Reproducibility in Biomedical Research

Mullane, Kevin; Curtis, Michael J.; Williams, Michael

doi:10.1016/b978-0-12-804725-5.00001-x

Cited by 4 publications

(3 citation statements)

References 269 publications

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“…One protocol recommends a final concentration of 7 × 10 6 cells/well in a 6 well plate, equivalent to 7.3 × 10 5 cells/cm 2 (∼450x higher than the luciferase assay) whereas another ChIP-seq protocol suggested a lower density of 1 × 10 5 cells/cm 2 ( Song et al., 2015 ; Sullivan and Santos 2020 ). These discrepancies may contribute to reproducibility concerns in biomedical research ( Mullane et al., 2018 ). Though many factors may be involved, including inconsistencies in reagents as well as human errors, we surmise that such variations in cell seeding density may contribute to lack of reproducibility.…”

Section: Introductionmentioning

confidence: 99%

β-catenin links cell seeding density to global gene expression during mouse embryonic stem cell differentiation

et al. 2022

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Summary Although cell density is known to affect numerous biological processes including gene expression and cell fate specification, mechanistic understanding of what factors link cell density to global gene regulation is lacking. Here, we reveal that the expression of thousands of genes in mouse embryonic stem cells (mESCs) is affected by cell seeding density and that low cell density enhances the efficiency of differentiation. Mechanistically, β-catenin is localized primarily to adherens junctions during both self-renewal and differentiation at high density. However, when mESCs differentiate at low density, β-catenin translocates to the nucleus and associates with Tcf7l1, inducing co-occupied lineage markers. Meanwhile, Esrrb sustains the expression of pluripotency-associated genes while repressing lineage markers at high density, and its association with DNA decreases at low density. Our results provide new insights into the previously neglected but pervasive phenomenon of density-dependent gene regulation.

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Section: Introductionmentioning

confidence: 99%

β-catenin links cell seeding density to global gene expression during mouse embryonic stem cell differentiation

et al. 2022

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“…We will employ the Wilcoxon rank-sum test to compare differences between working groups, as well as compare professional member and PPIE contributor experiences at each survey time point. We will compare within group changes over time using the Wilcoxon signed-rank test for comparison of the first two timepoints and the Friedman test to allow inclusion of more than two timepoints [ 33 ].…”

Section: Resultsmentioning

confidence: 99%

Patient and Public Involvement and Engagement in the Development of a Platform Clinical Trial for Parkinson’s Disease: An Evaluation Protocol

Zeissler,

Bakshi,

Bartlett

et al. 2024

JPD

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Background: Patient and public involvement and engagement (PPIE) in the design of trials is important, as participant experience critically impacts delivery. The Edmond J Safra Accelerating Clinical Trials in PD (EJS ACT-PD) initiative is a UK consortium designing a platform trial for disease modifying therapies in PD. Objective: The integration of PPIE in all aspects of trial design and its evaluation throughout the project. Methods: PwP and care partners were recruited to a PPIE working group (WG) via UK Parkinson’s charities, investigator patient groups and participants of a Delphi study on trial design. They are supported by charity representatives, trial delivery experts, researchers and core project team members. PPIE is fully embedded within the consortium’s five other WGs and steering group. The group’s terms of reference, processes for effective working and PPIE evaluation were co-developed with PPIE contributors. Results: 11 PwP and 4 care partners have supported the PPIE WG and contributed to the development of processes for effective working. A mixed methods research-in-action study is ongoing to evaluate PPIE within the consortium. This includes the Patient Engagement in Research Scale -a quantitative PPIE quality measure; semi-structured interviews -identifying areas for improvement and overall impressions of involvement; process fidelity- recording adherence; project documentation review – identifying impact of PPIE on project outputs. Conclusions: We provide a practical example of PPIE in complex projects. Evaluating feasibility, experiences and impact of PPIE involvement in EJS ACT-PD will inform similar programs on effective strategies. This will help enable future patient-centered research.

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“…Reproducibility, which we limit to the reproducibility of results, is defined as the ability to perform and confirm a previously reported finding by using procedures that are the same or closely matched to those in the original setting [ 113 ]. It is an important criterion in assessing the fabrication and the performance of a device.…”

Section: Fabrication Of µPadsmentioning

confidence: 99%

Recent Advances in Microfluidic Paper-Based Analytical Devices toward High-Throughput Screening

et al. 2020

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Microfluidic paper-based analytical devices (µPADs) have become promising tools offering various analytical applications for chemical and biological assays at the point-of-care (POC). Compared to traditional microfluidic devices, µPADs offer notable advantages; they are cost-effective, easily fabricated, disposable, and portable. Because of our better understanding and advanced engineering of µPADs, multistep assays, high detection sensitivity, and rapid result readout have become possible, and recently developed µPADs have gained extensive interest in parallel analyses to detect biomarkers of interest. In this review, we focus on recent developments in order to achieve µPADs with high-throughput capability. We discuss existing fabrication techniques and designs, and we introduce and discuss current detection methods and their applications to multiplexed detection assays in relation to clinical diagnosis, drug analysis and screening, environmental monitoring, and food and beverage quality control. A summary with future perspectives for µPADs is also presented.

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Reproducibility in Biomedical Research

Cited by 4 publications

References 269 publications

β-catenin links cell seeding density to global gene expression during mouse embryonic stem cell differentiation

β-catenin links cell seeding density to global gene expression during mouse embryonic stem cell differentiation

Patient and Public Involvement and Engagement in the Development of a Platform Clinical Trial for Parkinson’s Disease: An Evaluation Protocol

Recent Advances in Microfluidic Paper-Based Analytical Devices toward High-Throughput Screening

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