Please note: To accommodate reviewer and recommender holiday schedules, we will be closed to submissions from 1st July — 1st September. During this time, reviewers will be able to submit reviews and recommenders will issue decisions, but no new or revised submissions can be made by authors. The one exception to this rule is that authors using the scheduled track who submit their initial Stage 1 snapshot prior to 1st July can choose a date within the shutdown period to submit their full Stage 1 manuscript.
We are recruiting recommenders (editors) from all research fields!
Your feedback matters! If you have authored or reviewed a Registered Report at Peer Community in Registered Reports, then please take 5 minutes to leave anonymous feedback about your experience, and view community ratings.
Latest recommendations
| Id | Title * | Authors * | Abstract * | Picture | Thematic fields * ▲ | Recommender | Reviewers | Submission date | |
|---|---|---|---|---|---|---|---|---|---|
19 Jun 2024
STAGE 1
Culture-Driven Neural Plasticity and Imprints of Body-Movement Pace on Musical Rhythm ProcessingThe interplay of music, movement, and culture on rhythm processingRecommended by Juan David Leongómez based on reviews by Anne Keitel and 1 anonymous reviewer
The interplay of music, movement, and cultural experience shapes rhythm perception. From bouncing babies and children at play, to tapping, clapping, and dancing, music often triggers synchronous body movements that can influence how we process rhythm. And, at the same time, long-term exposure to specific musical traditions shapes how we perceive and interpret rhythms.
However, direct behavioural and neuroscientific evidence on how these processes occur remains scarce. In this programmatic submission, comprising two complementary Stage 2 reports, Guérin et al. (2024) will investigate how body movements shape the processing of auditory information, and how previous short-term motor practice and long-term cultural experience interact to shape neural and behavioural responses to rhythmic stimuli. The authors will record in separate sessions both electroencephalography (EEG) and hand clapping, in response to rhythms from West/Central Africa. These recordings will be conducted before and after a session in which participants will clap/step to either a three or a four-beat metre that is expected to influence how they interpret a rhythm.
The first Stage 2 report, which will be conducted on African-enculturated participants, aims to demonstrate how body-movement pace flexibly imprints on human sensory processing. The authors build on various theoretical models that emphasise the role of motor production in metre perception, and predict that both neural and behavioural entrainment will improve following movement, matching the rhythmic pattern set by the previous body movements.
The second Stage 2 report aims to uncover how short-term motor practice and long-term cultural experience interact to shape responses to rhythmic stimuli, by integrating short-term motor practice and long-term cultural experience. For this, the authors will test separate groups of participants from distinct cultural backgrounds (African vs. Western-enculturated), which are predicted to show neural and behavioural differences in their preferred metric mapping before body movement, and expect that neural and behavioural entrainment will improve after movement, especially for the metre set by prior movements, and more significantly for the metre common in the participant's culture.
Together, the findings from the planned Stage 2 reports are expected to clarify how long-term cultural background and short-term motor practice imprint onto rhythm processing in humans. This research will enhance our understanding of how cultural experience, body movement, and neural plasticity interact in music processing.
The Stage 1 manuscript was evaluated over three rounds of in-depth review. Based on detailed responses to the reviewers' and recommender's comments, the recommender judged that the manuscript met the Stage 1 criteria and awarded in-principle acceptance (IPA).
URL to the preregistered Stage 1 protocol: https://osf.io/skuyc
Level of bias control achieved: Level 6. Data collection commenced during the later part of Stage 1 peer review; however, since no changes to the design were made after this point, the risk of bias due to prior data observation remains zero and the manuscript therefore qualifies for Level 6. List of eligible PCI RR-friendly journals: References
Guérin, S. M. R., Coulon, E., Lenc, T., Polak, R., Keller, P. E., & Nozaradan, S. (2024). Culture-Driven Neural Plasticity and Imprints of Body-Movement Pace on Musical Rhythm Processing. In principle acceptance of Version 2.1 by Peer Community in Registered Reports. https://osf.io/skuyc
| Culture-Driven Neural Plasticity and Imprints of Body-Movement Pace on Musical Rhythm Processing | Ségolène M. R. Guérin, Emmanuel Coulon, Tomas Lenc, Rainer Polak, Peter E. Keller, Sylvie Nozaradan | <p>The proposed programmatic registered report aims at capturing direct neuroscientific evidence for the rhythmic, movement-related shaping of auditory information with a cross-cultural perspective. Specifically, West/Central African- and Western-... | | Life Sciences | Juan David Leongómez | Anonymous | 2023-11-30 11:36:06 | |
17 Jun 2024
STAGE 1
Neophobia across social contexts in juvenile Herring gullsDoes social context influence neophobia in juvenile herring gulls (Larus argentatus)?Recommended by Ljerka Ostojic based on reviews by 2 anonymous reviewers
Many animals are increasingly reliant on living close or in urban environments. For them, neophobia – a trait that denotes the fearfulness of novelty (Mettke-Hoffmann, 2022) – may influence how well the species but also individuals of the same species adjust to the (human-induced) changes that characterise these environments (Lowry et al., 2013).
