| 1. |
- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 2. |
- Artiaco, Claudia, et al.
(författare)
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Hard-sphere jamming through the lens of linear optimization
- 2022
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Ingår i: Physical review. E. - : American Physical Society (APS). - 2470-0045 .- 2470-0053. ; 106:5
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Tidskriftsartikel (refereegranskat)abstract
- The jamming transition is ubiquitous. It is present in granular matter, foams, colloids, structural glasses, and many other systems. Yet, it defines a critical point whose properties still need to be fully understood. Recently, a major breakthrough came about when the replica formalism was extended to build a mean-field theory that provides an exact description of the jamming transition of spherical particles in the infinite-dimensional limit. While such theory explains the jamming critical behavior of both soft and hard spheres, investigating the transition in finite-dimensional systems poses very difficult and different problems, in particular from the numerical point of view. Soft particles are modeled by continuous potentials; thus, their jamming point can be reached through efficient energy minimization algorithms. In contrast, the latter methods are inapplicable to hard-sphere (HS) systems since the interaction energy among the particles is always zero by construction. To overcome these difficulties, here we recast the jamming of hard spheres as a constrained optimization problem and introduce the CALiPPSO algorithm, capable of readily producing jammed HS packings without including any effective potential. This algorithm brings a HS configuration of arbitrary dimensions to its jamming point by solving a chain of linear optimization problems. We show that there is a strict correspondence between the force balance conditions of jammed packings and the properties of the optimal solutions of CALiPPSO, whence we prove analytically that our packings are always isostatic and in mechanical equilibrium. Furthermore, using extensive numerical simulations, we show that our algorithm is able to probe the complex structure of the free-energy landscape, finding qualitative agreement with mean-field predictions. We also characterize the algorithmic complexity of CALiPPSO and provide an open-source implementation of it.
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| 3. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 4. |
- Canales, Javier, et al.
(författare)
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Gene expression profiling in the stem of young maritime pine trees : detection of ammonium stress-responsive genes in the apex
- 2011
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Ingår i: Trees. - : Springer Science and Business Media LLC. - 0931-1890 .- 1432-2285. ; 26:2, s. 609-619
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Tidskriftsartikel (refereegranskat)abstract
- The shoots of young conifer trees represent an interesting model to study the development and growth of conifers from meristematic cells in the shoot apex to differentiated tissues at the shoot base. In this work, microarray analysis was used to monitor contrasting patterns of gene expression between the apex and the base ofmaritime pine shoots. A group of differentially expressed genes were selected and validated by examining their relative expression levels in different sections along thestem, from the top to the bottom. After validation of the microarray data, additional geneexpression analyses were also performed in the shoots of young maritime pine treesexposed to different levels of ammonium nutrition. Our results show that the apex ofmaritime pine trees is extremely sensitive to conditions of ammonium excess or deficiency, as revealed by the observed changes in the expression of stress-responsivegenes. This new knowledge may be used to precocious detection of early symptoms of nitrogen nutritional stresses, thereby increasing survival and growth rates of young treesin managed forests.
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| 5. |
- Cañas, Rafael A, et al.
(författare)
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Molecular and functional analyses support a role of Ornithine-{delta}-aminotransferase in the provision of glutamate for glutamine biosynthesis during pine germination
- 2008
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 148:1, s. 77-88
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Tidskriftsartikel (refereegranskat)abstract
- We report the molecular characterization and functional analysis of a gene (PsdeltaOAT) from Scots pine (Pinus sylvestris) encoding Orn-delta-aminotransferase (delta-OAT; EC 2.6.1.13), an enzyme of arginine metabolism. The deduced amino acid sequence contains a putative N-terminal signal peptide for mitochondrial targeting. The polypeptide is similar to other delta-OATs from plants, yeast, and mammals and encoded by a single-copy gene in pine. PsdeltaOAT encodes a functional delta-OAT as determined by expression of the recombinant protein in Escherichia coli and analysis of the active enzyme. The expression of PsdeltaOAT was undetectable in the embryo, but highly induced at early stages of germination and seedling development in all different organs. Transcript levels decreased in later developmental stages, although an increase was observed in lignified stems of 90-d-old plants. An increase of delta-OAT activity was observed in germinating embryos and seedlings and appears to mirror the observed alterations in PsdeltaOAT transcript levels. Similar expression patterns were also observed for genes encoding arginase and isocitrate dehydrogenase. Transcripts of PsdeltaOAT and the arginase gene were found widely distributed in different cell types of pine organs. Consistent with these results a metabolic pathway is proposed for the nitrogen flow from the megagametophyte to the developing seedling, which is also supported by the relative abundance of free amino acids in embryos and seedlings. Taken together, our data support that delta-OAT plays an important role in this process providing glutamate for glutamine biosynthesis during early pine growth.
