{"title":"Photoaffinity labelling with small molecules","authors":"","doi":"10.1038/s43586-024-00317-3","DOIUrl":"10.1038/s43586-024-00317-3","url":null,"abstract":"This PrimeView highlights the different types of reporter tags that can be paired with photoreactive groups for photoaffinity labeling.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":0.0,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00317-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140819065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ulrike G. K. Wegst, Paul H. Kamm, Kaiyang Yin, Francisco García-Moreno
{"title":"Freeze casting","authors":"Ulrike G. K. Wegst, Paul H. Kamm, Kaiyang Yin, Francisco García-Moreno","doi":"10.1038/s43586-024-00307-5","DOIUrl":"10.1038/s43586-024-00307-5","url":null,"abstract":"When solutions and slurries are directionally solidified, complex dynamics of solvent crystal growth and solvent templating determine the final hierarchical architecture of the freeze-cast material. With continuous X-ray tomoscopy, it is now possible to study in situ intricate and otherwise elusive ice crystal growth and solvent-templating phenomena. Quantifying these phenomena both time-resolved and in three dimensions provides novel insights into the formation of performance-defining features of freeze-cast cellular solids at several length scales: the material’s pore morphology (first hierarchical level), the molecular, fibrillar and particle self-assembly of components in the cell walls (second level) and the cell wall surface structures (third level). The freeze casting process is attractive because the features of the final hierarchical material architecture — which determine the material’s structural, mechanical and physical properties — can be custom designed for a given application. Overall porosity, pore size, geometry, orientation, particle packing in cell walls and cell wall surface features can be tailored for applications in, for example, biomedicine, environmental engineering, catalysis, power conversion, and energy generation and storage. Freeze casting involves directional solidification of solutions or slurries followed by removal of the solid solvent phase. This Primer introduces the freeze casting technique, including experimental and analysis methods, with a particular focus on using X-ray tomoscopy for real-time, 3D observations of freeze casting dynamics.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-23"},"PeriodicalIF":0.0,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140642047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Freeze casting","authors":"","doi":"10.1038/s43586-024-00316-4","DOIUrl":"10.1038/s43586-024-00316-4","url":null,"abstract":"This PrimeView highlights the structures formed with different freeze casting moulds.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":0.0,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00316-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140642057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Quantitative text analysis","authors":"","doi":"10.1038/s43586-024-00310-w","DOIUrl":"10.1038/s43586-024-00310-w","url":null,"abstract":"This PrimeView highlights the use of quantitative text analysis in various analytical tasks, from categorizing information to analyzing sentiment and making predictions.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":0.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00310-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140544572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kristoffer L. Nielbo, Folgert Karsdorp, Melvin Wevers, Alie Lassche, Rebekah B. Baglini, Mike Kestemont, Nina Tahmasebi
{"title":"Quantitative text analysis","authors":"Kristoffer L. Nielbo, Folgert Karsdorp, Melvin Wevers, Alie Lassche, Rebekah B. Baglini, Mike Kestemont, Nina Tahmasebi","doi":"10.1038/s43586-024-00302-w","DOIUrl":"10.1038/s43586-024-00302-w","url":null,"abstract":"Text analysis has undergone substantial evolution since its inception, moving from manual qualitative assessments to sophisticated quantitative and computational methods. Beginning in the late twentieth century, a surge in the utilization of computational techniques reshaped the landscape of text analysis, catalysed by advances in computational power and database technologies. Researchers in various fields, from history to medicine, are now using quantitative methodologies, particularly machine learning, to extract insights from massive textual data sets. This transformation can be described in three discernible methodological stages: feature-based models, representation learning models and generative models. Although sequential, these stages are complementary, each addressing analytical challenges in the text analysis. The progression from feature-based models that require manual feature engineering to contemporary generative models, such as GPT-4 and Llama2, signifies a change in the workflow, scale and computational infrastructure of the quantitative text analysis. This Primer presents a detailed introduction of some of these developments, offering insights into the methods, principles and applications pertinent to researchers embarking on the quantitative text analysis, especially within the field of machine learning. Quantitative text analysis is a range of computational methods to analyse text data statistically and mathematically. In this Primer, Kristoffer Nielbo et al. introduce the methods, principles and applications of the quantitative text analysis across disciplines.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-16"},"PeriodicalIF":0.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00302-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140544591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
René Tanious, Rumen Manolov, Patrick Onghena, Johan W. S. Vlaeyen