Typically, neophobia in non-human animals is assessed through behavioural tests, most often by measuring the time it takes an individual to approach a novel object or food that is positioned next to a novel object. Increasingly, resarchers are acknowledging that the social context may influence the behaviour of individuals in such situations, and several hypotheses have been proposed to explain a potential influence of social context on neophobic responses.
In the current study, Allaert et al. (2024) will use a within-subject design to test three hypotheses with juvenile herring gulls (Larus argentatus): 1) the risk dilution hypothesis, accoding to which gulls will exhibit smaller neophobic responses when tested in a group than when tested alone, 2) the negotiation hypothesis, according to which gulls will exhibit stronger neophobic responses when tested in a group than when tested alone, and 3) the social conformity hypothesis, according to which those more neophobic individuals will show a smaller neohobic response when tested in a group than when tested alone while less neophobic individuals will exhibit the opposite pattern.
The Stage 1 manuscript was evaluated by two reviewers over two rounds of revisions. During the revisions, the authors clarified the conceptual arguments of the manuscript (including why juveniles are being tested), and edited the methods, including timing of testing, adjustments to the way that the experimental and control conditions will be run, how the planned sample size will be ensured given that at the time of testing, some chicks may be of a different species (this will become evident later on), how relatedness between the chicks will be dealt with, as well as how the behavioural coding will be conducted. Thus, the recommender judged that the manuscript met the Stage 1 criteria and awarded in-principle acceptance (IPA).
URL to the preregistered Stage 1 protocol: https://osf.io/u4b7q
Level of bias control achieved: Level 6. No part of the data or evidence that will be used to answer the research question yet exists and no part will be generated until after IPA. List of eligible PCI RR-friendly journals:
References
1. Mettke-Hofmann, C. (2022). Neophobia. In: Vonk, J., Shackelford, T.K. (eds) Encyclopedia of Animal Cognition and Behavior. Springer, Cham. https://doi.org/10.1007/978-3-319-55065-7_908
2. Lowry, H., Lill, A., & Wong, B. B. (2013). Behavioural responses of wildlife to urban environments. Biological Reviews, 88, 537-549. https://doi.org/10.1111/brv.12012
3. Allaert, R., Knoch, S., Braem, S., Debeer, D, Martel, A., Müller, W., Stienen E., Lens, L., & Verbruggen. F. (2024) In principle acceptance of Version 3 by Peer Community in Registered Reports. https://osf.io/u4b7q
| Neophobia across social contexts in juvenile Herring gulls | Reinoud Allaert, Sophia Knoch, An Martel, Wendt Müller, Eric Stienen, Luc Lens, Frederick Verbruggen | <p>Neophobia, the fear or avoidance of the unfamiliar, can have significant fitness consequences. It is typically assessed by exposing individuals to unfamiliar objects when they are alone, but in social species the presence of conspecifics can in... | Life Sciences | Ljerka Ostojic | 2024-02-16 14:50:02 | |||
Registered Report: Are anticipatory auditory predictions enhanced in tinnitus and independent of hearing loss?Evidence for the role of predictive coding in subjective tinnitusRecommended by Chris Chambers based on reviews by Will Sedley, Pia Brinkmann and Emilie Cardon
Subjective tinnitus is a common disorder in which people experience a persistent sound in the absence of any external source. The underlying causes of tinnitus are debated – although the condition is strongly associated with hearing loss resulting from auditory damage, much remains to be understood about the neural processes that give rise to the phantom perception. Various classes of neurophysiological theories have been proposed, including the “altered gain” model – in which neurons in the auditory pathway increase their responsiveness to compensate for reduced auditory input following hearing loss – and the “noise cancellation” model – in which disrupted feedback connections from limbic regions are unable to tune out phantom signals. Although these theories account for much observed data, they have not been conclusively supported, and their ability to explain tinnitus is limited by the fact that hearing loss and tinnitus can arise independently and at different times.
In the current study, Reisinger et al. (2024) tested an emerging alternative theory based on a Bayesian predictive-coding framework (Sedley et al., 2016) in which the alteration of perceptual priors leads the auditory system to expect a sound that, if functioning normally, it should not expect. Using magnetoencephalography (MEG) in a sample of tinnitus patients (and carefully-matched controls for age, gender, and level of hearing loss), they asked whether tinnitus is associated with anticipatory brain activation, tuned to the carrier-frequency of an expected auditory stimulus. Specifically, the authors predicted that if the predictive-coding framework is correct then individuals with tinnitus should show different regularity-dependent pre-activations of carrier- frequency-specific information compared to the control group, while tone carrier-frequencies should be processed normally in tinnitus patients. They also predicted that any such pre-activations should not be related to levels of reported subjective tinnitus distress, as measured with the short version of the Tinnitus Questionnaire (mini-TQ).
