More Like this

1. Enhancing reproducibility in single cell research with biocytometry: An inter-laboratory study

   https://doi.org/10.1371/journal.pone.0314992  

   Fikar, Pavel; Alvarez, Laura; Berne, Laura; Cienciala, Martin; Kan, Christopher; Kasl, Hynek; Luo, Mona; Novackova, Zuzana; Ordonez, Sheyla; Sramkova, Zuzana; et al (December 2024, PLOS ONE)

   Fu, Elain (Ed.)

   Biomedicine today is experiencing a shift towards decentralized data collection, which promises enhanced reproducibility and collaboration across diverse laboratory environments. This inter-laboratory study evaluates the performance of biocytometry, a method utilizing engineered bioparticles for enumerating cells based on their surface antigen patterns. In centralized and aggregated inter-lab studies, biocytometry demonstrated significant statistical power in discriminating numbers of target cells at varying concentrations as low as 1 cell per 100,000 background cells. User skill levels varied from expert to beginner capturing a range of proficiencies. Measurement was performed in a decentralized environment without any instrument cross-calibration or advanced user training outside of a basic instruction manual. The results affirm biocytometry to be a viable solution for immunophenotyping applications demanding sensitivity as well as scalability and reproducibility and paves the way for decentralized analysis of rare cells in heterogeneous samples. 

   more » « less
2. A network correspondence toolbox for quantitative evaluation of novel neuroimaging results

   https://doi.org/10.1038/s41467-025-58176-9  

   Kong, Ru; Spreng, R Nathan; Xue, Aihuiping; Betzel, Richard F; Cohen, Jessica R; Damoiseaux, Jessica S; De_Brigard, Felipe; Eickhoff, Simon B; Fornito, Alex; Gratton, Caterina; et al (December 2025, Nature Communications)

   Abstract The brain can be decomposed into large-scale functional networks, but the specific spatial topographies of these networks and the names used to describe them vary across studies. Such discordance has hampered interpretation and convergence of research findings across the field. We have developed theNetwork Correspondence Toolbox(NCT) to permit researchers to examine and report spatial correspondence between their novel neuroimaging results and multiple widely used functional brain atlases. We provide several exemplar demonstrations to illustrate how researchers can use the NCT to report their own findings. The NCT provides a convenient means for computing Dice coefficients with spin test permutations to determine the magnitude and statistical significance of correspondence among user-defined maps and existing atlas labels. The adoption of the NCT will make it easier for network neuroscience researchers to report their findings in a standardized manner, thus aiding reproducibility and facilitating comparisons between studies to produce interdisciplinary insights. 

   more » « less
3. Your notebook is not crumby enough, REPLace it

   Michael Brachmann, William Spoth (January 2020, Conference on Innovative Data Systems Research (CIDR))

   Notebook and spreadsheet systems are currently the de-facto standard for data collection, preparation, and analysis. However, these systems have been criticized for their lack of reproducibility, versioning, and support for sharing. These shortcomings are particularly detrimental for data curation where data scientists iteratively build workflows to clean up and integrate data as a prerequisite for analysis. We present Vizier, an open-source tool that helps analysts to build and refine data pipelines. Vizier combines the flexibility of notebooks with the easy-to-use data manipulation interface of spreadsheets. Combined with advanced provenance tracking for both data and computational steps this enables reproducibility, versioning, and streamlined data exploration. Unique to Vizier is that it exposes potential issues with data, no matter whether they already exist in the input or are introduced by the operations of a notebook. We refer to such potential errors as data caveats. Caveats are propagated alongside data using principled techniques from uncertain data management. Vizier provides extensive user interface support for caveats, e.g., exposing them as summaries in a dedicated error view and highlighting cells with caveats in spreadsheets. 

   more » « less
4. Growth produces coordination trade-offs in Trichoplax adhaerens , an animal lacking a central nervous system

   https://doi.org/10.1073/pnas.2206163120  

   Davidescu, Mircea R.; Romanczuk, Pawel; Gregor, Thomas; Couzin, Iain D. (March 2023, Proceedings of the National Academy of Sciences)

   How collectives remain coordinated as they grow in size is a fundamental challenge affecting systems ranging from biofilms to governments. This challenge is particularly apparent in multicellular organisms, where coordination among a vast number of cells is vital for coherent animal behavior. However, the earliest multicellular organisms were decentralized, with indeterminate sizes and morphologies, as exemplified by Trichoplax adhaerens , arguably the earliest-diverged and simplest motile animal. We investigated coordination among cells in T. adhaerens by observing the degree of collective order in locomotion across animals of differing sizes and found that larger individuals exhibit increasingly disordered locomotion. We reproduced this effect of size on order through a simulation model of active elastic cellular sheets and demonstrate that this relationship is best recapitulated across all body sizes when the simulation parameters are tuned to a critical point in the parameter space. We quantify the trade-off between increasing size and coordination in a multicellular animal with a decentralized anatomy that shows evidence of criticality and hypothesize as to the implications of this on the evolution hierarchical structures such as nervous systems in larger organisms. 

   more » « less
5. Importance of Standardizing Analytical Characterization Methodology for Improved Reliability of the Nanomedicine Literature

   https://doi.org/10.1007/s40820-022-00922-5  

   Sharifi, Shahriar; Mahmoud, Nouf N.; Voke, Elizabeth; Landry, Markita P.; Mahmoudi, Morteza (December 2022, Nano-Micro Letters)

   Abstract Understanding the interaction between biological structures and nanoscale technologies, dubbed the nano-bio interface, is required for successful development of safe and efficient nanomedicine products. The lack of a universal reporting system and decentralized methodologies for nanomaterial characterization have resulted in a low degree of reliability and reproducibility in the nanomedicine literature. As such, there is a strong need to establish a characterization system to support the reproducibility of nanoscience data particularly for studies seeking clinical translation. Here, we discuss the existing key standards for addressing robust characterization of nanomaterials based on their intended use in medical devices or as pharmaceuticals. We also discuss the challenges surrounding implementation of such standard protocols and their implication for translation of nanotechnology into clinical practice. We, however, emphasize that practical implementation of standard protocols in experimental laboratories requires long-term planning through integration of stakeholders including institutions and funding agencies. 

   more » « less