bioRxiv

Cooperation Destabilizes Communities, but Competition Pays the Price

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URL https://www.biorxiv.org/content/10.1101/2023.12.26.573354v2.full.pdf Stage Normal Science Paradigm framing Community Ecology, Population Dynamics, and the paradigm of diversity-stability relationships within ecological communities. Highlights This preprint investigates a well-established problem within community ecology: the seemingly paradoxical prevalence of cooperation in natural communities despite theoretical predictions that cooperation destabilizes communities. This places the research firmly within the 'normal science' […]

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Solving three core challenges in transient dynamics analysis of matrix population models

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URL https://www.biorxiv.org/content/10.1101/2025.05.29.656837v1.full.pdf Stage Normal Science Paradigm framing The paper operates within the dominant paradigm of matrix population models in ecology and demography. Highlights This preprint presents a refinement of existing analytical tools within the established paradigm of matrix population models. It addresses specific technical challenges related to the interpretation of transient dynamics, proposing solutions like

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Deviation Error: assessing machine learning predictions for replicate measurements in genomics and beyond

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URL https://www.biorxiv.org/content/10.1101/2025.05.29.656931v1.full.pdf Stage Normal Science Paradigm framing The preprint operates within the paradigm of machine learning applied to genomics, specifically focusing on predictive modeling for replicate measurements. It accepts the established methods and assumptions of this field, such as the use of standard loss functions and the focus on minimizing prediction error. Highlights This preprint

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D1/D5 Receptor Activation Promotes Long-Term Potentiation and Synaptic Tagging/Capture in Hippocampal Area CA2

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URL https://www.biorxiv.org/content/10.1101/2025.06.01.657216v2.full.pdf Stage Normal Science Paradigm framing Long-term potentiation (LTP) as a cellular model of learning and memory Highlights This preprint investigates the effects of dopamine D1/D5 receptor activation on synaptic plasticity in the hippocampal CA2 region, an area implicated in social memory. While the broader paradigm of LTP as a correlate of learning and

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FoldMark: Safeguarding Protein Structure Generative Models with Distributional and Evolutionary Watermarking

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URL https://www.biorxiv.org/content/10.1101/2024.10.23.619960v6.full.pdf Stage Normal Science Paradigm framing The preprint operates within the dominant paradigm of protein structure prediction and design, heavily influenced by recent advancements in machine learning, particularly deep learning models like AlphaFold. It acknowledges the transformative impact of these models while addressing emerging concerns within this paradigm. Highlights This preprint presents FoldMark, a

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MARLOWE: Taxonomic Characterization of Unknown Samples for Forensics Using De Novo Peptide Identification

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URL https://www.biorxiv.org/content/10.1101/2024.09.30.615220v2.full.pdf Stage Normal Science Paradigm framing The preprint operates within the paradigm of forensic proteomics and metaproteomics, specifically focusing on taxonomic characterization of unknown biological samples using mass spectrometry data. Highlights This preprint presents MARLOWE, a new computational tool for taxonomic characterization using de novo peptide sequencing combined with a statistical approach. While it

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Synthetic Serum Markers Enable Noninvasive Monitoring of Gene Expression in Primate Brains

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URL https://www.biorxiv.org/content/10.1101/2025.06.01.657212v1.full.pdf Stage Normal Science Paradigm framing The current paradigm is the use of invasive methods, such as positron emission tomography (PET), magnetic resonance imaging (MRI) or, in some cases, electrophysiology, to monitor gene expression in the primate brain, especially long-term. Highlights The preprint presents Released Markers of Activity (RMAs) as an innovative approach for

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Non-canonical enhancers control gene expression and cell fate in human pluripotent stem cells

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URL https://www.biorxiv.org/content/10.1101/2025.06.01.657118v1.full.pdf Stage Normal Science Paradigm framing The preprint operates within the dominant paradigm of gene regulation, where enhancers play a crucial role in controlling gene expression. It specifically focuses on enhancers in human-induced pluripotent stem cells (hiPSCs). Highlights This research refines the existing understanding of enhancers by identifying a class of “non-canonical enhancers” that

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Disentangling objects′ contextual associations from perceptual and conceptual attributes using time-resolved neural decoding

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URL https://www.biorxiv.org/content/10.1101/2025.05.29.656895v2.full.pdf Stage Normal Science Paradigm framing The preprint operates within the established paradigm of cognitive neuroscience, specifically focusing on visual object recognition and its neural underpinnings. It adheres to the dominant assumption that object knowledge is represented in a distributed and dynamic manner in the brain, with perceptual and conceptual features playing distinct roles.

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Slow-Timescale Regulation of Dopamine Release and Mating Drive over Days

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URL https://www.biorxiv.org/content/10.1101/2025.05.29.656898v1.full.pdf Stage Normal Science Paradigm framing The preprint operates within the established paradigm of neuroendocrine regulation of behavior, specifically focusing on the role of dopamine in modulating mating drive. Highlights This research utilizes established experimental techniques like fluorescence lifetime imaging microscopy, electrophysiology, and optogenetics to investigate a specific aspect of dopamine’s function in mating

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