The results broadly confirmed the hypotheses, with some caveats. Statistically significant differences in regularity-dependent pre-activations were observed between the tinnitus and control groups, however – curiously – the effects appear to be driven by below-chance decoding in the control group, complicating the interpretration. At the same time, consistent with expectations, frequency processing did not differ significantly between individuals with and without tinnitus, and the observed pre-activations were not significantly related to tinnitus distress. Overall, the findings cautiously support the conclusion that chronic tinnitus is associated with maladaptively upregulated predictive neural processing, and that this phenomenon is unlikely to be explained by either tinnitus distress or hearing loss.
The Stage 2 manuscript was evaluated over one round of in-depth review. Based on detailed responses to the reviewers' comments, the recommender judged that the manuscript met the Stage 2 criteria and awarded a positive recommendation.
URL to the preregistered Stage 1 protocol: https://osf.io/6gvpy
Level of bias control achieved: Level 3. At least some data/evidence that was used to the answer the research question had been previously accessed by the authors (e.g. downloaded or otherwise received), but the authors certify that they had yet observed any part of the data/evidence prior to Stage 1 IPA.
List of eligible PCI RR-friendly journals:
References
1. Reisinger, L., Demarchi, G., Rösch, , S., Trinka, E., Obleser, L., & Weisz, N. (2024). Registered Report: Are anticipatory auditory predictions enhanced in tinnitus and independent of hearing loss? [Stage 2] Acceptance of Version 3 by Peer Community in Registered Reports. https://osf.io/9wqjh
2. Sedley, W., Friston, K. J., Gander, P. E., Kumar, S., & Griffiths, T. D. (2016). An integrative tinnitus model based on sensory precision. Trends in Neurosciences, 39, 799-812. https://doi.org/10.1016/j.tins.2016.10.004
| Registered Report: Are anticipatory auditory predictions enhanced in tinnitus and independent of hearing loss? | L. Reisinger, G. Demarchi, S. Rösch, E. Trinka, J. Obleser, N. Weisz | <p>Phantom perceptions occur without any identifiable environmental or bodily source. The mechanisms and key drivers behind phantom perceptions like tinnitus are not well understood. The dominant “altered-gain”-framework suggests that tinnitus res... | Life Sciences | Chris Chambers | 2024-02-21 16:17:33 | |||
12 Jul 2024
STAGE 1
Associations between anxiety-related traits and fear acquisition and extinction - an item-based content and meta-analysisIntegrative meta-analysis of anxiety-related traits and fear processing: bridging research to clinical applicationRecommended by Sara Garofalo based on reviews by Yoann Stussi, Luigi Degni, Marco Badioli and 1 anonymous reviewer
The paper aims to bridge gaps in understanding the relationship between anxiety-related traits and fear processing, with a specific focus on fear acquisition and extinction. Fear and safety processing are known to be linked to anxiety symptoms and traits such as neuroticism and intolerance of uncertainty (Lonsdorf et al., 2017; Morriss et al., 2021). However, the diversity in study focus and measurement methods makes it difficult to integrate findings into clinical practice effectively.
To address this issue, Brunsch et al. (2024) propose a systematic literature search and meta-analysis, following PRISMA guidelines, to explore these associations. They plan to use nested random effects models to analyze both psychophysiological and self-report outcome measures. Additionally, they will examine the role of different questionnaires used to assess anxiety-related traits and conduct a content analysis of these tools to evaluate trait overlaps.
Current knowledge from the literature indicates that individuals with anxiety disorders exhibit differences in fear acquisition and extinction compared to those without such disorders (Lonsdorf et al., 2017; Morriss et al., 2021). Previous meta-analyses have shown associations between anxiety traits and fear generalization/extinction, but these studies are limited in their scope and focus.
The primary aim of the research is to provide a comprehensive summary of the associations between anxiety-related traits and conditioned responding during fear acquisition and extinction across multiple measures. Another goal is to investigate whether different anxiety-related trait questionnaires yield different associations with fear and extinction learning. The authors will also conduct a content analysis to better interpret the results of their meta-analysis by examining the overlap in questionnaire content.
A secondary aim of the study is to evaluate how sample characteristics, experimental specifics, and study quality influence the associations between anxiety-related traits and fear acquisition and extinction. By addressing these aims, the study seeks to advance the understanding of fear-related processes in anxiety and inform more targeted prevention and intervention strategies.
The Stage 1 manuscript underwent two rounds of thorough review. After considering the detailed responses to the reviewers' comments, the recommender determined that the manuscript met the Stage 1 criteria and granted in-principle acceptance (IPA).
URL to the preregistered Stage 1 protocol: https://osf.io/4mndj
Level of bias control achieved: Level 3. At least some data/evidence that will be used to the answer the research question has been previously accessed by the authors (e.g. downloaded or otherwise received), but the authors certify that they have not yet observed ANY part of the data/evidence.