{"title":"Single-case experimental designs: the importance of randomization and replication","authors":"René Tanious, Rumen Manolov, Patrick Onghena, Johan W. S. Vlaeyen","doi":"10.1038/s43586-024-00312-8","DOIUrl":"10.1038/s43586-024-00312-8","url":null,"abstract":"Single-case experimental designs are rapidly growing in popularity. This popularity needs to be accompanied by transparent and well-justified methodological and statistical decisions. Appropriate experimental design including randomization, proper data handling and adequate reporting are needed to ensure reproducibility and internal validity. The degree of generalizability can be assessed through replication.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-2"},"PeriodicalIF":0.0,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140348855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Near-infrared II fluorescence imaging","authors":"","doi":"10.1038/s43586-024-00309-3","DOIUrl":"10.1038/s43586-024-00309-3","url":null,"abstract":"This PrimeView highlights how to overcome challenges when performing fluorescence imaging in the second near-infrared window.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":0.0,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00309-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140345827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Elizabeth Lea Schmidt, Zihao Ou, Erving Ximendes, Han Cui, Carl H. C. Keck, Daniel Jaque, Guosong Hong
{"title":"Near-infrared II fluorescence imaging","authors":"Elizabeth Lea Schmidt, Zihao Ou, Erving Ximendes, Han Cui, Carl H. C. Keck, Daniel Jaque, Guosong Hong","doi":"10.1038/s43586-024-00301-x","DOIUrl":"10.1038/s43586-024-00301-x","url":null,"abstract":"Fluorescence imaging in the second near-infrared (NIR-II) window enables deep-tissue imaging with high resolution and improved contrast by taking advantage of the reduced light scattering and tissue autofluorescence in this region of the spectrum. NIR-II fluorescence imaging uses photoluminescent contrast agents — including carbon nanotubes, quantum dots, rare earth-doped nanocrystals, gold nanoclusters, small molecules and their aggregates — and fluorescent proteins, which all exhibit fluorescence in the 1,000–3,000 nm range. After administration of these fluorophores in vivo, live animals can be imaged with specialized detectors and optical instruments, yielding images with contrast and resolution unparalleled by conventional visible and near-infrared fluorescence imaging. This powerful approach enables dynamic imaging of vascular structures and haemodynamics; molecular imaging and image-guided surgery of tumours; and visualization of deep-seated structures, such as the gastrointestinal system. NIR-II fluorescence imaging has revolutionized biomedical imaging over the past 15 years and is poised to make comparable advancements in cardiology, neurobiology and gastroenterology. This Primer describes the principles of NIR-II fluorescence imaging, reviews the most used fluorophores, outlines implementation approaches and discusses specific scientific and clinical applications. Furthermore, the limitations of NIR-II fluorescence imaging are addressed and future opportunities across various scientific domains are explored. Deep tissues can be imaged with high resolution and greater contrast by performing fluorescence imaging in the second near-infrared (NIR-II) window. This Primer summarizes how NIR-II fluorescence imaging can be used in animal models, exploring commonly used fluorophores and implementation approaches across a range of scientific and clinical applications.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-22"},"PeriodicalIF":0.0,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140345830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Fluorescence resonance energy transfer at the single-molecule level","authors":"","doi":"10.1038/s43586-024-00306-6","DOIUrl":"10.1038/s43586-024-00306-6","url":null,"abstract":"This PrimeView highlights the fluorophores used in smFRET experiments and how they affect measurement of energy transfer at the single-molecule level.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":0.0,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00306-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140310409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Taekjip Ha, Jingyi Fei, Sonja Schmid, Nam Ki Lee, Ruben L. Gonzalez Jr, Sneha Paul, Sanghun Yeou
{"title":"Fluorescence resonance energy transfer at the single-molecule level","authors":"Taekjip Ha, Jingyi Fei, Sonja Schmid, Nam Ki Lee, Ruben L. Gonzalez Jr, Sneha Paul, Sanghun Yeou","doi":"10.1038/s43586-024-00298-3","DOIUrl":"10.1038/s43586-024-00298-3","url":null,"abstract":"Fluorescence resonance energy transfer (FRET) is a powerful spectroscopic method for measuring distances in the 2–8 nm range. Often, conformational changes and molecular interactions are difficult or impossible to synchronize, or too rare or transient to detect using ensemble FRET. Single-molecule FRET (smFRET) opens new opportunities to probe biomolecular conformational changes or interactions that are missing in static snapshots provided by traditional structural biology tools, as well as to measure the kinetics of these dynamics on various timescales and under physiological conditions, including inside cells. Advances in labelling technologies, combining smFRET with optical and magnetic tweezers and Bayesian inference-based and information theory-based analysis tools are revealing rich biomolecular dynamics. We also discuss the challenges and opportunities in integrating dynamics into traditionally static structural biology approaches, extending smFRET into cells and tissues, advancing technical innovations and democratizing the practice of smFRET. Analysing single-molecule fluorescence resonance energy transfer (smFRET) enables an unprecedented view of the dynamics and kinetics of biomolecular conformational changes and interactions. In this Primer, Ha et al. discuss technological advances that have led to smFRET and how the method can be adapted to address various research questions in structural and molecular biology.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-18"},"PeriodicalIF":0.0,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140310419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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