Reproducibility in Sleep and Circadian Science

A special issue of Clocks & Sleep (ISSN 2624-5175). This special issue belongs to the section "Open & Reproducible Science".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 11496

Special Issue Editor

1. Translational Sensory & Circadian Neuroscience, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
2. Chronobiology & Health, TUM Department of Sport and Health Sciences (TUM SG), Technical University of Munich, Munich, Germany
3. TUM Institute for Advanced Study (TUM-IAS), Technical University of Munich, Garching, Germany
Interests: human chronobiology; visual neuroscience; melatonin suppression; non-visual effects of light; melanopsin; ipRGCs

Special Issue Information

Dear Colleagues,

We are pleased to announce the Special Issue “Reproducibility in sleep and circadian science”. The focus of this collection of articles is to bring open and reproducible science to the attention of sleep and circadian researchers.

This Special Issue aims to provide a platform for discussing open science and reproducibility—including its challenges—with a specific focus on circadian and sleep research.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

  • Original research articles employing open and reproducible science principles, such as registered reports;
  • Original meta-research articles on open and reproducible science practices in the field;
  • Perspective pieces and opinions, as well as commentary and narratives;
  • Articles describing software and resources to make research workflows reproducible;
  • Reviews.

We are also interested in allowing you to open your file drawer, i.e., well-designed and adequately powered but failed experiments or studies that you have not published, and failed replications.

We look forward to receiving your contributions.

Prof. Dr. Manuel Spitschan
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Clocks & Sleep is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • open science
  • open scholarship
  • reproducibility
  • data sharing
  • data standards

Published Papers (7 papers)

