Commentary: Expanding the vision of Registered Reports for qualitative mental health research: A response and extension to 'Misaligned incentives in mental health research - the case for Registered Reports', Baldwin (2023).

There is a growing exploration of how Registered Reports can benefit individual researchers and wider research fields as part of a wider shift towards open research principles and practices. In 'Misaligned incentives in mental health research - the case for Registered Reports', Baldwin examines this in the context of mental health research, arguing that Registered Reports (RRs) can be a valuable solution to misaligned incentive structures in the field. However, this original piece was generally inclined towards how such incentives and the use of RRs can play out in the context of quantitative research. Such reflection is valuable, but to examine the case for RRs in mental health research as a field, we must also explore such practices within the context of qualitative research. In this commentary, we therefore expand and reframe this discussion to make the case for RRs in qualitative mental health research. We explore the place for qualitative research in the mental health research field and examine possibilities for how RRs fit within principles and practices in such methods. We discuss the various benefits and challenges of RRs in qualitative research, reflecting on our experiences as authors and reviewers of qualitative RRs and exploring how research infrastructure can facilitate engagement with this publishing approach.

Design and validation of a conceptual model regarding impact of open science on healthcare research processes.

INTRODUCTION: The development and use of digital tools in various stages of research highlight the importance of novel open science methods for an integrated and accessible research system. The objective of this study was to design and validate a conceptual model of open science on healthcare research processes. METHODS: This research was conducted in three phases using a mixed-methods approach. The first phase employed a qualitative method, namely purposive sampling and semi-structured interview guides to collect data from healthcare researchers and managers. Influential factors of open science on research processes were extracted for refining the components and developing the proposed model; the second phase utilized a panel of experts and collective agreement through purposive sampling. The final phase involved purposive sampling and Delphi technique to validate the components of the proposed model according to researchers' perspectives. FINDINGS: From the thematic analysis of 20 interview on the study topic, 385 codes, 38 sub-themes, and 14 main themes were extracted for the initial proposed model. These components were reviewed by expert panel members, resulting in 31 sub-themes, 13 main themes, and 4 approved themes. Ultimately, the agreed-upon model was assessed in four layers for validation by the expert panel, and all the components achieved a score of > 75% in two Delphi rounds. The validated model was presented based on the infrastructure and culture layers, as well as supervision, assessment, publication, and sharing. CONCLUSION: To effectively implement these methods in the research process, it is essential to create cultural and infrastructural backgrounds and predefined requirements for preventing potential abuses and privacy concerns in the healthcare system. Applying these principles will lead to greater access to outputs, increasing the credibility of research results and the utilization of collective intelligence in solving healthcare system issues.

Searching COVID-19 Clinical Research Using Graph Queries: Algorithm Development and Validation.

BACKGROUND: Since the beginning of the COVID-19 pandemic, >1 million studies have been collected within the COVID-19 Open Research Dataset, a corpus of manuscripts created to accelerate research against the disease. Their related abstracts hold a wealth of information that remains largely unexplored and difficult to search due to its unstructured nature. Keyword-based search is the standard approach, which allows users to retrieve the documents of a corpus that contain (all or some of) the words in a target list. This type of search, however, does not provide visual support to the task and is not suited to expressing complex queries or compensating for missing specifications. OBJECTIVE: This study aims to consider small graphs of concepts and exploit them for expressing graph searches over existing COVID-19-related literature, leveraging the increasing use of graphs to represent and query scientific knowledge and providing a user-friendly search and exploration experience. METHODS: We considered the COVID-19 Open Research Dataset corpus and summarized its content by annotating the publications' abstracts using terms selected from the Unified Medical Language System and the Ontology of Coronavirus Infectious Disease. Then, we built a co-occurrence network that includes all relevant concepts mentioned in the corpus, establishing connections when their mutual information is relevant. A sophisticated graph query engine was built to allow the identification of the best matches of graph queries on the network. It also supports partial matches and suggests potential query completions using shortest paths. RESULTS: We built a large co-occurrence network, consisting of 128,249 entities and 47,198,965 relationships; the GRAPH-SEARCH interface allows users to explore the network by formulating or adapting graph queries; it produces a bibliography of publications, which are globally ranked; and each publication is further associated with the specific parts of the query that it explains, thereby allowing the user to understand each aspect of the matching. CONCLUSIONS: Our approach supports the process of query formulation and evidence search upon a large text corpus; it can be reapplied to any scientific domain where documents corpora and curated ontologies are made available.

