| 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. |
- Luo, Jun, et al.
(författare)
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Thermal Stability and Dopant Segregation for Schottky Diodes With Ultrathin Epitaxial NiSi(2-y)
- 2011
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Ingår i: IEEE Electron Device Letters. - : Institute of Electrical and Electronics Engineers (IEEE). - 0741-3106 .- 1558-0563. ; 32:8, s. 1029-1031
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Tidskriftsartikel (refereegranskat)abstract
- The Schottky barrier height (SBH) of an ultrathin epitaxial NiSi(2-y) film grown on Si(100) is modified significantly by means of dopant segregation (DS). The DS process begins with the NiSi(2-y) formation and is followed by dopant implantation and drive-in annealing. The rapid lattice restoration and superior morphological stability upon heat treatment up to 800 degrees C allow the epitaxial NiSi(2-y) film to take full advantage of the DS process. For drive-in annealing below 750 degrees C, the effective SBH is altered to similar to 0.9-1 eV for both electrons and holes by B-DS and As-DS, respectively, without deteriorating the integrity of the NiSi(2-y) film.
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| 3. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 4. |
- Hudson, Thomas J., et al.
(författare)
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International network of cancer genome projects
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7291, s. 993-998
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Tidskriftsartikel (refereegranskat)abstract
- The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.
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| 5. |
- Lu, Jun, et al.
(författare)
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On Epitaxy of Ultrathin Ni1-xPtx Silicide Films on Si(001)
- 2010
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Ingår i: Electrochemical and solid-state letters. - : The Electrochemical Society. - 1099-0062 .- 1944-8775. ; 13:10, s. H360-H362
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Tidskriftsartikel (refereegranskat)abstract
- Epitaxial Ni(Pt)Si2-y (y < 1) films readily grow upon thermal treatment of 2 nm thick Ni and Ni0.96Pt0.04 films deposited on Si(001). For annealing at 500 degrees C, the films are 5.4-5.6 nm thick with 61-70 mu cm in resistivity. At 750 degrees C, the epitaxial Ni(Pt)Si2-y films become 6.1-6.2 nm thick with a resistivity of 42-44 mu cm. Structural analysis reveals twins, facet wedges, and thickness inhomogeneities in the films grown at 500 degrees C. For higher temperature, an almost defect-free NiSi2-y film with a flat and sharp interface is formed. The presence of Pt makes the aforementioned imperfections more persistent.
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| 6. |
- Lu, Lu, et al.
(författare)
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Theoretical analysis of natural-gas leakage in urban medium-pressure pipelines
- 2014
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Ingår i: Journal of Environment and Human. - 2373-8324 .- 2373-8332. ; 1:2, s. 71-86
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Tidskriftsartikel (refereegranskat)abstract
- With widespread deployment of the urban natural gas industry, the energy security is now becoming one of the priorities in practice. Gas leakage may occur from the pipeline during the collection and transportation process. This article therefore presented a theoretical study on the urban natural gas pipeline leakage in order to provide the basic theory of the rescue policy making in emergent occasions. The investigation was undertaken through the fundamental analysis based on derivation of gas leakage models. The gas leakage model was applied to analyze the pressure, temperature and flow rate of gas leakage over time under both the steady-state and dynamic conditions. Two main impacting factors, pressure and hole size, were subsequently discussed. It is concluded that for the steady leakage the flow rate increases with the increase of pipeline pressure and hole size. And the distribution of pressure, temperature, density and velocity were calculated along the pipeline. For the unsteady leakage, the time of leakage is very short under different initial pressure and hole size, and the total leakage and average leakage rates were analyzed.
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| 7. |
- Luo, Jun, et al.
