| 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. |
- Cerhan, James R., et al.
(författare)
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Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma
- 2014
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 46:11, s. 1233-1238
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Tidskriftsartikel (refereegranskat)abstract
- Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma subtype and is clinically aggressive. To identify genetic susceptibility loci for DLBCL, we conducted a meta-analysis of 3 new genome-wide association studies (GWAS) and 1 previous scan, totaling 3,857 cases and 7,666 controls of European ancestry, with additional genotyping of 9 promising SNPs in 1,359 cases and 4,557 controls. In our multi-stage analysis, five independent SNPs in four loci achieved genome-wide significance marked by rs116446171 at 6p25.3 (EXOC2; P = 2.33 x 10(-21)), rs2523607 at 6p21.33 (HLA-B; P = 2.40 x 10(-10)), rs79480871 at 2p23.3 (NCOA1; P = 4.23 x 10(-8)) and two independent SNPs, rs13255292 and rs4733601, at 8q24.21 (PVT1; P = 9.98 x 10(-13) and 3.63 x 10(-11), respectively). These data provide substantial new evidence for genetic susceptibility to this B cell malignancy and point to pathways involved in immune recognition and immune function in the pathogenesis of DLBCL.
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| 3. |
- Skibola, Christine F, et al.
(författare)
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Genome-wide Association Study Identifies Five Susceptibility Loci for Follicular Lymphoma outside the HLA Region.
- 2014
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 95:4, s. 462-471
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWASs) of follicular lymphoma (FL) have previously identified human leukocyte antigen (HLA) gene variants. To identify additional FL susceptibility loci, we conducted a large-scale two-stage GWAS in 4,523 case subjects and 13,344 control subjects of European ancestry. Five non-HLA loci were associated with FL risk: 11q23.3 (rs4938573, p = 5.79 × 10(-20)) near CXCR5; 11q24.3 (rs4937362, p = 6.76 × 10(-11)) near ETS1; 3q28 (rs6444305, p = 1.10 × 10(-10)) in LPP; 18q21.33 (rs17749561, p = 8.28 × 10(-10)) near BCL2; and 8q24.21 (rs13254990, p = 1.06 × 10(-8)) near PVT1. In an analysis of the HLA region, we identified four linked HLA-DRβ1 multiallelic amino acids at positions 11, 13, 28, and 30 that were associated with FL risk (pomnibus = 4.20 × 10(-67) to 2.67 × 10(-70)). Additional independent signals included rs17203612 in HLA class II (odds ratio [ORper-allele] = 1.44; p = 4.59 × 10(-16)) and rs3130437 in HLA class I (ORper-allele = 1.23; p = 8.23 × 10(-9)). Our findings further expand the number of loci associated with FL and provide evidence that multiple common variants outside the HLA region make a significant contribution to FL risk.
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| 4. |
- Graeger, R., et al.
(författare)
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Experimental Study of the 238U(36S,3-5n)269-271Hs Reaction Leading to the Observation of 270Hs
- 2010
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Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 81:6
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Tidskriftsartikel (refereegranskat)abstract
- The deformed doubly magic nucleus (270)Hs has so far only been observed as the four-neutron (4n) evaporation residue of the reaction Mg-26+Cm-248, where a maximum cross section of 3 pb was measured. Theoretical studies on the formation of (270)Hs in the 4n evaporation channel of fusion reactions with different entrance channel asymmetry in the framework of a two-parameter Smoluchowski equation predict that the reactions Ca-48+Ra-226 and S-36+U-238 result in higher cross sections due to lower reaction Q values, in contrast to simple arguments based on the reaction asymmetry, which predict opposite trends. Calculations using HIVAP predict cross sections for the reaction S-36+U-238 that are similar to those of the Mg-26+Cm-248 reaction. Here, we report on the first measurement of evaporation residues formed in the complete nuclear fusion reaction S-36+U-238 and the observation of (270)Hs, which is produced in the 4n evaporation channel, with a measured cross section of 0.8(-0.7)(+2.6) pb at 51-MeV excitation energy. The one-event cross-section limits (68% confidence level) for the 3n, 4n, and 5n evaporation channels at 39-MeV excitation energy are 2.9 pb, while the cross-section limits of the 3n and 5n channel at 51 MeV are 1.5 pb. This is significantly lower than the 5n cross section of the Mg-26+Cm-248 reaction at similar excitation energy.
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| 5. |
- Brawand, David, et al.
