| 1. |
- 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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| 2. |
- Lindblad-Toh, Kerstin, et al.
(författare)
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Genome sequence, comparative analysis and haplotype structure of the domestic dog.
- 2005
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
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Tidskriftsartikel (refereegranskat)abstract
- Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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| 3. |
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| 4. |
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| 5. |
- Bednar, Peter, et al.
(författare)
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Diversity Networks in Digital Investigations
- 2009
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Ingår i: [Host publication title missing]. - 9781841022307 ; , s. 63-71
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Konferensbidrag (refereegranskat)abstract
- This paper is built upon recognizing the need that digital forensic investigators are required in many cases to investigate, understand and report on all kind of cyber-crime including novel security breaches which have not been performed in the past. When an investigator is faced with the challenge to explore a new threat, we argue that the inquiry dynamics do not differ from an organisational employee challenged to perform innovation. This is not just about challenging one’s own assumptions; not just challenging the assumptions of one’s colleagues but creating a dialogue among colleagues about the processes of questioning assumptions in order to uncover a richer appreciation of the uncertainties of the problem-space to be the subject of inquiry. This paper draws upon the approach of diversity networks which is used to support inquiry into complex problem spaces including the necessary requirement for innovation, and it is shown how this paradigm could be adopted by the forensic investigator to shed light on the uncertainty aspects of a cyber crime scene.
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| 6. |
- Beers, Timothy C., et al.
(författare)
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Broadband UBVRCIC photometry of horizontal-branch and metal-poor candidates from the HK and Hamburg/ESO surveys. I.
- 2007
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Ingår i: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 168:1, s. 128-139
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Tidskriftsartikel (refereegranskat)abstract
- We report broadband UBV and/or BVRCIC CCD photometry for a total of 1857 stars in the thick-disk and halo populations of the Galaxy. The majority of our targets were selected as candidate field horizontal-branch or other A-type stars (FHB/ A, N = 576), or candidate low-metallicity stars (N = 1221), from the HK and Hamburg/ESO objective-prism surveys. Similar data for a small number of additional stars from other samples are also reported. These data are being used for several purposes. In the case of the FHB/ A candidates they are used to accurately separate the lower gravity FHB stars from various higher gravity A-type stars, a subsample that includes the so-called blue metal poor stars, halo and thick-disk blue stragglers, main-sequence A-type dwarfs, and Am and Ap stars. These data are also being used to derive photometric distance estimates to high-velocity hydrogen clouds in the Galaxy and for improved measurements of the mass of the Galaxy. Photometric data for the metal-poor candidates are being used to refine estimates of stellar metallicity for objects with available medium-resolution spectroscopy, to obtain distance estimates for kinematic analyses, and to establish initial estimates of effective temperature for analysis of high-resolution spectroscopy of the stars for which this information now exists.
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| 7. |
- Behnam, Moris, et al.
(författare)
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Subsystem-Interface Generation in the Presence of Shared Resources
- 2009
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Ingår i: Proceedings of the 2nd Workshop on Compositional Theory and Technology for Real-Time Embedded Systems (CRTS'09) in conjunction with the 30th IEEE International Real-Time Systems Symposium (RTSS'09). - Washington DC, USA.
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Konferensbidrag (refereegranskat)abstract
- The Hierarchical Scheduling Framework (HSF) has been introduced as a design-time framework enabling compositional schedulability analysis of embedded software systems with real-time properties. However, supporting resource sharing in HSF is a major challenge, since it increases the amount of the CPU resources required to guarantee the schedulability of the hard real time tasks and decreases the composability at the system level. In this paper, we discuss and identify the key parameters of a compositional framework called the bounded-delay resource open environment (BROE) server to support global resource sharing, that have a great effect on how the framework will utilize CPU resources. Furthermore, we provide an algorithm, that has a pseudo-polynomial complexity, to evaluate the ”optimal” setting for the BROE server. In addition, we provide a polynomial-time approximation algorithm for generating near-optimal setting for the BROE server. The performance of the BROE server, as well as the efficiency of the approximated algorithm, is evaluated by the means of simulation analysis.
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| 8. |
- Bengtson, Per, et al.
