Search

Your search keyword '"Baker, Bradley J."' showing total 143 results
Start Over Author "Baker, Bradley J."
143 results on '"Baker, Bradley J."'

104. Voltage and Calcium Imaging of Brain Activity

Author

Sepehri Rad, Masoud, primary, Choi, Yunsook, additional, Cohen, Lawrence B., additional, Baker, Bradley J., additional, Zhong, Sheng, additional, Storace, Douglas A., additional, and Braubach, Oliver R., additional

Published
2017
Full Text
View/download PDF

128. Combinatorial Mutagenesis of the Voltage-Sensing Domain Enables the Optical Resolution of Action Potentials Firing at 60 Hz by a Genetically Encoded Fluorescent Sensor of Membrane Potential.

Author

Hong Hua Piao, Rajakumar, Dhanarajan, Bok Eum Kang, Eun Ha Kim, and Baker, Bradley J.

Subjects
MUTAGENESIS, MEMBRANE potential, GENETIC mutation, MEMBRANE proteins, NEURONS
Abstract

ArcLight is a genetically encoded fluorescent voltage sensor using the voltage-sensing domain of the voltage-sensing phosphatase from Ciona intestinalis that gives a large but slow-responding optical signal in response to changes in membrane potential (Jin et al., 2012). Fluorescent voltage sensors using the voltage-sensing domain from other species give faster yet weaker optical signals (Baker et al., 2012; Han et al., 2013). Sequence alignment of voltage-sensing phosphatases from different species revealed conserved polar and charged residues at 7 aa intervals in the S1-S3 transmembrane segments of the voltage-sensing domain, suggesting potential coil-coil interactions. The contribution of these residues to the voltage-induced optical signal was tested using a cassette mutagenesis screen by flanking each transmembrane segment with unique restriction sites to allow for the testing of individual mutations in each transmembrane segment, as well as combinations in all four transmembrane segments. Addition of a counter charge in S2 improved the kinetics of the optical response. A double mutation in the S4 domain dramatically reduced the slow component of the optical signal seen in ArcLight. Combining that double S4 mutant with the mutation in the S2 domain yielded a probe with kinetics <10 ms. Optimization of the linker sequence between S4 and the fluorescent protein resulted in a new ArcLight-derived probe, Bongwoori, capable of resolving action potentials in a hippocampal neuron firing at 60 Hz. Additional manipulation of the voltage-sensing domain could potentially lead to fluorescent sensors capable of optically resolving neuronal inhibition and subthreshold synaptic activity. [ABSTRACT FROM AUTHOR]

