| 1. |
- Beier, Sebastian, et al.
(author)
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Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
- 2017
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In: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4
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Journal article (peer-reviewed)abstract
- Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. â € Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).
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| 2. |
- Grasso, Silvia, et al.
(author)
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The scaffold protein p140Cap limits ERBB2-mediated breast cancer progression interfering with Rac GTPase-controlled circuitries
- 2017
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8
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Journal article (peer-reviewed)abstract
- The docking protein p140Cap negatively regulates tumour cell features. Its relevance on breast cancer patient survival, as well as its ability to counteract relevant cancer signalling pathways, are not fully understood. Here we report that in patients with ERBB2-amplified breast cancer, a p140Cap-positive status associates with a significantly lower probability of developing a distant event, and a clear difference in survival. p140Cap dampens ERBB2-positive tumour cell progression, impairing tumour onset and growth in the NeuT mouse model, and counteracting epithelial mesenchymal transition, resulting in decreased metastasis formation. One major mechanism is the ability of p140Cap to interfere with ERBB2-dependent activation of Rac GTPase-controlled circuitries. Our findings point to a specific role of p140Cap in curbing the aggressiveness of ERBB2-amplified breast cancers and suggest that, due to its ability to impinge on specific molecular pathways, p140Cap may represent a predictive biomarker of response to targeted anti-ERBB2 therapies.
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| 3. |
- Mascher, Martin, et al.
(author)
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A chromosome conformation capture ordered sequence of the barley genome
- 2017
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 544:7651, s. 427-433
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Journal article (peer-reviewed)abstract
- Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
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| 4. |
- Burrello, Stefano, et al.
(author)
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Towards a power counting in nuclear energy–density–functional theories through a perturbative analysis
- 2020
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In: Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 811
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Journal article (peer-reviewed)abstract
- We illustrate a step towards the construction of a power counting in energy–density–functional (EDF) theories, by analyzing the equations of state (EOSs) of both symmetric and neutron matter. Within the adopted strategy, next–to–leading order (NLO) EOSs are introduced which contain renormalized first–order–type terms and an explicit second–order finite part. Employing as a guide the asymptotic behavior of the introduced renormalized parameters, we focus our analysis on two aspects: (i) With a minimum number of counterterms introduced at NLO, we show that each energy contribution entering in the EOS has a regular evolution with respect to the momentum cutoff (introduced in the adopted regularization procedure) and is found to converge to a cutoff–independent curve. The convergence features of each term are related to its Fermi–momentum dependence. (ii) We find that the asymptotic evolution of the second–order finite–part coefficients is a strong indication of a perturbative behavior, which in turns confirms that the adopted strategy is coherent with a possible underlying power counting in the chosen Skyrme–inspired EDF framework.
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| 5. |
- Young, Briana, et al.
(author)
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Parallel Implementation of Instinctual and Learning Neural Mechanisms in a Simulated Mobile Robot
- 2012
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In: Biomimetic and Biohybrid Systems. - Berlin, Heidelberg : Springer. - 9783642315244 - 9783642315251 ; , s. 298-308
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Conference paper (peer-reviewed)abstract
- The question of how biological learning and instinctive neural mechanisms interact with each other in the course of development to produce novel, adaptive behaviors was explored via a robotic simulation. Instinctive behavior in the agent was implemented in a hard-wired network which produced obstacle avoidance. Phototactic behavior was produced in two serially connected plastic layers. A self-organizing feature map was combined with a reinforcement learning layer to produce a learning network. The reinforcement came from an internally generated signal. Both the adaptive and fixed networks supplied motor control signals to the robot motors. The sizes of the self-organizing layer, reinforcement layer, and the complexity of the environment were varied and effects on robot phototactic efficiency and accuracy in the mature networks were measured. A significant interaction of the three independent variables was found, supporting the idea that organisms evolve distinct combinations of instinctive and plastic neural mechanisms which are tailored to the demands of the environment in which their species evolved.
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