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Latest recommendations
| Id | Title * | Authors * | Abstract * | Picture | Thematic fields * ▼ | Recommender | Reviewers | Submission date | |
|---|---|---|---|---|---|---|---|---|---|
Positive Treatment Effects and High Heterogeneity of Hormonal Contraceptive Use on Women's SexualityThe Causal Effects of Hormonal Contraceptives on Sexuality OutcomesRecommended by Thomas Evans based on reviews by Summer Mengelkoch and 1 anonymous reviewer
Ensuring universal access to sexual and reproductive health and reproductive rights is a global concern, exemplified by goal 5.6 of the Sustainable Development Goals (UN General Assembly, 2015). Whilst the range of contraceptive options have increased, our understanding of the impacts of use for women are inadequate and represent a key barrier to positive change in policies and practices. In particular, we have few consensuses on the expected impacts of hormonal contraceptive use on women's sexuality and wellbeing.
In their Stage 1 Report, Botzet et al. (2023) argued that this inconclusive evidence base could be due to the wide heterogeneity in responses, the impacts of this heterogeneity upon attrition, differences in contraceptive methods and dosage effects, confounders, and the potential for reverse causality. Tackling some of these potential factors, Botzet (2023) planned to explore whether hormonal contraceptive use influences sexuality and well-being outcomes, and whether (and to what extent) the effects vary between women. To achieve this they proposed analysis of longitudinal data from the German Family Panel (PAIRFAM) which included annual waves of data collection, with separate Stage 2 submissions planned to report findings based on sexuality and well-being.
This specific Stage 2 Report, Botzet et al. (2025) focus upon the sexuality-based outcomes of the programme of work and found positive effects of hormonal contraceptives on sexual frequency and sexual satisfaction (but not desired sexual frequency), having controlled for a number of potential confounding variables. However, they also found relatively high heterogeneity for individual treatment effects, suggesting that predicting its effect for any given individual may be difficult. This work is a rigorous starting point for better understanding the impacts of hormonal contraceptives and the possibility for tailored approaches to contraception.
The Stage 2 manuscript was evaluated following one round of in-depth review. Based on detailed responses to the reviewers' and recommenders' comments, the recommender judged that the manuscript met the Stage 2 criteria and therefore awarded a positive recommendation.
URL to the preregistered Stage 1 protocol: https://osf.io/kj3h2
Level of bias control achieved: Level 3. At least some of the data/evidence that was used to answer the research question existed and was accessible in principle prior to IPA but the authors certify that they did not access any part of that data/evidence until after IPA. List of eligible PCI-RR-friendly journals:
References
1. Botzet, L. J., Rohrer, J. M., Penke, L. & Arslan, R. C. (2023). Hormonal Contraceptive Use and Women's Sexuality and Well-Being: Estimating Treatment Effects and Their Heterogeneity Based on Longitudinal Data [Stage 1]. In principle acceptance of Version 3 by Peer Community in Registered Reports. https://osf.io/kj3h2
2. Botzet, L. J., Rohrer, J. M., Penke, L. & Arslan, R. C. (2025). Positive Treatment Effects and High Heterogeneity of Hormonal Contraceptive Use on Women's Sexuality [Stage 2]. Acceptance of Version 3 by Peer Community in Registered Reports.
