RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods

Bandrowski, Anita; Martone, Maryann E.

doi:10.1016/j.neuron.2016.04.030

Cited by 70 publications

(59 citation statements)

References 12 publications

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“…Therefore, this method can lead to a comprehensive evaluation of cryopreservation protocols, and to the strengthening and standardization of overall quality control strategies. Given the expanding emphasis that is being placed on strategies to assure reproducibility in science overall (Bandrowski and Martone, 2016; Nuzzo, 2015), the evaluation of cell fixatives suitable for fish sperm provides a valuable alternative to the current limited methods, especially when making comparisons among laboratories.…”

Section: Discussionmentioning

confidence: 99%

Amine reactive dyes: An alternative to estimate membrane integrity in fish sperm cells

Torres

Tiersch

2016

Aquaculture

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Fluorescent dyes that binds irreversibly to cellular amines, come in several available emission spectra, and do not poses health concerns were used to evaluate membrane integrity in fish sperm cells. The objectives of the present study were to determine: (1) a working dye concentration for fish sperm samples, and (2) if the traditional propidium iodide/SYBR-14 staining combination was comparable with the amine reactive dye (ARD) methods at identifying cell populations with intact and compromised membranes after sperm activation, refrigerated storage, and exposure to cryoprotectant and surfactant. Zebrafish (Danio rerio) sperm were obtained by stripping, and pooled samples (in triplicate) were used in all tests. Six dilutions of the amine dye (ranging from 0.625 to 0.02 μL/mL) were evaluated, and compared with the traditional staining protocol. A concentration of 0.5 μL/mL ARD was selected to be used in subsequent assays. Sperm suspensions were activated with deionized water to simulate urine contamination. After 10 sec, osmolality was increased to stop activation, and the procedure was repeated in 10-sec intervals until the sperm remained activated for 120 consecutive sec; membrane integrity was analyzed at each time interval. For the storage assay, sperm suspensions were prepared in Hanks’ balanced salt solution at 302 mOsm/kg osmolality (HBSS302), HBSS354 and HBSS402, and evaluated every 2 hr for 8 hr, and every 24 hr for 72 hr. Cryoprotectant toxicity was tested by diluting sperm suspensions in HBSS340 with methanol at 5, 10 and 15% final concentrations. Surfactant toxicity was tested by diluting sperm suspensions in HBSS354 with Triton X-100 at 0.2, 0.15 and 0.1 mM final concentrations. In each toxicity assay, membrane integrity was tested every 20 min for 80 min. The number of membrane-intact cells significantly decreased across time in all treatments (p < 0.05). Significant differences between staining protocols were observed after activation and after exposure to methanol at 10 and 15%, and to Triton X-100 (p < 0.05). The average difference, however, was minor (between 1 and 6% in average) in relation to the typical values used for decision making based on this assay. Results showed that this method has the potential to contribute greatly to the standardization of cryopreservation in aquatic species.

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Section: Discussionmentioning

confidence: 99%

Amine reactive dyes: An alternative to estimate membrane integrity in fish sperm cells

Torres

Tiersch

2016

Aquaculture

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“…NeuroLex 60,61 provides a common platform that gathers terms from different sources (including previous vocabularies developed by NIF, BIRN…). Interestingly, Neurolex was part of the recent Resource Identification Initiative (RII) 62,63 that publicized the use of those identifiers (e.g., ‘RRID:SCR_007037’ for SPM 64 ) in research papers. RII is currently focused on the identification of biological resources and has been quickly adopted, with more than 100 journals participating to date.…”

Section: Methodsmentioning

confidence: 99%

Sharing brain mapping statistical results with the neuroimaging data model

et al. 2016

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Only a tiny fraction of the data and metadata produced by an fMRI study is finally conveyed to the community. This lack of transparency not only hinders the reproducibility of neuroimaging results but also impairs future meta-analyses. In this work we introduce NIDM-Results, a format specification providing a machine-readable description of neuroimaging statistical results along with key image data summarising the experiment. NIDM-Results provides a unified representation of mass univariate analyses including a level of detail consistent with available best practices. This standardized representation allows authors to relay methods and results in a platform-independent regularized format that is not tied to a particular neuroimaging software package. Tools are available to export NIDM-Result graphs and associated files from the widely used SPM and FSL software packages, and the NeuroVault repository can import NIDM-Results archives. The specification is publically available at: http://nidm.nidash.org/specs/nidm-results.html.

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“…As Van Horn and Gazzaniga observed, “the reality remains that very little of the neuroimaging data gathered each day in the field have been made available to those who could help provide much needed understanding.” While we agree that this assessment still holds, we see other evidence that points toward a very different future. There is increasing recognition that greater openness and transparency, reflected in data, materials, and code sharing, offers individual investigators and the field as a whole far more benefits than risks . While significant challenges remain in developing technology and workflow practices that make open and transparent workflows easy to generate and data readily shareable, that progress is being made.…”

Section: The Futurementioning

confidence: 99%

Progress toward openness, transparency, and reproducibility in cognitive neuroscience

Gilmore

Diaz

Wyble

et al. 2017

Annals of the New York Academy of Sciences

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Accumulating evidence suggests that many findings in psychological science and cognitive neuroscience may prove difficult to reproduce; statistical power in brain imaging studies is low, and has not improved recently; software errors in common analysis tools are common, and can go undetected for many years; and, a few large scale studies notwithstanding, open sharing of data, code, and materials remains the rare exception. At the same time, there is a renewed focus on reproducibility, transparency, and openness as essential core values in cognitive neuroscience. The emergence and rapid growth of data archives, meta-analytic tools, software pipelines, and research groups devoted to improved methodology reflects this new sensibility. We review evidence that the field has begun to embrace new open research practices, and illustrate how these can begin to address problems of reproducibility, statistical power, and transparency in ways that will ultimately accelerate discovery.

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RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods

Cited by 70 publications

References 12 publications

Amine reactive dyes: An alternative to estimate membrane integrity in fish sperm cells

Amine reactive dyes: An alternative to estimate membrane integrity in fish sperm cells

Sharing brain mapping statistical results with the neuroimaging data model

Progress toward openness, transparency, and reproducibility in cognitive neuroscience

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