Published
2015
Full Text
View/download PDF

129. A community-sourced glossary of open scholarship terms

Author

Parsons, Sam, Azevedo, Flávio, Elsherif, Mahmoud M, Guay, Samuel, Shahim, Owen N, Govaart, Gisela H, Norris, Emma, O'Mahony, Aoife, Parker, Adam J, Todorovic, Ana, Pennington, Charlotte R, Garcia-Pelegrin, Elias, Lazić, Aleksandra, Robertson, Olly, Middleton, Sara L, Valentini, Beatrice, McCuaig, Joanne, Baker, Bradley J, Collins, Elizabeth, Fillon, Adrien A, Lonsdorf, Tina B, Lim, Michele C, Vanek, Norbert, Kovacs, Marton, Roettger, Timo B, Rishi, Sonia, Miranda, Jacob F, Jaquiery, Matt, Stewart, Suzanne L K, Agostini, Valeria, Stewart, Andrew J, Izydorczak, Kamil, Ashcroft-Jones, Sarah, Hartmann, Helena, Ingham, Madeleine, Yamada, Yuki, Vasilev, Martin R, Dechterenko, Filip, Albayrak-Aydemir, Nihan, Yang, Yu-Fang, LaPlume, Annalise A, Wolska, Julia K, Henderson, Emma L, Zaneva, Mirela, Farrar, Benjamin G, Mounce, Ross, Kalandadze, Tamara, Li, Wanyin, Xiao, Qinyu, Ross, Robert M, Yeung, Siu Kit, Liu, Meng, Vandegrift, Micah L, Kekecs, Zoltan, Topor, Marta K, Baum, Myriam A, Williams, Emily A, Assaneea, Asma A, Bret, Amélie, Cashin, Aidan G, Ballou, Nick, Dumbalska, Tsvetomira, Kern, Bettina M J, Melia, Claire R, Arendt, Beatrix, Vineyard, Gerald H, Pickering, Jade S, Evans, Thomas R, Laverty, Catherine, Woodward, Eliza A, Moreau, David, Roche, Dominique G, Rinke, Eike M, Reid, Graham, Garcia-Garzon, Eduardo, Verheyen, Steven, Kocalar, Halil E, Blake, Ashley R, Cockcroft, Jamie P, Micheli, Leticia, Bret, Brice Beffara, Flack, Zoe M, Szaszi, Barnabas, Weinmann, Markus, Lecuona, Oscar, Schmidt, Birgit, Ngiam, William X, Mendes, Ana Barbosa, Francis, Shannon, Gall, Brett J, Paul, Mariella, Keating, Connor T, Grose-Hodge, Magdalena, Bartlett, James E, Iley, Bethan J, Spitzer, Lisa, Pownall, Madeleine, Graham, Christopher J, Wingen, Tobias, Terry, Jenny, Oliveira, Catia Margarida F, Millager, Ryan A, Fox, Kerry J, AlDoh, Alaa, Hart, Alexander, van den Akker, Olmo R, Feldman, Gilad, Kiersz, Dominik A, Pomareda, Christina, Krautter, Kai, Al-Hoorie, Ali H, Aczel, Balazs, Parsons, Sam, Azevedo, Flávio, Elsherif, Mahmoud M, Guay, Samuel, Shahim, Owen N, Govaart, Gisela H, Norris, Emma, O'Mahony, Aoife, Parker, Adam J, Todorovic, Ana, Pennington, Charlotte R, Garcia-Pelegrin, Elias, Lazić, Aleksandra, Robertson, Olly, Middleton, Sara L, Valentini, Beatrice, McCuaig, Joanne, Baker, Bradley J, Collins, Elizabeth, Fillon, Adrien A, Lonsdorf, Tina B, Lim, Michele C, Vanek, Norbert, Kovacs, Marton, Roettger, Timo B, Rishi, Sonia, Miranda, Jacob F, Jaquiery, Matt, Stewart, Suzanne L K, Agostini, Valeria, Stewart, Andrew J, Izydorczak, Kamil, Ashcroft-Jones, Sarah, Hartmann, Helena, Ingham, Madeleine, Yamada, Yuki, Vasilev, Martin R, Dechterenko, Filip, Albayrak-Aydemir, Nihan, Yang, Yu-Fang, LaPlume, Annalise A, Wolska, Julia K, Henderson, Emma L, Zaneva, Mirela, Farrar, Benjamin G, Mounce, Ross, Kalandadze, Tamara, Li, Wanyin, Xiao, Qinyu, Ross, Robert M, Yeung, Siu Kit, Liu, Meng, Vandegrift, Micah L, Kekecs, Zoltan, Topor, Marta K, Baum, Myriam A, Williams, Emily A, Assaneea, Asma A, Bret, Amélie, Cashin, Aidan G, Ballou, Nick, Dumbalska, Tsvetomira, Kern, Bettina M J, Melia, Claire R, Arendt, Beatrix, Vineyard, Gerald H, Pickering, Jade S, Evans, Thomas R, Laverty, Catherine, Woodward, Eliza A, Moreau, David, Roche, Dominique G, Rinke, Eike M, Reid, Graham, Garcia-Garzon, Eduardo, Verheyen, Steven, Kocalar, Halil E, Blake, Ashley R, Cockcroft, Jamie P, Micheli, Leticia, Bret, Brice Beffara, Flack, Zoe M, Szaszi, Barnabas, Weinmann, Markus, Lecuona, Oscar, Schmidt, Birgit, Ngiam, William X, Mendes, Ana Barbosa, Francis, Shannon, Gall, Brett J, Paul, Mariella, Keating, Connor T, Grose-Hodge, Magdalena, Bartlett, James E, Iley, Bethan J, Spitzer, Lisa, Pownall, Madeleine, Graham, Christopher J, Wingen, Tobias, Terry, Jenny, Oliveira, Catia Margarida F, Millager, Ryan A, Fox, Kerry J, AlDoh, Alaa, Hart, Alexander, van den Akker, Olmo R, Feldman, Gilad, Kiersz, Dominik A, Pomareda, Christina, Krautter, Kai, Al-Hoorie, Ali H, and Aczel, Balazs

Abstract

Open scholarship has transformed research, and introduced a host of new terms in the lexicon of researchers. The ‘Framework for Open and Reproducible Research Teaching’ (FORRT) community presents a crowdsourced glossary of open scholarship terms to facilitate education and effective communication between experts and newcomers.

130. The replication crisis has led to positive structural, procedural, and community changes

Author

Korbmacher, Max, Azevedo, Flavio, Pennington, Charlotte R., Hartmann, Helena, Pownall, Madeleine, Schmidt, Kathleen, Elsherif, Mahmoud, Breznau, Nate, Robertson, Olly, Kalandadze, Tamara, Yu, Shijun, Baker, Bradley J., O’Mahony, Aoife, Olsnes, Jørgen Ø. -S., Shaw, John J., Gjoneska, Biljana, Yamada, Yuki, Röer, Jan P., Murphy, Jennifer, Alzahawi, Shilaan, Grinschgl, Sandra, Oliveira, Catia M., Wingen, Tobias, Yeung, Siu Kit, Liu, Meng, König, Laura M., Albayrak-Aydemir, Nihan, Lecuona, Oscar, Micheli, Leticia, Evans, Thomas, Korbmacher, Max, Azevedo, Flavio, Pennington, Charlotte R., Hartmann, Helena, Pownall, Madeleine, Schmidt, Kathleen, Elsherif, Mahmoud, Breznau, Nate, Robertson, Olly, Kalandadze, Tamara, Yu, Shijun, Baker, Bradley J., O’Mahony, Aoife, Olsnes, Jørgen Ø. -S., Shaw, John J., Gjoneska, Biljana, Yamada, Yuki, Röer, Jan P., Murphy, Jennifer, Alzahawi, Shilaan, Grinschgl, Sandra, Oliveira, Catia M., Wingen, Tobias, Yeung, Siu Kit, Liu, Meng, König, Laura M., Albayrak-Aydemir, Nihan, Lecuona, Oscar, Micheli, Leticia, and Evans, Thomas