List of eligible PCI RR-friendly journals:
References
1. Bruntsch, M., Abend, R., Chalkia, A., Cooper, S. E., Ehlers, M. R., Johnson, D. C., Klingelhöfer-Jens, M., Morriss, J., Zika, O., & Lonsdorf, T. B. (2024). Associations between anxiety-related traits and fear acquisition and extinction - an item-based content and meta-analysis. In principle acceptance of Version 3 by Peer Community in Registered Reports. https://osf.io/4mndj
2. Lonsdorf, T. B., & Merz, C. J. (2017). More than just noise: Inter-individual differences in fear acquisition, extinction and return of fear in humans - Biological, experiential, temperamental factors, and methodological pitfalls. Neuroscience & Biobehavioral Reviews, 80, 703–728. https://doi.org/10.1016/j.neubiorev.2017.07.007
3. Morriss, J., Wake, S., Elizabeth, C., & van Reekum, C. M. (2021). I Doubt It Is Safe: A Meta-analysis of Self-reported Intolerance of Uncertainty and Threat Extinction Training. Biological Psychiatry Global Open Science, 1, 171–179. https://doi.org/10.1016/j.bpsgos.2021.05.011
| Associations between anxiety-related traits and fear acquisition and extinction - an item-based content and meta-analysis | Maria Bruntsch, Samuel E Cooper, Rany Abend, Marian Boor, Anastasia Chalkia, Mana Ehlers, Artur Czeszumski, Dave Johnson, Maren Klingelhöfer-Jens, Jayne Morriss, Erik Mueller, Ondrej Zika, Tina Lonsdorf | <p>Background: Deficits in learning and updating of fear and safety associations have been reported in patients suffering from anxiety- and stress-related disorders. Also in healthy individuals, anxiety-related traits have been linked to altered f... | Life Sciences | Sara Garofalo | Anonymous, Luigi Degni, Marco Badioli, Yoann Stussi | 2024-03-15 14:48:20 | ||
15 Nov 2023
STAGE 1
Somatosensory Response Changes During Illusory Finger StretchingNeural responses to a finger-stretching illusion in human somatosensory cortexRecommended by D. Samuel Schwarzkopf based on reviews by Harry Farmer, Alexandra Mitchell and Susanne Stoll
Chronic pain is a major cause of disability that can often poorly managed with pharmacological treatments. This has prompted the exploration of other interventions like resizing illusions of body parts in augmented reality. These illusions have shown promise in conditions like osteoarthritis and complex regional pain syndrome, but it remains unclear how they alter the neural representation of body parts in the brain. The study by Hansford and colleagues aims to investigate these mechanisms in healthy participants, using somatosensory steady state evoked potentials (SSEP) and self-report questionnaires.
The study will involve finger stretching in an augmented reality setup that allows the researchers to independently manipulate visual and tactical stimulation. Assuming that multisensory stimulation indeed produces a robust illusion, the researchers will quantify the somatosensory evoked potentials in multisensory, unisensory, and two non-illusion control conditions. The study will provide inights into the neural mechanisms of these illusions and lay the ground for future investigations of these processes as a potential treatment for chronic pain.
The manuscript was evaluated over seven rounds of in-depth review by the recommender and three expert reviewers. After substantial revisions, the recommender judged that the manuscript met the Stage 1 criteria and awarded in-principle acceptance (IPA).
URL to the preregistered Stage 1 protocol: https://osf.io/u6gsb
Level of bias control achieved: Level 6. No part of the data or evidence that will be used to answer the research question yet exists and no part will be generated until after IPA. List of eligible PCI RR-friendly journals:
References 1. Hansford, K. J., Baker, D. H., McKenzie, K. J., & Preston, C. E. J. (2023). Somatosensory Response Changes During Illusory Finger Stretching. In principle acceptance of Version 7 by Peer Community in Registered Reports. https://osf.io/u6gsb | Somatosensory Response Changes During Illusory Finger Stretching | Kirralise J. Hansford, Daniel H. Baker, Kirsten J. McKenzie & Catherine E. J. Preston | <p>Resizing illusions, delivered using augmented reality, resize a body part through either stretching or shrinking manipulations. These resizing illusions have been investigated in visuotactile, visual-only and visuo-auditory presentations. Howev... | Life Sciences, Medical Sciences | D. Samuel Schwarzkopf | 2022-11-15 17:17:18 | |||
27 Jun 2023
STAGE 1
Functional MRI brain state occupancy in the presence of cerebral small vessel disease -- pre-registration for a replication analysis of the Hamburg City Health StudyTesting the replicability of dynamic functional connectivity correlates of cerebral small vessel disease in the Hamburg City Health StudyRecommended by Robert McIntosh based on reviews by Olivia Hamilton and 1 anonymous reviewer
A recent study has reported that the extent of cerebral small vessel disease (cSVD) shows associations with dynamic functional connectivity measures obtained from resting state functional MRI scans (Schlemm et al, 2022). Specifically, when the functional scan was parsed into time spent in discrete brain states, the proportion of time spent in the two most-occupied states was negatively related to a structural indicator of cSVD (volume of white matter hyperintensities of presumed vascular origin). This measure of 'fractional occupancy' was also associated with cognitive impairment as indicated by longer time to complete part B of the Trail Making Test. These findings were based on the analysis of data from 988 participants in the Hamburg City Health Study (HCHS).
