| 1. |
- Doverbratt, Isa, et al.
(author)
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Transferring Grains from Single-Grain Luminescence Discs to SEM Specimen Stubs
- 2019
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In: Methods & Protocols. - 2409-9279. ; 2:4
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Journal article (peer-reviewed)abstract
- The grain transfer protocol presents a step-by-step guide on how to successfully transfer positioned grains from a single-grain luminescence disc to a scanning electron microscope (SEM) specimen stub and how to transport them between laboratories. Single-grain luminescence analysis allows the determination of luminescence characteristics for individual sand-sized grains.By combining such luminescence data with other grain properties such as geochemical composition, shape, or structure also at single-grain level, it is possible to investigate factors controlling luminescence signals or study other material properties. The non-luminescence properties are typically measuredin another instrument; thus, grains need to be transferred between machines and sample holders, and sometimes also between laboratories. It is then important that the position of each grain is known and stable so that the properties from the same grain are compared. By providing an easily observableorientation marker on the specimen stub, the hundred numbered grains from the single-grain disc can be transferred and later identified when analyzed in the SEM.
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| 2. |
- Troein, Carl, et al.
(author)
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OCTAVVS : A graphical toolbox for high-throughput preprocessing and analysis of vibrational spectroscopy imaging data
- 2020
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In: Methods and Protocols. - : MDPI AG. - 2409-9279. ; 3:2, s. 1-15
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Journal article (peer-reviewed)abstract
- Modern vibrational spectroscopy techniques enable the rapid collection of thousands of spectra in a single hyperspectral image, allowing researchers to study spatially heterogeneous samples at micrometer resolution. A number of algorithms have been developed to correct for effects such as atmospheric absorption, light scattering by cellular structures and varying baseline levels. After preprocessing, spectra are commonly decomposed and clustered to reveal informative patterns and subtle spectral changes. Several of these steps are slow, labor-intensive and require programming skills to make use of published algorithms and code. We here present a free and platform-independent graphical toolbox that allows rapid preprocessing of large sets of spectroscopic images, including atmospheric correction and a new algorithm for resonant Mie scattering with improved speed. The software also includes modules for decomposition into constituent spectra using the popular Multivariate Curve Resolution–Alternating Least Squares (MCR-ALS) algorithm, augmented by region-of-interest selection, as well as clustering and cluster annotation.
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| 3. |
- Eriksson, Ida, et al.
(author)
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Real-Time Monitoring of Lysosomal Membrane Permeabilization Using Acridine Orange
- 2023
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In: METHODS AND PROTOCOLS. - : MDPI. - 2409-9279. ; 6:4
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Journal article (peer-reviewed)abstract
- Loss of lysosomal membrane integrity results in leakage of lysosomal hydrolases to the cytosol which might harm cell function and induce cell death. Destabilization of lysosomes often precede apoptotic or necrotic cell death and occur during both physiological and pathological conditions. The weak base acridine orange readily enters cells and accumulates in the acidic environment of lysosomes. Vital staining with acridine orange is a well-proven technique to observe lysosomal destabilization using fluorescence microscopy and flow cytometry. These analyses are, however, time consuming and only adapted for discrete time points, which make them unsuitable for large-scale approaches. Therefore, we have developed a time-saving, high-throughput microplate reader-based method to follow destabilization of the lysosomal membrane in real-time using acridine orange. This protocol can easily be adopted for patient samples since the number of cells per sample is low and the time for analysis is short.
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| 4. |
- Forslund, Emelie Butler, et al.
(author)
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A Protocol for Comprehensive Analysis of Gait in Individuals with Incomplete Spinal Cord Injury
- 2024
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In: Methods and Protocols. - : MDPI AG. - 2409-9279. ; 7:3
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Journal article (peer-reviewed)abstract
- This is a protocol for comprehensive analysis of gait and affecting factors in individuals with incomplete paraplegia due to spinal cord injury (SCI). A SCI is a devastating event affecting both sensory and motor functions. Due to better care, the SCI population is changing, with a greater proportion retaining impaired ambulatory function. Optimizing ambulatory function after SCI remains challenging. To investigate factors influencing optimal ambulation, a multi-professional research project was grounded with expertise from clinical rehabilitation, neurophysiology, and biomechanical engineering from Karolinska Institutet, the Spinalis Unit at Aleris Rehab Station (Sweden's largest center for specialized neurorehabilitation), and the Promobilia MoveAbility Lab at KTH Royal Institute of Technology. Ambulatory adults with paraplegia will be consecutively invited to participate. Muscle strength, sensitivity, and spasticity will be assessed, and energy expenditure, 3D movements, and muscle function (EMG) during gait and submaximal contractions will be analyzed. Innovative computational modeling and data-driven analyses will be performed, including the identification of clusters of similar movement patterns among the heterogeneous population and analyses that study the link between complex sensorimotor function and movement performance. These results may help optimize ambulatory function for persons with SCI and decrease the risk of secondary conditions during gait with a life-long perspective.
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| 5. |
- Huang, Junchi, et al.
(author)
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Magnetic Resonance Imaging as a Tool for Monitoring Intratibial Growth of Experimental Prostate Cancer Metastases in Mice
- 2023
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In: Methods and Protocols (MP). - 2409-9279. ; 6:6
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Journal article (peer-reviewed)abstract
- Bone metastases cause morbidity and mortality in several human cancer forms. Experimental models are used to unravel the mechanisms and identify possible treatment targets. The location inside the skeleton complicates accurate assessment. This study evaluates the performance of magnetic resonance imaging (MRI) of prostate cancer tumors growing intratibially in mice. MRI detected intratibial tumor lesions with a sensitivity and specificity of 100% and 89%, respectively, compared to histological evaluation. Location and some phenotypical features could also be readily detected with MRI. Regarding volume estimation, the correlation between MRI and histological assessment was high (p < 0.001, r = 0.936). In conclusion, this study finds MRI to be a reliable tool for in vivo, non-invasive, non-ionizing, real-time monitoring of intratibial tumor growth.
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