Exploring factors that influence the practice of Open Science by early career health researchers: a mixed methods study

Machine learning hypothesis-generation for patient stratification and target discovery in rare disease: our experience with Open Science in ALS

Introduction

Advances in machine learning (ML) methodologies, combined with multidisciplinary collaborations across biological and physical sciences, has the potential to propel drug discovery and development. Open Science fosters this collaboration by releasing datasets and methods into the public space; however, further education and widespread acceptance and adoption of Open Science approaches are necessary to tackle the plethora of known disease states.

Motivation

In addition to providing much needed insights into potential therapeutic protein targets, we also aim to demonstrate that small patient datasets have the potential to provide insights that usually require many samples (>5,000). There are many such datasets available and novel advancements in ML can provide valuable insights from these patient datasets.

Problem statement

Using a public dataset made available by patient advocacy group AnswerALS and a multidisciplinary Open Science approach with a systems biology augmented ML technology, we aim to validate previously reported drug targets in ALS and provide novel insights about ALS subpopulations and potential drug targets using a unique combination of ML methods and graph theory.

Methodology

We use NetraAI to generate hypotheses about specific patient subpopulations, which were then refined and validated through a combination of ML techniques, systems biology methods, and expert input.

Results

We extracted 8 target classes, each comprising of several genes that shed light into ALS pathophysiology and represent new avenues for treatment. These target classes are broadly categorized as inflammation, epigenetic, heat shock, neuromuscular junction, autophagy, apoptosis, axonal transport, and excitotoxicity. These findings are not mutually exclusive, and instead represent a systematic view of ALS pathophysiology. Based on these findings, we suggest that simultaneous targeting of ALS has the potential to mitigate ALS progression, with the plausibility of maintaining and sustaining an improved quality of life (QoL) for ALS patients. Even further, we identified subpopulations based on disease onset.

Conclusion

In the spirit of Open Science, this work aims to bridge the knowledge gap in ALS pathophysiology to aid in diagnostic, prognostic, and therapeutic strategies and pave the way for the development of personalized treatments tailored to the individual's needs.

Open Science Practices in Communication Sciences and Disorders: A Survey

PURPOSE

Open science is a collection of practices that seek to improve the accessibility, transparency, and replicability of science. Although these practices have garnered interest in related fields, it remains unclear whether open science practices have been adopted in the field of communication sciences and disorders (CSD). This study aimed to survey the knowledge, implementation, and perceived benefits and barriers of open science practices in CSD.

METHOD

An online survey was disseminated to researchers in the United States actively engaged in CSD research. Four-core open science practices were examined: preregistration, self-archiving, gold open access, and open data. Data were analyzed using descriptive statistics and regression models.

RESULTS

Two hundred twenty-two participants met the inclusion criteria. Most participants were doctoral students (38%) or assistant professors (24%) at R1 institutions (58%). Participants reported low knowledge of preregistration and gold open access. There was, however, a high level of desire to learn more for all practices. Implementation of open science practices was also low, most notably for preregistration, gold open access, and open data (< 25%). Predictors of knowledge and participation, as well as perceived barriers to implementation, are discussed.

CONCLUSION

Although participation in open science appears low in the field of CSD, participants expressed a strong desire to learn more in order to engage in these practices in the future. Supplemental Material and Open Science Form: https://doi.org/10.23641/asha.21569040.

Assessing the publishing priorities and preferences among STEM researchers at a large R1 institution

The cost of academic publishing has increased substantially despite the ease with which information can be shared on the web. Open Access publishing is a key mechanism for amplifying research access, inclusivity, and impact. Despite this, shifting to a free-to-read publishing environment requires navigating complex barriers that vary by career status and publishing expectations. In this article, we investigate the motivations and preferences of researchers situated within our large research institution as a case study for publishing attitudes at similar institutions. We surveyed the publishing priorities and preferences of researchers at various career stages in STEM fields as they relate to openness, data practices, and assessment of research impact. Our results indicate that publishing preferences, data management experience and research impact assessment vary by career status and departmental approaches to promotion. We find that open access publishing is widely appreciated regardless of career status, but financial limitations and publishing expectations were common barriers to publishing in Open Access journals. Our findings shed light on publishing attitudes and preferences among researchers at a major R1 research institution, and offer insight into advocacy strategies that incentivize open access publishing.

Establishing open science research priorities in health psychology: a research prioritisation Delphi exercise

OBJECTIVE

Research on Open Science practices in Health Psychology is lacking. This meta-research study aimed to identify research question priorities and obtain consensus on the Top 5 prioritised research questions for Open Science in Health Psychology.

METHODS AND MEASURES

An international Delphi consensus study was conducted. Twenty-three experts in Open Science and Health Psychology within the European Health Psychology Society (EHPS) suggested research question priorities to create a 'long-list' of items (Phase 1). Forty-three EHPS members rated the importance of these items, ranked their top five and suggested their own additional items (Phase 2). Twenty-four EHPS members received feedback on Phase 2 responses and then re-rated and re-ranked their top five research questions (Phase 3).

RESULTS

The top five ranked research question priorities were: 1. 'To what extent are Open Science behaviours currently practised in Health Psychology?', 2. 'How can we maximise the usefulness of Open Data and Open Code resources?', 3. 'How can Open Data be increased within Health Psychology?', 4. 'What interventions are effective for increasing the adoption of Open Science in Health Psychology?' and 5. 'How can we increase free Open Access publishing in Health Psychology?'.

CONCLUSION

Funding and resources should prioritise the research questions identified here.