2. UN General Assembly (2015). Transforming our world : the 2030 Agenda for Sustainable Development, 21 October 2015, A/RES/70/1. Available at: https://www.refworld.org/docid/57b6e3e44.html [accessed 27 September 2023]
| Positive Treatment Effects and High Heterogeneity of Hormonal Contraceptive Use on Women's Sexuality | Laura J. Botzet, Julia M. Rohrer, Lars Penke, Ruben C. Arslan | <p>Different women experience hormonal contraceptives differently, reporting side effects on their sexuality that range from negative to positive. But research on such causal effects of hormonal contraceptives on psychological outcomes struggles b... | Life Sciences, Social sciences | Thomas Evans | 2024-03-15 15:07:34 | |||
Impact of analytic decisions on test-retest reliability of individual and group estimates in functional magnetic resonance imaging: a multiverse analysis using the monetary incentive delay taskExploring determinants of test-retest reliability in fMRI: a study with the Monetary Incentive Delay TaskRecommended by Dorothy Bishop based on reviews by Xiangzhen Kong and 1 anonymous reviewer
Functional magnetic resonance imaging has been used to explore brain-behaviour relationships for many years, with proliferation of a wide range of sophisticated analytic procedures. However, rather scant attention has been paid to the reliability of findings. Concerns have been growing failures to replicate findings in some fields, but it is hard to know how far this is a consequence of underpowered studies, flexible analytic pipelines, or variability within and between participants. Demidenko et al. (2024) took advantage of the availability of three existing datasets, including the Adolescent Brain Cognitive Development (ABCD) study, the Michigan Longitudinal Study, and the Adolescent Risk Behavior Study, which all included a version of the Monetary Incentive Delay task measured in two sessions. These were entered into a multiverse analysis, which considered how within-subject and between-subject variance varies according to four analytic factors: smoothing (5 levels), motion correction (6 levels), task modelling (3 levels) and task contrasts (4 levels). They also considered how sample size affects estimates of reliability. The results have important implications for the those using fMRI with the Monetary Incentive Delay Task, and also raise questions more broadly about use of fMRI indices to study individual differences. Motion correction had relatively little impact on the ICC, and the effect size of the smoothing kernel was modest. Larger impacts on reliability were associated with choice of contrast (implicit baseline giving larger effects) and task parameterization. But perhaps the most sobering message from this analysis is that although activation maps from group data were reasonably reliable, the ICC, used as an index of reliability for individual levels of activation, was consistently low. This raises questions about the suitability of the Monetary Incentive Delay Task for studying individual differences. Another point is that reliability estimates become more stable as sample size increases; researchers may want to consider whether the trade-off between cost and gain in precision is justified for sample sizes above 250. I did a quick literature search on Web of Science: at the time of writing the search term ("Monetary Delay Task" AND fMRI) yielded 410 returns, indicating that this is a popular method in cognitive neuroscience. The detailed analyses reported here will repay study for those who are planning further research using this task. The Stage 2 manuscript was evaluated over one round of in-depth review. Based on detailed responses to the reviewer's and recommender's 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/nqgeh
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 IPA, but the authors certify that they had not yet sufficiently observed the key variables within the data to be able to answer the research questions and they took additional steps to maximise bias control and rigour.
List of eligible PCI RR-friendly journals:
References 1. Demidenko, M. I., Mumford, J. A., & Poldrack, R. A. (2024). Impact of analytic decisions on test-retest reliability of individual and group estimates in functional magnetic resonance imaging: a multiverse analysis using the monetary incentive delay task [Stage 2]. Acceptance of Version 5 by Peer Community in Registered Reports. https://www.biorxiv.org/content/10.1101/2024.03.19.585755v4 | Impact of analytic decisions on test-retest reliability of individual and group estimates in functional magnetic resonance imaging: a multiverse analysis using the monetary incentive delay task | Michael I. Demidenko, Jeanette A. Mumford, Russell A. Poldrack | <p>Empirical studies reporting low test-retest reliability of individual blood oxygen-level dependent (BOLD) signal estimates in functional magnetic resonance imaging (fMRI) data have resurrected interest among cognitive neuroscientists in methods... |  | Life Sciences, Social sciences | Dorothy Bishop | 2024-03-21 02:23:30 | ||
06 Mar 2025
STAGE 1
The role of extra-striate areas in conscious motor behavior: a registered report with Fast-Optical ImagingNeural underpinning of conscious perception of visual stimuli disentangled from motor confoundsRecommended by Anoushiravan Zahedi based on reviews by 3 anonymous reviewers
The debate about consciousness and its neural underpinnings is a hot topic in cognitive neuroscience that has driven innovative original research and theoretical frameworks (Dehaene et al., 2006; Lamme, 2006). Consciousness itself can be defined and studied from different perspectives, such as neuropsychology (Laureys et al., 2004; Monti, 2012), applied philosophy (Blanke & Metzinger, 2009), and experimental cognitive neuroscience (Dehaene & Changeux, 2011). However, after several decades of research via different methods and from different perspectives, basic questions regarding consciousness and its neural underpinnings are still debated (Chalmers, 2010). One of the reasons for this ongoing debate is that consciousness cannot be easily disentangled from confounds, such as involvement of other cognitive processes like memory, language, and so forth (Dehaene & Changeux, 2011).
In the current study, Colombari et al. (2025) focus on disentangling neural markers of conscious visual perception from motoric responses. To this end, the study uses a cutting-edge neuroimaging technique, Event-Related Optical Signal (EROS), to measure the neural responses during a Go/No-Go detection task, which is especially designed to gauge visual perception regardless of response production. The study, therefore, is instrumental in addressing the neural foundation of conscious visual perception and is well situated to advance our understanding of consciousness and its neural underpinnings.
