| 1. |
- Aguet, Francois, et al.
(författare)
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Molecular quantitative trait loci
- 2023
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Ingår i: NATURE REVIEWS METHODS PRIMERS. - : Springer Nature. - 2662-8449. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Understanding functional effects of genetic variants is one of the key challenges in human genetics, as much of disease-associated variation is located in non-coding regions with typically unknown putative gene regulatory effects. One of the most important approaches in this field has been molecular quantitative trait locus (molQTL) mapping, where genetic variation is associated with molecular traits that can be measured at scale, such as gene expression, splicing and chromatin accessibility. The maturity of the field and large-scale studies have produced a rich set of established methods for molQTL analysis, with novel technologies opening up new areas of discovery. In this Primer, we discuss the study design, input data and statistical methods for molQTL mapping and outline the properties of the resulting data as well as popular downstream applications. We review both the limitations and caveats of molQTL mapping as well as future potential approaches to tackle them. With technological development now providing many complementary methods for functional characterization of genetic variants, we anticipate that molQTLs will remain an important part of this toolkit as the only existing approach that can measure human variation in its native genomic, cellular and tissue context.
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| 2. |
- Christopher, JA, et al.
(författare)
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Subcellular proteomics
- 2021
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Ingår i: Nature reviews. Methods primers. - : Springer Science and Business Media LLC. - 2662-8449. ; 1
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Fresch, Elisa, et al.
(författare)
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Two-dimensional electronic spectroscopy
- 2023
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Ingår i: Nature Reviews Methods Primers. - 2662-8449. ; 3:1
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Forskningsöversikt (refereegranskat)abstract
- Two-dimensional electronic spectroscopy (2DES) is a popular technique that can track ultrafast coherent and incoherent processes in real time. Since its development in the late 1990s, 2DES has become a powerful tool for investigating ultrafast dynamics in a range of systems, including nanomaterials and optoelectronic devices. This Primer explains the underlying physical principles of 2DES and how it can be applied to study dynamic photophysical processes. The article discusses how to collect, process and analyse data, with a summary of currently available experimental configurations. Common issues and challenges are considered, focusing on the limitations and reproducibility of the technique, finishing with an exploration of potential future advances and applications.
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| 4. |
- Greczynski, Grzegorz, et al.
(författare)
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X-ray photoelectron spectroscopy of thin films
- 2023
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Ingår i: NATURE REVIEWS METHODS PRIMERS. - : SPRINGERNATURE. - 2662-8449. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- X-ray photoelectron spectroscopy (XPS) is a popular analytical technique in materials science as it can assess the surface chemistry of a broad range of samples. This Primer concerns best practice in XPS analysis, aimed at both entry-level and advanced users, with a focus on thin film samples synthesized under vacuum conditions. The high surface to volume ratio of thin films means that factors such as substrate choice and air exposure time are important for the final result. Essential concepts are introduced, such as binding energy, photoelectric effect, spectral referencing and chemical shift, as well as practical aspects including surface sensitivity, probing depth, energy resolution, sample handling and sputter etching. Correct procedures for experimental planning, instrument set-up, sample preparation, data acquisition, results analysis and presentation are reviewed in connection with physical principles and common applications. Typical problems, including charging, spectral overlap, sputter damage and binding energy referencing, are discussed along with possible solutions or workarounds. Finally, a workflow is presented for arriving at high-quality results. X-ray photoelectron spectroscopy (XPS) can be used to investigate chemical bonding and elemental composition. This Primer discusses how XPS can be used to characterize thin films, including key considerations for sample preparation, experimental set-up and data analysis.
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| 5. |
- Hendrix, A., et al.
(författare)
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Extracellular vesicle analysis
- 2023
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Ingår i: Nature Reviews Methods Primers. - 2662-8449. ; 3:1
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Forskningsöversikt (refereegranskat)abstract
- Cells release small, phospholipid membrane-enclosed particles, collectively referred to as extracellular vesicles (EVs), into their surroundings to enable intercellular communication. EVs have numerous functions in physiological and pathophysiological processes and show considerable promise for diagnostic and therapeutic applications. Technologies have rapidly evolved over the past two decades, providing a powerful, versatile toolset for preparing and characterizing EVs to facilitate research and translational efforts. However, considering the plethora of methods available, it is challenging to understand what makes one method more suited for a given experiment than another. The heterogeneity of EVs as well as the diversity in composition of their surroundings further add to this challenge. This Primer provides guidance for EV analysis across ecosystems, including accessible body- and environment-derived sources. We summarize the multi-step process of EV preparation, cover the guiding principles and considerations when performing and interpreting EV experiments, and reflect on the limitations and challenges in the fields of fundamental biology, biomarker development and therapeutic strategies. Extracellular vesicles (EVs) have vital functions and promise diagnostic and therapeutic applications. In this Primer, Hendrix and colleagues discuss tools for isolating and characterizing EVs obtained from various sources, including the body and the environment.