Abstract

The emergence of large-scale replication projects yielding successful rates substantially lower than expected caused the behavioural, cognitive, and social sciences to experience a so-called ‘replication crisis’. In this Perspective, we reframe this ‘crisis’ through the lens of a credibility revolution, focusing on positive structural, procedural and community-driven changes. Second, we outline a path to expand ongoing advances and improvements. The credibility revolution has been an impetus to several substantive changes which will have a positive, long-term impact on our research environment.

131. Teaching open and reproducible scholarship: a critical review of the evidence base for current pedagogical methods and their outcomes

Author

Pownall, Madeleine, Azevedo, Flávio, König, Laura M., Slack, Hannah R., Evans, Thomas Rhys, Flack, Zoe, Grinschgl, Sandra, Elsherif, Mahmoud M., Gilligan-Lee, Katie A., de Oliveira, Catia M. F., Gjoneska, Biljana, Kalandadze, Tamara, Button, Katherine, Ashcroft-Jones, Sarah, Terry, Jenny, Albayrak-Aydemir, Nihan, Děchtěrenko, Filip, Alzahawi, Shilaan, Baker, Bradley J., Pittelkow, Merle-Marie, Riedl, Lydia, Schmidt, Kathleen, Pennington, Charlotte R., Shaw, John J., Lüke, Timo, Makel, Matthew C., Hartmann, Helena, Zaneva, Mirela, Walker, Daniel, Verheyen, Steven, Cox, Daniel, Mattschey, Jennifer, Gallagher-Mitchell, Tom, Branney, Peter, Weisberg, Yanna, Izydorczak, Kamil, Al-Hoorie, Ali H., Creaven, Ann-Marie, Stewart, Suzanne L. K., Krautter, Kai, Matvienko-Sikar, Karen, Westwood, Samuel J., Arriaga, Patrícia, Liu, Meng, Baum, Myriam A., Wingen, Tobias, Ross, Robert M., O'Mahony, Aoife, Bochynska, Agata, Jamieson, Michelle, Tromp, Myrthe Vel, Yeung, Siu Kit, Vasilev, Martin R., Gourdon-Kanhukamwe, Amélie, Micheli, Leticia, Konkol, Markus, Moreau, David, Bartlett, James E., Clark, Kait, Brekelmans, Gwen, Gkinopoulos, Theofilos, Tyler, Samantha L., Röer, Jan Philipp, Ilchovska, Zlatomira G., Madan, Christopher R., Robertson, Olly, Iley, Bethan J., Guay, Samuel, Sladekova, Martina, Sadhwani, Shanu, Pownall, Madeleine, Azevedo, Flávio, König, Laura M., Slack, Hannah R., Evans, Thomas Rhys, Flack, Zoe, Grinschgl, Sandra, Elsherif, Mahmoud M., Gilligan-Lee, Katie A., de Oliveira, Catia M. F., Gjoneska, Biljana, Kalandadze, Tamara, Button, Katherine, Ashcroft-Jones, Sarah, Terry, Jenny, Albayrak-Aydemir, Nihan, Děchtěrenko, Filip, Alzahawi, Shilaan, Baker, Bradley J., Pittelkow, Merle-Marie, Riedl, Lydia, Schmidt, Kathleen, Pennington, Charlotte R., Shaw, John J., Lüke, Timo, Makel, Matthew C., Hartmann, Helena, Zaneva, Mirela, Walker, Daniel, Verheyen, Steven, Cox, Daniel, Mattschey, Jennifer, Gallagher-Mitchell, Tom, Branney, Peter, Weisberg, Yanna, Izydorczak, Kamil, Al-Hoorie, Ali H., Creaven, Ann-Marie, Stewart, Suzanne L. K., Krautter, Kai, Matvienko-Sikar, Karen, Westwood, Samuel J., Arriaga, Patrícia, Liu, Meng, Baum, Myriam A., Wingen, Tobias, Ross, Robert M., O'Mahony, Aoife, Bochynska, Agata, Jamieson, Michelle, Tromp, Myrthe Vel, Yeung, Siu Kit, Vasilev, Martin R., Gourdon-Kanhukamwe, Amélie, Micheli, Leticia, Konkol, Markus, Moreau, David, Bartlett, James E., Clark, Kait, Brekelmans, Gwen, Gkinopoulos, Theofilos, Tyler, Samantha L., Röer, Jan Philipp, Ilchovska, Zlatomira G., Madan, Christopher R., Robertson, Olly, Iley, Bethan J., Guay, Samuel, Sladekova, Martina, and Sadhwani, Shanu