The Stage 1 submission was evaluated by three expert reviewers. After several rounds of revision, the recommender determined that the manuscript met the Stage 1 criteria and awarded in-principle acceptance (IPA).
URL to the preregistered Stage 1 protocol: https://osf.io/8ya2t
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. Blanke, O., & Metzinger, T. (2009). Full-body illusions and minimal phenomenal selfhood. Trends in Cognitive Sciences, 13, 7-13. https://doi.org/10.1016/j.tics.2008.10.003
2. Chalmers, D. J. (2010). Facing Up to the Problem of Consciousness. In The Character of Consciousness (pp. 3-34). Oxford University Press. https://doi.org/10.1093/acprof:oso/9780195311105.003.0001 3. Colombari, E., Parisi, G., Mele, S., Mazzi, C., & Savazzi, S. (2025). The role of extra-striate areas in conscious motor behavior: a registered report with Fast-Optical Imaging. In principle acceptance of Version 5 by Peer Community in Registered Reports. https://osf.io/8ya2t
4. Dehaene, S., & Changeux, J. P. (2011). Experimental and theoretical approaches to conscious processing. Neuron, 70, 200-227. https://doi.org/10.1016/j.neuron.2011.03.018
5. Dehaene, S., Changeux, J. P., Naccache, L., Sackur, J., & Sergent, C. (2006). Conscious, preconscious, and subliminal processing: a testable taxonomy. Trends in Cognitive Sciences, 10, 204-211. https://doi.org/10.1016/j.tics.2006.03.007
6. Lamme, V. A. (2006). Towards a true neural stance on consciousness. Trends in Cognitive Sciences, 10, 494-501. https://doi.org/10.1016/j.tics.2006.09.001
7. Laureys, S., Owen, A. M., & Schiff, N. D. (2004). Brain function in coma, vegetative state, and related disorders. The Lancet Neurology, 3, 537-546. https://doi.org/10.1016/s1474-4422(04)00852-x
8. Monti, M. M. (2012). Cognition in the vegetative state. Annual Review of Clinical Psychology, 8, 431-454. https://doi.org/10.1146/annurev-clinpsy-032511-143050
| The role of extra-striate areas in conscious motor behavior: a registered report with Fast-Optical Imaging | Elisabetta Colombari, Giorgia Parisi, Sonia Mele, Chiara Mazzi, Silvia Savazzi | <p>Disclosing the brain areas responsible for the emergence of visual awareness and their timing of activation represents one of the major challenges in consciousness research. In particular, isolating the neural processes strictly related to cons... | Life Sciences, Social sciences | Anoushiravan Zahedi | 2024-04-26 22:44:25 | |||
17 Oct 2024
STAGE 1
Is subjective perceptual similarity metacognitive?The relationship between perceptual discriminability and subject similarityRecommended by D. Samuel Schwarzkopf based on reviews by Haiyang Jin and 1 anonymous reviewer
Much of how we use our perception involves judgements on how similar things are: You might vaguely recognise an actor's face in a movie but not immediately recognise where you have seen it before. Some people claim to be "bad with faces". Is that in fact based on objectively poorer ability to recognise faces? Psychophysical lab studies of perception typically use forced-choice discrimination tasks in which participants must make explicit, and usually binary, decisions. Such designs can yield parametric information about underlying perceptual processes, but it is very different from how we use perception in daily life.
Here, Moharramipour and colleagues (2024) seek to better understand the link between such subjective similarity jugdements and objective discrimination ability. They argue that subjective similarity can be considered a metacognitive process, reflecting the person's awareness of their perceptual capacity. Participants will be asked to discriminate face pairs across a spectrum of morphing steps in a classical forced-choice paradigm to estimate perceptual threshold performance, as well as provide subjective ratings of similarity of the face pairs. The researchers hypothesise a correlation between objective perceptual ability and subjective similarity judgements. They will evaluate this at the group level, and also use a resampling approach to determine the specificity of this relationship in individual participants. Confirming this hypothesis would advance our knowledge of how perceptual ability links with our metacognitive introspection of it. Are you really "bad with faces" or do you only think you are?
