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Differential Analysis Reveals Isoform Switching Following Pneumococcal Vaccination

Leave a Comment / bioRxiv, Normal Science / Preprint Watch

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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Navigating contradictions: Salmonella Typhimurium chemotaxis amidst conflicting stimuli of the intestinal environment

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URL https://www.biorxiv.org/content/10.1101/2024.01.18.576330v4.full.pdf Stage Normal Science Paradigm framing Chemotaxis Highlights The preprint investigates the role of chemotaxis in *Salmonella Typhimurium* within the complex chemical environment of the gut, specifically focusing on the interaction between indole and other chemoeffectors. This research falls under normal science as it operates within the established paradigm of chemotaxis, seeking to refine

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Constraints on maximum neutron star mass from proto-neutron star evolution

Leave a Comment / Model Drift, Research Square / Preprint Watch

URL https://assets-eu.researchsquare.com/files/rs-6757777/v1_covered_31f5efe7-da24-4f9b-8d0b-4fac1e3d3fcc.pdf?c=1748452055 Stage Model Drift Paradigm framing The current paradigm for neutron stars is that they are composed primarily of neutrons, with some protons and leptons. There are a number of variations to this paradigm, including the presence of hyperons, kaons, or deconfined quarks. Highlights This preprint explores the impact of hyperons on the equation

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Reappraisal of the place of cultivated plants in the carbon budget

Leave a Comment / bioRxiv, Model Drift / Preprint Watch

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

Herbaria provide a valuable resource for obtaining informative mRNA Read More »

Separating the genetics of disease, treatment and treatment response using graphical modeling and large-scale electronic health records

Leave a Comment / medRxiv, Normal Science / Preprint Watch

URL https://www.medrxiv.org/content/10.1101/2025.04.29.25326633v1.full.pdf Stage Normal Science Paradigm framing The preprint operates within the established paradigm of genome-wide association studies (GWAS) and their application to pharmacogenomics. It adheres to the standard assumptions of this paradigm, such as the common disease-common variant hypothesis and the additive effect of genetic variants. It utilizes established methodologies for genomic data analysis

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Evidence for complex fixed points in pandemic data

Leave a Comment / Model Revolution, Paradigm Shift, Research Square / Preprint Watch

URL https://assets-eu.researchsquare.com/files/rs-70238/v1_covered.pdf?c=1631840663 Stage Model Revolution / Paradigm Change Paradigm framing The preprint attempts to revolutionize the existing paradigm of epidemiological modeling, by introducing complex fixed points into the Renormalization Group (RG) framework. It challenges the conventional compartmental models and complex network diffusion techniques, which primarily focus on initial growth, by proposing a unified way to

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Women and men exhibit distinct gut microbial profiles linked to colorectal cancer development

Leave a Comment / medRxiv, Normal Science / Preprint Watch

URL https://www.medrxiv.org/content/10.1101/2025.05.16.25327767v1.full.pdf Stage Normal Science Paradigm framing The paradigm of this research is the established understanding of the human gut microbiome's role in health and disease, specifically in the context of colorectal cancer (CRC). The study operates within the bounds of existing methodologies like metagenomic sequencing and statistical analysis, aiming to refine and expand upon

Women and men exhibit distinct gut microbial profiles linked to colorectal cancer development Read More »