Abstract

In recent years, the scientific community has called for improvements in the credibility, robustness and reproducibility of research, characterized by increased interest and promotion of open and transparent research practices. While progress has been positive, there is a lack of consideration about how this approach can be embedded into undergraduate and postgraduate research training. Specifically, a critical overview of the literature which investigates how integrating open and reproducible science may influence student outcomes is needed. In this paper, we provide the first critical review of literature surrounding the integration of open and reproducible scholarship into teaching and learning and its associated outcomes in students. Our review highlighted how embedding open and reproducible scholarship appears to be associated with (i) students’ scientific literacies (i.e. students’ understanding of open research, consumption of science and the development of transferable skills); (ii) student engagement (i.e. motivation and engagement with learning, collaboration and engagement in open research) and (iii) students’ attitudes towards science (i.e. trust in science and confidence in research findings). However, our review also identified a need for more robust and rigorous methods within pedagogical research, including more interventional and experimental evaluations of teaching practice. We discuss implications for teaching and learning scholarship.

132. A community-sourced glossary of open scholarship terms

Author

Parsons, Sam, Azevedo, Flávio, Elsherif, Mahmoud M, Guay, Samuel, Shahim, Owen N, Govaart, Gisela H, Norris, Emma, O'Mahony, Aoife, Parker, Adam J, Todorovic, Ana, Pennington, Charlotte R, Garcia-Pelegrin, Elias, Lazić, Aleksandra, Robertson, Olly, Middleton, Sara L, Valentini, Beatrice, McCuaig, Joanne, Baker, Bradley J, Collins, Elizabeth, Fillon, Adrien A, Lonsdorf, Tina B, Lim, Michele C, Vanek, Norbert, Kovacs, Marton, Roettger, Timo B, Rishi, Sonia, Miranda, Jacob F, Jaquiery, Matt, Stewart, Suzanne L K, Agostini, Valeria, Stewart, Andrew J, Izydorczak, Kamil, Ashcroft-Jones, Sarah, Hartmann, Helena, Ingham, Madeleine, Yamada, Yuki, Vasilev, Martin R, Dechterenko, Filip, Albayrak-Aydemir, Nihan, Yang, Yu-Fang, LaPlume, Annalise A, Wolska, Julia K, Henderson, Emma L, Zaneva, Mirela, Farrar, Benjamin G, Mounce, Ross, Kalandadze, Tamara, Li, Wanyin, Xiao, Qinyu, Ross, Robert M, Yeung, Siu Kit, Liu, Meng, Vandegrift, Micah L, Kekecs, Zoltan, Topor, Marta K, Baum, Myriam A, Williams, Emily A, Assaneea, Asma A, Bret, Amélie, Cashin, Aidan G, Ballou, Nick, Dumbalska, Tsvetomira, Kern, Bettina M J, Melia, Claire R, Arendt, Beatrix, Vineyard, Gerald H, Pickering, Jade S, Evans, Thomas R, Laverty, Catherine, Woodward, Eliza A, Moreau, David, Roche, Dominique G, Rinke, Eike M, Reid, Graham, Garcia-Garzon, Eduardo, Verheyen, Steven, Kocalar, Halil E, Blake, Ashley R, Cockcroft, Jamie P, Micheli, Leticia, Bret, Brice Beffara, Flack, Zoe M, Szaszi, Barnabas, Weinmann, Markus, Lecuona, Oscar, Schmidt, Birgit, Ngiam, William X, Mendes, Ana Barbosa, Francis, Shannon, Gall, Brett J, Paul, Mariella, Keating, Connor T, Grose-Hodge, Magdalena, Bartlett, James E, Iley, Bethan J, Spitzer, Lisa, Pownall, Madeleine, Graham, Christopher J, Wingen, Tobias, Terry, Jenny, Oliveira, Catia Margarida F, Millager, Ryan A, Fox, Kerry J, AlDoh, Alaa, Hart, Alexander, van den Akker, Olmo R, Feldman, Gilad, Kiersz, Dominik A, Pomareda, Christina, Krautter, Kai, Al-Hoorie, Ali H, Aczel, Balazs, Parsons, Sam, Azevedo, Flávio, Elsherif, Mahmoud M, Guay, Samuel, Shahim, Owen N, Govaart, Gisela H, Norris, Emma, O'Mahony, Aoife, Parker, Adam J, Todorovic, Ana, Pennington, Charlotte R, Garcia-Pelegrin, Elias, Lazić, Aleksandra, Robertson, Olly, Middleton, Sara L, Valentini, Beatrice, McCuaig, Joanne, Baker, Bradley J, Collins, Elizabeth, Fillon, Adrien A, Lonsdorf, Tina B, Lim, Michele C, Vanek, Norbert, Kovacs, Marton, Roettger, Timo B, Rishi, Sonia, Miranda, Jacob F, Jaquiery, Matt, Stewart, Suzanne L K, Agostini, Valeria, Stewart, Andrew J, Izydorczak, Kamil, Ashcroft-Jones, Sarah, Hartmann, Helena, Ingham, Madeleine, Yamada, Yuki, Vasilev, Martin R, Dechterenko, Filip, Albayrak-Aydemir, Nihan, Yang, Yu-Fang, LaPlume, Annalise A, Wolska, Julia K, Henderson, Emma L, Zaneva, Mirela, Farrar, Benjamin G, Mounce, Ross, Kalandadze, Tamara, Li, Wanyin, Xiao, Qinyu, Ross, Robert M, Yeung, Siu Kit, Liu, Meng, Vandegrift, Micah L, Kekecs, Zoltan, Topor, Marta K, Baum, Myriam A, Williams, Emily A, Assaneea, Asma A, Bret, Amélie, Cashin, Aidan G, Ballou, Nick, Dumbalska, Tsvetomira, Kern, Bettina M J, Melia, Claire R, Arendt, Beatrix, Vineyard, Gerald H, Pickering, Jade S, Evans, Thomas R, Laverty, Catherine, Woodward, Eliza A, Moreau, David, Roche, Dominique G, Rinke, Eike M, Reid, Graham, Garcia-Garzon, Eduardo, Verheyen, Steven, Kocalar, Halil E, Blake, Ashley R, Cockcroft, Jamie P, Micheli, Leticia, Bret, Brice Beffara, Flack, Zoe M, Szaszi, Barnabas, Weinmann, Markus, Lecuona, Oscar, Schmidt, Birgit, Ngiam, William X, Mendes, Ana Barbosa, Francis, Shannon, Gall, Brett J, Paul, Mariella, Keating, Connor T, Grose-Hodge, Magdalena, Bartlett, James E, Iley, Bethan J, Spitzer, Lisa, Pownall, Madeleine, Graham, Christopher J, Wingen, Tobias, Terry, Jenny, Oliveira, Catia Margarida F, Millager, Ryan A, Fox, Kerry J, AlDoh, Alaa, Hart, Alexander, van den Akker, Olmo R, Feldman, Gilad, Kiersz, Dominik A, Pomareda, Christina, Krautter, Kai, Al-Hoorie, Ali H, and Aczel, Balazs