(författare)
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Links between methanotroph community composition and CH(4) oxidation in a pine forest soil
- 2009
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Ingår i: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 1574-6941 .- 0168-6496. ; 70:3, s. 356-366
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Tidskriftsartikel (refereegranskat)abstract
- The main gap in our knowledge about what determines the rate of CH(4) oxidation in forest soils is the biology of the microorganisms involved, the identity of which remains unclear. In this study, we used stable-isotope probing (SIP) following (13)CH(4) incorporation into phospholipid fatty acids (PLFAs) and DNA/RNA, and sequencing of methane mono-oxygenase (pmoA) genes, to identify the influence of variation in community composition on CH(4) oxidation rates. The rates of (13)C incorporation into PLFAs differed between horizons, with low (13)C incorporation in the organic soil and relatively high (13)C incorporation into the two mineral horizons. The microbial community composition of the methanotrophs incorporating the (13)C label also differed between horizons, and statistical analyses suggested that the methanotroph community composition was a major cause of variation in CH(4) oxidation rates. Both PLFA and pmoA-based data indicated that CH(4) oxidizers in this soil belong to the uncultivated 'upland soil cluster alpha'. CH(4) oxidation potential exhibited the opposite pattern to (13)C incorporation, suggesting that CH(4) oxidation potential assays may correlate poorly with in situ oxidation rates. The DNA/RNA-SIP assay was not successful, most likely due to insufficient (13)C-incorporation into DNA/RNA. The limitations of the technique are briefly discussed.
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| 9. |
- Bromley, Elizabeth H. C., et al.
(författare)
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The Tumbleweed: towards a synthetic protein motor
- 2009
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Ingår i: HFSP Journal. - : Informa UK Limited. - 1955-2068. ; 3:3, s. 204-212
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Tidskriftsartikel (refereegranskat)abstract
- Biomolecular motors have inspired the design and construction of artificial nanoscale motors and machines based on nucleic acids, small molecules, and inorganic nanostructures. However, the high degree of sophistication and efficiency of biomolecular motors, as well as their specific biological function, derives from the complexity afforded by protein building blocks. Here, we discuss a novel bottom-up approach to understanding biological motors by considering the construction of synthetic protein motors. Specifically, we present a design for a synthetic protein motor that moves along a linear track, dubbed the "Tumbleweed." This concept uses three discrete ligand-dependent DNA-binding domains to perform cyclically ligand-gated, rectified diffusion along a synthesized DNA molecule. Here we describe how de novo peptide design and molecular biology could be used to produce the Tumbleweed, and we explore the fundamental motor operation of such a design using numerical simulations. The construction of this and more sophisticated protein motors is an exciting challenge that is likely to enhance our understanding of the structure-function relationship in biological motors. [DOI: 10.2976/1.3111282]
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| 10. |
- Canadel, Josep G., et al.
(författare)
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Contributions to accelerating atmospheric CO2 growth from economic activity, carbon intensity, and efficiency of natural sinks
- 2007
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 104:47, s. 18866-18870
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Tidskriftsartikel (refereegranskat)abstract
- The growth rate of atmospheric carbon dioxide (CO2), the largest human contributor to human-induced climate change, is increasing rapidly. Three processes contribute to this rapid increase. Two of these processes concern emissions. Recent growth of the world economy combined with an increase in its carbon intensity have led to rapid growth in fossil fuel CO2 emissions since 2000: comparing the 1990s with 2000–2006, the emissions growth rate increased from 1.3% to 3.3% y −1. The third process is indicated by increasing evidence (P = 0.89) for a long-term (50-year) increase in the airborne fraction (AF) of CO2 emissions, implying a decline in the efficiency of CO2 sinks on land and oceans in absorbing anthropogenic emissions. Since 2000, the contributions of these three factors to the increase in the atmospheric CO2 growth rate have been ≈65 ± 16% from increasing global economic activity, 17 ± 6% from the increasing carbon intensity of the global economy, and 18 ± 15% from the increase in AF. An increasing AF is consistent with results of climate–carbon cycle models, but the magnitude of the observed signal appears larger than that estimated by models. All of these changes characterize a carbon cycle that is generating stronger-than-expected and sooner-than-expected climate forcing.
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