| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)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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| 2. |
- Chu, M.S., et al.
(författare)
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Response of a resistive and rotating tokamak to external magnetic perturbations below the Alfven frequency
- 2011
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Ingår i: Nuclear Fusion. - 1741-4326 .- 0029-5515. ; 51, s. 073036-
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Tidskriftsartikel (refereegranskat)abstract
- Motivated by the recent experimental observation that plasma stability can be improved by external magnetic perturbations, the general problem of plasma response to external magnetic perturbations is investigated. Different (vacuum, ideal and resistive) plasma response models are considered and compared. Plasma response, in experiments where stabilization was achieved, is obtained through computation using the MARS-F code, with a plasma model that includes both plasma resistivity and rotation. The resultant magnetic field line stochasticity is much reduced from that obtained formerly using the vacuum plasma model. This reduced stochasticity is more consistent with the favourable experimental observation of enhanced stability. Examples are given for the response of an ITER plasma to perturbations generated by the correction coils; and the response of a plasma to external coils (antenna) up to the Alfvén frequency.
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| 3. |
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| 4. |
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| 5. |
- Kushnir, Mark M., et al.
(författare)
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Liquid chromatography tandem mass spectrometry for analysis of steroids in clinical laboratories
- 2011
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Ingår i: Clinical Biochemistry. - : Elsevier BV. - 0009-9120 .- 1873-2933. ; 44:1, s. 77-88
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Forskningsöversikt (refereegranskat)abstract
- Liquid chromatography tandem mass spectrometry is one of the most specific techniques available in clinical laboratories. In the past, immunoassays were the primary methodology for analysis of steroids in biological samples because they are rapid and easy to perform. However, these methods were shown to suffer from the lack of specificity for measuring many of the diagnostically important steroids. LC-MS/MS overcomes many of the limitations of immunoassays, enhances diagnostic utility of the testing, and expands diagnostic capabilities in endocrinology. In addition to the superior quality of the measurements, LC-MS/MS allows high throughput testing using small sample volume with minimal sample preparation, and frees the laboratory from dependence on suppliers of assay specific reagents. LC-MS/MS is being widely employed for routine measurement of steroids, and the methodology plays an important role in the standardization and harmonization of measurements among clinical laboratories.
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| 6. |
- Chapman, Christopher H., et al.
(författare)
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Diffusion Tensor Imaging of Normal-Appearing White Matter as Biomarker for Radiation-Induced Late Delayed Cognitive Decline
- 2012
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Ingår i: International Journal of Radiation Oncology, Biology, Physics. - : Elsevier BV. - 0360-3016. ; 82:5, s. 2033-2040
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To determine whether early assessment of cerebral white matter degradation can predict late delayed cognitive decline after radiotherapy (RT). Methods and Materials: Ten patients undergoing conformal fractionated brain RT participated in a prospective diffusion tensor magnetic resonance imaging study. Magnetic resonance imaging studies were acquired before RT, at 3 and 6 weeks during RT, and 10, 30, and 78 weeks after starting RT. The diffusivity variables in the parahippocampal cingulum bundle and temporal lobe white matter were computed. A quality-of-life survey and neuro-cognitive function tests were administered before and after RT at the magnetic resonance imaging follow-up visits. Results: In both structures, longitudinal diffusivity (lambda(parallel to)) decreased and perpendicular diffusivity (lambda(perpendicular to)) increased after RT, with early changes correlating to later changes (p < .05). The radiation dose correlated with an increase in cingulum lambda(perpendicular to) at 3 weeks, and patients with >50% of cingula volume receiving >12 Gy had a greater increase in lambda(perpendicular to) at 3 and 6 weeks (p < .05). The post-RT changes in verbal recall scores correlated linearly with the late changes in cingulum lambda(parallel to) (30 weeks, p < .02). Using receiver operating characteristic curves, early cingulum lambda(parallel to) changes predicted for post-RT changes in verbal recall scores (3 and 6 weeks, p < .05). The neurocognitive test scores correlated significantly with the quality-of-life survey results. Conclusions: The correlation between early diffusivity changes in the parahippocampal cingulum and the late decline in verbal recall suggests that diffusion tensor imaging might be useful as a biomarker for predicting late delayed cognitive decline. (C) 2012 Elsevier Inc.