Abstract

Open scholarship has transformed research, and introduced a host of new terms in the lexicon of researchers. The ‘Framework for Open and Reproducible Research Teaching’ (FORRT) community presents a crowdsourced glossary of open scholarship terms to facilitate education and effective communication between experts and newcomers.

135. What’s in a Badge? A Computational Reproducibility Investigation of the Open Data Badge Policy in One Issue of Psychological Science

Author

Sophia Crüwell, Deborah Apthorp, Bradley J. Baker, Lincoln Colling, Malte Elson, Sandra J. Geiger, Sebastian Lobentanzer, Jean Monéger, Alex Patterson, D. Samuel Schwarzkopf, Mirela Zaneva, Nicholas J. L. Brown, Crüwell, Sophia [0000-0003-4178-5820], Apthorp, Deborah [0000-0001-5785-024X], Baker, Bradley J [0000-0002-1697-4198], Colling, Lincoln [0000-0002-3572-7758], Elson, Malte [0000-0001-7806-9583], Geiger, Sandra J [0000-0002-3262-5609], Monéger, Jean [0000-0003-1178-1896], Patterson, Alex [0000-0002-7780-4192], Zaneva, Mirela [0000-0003-3569-931X], Brown, Nicholas JL [0000-0003-1579-0730], and Apollo - University of Cambridge Repository

Subjects
Policy, journal policy, data sharing, open badges, open data, Humans, Reproducibility of Results, Disclosure, 150 Psychology, reproducibility, General Psychology
Abstract

[Preprint; Manuscript accepted at Psychological Science] In April 2019, Psychological Science published its first issue in which all research articles received the Open Data badge. We used that issue to investigate the effectiveness of this badge, focusing on the adherence to its aim at Psychological Science: sharing both data and code to ensure reproducibility of results. Twelve researchers of varying experience levels attempted to reproduce the results of the empirical articles in the target issue (at least three researchers per article). We found that while all 14 articles provided at least some data and six provided analysis code, only one article was rated to be exactly reproducible, and three essentially reproducible with minor deviations. We suggest that researchers should be encouraged to adhere to the higher standard in force at Psychological Science. Moreover, a check of reproducibility during peer review may be preferable to the ‘disclosure method’ of awarding badges.

Published
2023

136. The potential of preregistration in psychology: Assessing preregistration producibility and preregistration-study consistency.

