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Current in vitro sonication experiments show immense variability in experimental set-ups and methods used. As a result, there is uncertainty in the ultrasound field parameters experienced by sonicated samples, poor reproducibility of these experiments and thus reduced scientific value of the results obtained. The scope of this narrative review is to briefly describe mechanisms of action of ultrasound, list the most frequently used experimental set-ups and focus on a description of factors influencing the outcomes and reproducibility of these experiments. The factors assessed include: proper reporting of ultrasound exposure parameters, experimental geometry, coupling medium quality, influence of culture vessels, formation of standing waves, motion/rotation of the sonicated sample and the characteristics of the sample itself. In the discussion we describe pros and cons of particular exposure geometries and factors, and make a few recommendations as to how to increase the reproducibility and validity of the experiments performed.

Book

Kinetic data analysis, design and analysis of enzyme and pharmacokinetic experiments : proceedings of a sattelite symposium held July 14, 1979 in Toronto

Endrenyi, Laszlo
Author Endrenyi, Laszlo

New York : Plenum Press, 1981

427 s. : il.

Article

Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR)

... This design enables the expression of one reporter to be influenced by the specific mechanism under investigation ...

Nature structural & molecular biology. 2025 ; 32 (3) : 418-430. [pub] 20250303

Nat Struct Mol Biol
ISSN 1545-9985
Medvik
Source

Dual reporters encoding two distinct proteins within the same mRNA have had a crucial role in identifying and characterizing unconventional mechanisms of eukaryotic translation. These mechanisms include initiation via internal ribosomal entry sites (IRESs), ribosomal frameshifting, stop codon readthrough and reinitiation. This design enables the expression of one reporter to be influenced by the specific mechanism under investigation, while the other reporter serves as an internal control. However, challenges arise when intervening test sequences are placed between these two reporters. Such sequences can inadvertently impact the expression or function of either reporter, independent of translation-related changes, potentially biasing the results. These effects may occur due to cryptic regulatory elements inducing or affecting transcription initiation, splicing, polyadenylation and antisense transcription as well as unpredictable effects of the translated test sequences on the stability and activity of the reporters. Unfortunately, these unintended effects may lead to misinterpretation of data and the publication of incorrect conclusions in the scientific literature. To address this issue and to assist the scientific community in accurately interpreting dual-reporter experiments, we have developed comprehensive guidelines. These guidelines cover experimental design, interpretation and the minimal requirements for reporting results. They are designed to aid researchers conducting these experiments as well as reviewers, editors and other investigators who seek to evaluate published data.

Online article

The influence of past research on the design of experiments with dissolved organic matter and engineered nanoparticles

... plausibility of this hypothesis, we developed an agent-based model simulating the material choice in the experiments ...

PLoS One. 2018 ; 13 (5) : e0196549. [pub] 20180507

ISSN 1932-6203
Medvik
Source

To assess the environmental fate of engineered nanoparticles (ENPs), it is essential to understand their interactions with dissolved organic matter (DOM). The highly complex nature of the interactions between DOM and ENPs and other particulate matter (PM) requires investigating a wide range of material types under different conditions. However, despite repeated calls for an increased diversity of the DOM and PM studied, researchers increasingly focus on certain subsets of DOM and PM. Considering the discrepancy between the calls for more diversity and the research actually carried out, we hypothesize that materials that were studied more often are more visible in the scientific literature and therefore are more likely to be studied again. To investigate the plausibility of this hypothesis, we developed an agent-based model simulating the material choice in the experiments studying the interaction between DOM and PM between 1990 and 2015. The model reproduces the temporal trends in the choice of materials as well as the main properties of a network that displays the DOM and PM types investigated experimentally. The results, which support the hypothesis of a positive reinforcing material choice, help to explain why calls to increase the diversity of the materials studied are repeatedly made and why recent criticism states that the selection of materials is unbalanced.