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Bruinsma, S.

Publications and source records attributed to Bruinsma, S..

2 recordsLinked to original sources

A parietal grid-like code rotates with cognitive maps but lags rapid behavioral transfer

The neural grid code has been proposed to provide a mechanism for generalization and transfer of relational knowledge between situations enabling rapid adaptation of behavior in novel circumstances. However, to date, very little is known about the dynamics with which grid representations change at context transitions, or how such dynamics relate to downstream behavioral adaptation. Here we tested whether grid representations measured with fMRI rotate to match behavioral goals at context transitions and whether such rotations underlie knowledge transfer. Human participants performed a task that included unsignaled state changes at which the position of multiple target locations abruptly and synchronously rotated by the same degree. After state changes, participants were able to leverage the relative positions of the targets to rapidly infer locations, even novel ones, constituting a form of zero-shot transfer. We observed a cognitive grid-like code in the right posterior parietal cortex with a consistent phase angle that rotated with the relative positions of the targets. However, this rotation was too slow to account for rapid improvements in performance after a state change, and instead these improvements were more closely related to representations of the identity and location of spatial targets in the frontoparietal and orbitofrontal cortex, respectively. Our results highlight the ability of humans to rapidly transfer knowledge and demonstrate that a parietal grid-like code rotates into behaviorally relevant reference frames, but raise questions about the function of such rotations, pointing instead to alternate neural mechanisms for rapid knowledge transfer.

neuroscience↗

The SEQC2 Epigenomics Quality Control (EpiQC) Study: Comprehensive Characterization of Epigenetic Methods, Reproducibility, and Quantification

Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and a global resource for epigenetics research from the FDAs Epigenomics Quality Control (EpiQC) Group. The study design leverages seven human cell lines that are designated as reference materials and publicly available from the National Institute of Standards and Technology (NIST) and Genome in a Bottle (GIAB) consortium. These samples were subject to a variety of genome-wide methylation interrogation approaches across six independent laboratories, with a primary focus was on 5-methylcytosine modifications. Each sample was processed in two or more technical replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), one enzymatic deamination method (EMseq), targeted methylation sequencing (Illumina Methyl Capture EPIC), and single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, BWAMeth, and GemBS), we found overall high concordance between assays (R=0.87-R0.93), differences in efficency of read mapping and CpG capture and coverage, and platform performance. The data provided herein can guide continued used of these reference materials in epigenomics assays, as well as provide best practices for epigenomics research and experimental design in future studies.

genomics↗