Author

van den Akker OR, Bakker M, van Assen MALM, Pennington CR, Verweij L, Elsherif MM, Claesen A, Gaillard SDM, Yeung SK, Frankenberger JL, Krautter K, Cockcroft JP, Kreuer KS, Evans TR, Heppel FM, Schoch SF, Korbmacher M, Yamada Y, Albayrak-Aydemir N, Alzahawi S, Sarafoglou A, Sitnikov MM, Děchtěrenko F, Wingen S, Grinschgl S, Hartmann H, Stewart SLK, de Oliveira CMF, Ashcroft-Jones S, Baker BJ, and Wicherts JM

Abstract

Study preregistration has become increasingly popular in psychology, but its potential to restrict researcher degrees of freedom has not yet been empirically verified. We used an extensive protocol to assess the producibility (i.e., the degree to which a study can be properly conducted based on the available information) of preregistrations and the consistency between preregistrations and their corresponding papers for 300 psychology studies. We found that preregistrations often lack methodological details and that undisclosed deviations from preregistered plans are frequent. These results highlight that biases due to researcher degrees of freedom remain possible in many preregistered studies. More comprehensive registration templates typically yielded more producible preregistrations. We did not find that the producibility and consistency of preregistrations differed over time or between original and replication studies. Furthermore, we found that operationalizations of variables were generally preregistered more producible and consistently than other study parts. Inconsistencies between preregistrations and published studies were mainly encountered for data collection procedures, statistical models, and exclusion criteria. Our results indicate that, to unlock the full potential of preregistration, researchers in psychology should aim to write more producible preregistrations, adhere to these preregistrations more faithfully, and more transparently report any deviations from their preregistrations. This could be facilitated by training and education to improve preregistration skills, as well as the development of more comprehensive templates. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Published
2024
Full Text
View/download PDF

137. Hydrophobic residues in S1 modulate enzymatic function and voltage sensing in voltage-sensing phosphatase.

Author

Rayaprolu V, Miettinen HM, Baker WD, Young VC, Fisher M, Mueller G, Rankin WO, Kelley JT, Ratzan WJ, Leong LM, Davisson JA, Baker BJ, and Kohout SC

Subjects
Animals, Humans, Hydrophobic and Hydrophilic Interactions, Kinetics, Mutation, Phosphorylation, Protein Domains, Xenopus laevis, Xenopus Proteins chemistry, Xenopus Proteins metabolism, Xenopus Proteins physiology, Phosphoric Monoester Hydrolases metabolism, Phosphoric Monoester Hydrolases genetics, Phosphoric Monoester Hydrolases chemistry
Abstract

The voltage-sensing domain (VSD) is a four-helix modular protein domain that converts electrical signals into conformational changes, leading to open pores and active enzymes. In most voltage-sensing proteins, the VSDs do not interact with one another, and the S1-S3 helices are considered mainly scaffolding, except in the voltage-sensing phosphatase (VSP) and the proton channel (Hv). To investigate its contribution to VSP function, we mutated four hydrophobic amino acids in S1 to alanine (F127, I131, I134, and L137), individually or in combination. Most of these mutations shifted the voltage dependence of activity to higher voltages; however, not all substrate reactions were the same. The kinetics of enzymatic activity were also altered, with some mutations significantly slowing down dephosphorylation. The voltage dependence of VSD motions was consistently shifted to lower voltages and indicated a second voltage-dependent motion. Additionally, none of the mutations broke the VSP dimer, indicating that the S1 impact could stem from intra- and/or intersubunit interactions. Lastly, when the same mutations were introduced into a genetically encoded voltage indicator, they dramatically altered the optical readings, making some of the kinetics faster and shifting the voltage dependence. These results indicate that the S1 helix in VSP plays a critical role in tuning the enzyme's conformational response to membrane potential transients and influencing the function of the VSD., (© 2024 Rayaprolu et al.)

Published
2024
Full Text
View/download PDF

138. S1 hydrophobic residues modulate voltage sensing phosphatase enzymatic function and voltage sensing.

Author

Rayaprolu V, Miettinen HM, Baker W, Young VC, Fisher M, Mueller G, Rankin WO, Kelley JJ, Ratzan W, Leong LM, Davisson JA, Baker BJ, and Kohout SC

Abstract

The voltage sensing domain (VSD) is a four-helix modular protein domain that converts electrical signals into conformational changes, leading to open pores and active enzymes. In most voltage sensing proteins, the VSDs do not interact with one another and the S1-S3 helices are considered mainly as scaffolding. The two exceptions are the voltage sensing phosphatase (VSP) and the proton channel (Hv). VSP is a voltage-regulated enzyme and Hvs are channels that only have VSDs. To investigate the S1 contribution to VSP function, we individually mutated four hydrophobic amino acids in S1 to alanine (F127, I131, I134 and L137). We also combined these mutations to generate quadruple mutation designated S1-Q. Most of these mutations shifted the voltage dependence of activity to higher voltages though interestingly, not all substrate reactions were the same. The kinetics of enzymatic activity were also altered with some mutations significantly slowing down dephosphorylation. The voltage dependence of VSD motions were consistently shifted to lower voltages and indicated a second voltage dependent motion. Co-immunoprecipitation demonstrated that none of the mutations broke the VSP dimer indicating that the S1 impact could stem from intrasubunit and/or intersubunit interactions. Lastly, when the same alanine mutations were introduced into a genetically encoded voltage indicator, they dramatically altered the optical readings, making some of the kinetics faster and shifting the voltage dependence. These results indicate that the S1 helix in VSP plays a critical role in tuning the enzymes conformational response to membrane potential transients and influencing the function of the VSD.