In the present Registered Report, Schlemm (2023) will test whether these associations can be replicated in an independent sample of participants from the HCHS, not included in the earlier analysis (projected N for new analysis ~1500). In addition to the two main hypothesis tests, an exploratory multiverse analysis will be reported, systematically varying some key parameters of the MRI processing pipeline to provide further information about the robustness of the outcome of the primary hypothesis test.
The Stage 1 plan was refined over two rounds of review by two relevant experts, with additional input from the recommender on the specification of the registered plan. Both reviewers are satisfied that the plan constitutes an appropriate approach to this question, and on the basis of their comments and his own evaluation, the recommender judged that the Stage 1 report meets the criteria for in-principle acceptance.
URL to the preregistered Stage 1 protocol: https://osf.io/9yhzc
Level of bias control achieved: Level 2. At least some data/evidence that will be used to answer the research question has been accessed and partially observed by the authors, but the authors certify that they have not yet observed the key variables within the data that will be used to answer the research question AND they have taken additional steps to maximise bias control and rigour. List of eligible PCI RR-friendly journals:
References
1. Schlemm, E., Frey, B. M., Mayer, C., Petersen, M., Fiehler, J., Hanning, U., Kühn, S., Twerenbold, R., Gallinat, J., Gerloff, C., Thomalla, G. & Cheng, B. (2022). Equalization of brain state occupancy accompanies cognitive impairment in cerebral small vessel disease. Biological Psychiatry, 92, 592-602. https://doi.org/10.1016/j.biopsych.2022.03.019
2. Schlemm, E. (2023). Functional MRI brain state occupancy in the presence of cerebral small vessel disease – pre-registration for a replication analysis of the Hamburg City Health Study. In principle acceptance of Version 1.5 by Peer Community in Registered Reports. https://osf.io/9yhzc
| Functional MRI brain state occupancy in the presence of cerebral small vessel disease -- pre-registration for a replication analysis of the Hamburg City Health Study | Eckhard Schlemm | <p>Objective: To replicate recent findings about the association between the extent of cerebral small vessel disease (cSVD), functional brain network dedifferentiation and cognitive impairment.</p> <p>Methods: We will analyze demographic, imaging... | Life Sciences, Medical Sciences | Robert McIntosh | 2022-11-19 14:21:28 | |||
16 Nov 2023
STAGE 1
The effect of stimulus saliency on the modulation of pain-related ongoing neural oscillations: a Registered ReportAre there oscillatory markers of pain intensity?Recommended by Zoltan Dienes based on reviews by Markus Ploner and Björn Horing
Rhythmic changes in pain can lead to corresponding modulations of EEG amplitudes in theta, alpha, and beta bands. But the question remains open as to whether these modulations are actually tracking pain, or maybe rather saliency or stimulus intensity. The question is of some importance because a marker of pain per se could be useful for tracking felt pain without a verbal response, and could be useful in investigating interventions for treating pain (such as suggestion). Here, Leu et al. (2023) will address the question of whether modulations reflect saliency or else the intensity of pain, by using an oddball paradigm in which most trials are a pain stimulus of a certain intensity, and oddball trials will sometimes occur, at either a higher intensity or a lower intensity than the baseline ones. If the modulations reflect salience, the modulation at the frequency of the oddball will be similar for high and low intensity oddballs. However, if the modulations reflect pain intensity, the modulations for the low rather than high oddball condition will be lower.
The Stage 1 manuscript was evaluated over three rounds of in-depth peer review, the first two consisting of substantial comments from two scholars with relevant expertise, and the third consisting of a close review by the recommender. Based on detailed responses to the reviewers' comments, the recommender judged that the manuscript met the Stage 1 criteria and therefore awarded in-principle acceptance (IPA).
URL to the preregistered Stage 1 protocol: https://osf.io/qbrf2
Level of bias control achieved: Level 6. No part of the data or evidence that will be used to answer the research question yet exists and no part will be generated until after IPA. List of eligible PCI RR-friendly journals:
References
1. Leu, C., Forest, S., Legrain, V., & Liberati, G. (2023). The effect of stimulus saliency on the modulation of pain-related ongoing neural oscillations: a Registered Report. In principle acceptance of Version 4 by Peer Community in Registered Reports. https://osf.io/qbrf2 | The effect of stimulus saliency on the modulation of pain-related ongoing neural oscillations: a Registered Report | Chiara Leu, Sébastien Forest, Valéry Legrain, Giulia Liberati | <p>Ongoing oscillations have been shown to be modulated in different frequency bands following phasic, tonic as well as periodic thermonociceptive stimulation. Yet, it remains unclear whether these modulations are related to pain perception, salie... | Life Sciences, Medical Sciences | Zoltan Dienes | 2023-09-06 15:15:19 | |||
Functional MRI brain state occupancy in the presence of cerebral small vessel disease -- a pre-registered replication analysis of the Hamburg City Health StudyReplicable dynamic functional connectivity and cognitive correlates of cerebral small vessel disease in the Hamburg City Health StudyRecommended by Robert McIntosh based on reviews by 1 anonymous reviewer
In a previous analysis of data from 988 participants in the Hamburg City Health Study (HCHS), Schlemm and colleagues (2022) reported significant associations between the extent of cerebral small vessel disease (cSVD) and dynamic functional connectivity measures from resting state fMRI. Specifically, the volume of white matter hyperintensities of presumed vascular origin, a structural indicator of cSVD, was negatively related to the proportion of time (‘fractional occupancy’) spent in the two most occupied functional brain states. Reduced fractional occupancy was also associated with longer times to complete part B of the Trail Making Test.
