| 1. |
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| 2. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
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| 5. |
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| 6. |
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| 7. |
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- 2019
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Journal article (peer-reviewed)
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| 8. |
- Fenstermacher, M.E., et al.
(author)
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DIII-D research advancing the physics basis for optimizing the tokamak approach to fusion energy
- 2022
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In: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 62:4
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Journal article (peer-reviewed)abstract
- DIII-D physics research addresses critical challenges for the operation of ITER and the next generation of fusion energy devices. This is done through a focus on innovations to provide solutions for high performance long pulse operation, coupled with fundamental plasma physics understanding and model validation, to drive scenario development by integrating high performance core and boundary plasmas. Substantial increases in off-axis current drive efficiency from an innovative top launch system for EC power, and in pressure broadening for Alfven eigenmode control from a co-/counter-I p steerable off-axis neutral beam, all improve the prospects for optimization of future long pulse/steady state high performance tokamak operation. Fundamental studies into the modes that drive the evolution of the pedestal pressure profile and electron vs ion heat flux validate predictive models of pedestal recovery after ELMs. Understanding the physics mechanisms of ELM control and density pumpout by 3D magnetic perturbation fields leads to confident predictions for ITER and future devices. Validated modeling of high-Z shattered pellet injection for disruption mitigation, runaway electron dissipation, and techniques for disruption prediction and avoidance including machine learning, give confidence in handling disruptivity for future devices. For the non-nuclear phase of ITER, two actuators are identified to lower the L-H threshold power in hydrogen plasmas. With this physics understanding and suite of capabilities, a high poloidal beta optimized-core scenario with an internal transport barrier that projects nearly to Q = 10 in ITER at ∼8 MA was coupled to a detached divertor, and a near super H-mode optimized-pedestal scenario with co-I p beam injection was coupled to a radiative divertor. The hybrid core scenario was achieved directly, without the need for anomalous current diffusion, using off-axis current drive actuators. Also, a controller to assess proximity to stability limits and regulate β N in the ITER baseline scenario, based on plasma response to probing 3D fields, was demonstrated. Finally, innovative tokamak operation using a negative triangularity shape showed many attractive features for future pilot plant operation.
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| 9. |
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| 10. |
- Hu, R., et al.
(author)
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Biofeedback neuromuscular electrical stimulation front-end for dysphagia treatment
- 2014
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In: IEEE 2014 Biomedical Circuits and Systems Conference, BioCAS 2014 - Proceedings. - : IEEE Press. - 9781479923465 ; , s. 612-615
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Conference paper (peer-reviewed)abstract
- A dedicated front-end for biofeedback neuromuscular electrical stimulation (NESM) system is proposed. For controllable dysphagia treatment, the integrated circuit (IC) provides a stimulator front-end with programmable stimulation parameters (2μA-1mA current amplitude, DC-2KHz frequency, and variable duty cycle) and an electromyogram/impedance (EMG/ETI) readout front-end with programmable gain and bandwidth (42-80dB, 0.1Hz-1.2KHz) for biofeedback. Area-efficient, low-power but high precision current controlling is achieved by inducing the sigma-delta modulator technique in the stimulation channel. The measured impedance and EMG signal are used to determine the stimulation parameters, enabling a closed loop optimized treatment. The proposed front-end is fabricated in a 0.18 μm standard CMOS process technology and dissipates a peak power of 2.3 mW at the supply voltage of 1.8 V. Measurement results on a live person are also provided to validate the system's effectiveness.
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| 11. |
- Jin, Han, et al.
(author)
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A Mobile-Based High Sensitivity On-Field Organophosphorus Compounds Detecting System for IoT-Based Food Safety Tracking
- 2017
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In: Journal of Sensors. - : Hindawi Publishing Corporation. - 1687-725X .- 1687-7268.
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Journal article (peer-reviewed)abstract
- A mobile-based high sensitivity absorptiometer is presented to detect organophosphorus (OP) compounds for Internet-of-Things based food safety tracking. This instrument consists of a customized sensor front-end chip, LED-based light source, low power wireless link, and coin battery, along with a sample holder packaged in a recycled format. The sensor front-end integrates optical sensor, capacitive transimpedance amplifier, and a folded-reference pulse width modulator in a single chip fabricated in a 0.18 mu m 1-poly 5-metal CMOS process and has input optical power dynamic range of 71 dB, sensitivity of 3.6 nW/cm(2) (0.77 pA), and power consumption of 14.5 mu W. Enabled by this high sensitivity sensor front-end chip, the proposed absorptiometer has a small size of 96 cm(3), with features including on-field detection and wireless communication with a mobile. OP compound detection experiments of the handheld system demonstrate a limit of detection (LOD) of 0.4 mu mol/L, comparable to that of a commercial spectrophotometer. Meanwhile, an android-based application (APP) is presented which makes the absorptiometer access to the Internet-of-Things (IoT).
