| 1. |
- Lensink, Marc F., et al.
(författare)
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
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Ingår i: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
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Tidskriftsartikel (refereegranskat)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
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| 2. |
- Takeuchi, Fumihiko, et al.
(författare)
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Interethnic analyses of blood pressure loci in populations of East Asian and European descent
- 2018
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Blood pressure (BP) is a major risk factor for cardiovascular disease and more than 200 genetic loci associated with BP are known. Here, we perform a multi-stage genome-wide association study for BP (max N = 289,038) principally in East Asians and meta-analysis in East Asians and Europeans. We report 19 new genetic loci and ancestry-specific BP variants, conforming to a common ancestry-specific variant association model. At 10 unique loci, distinct non-rare ancestry-specific variants colocalize within the same linkage disequilibrium block despite the significantly discordant effects for the proxy shared variants between the ethnic groups. The genome-wide transethnic correlation of causal-variant effect-sizes is 0.898 and 0.851 for systolic and diastolic BP, respectively. Some of the ancestry-specific association signals are also influenced by a selective sweep. Our results provide new evidence for the role of common ancestry-specific variants and natural selection in ethnic differences in complex traits such as BP.
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| 3. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 4. |
- He, Liming, et al.
(författare)
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A new relativistic Hartree-Fock calculation scheme and its application to the evaluation of fine-structure intervals for nd (n=3-40) series of sodium
- 2011
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Ingår i: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 44:22, s. 225007-
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Tidskriftsartikel (refereegranskat)abstract
- We present a new second-order representation of the relativistic Hartree-Fock equation, which can be solved by the standard Hartree-Fock technique. An alternative reduction for the magnetic part of the Breit interaction is presented in an explicit expression. A corresponding program has been developed, which improves significantly the scaled linear mesh introduced by Herman and Skillman. The structures for a number of atoms and ions are calculated and the agreement of our results with those published is excellent. We evaluate the fine-structure intervals of nd(n = 3-40) Rydberg series for sodium. The inverted fine-structure splitting values are obtained directly as the differences of eigenvalues obtained from a self-consistent field procedure. Taking into account the Gaunt effect enables the accuracy of the calculation to be substantially improved. The complete treatments reproduce very well the inverted fine structures along the Rydberg series and the relative difference between the present results and the experiments does not exceed 4.4%.
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| 5. |
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| 6. |
- Lu, Qinghua, et al.
(författare)
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MapReduce Job Optimization : A Mapping Study
- 2016
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Ingår i: Proceedings - 2015 International Conference on Cloud Computing and Big Data, CCBD 2015. - 9781467383509 ; , s. 81-88
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Konferensbidrag (refereegranskat)abstract
- MapReduce has become the standard model for supporting big data analytics. In particular, MapReduce job optimization has been widely considered to be crucial in the implementations of big data analytics. However, there is still a lack of guidelines especially for practitioners to understand how the MapReduce jobs can be optimized. This paper aims to systematic identify and taxonomically classify the existing work on job optimization. We conducted a mapping study on 47 selected papers that were published between 2004 and 2014. We classified and compared the selected papers based on a 5WH-based characterization framework. This study generates a knowledge base of current job optimization solutions and also identifies a set of research gaps and opportunities. This study concludes that job optimization is still in an early stage of maturity. More attentions need to be paid to the cross-data center, cluster or rack job optimization to improve communication efficiency.
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| 7. |
- Lu, Zhaohui, et al.
(författare)
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Microseismic Monitoring of Hydraulic Fracture Propagation and Seismic Risks in Shale Reservoir with a Steep Dip Angle
- 2022
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Ingår i: Natural Resources Research. - : Springer Nature. - 1520-7439 .- 1573-8981. ; 31:5, s. 2973-2993
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Tidskriftsartikel (refereegranskat)abstract
- Hydraulic fracturing is an essential technique to increase reservoir permeability and enhance the production of shale gas. When the dip angle is steep and geological condition is complex, hydraulic fractures may behave complexly, and research on this topic is critical for the shale gas industry. This paper reports a case study of hydraulic fracturing in a shale reservoir with a steep dip angle. We monitored pump data, including the injection rate and fluid pressure. Microseismic monitoring was also used to record the seismic events and monitor the hydraulic fracture propagation. Our results validated that microseismic monitoring is a feasible technique to monitor the hydraulic fracture propagation in shale reservoirs with steep dip angles. Moreover, the variation in depth of shale reservoir induces significant alternation of local in situ stress states, in which cases the fracture propagation pathway is more complex, and where microseismic monitoring is necessary to acquire the hydraulic fracture distribution. Besides, all sound sources, including quarries and rivers, should be eliminated during microseismic station arrangement to improve accuracy of microseismic signals. Moreover, the relationship between the maximum magnitude of seismic event and fluid injection volume was validated further in this study. Finally, unexpected faults and aquifers may affect hydraulic fracture propagation due to the steep dip angle of the target shale reservoir. Thus, a comprehensive geological survey is essential for better hydraulic fracturing design. Our results provide first-hand in situ hydraulic fracturing data and provide important implications for shale gas development, especially for those shale reservoirs with steep dip angles.
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| 8. |
- Mejia, Max, et al.
(författare)
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Adapting the AcciMap for an Analysis of Maritime Security Incidents
- 2007
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Ingår i: Interaction of Science, Technology and Engineering. - 9787801446824 ; , s. 333-337
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Konferensbidrag (refereegranskat)abstract
- This study aims to: (1) identify some of the active and latent conditions that allow maritime security incidents to occur, and (2) explore the feasibility of adapting the Rasmussen-Svedung AcciMap as a tool for maritime security management. These twin objectives are pursued by applying concepts and principles, propounded by Rasmussen and Svedung, to a case study of the 1999 hijacking of the Alondra Rainbow. The case study is based on information gathered from official and journalistic investigations conducted into the incident. As its preliminary result, this study presents a SecInciMap of the Alondra Rainbow hijacking which helps identify some of the conditions relevant to the hijacking of ships; supports the SecInciMap’s feasibility; but which raises questions as to how readily adaptable safety and risk management concepts can be in the context of security.
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