Published
2024
Full Text
View/download PDF

139. We don't know what you did last summer. On the importance of transparent reporting of reaction time data pre-processing.

Author

Loenneker HD, Buchanan EM, Martinovici A, Primbs MA, Elsherif MM, Baker BJ, Dudda LA, Đurđević DF, Mišić K, Peetz HK, Röer JP, Schulze L, Wagner L, Wolska JK, Kührt C, and Pronizius E

Subjects
Humans, Checklist, Research Design standards, Reproducibility of Results, Reaction Time physiology
Abstract

In behavioral, cognitive, and social sciences, reaction time measures are an important source of information. However, analyses on reaction time data are affected by researchers' analytical choices and the order in which these choices are applied. The results of a systematic literature review, presented in this paper, revealed that the justification for and order in which analytical choices are conducted are rarely reported, leading to difficulty in reproducing results and interpreting mixed findings. To address this methodological shortcoming, we created a checklist on reporting reaction time pre-processing to make these decisions more explicit, improve transparency, and thus, promote best practices within the field. The importance of the pre-processing checklist was additionally supported by an expert consensus survey and a multiverse analysis. Consequently, we appeal for maximal transparency on all methods applied and offer a checklist to improve replicability and reproducibility of studies that use reaction time measures., (Crown Copyright © 2023. Published by Elsevier Ltd. All rights reserved.)

Published
2024
Full Text
View/download PDF

140. The replication crisis has led to positive structural, procedural, and community changes.

Author

Korbmacher M, Azevedo F, Pennington CR, Hartmann H, Pownall M, Schmidt K, Elsherif M, Breznau N, Robertson O, Kalandadze T, Yu S, Baker BJ, O'Mahony A, Olsnes JØ, Shaw JJ, Gjoneska B, Yamada Y, Röer JP, Murphy J, Alzahawi S, Grinschgl S, Oliveira CM, Wingen T, Yeung SK, Liu M, König LM, Albayrak-Aydemir N, Lecuona O, Micheli L, and Evans T

Abstract

The emergence of large-scale replication projects yielding successful rates substantially lower than expected caused the behavioural, cognitive, and social sciences to experience a so-called 'replication crisis'. In this Perspective, we reframe this 'crisis' through the lens of a credibility revolution, focusing on positive structural, procedural and community-driven changes. Second, we outline a path to expand ongoing advances and improvements. The credibility revolution has been an impetus to several substantive changes which will have a positive, long-term impact on our research environment., (© 2023. The Author(s).)

Published
2023
Full Text
View/download PDF

141. Teaching open and reproducible scholarship: a critical review of the evidence base for current pedagogical methods and their outcomes.

Author

Pownall M, Azevedo F, König LM, Slack HR, Evans TR, Flack Z, Grinschgl S, Elsherif MM, Gilligan-Lee KA, de Oliveira CMF, Gjoneska B, Kalandadze T, Button K, Ashcroft-Jones S, Terry J, Albayrak-Aydemir N, Děchtěrenko F, Alzahawi S, Baker BJ, Pittelkow MM, Riedl L, Schmidt K, Pennington CR, Shaw JJ, Lüke T, Makel MC, Hartmann H, Zaneva M, Walker D, Verheyen S, Cox D, Mattschey J, Gallagher-Mitchell T, Branney P, Weisberg Y, Izydorczak K, Al-Hoorie AH, Creaven AM, Stewart SLK, Krautter K, Matvienko-Sikar K, Westwood SJ, Arriaga P, Liu M, Baum MA, Wingen T, Ross RM, O'Mahony A, Bochynska A, Jamieson M, Tromp MV, Yeung SK, Vasilev MR, Gourdon-Kanhukamwe A, Micheli L, Konkol M, Moreau D, Bartlett JE, Clark K, Brekelmans G, Gkinopoulos T, Tyler SL, Röer JP, Ilchovska ZG, Madan CR, Robertson O, Iley BJ, Guay S, Sladekova M, and Sadhwani S

Abstract

In recent years, the scientific community has called for improvements in the credibility, robustness and reproducibility of research, characterized by increased interest and promotion of open and transparent research practices. While progress has been positive, there is a lack of consideration about how this approach can be embedded into undergraduate and postgraduate research training. Specifically, a critical overview of the literature which investigates how integrating open and reproducible science may influence student outcomes is needed. In this paper, we provide the first critical review of literature surrounding the integration of open and reproducible scholarship into teaching and learning and its associated outcomes in students. Our review highlighted how embedding open and reproducible scholarship appears to be associated with (i) students' scientific literacies (i.e. students' understanding of open research, consumption of science and the development of transferable skills); (ii) student engagement (i.e. motivation and engagement with learning, collaboration and engagement in open research) and (iii) students' attitudes towards science (i.e. trust in science and confidence in research findings). However, our review also identified a need for more robust and rigorous methods within pedagogical research, including more interventional and experimental evaluations of teaching practice. We discuss implications for teaching and learning scholarship., Competing Interests: We declare we have no competing interests., (© 2023 The Authors.)

