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- Bradnam, K. R., et al.
(author)
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Assemblathon 2 : Evaluating de novo methods of genome assembly in three vertebrate species
- 2013
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In: GigaScience. - : BioMed Central (BMC). - 2047-217X. ; 2:1
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Journal article (peer-reviewed)abstract
- Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
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| 3. |
- Barrat, Jean-Louis, et al.
(author)
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Soft matter roadmap
- 2024
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In: Journal of Physics. - : Institute of Physics Publishing (IOPP). - 2515-7639. ; 7:1
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Research review (peer-reviewed)abstract
- Soft materials are usually defined as materials made of mesoscopic entities, often self-organised, sensitive to thermal fluctuations and to weak perturbations. Archetypal examples are colloids, polymers, amphiphiles, liquid crystals, foams. The importance of soft materials in everyday commodity products, as well as in technological applications, is enormous, and controlling or improving their properties is the focus of many efforts. From a fundamental perspective, the possibility of manipulating soft material properties, by tuning interactions between constituents and by applying external perturbations, gives rise to an almost unlimited variety in physical properties. Together with the relative ease to observe and characterise them, this renders soft matter systems powerful model systems to investigate statistical physics phenomena, many of them relevant as well to hard condensed matter systems. Understanding the emerging properties from mesoscale constituents still poses enormous challenges, which have stimulated a wealth of new experimental approaches, including the synthesis of new systems with, e.g. tailored self-assembling properties, or novel experimental techniques in imaging, scattering or rheology. Theoretical and numerical methods, and coarse-grained models, have become central to predict physical properties of soft materials, while computational approaches that also use machine learning tools are playing a progressively major role in many investigations. This Roadmap intends to give a broad overview of recent and possible future activities in the field of soft materials, with experts covering various developments and challenges in material synthesis and characterisation, instrumental, simulation and theoretical methods as well as general concepts.
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| 4. |
- Ganapathy, S., et al.
(author)
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Chromium IV exposure, via Src/Ras signaling, promotes cell transformation
- 2017
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In: Molecular Carcinogenesis. - : Wiley. - 0899-1987. ; 56:7, s. 1808-1815
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Journal article (peer-reviewed)abstract
- Hexavalent chromium [Cr(VI)] is a well-known environment carcinogen. The exposure of Cr(VI) through contaminated soil, air particles, and drinking water is a strong concern for the public health worldwide. While many studies have been done, it remains unclear which intracellular molecules transduce Cr(VI)-mediated carcinogenic signaling in cells to promote cancer. In this study, we demonstrated that upon Cr(VI) treatment, the intracellular receptor src was activated, which further upregulated Ras activity, leading to the augmentation of ROS and onset of ER stress in human lung epithelial BEAS-2B or keratinocytes. These cells were formed colonies in soft agar cultures following the persistent Cr(VI) treatment. Furthermore, anti-apoptotic factor Bcl-2 was upregulated and activated in the colonies. Thus, our study suggests that Cr(VI), though activating the src and Ras signaling axis, perturbs redox state and invokes ER stress for the establishment of carcinogenic actions in the cells. In this process, Bcl-2 appears playing an important role. By uncovering these intracellular targets, our study may help developing novel strategies for better environmental protection, especially in areas contaminated or polluted by Cr(VI) as well as for effective cancer treatments. © 2017 Wiley Periodicals, Inc.
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| 5. |
- Winkler, A., et al.
(author)
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Magnetism in Re-based ferrimagnetic double perovskites
- 2009
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In: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 11, s. 073047-
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Journal article (peer-reviewed)abstract
- We have investigated spin and orbital magnetic moments of the Re 5d ion in the double perovskites A(2)FeReO(6) (A = Ba, Sr, Ca) by x-ray magnetic circular dichroism (XMCD) at the Re L(2,3) edges. In these ferrimagnetic compounds, an unusually large negative spin and positive orbital magnetic moment at the Re atoms was detected. The presence of a finite spin magnetic moment in a 'non-magnetic' double perovskite as observed in the double perovskite Sr(2)ScReO(6) proves that Re has also a small, but finite intrinsic magnetic moment. We further show for the examples of Ba and Ca that the usually neglected alkaline earth ions undoubtedly also contribute to the magnetism in the ferrimagnetic double perovskites.
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| 6. |
- Zhang, Guojie, et al.
(author)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Journal article (peer-reviewed)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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