The Stage 1 manuscript was evaluated over two rounds of in-depth review. Based on detailed responses to the reviewers' 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/pzugy
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
Moharramipour, A., Zhou, W., Rahnev, D., & Lau, H. (2024). Is subjective perceptual similarity metacognitive? In principle acceptance of Version 4 by Peer Community in Registered Reports. https://osf.io/pzugy
| Is subjective perceptual similarity metacognitive? | Ali Moharramipour, William Zhou, Dobromir Rahnev, Hakwan Lau | <p>Perceptual similarity is a cornerstone for human learning and generalization. However, in assessing the similarity between two stimuli differing in multiple dimensions, it is not well-defined which feature(s) one should focus on. The problem ha... | Life Sciences, Social sciences | D. Samuel Schwarzkopf | 2024-06-15 15:27:08 | |||
Do Ecological Valid Stop Signals Aid Detour Performance? A Comparison of Four Bird SpeciesWhat is the role of sensory perception in cognitive task performance? An improved replication of detour performance in four different bird speciesRecommended by Dieter Lukas based on reviews by Christian Nawroth and 1 anonymous reviewer
The detour task, where an individual has to go around a see-through barrier in order to reach a goal, is one of the oldest paradigms used in animal cognition research (Kabadayi et al. 2018). While these previous tests have documented variation in the ability of animals to inhibit going straight for the visible reward, the cognitive underpinnings of this behaviour are as yet not fully understood. In the current study, Dewulf et al. (2025) assessed one of the specific cognitive processes that might be involved in this behaviour, the ability to identify the transparent object as a barrier. Through experimental procedures relying on large samples of individuals from four bird species, they compared the role of signal detection in inhibitory response performance in a detour task. The authors found that, unlike suggested in previous work with these four species (Regolin et al. 1994, Zucca et al. 2005), changing the markings on the barriers to potentially better match those experienced by individuals in their natural environments did not improve their performance. Nevertheless, the detailed further explorations suggest that in order to understand variation in how quickly individuals and species solve the detour task, it is important to consider that different cognitive processes are involved. Their work therefore provides a basis to better understand and further investigate why species might differ in their performance in the detour task.
The Stage 2 manuscript was evaluated over two rounds of in-depth review, the first round consisting of detailed comments from two reviewers and the second round consisting of a close read by the recommender. Based on detailed responses to the reviewers' comments, the recommender judged that the manuscript met the Stage 2 criteria and awarded a positive recommendation.
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.
URL to the preregistered Stage 1 protocol: https://osf.io/qvxgh
List of eligible PCI RR-friendly journals:
References
1. Dewulf, A., Garcia-Co, C., Müller, W., Madden, J.R., Martel, A., Lens, L. & Verbruggen, F. (2025). Do Ecological Valid Stop Signals Aid Detour Performance? A Comparison of Four Bird Species [Stage 2]. Acceptance of Version 3 by Peer Community in Registered Reports. https://osf.io/j2k9h
2. Kabadayi, C., Bobrowicz, K., & Osvath, M. (2018). The detour paradigm in animal cognition. Animal Cognition, 21, 21-35. https://doi.org/10.1007/s10071-017-1152-0
3. Regolin, L., Vallortigara, G., & Zanforlin, M. (1995). Object and spatial representations in detour problems by chicks. Animal Behaviour, 49, 195-199. https://doi.org/10.1016/0003-3472(95)80167-7
4. Zucca, P., Antonelli, F., & Vallortigara, G. (2005). Detour behaviour in three species of birds: quails (Coturnix sp.), herring gulls (Larus cachinnans) and canaries (Serinus canaria). Animal Cognition, 8, 122-128. https://doi.org/10.1007/s10071-004-0243-x
| Do Ecological Valid Stop Signals Aid Detour Performance? A Comparison of Four Bird Species | Anneleen Dewulf, Clara Garcia-Co, Wendt Müller, Joah R. Madden, An Martel, Luc Lens, Frederick Verbruggen | <p>Response inhibition, or the stopping of actions, is considered a key component of flexible and adaptive behaviour. Across fields, response inhibition is often treated as a unitary cognitive mechanism. However, we propose that response inhibitio... | Life Sciences, Social sciences | Dieter Lukas | 2024-10-22 14:00:30 | |||
24 Oct 2022
STAGE 1
Does childhood adversity alter opioid drug reward? A conceptual replication in outpatients before surgeryIs childhood adversity associated with a heightened response to opioids?Recommended by Chris Chambers based on reviews by Zoltan Dienes, Yuki Yamada and 1 anonymous reviewer
A convergence of evidence suggests that early life adversity may cause dysfunction in opioid-sensitive reward systems. Childhood adversity is associated with opioid use, potentially by altering reward and motivation networks, and experimental models in animals have found that early life adversity increases and consolidates opioid seeking behaviours. Further, in a recent controlled experiment, Carlyle et al. (2021) found that opioid administration produced stronger positive responses, and weaker negative responses, in adults with a history of childhood abuse and neglect.
