| 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. |
- Wu, Chen, et al.
(författare)
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Genome-wide association study of survival in patients with pancreatic adenocarcinoma
- 2014
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Ingår i: Gut. - : BMJ Publishing Group. - 0017-5749 .- 1468-3288. ; 63:1, s. 152-160
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND AND OBJECTIVE: Survival of patients with pancreatic adenocarcinoma is limited and few prognostic factors are known. We conducted a two-stage genome-wide association study (GWAS) to identify germline variants associated with survival in patients with pancreatic adenocarcinoma. METHODS: We analysed overall survival in relation to single nucleotide polymorphisms (SNPs) among 1005 patients from two large GWAS datasets, PanScan I and ChinaPC. Cox proportional hazards regression was used in an additive genetic model with adjustment for age, sex, clinical stage and the top four principal components of population stratification. The first stage included 642 cases of European ancestry (PanScan), from which the top SNPs (p≤10(-5)) were advanced to a joint analysis with 363 additional patients from China (ChinaPC). RESULTS: In the first stage of cases of European descent, the top-ranked loci were at chromosomes 11p15.4, 18p11.21 and 1p36.13, tagged by rs12362504 (p=1.63×10(-7)), rs981621 (p=1.65×10(-7)) and rs16861827 (p=3.75×10(-7)), respectively. 131 SNPs with p≤10(-5) were advanced to a joint analysis with cases from the ChinaPC study. In the joint analysis, the top-ranked SNP was rs10500715 (minor allele frequency, 0.37; p=1.72×10(-7)) on chromosome 11p15.4, which is intronic to the SET binding factor 2 (SBF2) gene. The HR (95% CI) for death was 0.74 (0.66 to 0.84) in PanScan I, 0.79 (0.65 to 0.97) in ChinaPC and 0.76 (0.68 to 0.84) in the joint analysis. CONCLUSIONS: Germline genetic variation in the SBF2 locus was associated with overall survival in patients with pancreatic adenocarcinoma of European and Asian ancestry. This association should be investigated in additional large patient cohorts.
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| 3. |
- Chen, Eric Zhi, 1963-
(författare)
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Flipped classroom model and its implementation in a computer programming course
- 2014
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Ingår i: Lärarlärdom. - 9789172959682 ; , s. 180-200
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Konferensbidrag (refereegranskat)abstract
- The flipped classroom approach provides implementation of a student-centered learning environment. By changing the traditional classroom lectures and homework elements of a course, it facilitates active learning and higher-order understanding. This paper presents initial experiments on a flipped classroom approach and its application in a programming course. The course results and evaluation show that this approach is rewarding, and why it deserves further investigation.
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| 4. |
- Chen, Eric Zhi
(författare)
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Flipped classroom model and its implementation in a computer programming course
- 2014
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The flipped classroom approach provides implementation of a student-centered learning environment. By changing the traditional classroom lectures and homework elements of a course, it facilitates active learning and higher-order understanding. This paper presents initial experiments on a flipped classroom approach and its application in a programming course. The course results and evaluation show that this approach is rewarding, and why it deserves further investigation.
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| 5. |
- Chen, Eric Zhi, et al.
(författare)
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New databases of linear codes over GF(11) and GF(13)
- 2014
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Ingår i: Proceedings of Karatekin mathematics days 2014. ; , s. 22-22
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Konferensbidrag (refereegranskat)abstract
- One central problem in coding theory is to optimize the parameters of a linear code and construct codes with best possible parameters. There are tables of best-known linear codes over nite elds of sizes up to 9. Recently, there has been a growing interest in codes over GF(11), over GF(13) and other elds of size greater than 9. The main purpose of this work is to present new databases of best-known linear codes over the elds GF(11) and GF(13) together with upper bounds on the minimum distances. To nd good linear codes to establish lower bounds on minimum distances, an iterative heuristic computer search algorithm is employed to construct quasi-twisted (QT) codes over these elds with high minimum distances. A large number of new linear codes have been found, improving previously best-known results. Tables of [pm, m] QT codes over the two elds with best-known minimum distances as well as a table of lower and upper bounds on the minimum distances for linear codes of length up to 150 and dimension up to 6 are presented.
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| 6. |
- Chen, Eric Zhi, et al.
(författare)
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New databases of linear codes over GF(11) and GF(13)
- 2014
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- One central problem in coding theory is to optimize the parameters of a linear code and construct codes with best possible parameters. There are tables of best-known linear codes over nite elds of sizes up to 9. Recently, there has been a growing interest in codes over GF(11), over GF(13) and other elds of size greater than 9. The main purpose of this work is to present new databases of best-known linear codes over the elds GF(11) and GF(13) together with upper bounds on the minimum distances. To nd good linear codes to establish lower bounds on minimum distances, an iterative heuristic computer search algorithm is employed to construct quasi-twisted (QT) codes over these elds with high minimum distances. A large number of new linear codes have been found, improving previously best-known results. Tables of [pm, m] QT codes over the two elds with best-known minimum distances as well as a table of lower and upper bounds on the minimum distances for linear codes of length up to 150 and dimension up to 6 are presented.
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