bioRxiv

Transcriptome-wide alternative mRNA splicing analysis reveals post-transcriptional regulation of neuronal differentiation

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URL https://www.biorxiv.org/content/10.1101/2024.07.16.603656v1.full.pdf Stage Normal Science Paradigm framing The preprint operates within the dominant paradigm of molecular biology, specifically focusing on post-transcriptional gene regulation mechanisms and their role in neuronal differentiation. It utilizes established techniques like RNA-seq and shRNA knockdown to investigate these processes. Highlights This research solidifies existing understanding within the field by providing a […]

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Tongue bite apparatus highlights functional innovation in a 310-million-year-old ray- finned fish

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URL https://www.biorxiv.org/content/10.1101/2025.05.10.653277v1.full.pdf Stage Normal Science Paradigm framing The paradigm is the established understanding of the evolution of feeding mechanisms in ray-finned fishes, specifically focusing on the development of the tongue bite. This includes the existing knowledge of the timing, anatomical variations, and phylogenetic distribution of this adaptation across different lineages. Highlights This preprint presents a

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Differential Analysis Reveals Isoform Switching Following Pneumococcal Vaccination

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URL https://www.biorxiv.org/content/10.1101/2025.03.09.642237v2.full.pdf Stage Normal Science Paradigm framing The preprint operates within the current paradigm of bioinformatics and transcriptomics, utilizing established RNA-seq technologies and analysis methods. It specifically focuses on the well-established concepts of differential gene expression and isoform switching. Highlights This preprint represents a clear example of normal science. It operates within the accepted paradigm

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Reappraisal of the place of cultivated plants in the carbon budget

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URL https://www.biorxiv.org/content/10.1101/2025.05.17.654640v1.full.pdf Stage Model Drift Paradigm framing Carbon Budget and Climate Change Highlights The preprint "Reappraisal of the place of cultivated plants in the carbon budget" challenges the current paradigm of carbon budget accounting within the broader climate change discourse. The established paradigm largely neglects the carbon capture and storage contribution of annual crops, focusing

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Non-enzymatic isothermal strand displacement and amplification (NISDA) does not enable sensitive nucleic acid quantification

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URL https://www.biorxiv.org/content/10.1101/2025.05.19.654176v1.full.pdf Stage Model Drift Paradigm framing Nucleic acid quantification using enzyme-free isothermal amplification methods Highlights This preprint presents an attempt to replicate and validate the non-enzymatic isothermal strand displacement and amplification (NISDA) assay, a recently introduced method for nucleic acid detection. The authors’ inability to reproduce the sensitivity levels reported in the original NISDA

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Herbaria provide a valuable resource for obtaining informative mRNA

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URL https://www.biorxiv.org/content/10.1101/2025.02.12.637878v1.full.pdf Stage Normal Science Paradigm framing Transcriptomics and Molecular Biology Highlights This preprint investigates the utility of herbarium specimens for mRNA transcriptomics, a field traditionally reliant on DNA. While acknowledging the established paradigm of RNA instability, the authors challenge the assumption that herbarium specimens are unsuitable for RNA-based studies. By successfully assembling transcriptomes from

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Shared Hierarchical Representations Explain Temporal Correspondence Between Brain Activity and Deep Neural Networks

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URL https://www.biorxiv.org/content/10.1101/2025.05.19.655003v2.full.pdf Stage Normal Science Paradigm framing The preprint operates within the broader paradigm of cognitive neuroscience, specifically focusing on visual object recognition. Within this field, the dominant paradigm involves hierarchical processing of visual information in both biological and artificial systems. Highlights This preprint investigates the temporal correspondence between brain activity (measured via EEG) and

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Closed-form expressions for the directions of maximum modulation depth in temporal interference electrical brain stimulation.

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URL https://www.biorxiv.org/content/10.1101/2025.05.16.654079v2.full.pdf Stage Normal Science / Model Drift Paradigm framing The preprint operates within the dominant paradigm of bioelectromagnetism, specifically focusing on the use of electric fields for neuromodulation. It uses established methodologies of computational bioelectromagnetism to analyze and model electric fields interaction with neural tissue. Highlights The preprint primarily contributes to "normal science" by

Closed-form expressions for the directions of maximum modulation depth in temporal interference electrical brain stimulation. Read More »

Draft genome and transcriptomic sequence data of three invasive insect species

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URL https://www.biorxiv.org/content/10.1101/2024.12.02.626401v3.full.pdf Stage Normal Science Paradigm framing Genomics and Bioinformatics Highlights This preprint presents genomic and transcriptomic data for three invasive insect species. It falls under the "normal science" stage of Kuhn's paradigm cycle. The research operates within the established paradigms of genomics and bioinformatics, utilizing accepted methods like whole-genome sequencing, RNA-seq, and Hi-C sequencing.

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Otoacoustic emissions but not behavioral measurements predict cochlear-nerve frequency tuning in an avian vocal-communication specialist

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URL https://www.biorxiv.org/content/10.1101/2024.08.29.610326v4.full.pdf Stage Normal Science Paradigm framing The current paradigm in auditory research is the power spectrum model of masking. The dominant theory is that behavioral frequency selectivity measurements should roughly correspond to cochlear frequency tuning, at least at lower sound levels. This assumes that the behavioral responses are largely driven by cochlear processes. Highlights

Otoacoustic emissions but not behavioral measurements predict cochlear-nerve frequency tuning in an avian vocal-communication specialist Read More »