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| 12. |
- Zhang, Huai, et al.
(author)
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A global survey on the use of the international classification of diseases codes for metabolic dysfunction-associated fatty liver disease.
- 2024
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In: Hepatology international. - 1936-0541.
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Journal article (peer-reviewed)abstract
- With the implementation of the 11th edition of the International Classification of Diseases (ICD-11) and the publication of the metabolic dysfunction-associated fatty liver disease (MAFLD) nomenclature in 2020, it is important to establish consensus for the coding of MAFLD in ICD-11. This will inform subsequent revisions of ICD-11.Using the Qualtrics XM and WJX platforms, questionnaires were sent online to MAFLD-ICD-11 coding collaborators, authors of papers, and relevant association members.A total of 890 international experts in various fields from 61 countries responded to the survey. We also achieved full coverage of provincial-level administrative regions in China. 77.1% of respondents agreed that MAFLD should be represented in ICD-11 by updating NAFLD, with no significant regional differences (77.3% in Asia and 76.6% in non-Asia, p=0.819). Over 80% of respondents agreed or somewhat agreed with the need to assign specific codes for progressive stages of MAFLD (i.e. steatohepatitis) (92.2%), MAFLD combined with comorbidities (84.1%), or MAFLD subtypes (i.e., lean, overweight/obese, and diabetic) (86.1%).This global survey by a collaborative panel of clinical, coding, health management and policy experts, indicates agreement that MAFLD should be coded in ICD-11. The data serves as a foundation for corresponding adjustments in the ICD-11 revision.
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| 13. |
- Aad, G., et al.
(author)
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- 2011
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swepub:Mat__t (peer-reviewed)
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| 14. |
- Aad, G., et al.
(author)
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- 2011
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Journal article (peer-reviewed)
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| 15. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 16. |
- Aad, G., et al.
(author)
-
- 2012
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swepub:Mat__t (peer-reviewed)
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| 17. |
- Aad, G., et al.
(author)
-
- 2013
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swepub:Mat__t (peer-reviewed)
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| 18. |
- Aad, G., et al.
(author)
-
- 2012
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swepub:Mat__t (peer-reviewed)
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| 19. |
- Aad, G., et al.
(author)
-
- 2012
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swepub:Mat__t (peer-reviewed)
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| 20. |
- Aad, G., et al.
(author)
-
- 2012
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swepub:Mat__t (peer-reviewed)
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| 21. |
- Aad, G., et al.
(author)
-
- 2012
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swepub:Mat__t (peer-reviewed)
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| 22. |
- Aad, G., et al.
(author)
-
- 2012
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swepub:Mat__t (peer-reviewed)
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| 23. |
- Aad, G., et al.
(author)
-
- 2012
-
swepub:Mat__t (peer-reviewed)
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| 24. |
- Aad, G., et al.
(author)
-
- 2012
-
swepub:Mat__t (peer-reviewed)
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| 25. |
- Aad, G., et al.
(author)
-
- 2012
-
swepub:Mat__t (peer-reviewed)
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| 26. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 27. |
- Aad, G., et al.
(author)
-
- 2011
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swepub:Mat__t (peer-reviewed)
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| 28. |
- Aad, G., et al.
(author)
-
- 2011
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swepub:Mat__t (peer-reviewed)
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| 29. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 30. |
- Aad, G., et al.
(author)
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- 2012
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Journal article (peer-reviewed)
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| 31. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 32. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 33. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 34. |
- Aad, G., et al.
(author)
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- 2013
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swepub:Mat__t (peer-reviewed)
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| 35. |
- Aad, G., et al.
(author)
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- 2012
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Journal article (peer-reviewed)
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| 36. |
- Aad, G., et al.
(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 37. |
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(author)
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- 2011
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swepub:Mat__t (peer-reviewed)
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| 38. |
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(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 39. |
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(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 40. |
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(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 41. |
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(author)
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- 2012
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Journal article (peer-reviewed)
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| 42. |
- Aad, G., et al.
(author)
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- 2011
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swepub:Mat__t (peer-reviewed)
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| 43. |
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(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 44. |
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(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 45. |
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(author)
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- 2011
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swepub:Mat__t (peer-reviewed)
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| 46. |
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(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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| 47. |
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(author)
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- 2011
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Journal article (peer-reviewed)
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| 48. |
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swepub:Mat__t (peer-reviewed)
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| 49. |
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- 2012
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swepub:Mat__t (peer-reviewed)
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(author)
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- 2012
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swepub:Mat__t (peer-reviewed)
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