In the present Registered Report, Ingwersen and colleagues (2023) successfully replicated these associations between structural, functional and cognitive measures in a sample of 1651 HCHS participants not included in the earlier study. An exploratory multiverse analysis found that the associations were generally robust to different brain parcellation and confound regression strategies. These replicable patterns reinforce the idea that cSVD may disrupt the brain’s ability to enter and maintain distinct functional modes, and that these changes in functional dynamics are predictive of cognitive impairment.
The Stage 2 manuscript was assessed over one round of in-depth review. The recommender judged that responses to reviewer comments were appropriate, and that the manuscript met the Stage 2 criteria for recommendation.
URL to the preregistered Stage 1 protocol: https://osf.io/9yhzc
Level of bias control achieved: Level 2. At least some data/evidence that was used to answer the research question had been accessed and partially observed by the authors prior to Stage 1 in-principle acceptance, but the authors certify that they had not yet observed the key variables within the data that were used to answer the research question AND they took additional steps to maximise bias control and rigour. List of eligible PCI RR-friendly journals:
References
1. Schlemm, E., Frey, B. M., Mayer, C., Petersen, M., Fiehler, J., Hanning, U., Kühn, S., Twerenbold, R., Gallinat, J., Gerloff, C., Thomalla, G. & Cheng, B. (2022). Equalization of brain state occupancy accompanies cognitive impairment in cerebral small vessel disease. Biological Psychiatry, 92, 592-602. https://doi.org/10.1016/j.biopsych.2022.03.019
2. Ingwersen, T., Mayer, C., Petersen, M., Frey, B. M., Fiehler, J., Hanning, U., Kühn, S., Gallinat, J., Twerenbold, R., Gerloff, C., Cheng, B., Thomalla, G. & Schlemm, E. (2023). Functional MRI brain state occupancy in the presence of cerebral small vessel disease -- a pre-registered replication analysis of the Hamburg City Health Study. Acceptance of Version 2.01 by Peer Community in Registered Reports. https://github.com/csi-hamburg/HCHS-brain-states-RR/blob/f9d00adbbcf9593d8d191bf5b93912141b80ab1b/manuscript/build/main.pdf
| Functional MRI brain state occupancy in the presence of cerebral small vessel disease -- a pre-registered replication analysis of the Hamburg City Health Study | Thies Ingwersen, Carola Mayer, Marvin Petersen, Benedikt M. Frey, Jens Fiehler, Uta Hanning, Simone Kühn, Jürgen Gallinat, Raphael Twerenbold, Christian Gerloff, Bastian Cheng, Götz Thomalla, Eckhard Schlemm, | <p><strong>Objective</strong>: To replicate recent findings on the association between the extent of cerebral small vessel disease (cSVD), functional brain network dedifferentiation, and cognitive impairment.</p> <p><strong>Methods:</strong> We a... | Life Sciences, Medical Sciences | Robert McIntosh | 2023-10-17 09:53:02 | |||
Cue-based modulation of pain stimulus expectation: do ongoing oscillations reflect changes in pain perception? A Registered ReportUnderstanding oscillatory correlates of pain expectationRecommended by Gemma Learmonth based on reviews by Zoltan Dienes, Chris Chambers and Markus Ploner
Recent studies using an EEG frequency tagging approach have reported modulations of alpha, beta and theta bands at the stimulation frequency during nociceptive/painful thermal stimulation compared to non-nociceptive/non-painful vibrotactile stimulation. Prior expectations of the intensity of upcoming painful stimuli are known to strongly modulate the subjective experience of those stimuli. Thus, modulating the expectation of pain should result in a change in the modulation of oscillations if these factors are indeed linked.
In this study, Leu, Glineur and Liberati modulated expectations of pain (low or high intensity) in 40 participants prior to delivering thermal cutaneous stimulation (low, medium or high intensity). They recorded how intense participants expected the pain to be, and how intense they felt it to be, as well as EEG to assess oscillatory differences across the expectation and intensity conditions.
The results confirmed that there was a strong effect of expectation on the perceived stimulus intensity. However, contrary to the hypotheses, this was not reflected in the cortical oscillations. Overall this indicates a possible dissociation between perceived pain and modulation of ongoing oscillations in the theta, alpha and beta bands.
The Stage 2 manuscript was evaluated over one round of in-depth review. Based on detailed responses to the reviewers' comments, the recommender judged that the manuscript met the Stage 2 criteria and awarded a positive recommendation.
