R., Sanz-Morales, Emilio, Schlichting, Margaret L., Schultz, Douglas H., Shen, Qiang, Sheridan, Margaret A., Silvers, Jennifer A., Skagerlund, Kenny, Smith, Alec, Smith, David V., Sokol-Hessner, Peter, Steinkamp, Simon R., Tashjian, Sarah M., Thirion, Bertrand, Thorp, John N., Tinghög, Gustav, Tisdall, Loreen, Tompson, Steven H., Toro-Serey, Claudio, Torre Tresols, Juan Jesus, Tozzi, Leonardo, Truong, Vuong, Turella, Luca, van ‘t Veer, Anna E., Verguts, Tom, Vettel, Jean M., Vijayarajah, Sagana, Vo, Khoi, Wall, Matthew B., Weeda, Wouter D., Weis, Susanne, White, David J., Wisniewski, David, Xifra-Porxas, Alba, Yearling, Emily A., Yoon, Sangsuk, Yuan, Rui, Yuen, Kenneth S. L., Lei Zhang, Zhang, Xu, Zosky, Joshua E., Thomas E. Nichols, Poldrack, Rusell A., Schonberg, Tom, and Melero Carrasco, Helena

Abstract

Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses1. The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. This flexibility resulted in sizeable variation in the results of hypothesis tests, even for teams whose statistical maps were highly correlated at intermediate stages of the analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Notably, a meta-analytical approach that aggregated information across teams yielded a significant consensus in activated regions. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset2–5. Our findings show that analytical flexibility can have substantial effects on scientific conclusions, and identify factors that may be related to variability in the analysis of functional magnetic resonance imaging. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for performing and reporting multiple analyses of the same data. Potential approaches that could be used to mitigate issues related to analytical variability are discussed., Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

Published
2024

14. LACITEP in Action: Primary Teacher Language Education through Partial-Immersion.

Author

Cox, R.

Abstract

The Language and Culture Initial Teacher Education: Primary (LACITEP) program in Australia, a preservice teacher education program designed to train elementary school teachers as specialists in Japanese language teaching, is described. In the partial immersion format, at least half the courses are taught in Japanese. Courses in the first year emphasize the learning process. In the second year they focus on improving learning processes, and in the third year on the sociocultural context of learning. The six curriculum components are: foundation subjects; second language teacher development; second language teaching methodology; curriculum subjects; second language enhancement subjects; and practicum and study in Japan. In each year, the components take on the particular focus of that year's instruction. The program recruits top students from high school graduating classes for the 22 student places available. The first cohort began the program in February 1993. Even in its early stages, the program has given evidence of success in terms of students' Japanese linguistic proficiency and teaching skills. It is seen as a promising means for improving second language teaching in Australia and supporting the national policy of extensive elementary and secondary school second language instruction. (MSE)

Published
1993

27. Synchrotron Nano-Mechanical Imaging Techniques to Understand How Altered Bone Quality Increases Fracture Risk in Secondary Osteoporosis

Author

Karunaratne, A., Bentley, L., Cox, R., Boyde, A., Esapa, C. T., Terrill, N. J., Davis, G. R., Brown, S. D. M, Thakker, R. V., Gupta, H. S., MAGJAREVIC, Ratko, Editor-in-chief, Ładyzynsk, Piotr, Series editor, Ibrahim, Fatimah, Series editor, Lackovic, Igor, Series editor, Rock, Emilio Sacristan, Series editor, and Goh, James, editor

Published
2014
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30. Crystal structure of human Cathepsin L after incubation with Sulfo-Calpeptin

Author

Reinke, P.Y.A., primary, Falke, S., additional, Lieske, J., additional, Ewert, W., additional, Loboda, J., additional, Rahmani Mashhour, A., additional, Hauser, M., additional, Karnicar, K., additional, Usenik, A., additional, Lindic, N., additional, Lach, M., additional, Boehler, H., additional, Beck, T., additional, Cox, R., additional, Chapman, H.N., additional, Hinrichs, W., additional, Turk, D., additional, Guenther, S., additional, and Meents, A., additional

Published
2022
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31. Crystal structure of human Cathepsin L in complex with covalently bound GC376

Author

Reinke, P.Y.A., primary, Falke, S., additional, Lieske, J., additional, Ewert, W., additional, Loboda, J., additional, Rahmani Mashhour, A., additional, Hauser, M., additional, Karnicar, K., additional, Usenik, A., additional, Lindic, N., additional, Lach, M., additional, Boehler, H., additional, Beck, T., additional, Cox, R., additional, Chapman, H.N., additional, Hinrichs, W., additional, Turk, D., additional, Guenther, S., additional, and Meents, A., additional

Published
2022
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32. Crystal structure of SARS-CoV-2 Main Protease in complex with covalently bound GC376