Published
2023
Full Text
View/download PDF

142. A community-sourced glossary of open scholarship terms.

Author

Parsons S, Azevedo F, Elsherif MM, Guay S, Shahim ON, Govaart GH, Norris E, O'Mahony A, Parker AJ, Todorovic A, Pennington CR, Garcia-Pelegrin E, Lazić A, Robertson O, Middleton SL, Valentini B, McCuaig J, Baker BJ, Collins E, Fillon AA, Lonsdorf TB, Lim MC, Vanek N, Kovacs M, Roettger TB, Rishi S, Miranda JF, Jaquiery M, Stewart SLK, Agostini V, Stewart AJ, Izydorczak K, Ashcroft-Jones S, Hartmann H, Ingham M, Yamada Y, Vasilev MR, Dechterenko F, Albayrak-Aydemir N, Yang YF, LaPlume AA, Wolska JK, Henderson EL, Zaneva M, Farrar BG, Mounce R, Kalandadze T, Li W, Xiao Q, Ross RM, Yeung SK, Liu M, Vandegrift ML, Kekecs Z, Topor MK, Baum MA, Williams EA, Assaneea AA, Bret A, Cashin AG, Ballou N, Dumbalska T, Kern BMJ, Melia CR, Arendt B, Vineyard GH, Pickering JS, Evans TR, Laverty C, Woodward EA, Moreau D, Roche DG, Rinke EM, Reid G, Garcia-Garzon E, Verheyen S, Kocalar HE, Blake AR, Cockcroft JP, Micheli L, Bret BB, Flack ZM, Szaszi B, Weinmann M, Lecuona O, Schmidt B, Ngiam WX, Mendes AB, Francis S, Gall BJ, Paul M, Keating CT, Grose-Hodge M, Bartlett JE, Iley BJ, Spitzer L, Pownall M, Graham CJ, Wingen T, Terry J, Oliveira CMF, Millager RA, Fox KJ, AlDoh A, Hart A, van den Akker OR, Feldman G, Kiersz DA, Pomareda C, Krautter K, Al-Hoorie AH, and Aczel B

Subjects
Humans, Fellowships and Scholarships
Published
2022
Full Text
View/download PDF

143. Combinatorial mutagenesis of the voltage-sensing domain enables the optical resolution of action potentials firing at 60 Hz by a genetically encoded fluorescent sensor of membrane potential.

Author

Piao HH, Rajakumar D, Kang BE, Kim EH, and Baker BJ

Subjects
Amino Acid Sequence, Animals, Ciona intestinalis, HEK293 Cells, Humans, Ion Channels physiology, Luminescent Proteins analysis, Membrane Potentials physiology, Mice, Inbred C57BL, Molecular Sequence Data, Action Potentials physiology, Fluorescent Dyes analysis, Ion Channel Gating physiology, Mutagenesis physiology, Optogenetics methods, Sequence Homology
Abstract

ArcLight is a genetically encoded fluorescent voltage sensor using the voltage-sensing domain of the voltage-sensing phosphatase from Ciona intestinalis that gives a large but slow-responding optical signal in response to changes in membrane potential (Jin et al., 2012). Fluorescent voltage sensors using the voltage-sensing domain from other species give faster yet weaker optical signals (Baker et al., 2012; Han et al., 2013). Sequence alignment of voltage-sensing phosphatases from different species revealed conserved polar and charged residues at 7 aa intervals in the S1-S3 transmembrane segments of the voltage-sensing domain, suggesting potential coil-coil interactions. The contribution of these residues to the voltage-induced optical signal was tested using a cassette mutagenesis screen by flanking each transmembrane segment with unique restriction sites to allow for the testing of individual mutations in each transmembrane segment, as well as combinations in all four transmembrane segments. Addition of a counter charge in S2 improved the kinetics of the optical response. A double mutation in the S4 domain dramatically reduced the slow component of the optical signal seen in ArcLight. Combining that double S4 mutant with the mutation in the S2 domain yielded a probe with kinetics <10 ms. Optimization of the linker sequence between S4 and the fluorescent protein resulted in a new ArcLight-derived probe, Bongwoori, capable of resolving action potentials in a hippocampal neuron firing at 60 Hz. Additional manipulation of the voltage-sensing domain could potentially lead to fluorescent sensors capable of optically resolving neuronal inhibition and subthreshold synaptic activity., (Copyright © 2015 the authors 0270-6474/15/350372-15$15.00/0.)

Published
2015
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results