Browsing by Subject "reproducibility"

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    ItemOpen Access
    An Online Repository for Pre-Clinical Imaging Protocols (PIPs).
    (Tomography (Ann Arbor, Mich.), 2023-03) Gammon, Seth T; Cohen, Allison S; Lehnert, Adrienne L; Sullivan, Daniel C; Malyarenko, Dariya; Manning, Henry Charles; Hormuth, David A; Daldrup-Link, Heike E; An, Hongyu; Quirk, James D; Shoghi, Kooresh; Pagel, Mark David; Kinahan, Paul E; Miyaoka, Robert S; Houghton, A McGarry; Lewis, Michael T; Larson, Peder; Sriram, Renuka; Blocker, Stephanie J; Pickup, Stephen; Badea, Alexandra; Badea, Cristian T; Yankeelov, Thomas E; Chenevert, Thomas L
    Providing method descriptions that are more detailed than currently available in typical peer reviewed journals has been identified as an actionable area for improvement. In the biochemical and cell biology space, this need has been met through the creation of new journals focused on detailed protocols and materials sourcing. However, this format is not well suited for capturing instrument validation, detailed imaging protocols, and extensive statistical analysis. Furthermore, the need for additional information must be counterbalanced by the additional time burden placed upon researchers who may be already overtasked. To address these competing issues, this white paper describes protocol templates for positron emission tomography (PET), X-ray computed tomography (CT), and magnetic resonance imaging (MRI) that can be leveraged by the broad community of quantitative imaging experts to write and self-publish protocols in protocols.io. Similar to the Structured Transparent Accessible Reproducible (STAR) or Journal of Visualized Experiments (JoVE) articles, authors are encouraged to publish peer reviewed papers and then to submit more detailed experimental protocols using this template to the online resource. Such protocols should be easy to use, readily accessible, readily searchable, considered open access, enable community feedback, editable, and citable by the author.
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    ItemOpen Access
    Quantifying Sources of Variability in Infancy Research Using the Infant-Directed-Speech Preference
    (Advances in Methods and Practices in Psychological Science, 2020-03) Frank, MC; Alcock, KJ; Arias-Trejo, N; Aschersleben, G; Baldwin, D; Barbu, S; Bergelson, E; Bergmann, C; Black, AK; Blything, R; Böhland, MP; Bolitho, P; Borovsky, A; Brady, SM; Braun, B; Brown, A; Byers-Heinlein, K; Campbell, LE; Cashon, C; Choi, M; Christodoulou, J; Cirelli, LK; Conte, S; Cordes, S; Cox, C; Cristia, A; Cusack, R; Davies, C; de Klerk, M; Delle Luche, C; de Ruiter, L; Dinakar, D; Dixon, KC; Durier, V; Durrant, S; Fennell, C; Ferguson, B; Ferry, A; Fikkert, P; Flanagan, T; Floccia, C; Foley, M; Fritzsche, T; Frost, RLA; Gampe, A; Gervain, J; Gonzalez-Gomez, N; Gupta, A; Hahn, LE; Hamlin, JK; Hannon, EE; Havron, N; Hay, J; Hernik, M; Höhle, B; Houston, DM; Howard, LH; Ishikawa, M; Itakura, S; Jackson, I; Jakobsen, KV; Jarto, M; Johnson, SP; Junge, C; Karadag, D; Kartushina, N; Kellier, DJ; Keren-Portnoy, T; Klassen, K; Kline, M; Ko, ES; Kominsky, JF; Kosie, JE; Kragness, HE; Krieger, AAR; Krieger, F; Lany, J; Lazo, RJ; Lee, M; Leservoisier, C; Levelt, C; Lew-Williams, C; Lippold, M; Liszkowski, U; Liu, L; Luke, SG; Lundwall, RA; Cassia, VM; Mani, N; Marino, C; Martin, A; Mastroberardino, M; Mateu, V; Mayor, J; Menn, K; Michel, C; Moriguchi, Y; Morris, B; Nave, KM; Nazzi, T
    Psychological scientists have become increasingly concerned with issues related to methodology and replicability, and infancy researchers in particular face specific challenges related to replicability: For example, high-powered studies are difficult to conduct, testing conditions vary across labs, and different labs have access to different infant populations. Addressing these concerns, we report on a large-scale, multisite study aimed at (a) assessing the overall replicability of a single theoretically important phenomenon and (b) examining methodological, cultural, and developmental moderators. We focus on infants’ preference for infant-directed speech (IDS) over adult-directed speech (ADS). Stimuli of mothers speaking to their infants and to an adult in North American English were created using seminaturalistic laboratory-based audio recordings. Infants’ relative preference for IDS and ADS was assessed across 67 laboratories in North America, Europe, Australia, and Asia using the three common methods for measuring infants’ discrimination (head-turn preference, central fixation, and eye tracking). The overall meta-analytic effect size (Cohen’s d) was 0.35, 95% confidence interval = [0.29, 0.42], which was reliably above zero but smaller than the meta-analytic mean computed from previous literature (0.67). The IDS preference was significantly stronger in older children, in those children for whom the stimuli matched their native language and dialect, and in data from labs using the head-turn preference procedure. Together, these findings replicate the IDS preference but suggest that its magnitude is modulated by development, native-language experience, and testing procedure.
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    Reproducibility assessment of a biomechanical model-based elasticity imaging method for identifying changes in left ventricular mechanical stiffness.
    (Journal of medical imaging (Bellingham, Wash.), 2022-09) Miller, Caroline E; Jordan, Jennifer H; Douglas, Emily; Ansley, Katherine; Thomas, Alexandra; Weis, Jared A

    Purpose

    Cardiotoxicity of antineoplastic therapies is increasingly a risk to cancer patients treated with curative intent with years of life to protect. Studies highlight the importance of identifying early cardiac decline in cancer patients undergoing cardiotoxic therapies. Accurate tools to study this are a critical clinical need. Current and emerging methods for assessing cardiotoxicity are too coarse for identifying preclinical cardiac degradation or too cumbersome for clinical implementation.

    Approach

    In the previous work, we developed a noninvasive biomechanical model-based elasticity imaging methodology (BEIM) to assess mechanical stiffness changes of the left ventricle (LV) based on routine cine cardiac magnetic resonance (CMR) images. We examine this methodology to assess methodological reproducibility. We assessed a cohort of 10 participants that underwent test/retest short-axis CMR imaging at baseline and follow-up sessions as part of a previous publicly available study. We compare test images to retest images acquired within the same session to assess within-session reproducibility. We also compare test and retest images acquired at the baseline imaging session to test and retest images acquired at the follow-up imaging session to assess between-session reproducibility.

    Results

    We establish the within-session and between-session reproducibility of our method, with global elasticity demonstrating repeatability within a range previously demonstrated in cardiac strain imaging studies. We demonstrate increased repeatability of global elasticity compared to segmental elasticity for both within-session and between-session. Within-subject coefficients of variation for within-session test/retest images globally for all modulus directions and a mechanical fractional mechanical stiffness anisotropy metric ranged from 11% to 28%.

    Conclusions

    Results suggest that our methodology can reproducibly generate estimates of relative mechanical elasticity of the LV and provides a threshold for distinguishing true changes in myocardial mechanical stiffness from experimental variation. BEIM has applications in identifying preclinical cardiotoxicity in breast cancer patients undergoing antineoplastic therapies.