URL to the preregistered Stage 1 protocol: https://osf.io/y6fb8
Level of bias control achieved: Level 6. No part of the data or evidence that was used to answer the research question was generated until after IPA. List of eligible PCI RR-friendly journals: References
1. Leu, C., Glineur, E. & Liberati, G. (2023). Cue-based modulation of pain stimulus expectation: do ongoing oscillations reflect changes in pain perception? [Stage 2] Acceptance of Version 2 by Peer Community in Registered Reports. https://osf.io/awrge | Cue-based modulation of pain stimulus expectation: do ongoing oscillations reflect changes in pain perception? A Registered Report | Chiara Leu, Esther Glineur, Giulia Liberati | <p style="text-align: justify;">A promising stream of investigations is targeting ongoing neural oscillations and whether their modulation could be related to the perception of pain. Using an electroencephalography (EEG) frequency tagging approach... | Life Sciences, Medical Sciences | Gemma Learmonth | 2024-01-23 19:35:39 | |||
22 Jul 2024
STAGE 1
Replication of “Carbon-Dot-Based Dual-Emission Nanohybrid Produces a Ratiometric Fluorescent Sensor for In Vivo Imaging of Cellular Copper Ions”Replicating, Revising and Reforming: Unpicking the Apparent Nanoparticle Endosomal Escape ParadoxRecommended by Emily Linnane and Yuki Yamada based on reviews by Cecilia Menard-Moyon and Zeljka Krpetic
Context
Over the past decade there has been an exponential increase in the number of research papers utlising nanoparticles for biological applications such as intracellular sensing [1, 2], theranostics [3-5] and more recently drug delivery and precision medicine [6, 7]. Despite the success stories, there is a disconnect regarding current dogma on issues such as nanoparticle uptake and trafficking, nanoparticle delivery via the enhanced permeability and retention (EPR) effect, and endosomal escape. Critical re-evaluation of these concepts both conceptually and experimentally is needed for continued advancement in the field.
For this preregistration, Said et al. (2024) focus on nanoparticle intracellular trafficking, specifically endosomal escape [8]. The current consensus in the literature is that nanoparticles enter cells via endocytosis [9, 10] but reportedly just 1-2% of nanoparticles/ nanoparticle probes escape endosomes and enter the cytoplasm [11-13]. There is therefore an apparent paradox over how sensing nanoparticles can detect their intended targets in the cytoplasm if they are trapped within the cell endosomes. To address this fundamental issue of nanoparticle endosomal escape, Lévy and coworkers are carrying out replication studies to thoroughly and transparently replicate the most influential papers in the field of nanoparticle sensing. The aim of these replication studies is twofold: to establish a robust methodology to study endosomal escape of nanoparticles, and to encourage discussions, transparency and a step-change in the field.
Replication of “Carbon-Dot-Based Dual-Emission Nanohybrid Produces a Ratiometric Fluorescent Sensor for In Vivo Imaging of Cellular Copper Ions”
For this replication study, the authors classified papers on the topic of nanoparticle sensing and subsequently ranked them by number of citations. Based on this evaluation they selected a paper by Zhu and colleagues [14] entitled “Carbon-Dot-Based Dual-Emission Nanohybrid Produces a Ratiometric Fluorescent Sensor for In Vivo Imaging of Cellular Copper Ions” for their seminal replication study. To determine the reproducibility of the results from Zhu et al., the authors aim to establish the proportion of endosomal escape of the nanoparticles, and to examine the data in a biological context relevant to the application of the probe.
Beyond Replication
The authors plan to replicate the exact conditions reported in the materials and methods section of the selected paper such as nanoparticle probe synthesis of CdSe@C-TPEA nanoparticles, assessment of particle size, stability and reactivity and effect on cells (TEM, pH experiments, fluorescent responsivity to metal ions and cell viability). In addition, Said et al., plan to include further experimental characterisation to complement the existing study by Zhu and colleagues. They will incorporate additional controls and methodology to determine the intracellular location of nanoparticle probes in cells including: quantifying excess fluorescence in the culture medium, live cell imaging analysis, immunofluorescence with endosomal and lysosomal markers, and electron microscopy of cell sections. The authors will also include supplementary viability studies to assess the impact of the nanoparticles on HeLa cells as well as an additional biologically relevant cell line (for use in conjunction with the HeLa cells as per the original paper).
The Stage 1 manuscript underwent two rounds of thorough in-depth review. After considering the detailed responses to the reviewers' comments, the recommenders determined that the manuscript met the Stage 1 criteria and awarded in-principle acceptance (IPA).
The authors have thoughtfully considered their experimental approach to the replication study, whilst acknowledging any potential limitations. Given that conducting such a replication study is novel in the field of Nanotechnology and there is currently no ‘gold standard’ approach in doing so, the authors have showed thoughtful regard of statistical analysis and unbiased methodology where possible.
Based on current information, this study is the first use of preregistration via Peer Community in Registered Reports and the first formalised replication study in Nanotechnology for Biosciences. The outcomes of this of this study will be significant both scientifically and in the wider context in discussion of the scientific method.