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| 7. |
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| 8. |
- Hugerth, Luisa W., et al.
(författare)
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Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:4, s. 095567-
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Tidskriftsartikel (refereegranskat)abstract
- High-throughput sequencing of ribosomal RNA gene (rDNA) amplicons has opened up the door to large-scale comparative studies of microbial community structures. The short reads currently produced by massively parallel sequencing technologies make the choice of sequencing region crucial for accurate phylogenetic assignments. While for 16S rDNA, relevant regions have been well described, no truly systematic design of 18S rDNA primers aimed at resolving eukaryotic diversity has yet been reported. Here we used 31,862 18S rDNA sequences to design a set of broad-taxonomic range degenerate PCR primers. We simulated the phylogenetic information that each candidate primer pair would retrieve using paired-or single-end reads of various lengths, representing different sequencing technologies. Primer pairs targeting the V4 region performed best, allowing discrimination with paired-end reads as short as 150 bp (with 75% accuracy at genus level). The conditions for PCR amplification were optimised for one of these primer pairs and this was used to amplify 18S rDNA sequences from isolates as well as from a range of environmental samples which were then Illumina sequenced and analysed, revealing good concordance between expected and observed results. In summary, the reported primer sets will allow minimally biased assessment of eukaryotic diversity in different microbial ecosystems.
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| 9. |
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| 11. |
- Mao, Wendy L., et al.
(författare)
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Distortions and stabilization of simple-cubic calcium at high pressure and low temperature
- 2010
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 107:22, s. 9965-9968
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Tidskriftsartikel (refereegranskat)abstract
- Ca-III, the first superconducting calcium phase under pressure, was identified as simple-cubic (sc) by previous X-ray diffraction (XRD) experiments. In contrast, all previous theoretical calculations showed that sc had a higher enthalpy than many proposed structures and had an imaginary (unstable) phonon branch. By using our newly developed submicrometer high-pressure single-crystal XRD, cryogenic high-pressure XRD, and theoretical calculations, we demonstrate that Ca-III is neither exactly sc nor any of the lower-enthalpy phases, but sustains the sc-like, primitive unit by a rhombohedral distortion at 300 K and a monoclinic distortion below 30 K. This surprising discovery reveals a scenario that the high-pressure structure of calcium does not go to the zero-temperature global enthalpy minimum but is dictated by high-temperature anharmonicity and low-temperature metastability fine-tuned with phonon stability at the local minimum.
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| 12. |
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| 13. |
- Schreier, M. M., et al.
(författare)
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Atmospheric parameters in a subtropical cloud regime transition derived by AIRS and MODIS : observed statistical variability compared to ERA-Interim
- 2014
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Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 14:7, s. 3573-3587
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Tidskriftsartikel (refereegranskat)abstract
- Cloud occurrence, microphysical and optical properties, and atmospheric profiles within a subtropical cloud regime transition in the northeastern Pacific Ocean are obtained from a synergistic combination of the Atmospheric Infrared Sounder (AIRS) and the MODerate resolution Imaging Spectroradiometer (MODIS). The observed cloud parameters and atmospheric thermodynamic profile retrievals are binned by cloud type and analyzed based on their probability density functions (PDFs). Comparison of the PDFs to data from the European Centre for Medium Range Weather Forecasting reanalysis (ERA-Interim) shows a strong difference in the occurrence of the different cloud types compared to clear sky. An increasing non-Gaussian behavior is observed in cloud optical thickness (tau(c)), effective radius (r(e)) and cloud-top temperature (T-c) distributions from stratocumulus to trade cumulus, while decreasing values of lowertropospheric stability are seen. However, variations in the mean, width and shape of the distributions are found. The AIRS potential temperature (theta) and water vapor (q) profiles in the presence of varying marine boundary layer (MBL) cloud types show overall similarities to the ERA-Interim in the mean profiles, but differences arise in the higher moments at some altitudes. The differences between the PDFs from AIRS+MODIS and ERA-Interim make it possible to pinpoint systematic errors in both systems and help to understand joint PDFs of cloud properties and coincident thermodynamic profiles from satellite observations.