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| 6. |
- Mohanty, Amar K., et al.
(författare)
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Biocarbon materials
- 2024
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Ingår i: Nature Reviews Methods Primers. - : Springer Nature. - 2662-8449. ; 4:1
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Tidskriftsartikel (refereegranskat)
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| 7. |
- Mohanty, A. K., et al.
(författare)
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Sustainable polymers
- 2022
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Ingår i: Nature Reviews Methods Primers. - : Springer Nature. - 2662-8449. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- Sustainable polymers are materials derived from renewable, recycled and waste carbon resources and their combinations, which at the end of life can be recycled, biodegraded or composted. Sustainable polymers also exhibit reduced environmental impact throughout their life cycle. This Primer presents an overview of the research in and potential of sustainable polymers, with a focus on their life cycle, synthetic routes from renewable carbon feedstocks, production, material characterization, applications, end of life, data reproducibility and limitations faced, and provides a brief outlook. The Primer also briefly covers other carbon feedstocks such as carbon dioxide and wastes, including agricultural and woody residues. Although still in their infancy, new sustainable polymers are already finding applications in packaging, automotive parts and 3D printing. This Primer also discusses the headwinds facing the adoption of sustainable polymers, including complexities of recycling and composting, manufacturing scale-up, data reproducibility, deposition and potential solutions. Development of sustainable polymers will accelerate the age of sustainable polymers and create a truly circular economy for plastics by reducing production and use of virgin plastics from finite resources.
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| 8. |
- Nielbo, Kristoffer L., et al.
(författare)
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Quantitative text analysis
- 2024
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Ingår i: Nature Reviews Methods Primers. - 2662-8449. ; 4:1
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Tidskriftsartikel (refereegranskat)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.
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| 9. |
- Rufo, Joseph, et al.
(författare)
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Acoustofluidics for biomedical applications
- 2022
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Ingår i: Nature Reviews Methods Primers. - : Springer Nature. - 2662-8449. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- Acoustofluidic technologies utilize acoustic waves to manipulate fluids and particles within fluids, all in a contact-free and biocompatible manner. Over the past decade, acoustofluidic technologies have enabled new capabilities in biomedical applications ranging from the precise patterning of heterogeneous cells for tissue engineering to the automated isolation of extracellular vesicles from biofluids for rapid, point-of-care diagnostics. In this Primer, we explain the underlying physical principles governing the design and operation of acoustofluidic technologies and describe the various implementations that have been developed for biomedical applications. We aim to demystify the rapidly growing field of acoustofluidics and provide a unified perspective that will allow end users to choose the acoustofluidic technology that is best suited for their research needs. The experimental set-ups for each type of acoustofluidic device are discussed along with their advantages and limitations. In addition, we review typical types of data that are obtained from acoustofluidic experiments and describe how to model different forces acting on particles within an acoustofluidic device. We also discuss data reproducibility and the need to establish standards for the deposition of data sets within the field. Finally, we provide our perspective on how to optimize device performance and discuss areas of future development.
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| 10. |
- Uffelmann, E., et al.
(författare)
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Genome-wide association studies
- 2021
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Ingår i: Nature Reviews Methods Primers. - : Springer Nature. - 2662-8449. ; 1:1
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) test hundreds of thousands of genetic variants across many genomes to find those statistically associated with a specific trait or disease. This methodology has generated a myriad of robust associations for a range of traits and diseases, and the number of associated variants is expected to grow steadily as GWAS sample sizes increase. GWAS results have a range of applications, such as gaining insight into a phenotype’s underlying biology, estimating its heritability, calculating genetic correlations, making clinical risk predictions, informing drug development programmes and inferring potential causal relationships between risk factors and health outcomes. In this Primer, we provide the reader with an introduction to GWAS, explaining their statistical basis and how they are conducted, describe state-of-the art approaches and discuss limitations and challenges, concluding with an overview of the current and future applications for GWAS results.
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