URL to the preregistered Stage 1 protocol: https://osf.io/qbxpf
Level of bias control achieved: Level 6. No part of the data or evidence that will be used to answer the research question yet exists and no part will be generated until after IPA. List of eligible PCI RR-friendly Journals:
References
1. Howes, P. D., Chandrawati, R., & Stevens, M. M. (2014). Colloidal nanoparticles as advanced biological sensors. Science, 346(6205), 1247390. https://doi.org/10.1126/science.1247390
2. Liu, C. G., Han, Y. H., Kankala, R. K., Wang, S. B., & Chen, A. Z. (2020). Subcellular performance of nanoparticles in cancer therapy. International Journal of Nanomedicine, 675-704. https://doi.org/10.2147/IJN.S226186
3. Tang, W., Fan, W., Lau, J., Deng, L., Shen, Z., & Chen, X. (2019). Emerging blood–brain-barrier-crossing nanotechnology for brain cancer theranostics. Chemical Society Reviews, 48(11), 2967-3014. https://doi.org/10.1039/C8CS00805A
4. Yoon, Y. I., Pang, X., Jung, S., Zhang, G., Kong, M., Liu, G., & Chen, X. (2018). Smart gold nanoparticle-stabilized ultrasound microbubbles as cancer theranostics. Journal of Materials Chemistry B, 6(20), 3235-3239. https://doi.org/10.1039%2FC8TB00368H
5. Lin, H., Chen, Y., & Shi, J. (2018). Nanoparticle-triggered in situ catalytic chemical reactions for tumour-specific therapy. Chemical Society Reviews, 47(6), 1938-1958. https://doi.org/10.1039/C7CS00471K
6. Hou, X., Zaks, T., Langer, R., & Dong, Y. (2021). Lipid nanoparticles for mRNA delivery. Nature Reviews Materials, 6(12), 1078-1094. https://doi.org/10.1038/s41578-021-00358-0
7. Mitchell, M. J., Billingsley, M. M., Haley, R. M., Wechsler, M. E., Peppas, N. A., & Langer, R. (2021). Engineering precision nanoparticles for drug delivery. Nature Reviews Drug Discovery, 20(2), 101-124. https://doi.org/10.1038/s41573-020-0090-8
8. Said, M., Gharib, M., Zrig, S., & Lévy, R. (2024). Replication of “Carbon-Dot-Based Dual-Emission Nanohybrid Produces a Ratiometric Fluorescent Sensor for In Vivo Imaging of Cellular Copper Ions”. In principle acceptance of Version 3 by Peer Community in Registered Reports. https://osf.io/qbxpf
9. Behzadi, S., Serpooshan, V., Tao, W., Hamaly, M. A., Alkawareek, M. Y., Dreaden, E. C., ... & Mahmoudi, M. (2017). Cellular uptake of nanoparticles: Journey inside the cell. Chemical Society Reviews, 46(14), 4218-4244. https://doi.org/10.1039/C6CS00636A
10. de Almeida, M. S., Susnik, E., Drasler, B., Taladriz-Blanco, P., Petri-Fink, A., & Rothen-Rutishauser, B. (2021). Understanding nanoparticle endocytosis to improve targeting strategies in nanomedicine. Chemical society reviews, 50(9), 5397-5434. https://doi.org/10.1039/D0CS01127D
11. Smith, S. A., Selby, L. I., Johnston, A. P., & Such, G. K. (2018). The endosomal escape of nanoparticles: toward more efficient cellular delivery. Bioconjugate Chemistry, 30(2), 263-272. http://dx.doi.org/10.1021/acs.bioconjchem.8b00732
12. Cupic, K. I., Rennick, J. J., Johnston, A. P., & Such, G. K. (2019). Controlling endosomal escape using nanoparticle composition: current progress and future perspectives. Nanomedicine, 14(2), 215-223. https://doi.org/10.2217/nnm-2018-0326
13. Wang, Y., & Huang, L. (2013). A window onto siRNA delivery. Nature Biotechnology, 31(7), 611-612. https://doi.org/10.1038/nbt.2634
14. Zhu, A., Qu, Q., Shao, X., Kong, B., & Tian, Y. (2012). Carbon-dot-based dual-emission nanohybrid produces a ratiometric fluorescent sensor for in vivo imaging of cellular copper ions. Angewandte Chemie (International ed. in English), 51(29), 7185-7189. https://doi.org/10.1002/anie.201109089
| Replication of “Carbon-Dot-Based Dual-Emission Nanohybrid Produces a Ratiometric Fluorescent Sensor for In Vivo Imaging of Cellular Copper Ions” | Maha Said, Mustafa Gharib, Samia Zrig, Raphaël Lévy | <p>In hundreds of articles published over the past two decades, nanoparticles have been described as probes for sensing and imaging of a variety of intracellular cytosolic targets. However, nanoparticles generally enter cells by endocytosis with o... | | Life Sciences, Medical Sciences, Physical Sciences | Emily Linnane | 2023-11-29 19:14:03 |