Iranian researchers' perspective about concept and effect of open science on research publication.

BACKGROUND: Sharing research outputs with open science methods for different stakeholders causes better access to different studies to solve problems in diverse fields, which leads to equal access conditions to research resources, as well as greater scientific productivity. Therefore, the aim of this study was to perceive the concept of openness in research among Iranian health researchers. METHODS: From the beginning of August to the middle of November 2021, twenty semi-structured interviews were held with Iranian health researchers from different fields using purposeful, snowball, and convenience sampling. The interviews continued until data saturation. Data analysis was performed with thematic analysis using MAXQDA 20. Finally, seven main issues related to open science were identified. RESULTS: Through analysis of the interviews, 235 primary codes and 173 main codes were extracted in 22 subclasses. After careful evaluation and integration of subclasses and classes, they were finally classified into nine categories and three main themes. Analysis showed that openness in research was related to three main themes: researchers' understanding of open science, the impact of open science on publication and sharing of research, concerns and reluctance to open research. CONCLUSION: The conditions of access to research output should be specified given the diversity of studies conducted in the field of health; issues like privacy as an important topic of access to data and information in the health system should also be specified. Our analysis indicated that the conditions of publication and sharing of research processes should be stated according to different scopes of health fields. The concept of open science was related to access to findings and other research items regardless of cost, political, social, or racial barriers, which could create collective wisdom in the development of knowledge. The process of publication and sharing of research related to open access applies to all types of outputs, conditions of access, increasing trust in research, creation of diverse publication paths, and broader participation of citizens in research. Open science practices should be promoted to increase the circulation and exploitation rates of knowledge while adjusting and respecting the limits of privacy, intellectual property and national security rights of countries.

Using text mining to glean insights from COVID-19 literature.

The purpose of this study is to develop a text clustering-based analysis of COVID-19 research articles. Owing to the proliferation of published COVID-19 research articles, researchers need a method for reducing the number of articles they have to search through to find material relevant to their expertise. The study analyzes 83,264 abstracts from research articles related to COVID-19. The textual data are analysed using singular value decomposition (SVD) and the expectation-maximisation (EM) algorithm. Results suggest that text clustering can both reveal hidden research themes in the published literature related to COVID-19, and reduce the number of articles that researchers need to search through to find material relevant to their field of interest.

The Power of Chemists Is in What They Can Learn, Not What They Already Know.

In this viewpoint, the concepts that chemistry transcends the laboratory into the clinic and beyond is explored from the perspective of a single individual who began strictly within synthetic chemistry. They learned through their training that in reality, chemists are capable of anything, requiring mentorship, open discussion, and some frontend work to learn something new.

The case for free and open source software in research and scholarship.

Free and open source software (FOSS) is any computer program released under a licence that grants users rights to run the program for any purpose, to study it, to modify it, and to redistribute it in original or modified form. Our aim is to explore the intersection between FOSS and computational reproducibility. We begin by situating FOSS in relation to other 'open' initiatives, and specifically open science, open research, and open scholarship. In this context, we argue that anyone who actively contributes to the research process today is a computational researcher, in that they use computers to manage and store information. We then provide a primer to FOSS suitable for anyone concerned with research quality and sustainability-including researchers in any field, as well as support staff, administrators, publishers, funders, and so on. Next, we illustrate how the notions introduced in the primer apply to resources for scientific computing, with reference to the GNU Scientific Library as a case study. We conclude by discussing why the common interpretation of 'open source' as 'open code' is misplaced, and we use this example to articulate the role of FOSS in research and scholarship today. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'.

Standardization of patient modeling in hyperthermia simulation studies: introducing the Erasmus Virtual Patient Repository.