(författare)
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On Different Process Schemes for MOSFETs With a Controllable NiSi-Based Metallic Source/Drain
- 2011
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Ingår i: IEEE Transactions on Electron Devices. - : IEEE Institute of Electrical and Electronics. - 0018-9383 .- 1557-9646. ; 58:7, s. 1898-1906
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Tidskriftsartikel (refereegranskat)abstract
- This paper focuses on different silicidation schemes toward a controllable NiSi-based metallic source/drain (MSD) process with restricted lateral encroachment of NiSi. These schemes include thickness control of Ni, Ni-Pt alloying, and two-step annealing. Experimental results show that all the three process schemes can give rise to effective control of lateral encroachment during Ni silicidation. By controlling t(Ni), NiSi-based MSD metal-oxide-semiconductor field-effect transistors (MOSFETs) of gate length L-G = 55 nm are readily realized on ultrathin-body silicon-on-insulator substrates with 20-nm surface Si thickness. With the aid of dopant segregation (DS) to modifying the Schottky barrier heights of NiSi, both n- and p-type MSD MOSFETs show significant performance improvement, compared to reference devices without DS.
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| 8. |
- Luo, Jun, et al.
(författare)
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Surface-energy triggered phase formation and epitaxy in nanometer-thick Ni1-xPtx silicide films
- 2010
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 96:3
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Tidskriftsartikel (refereegranskat)abstract
- The formation of ultrathin silicide films of Ni1-xPtx at 450-850 degrees C is reported. Without Pt (x=0) and for t(Ni)< 4 nm, epitaxially aligned NiSi2-y films readily grow and exhibit extraordinary morphological stability up to 800 degrees C. For t(Ni)>= 4 nm, polycrystalline NiSi films form and agglomerate at lower temperatures for thinner films. Without Ni (x=1) and for t(Pt)=1-20 nm, the annealing behavior of the resulting PtSi films follows that for the NiSi films. The results for Ni1-xPtx of other compositions support the above observations. Surface energy is discussed as the cause responsible for the distinct behavior in phase formation and morphological stability.
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| 9. |
- Ma, Tao, et al.
(författare)
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Genomic insights into salt adaptation in a desert poplar
- 2013
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2797-
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Tidskriftsartikel (refereegranskat)abstract
- Despite the high economic and ecological importance of forests, our knowledge of the genomic evolution of trees under salt stress remains very limited. Here we report the genome sequence of the desert poplar, Populus euphratica, which exhibits high tolerance to salt stress. Its genome is very similar and collinear to that of the closely related mesophytic congener, P. trichocarpa. However, we find that several gene families likely to be involved in tolerance to salt stress contain significantly more gene copies within the P. euphratica lineage. Furthermore, genes showing evidence of positive selection are significantly enriched in functional categories related to salt stress. Some of these genes, and others within the same categories, are significantly upregulated under salt stress relative to their expression in another salt-sensitive poplar. Our results provide an important background for understanding tree adaptation to salt stress and facilitating the genetic improvement of cultivated poplars for saline soils.
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| 10. |
- Wu, Lu-Lu, et al.
(författare)
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Witness of unsatisfiability for a random 3-satisfiability formula
- 2013
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1539-3755 .- 1550-2376. ; 87:5, s. 052807-
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Tidskriftsartikel (refereegranskat)abstract
- The random 3-satisfiability (3-SAT) problem is in the unsatisfiable (UNSAT) phase when the clause density alpha exceeds a critical value alpha(s) approximate to 4.267. Rigorously proving the unsatisfiability of a given large 3-SAT instance is, however, extremely difficult. In this paper we apply the mean-field theory of statistical physics to the unsatisfiability problem, and show that a reduction to 3-XORSAT, which permits the construction of a specific type of UNSAT witnesses (Feige-Kim-Ofek witnesses), is possible when the clause density alpha > 19. We then construct Feige-Kim-Ofek witnesses for single 3-SAT instances through a simple random sampling algorithm and a focused local search algorithm. The random sampling algorithm works only when a scales at least linearly with the variable number N, but the focused local search algorithm works for clause density alpha > cN(b) with b approximate to 0.59 and prefactor c approximate to 8. The exponent b can be further decreased by enlarging the single parameter S of the focused local search algorithm.
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