(författare)
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The genomic substrate for adaptive radiation in African cichlid fish
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 513:7518, s. 375-381
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Tidskriftsartikel (refereegranskat)abstract
- Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand themolecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
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| 6. |
- Ruffini, M., et al.
(författare)
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DISCUS : An End-to-End Solution for Ubiquitous Broadband Optical Access
- 2014
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Ingår i: IEEE Communications Magazine. - 0163-6804 .- 1558-1896. ; 52:2, s. S24-S32
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Tidskriftsartikel (refereegranskat)abstract
- Fiber to the premises has promised to increase the capacity in telecommunications access networks for well over 30 years. While it is widely recognized that optical-fiber-based access networks will be a necessity in the shortto medium-term future, its large upfront cost and regulatory issues are pushing many operators to further postpone its deployment, while installing intermediate unambitious solutions such as fiber to the cabinet. Such high investment cost of both network access and core capacity upgrade often derives from poor planning strategies that do not consider the necessity to adequately modify the network architecture to fully exploit the cost benefit that a fiber-centric solution can bring. DISCUS is a European Framework 7 Integrated Project that, building on optical-centric solutions such as long-reach passive optical access and flat optical core, aims to deliver a cost-effective architecture for ubiquitous broadband services. DISCUS analyzes, designs, and demonstrates end-to-end architectures and technologies capable of saving cost and energy by reducing the number of electronic terminations in the network and sharing the deployment costs among a larger number of users compared to current fiber access systems. This article describes the network architecture and the supporting technologies behind DISCUS, giving an overview of the concepts and methodologies that will be used to deliver our end-to-end network solution.
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| 7. |
- Wang, F., et al.
(författare)
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FE modeling of the human neck responses in low-speed car collisions
- 2010
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Ingår i: International Federation for Medical and Biological Engineering Proceedings. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 1680-0737. - 9783540790389 ; 31, s. 513-516
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Konferensbidrag (refereegranskat)abstract
- The main goal of the current study is to improve an FE neck model with human like response in vehicle frontal, rear-end and side collisions based on an existing model developed in Hunan University. This model consists of the cervical vertebrae, intervertebral discs, ligaments and muscles that are modeled with various element types. The neck model is validated against kinematics data from volunteer tests. The response of the model generally shows a good agreement with the test results for the main part of the time history of the collision events. Sensitivity analysis of the model shows that the Young's modulus of the disc has a great influence on the head-neck kinematics. © 2010 International Federation for Medical and Biological Engineering.
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| 8. |
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| 9. |
- Zhang, Zhi Y, et al.
(författare)
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PINCH mRNA Overexpression in Colorectal Carcinomas Correlated with VEGF and FAS mRNA Expression
- 2011
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Ingår i: Anticancer Research. - : International Institute of Anticancer Research (IIAR). - 0250-7005 .- 1791-7530. ; 31:12, s. 4127-4133
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND:Particularly interesting new cysteine-histidine-rich protein (PINCH) was found to be up-regulated in the stroma of colorectal carcinomas (CRCs) in our previous studies and was involved in angiogenesis through activation of fibroblasts in extracellular matrix (ECM) in response to tumors. Here, we examined PINCH mRNA expression in colorectal cancer and investigated its relationship with the clinicopathological features and proliferation cell nuclear antigen (PCNA), vascular endothelial growth factor (VEGF) and FAS.MATERIALS AND METHODS:The primary cancer tissues, adjacent noncancerous tissues and the proximal and distant margins of normal mucosa were collected from 81 colorectal cancer patients during surgery. PINCH, PCNA, VEGF and FAS mRNA expression was examined by reverse transcriptional PCR (RT-PCR).RESULTS:PINCH mRNA expression was significantly increased in primary tumors compared with that in adjacent noncancerous tissues, and the proximal and distant margins of normal mucosa (p<0.0001). Expression of PINCH mRNA in colon cancer tended to be higher than expression in rectal cancer (p=0.051). Tumors which had infiltrated through the wall of the colorectum trended to have higher PINCH mRNA expression (p=0.073). PINCH mRNA expression in primary tumors was positively related to the expression of PCNA mRNA (r=0.534, p=0.010), VEGF mRNA (r=0.431, p=0.022) and FAS mRNA (r=0.542, p=0.012).CONCLUSION:PINCH mRNA was overexpressed in colorectal cancer and associated with PCNA mRNA, VEGF mRNA and FAS mRNA expression. PINCH mRNA was involved in the development of colorectal cancer and might play a role in the epithelial mesenchymal transition in the rectum differently than in the colon, through the adenomatous polyposis coli (APC)/catenin pathway.
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