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Research

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15 pages, 6621 KiB  
Article
Power Analysis for Human Melatonin Suppression Experiments
Clocks & Sleep 2024, 6(1), 114-128; https://doi.org/10.3390/clockssleep6010009 - 26 Feb 2024
Viewed by 381
Abstract
In humans, the nocturnal secretion of melatonin by the pineal gland is suppressed by ocular exposure to light. In the laboratory, melatonin suppression is a biomarker for this neuroendocrine pathway. Recent work has found that individuals differ substantially in their melatonin-suppressive response to [...] Read more.
In humans, the nocturnal secretion of melatonin by the pineal gland is suppressed by ocular exposure to light. In the laboratory, melatonin suppression is a biomarker for this neuroendocrine pathway. Recent work has found that individuals differ substantially in their melatonin-suppressive response to light, with the most sensitive individuals being up to 60 times more sensitive than the least sensitive individuals. Planning experiments with melatonin suppression as an outcome needs to incorporate these individual differences, particularly in common resource-limited scenarios where running within-subjects studies at multiple light levels is costly and resource-intensive and may not be feasible with respect to participant compliance. Here, we present a novel framework for virtual laboratory melatonin suppression experiments, incorporating a Bayesian statistical model. We provide a Shiny web app for power analyses that allows users to modify various experimental parameters (sample size, individual-level heterogeneity, statistical significance threshold, light levels), and simulate a systematic shift in sensitivity (e.g., due to a pharmacological or other intervention). Our framework helps experimenters to design compelling and robust studies, offering novel insights into the underlying biological variability in melatonin suppression relevant for practical applications. Full article
(This article belongs to the Special Issue Reproducibility in Sleep and Circadian Science)
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25 pages, 4218 KiB  
Article
Integrative Lighting Aimed at Patients with Psychiatric and Neurological Disorders
Clocks & Sleep 2023, 5(4), 806-830; https://doi.org/10.3390/clockssleep5040052 - 15 Dec 2023
Viewed by 1753
Abstract
The purpose of this paper is to investigate the impact of circadian lighting-induced melatonin suppression on patients with psychiatric and neurological disorders in hospital wards by using an ad-hoc metrology framework and the subsequent metrics formalized by the CIE in 2018. A measurement [...] Read more.
The purpose of this paper is to investigate the impact of circadian lighting-induced melatonin suppression on patients with psychiatric and neurological disorders in hospital wards by using an ad-hoc metrology framework and the subsequent metrics formalized by the CIE in 2018. A measurement scheme was conducted in hospital ward rooms in the Department of Neurology, Zealand University Hospital, at Roskilde in Denmark, to evaluate the photometric and colorimetric characteristics of the lighting system, as well as its influence on the circadian rhythm of the occupants. The measurement scheme included point measurements and data logging, using a spectrophotometer mounted on a tripod with adjustable height to assess the newly installed circadian lighting system. The measured spectra were uploaded to the Luox platform to calculate illuminance, CCT, MEDI, etc., in accordance with the CIE S026 standard. Furthermore, the MLIT based on MEDI data logging results was calculated. In addition to CIE S026, we have investigated the usefulness of melatonin suppression models for the assessment of circadian performance regarding measured light. From the results, the lighting conditions in the patient room for both minimal and abundant daylight access were evaluated and compared; we found that access to daylight is essential for both illumination and circadian entrainment. It can be concluded that the measurement scheme, together with the use of the Luox platform and Canva template, is suitable for the accurate and satisfactory measurement of integrative lighting that aligns with CIE requirements and recommendations. Full article
(This article belongs to the Special Issue Reproducibility in Sleep and Circadian Science)
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16 pages, 2123 KiB  
Communication
Seasonal Variation in the Responsiveness of the Melanopsin System to Evening Light: Why We Should Report Season When Collecting Data in Human Sleep and Circadian Studies
Clocks & Sleep 2023, 5(4), 651-666; https://doi.org/10.3390/clockssleep5040044 - 01 Nov 2023
Cited by 1 | Viewed by 2372
Abstract
It is well known that variations in light exposure during the day affect light sensitivity in the evening. More daylight reduces sensitivity, and less daylight increases it. On average days, we spend less time outdoors in winter and receive far less light than [...] Read more.
It is well known that variations in light exposure during the day affect light sensitivity in the evening. More daylight reduces sensitivity, and less daylight increases it. On average days, we spend less time outdoors in winter and receive far less light than in summer. Therefore, it could be relevant when collecting research data on the non-image forming (NIF) effects of light on circadian rhythms and sleep. In fact, studies conducted only in winter may result in more pronounced NIF effects than in summer. Here, we systematically collected information on the extent to which studies on the NIF effects of evening light include information on season and/or light history. We found that more studies were conducted in winter than in summer and that reporting when a study was conducted or measuring individual light history is not currently a standard in sleep and circadian research. In addition, we sought to evaluate seasonal variations in a previously published dataset of 72 participants investigating circadian and sleep effects of evening light exposure in a laboratory protocol where daytime light history was not controlled. In this study, we selectively modulated melanopic irradiance at four different light levels (<90 lx). Here, we aimed to retrospectively evaluate seasonal variations in the responsiveness of the melanopsin system by combining all data sets in an exploratory manner. Our analyses suggest that light sensitivity is indeed reduced in summer compared to winter. Thus, to increase the reproducibility of NIF effects on sleep and circadian measures, we recommend an assessment of the light history and encourage standardization of reporting guidelines on the seasonal distribution of measurements. Full article
(This article belongs to the Special Issue Reproducibility in Sleep and Circadian Science)
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23 pages, 9747 KiB  
Article
Influence of the Human Field of View on Visual and Non-Visual Quantities in Indoor Environments
Clocks & Sleep 2023, 5(3), 476-498; https://doi.org/10.3390/clockssleep5030032 - 29 Aug 2023
Cited by 1 | Viewed by 1680
Abstract
The visual and non-visual effectiveness of light is often determined by measuring the spectrally weighed irradiance on the corneal plane. This is typically achieved using spectral irradiance or illuminance measurements, captured in a hemispheric (2π) geometry with a diffuser. However, the human binocular [...] Read more.
The visual and non-visual effectiveness of light is often determined by measuring the spectrally weighed irradiance on the corneal plane. This is typically achieved using spectral irradiance or illuminance measurements, captured in a hemispheric (2π) geometry with a diffuser. However, the human binocular field of view (FOV) is not a perfect hemisphere, as it is occluded both upward and downward. Previous research on FOV-restricted measurements is limited, leaving the error from using hemispheric measurements for non-visual quantities undefined. In our study, we tackled this issue by designing and 3D printing FOV occlusions as attachments to spectral measurement devices. We took measurements with and without the occlusion in various laboratory (light from different directions) and real-world lighting situations (light typically from above). Our findings reveal a reduction of visual and melanopic values due to the FOV occlusion. These ranged from negligible to more than 60% in realistic scenarios. Interestingly, the reduction was consistent for both visual and melanopic parameters, as the distribution of light in the FOV was generally spectrally homogeneous. An exception occurred in a specific artificial laboratory situation, where the melanopic daylight (D65) efficacy ratio changed by more than a factor of 2 solely because of the FOV occlusion. Additionally, we observed that head orientation had a marked effect on all quantities measured. In conclusion, our results highlight the potential for substantial errors when solely relying on vertical, hemispheric measurements in experiments and non-visual lighting design projects. We encourage the (additional) use of FOV occlusion in eye-level measurements for typical viewing directions, and we are providing open-source 3D-print files to facilitate this practice. Full article
(This article belongs to the Special Issue Reproducibility in Sleep and Circadian Science)
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Review