Purpose: Thermal dose-effect relations have demonstrated that clinical effectiveness of hyperthermia would benefit from more controlled heating of the tumor. Hyperthermia treatment planning (HTP) is a potent tool to study strategies enabling target conformal heating, but its accuracy is affected by patient modeling approximations. Homogeneous phantoms models are being used that do not match the body shape of patients in treatment position and often have unrealistic target volumes. As a consequence, simulation accuracy is affected, and performance comparisons are difficult. The aim of this study is to provide the first step toward standardization of HTP simulation studies in terms of patient modeling by introducing the Erasmus Virtual Patient Repository (EVPR): a virtual patient model database.Methods: Four patients with a tumor in the head and neck or the pelvis region were selected, and corresponding models were created using a clinical segmentation procedure. Using the Erasmus University Medical Center standard procedure, HTP was applied to these models and compared to HTP for commonly used surrogate models.Results: Although this study was aimed at presenting the EVPR database, our study illustrates that there is a non-negligible difference in the predicted SAR patterns between patient models and homogeneous phantom-based surrogate models. We further demonstrate the difference between actual and simplified target volumes being used today.Conclusion: Our study describes the EVPR for the research community as a first step toward standardization of hyperthermia simulation studies.

Exploring the current dynamics of preprints.

Preprints are non-peer-reviewed and publicly available articles for open and transparent research communication. Preprint servers host the submission of such manuscripts, and despite the presence of established preprint servers, their numbers have continued to rise in recent times. A steep increasing pattern in posted preprints and their accommodating servers has been observed over the last decade. In this article, we explored the global trends in the preprint adoption and its involvement in promoting open and transparent research findings across various domains. We further emphasized the importance of preprinting, highlighting its significant impact during the pandemic through effective information sharing, and advocating for its broader integration in scholarly communication.

Navigating University Openness in Research Policy Inconsistent with Indigenous Data Sovereignty: A Case Analysis.

Indigenous nations and communities in the United States have rights as sovereign governments to exercise control and ownership over all data and information generated by or from the tribes, tribal members, or tribal resources. Indigenous nations exercise these rights through data ownership policies established in response to unethical research practices in research involving Indigenous communities. Most universities in the U.S. have "openness in research" policies to ensure academic freedom to publish freely, exercised by retaining university control of data. Here, we describe our study of cultural ecosystem services in the St. Louis River estuary region (Nagaajiwanaang in the language Ojibwemowin) in Duluth, Minnesota, and Superior, Wisconsin, U.S., an area that includes portions of the 1854 and 1842 Ceded Territories and reservation lands of a local band of Ojibwe (hereafter referred to as "the Band"). In this university-led, Band-supported study, both the university and the Band sought ownership of data collected based on their respective policies, resulting in a research delay of nearly a year. We found that open research policies that do not consider Indigenous sovereignty can hamper collaboration between university researchers and tribal nations, even when there is broad agreement on research goals and objectives. University open research policies that do not explicitly address Indigenous sovereignty fall short of the open research principles they intend to support and should be revised. Formal adoption of principles for ethical research with sovereign tribal governments by universities is needed to improve coordination and trust among university and tribal researchers and members.

Accelerating the open research agenda to solve global challenges.

Harnessing science-based policy is key to addressing global challenges like the biodiversity and climate crises. Open research principles underpin effective science-based policy, but the uptake of these principles is likely constrained by the politicisation, commoditisation and conflicting motives of stakeholders in the research landscape. Here, using the mission and vision statements from 129 stakeholders from across the research landscape, we explore alignment in open research principles between stakeholders. We find poor alignment between stakeholders, largely focussed around journals, societies and funders, all of which have low open research language-use. We argue that this poor alignment stifles knowledge flow within the research landscape, ultimately limiting the mobilisation of impactful science-based policy. We offer recommendations on how the research landscape could embrace open research principles to accelerate societies' ability to solve global challenges.

Changing the paradigm for primary research dissemination.

