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- Deutsch, Eric W., et al.
(författare)
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Expanding the Use of Spectral Libraries in Proteomics
- 2018
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 17:12, s. 4051-4060
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Tidskriftsartikel (refereegranskat)abstract
- The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on ABSTRACT: The 2017 Dagstuhl Seminar on Computational the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.
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- Kuster, RP, et al.
(författare)
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Measuring Sedentary Behavior by Means of Muscular Activity and Accelerometry
- 2018
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Ingår i: Sensors (Basel, Switzerland). - : MDPI AG. - 1424-8220. ; 18:11
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Tidskriftsartikel (refereegranskat)abstract
- Sedentary Behavior (SB) is among the most frequent human behaviors and is associated with a plethora of serious chronic lifestyle diseases as well as premature death. Office workers in particular are at an increased risk due to their extensive amounts of occupational SB. However, we still lack an objective method to measure SB consistent with its definition. We have therefore developed a new measurement system based on muscular activity and accelerometry. The primary aim of the present study was to calibrate the new-developed 8-CH-EMG+ for measuring occupational SB against an indirect calorimeter during typical desk-based office work activities. In total, 25 volunteers performed nine office tasks at three typical workplaces. Minute-by-minute posture and activity classification was performed using subsequent decision trees developed with artificial intelligence data processing techniques. The 8-CH-EMG+ successfully identified all sitting episodes (AUC = 1.0). Furthermore, depending on the number of electromyography channels included, the device has a sensitivity of 83–98% and 74–98% to detect SB and active sitting (AUC = 0.85–0.91). The 8-CH-EMG+ advances the field of objective SB measurements by combining accelerometry with muscular activity. Future field studies should consider the use of EMG sensors to record SB in line with its definition.
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- Bernhardt, A. M., et al.
(författare)
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A unified classification approach rating clinical utility of protein biomarkers across neurologic diseases
- 2023
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Ingår i: Ebiomedicine. - : Elsevier BV. - 2352-3964. ; 89
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Tidskriftsartikel (refereegranskat)abstract
- A major evolution from purely clinical diagnoses to biomarker supported clinical diagnosing has been occurring over the past years in neurology. High-throughput methods, such as next-generation sequencing and mass spectrometry-based proteomics along with improved neuroimaging methods, are accelerating this development. This calls for a consensus framework that is broadly applicable and provides a spot-on overview of the clinical validity of novel biomarkers. We propose a harmonized terminology and a uniform concept that stratifies biomarkers according to clinical context of use and evidence levels, adapted from existing frameworks in oncology with a strong focus on (epi) genetic markers and treatment context. We demonstrate that this framework allows for a consistent assessment of clinical validity across disease entities and that sufficient evidence for many clinical applications of protein biomarkers is lacking. Our framework may help to identify promising biomarker candidates and classify their applications by clinical context, aiming for routine clinical use of (protein) biomarkers in neurology. Copyright (c) 2023 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
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- Hashimoto, F., et al.
(författare)
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Abrasive fine-finishing technology
- 2016
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Ingår i: CIRP Annals - Manufacturing Technology. - : Elsevier BV. - 1726-0604 .- 0007-8506. ; 65:2, s. 597-620
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Tidskriftsartikel (refereegranskat)abstract
- Abrasive fine-finishing technology is often applied as a final finishing process, and the selection of the right technology is crucial to obtaining the desired performance of functions such as fatigue life. This paper begins with classifications of the technology along with fundamentals and brief histories of the individual methods. The material removal mechanisms, specific energies, and finishing characteristics of the various technologies are summarized giving assessments of the surfaces created by them. Guidelines developed for selecting the appropriate methods, and case studies illustrate the effectiveness of various methods. This paper ends with a discussion of the future prospects of the technology. (C) 2016
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| 10. |
- Zhou Hagström, Nanna, 1993-, et al.
(författare)
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Megahertz-rate Ultrafast X-ray Scattering and Holographic Imaging at the European XFEL
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The advent of X-ray free-electron lasers (XFELs) has revolutionized fundamental science, from atomic to condensed matter physics, from chemistry to biology, giving researchers access to X-rays with unprecedented brightness, coherence, and pulse duration. All XFEL facilities built until recently provided X-ray pulses at a relatively low repetition rate, with limited data statistics. Here, we present the results from the first megahertz repetition rate X-ray scattering experiments at the Spectroscopy and Coherent Scattering (SCS) instrument of the European XFEL. We illustrate the experimental capabilities that the SCS instrument offers, resulting from the operation at MHz repetition rates and the availability of the novel DSSC 2D imaging detector. Time-resolved magnetic X-ray scattering and holographic imaging experiments in solid state samples were chosen as representative examples, providing an ideal test-bed for operation at megahertz rates. Nevertheless, our results are relevant and applicable to any other non-destructive XFEL experiments in the soft X-ray range.
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