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| 14. |
- Wang, Z. B., et al.
(författare)
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Characteristics of regional new particle formation in urban and regional background environments in the North China Plain
- 2013
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Ingår i: Atmos. Chem. Phys.. - : Copernicus Publications. - 1680-7324. ; 13:24, s. 12495-12506
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Tidskriftsartikel (refereegranskat)abstract
- Long-term measurements of particle number size distributions were carried out both at an urban background site (Peking University, PKU) and a regional Global Atmospheric Watch station (Shangdianzi, SDZ) from March to November in 2008. In total, 52 new particle formation (NPF) events were observed simultaneously at both sites, indicating that this is a regional phenomenon in the North China Plain. On average, the mean condensation sink value before the nucleation events started was 0.025 s−1 in the urban environment, which was 1.6 times higher than that at regional site. However, higher particle formation and growth rates were observed at PKU (10.8 cm−3 s−1 and 5.2 nm h−1) compared with those at SDZ (4.9 cm−3 s−1 and 4.0 nm h−1). These results implied that precursors were much more abundant in the polluted urban environment. Different from the observations in cleaner environments, the background conditions of the observed particle homogeneous nucleation events in the North China Plain could be characterized as the co-existing of a stronger source of precursor gases and a higher condensational sink of pre-existing aerosol particles. Secondary aerosol formation following nucleation events results in an increase of particle mass concentration, particle light scattering coefficient, and cloud condensation nuclei (CCN) number concentration, with consequences on visibility, radiative effects, and air quality. Typical regional NPF events with significant particle nucleation rates and subsequent particle growth over a sufficiently long time period at both sites were chosen to investigate the influence of NPF on the number concentration of "potential" CCN. As a result, the NPF and the subsequent condensable growth increased the CCN number concentration in the North China Plain by factors in the range from 5.6 to 8.7. Moreover, the potential contribution of anthropogenic emissions to the CCN number concentration was more than 50%, to which more attention should be drawn in regional and global climate modeling, especially in the polluted urban areas.
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| 15. |
- Yan, J. Y., et al.
(författare)
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Growth of metamorphic InGaP layers on GaAs substrates
- 2013
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Ingår i: Journal of Crystal Growth. - : Elsevier BV. - 0022-0248. ; 378, s. 141-144
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Tidskriftsartikel (refereegranskat)abstract
- We report on the growth of InGaP metamorphic layer by gas source molecular-beam epitaxy. After optimization of the growth temperatures of the compositionally graded InGaP layer and the indium content in the top metamorphic InGaP layer, almost fully relaxed metamorphic layer was obtained with surface roughness of only about 2.17 nm. Strong photoluminescence signals were measured from both InGaAs quantum well and InAs quantum dots embedded in the metamorphic layer, indicating that the top metamorphic layer had low density of threading dislocations. (c) 2013 Elsevier B.V. All rights reserved.
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| 16. |
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| 17. |
- Yue, C., et al.
(författare)
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Modeling of the effective thermal conductivity of composite materials with FEM based on resistor networks approach
- 2010
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Ingår i: Microsystem Technologies. - : Springer Science and Business Media LLC. - 0946-7076 .- 1432-1858. ; 16:4, s. 633-639
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Tidskriftsartikel (refereegranskat)abstract
- In the present paper, a novel and efficient model was developed for predicting the effective thermal conductivity of the composite materials at different filler percentages. By introducing the relative radius as a parameter, the effective thermal conductivity can be predicted precisely when the thermal properties of filler and matrix are prescribed. The model employed the resistor network strategy to achieve a highly efficient prediction during the overall conductivity calculation. To verify this model, a wide range of two-phase composites, including Cu/PP, AlN/PI and a self-developed thermal conductive adhesive, were analyzed. The model-based simulation values showed good agreement with the experimental results. Moreover, a discussion on the effects of the newly-introduced parameter was given. Finally, the relationship between the filler radius variation and the thermal conductivity of the composite was studied.
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