The predominant research publishing system is not equitable by design, nor optimised to advance research to create knowledge and ultimately to benefit society. Open Research Central (ORC) was created to foster the re-imagination of the research dissemination system to facilitate trust, transparency and equitable participation. In five years of operation, before dissolving, the non-profit organisation produced outputs and learnings valuable to the development of a responsible research dissemination system. We are sharing our experience in the hope that it will provide others who share the same vision and goals with useful materials to build on. We think that there remains a need for global, cross-stakeholder exploration to build collective understanding of research validation and dissemination and to pilot solutions. However, as this article will explore, enabling and supporting the development of such a collective voice and consequent action is a challenging endeavour in the current landscape and funding environment.

A grassroots approach to peer support by the Danish Reproducibility Network.

The Danish Reproducibility Network (DKRN) is a grassroots initiative for establishing a peer-supportive reproducibility-focused academic network in Denmark. We modelled our approach on already existing national Reproducibility Networks. We consulted with researchers and research support professionals to identify the needs of the research community. Three themes emerged around policy implementation, training and the appropriate application of reproducible practices. The network aims to address these three themes in a strategic plan, which harnesses the benefits of grassroots initiatives. The mission of the DKRN is therefore to facilitate communication, peer-support, and the exchange of ideas through a network of topic and geographical nodes. The network is open to researchers and research support professionals from all career stages and disciplines. It aligns with broader international initiatives, and national institutions, positioning itself as a contributor to the Danish research ecosystem.

Demystifying Open Science in health psychology and behavioral medicine: a practical guide to Registered Reports and Data Notes.

Open Science practices are integral to increasing transparency, reproducibility, and accessibility of research in health psychology and behavioral medicine. Drives to facilitate Open Science practices are becoming increasingly evident in journal editorial policies, including the establishment of new paper formats such as Registered Reports and Data Notes. This paper provides: (i) an overview of the current state of Open Science policies within health psychology and behavioral medicine, (ii) a call for submissions to an Article Collection of Registered Reports and Data Notes as new paper formats within the journal of Health Psychology & Behavioral Medicine, (iii) an overview of Registered Reports and Data Notes, and (iv) practical considerations for authors and reviewers of Registered Reports and Data Notes.

Reflection over compliance: Critiquing mandatory data sharing policies for qualitative research.

Many journals are moving towards a 'Mandatory Inclusion of Raw Data' (MIRD) model of data sharing, where it is expected that raw data be publicly accessible at article submission. While open data sharing is beneficial for some research topics and methodologies within health psychology, in other cases it may be ethically and epistemologically questionable. Here, we outline several questions that qualitative researchers might consider surrounding the ethics of open data sharing. Overall, we argue that universal open raw data mandates cannot adequately represent the diversity of qualitative research, and that MIRD may harm rigorous and ethical research practice within health psychology and beyond. Researchers should instead find ways to demonstrate rigour thorough engagement with questions surrounding data sharing. We propose that all researchers utilise the increasingly common 'data availability statement' to demonstrate reflexive engagement with issues of ethics, epistemology and participant protection when considering whether to open data.

Selective outcome reporting in trials of behavioural health interventions in health psychology and behavioural medicine journals: a review.

Selective outcome reporting can result in overestimation of treatment effects, research waste, and reduced openness and transparency. This review aimed to examine selective outcome reporting in trials of behavioural health interventions and determine potential outcome reporting bias. A review of nine health psychology and behavioural medicine journals was conducted to identify randomised controlled trials of behavioural health interventions published since 2019. Discrepancies in outcome reporting were observed in 90% of the 29 trials with corresponding registrations/protocols. Discrepancies included 72% of trials omitting prespecified outcomes; 55% of trials introduced new outcomes. Thirty-eight percent of trials omitted prespecified and introduced new outcomes. Three trials (10%) downgraded primary outcomes in registrations/protocols to secondary outcomes in final reports; downgraded outcomes were not statistically significant in two trials. Five trials (17%) upgraded secondary outcomes to primary outcomes; upgraded outcomes were statistically significant in all trials. In final reports, three trials (7%) omitted outcomes from the methods section; three trials (7%) introduced new outcomes in results that were not in the methods. These findings indicate that selective outcome reporting is a problem in behavioural health intervention trials. Journal- and trialist-level approaches are needed to minimise selective outcome reporting in health psychology and behavioural medicine.

A scoping review on what constitutes a good research culture.