In the current study, Carlyle et al. seek to test the generalisability of these previous findings in a pre-operative clinical setting. Using partially observed data from an existing cohort study (N=155), the authors will test whether patients with greater experience of childhood trauma in turn exhibit a larger mood boost and express greater subjective pleasure following opioid administration. Although not a randomised experimental design, this study provides the opportunity to examine the relationship between opioid response and history of childhood adversity in a naturalistic setting, and thus has the potential to either support or cast doubt on the theory that adversity elevates risk of opioid addiction by altering sensitivity to subjectively pleasurable effects.
Following three rounds of in-depth review, 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/7ymts 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. Carlyle M., Broomby R., Simpson G., Hannon R., Fawaz L., Mollaahmetoglu O.M., Drain, J., Mostazir, M., & Morgan C. (2021). A randomised, double‐blind study investigating the relationship between early childhood trauma and the rewarding effects of morphine. Addiction Biology, 26(6):e13047.
2. Carlyle, M., Kvande, M., Leknes, S., Meier, I., Buen, K., Jensen, E. N., Ernst, G. & Eikemo, M. (2022). Does childhood adversity alter opioid drug reward? A conceptual replication in outpatients before surgery, in principle acceptance of Version 4 by Peer Community in Registered Reports. https://osf.io/7ymts
| Does childhood adversity alter opioid drug reward? A conceptual replication in outpatients before surgery | Molly Carlyle*, Malin Kvande*, Siri Leknes, Isabell Meier, Kaja Buen, Eira Nordeng Jensen, Gernot Ernst, Marie Eikemo. *denotes equal contribution. | <p>PCI-RR Snapshot only</p> | Life Sciences, Medical Sciences, Social sciences | Chris Chambers | 2022-03-15 10:07:29 | |||
30 May 2024
STAGE 1
The role of resource dynamics in the distribution of life cycles within a female human populationAn agent-based model of the role of resource dynamics and the environment in human female life cyclesRecommended by Claudio Tennie based on reviews by Cecilia Padilla-Iglesias and 1 anonymous reviewer
Among primates, the human female life cycle appears special. Aspects of these life cycles have been linked to the acquisition and distribution of resources and to environmental factors, as well as to individual differences across human females. Many questions remain regarding the causal roles that these (or also other) factors might have played in the evolution of human female life cycles – and also whether generalizing statements about these life cycles can adequately capture the wide range of the observed phenomena.
In the current study, Varas Enriquez et al. (2024) outline a plan for an agent-based model approach to study the factors that guide and channel variability in female life cycles in humans (within biological constraints), via the effects that their model will capture. The authors’ model has a particular eye towards the effects of resource dynamics (resource production and resource transfers) and environmental conditions – and their interplay. The results of this agent based model will be thoroughly analysed to better understand the evolution of the specific female human life cycle range.
The study plan was refined after one round of review, which led to input from two external reviewers and the recommender. The revised (second) version was judged to satisfy the Stage 1 criteria for in-principle acceptance.
URL to the preregistered Stage 1 protocol: https://osf.io/24c7z
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 (e.g. conservative statistical threshold; recruitment of a blinded analyst; robustness testing, multiverse/specification analysis, or other approach) List of eligible PCI RR-friendly journals: References
Varas Enríquez, P. J., Lukas, D., Colleran, H, Mulder, M. B., & Redhead, D. (2024) The role of resource dynamics in the distribution of life cycles within a female human population. In principle acceptance of Version 2 by Peer Community in Registered Reports. https://osf.io/24c7z
| The role of resource dynamics in the distribution of life cycles within a female human population | Pablo J. Varas Enríquez, Daniel Redhead, Monique Borgerhoff Mulder, Heidi Colleran, Dieter Lukas | <p>The evolution of the female human life cycle, which is characterised by having a reproductive career nested within juvenile and post-reproductive periods, has been linked to the surplus of adult resource production and downwards inter-generatio... | | Life Sciences, Medical Sciences, Social sciences | Claudio Tennie | 2023-11-13 15:45:52 | ||
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 | ||
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 |
