Nicholas P. Lockyer, Satoka Aoyagi, John S. Fletcher, Ian S. Gilmore, Paul A. W. van der Heide, Katie L. Moore, Bonnie J. Tyler, Lu-Tao Weng
{"title":"Secondary ion mass spectrometry","authors":"Nicholas P. Lockyer, Satoka Aoyagi, John S. Fletcher, Ian S. Gilmore, Paul A. W. van der Heide, Katie L. Moore, Bonnie J. Tyler, Lu-Tao Weng","doi":"10.1038/s43586-024-00311-9","DOIUrl":"10.1038/s43586-024-00311-9","url":null,"abstract":"Secondary ion mass spectrometry (SIMS) is a technique for chemical analysis and imaging of solid materials, with applications in many areas of science and technology. It involves bombarding a sample surface under high vacuum with energetic primary ions. The ejected secondary ions undergo mass-to-charge ratio (m/z) analysis and are detected. The resulting mass spectrum contains detailed surface chemical information with sub-monolayer sensitivity. Different experimental configurations provide chemically resolved depth distribution and 2D or 3D images. SIMS is complementary to other surface analysis techniques, such as X-ray photoelectron spectroscopy; chemical imaging techniques, for example, vibrational microspectroscopy methods such as Fourier transform infrared spectroscopy and Raman spectroscopy; and other mass spectrometry imaging techniques, including desorption electrospray ionization and matrix-assisted laser desorption ionization. Features of SIMS include high spatial resolution, high depth resolution and broad chemical sensitivity to all elements, isotopes and molecules up to several thousand mass units. This Primer describes the operating principles of SIMS and outlines how the instrument geometry and operational parameters enable different modes of operation and information to be obtained. Applications, including materials science, surface science, electronic devices, geosciences and life sciences, are explored, finishing with an outlook for the technique. Solid samples can be imaged and chemically analysed using secondary ion mass spectrometry. This Primer describes the secondary ion mass spectrometry experimental setup, in which a primary ion beam sputters secondary ions that are analysed and detected by a mass spectrometer, and explores applications in materials, geological and life sciences.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-21"},"PeriodicalIF":0.0,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140895320","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}
Rick A. Homan, John D. Lapek, Christina M. Woo, Sherry Niessen, Lyn H. Jones, Christopher G. Parker
{"title":"Photoaffinity labelling with small molecules","authors":"Rick A. Homan, John D. Lapek, Christina M. Woo, Sherry Niessen, Lyn H. Jones, Christopher G. Parker","doi":"10.1038/s43586-024-00308-4","DOIUrl":"10.1038/s43586-024-00308-4","url":null,"abstract":"Small molecules can serve as leads for new therapeutics as well as powerful tools to investigate biological processes. Understanding the interactions of these molecules, particularly in native biological environments, is fundamentally critical to their utility. Photoaffinity labelling (PAL) represents one of the few strategies that enable the direct mapping of interactions of small molecules with proteins. PAL uses latent functional groups that form reactive intermediates only upon exposure to light of specific wavelengths that, subsequently, covalently adduct to proximal biomolecules, allowing for their enrichment and identification. Although the original applications of PAL date to six decades ago, the more recent integration with powerful mass spectrometry-based proteomic methods has profoundly impacted the ability to illuminate molecular interactions on a global scale. In this Primer, we discuss the current state-of-the-art of PAL-based strategies for studying molecular interactions in native systems, with a focus on investigations of small molecule–protein interactions. We cover topics including the basic principles of PAL chemistries, PAL probe design, experimental considerations, data analysis and applications of PAL illustrated by recent examples. Finally, we provide our perspective on persistent challenges and our outlook on the field. Photoaffinity labelling (PAL) enables the direct mapping of interactions of small molecules with proteins. In this Primer, Homan et al. discuss the basic principles and considerations involved in the design and implementation of PAL reagents and methods.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-23"},"PeriodicalIF":0.0,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140819055","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":"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}
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