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RNA velocities and generalizations emerge as powerful approaches for extracting time-resolved information from high-throughput snapshot single-cell data. Yet, several inherent limitations restrict applying the approaches to genes not suitable for RNA velocity inference due to complex transcriptional dynamics, low expression, or lacking splicing dynamics, or data of non-transcriptomic modality. Here, we present GraphVelo, a graph-based machine learning procedure that uses as input the RNA velocities inferred from existing methods and infers velocity vectors lying in the tangent space of the low-dimensional manifold formed by the single cell data.
View Article and Find Full Text PDFPopulation imaging of internal state circuits relevant to psychiatric disease: a review.
Neurophotonics
January 2025
University of Pittsburgh, Department of Psychiatry, Translational Neuroscience Program, Pittsburgh, Pennsylvania, United States.
Internal states involve brain-wide changes that subserve coordinated behavioral and physiological responses for adaptation to changing environments and body states. Investigations of single neurons or small populations have yielded exciting discoveries for the field of neuroscience, but it has been increasingly clear that the encoding of internal states involves the simultaneous representation of multiple different variables in distributed neural ensembles. Thus, an understanding of the representation and regulation of internal states requires capturing large population activity and benefits from approaches that allow for parsing intermingled, genetically defined cell populations.
View Article and Find Full Text PDFNationwide guideline implementation: a qualitative study of barriers and facilitators from the perspective of guideline organizations.
BMC Health Serv Res
January 2025
Amsterdam UMC, Department of Public and Occupational Health, Vrije Universiteit Amsterdam, Amsterdam Public Health research institute, Van der Boechorststraat 7, NL-1081 BT, Amsterdam, The Netherlands.
Background: Although the number of Dutch guidelines is growing, their uptake and impact in clinical practice lag behind. Dutch guideline organizations, including guideline developers, governmental agencies, health insurers and other national organizations, play a crucial role in developing, authorizing and/or supporting the use of guidelines. They influence end users' awareness, accessibility, understanding, acceptability and applicability of guidelines.
View Article and Find Full Text PDFIntegrating representation learning, permutation, and optimization to detect lineage-related gene expression patterns.
Nat Commun
January 2025
Laboratory for Information and Decision Systems, Massachusetts Institute of Technology, Cambridge, MA, USA.
Recent barcoding technologies allow reconstructing lineage trees while capturing paired single-cell RNA-sequencing (scRNA-seq) data. Such datasets provide opportunities to compare gene expression memory maintenance through lineage branching and pinpoint critical genes in these processes. Here we develop Permutation, Optimization, and Representation learning based single Cell gene Expression and Lineage ANalysis (PORCELAN) to identify lineage-informative genes or subtrees where lineage and expression are tightly coupled.
View Article and Find Full Text PDFScaling of ventral hippocampal activity during anxiety.
J Neurosci
January 2025
Laboratory of Systems Neuroscience, Department of Physiology, University of Bern, Bern, Switzerland.
The hippocampus supports a multiplicity of functions, with the dorsal region contributing to spatial representations and memory, and the ventral hippocampus (vH) being primarily involved in emotional processing. While spatial encoding has been extensively investigated, how the vH activity is tuned to emotional states, e.g.
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