Background: The crisis in research culture is well documented, covering issues such as a tendency for quantity over quality, unhealthy competitive environments, and assessment based on publications, journal prestige and funding. In response, research institutions need to assess their own practices to promote and advocate for change in the current research ecosystem. The purpose of the scoping review was to explore ' What does the evidence say about the 'problem' with 'poor' research culture, what are the benefits of 'good' research culture, and what does 'good' look like?' Aims: To examine the peer-reviewed and grey literature to explore the interplay between research culture, open research, career paths, recognition and rewards, and equality, diversity, and inclusion, as part of a larger programme of activity for a research institution. Methods: A scoping review was undertaken. Six databases were searched along with grey literature. Eligible literature had relevance to academic research institutions, addressed research culture, and were published between January 2017 to May 2022. Evidence was mapped and themed to specific categories. The search strategy, screening and analysis took place between April-May 2022. Results: 1666 titles and abstracts, and 924 full text articles were assessed for eligibility. Of these, 253 articles met the eligibility criteria for inclusion. A purposive sampling of relevant websites was drawn from to complement the review, resulting in 102 records included in the review. Key areas for consideration were identified across the four themes of job security, wellbeing and equality of opportunity, teamwork and interdisciplinary, and research quality and accountability. Conclusions: There are opportunities for research institutions to improve their own practice, however institutional solutions cannot act in isolation. Research institutions and research funders need to work together to build a more sustainable and inclusive research culture that is diverse in nature and supports individuals' well-being, career progression and performance.

Compound management in a virtual research organization: The cornerstone of a reliable MMV discovery engine.

Despite the efforts towards malaria eradication, latest estimates show that the number of malaria cases is still rising, and malaria continues to have a devastating impact on people's health and livelihoods particularly in populations located in sub-Saharan Africa 1. As a Product Development Partnership (PDP), MMV Medicines for Malaria Venture (MMV) plays a crucial role by using public and philanthropic funds to engage the pharmaceutical industry and academic research institutions to discover, develop and deliver the new drugs needed to control and eradicate malaria. MMV Discovery, working with partners, has developed a robust pipeline of molecules and a reliable discovery engine able to support research projects from screening to candidate nomination, providing access to centers of expertise and evaluating the profile and potential of molecules. To efficiently support this malaria discovery effort, MMV and its partners have established a state-of-the-art compound management network, supporting all discovery activities. This network serves both discovery projects and open innovation initiatives, such as MMV Open, tailoring workflows to align with distinct project objectives. In addition to this, MMV has implemented reliable integrated logistic tools and interfaces. These tools enable the efficient management and tracking of individual not solubilized (dry) samples of project compounds, as well as dedicated, solubilized libraries of compounds designated for primary screens targeting malaria and other neglected diseases.

The UK Reproducibility Network: A progress report.

There is growing awareness that the ways in which academic research is conducted could be improved. A number of exciting innovations are emerging, alongside a broader agenda that includes a growing emphasis on open research. This short article outlines the rationale, progress and plans of the UK Reproducibility Network, which is one of a growing number of similar initiatives internationally that promote more rigorous and transparent research.

Designing, conducting, and reporting reproducible animal experiments.

In biomedicine and many other fields, there are growing concerns around the reproducibility of research findings, with many researchers being unable to replicate their own or others' results. This raises important questions as to the validity and usefulness of much published research. In this review, we aim to engage researchers in the issue of research reproducibility and equip them with the necessary tools to increase the reproducibility of their research. We first highlight the causes and potential impact of non-reproducible research and emphasise the benefits of working reproducibly for the researcher and broader research community. We address specific targets for improvement and steps that individual researchers can take to increase the reproducibility of their work. We next provide recommendations for improving the design and conduct of experiments, focusing on in vivo animal experiments. We describe common sources of poor internal validity of experiments and offer practical guidance for limiting these potential sources of bias at different experimental stages, as well as discussing other important considerations during experimental design. We provide a list of key resources available to researchers to improve experimental design, conduct, and reporting. We then discuss the importance of open research practices such as study preregistration and the use of preprints and describe recommendations around data management and sharing. Our review emphasises the importance of reproducible work and aims to empower every individual researcher to contribute to the reproducibility of research in their field.