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10 pages, 1475 KiB  
Review
Primer on Reproducible Research in R: Enhancing Transparency and Scientific Rigor
Clocks & Sleep 2024, 6(1), 1-10; https://doi.org/10.3390/clockssleep6010001 - 20 Dec 2023
Viewed by 1023
Abstract
Achieving research reproducibility is a precarious aspect of scientific practice. However, many studies across disciplines fail to be fully reproduced due to inadequate dissemination methods. Traditional publication practices often fail to provide a comprehensive description of the research context and procedures, hindering reproducibility. [...] Read more.
Achieving research reproducibility is a precarious aspect of scientific practice. However, many studies across disciplines fail to be fully reproduced due to inadequate dissemination methods. Traditional publication practices often fail to provide a comprehensive description of the research context and procedures, hindering reproducibility. To address these challenges, this article presents a tutorial on reproducible research using the R programming language. The tutorial aims to equip researchers, including those with limited coding knowledge, with the necessary skills to enhance reproducibility in their work. It covers three essential components: version control using Git, dynamic document creation using rmarkdown, and managing R package dependencies with renv. The tutorial also provides insights into sharing reproducible research and offers specific considerations for the field of sleep and chronobiology research. By following the tutorial, researchers can adopt practices that enhance the transparency, rigor, and replicability of their work, contributing to a culture of reproducible research and advancing scientific knowledge. Full article
(This article belongs to the Special Issue Reproducibility in Sleep and Circadian Science)
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13 pages, 1533 KiB  
Review
Methods for REM Sleep Density Analysis: A Scoping Review
Clocks & Sleep 2023, 5(4), 793-805; https://doi.org/10.3390/clockssleep5040051 - 14 Dec 2023
Viewed by 1243
Abstract
Rapid eye movements (REM) sleep density is the parameter proposed to explain the variability in the amount of eye movements during REM sleep. Alterations in REM sleep density have been proposed as a screening criterion for individuals with depression and other mental health [...] Read more.
Rapid eye movements (REM) sleep density is the parameter proposed to explain the variability in the amount of eye movements during REM sleep. Alterations in REM sleep density have been proposed as a screening criterion for individuals with depression and other mental health conditions, but its accuracy has not been properly evaluated. The lack of consensus and the variability of the methods used to score it reduces the external validity of the results, hindering an adequate analysis of its diagnostic accuracy and clinical applicability. This scoping review aimed to identify and quantify the methods used to score REM sleep density, describing their main characteristics. A literature search was conducted in PubMed, Scopus, PsycInfo, and Web of Science. Only studies with objective measures for REM sleep density analysis in individuals with depression were considered eligible. The final sample comprised 57 articles, covering 64 analyses of REM sleep density. The relative frequency methods were the predominant measurement parameter for analyzing REM sleep density across studies. The most frequently adopted REM estimation unit was the number of REM events followed by mini-epochs containing REM. The most common unit of measurement were frequency/time measures. The results demonstrate that there is no consistency in the methods used to calculate REM sleep density in the literature, and a high percentage of studies do not describe their methods in sufficient detail. The most used method was the number of REM episodes per minute of REM sleep, but its use is neither unanimous nor consensual. The methodological inconsistencies and omissions among studies limit the replicability, comparability, and clinical applicability of REM sleep density. Future guidelines should discuss and include a specific methodology for the scoring of REM sleep density, so it can be consensually implemented in clinical services and research. Full article
(This article belongs to the Special Issue Reproducibility in Sleep and Circadian Science)
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Other

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8 pages, 857 KiB  
Opinion
Keep It Simple: Using README Files to Advance Standardization in Chronobiology
Clocks & Sleep 2023, 5(3), 499-506; https://doi.org/10.3390/clockssleep5030033 - 30 Aug 2023
Viewed by 1848
Abstract
Standardization plays a crucial role in ensuring the reliability, reproducibility, and interoperability of research data in the biomedical sciences. Metadata standards are one foundation for the FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data management. They facilitate data discovery, understanding, and reuse. [...] Read more.
Standardization plays a crucial role in ensuring the reliability, reproducibility, and interoperability of research data in the biomedical sciences. Metadata standards are one foundation for the FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data management. They facilitate data discovery, understanding, and reuse. However, the adoption of metadata standards in biological research lags in practice. Barriers such as complexity, lack of incentives, technical challenges, resource constraints, and resistance to change hinder widespread adoption. In the field of chronobiology, standardization is essential but faces particular challenges due to the longitudinal nature of experimental data, diverse model organisms, and varied measurement techniques. To address these challenges, we propose an approach that emphasizes simplicity and practicality: the development of README templates tailored for particular data types and species. Through this opinion article, our intention is to initiate a dialogue and commence a community-driven standardization process by engaging potential contributors and collaborators. Full article
(This article belongs to the Special Issue Reproducibility in Sleep and Circadian Science)
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