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| 6. |
- Miettinen, Kaisa, 1965-, et al.
(författare)
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Using Box Indices in Supporting Comparison in Multiobjective Optimization
- 2009
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Ingår i: European Journal of Operational Research. - : Elsevier BV. - 0377-2217 .- 1872-6860. ; 197:1, s. 17-24
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Tidskriftsartikel (refereegranskat)abstract
- Because of the conflicting nature of criteria or objectives, solving a multiobjective optimization problem typically requires interaction with a decision maker who can specify preference information related to the objectives in the problem in question. Due to the difficulties of dealing with multiple objectives, the way information is presented plays a very important role. Questions posed to the decision maker must be simple enough and information shown must be easy to understand. For this purpose, visualization and graphical representations can be useful and constitute one of the main tools used in the literature. In this paper, we propose to use box indices to represent information related to different solution alternatives of multiobjective optimization problems involving at least three objectives. Box indices are an intelligible and easy to handle way to represent data. They are based on evaluating the solutions in a natural and rough enough scale in order to let the decision maker easily recognize the main characteristics of a solution at a glance and to facilitate comparison of two or more solutions in an easily understandable way.
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| 7. |
- Morell, Maybi, et al.
(författare)
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Personal epistemology and spontaneous small groups
- 2020
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Ingår i: Educational Psychology. - : Routledge. - 0144-3410 .- 1469-5820.
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Tidskriftsartikel (refereegranskat)abstract
- We explore the structure of epistemological beliefs and its relation with the spontaneous formation of study groups in a sample of biomedical engineering students. The sophistication of the beliefs as well as the size and distribution of spontaneous small groups were measured for subjects in three different academic years: junior, intermediate and senior. Through principal components analysis, a four-factor structure was found for the epistemological beliefs, additionally validated with confirmatory factor analysis. The spontaneous small groups were determined by a clustering algorithm with data from a survey applied to 151 participants. Using parametric and non-parametric methods, it was found that the size of the group for junior students was positively correlated to naive beliefs about the source of knowledge. For senior students, however, both size and number of groups were inversely correlated to the passiveness in learning. These results are discussed in the frame of the interplay between group praxis and mental representations in the learning process. In addition, general differences were encountered between learners in spontaneous small groups and lone learners concerning the belief about the speed of learning, which also showed an overall difference across gender.
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| 8. |
- Villalobos, David P., et al.
(författare)
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Reprogramming of gene expression during compression wood formation in pine : Coordinated modulation of S-adenosylmethionine, lignin and lignan related genes
- 2012
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Ingår i: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 12, s. 100-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Transcript profiling of differentiating secondary xylem has allowed us to draw a general picture of the genes involved in wood formation. However, our knowledge is still limited about the regulatory mechanisms that coordinate and modulate the different pathways providing substrates during xylogenesis. The development of compression wood in conifers constitutes an exceptional model for these studies. Although differential expression of a few genes in differentiating compression wood compared to normal or opposite wood has been reported, the broad range of features that distinguish this reaction wood suggest that the expression of a larger set of genes would be modified. Results: By combining the construction of different cDNA libraries with microarray analyses we have identified a total of 496 genes in maritime pine (Pinus pinaster, Ait.) that change in expression during differentiation of compression wood (331 up-regulated and 165 down-regulated compared to opposite wood). Samples from different provenances collected in different years and geographic locations were integrated into the analyses to mitigate the effects of multiple sources of variability. This strategy allowed us to define a group of genes that are consistently associated with compression wood formation. Correlating with the deposition of a thicker secondary cell wall that characterizes compression wood development, the expression of a number of genes involved in synthesis of cellulose, hemicellulose, lignin and lignans was up-regulated. Further analysis of a set of these genes involved in S-adenosylmethionine metabolism, ammonium recycling, and lignin and lignans biosynthesis showed changes in expression levels in parallel to the levels of lignin accumulation in cells undergoing xylogenesis in vivo and in vitro. Conclusions: The comparative transcriptomic analysis reported here have revealed a broad spectrum of coordinated transcriptional modulation of genes involved in biosynthesis of different cell wall polymers associated with within-tree variations in pine wood structure and composition. In particular, we demonstrate the coordinated modulation at transcriptional level of a gene set involved in S-adenosylmethionine synthesis and ammonium assimilation with increased demand for coniferyl alcohol for lignin and lignan synthesis, enabling a better understanding of the metabolic requirements in cells undergoing lignification.
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