Author

Reinke, P.Y.A., primary, Falke, S., additional, Lieske, J., additional, Ewert, W., additional, Loboda, J., additional, Rahmani Mashhour, A., additional, Hauser, M., additional, Karnicar, K., additional, Usenik, A., additional, Lindic, N., additional, Lach, M., additional, Boehler, H., additional, Beck, T., additional, Cox, R., additional, Chapman, H.N., additional, Hinrichs, W., additional, Turk, D., additional, Guenther, S., additional, and Meents, A., additional

Published
2022
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33. Crystal structure of human Cathepsin L in complex with covalently bound MG132

Author

Reinke, P.Y.A., primary, Falke, S., additional, Lieske, J., additional, Ewert, W., additional, Loboda, J., additional, Rahmani Mashhour, A., additional, Hauser, M., additional, Karnicar, K., additional, Usenik, A., additional, Lindic, N., additional, Lach, M., additional, Boehler, H., additional, Beck, T., additional, Cox, R., additional, Chapman, H.N., additional, Hinrichs, W., additional, Turk, D., additional, Guenther, S., additional, and Meents, A., additional

Published
2022
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39. An Interaction-Dominant Perspective on Reading Fluency and Dyslexia

Author

Wijnants, M. L., Hasselman, F., and Cox, R. F. A.

Abstract

The background noise of response times is often overlooked in scientific inquiries of cognitive performances. However, it is becoming widely acknowledged in psychology, medicine, physiology, physics, and beyond that temporal patterns of variability constitute a rich source of information. Here, we introduce two complexity measures (1/f scaling and recurrence quantification analysis) that employ background noise as metrics of reading fluency. These measures gauge the extent of interdependence across, rather than within, cognitive components. In this study, we investigated dyslexic and non-dyslexic word-naming performance in beginning readers and observed that these complexity metrics differentiate reliably between dyslexic and average response times and correlate strongly with the severity of the reading impairment. The direction of change in the introduced metrics suggests that developmental dyslexia resides from dynamical instabilities in the coordination among the many components necessary to read, which could explain why dyslexic readers score below average on so many distinct tasks and modalities. (Contains 6 figures and 2 tables.)

Published
2012
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40. Low Vision Aids for Visually Impaired Children

Author

Schurink, J., Cox, R. F. A., and Cillessen, A. H. N.

Abstract

It is a widely accepted belief in clinical practice that children with a visual impairment can profit from the use of a low vision aid (LVA). However, we found a considerable gap in our scientific understanding of LVA use, particularly in young children. This is the reason for the analysis presented in this paper. A selected overview of LVA use in adults is given, from which valuable insights are taken. Additionally, an action perspective for analysing LVA use is discussed as well as the results of tool-use studies in children. Mainly based on these three ingredients, we developed a conceptual framework for LVA use. The framework consists of three interacting relations between LVA, child and task. Performance of a particular child on a specific task with a certain LVA is constrained by the following three reciprocal and dynamic relations: the Child-to-Task relation (related to goal-information), the Child-to-LVA relation (related to control-information), and the LVA-to-Task relation (related to topology information).

Published
2011
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41. Improvement of Fine Motor Skills in Children with Visual Impairment: An Explorative Study

Author

Reimer, A. M., Cox, R. F. A., and Nijhuis-Van der Sanden, M. W. G.

Abstract

In this study we analysed the potential spin-off of magnifier training on the fine-motor skills of visually impaired children. The fine-motor skills of 4- and 5-year-old visually impaired children were assessed using the manual skills test for children (6-12 years) with a visual impairment (ManuVis) and movement assessment for children (Movement ABC), before and after receiving a 12-sessions training within a 6-weeks period. The training was designed to practice the use of a stand magnifier, as part of a larger research project on low-vision aids. In this study, fifteen children trained with a magnifier; seven without. Sixteen children had nystagmus. In this group head orientation (ocular torticollis) was monitored. Results showed an age-related progress in children's fine-motor skills after the training, irrespective of magnifier condition: performance speed of the ManuVis items went from 333.4 s to 273.6 s on average. Accuracy in the writing tasks also increased. Finally, for the children with nystagmus, an increase of ocular torticollis was found. These results suggest a careful reconsideration of which intervention is most effective for enhancing perceptuomotor performance in visually impaired children: specific "fine-motor" training or "non-specific" visual-attention training with a magnifier. (Contains 3 figures and 3 tables.)

Published
2011
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47. Advances in Laboratory and Field Measurements

Author

Tyndall, Geoffrey S., Winker, David M., Anderson, Theodore L., Eisele, Fred L., Apel, Eric C., Brenninkmeijer, Carl A. M., Calvert, Jack G., Covert, David S., Anthony Cox, R., Crosley, David R., Davidson, Clifford I., Drummond, James R., Grant, William B., Guenther, Alex B., Huebert, Barry, Kent, Geoffrey S., Lowe, David C., McGillis, Wade R., Miller, John M., Montzka, Steve A., Orlando, John J., Platt, Ulrich, Swietlicki, Eric, Trivett, Neil B. A., Wexler, Anthony S., Brasseur, Guy P., editor, Prinn, Ronald G., editor, and Pszenny, Alexander A. P., editor

Published
2003
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