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| 2. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 3. |
- Loarer, T., et al.
(författare)
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Gas balance and fuel retention in fusion devices
- 2007
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 47:9, s. 1112-1120
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Tidskriftsartikel (refereegranskat)abstract
- The evaluation of hydrogenic retention in present tokamaks is of crucial importance to estimate the expected tritium (T) vessel inventory in ITER, limited from safety considerations to 350 g. In the framework of the European Task Force on Plasma Wall Interaction (EU TF on PWI) efforts are underway to investigate gas balance and fuel retention during discharges, and to compare the data obtained with those from post-mortem analysis of in-vessel components exposed over whole experimental campaigns. This paper summarizes the principal findings from coordinated studies on gas balance and fuel retention from a number of European tokamaks, namely, ASDEX-Upgrade (AUG), JET, TEXTOR and Tore Supra (TS). For most devices, the long-term retention fraction deduced from integrated particle balance is similar to 10-20%. This is larger than the similar to 3-4% deduced from post-mortem analysis of plasma facing components (PFCs). However, from the database available for tokamaks with their main PFCs made of carbon, the important conclusion is that the T inventory limit (set by the working guideline for operations) could be reached in ITER within fewer than 100 discharges. This, therefore, would seriously impact on operation of the device unless efficient T removal processes are developed.
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| 6. |
- Loarer, T., et al.
(författare)
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Fuel retention in L and H mode experiments in JET
- 2007
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Ingår i: 34th EPS Conference on Plasma Physics 2007, EPS 2007 - Europhysics Conference Abstracts. - 9781622763344 ; , s. 13-16
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Konferensbidrag (refereegranskat)abstract
- The fuel retention has been studied out in JET in L mode, Type III and Type I ELMy H-modes using gas balance in series of repetitive pulses with an overall accuracy of about 1.2%. The short term (dynamic) retention is important for both L mode and Type III ELMy H-mode over the heating phases (respectively 13 and 17 sec) but decreases already significantly during the pulse. It becomes small already after 6 sec for the Type I ELMy H-mode conditions. In all the cases, the recovery after the pulse contributes for a weak part in the gas balance and in the overall fuel retention. The absolute long term fuel retention (on the time basis of typically 5 hours) for the different plasma conditions is between 1.3 and 2.8 1021Ds-1 (averaged over the plasma heating time) and in reasonable agreement with the value deduced from post mortem tile analysis of about 5 1020Ds-1 considering the additional long term outgassing, conditioning and disruptions included in the post mortem analysis. The increase of the long term retention observed from L mode to Type I ELMy H-mode is associated to the increase of the recycling flux and the ELM energy. This larger long term retention is attributed to an enhanced carbon erosion and transport in the SOL leading to stronger carbon deposition and fuel codeposition. The results confirm the strong concerns about fuel retention in a carbon clad tokamak and a possible full carbon wall ITER which could reach the T-inventory limit in only a small number of high performance shots. A reasonable ITER operation time depends thus on a significant reduced T codeposition under the different ITER material conditions (which has to be confirmed in a relevant tokamak experiment such as the JET ILW project) and an effective routine T removal technique.
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| 7. |
- Margulies, Elliott H, et al.
(författare)
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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- 2007
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 17:6, s. 760-774
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Tidskriftsartikel (refereegranskat)abstract
- A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.
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| 9. |
- Hatemi-J, Abdulnasser, et al.
(författare)
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Liberalized emerging markets and the world economy : testing for increased integration with time-varying volatility
- 2007
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Ingår i: Applied Financial Economics. - : Routledge. - 0960-3107 .- 1466-4305. ; 17:15, s. 1245-1250
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Tidskriftsartikel (refereegranskat)abstract
- Due to increasing globalization and its potential benefits, many emerging markets have introduced capital liberalization policies to attract much needed foreign direct investment. The objective of this article is to empirically investigate whether the conducted deregulation policies resulted in greater integration of emerging financial markets with the world market. For this purpose, a novel method introduced by Hatemi-J and Hacker (2005) is utilized to calculate the parameters as well as to test the significance of these parameters. This method is shown to be robust to nonnormality and time-varying volatility that usually characterize financial data and therefore it can provide more accurate inference compared to other methods. We find that only four of 17 emerging markets have become more integrated with the world market after implementing the liberalization policy.
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